****************************************************************************** From: Olivier Plaut Date: Mon, 05 Jan 2004 12:51:40 +0100 Subject: Re: Agilent filaments Organization: * I was told by an Agilent tech that they received bad batches... The tech told me to put new filaments in methanol and to sonicate them before mounting. Olivier Gun Blomkvist a écrit : } We have been using an Agilent 5973 instrument for about two years, } mainly for analysis of organohalogens with NCI/methane. Earlier this } year we began experiencing problems with the filaments; shortly after } installation of a new filament, sensitivity started to decrease } rapidly and we found that the filament was bent. As this has been } repeated several times, it seems that Agilent's production methods } have changed somehow. } Two questions: } 1) Has anybody else had the same problem? } 2) We have found that older batches of filaments, part no. } G.1099-80053, batch no beginning with 0, work well. Does anybody have } one or more of these and is willing to part with them? } } Regards, } Gun ****************************************************************************** From: Thomas Frenzel Date: 5 Jan 2004 05:15:30 -0800 Subject: handbook on high resolution mass spectrometry Organization: * Does anybody know a comprehensive textbook covering theory and application of high resolution mass spectrometry by means of magnetic sector field instruments? Thank you for your help. Thomas ****************************************************************************** From: John M Roman Date: 5 Jan 2004 10:32:23 -0800 Subject: Re: gcms methods Organization: * Becky: Try this reference for glucose analysis by gc/ms: MG Kienle, et al, Journal of Chrom.,Biomedia Applications, 573(1992)127-131, "Determination of plasma[6,6-2H2) glucose by GC/MS" I've been quantitating glucose in plasma and serum by gc/ms since 1998. I'm measuring deuterated(2-H2) to non-deuterated (0-H2)ratios. In this paper they measure m/z187 and 189. I'm using m/z 217 and 219. I receive my samples as methanolic/water solutions. Transfer the samples to glass vials, evaporate under N2, add ~1-2mg hydroxylamine HCl + 100uL pyridine; cap, vortex, heat 30mins @ 90 deg C; uncap, add ~100uL actic anhydride, cap, vortex, heat 30mins @ 90 deg C; uncap, quantitative transfer to autosmpler vial with acetonitrile; adjust to final volume, gc/ms. John M.Roman MS Lab SAIC-Frederick NCI-Frederick PO Box B Frederick, MD 21702 ****************************************************************************** From: David Sparkman Date: Mon, 5 Jan 2004 11:20:02 -0800 Subject: Re: handbook on high resolution mass spectrometry Organization: * Thomas, I assume you mean double-focusing mass spectrometers. I never likes that sector field terminology. both the electric sector and the magnetic field are fields and sectors. JEOL (http://www.jeol.com) has some good information under the Essays/Tutorial section. The book by John Roboz written in the 1968 is a very good source. This book has been reprinted by ASMS. Regards; David "Thomas Frenzel" wrote in message news:btbsnc$qqs$1@news-int2.gatech.edu... } } Does anybody know a comprehensive textbook covering theory and } application of high resolution mass spectrometry by means of magnetic } sector field instruments? } } Thank you for your help. } } Thomas } ****************************************************************************** From: Kjell Mortier Date: Tue, 6 Jan 2004 17:42:29 +0100 Subject: zero air or nitrogen in LC-MS ionization Organization: * A question concerning installation of LC-MS/MS API4000. We have to choose between using zero grade air and nitrogen as nebulizer and auxillary gas for an API (applied biosystems) instrument with the turbo V source. Does anyone has some experience if this can effect the ionization of your compound (electrospray or APCI). Does the oxygen has an effect on the ionization? Why would you prefer the one or the other gas, aside from costs? According to the pre-installation guide, both gases work fine, but the people from AB would advize zero grade air. This would be an additional cost for us, so we prefer nitrogen (very pure grade). thanks for any comments ****************************************************************************** From: Michael Sherrell Date: Mon, 12 Jan 2004 21:23:12 -0800 Subject: Seqs, synths, mass specs/MALDIs, liquid handlers available Organization: * Grizzly Analytical: Sequencers, synthesizers, mass specs, MALDIs, liquid handlers, cytometers etc. for sale New engineering development, service and retail facility: 377 Oyster Pt Blvd #11, South San Francisco CA 94080 **Oligosynthesizers: ABI 3900: $75,000. 90-day parts & labor warranty. (3900 parts: independent sources; savings over list prices.) Expedite 8909: $14,500. Includes M.O.S.S, rebuilt w/ new ABI valves, 90-day warranty. + $3,500/trityl. ABI 394: $14,200. Rebuilt; 90-day warranty. ABI 394: $19,900. Trityl, MAC, rebuilt: about as good as the new 3400. ABI 392: $12,200. Rebuilt; 90-day warranty. ABI 3948: $25,000. Rebuilt/installed w/ 90-day warranty. ABI 390Z: $11,000. Rebuilt/warranteed. (Oligosynthesis reagents, ~75% off list: Oxidizer, Cap A, Cap B, Activator, Deblock, amadites, + 8909 columns) Beckman 1000M: $11,000. Excellent condition; guaranteed. CyClone: $7,500. New-in-box; 90 day parts warranty. Similar to ABI 392. Biosearch 8700: $10,000. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. BioSearch 8750: $10,500. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. Biosearch 8700: $8,000. Rebuilt; 90-day warr. + $2K/Windows. BioSearch 8750. ~$4,000. Have 5; cheaper & faster than 394s. Cruachem PS250. <=$2,500. 6 available. *High throughput synthesizers: BLP 192: $125,000. 2 plates, 8 min. cycle time. New; incl. install + 1 yr. warr. Polygen 10. Call if interested. Polyplex Gene Machine: $89,000. Installed/warranteed. **Oligosequencers: ABI 3100: $90,000. Includes factory install, software license. ABI 310: $28,000. Mac. Includes factory install; guar. eligible for service. ABI 310: $31,000. PC. Includes factory install; guar. eligible for service. ABI 3700: $75,000. Includes factory install; guar. eligible for service. ABI 3700: $19,000. From major genome center; beautifully maintained. MegaBace 4000: Offers considered. Have three; currently under mfr. svc contract. MegaBace 1000: $22,000. Incl. installation by manufacturer. ABI 377: $15,500. 96-lane; install factory incl., eligible for service. (Also suitable for tiling.). Genescan: $5,000. Licensed software for the 377, 310 or 373. ABI 373 stretch: $9,000. Big Dye upgrade. Pharmacia ALF Express: $14,000, incl. 90-day parts & labor warr. Visible Genetics: $20,000. Unused. Have 3. LiCor 4200: $25,000. Incl. Global Upgrade; guaranteed installable. LiCor 4000LS <: $20,000. 1994 model; can have Global Upgrade. Genomyx LR: $2,500. Boots; many accessories. MJ Basestation 51. Call for pricing. No robotic loading, 2 years old, under service contract. MJ Research BaseStation: $105,000. 2 yrs old; still under svc. contract. MJ Research BaseStation: $125,000. 6 mos. old; still under svc. contract. **Real-time PCR: ABI 7700: $34,000. Installed/warranteed. BioRad iCycler: $32,000. 90-day warranty. **Peptide synthesizers: ABI 433: $33,000. Original, ABI-supportible 433. These come and go; call/email to reserve. 90-day warr. ABI 433: $24,000. Upgraded from 431. We support. Rebuilt, 90-day warr. ABI 431: $16,000. Rebuilt, 90-day warr. ABI 430: $10,500. Rebuilt, 90-day warranty. ABI 432: $15,000. Rebuilt, 90-day warranty. Capriccio 1: $65,000. New instrument. Benchtop, large scale; faster and more efficient than ACT 400. Incl. install, 1 yr svc. PerSeptive 9500: $12,750. Rebuilt w/ 90-day warranty. PerSeptive 9050: $16,000. Rebuilt w/ 90-day warranty. CS Bio 336. ~$27,000. 6 mos old; lease default. 3 peps simultaneous; .05-.25 mmol. ACT LabTech III: $15,000. 30-day warranty. Pioneer: $40,000. Includes factory install, eligible for svc. contract MPS unit for the Pioneer peptide synthesizer: $5,000. New and unused; price = 25% of new cost. ACT 396 MPS: $42,000. Factory refurb; includes 120-day warranty. PerSeptive 9600: $13,750. Rebuilt, warranteed. ACT Vantage: $79,000. Excellent condition. ACT 357-MPS. Call for pricing. ACT 90: $16,250. Only used twice. Incl. install; guar. eligible for svc. Argonaut Quest 205: $27,000. ASW model. Argonaut Quest 210: $19,000. ASW model. **Peptide sequencers: ABI 494 HT: $55,000. Installed, guaranteed ok for service contract. ABI 494 cLc. Offers considered. ABI 492: $20,000 installed, eligible for service contract. Beckman 6300. Various prices. Have several; can rebuild or sell for parts. ABI 421: $10,000. Offers considered. ABI 477/120: $1,500. Good working order or right of return. ABI 477. Service, parts available. ABI 473/476: $15,000. Good working order; install/service available. ABI 470A: $2,000. For parts. Many extra parts. *[Note: various other ABI, HP, Millipore, Biosearch, Beckman, etc. sequencers, synthesizers etc. available; please inquire.] **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000 upgrade: $35,000. HSID interface: higher sensitivity and s/n at high flow rates; comparable to API 4000. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 365: $49,000. Sciex upgraded from original 300. Incl. turboionspray, installation, guaranteed eligible for service contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex APCI source: $7,900. For API 150 or 300 or Q-Star Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $165,000. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $30,000. ES, API 1, Alpha station, good working order. +$20K/current Xcalibur, installation and 30-day warranty. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. MM Autospec M: $115,000. Mag Sector; orthogonal TOF MS/MS; 4 sources, FPD and TOF included; currently working well. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE STR. $129,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $45,000. Extensively refurbished. Voyager DE: $76,000. Incl. install. 2002 model. ABI 4700: Must sell; all offers considered. TOF/TOF MS/MS Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $275,000. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$200,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $50,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. HP G2025A LD-TOF: free for parts, you pay shipping. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. **Liquid handlers: Biomek FX (core system): $450,000 good working order. Includes 3 meter Orca, fluorometer, incubator, more. Biomek FX: $60,000. Single arm. Biomek 2000, no side loader, $49,000. Beckman Multimek, $34,000. Zymark Sciclone: 1.5 years old; $43K. Zymark Staccato system: $250,000 and up, depending on accessories, install, warranty. XP-arm based Zymarks: $10,000 and $20,000, depending on accessories. Tecan RSP-200/8 ID Robot Sample Processor, fully equipped: call/email if interested. Hamilton MicroLab AT2 Plus robot, $38,000 Packard Multiprobe 20400 and CP20400, Packard refurbed, $16,500 for either Transgenomic WAVE system, $22,000 incl. installation, eligible for svc. Quantity discounts for up to 20 units. Tecan Genesis RSP 150, no Roma, $52,000 delivered w/ 90-day warranty. Tecan Genesis RSP 100, $41,000 delivered w/ 90-day warranty. LC Packings UltiMate NanoLC system w/ FAMOS autosampler, $37,300 Scitec robotic liquid handling system, 3-meter rail, $60,000 guaranteed working Tom-Tec Quadras, various configurations, refurbished and warrantied. Hamilton Microlab 2200: call for pricing. Gilson 215: call for price. ABI 877 Catalyst Turbo: $12,000 or best offer Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically 96-well microplate source, glass slide, microwell plate or membrane target), ~ 5 years old. **Other expensive hi-tech items: *NMRs: Bruker Avance 700 NMR, shielded, 2 yrs old, $1.26M new, $850K installed + ship; excl. $15K site license. Varian Inova 600 NMR: $275,000 guaranteed installable; +$25K/install. FX90Q NMR w/ Tek-Mag, $19,500. Others available; inquire if interested. *Flow cytometers: COULTER® EPICS XL-MCL^Ù: $45,000. 4 color with Multi Carousel Loader includes rebuilt, installation and one-year warranty. Coulter Epics Elite: 9 years old but never used. Call/email if interested. COULTER® EPICS XL^ÙFlow Cytometer: $45,000.00 Currently in operation. Includes XL2, EXPO and Data Mate Software, APC UPS Back-up, factory installation, and other options. FACS Vantage SE with the DIVA option: $160,500. (2 lasers: 488nm and UV tunable). Bought in June '02 and never used. BD FACSCalibur w/ FACSLoader: $84,000. 4 color. 2001; excellent condition. BD FACScan; offers considered. 3 color w/ argon laser, FITC, PE & 7 AAD BD FACSort Cell Sorter, $39,000. 3 color, MAC G3, Cellquest, install included MoFlo Analyzer with MoSkeeto System: $99,750.00. 6-channel / 5-color detector, Carvo MSP - 9000 Auto sampler, Summit 3.1 Software, Laser. Scanning Cytometer: Microscope-based. Two-laser system. $85,000 guaranteed installable. Others available; inquire if interested. *Arrayers/spotters/readers: HP/Affymetrix GeneArray G2500A system, $117,500. Complete system, factory install, guar. eligible for factory service contract. New list: $199K. Affymetrix GeneChip system: $120,000. 2003; unused. HP GeneArray G2500A reader w/ laser, $22,000, including new data system but no fluidics station. Affymetrix 417 Arrayer/spotter: seller considering rather low offers; call if interested. Affymetrix 417 Arrayer/spotter: $34,500 reconditioned with 1 year warranty HP/Affymetrix GeneArray Scanner Model G2500A, unused, $49,000. CELLOMICS ScanArray HCS: 2003 model. Factory install, license discount available; offers considered. Packard ScanArray 4000: $35,950. 2000 instrument. Incl. factory install; eligible for service contract. Packard ScanArray 3000: $17,250. Incl. factory install; eligible for service contract. Genomic Solutions GeneTAC microarray Hybridization Station: $27,000. (for details see www.genomicsolutions.com/products/bio/hyb.html) Amersham Lucidea SLIDE PRO Hybridization Station: $18,500. Ciphergen ProteinChip Reader PBS II: $65,000. Current upgrades; includes factory install, 30-day warranty. *Spot pickers: Genetix QPix2 benchtop: $79,570 installed. Incl. 96-well picking head, gridding option, etc; Q-Fill optional. Genetix QBot picker/arrayer. Call/email if interested. BioRobotics BioPick automatic colony picker. Excellent condition. ~$60,000 Genomic Solutions Flexys; much less than new price; call/email if interested. *Microscopes: ZEISS Axioskop Trinocular Microscope, $24,650 For phase contrast, DIC and Epi-Flourscence Cambridge Stereoscope S90B SEM w/ Kevex EDX: $25,000. Incl. secondary and backscattering detectors, Polaroid system, some options, factory installation. Working now. Optional one year service sontracts available. Meridian ACAS 570C LSCM. Other Laser Scanning Confocal microscopes available, call or email for list. Leica Confocal TCS-4D: $51,000. NT upgrades, 2 or 3 laser w/ DMRBE microscope bought new in 1997. Includes factory installation. Various (SEM) Scanning Electron Microscopes, $9,500-$375,000. Call or email for list. Various (TEM) Transmission Electron Microscopes, call or email for list. Various surgical, neuro surgical microscopes, call or email for list. Various optical microscopes, call or email for list. *Truly miscellaneous: Molecular Devices/LJL Biosystems Criterion Analyst HT System: $35,000. Amersham Typhoon 9410 scanner: Accepting offers. 2003 system, top condition. The first large-format gel , blot and microarray imager; also optimized for protein research. Perkin Elmer 1010M Micro Densitometer: was $325,000 new. Now in Japan. Call if interested. Amersham FARCyte/Tecan Ultra fluorescence plate reader, new in box, $50,000. List: $80K. Accutag Radio Frequency Reader/10k Automated Microreactor Sorting System, $80,000 Genevac's Mega 1200 ultra high throughput solvent evaporation system, 1.5 yrs old but unused, $200,000 or best offer. New Brunswick Bioflo 3000 bioreactor: $18,900. 10 liter; new probes; 90-day warr. Process Engineers 29 liter mammalian cell bioreactor, new/unused, ~$35,000 or best offer. *(other bioreactors/fermenters available; inquire if interested.) Cambridge Stereoscope S90B SEM w/ Kevex EDX: $10,000. Incl. secondary and backscattering detectors, Polaroid system, some options. Working now. **Too hard to classify: Li-Cor Odyssey: $25,000 ($40K new). Guaranteed good working order. See for specs. BioCAD 20s and 60s w/ 90-day warr. available for $10-15,000, depending on details. 700E also avail. ABI VISION Workstation (souped-up BioCAD; see AB website for details): offers considered. Luminex LX100 (simultaneous assay of multiple analytes): $29,000. Glycoprep 1000 automated hydrazinolysis machine: $9,000; good working order Packard Topcount 12-detector 96 well microplate scintillation counter, $35,000 Jasco FP6500 Fluorescence Spectrometer. Excellent condition. $11,500. ABI 120 HPLC, $1,500 ABI 877: have several; different configs, prices, none very expensive; call PE 9600 thermalcyclers: $3,750 w/ 90-day warranty PE 9700 96-well thermalcyclers: $5,300 w/ 90-day warranty PE 9700 384-well thermalcyclers: $5,450 w/ 1 yr. warranty PE 2400 thermalcyclers: $2,450 w/ 90-day warranty PE 480 thermalcyclers: $3,000 guaranteed working; have several Beckman P/ACE MDQ: $24,000 Beckman P/ACE 5510: $19,500. Refurbed, warranteed. MD PhosphorImager Storm 860, $30,000. MD FSI FluorImager, $15,000 MD Personal Densitometer SI -- call to discuss price MD Cytosensor, $8,750. 4 channel; virtually unused. **Service: We rebuild valve blocks for ABI 430, 431 and 39x @ $65/port, 90-day warranty Service and contracts on ABI 39n and PerSeptive 8909/8905s available. Service contracts on Hewlett Packard HPLCs, GCs and MSs available at a savings over HP rates **Also available: Agilent 1100 HPLCs, virtually all configurations/detectors. HPLCs, ICs, CEs, FPLCs: microbore to prep scale. A variety of other lab instruments. Call or check the website: www. grizzlyanalytical. com. Please call or email for more information or if you have items to sell. Michael Sherrell Grizzly Analytical (USA) www.grizzlyanalytical.com 707 887 2919/fax 707 887 9834 [All the items are subject to prior sale.] [If you do not wish to receive my emails, please return this with "Stop" in the subject line, and accept my apologies for the inconvenience.] ****************************************************************************** From: "Skorich, Steven" Subject: Library Search Glitch Date: Mon, 12 Jan 2004 18:11:53 -0600 Organization: * I am running ThermoQuest Mass Lab 1.33 nder Windows 95, with an old VG Trio-1 and HP5890. Quite suddenly, my library search function has ceased to operate. If I attempt to search a library with a query spectrum, the library function locks up the computer, and I have to reboot. I have reloaded the NIST library from CD-ROM without apparent effect on the problem. The data acquisition and instrument control functions work, the instrument calibrates. It is only the library search that causes this error. Can anyone give me some pointers on what files to look for (and where to look) to determine if files that should be there are missing? I'm reluctant to reinstall the whole system unless I absolutely must. Any help that anyone can give me will be appreciated greatly. Thanks! Steven R. Skorich Medtronic Energy and Component Center Analytical Chemistry laboratory ****************************************************************************** From: "Little, James - Eastman" Date: Sun, 18 Jan 2004 11:23:00 -0500 Subject: Interpretation of CID Spectra Organization: * We are interested in gaining expertise in the interpretation of CID spectra of relative small organic molecules (100-1000, not peptides). I am trying to justify with my management having a course taught at our laboratory. I noticed three different courses on the internet. 1. Advanced LC/MS III, Interpretation of CID Mass Spectra, Jack Henion, Cornell University 2. Advanced Interpretation of CID Mass Spectra from LC/MS,Developing a systematic methodology for Special Interpretation, Robert D. Voyksner, Ph. D., LCMS Limited 3. Interpretation of MS-MS Mass Spectra, Hyphen MassSpec Consultancy Has anyone taken any of these classes? Was the information useful in the identification of unknowns in your work? James Little Tel. No. 423-229-8685 office Tel. No. 423-229-8022 lab "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ ****************************************************************************** From: Jenny Date: 21 Jan 2004 23:17:55 -0800 Subject: Contaminant peaks Organization: * I am presently trying to set up a mass spectrometer with an electrospray source to be able to run protein non-covalent complexes regularly. This requires aqueous solvents. Unfortunatly when I run water based solvents I am always seeing the following masses in my spectra. 214.09, 257.24, 315.25, 391.28, 419.28, 447.34, (Phthalates) 519.12, 593.15, 667.17, 741.20 (A series increasing in increments of 74 (C3H6O2). I think these peaks are the sodium adducts of the series, meaning the M+H masses are 497, 571, 645, 719) These peaks also have a tendency to stay in the instrument, and I need to clean the source thoroughly to get rid of them. They also charge more readily than my samples, leading to signal suppression. Can anyone identify these peaks with possible suggestions as to where they are coming from? Thanks, Jenny Mitchell PS. Is there a reference list of masses of common contaminants anywhere? ****************************************************************************** From: Tony Bristow Date: Thu, 22 Jan 2004 17:41:12 +0000 Subject: Re: Contaminant peaks Organization: * Hi Jenny With regards to a reference list of masses of common contaminants, see JASMS, 1999, 10, 1174-1187. Also, see the University of Southampton MS website at http://www.soton.ac.uk/~msweb/help.htm. Best Wishes Tony Bristow ******************************************************************* This email and any attachments are confidential. Any use, copying or disclosure other than by the intended recipient is unauthorised. If you have received this message in error, please notify the sender immediately via +44(0)20 8943 7000 or notify postmaster@lgc.co.uk and delete this message and any copies from your computer and network. LGC Limited. Registered in England 2991879. Registered office: Queens Road, Teddington, Middlesex, TW11 0LY, UK ****************************************************************************** From: David Stranz Date: Thu, 22 Jan 2004 09:33:11 -0600 Subject: Re: Contaminant peaks Organization: * Jenny wrote in news:buonhp$pjq$1@news-int.gatech.edu: } I am presently trying to set up a mass spectrometer with an } electrospray source to be able to run protein non-covalent } complexes regularly. This requires aqueous solvents. } Unfortunatly when I run water based solvents I am always seeing } the following masses in my spectra. } } 214.09, 257.24, 315.25, } } 391.28, 419.28, 447.34, } (Phthalates) } } 519.12, 593.15, 667.17, 741.20 } (A series increasing in increments of 74 (C3H6O2). I think } these peaks are the sodium adducts of the series, meaning the } M+H masses are 497, 571, 645, 719) } } These peaks also have a tendency to stay in the instrument, and } I need to clean the source thoroughly to get rid of them. They } also charge more readily than my samples, leading to signal } suppression. Can anyone identify these peaks with possible } suggestions as to where they are coming from? } } Thanks, } } Jenny Mitchell } } PS. Is there a reference list of masses of common contaminants } anywhere? } } Some links to identification of contaminants in MS spectra: http://www.iscpubs.com/articles/al/a9911kum.pdf (phthalates) http://www.proteinworks.com/contamin.htm http://prowl.rockefeller.edu/contam/contents.htm Detergents are known to cause severe signal suppression in ESI, and could also be responsible for dissolving the phthalates you're seeing. If your protein complexes are membrane-bound and you are using detergents in their isolation, that might be a source of the sodiated series you see. It might also be membrane lipids themselves. An email to Carol Robinson's group at Cambridge might get some advice on sample handling. Regards, David ****************************************************************************** From: Chip Cody Date: 23 Jan 2004 03:36:27 -0800 Subject: Re: Contaminant peaks Organization: * The m/z 214.09 is most likely to be N-butylbenzenesulfonamide (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and a contaminant that I have often seen in LC/MS and FTICR. I do not know the origin of this contamination, but I am quite certain of the identification because we have used exact mass, MS/MS, isotope ratios, etc. to identify it. Chip Cody David Stranz wrote in message news:... } Jenny wrote in } news:buonhp$pjq$1@news-int.gatech.edu: } } } I am presently trying to set up a mass spectrometer with an } } electrospray source to be able to run protein non-covalent } } complexes regularly. This requires aqueous solvents. } } Unfortunatly when I run water based solvents I am always seeing } } the following masses in my spectra. } } } } 214.09, 257.24, 315.25, } } } } ...remainder of message deleted.. ****************************************************************************** From: Eppendorf Date: Fri, 23 Jan 2004 16:59:59 GMT Subject: ICP-MS problems with Vanadium Organization: * Has anyone else seen problems with measuring V by ICP-MS? Specifically, the numbers tend to start out fine (cal verifications and QC checks) but the numbers tend to rise consistently as the run goes on. By the end of a standard ~20 sample run the numbers are way outside of QC limits. We measure V at 50.944. To make matters worse, the problem is somewhat intermittent. Sometimes (once in maybe 10 runs) it'll work just fine. I would greatly appreciate any input on this. Thanks in advance. ****************************************************************************** From: Kajjo Date: 24 Jan 2004 09:06:38 -0800 Subject: Old manuals? Varian SMS data file format for GC/MS? Organization: * Hi everyone! Does anyone know details of the SMS Varian data file format. As far as we know, old manuals contained a appendix or section describing the binary format (header, byte order etc) of the SMS files. Unfortunately, the new device came without any such description and we would like to write a program to automatically process our GC/MS data files. Any help much appreciated! Kajjo Please answer also by email to kajjo@gmx.de Thanks! ****************************************************************************** From: Giganews Date: Sat, 24 Jan 2004 15:36:42 -0600 Subject: Re: Contaminant peaks Organization: * Chip; We salso ee this ion fairly frequently. NBBS is a plasticizer used in production of some polyamides. It's reportedly neurotoxic. ....Dave Hachey "Chip Cody" wrote in message news:burbph$3c6$1@news-int.gatech.edu... } } The m/z 214.09 is most likely to be N-butylbenzenesulfonamide } (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and } a contaminant that I have often seen in LC/MS and FTICR. I do not } know the origin of this contamination, but I am quite certain of the } identification because we have used exact mass, MS/MS, isotope ratios, } etc. to identify it. } } Chip Cody } } } David Stranz wrote in message news:... } } Jenny wrote in } } news:buonhp$pjq$1@news-int.gatech.edu: } } } } } I am presently trying to set up a mass spectrometer with an } } } electrospray source to be able to run protein non-covalent } } } complexes regularly. This requires aqueous solvents. } } } Unfortunatly when I run water based solvents I am always seeing } } } the following masses in my spectra. } } } } } } 214.09, 257.24, 315.25, } } } } } } } ...remainder of message deleted.. } ****************************************************************************** From: Chip Cody Date: 26 Jan 2004 04:49:50 -0800 Subject: Re: Contaminant peaks Organization: * Thanks for the information, Dave. I have been trying to find where this could come from. We don't presently see it in our AccuTOF, but it has been a problem in the past on other machines that I have worked with. NBBS has been detected in plastic used for food wrapping -- a Google search will show you a paper from SIS about short-path thermal desorption used to detect this compound. It is frustrating to have a contamination problem that eventually goes away and we never find out where it came from. If we knew the origin (tubing, solvent containers, seals, or?), it would be easier to solve the problem. NBBS is particularly annoying because it has a high proton affinity and it can give strong signals even at low levels. In some old Nicolet FTMS systems, m/z 214 would be the only peak remaining if we trapped ions for very long times. Everything else transferred a proton to the NBBS. Chip Giganews wrote in message news:... } Chip; } } We salso ee this ion fairly frequently. NBBS is a plasticizer used in } production of some polyamides. It's reportedly neurotoxic. } } ....Dave Hachey } } } "Chip Cody" wrote in message } news:burbph$3c6$1@news-int.gatech.edu... } } } } The m/z 214.09 is most likely to be N-butylbenzenesulfonamide } } (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and } } a contaminant that I have often seen in LC/MS and FTICR. I do not } } know the origin of this contamination, but I am quite certain of the } } identification because we have used exact mass, MS/MS, isotope ratios, } } etc. to identify it. } } } } Chip Cody } } } } } } David Stranz wrote in } message news:... } } } Jenny wrote in } } } news:buonhp$pjq$1@news-int.gatech.edu: } } } } } } } I am presently trying to set up a mass spectrometer with an } } } } electrospray source to be able to run protein non-covalent } } } } complexes regularly. This requires aqueous solvents. } } } } Unfortunatly when I run water based solvents I am always seeing } } } } the following masses in my spectra. } } } } } } } } 214.09, 257.24, 315.25, } } } } } } } } } } ...remainder of message deleted.. } } ****************************************************************************** From: Giganews Date: Tue, 27 Jan 2004 04:20:57 -0600 Subject: Re: Contaminant peaks Organization: * Chip; Thanks for the comments on NBBS. It's not a major problem in our lab, we tend to see more PEG and PPG related polymers from detergents and cosmetics as frequent contaminants. We have also seen a lot of silicone polymers from silastic tubing and seals. The current generation of LC/MS instruments is so sensitive that contaminants are showing up everywhere. ....Dave Hachey "Chip Cody" wrote in message news:bv3720$20f$1@news-int.gatech.edu... } } Thanks for the information, Dave. I have been trying to find where } this could come from. We don't presently see it in our AccuTOF, but } it has been a problem in the past on other machines that I have worked } with. NBBS has been detected in plastic used for food wrapping -- a } Google search will show you a paper from SIS about short-path thermal } desorption used to detect this compound. } } It is frustrating to have a contamination problem that eventually goes } away and we never find out where it came from. If we knew the origin } (tubing, solvent containers, seals, or?), it would be easier to solve } the problem. NBBS is particularly annoying because it has a high } proton affinity and it can give strong signals even at low levels. In } some old Nicolet FTMS systems, m/z 214 would be the only peak } remaining if we trapped ions for very long times. Everything else } transferred a proton to the NBBS. } } Chip } } Giganews wrote in message news:... } } Chip; } } } } We salso ee this ion fairly frequently. NBBS is a plasticizer used in } } production of some polyamides. It's reportedly neurotoxic. } } } } ....Dave Hachey } } } } } } "Chip Cody" wrote in message } } news:burbph$3c6$1@news-int.gatech.edu... } } } } } } The m/z 214.09 is most likely to be N-butylbenzenesulfonamide } } } (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and } } } a contaminant that I have often seen in LC/MS and FTICR. I do not } } } know the origin of this contamination, but I am quite certain of the } } } identification because we have used exact mass, MS/MS, isotope ratios, } } } etc. to identify it. } } } } } } Chip Cody } } } } } } } } } David Stranz wrote in } } message news:... } } } } Jenny wrote in } } } } news:buonhp$pjq$1@news-int.gatech.edu: } } } } } } } } } I am presently trying to set up a mass spectrometer with an } } } } } electrospray source to be able to run protein non-covalent } } } } } complexes regularly. This requires aqueous solvents. } } } } } Unfortunatly when I run water based solvents I am always seeing } } } } } the following masses in my spectra. } } } } } } } } } } 214.09, 257.24, 315.25, } } } } } } } } } } } } } ...remainder of message deleted.. } } } } ****************************************************************************** From: usedlabequip Date: 30 Jan 2004 11:56:17 -0800 Subject: ABI SCIEX Q TRAP LC/MS/MS AVAILABLE Organization: * Applied Biosystems Q-TRAP LC/MS/MS with HTLCHPLC Cohesive system model 2300 turboflow available. The system is 1 year old. Please contact for further details. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 ****************************************************************************** From: Marc Rosen Date: Fri, 30 Jan 2004 23:00:15 -0500 Subject: Advice on MS/MS of a compound Organization: * I have a compound that we synthesized (a prodrug made from a natural product, modified by attaching a peptide ) The MW is 1648, verified by MALDI. When I analyze by electrospray I see very little M+1 but the doubly charged and triply charge species (m/z = 825.3 and 550.8, respectively) provide a significant signal. I'm using -a triple quad- an API3000, direct infusion dissolved in 50% CH3CN with 0.1% formic acid. (Should I switch to methanol?) Do you think I could do a product ion scan on the double charged and triple charged ions and arrive at the same fragments? Also, my guess is that I could produce fragments with an m/z greater than the two values I listed above. I'm still very new to MS (my other work pulls me away too much) and I won't get to try these experiments until late next week, so if anyone can offer some predictions I would appreciate it. Read you later, Marc ****************************************************************************** From: James Barnett Date: Sat, 31 Jan 2004 19:32:22 +0000 Subject: Re: Advice on MS/MS of a compound Organization: * Marc Rosen wrote: } I have a compound that we synthesized (a prodrug made from a natural } product, modified by attaching a peptide ) The MW is 1648, verified by } MALDI. When I analyze by electrospray I see very little M+1 but the doubly } charged and triply charge species (m/z = 825.3 and 550.8, respectively) increasing the source voltage can redue multi charge states, ut in creases fagmentation. } provide a significant signal. I'm using -a triple quad- an API3000, direct } infusion dissolved in 50% CH3CN with 0.1% formic acid. (Should I switch to } methanol?) Yup MeCN reduces the charge on the droplet as the droplet desolvates. MeOH and isopropyl alcohol don't leak as much charge away from the droplet as it desolvates, hence larger signal. } Do you think I could do a product ion scan on the double charged and triple } charged ions and arrive at the same fragments? Also, my guess is that I } could produce fragments with an m/z greater than the two values I listed } above. your fragments will also have multiple charge states as well, the amino acid fragment for sure. } I'm still very new to MS (my other work pulls me away too much) and I won't } get to try these experiments until late next week, so if anyone can offer } some predictions I would appreciate it. } Read you later, } Marc Regards, James } } } ****************************************************************************** From: Freddy Smith Date: Sun, 01 Feb 2004 00:51:32 -0600 Subject: LC-MS (ion trap) Organization: * Just wondering if anyone had any feedback to give on the Finnigan LCQ Classic ion-traps ??? We are interested in possibly buying an instrument but have not had much experience with LC-MS-MS (only GC-MS). All comments welcomed ?? Freddy ****************************************************************************** From: ad@news1.news.xs4all.nl Date: Mon, 2 Feb 2004 19:40:51 +0100 Subject: Re: LC-MS (ion trap) Organization: * if you want any usefull info tell wat you want to do with the instrument. ad "Freddy Smith" wrote in message news:bvjric$gpl$1@news-int.gatech.edu... } Just wondering if anyone had any feedback to give on the Finnigan LCQ } Classic ion-traps ??? } } We are interested in possibly buying an instrument but have not had much } experience with LC-MS-MS (only GC-MS). } } All comments welcomed ?? } } Freddy } } ****************************************************************************** From: Mike Sherrell Date: Mon, 2 Feb 2004 12:47:17 -0800 Subject: LC/Mass specs and MALDIs for sale Organization: * Grizzly Analytical LC/Mass specs and MALDIs for sale. **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Q-Trap: $125,000 installed, eligible for service. Sciex API 3000 upgrade: $35,000. HSID interface: higher sensitivity and s/n at high flow rates; comparable to API 4000. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 300: $49,000. NT; has 365 interface. ES only. Install included; guar. eligible for svc contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex APCI source: $7,900. For API 150 or 300 or Q-Star Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $165,000. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $30,000. ES, API 1, Alpha station, good working order. +$20K/current Xcalibur, installation and 30-day warranty. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. MM Autospec M: $115,000. Mag Sector; orthogonal TOF MS/MS; 4 sources, FPD and TOF included; currently working well. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: Voyager DE: $69,500. 2000 instrument. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. ABI 4700: Must sell; all offers considered. TOF/TOF MS/MS Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com **Other mass specs, NMRs, DNA/protein sequencers & synthesizers available; check the website. All listed items subject to prior sale. ****************************************************************************** From: Jenny Date: 2 Feb 2004 17:44:46 -0800 Subject: Air compressors Organization: * Thought I'd send this out to see if anyone has any advice. In order to generate Nitrogen gas for electrospray nebulisation we have recently installed Nitrogen generators which are powered by oil-free air compressors. We use this system on both an FTMS and a triple quad instrument. This works well, except that we seem to be overworking the air compressors and they keep breaking down. The company that supplied the air compressors have been brilliant and they are very good and keep replacing the compressors, but we've been through three in five months - and this cannot go on for ever. We are using the air compressors within their operating specifics - though perhaps they do not like our 30 degree plus climate, and tropical storms. Anyone had similar difficulties - and more importantly found any solutions? Jenny ****************************************************************************** From: Freddy Smith Date: Tue, 03 Feb 2004 17:41:26 -0600 Subject: Re: LC-MS (ion trap) Organization: * We would like to be able to analyze low level impurities (100-500 ppm) in relatively dirty matrices to clean matrices (alot of other non-GC-able cmps). Would like to use for identification purposes in a lab where the MS would every now and then be plubed to an 1100 LC system (non-routine kinda stuff for plant support group). Thanking you ad@news1.news.xs4all.nl wrote: } if you want any usefull info tell wat you want to do with the instrument. } } ad } } "Freddy Smith" wrote in message } news:bvjric$gpl$1@news-int.gatech.edu... } } Just wondering if anyone had any feedback to give on the Finnigan LCQ } } Classic ion-traps ??? } } } } We are interested in possibly buying an instrument but have not had much } } experience with LC-MS-MS (only GC-MS). } } } } All comments welcomed ?? } } } } Freddy } } } } ****************************************************************************** From: Marc Rosen Date: Tue, 3 Feb 2004 21:36:37 -0500 Subject: Re: Air compressors Organization: * Hello Jenny, We purchased a suitable compressor to provide air for four N2 generators after discovering that our house compressor was not capable of servicing even one N2. Due to space constraints and noise level, the compressor resides in what was a darkroom that was fitted with additional ductwork to keep it at a tolerable 26-30 C. The compressor runs constantly and there have been no failures (yet). I will try to get more information tomorrow when i go into work. Marc "Jenny" wrote in message news:bvoagq$hth$1@news-int.gatech.edu... } } Thought I'd send this out to see if anyone has any advice. } } In order to generate Nitrogen gas for electrospray nebulisation we } have recently installed Nitrogen generators which are powered by } oil-free air compressors. We use this system on both an FTMS and a } triple quad instrument. This works well, except that we seem to be } overworking the air compressors and they keep breaking down. The } company that supplied the air compressors have been brilliant and they } are very good and keep replacing the compressors, but we've been } through three in five months - and this cannot go on for ever. We are } using the air compressors within their operating specifics - though } perhaps they do not like our 30 degree plus climate, and tropical } storms. Anyone had similar difficulties - and more importantly found } any solutions? } } Jenny } ****************************************************************************** From: Ilham Sanhaji Date: Wed, 4 Feb 2004 11:58:44 -0500 Subject: proteins in liquid matrices/ Maldi-Tof Organization: * Hi everybody First of all I ask you to excuse my English because i'm francophone I have few problems with Maldi -TOf i want to analyse proteins using liquid matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi don't succeed to have signal of proteins, large and small ones.but i can have signal of matrices. Another issue is that a vaccum in ionisation source take 4hours to be reached.so does someone have suggestions for solving these problems. thank you. ****************************************************************************** From: grober Date: Wed, 4 Feb 2004 20:15:50 -0000 Subject: Re: Air compressors Organization: * Hi Jenny, manufacturers do tend to be a bit optimistic when quoting "performance" figures for their units. I think that many rely on a "recovery period" i.e. the compressor unit recovering/cooling while the reservoir/tank supplies the output. If the compressor runs continuously it may not cope. The other possibility is that your voltage supply is marginal with respect to the voltage/current rating of the electric motor driving the compressor causing the motor to overheat/burn out. I have always found JUNAIR Compressors to be reliable units when rated correctly for the load demanded. "Jenny" wrote in message news:bvoagq$hth$1@news-int.gatech.edu... } } Thought I'd send this out to see if anyone has any advice. } } In order to generate Nitrogen gas for electrospray nebulisation we } have recently installed Nitrogen generators which are powered by } oil-free air compressors. We use this system on both an FTMS and a } triple quad instrument. This works well, except that we seem to be } overworking the air compressors and they keep breaking down. The } company that supplied the air compressors have been brilliant and they } are very good and keep replacing the compressors, but we've been } through three in five months - and this cannot go on for ever. We are } using the air compressors within their operating specifics - though } perhaps they do not like our 30 degree plus climate, and tropical } storms. Anyone had similar difficulties - and more importantly found } any solutions? } } Jenny } ****************************************************************************** From: motmot Date: Wed, 04 Feb 2004 22:25:20 -0500 Subject: check valve in nitrogen line Organization: * Does anyone know if installation of a check valve in the nitrogen line that supplies our mass specs might cause a contamination issue? We supply nitrogen to 2 triples, a QTOF and an LCQ from a dedicated nitrogen generator and the system works fabulously (and has been installed for over 2 years). I want to do some plumbing changes that would involve installing a check valve just after the nitrogen generator. When I look at catalogs that describe check valves, I see scary descriptions of the check valve components like "silicone base lubricant" or "molybdenum disulfide base lubricant" and things like Viton or fluorocarbon o-rings. I don't want to contaminate my nitrogen supply, but I want a check valve, but they all seem to have these components. Anyone have any experience with this? Thanks, Sue Hill Praecis Pharmaceuticals Waltham, Massachusetts susan.hill@praecis.com ****************************************************************************** From: Cory Date: 4 Feb 2004 21:52:18 -0800 Subject: LC/MS contaminants - your help appreciated Organization: * Hi, Having a hard time chasing a contaminant and hoping some one might be able to shed some light on the situation. This series of ions is very strong under electrospray conditions and appears in what should be clean water with 0.1% formic acid. 429, 445, 503, 519, 536, 593, 610 The most abundant peak at 445 is fragmented to give rise to the following species 429, 359, 341, 147, 73 - 341 is the base peak The issue is that this contamination has been completly intractible. It appears despite numerous bottles of water and acid and significant changes in composition and different spray setups. Another observation is that at low curtain gas levels the ions are strong and they can be significantly depressed with increased curtain gas. I'm at my wits end and hope that someone could help me with this - unfortunately I'm not well versed in small molecule mass spec so interpreting the ms/ms spectra will take me some time without a helping hand. I'm sure that someone will recognize this - my hunch is that this is a Si contaning compound - how it is showing up in our solvent I don't know yet... Thanks much, Cory ****************************************************************************** From: Dr. Dickie Date: Thu, 05 Feb 2004 17:54:06 -0500 Subject: Re: proteins in liquid matrices/ Maldi-Tof Organization: * On Wed, 4 Feb 2004 11:58:44 -0500, Ilham Sanhaji wrote: }Hi everybody } First of all I ask you to excuse my English because i'm francophone }I have few problems with Maldi -TOf i want to analyse proteins using liquid }matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with }Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi }don't succeed to have signal of proteins, large and small ones.but i can have }signal of matrices. Another issue is that a vaccum in ionisation source take }4hours to be reached.so does someone have suggestions for solving these }problems. thank you. If I could ask: why do you want to use those matrices? Why not use DHB or HCCA, or sinapinic for very high molecular weight proteins. Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: Simon Grist Date: Fri, 06 Feb 2004 14:18:41 +0000 Subject: Re: proteins in liquid matrices/ Maldi-Tof Organization: * Hi, from experience, glycerol is definately not compatable with MALDI techniques. Even a concentration as low as 0.5% v/v will interfere with protein crystallisation and ionisation. How big are the proteins you are looking at? Have you tried the following matrices - DHB or alpha-cyano for proteins smaller than 10KDa, or sinapinic acid for anything over 10KDa? For any of the above matrices, try 10mg/ml dissolved in 50:50 0.1%TFA/acetonitrile. Sime Ilham Sanhaji wrote: } Hi everybody } First of all I ask you to excuse my English because i'm francophone } I have few problems with Maldi -TOf i want to analyse proteins using liquid } matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with } Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi } don't succeed to have signal of proteins, large and small ones.but i can have } signal of matrices. Another issue is that a vaccum in ionisation source take } 4hours to be reached.so does someone have suggestions for solving these } problems. thank you. ****************************************************************************** From: Chip Cody Date: 6 Feb 2004 08:11:43 -0800 Subject: Re: LC/MS contaminants - your help appreciated Organization: * Are you suspecting silicon because of the m/z 73 peak? I don't recognize the contaminants, but if silicon is present, the M+2 isotope should be distinctive. As you probably know, the masses and relative isotopic of Si isotopes are: 27.976927 100.0000 28.976495 5.0778 29.973770 3.3473 So the M+2 isotope peak abundances will be quite distinctive for species containing multiple silicons. Good luck! Chip Cody JEOL USA, Inc. Cory wrote in message news:... } Hi, } } Having a hard time chasing a contaminant and hoping some one might be } able to shed some light on the situation. This series of ions is very } strong under electrospray conditions and appears in what should be } clean water with 0.1% formic acid. } } 429, 445, 503, 519, 536, 593, 610 } } The most abundant peak at 445 is fragmented to give rise to the } following species } } 429, 359, 341, 147, 73 - 341 is the base peak } } The issue is that this contamination has been completly intractible. } It appears despite numerous bottles of water and acid and significant } changes in composition and different spray setups. Another } observation is that at low curtain gas levels the ions are strong and } they can be significantly depressed with increased curtain gas. } } I'm at my wits end and hope that someone could help me with this - } unfortunately I'm not well versed in small molecule mass spec so } interpreting the ms/ms spectra will take me some time without a } helping hand. I'm sure that someone will recognize this - my hunch is } that this is a Si contaning compound - how it is showing up in our } solvent I don't know yet... } } Thanks much, } } Cory ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Sun, 08 Feb 2004 00:07:55 +0100 Subject: Re: LC/MS contaminants - your help appreciated Organization: * Hi Cory, these masses are very common in ESI, especially at low flow rates. We suggest them to originate from the fused silica tubing very often used in these systems. Try using FS tubing that is not deactivated. Your observation that a higher curtain gas level suppresses these ions might be caused by a general decrease of ion transmission. Best Regards Rainer Cory schrieb: } } Hi, } } Having a hard time chasing a contaminant and hoping some one might be } able to shed some light on the situation. This series of ions is very } strong under electrospray conditions and appears in what should be } clean water with 0.1% formic acid. } } 429, 445, 503, 519, 536, 593, 610 } } The most abundant peak at 445 is fragmented to give rise to the } following species } } 429, 359, 341, 147, 73 - 341 is the base peak } } The issue is that this contamination has been completly intractible. } It appears despite numerous bottles of water and acid and significant } changes in composition and different spray setups. Another } observation is that at low curtain gas levels the ions are strong and } they can be significantly depressed with increased curtain gas. } } I'm at my wits end and hope that someone could help me with this - } unfortunately I'm not well versed in small molecule mass spec so } interpreting the ms/ms spectra will take me some time without a } helping hand. I'm sure that someone will recognize this - my hunch is } that this is a Si contaning compound - how it is showing up in our } solvent I don't know yet... } } Thanks much, } } Cory ****************************************************************************** From: Bertram.Frank@epamail.epa.gov Date: Mon, 09 Feb 2004 11:31:45 -0500 Subject: Re: Air Compressors Organization: * Jenny: 1) I am not aware of any air compressors that are designed to run constantly. They all have a duty cycle in their specifications as far as I know, and to exceed that is asking for breakdown. Duty cycle is how long they can run and how long they have to rest to cool down before running again. They get very hot when they are running, and the compressor section will burn up eventually. 2) You didn't say what kind of failures you were experiencing. If they are on the electric motor side, then it could be your storms, where you can have spikes in the line voltage, and you can get protection on the line for that. Also, have the line voltage checked. If it is wrong, that can burn up a motor, especially if it is too low. (A low voltage causes more current draw and they get too hot.) 3) We have many zero air generators all over the building, plan to add N2 generators with the new mass specs, and we NOW feed them from a BIG compressor upstairs. We had problems galore in the past. We also had two cheap compressors that were a bad design ($300) and they were removed from the market. The piston rod disintegrated. If you have trouble keeping up with the N2 generators, you need more than one compressor for them, OR go to a bigger tank capacity with higher pressure (say 175 psi) so it doesn't have to run so often to refill the tank. 4) The compressor we now have is an oil-less, cast iron, 2-cylinder, 10 HP, 230 VAC, 3-phase, with 120 gallon receiving tank at 155 psi, and a refrigerated dryer on the output. It cost about $12,000, but it feeds the whole building, which is extensive. Ultimately, it is cheaper than all the problems we had before and all the down time. It also cured the wet air lines on the old building air. Before they would sometimes have water running out of them like a faucet because the coalescing filters overloaded and building maintenance couldn't seem to do anything about it. I am no expert but I have been through a bit of this, so if you have more questions, feel free. Frank ****************************************************************************** From: "Little, James - Eastman" Date: Tue, 10 Feb 2004 09:16:02 -0500 Subject: MW Calculator for Excel Organization: * Anyone got a copy of mm.xla an Excel Add-in written by Christain Hauck and described in Citation: Hauck, Christian. An Excel 4.0 Add-in Function to Calculate Molecular Mass J. Chem. Educ. 1996 73 431? I want something to calculate nominal MW in an Excel spreadsheet and possibly average and accurate. James Little Tel. No. 423-229-8685 office Tel. No. 423-229-8022 lab "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ "Twenty years from now you will be more disappointed by the things you didn't do than by the ones you did. So throw off the bowlines, sail away from the safe harbor. Catch the trade winds in your sails. Explore. Dream. Discover." ****************************************************************************** From: max Date: 10 Feb 2004 08:06:11 -0800 Subject: super basic mass spec tutorial Organization: * Hi, I'm working with a group that is using mass spec methods frequently and I don't have the technical background to get more than 30% of what they're saying. Can anyone recommend books or websites to get my feet wet? I only have a basic college chemistry background, so it would need to fairly low level. Thanks in advance for your help, Max ****************************************************************************** From: Chip Cody Date: 10 Feb 2004 10:17:37 -0800 Subject: Re: proteins in liquid matrices/ Maldi-Tof Organization: * Liquid-matrix MALDI is less common than solid-matrix MALDI, but it is an active area of research. Various matrix mixtures have been developed for lasers with different wavelegths. Take a look at the notes on the following web sites: http://www.chemistry.wustl.edu/~msf/damon/samp_prep_liquid.html www.chemistry.wustl.edu/~msf/ ASMS2002/Ying_Li_Poster.pdf The notes in the first site listed point out some potential problems, such as larger sample amounts required (1-10 pmol) than for solid-matrix MALDI, and limitations on mass range (25 kDa) and resolving power (a few hundred). Several reference articles on liquid-matrix MALDI are cited. If your ion source is not equipped for analysis of materials with higher vapor pressures, this may be difficult. We had good luck in using MALDI on a magnetic sector MS with the liquid matrix developed by Kolli and Orlando: V.S.K. Kolli, R. Orlando. 1996. A new matrix for MALDI on magnetic sector instruments with point detectors. Rapid Commun. Mass Spectrom. 10: 923-926. Another alternative is to use AP/MALDI, where vacuum problems are eliminated. Chip Cody JEOL USA, Inc. Ilham Sanhaji wrote in message news:... } Hi everybody } First of all I ask you to excuse my English because i'm francophone } I have few problems with Maldi -TOf i want to analyse proteins using liquid } matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with } Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi } don't succeed to have signal of proteins, large and small ones.but i can have } signal of matrices. Another issue is that a vaccum in ionisation source take } 4hours to be reached.so does someone have suggestions for solving these } problems. thank you. ****************************************************************************** From: Kendall Powell Date: 11 Feb 2004 06:12:29 -0800 Subject: Re: LC/MS contaminants - your help appreciated Organization: * Cory- An excellent paper detailing many of the common contaminants in ESI and APCI mass spec is: J. Am. Soc. Mass Spectrom 1999, 10, 1174-1187 In their table 3 they list the series of ions 355, 429, 503, 593, 667, 741, and 815 as coming from silicone rubber polymer - you also observed several of these ions. Hope that helps. -Kendall Cory wrote in message news:... } Hi, } } Having a hard time chasing a contaminant and hoping some one might be } able to shed some light on the situation. This series of ions is very } strong under electrospray conditions and appears in what should be } clean water with 0.1% formic acid. } } 429, 445, 503, 519, 536, 593, 610 } } The most abundant peak at 445 is fragmented to give rise to the } following species } } 429, 359, 341, 147, 73 - 341 is the base peak } } The issue is that this contamination has been completly intractible. } It appears despite numerous bottles of water and acid and significant } changes in composition and different spray setups. Another } observation is that at low curtain gas levels the ions are strong and } they can be significantly depressed with increased curtain gas. } } I'm at my wits end and hope that someone could help me with this - } unfortunately I'm not well versed in small molecule mass spec so } interpreting the ms/ms spectra will take me some time without a } helping hand. I'm sure that someone will recognize this - my hunch is } that this is a Si contaning compound - how it is showing up in our } solvent I don't know yet... } } Thanks much, } } Cory ****************************************************************************** From: Mudbunny Date: 11 Feb 2004 12:10:14 -0800 Subject: Question on HRMS Organization: * OK, this may be a silly question, but I can't seem to find the answer. I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One of the parameters which is open to change is sec/decade. I know that this has to do with the scan rate, but I can't find, anywhere, a definition of what this is. I am used to seeing it in terms of scans/second. Thanks Marcel ****************************************************************************** From: David Stranz Date: Thu, 12 Feb 2004 11:08:19 -0600 Subject: Re: Question on HRMS Organization: * Mudbunny wrote in news:c0e2mt$qad$1@news-int2.gatech.edu: } OK, this may be a silly question, but I can't seem to find the } answer. } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One } of the parameters which is open to change is sec/decade. I know } that this has to do with the scan rate, but I can't find, } anywhere, a definition of what this is. I am used to seeing it } in terms of scans/second. } } Thanks } } Marcel } } Try the Mass Spec Desk Reference by O. David Sparkman (ISBN0-9660813- 2-3). For magnetic sector instruments, a "decade" is an order of magnitude change in the m/z range, e.g. m/z 100 - 1000. sec/decade is therefore the rate at which the accelerating voltage is changed (assuming fixed magnetic field strength) in order to scan that m/z range. See page 49 of the Desk Reference for a more complete description; it is too lengthy to type here. David ****************************************************************************** From: Chip Cody Date: 12 Feb 2004 10:06:08 -0800 Subject: Re: Question on HRMS Organization: * Seconds per decade means the time it takes to scan an m/z range of M to 10M, i.e. the starting mass and the ending mass differ by a factor of 10. For example, 1 second per decade would allow you to scan from m/z 35 to m/z 350 in one second, or from m/z 500 to m/z 1000 in one second. The reason for this is the following: Traditional magnetic sector mass spectrometers scan the magnet exponentially. The scan law is: m(t) = m(o)e^kt Where e is 2.718281828..., m(t) is mass at time t, m(0) is the starting mass, k is a constant related to the scan speed and t is time. The exponential magnet scan provides a constant peak width independent of m/z. If you want to express the scan law in linear form (y=ax+b), you have to use logarithms. It is convenient to use base 10 logs, hence the use of the "decade". (If you used natural logs, you would have to express a scan range of M to 2.303M, not a very intuitive value!). Chip Cody (JEOL) Mudbunny wrote in message news:... } OK, this may be a silly question, but I can't seem to find the answer. } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One of } the parameters which is open to change is sec/decade. I know that this } has to do with the scan rate, but I can't find, anywhere, a definition } of what this is. I am used to seeing it in terms of scans/second. } } Thanks } } Marcel ****************************************************************************** From: Rod Buchanan Date: Thu, 12 Feb 2004 19:54:02 -0000 Subject: Re: Question on HRMS Organization: * "Mudbunny" wrote in message news:c0e2mt$qad$1@news-int2.gatech.edu... } OK, this may be a silly question, but I can't seem to find the answer. } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One of } the parameters which is open to change is sec/decade. I know that this } has to do with the scan rate, but I can't find, anywhere, a definition } of what this is. I am used to seeing it in terms of scans/second. } } Thanks } } Marcel } Brief answer: It is the time during scanning for the focussed mass to be reduced to one-tenth (i.e. by one decade of mass) such as from m/z 1000 to m/z 100. Thus the larger the number, the slower the scan. Explanation: On a magnetic sector instrument, such as the Concept, now manufactured and supported by MSI (Altrincham, England) the magnet is usually scanned with an exponential decay scan law. Traditionally this was achieved by allowing the magnetic current to decay through an R/C circuit, but is now frequently achieved by a programmed scan on a high resolution DAC. In terms of AMU per second the scan slows down the lower in mass that is scanned. The resolution of a sector instrument is usually defined in terms of the ratio of masses that may be resolved at a 10% valley. Thus on a Concept operating at 10,000 resolution, masses differing by 1 part in 10,000 are resolved, so it is possible to separate ion species at m/z 250.000 and 250.025. The resolution, as defined above, is approximately constant over the whole mass range so if an exponential scan law is used, the time that is needed to scan over a peak remains approximately constant. [The maths is a bit long for inclusion here] Data is collected at a fixed rate during the scan, thus the number of data points collected will be similar for every peak. This has considerable advantages in calculating peak centroids and peak areas. Please feel free to email me off group if you want more information. See below for the address. MACH 3x tip: You can get help on many of the parameters and buttons by placing the mouse over the item concerned an pressing the "Help" button on the keyboard. For the SunView version of MACH 3, help is obtained by clicking the middle mouse button on the item concerned. Rod Buchanan, MACH 3 programmer, Mass Spectrometry International, Altrincham, England rod (at) massint http://www massint.co.uk ****************************************************************************** From: Reinhard Stroh Date: Fri, 13 Feb 2004 11:12:32 +0100 Subject: Re: Air compressors Organization: * Jenny wrote: } Thought I'd send this out to see if anyone has any advice. } } In order to generate Nitrogen gas for electrospray nebulisation we } have recently installed Nitrogen generators which are powered by } oil-free air compressors. We use this system on both an FTMS and a } triple quad instrument. This works well, except that we seem to be } overworking the air compressors and they keep breaking down. The } company that supplied the air compressors have been brilliant and they } are very good and keep replacing the compressors, but we've been } through three in five months - and this cannot go on for ever. We are } using the air compressors within their operating specifics - though } perhaps they do not like our 30 degree plus climate, and tropical } storms. Anyone had similar difficulties - and more importantly found } any solutions? } } Jenny } Hi, Jenny, we evaluated compressors for use with nitrogen generators. We were told not to use oil-free compressors because they are not so robust. Instead, we use normal compressors, a cold-trap (2 degrees C) and a couple of spray- and dust filters as well as an activated coal filter. This works excellent since 4 years or so. We never had problems with the N2 quality so far. Of course, the filters have to be replaced in time. Our company is located in Austria, so you´ll have different suppliers. We use "MARK" Compressors (a subsidiary of Atlas Copco). In the US you may find "GARDNER" Compressors (Denver). regards Reinhard ****************************************************************************** From: Phil Date: Thu, 12 Feb 2004 00:01:10 +0100 Subject: Re: MW Calculator for Excel Organization: * [Moderator's note - Three files were attached to this, but the posting program does not handle attachments well. The files may be found at http://www.chemistry.gatech.edu/stms/Module1.bas http://www.chemistry.gatech.edu/stms/CalcForm.frx and http://www.chemistry.gatech.edu/stms/CalcForm.frm DB] Hi there James, Found your message tonight. I don't have any mm.xla addin but did quickly make this macro for you.. Maybe this can help. If not, feel free to modify and spread it around. I started off a Javascript I found on the net. Just fire up Excel and VBA, import these 2 files under the PERSONAL.XLS workbook and save it, then run it. This one is interactive, but could easily be modified to return the value as a function. If you don't see a PERSONAL.XLS workbook on the top left pane of the VBA environment, just start Tools/Macros/Record New macro. This will open a window asking you where you want to store the macros. Select Personal.xls. A small toolbar with a record button will show up. Just close this toolbar and your personal.xls file will be created. It is not fully tested and only expects that you type formulas exactly as they should be, that is, lower and upper cases. If I have a minute one day, I'll fix this. Hope this helps. Let me know Rgds from Paris, France Phil "Little, James - Eastman" a écrit dans le message de news:c0arhe$3r2$1@news-int.gatech.edu... } } Anyone got a copy of mm.xla an Excel Add-in written by Christain Hauck and described in Citation: Hauck, Christian. An Excel } 4.0 Add-in Function to Calculate Molecular Mass J. Chem. Educ. 1996 73 431? } } I want something to calculate nominal MW in an Excel spreadsheet and possibly average and accurate. } } } } } James Little } Tel. No. 423-229-8685 office } Tel. No. 423-229-8022 lab } "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle } Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ } } "Twenty years from now you will be more disappointed by the things you didn't do than by the ones you did. So throw off the } bowlines, sail away from the safe harbor. Catch the trade winds in your sails. Explore. Dream. Discover." } } ****************************************************************************** From: usedlabequip Date: 13 Feb 2004 10:13:30 -0800 Subject: Refurbished Analytical Equipment Available Organization: * !!!!FOR SALE!!!! 1. Applied BioSystems Prism 7900HT Real Time PCR 2. PerSeptive-ABI Mariner (ESI-TOF) Biospectrometry Workstation 3.) Cohesive Technologies model turboflow 2300 HTLC/HPLC system complete with HP 1100 # G1322A Degasser, # G1311A Quat. Pump, & # G1312 Binary Pump 4.) Perspective BioSystems VOYAGER-DE STR MALDI-TOF. 5.) Applied BioSystems Q-TRAP, LC/MS/MS 6.) Micromass Q-TOF II 7.) Thermo Finnigan TSQ 7000 with API II LC/MS/MS 8.) Thermo Finnigan LCQ Classic LC/MS/MS 9.) Micromass ZMD 2000 LC/MS 10.) Micromass Quattro Ultima LC/MS/MS 11.) Varian Unity Inova 300 MHz NMR 12.) Varian Mercury MVX 300 MHz NMR 13.) Bruker AC300 MHz Plus NMR 14.) Varian Unity Plus 400 MHz NMR 15.) Varian Unity 500 MHz NMR 16.) Bruker Avance 500 MHz LC/NMR 17.) Varian Inova 600 MHz LC/NMR 18.) Bruker Avance 700 MHz NMR 19.) Genomics Solutions GeneTAC Hybstation *Please call for further details. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 ****************************************************************************** From: Elijah Bailey Date: 14 Feb 2004 10:15:55 -0800 Subject: NewBie: Help Organization: * I got some mass spec data of blood samples (for cancer patients) to analyze and it is distributed in 4 directories. NormalControl, Benign, Malignant, Reference I understand Benign and Malignant stand for cancer. What might be NormalControl and Reference? I dont know any biology, just trying my luck here if someone could help. Thanks in Advance for your help/comments, --Elijah ****************************************************************************** From: Joerg Hau Date: Sun, 15 Feb 2004 10:49:43 +0100 Subject: Re: Question on HRMS Organization: * Hi David } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One } } of the parameters which is open to change is sec/decade. I know } } that this has to do with the scan rate, but I can't find, } } anywhere, a definition of what this is. I am used to seeing it } } in terms of scans/second. } } For magnetic sector instruments, a "decade" is an order of magnitude } change in the m/z range, e.g. m/z 100 - 1000. sec/decade is } therefore the rate at which the accelerating voltage is changed } (assuming fixed magnetic field strength) in order to scan that m/z } range. In theory I agree, but in practice may obtain rather bad mass spectra if you vary the accelerating voltage over such a large range (e.g. from 3000 to 300 V!). On a sector field instrument, voltage scanning is usually used only for very narrow mass ranges (e.g. ion source tuning), linked scans, or fast monitoring of multiple mass traces. Generally not more than 10% sweep of the full voltage. Common practice instead to keep the accelerating voltage constant and to scan the magnetic field. As Chip Cody and Rod Buchanan pointed out, peak width will be constant in time if you scan with an exponential scan law. Again, all this applies to sector field MS only ... ah, those good ol' sector machines ... Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: Maxell Date: 15 Feb 2004 04:06:49 -0800 Subject: Databases Organization: * Hi! Where can I find a good database that is searchable on molecular weight. It should preferably be free of charge. ****************************************************************************** From: David Stranz Date: Mon, 16 Feb 2004 08:29:57 -0600 Subject: Re: Question on HRMS Organization: * Joerg Hau wrote in news:c0ostl$67i$1@news-int.gatech.edu: } Hi David } } } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. } One } } of the parameters which is open to change is sec/decade. } I know } } that this has to do with the scan rate, but I can't } find, } } anywhere, a definition of what this is. I am used to } seeing it } } in terms of scans/second. } } } } For magnetic sector instruments, a "decade" is an order of } magnitude } change in the m/z range, e.g. m/z 100 - 1000. } sec/decade is } therefore the rate at which the accelerating } voltage is changed } (assuming fixed magnetic field strength) in } order to scan that m/z } range. } } In theory I agree, but in practice may obtain rather bad mass } spectra if you vary the accelerating voltage over such a large } range (e.g. from 3000 to 300 V!). On a sector field instrument, } voltage scanning is usually used only for very narrow mass } ranges (e.g. ion source tuning), linked scans, or fast } monitoring of multiple mass traces. Generally not more than 10% } sweep of the full voltage. } } Common practice instead to keep the accelerating voltage } constant and to scan the magnetic field. As Chip Cody and Rod } Buchanan pointed out, peak width will be constant in time if you } scan with an exponential scan law. } } Again, all this applies to sector field MS only ... ah, those } good ol' sector machines ... } } Cheers + HTH, } } - Joerg } } My comments were paraphrased from David Sparkman's MS Desk Reference, so I think your complaint is with him! I traded MS hardware for PC hardware a long time ago... I'm wary of magnetic fields now. Cheers, David ****************************************************************************** From: Darryl Date: 16 Feb 2004 11:50:52 -0800 Subject: HP5989 HELP Organization: * Hi, I have a 5989. I've spent 2500$ on having the HP engineer come out to repair but he and the people who designed it could not fix it. SOOOOOOOOO. The problem seems to be in the feedback portion of the mass filter electronics. Symptoms are 0 abundance. We swapped the RFPA board and controller board plus they soaked me for some consumables like HED and ceramic blocks. any advice please email me if you think you can help this is real pain to figure out thanks ****************************************************************************** From: Chip Cody Date: 19 Feb 2004 05:44:43 -0800 Subject: Re: Question on HRMS Organization: * As Joerg pointed out, the most common scan mode for a magnetic sector is to set the accelerating voltage and electrostatic sector analyzer (ESA) to pass ions of a set kinetic energy and then to scan the magnetic field. The advantage of this scan mode is that one can scan over the full m/z range of the spectrometer with (essentially) a constant sensitivity as a function of m/z. The disadvantage is that magnet hysteresis leads to small (ppm-level) variations from scan to scan that require an internal standard with lots of peaks if one wishes to measure exact masses. Exact calibration of a magnet scan requires four reference points to bracket each measured m/z. Voltage scanning is an alternative. In this scan mode, you "park" the magnet at a fixed value and scan the accelerating voltage and ESA. Magnet hysteresis is not a problem, but the response decreases as voltage decreases (and m/z increases) during the scan. If our mass spectrometers are adjusted correctly, we can scan the voltage from M to 2M (50% of the acclerating voltage range), but the signal at 2M will be decreased. Lock masses from known reference standards are used to correct slow ppm-level drift in the magnetic field due to temperature fluctuations. Electric field scans are linear, so calibration only requires two reference points. Scanning from M to 2M is more-or-less the maximum possible range for a voltage scan. Scanning over a decade would produce no signal for the high-m/z ions. The same comments apply to selected ion monitoring (SIM) measurements. Magnet switching is used for low-resolution SIM, and voltage switching is used for high-resolution SIM. There are exceptions to everything. We have performed magnet-switching HRSIM experiments, but they are uncommon. Magnetic sectos scans are discussed on our web page at: http://www.jeol.com/ms/docs/ms_analyzers.html Other scan modes involve scanning both the magnet and ESA together. Linked-scan MS/MS is discussed at: http://www.jeol.com/ms/docs/ms-ms.pdf Chip Cody (JEOL) ------------------------------------------------------- Joerg Hau wrote in message ... } } } } For magnetic sector instruments, a "decade" is an order of magnitude } } change in the m/z range, e.g. m/z 100 - 1000. sec/decade is } } therefore the rate at which the accelerating voltage is changed } } (assuming fixed magnetic field strength) in order to scan that m/z } } range. } } In theory I agree, but in practice may obtain rather bad mass spectra } if you vary the accelerating voltage over such a large range (e.g. } from 3000 to 300 V!). On a sector field instrument, voltage scanning } is usually used only for very narrow mass ranges (e.g. ion source } tuning), linked scans, or fast monitoring of multiple mass traces. } Generally not more than 10% sweep of the full voltage. } ****************************************************************************** From: Mudbunny Date: 19 Feb 2004 13:34:57 -0800 Subject: Re: Question on HRMS Organization: * Chip Cody wrote in message news:... } Seconds per decade means the time it takes to scan an m/z range of M } to 10M, i.e. the starting mass and the ending mass differ by a factor } of 10. For example, 1 second per decade would allow you to scan from } m/z 35 to m/z 350 in one second, or from m/z 500 to m/z 1000 in one } second. I am just trying to understand, so forgive the question. Shouln't the last example be from m/z 500(M) to m/z 5000(10M)?? ****************************************************************************** From: Mudbunny Date: 19 Feb 2004 13:42:13 -0800 Subject: Re: Question on HRMS Organization: * } In theory I agree, but in practice may obtain rather bad mass spectra } if you vary the accelerating voltage over such a large range (e.g. } from 3000 to 300 V!). On a sector field instrument, voltage scanning } is usually used only for very narrow mass ranges (e.g. ion source } tuning), linked scans, or fast monitoring of multiple mass traces. } Generally not more than 10% sweep of the full voltage. So then I can tell my bosses, who want me to use the Concept to do quantitation of pesticides by GC-MS (m/z range of about 60 to 450) that it is not really going to be useful? From what I understand from all of the response so far (thank you!! thank you!! thank you!!!) I will get decent response at the low masses, but as I get higher, the response is going to suck, thus making it very difficult to do quantitative analysis of compounds in the ppb concentration range. This then will lead them to the next question that I would like to confirm. They are then going to ask me to do SIM analysis of the pesticides. How can I go from a basic MS dataset to the exact masses required for a SIM experiment. I have a direct probe, so is it as simple as putting a sample of the pesticide on the end of the probe, sticking it in, and then using the scope to manually look for peaks?? Thanks again for all of your help. Marcel ****************************************************************************** From: Mudbunny Date: 19 Feb 2004 13:47:06 -0800 Subject: Re: Question on HRMS Organization: * } Voltage scanning is an alternative. In this scan mode, you "park" the } magnet at a fixed value and scan the accelerating voltage and ESA. } Magnet hysteresis is not a problem, but the response decreases as } voltage decreases (and m/z increases) during the scan. } } If our mass spectrometers are adjusted correctly, we can scan the } voltage from M to 2M (50% of the acclerating voltage range), but the } signal at 2M will be decreased. Lock masses from known reference } standards are used to correct slow ppm-level drift in the magnetic } field due to temperature fluctuations. Electric field scans are } linear, so calibration only requires two reference points. Scanning } from M to 2M is more-or-less the maximum possible range for a voltage } scan. Scanning over a decade would produce no signal for the high-m/z } ions. Ahhh. That'll teach me to reply before reading the whole thread. Thanks!! } The same comments apply to selected ion monitoring (SIM) measurements. } Magnet switching is used for low-resolution SIM, and voltage } switching is used for high-resolution SIM. There are exceptions to } everything. We have performed magnet-switching HRSIM experiments, but } they are uncommon. Ahhh. Interesting. I will, in the very near future, be using the instrument to do the quantitative high res SIM of various nitrosamines, with pfk as the reference. So what are the advantages and disadvantages of using the instrument in Field stabilisation mode vs. Current stabilisation mode? In this case, sensitivity is a must, as we will be looking at concentrations in ppt (parts per trillion) levels. Marcel ****************************************************************************** From: "Horler, R" Date: Fri, 20 Feb 2004 09:35:00 +0000 Subject: Tryptic digests Organization: * Hello To set the scene I am currently involved in a creating a new E coli database and part of what we plan to put in this database is a large collection of experimental data from published work. One problem I am having at the moment is a number of proteomic experiments show a predicted number of tryptic fragments but the actual numbers vary hugely between different published work. My understanding, as a geneticist, is that trypsin cuts like a restriction enzyme after arginine or lysine residues and therefore I would have thought that the number of fragments would be easy to predict. The numbers for specific proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. Could you tell me if my understanding of the specificity of trypsin digest is correct and if not what it is? If so why would the predicted number of fragemtns vary so much in the two examples? Regards Richard ****************************************************************************** From: Freddy Smith Date: Fri, 20 Feb 2004 07:07:16 -0600 Subject: Re: Question on HRMS Organization: * Mudbunny wrote: } } In theory I agree, but in practice may obtain rather bad mass spectra } } if you vary the accelerating voltage over such a large range (e.g. } } from 3000 to 300 V!). On a sector field instrument, voltage scanning } } is usually used only for very narrow mass ranges (e.g. ion source } } tuning), linked scans, or fast monitoring of multiple mass traces. } } Generally not more than 10% sweep of the full voltage. } } So then I can tell my bosses, who want me to use the Concept to do } quantitation of pesticides by GC-MS (m/z range of about 60 to 450) } that it is not really going to be useful? From what I understand from } all of the response so far (thank you!! thank you!! thank you!!!) I } will get decent response at the low masses, but as I get higher, the } response is going to suck, thus making it very difficult to do } quantitative analysis of compounds in the ppb concentration range. } } This then will lead them to the next question that I would like to } confirm. They are then going to ask me to do SIM analysis of the } pesticides. How can I go from a basic MS dataset to the exact masses } required for a SIM experiment. I have a direct probe, so is it as } simple as putting a sample of the pesticide on the end of the probe, } sticking it in, and then using the scope to manually look for peaks?? } I am new to the MS field but am of the thought that it will be very difficult to detect ppb components in a mix with the direct probe method. I would have imagined that one would require pre separation with a GC column. Even with SIM you would not be able to quantify your levels as you would not know which species are generating those ions, with the added problem that some of these ions might be secondary ions ?? More experienced users might be able to comment further and correct me on this if I am wrong ??? } } Thanks again for all of your help. } } Marcel ****************************************************************************** From: Freddy Smith Date: Fri, 20 Feb 2004 07:09:51 -0600 Subject: Ion traps Organization: * Just wondering if anyone had any feedback to give on the Finnigan LCQ Classic ion-traps ??? We are interested in possibly buying an instrument but have not had much experience with LC-MS-MS (only GC-MS). All comments welcomed ?? We would like to be able to analyze low level impurities (100-500 ppm) in relatively dirty matrices to clean matrices (alot of other non-GC-able cmps). Would like to use for identification purposes in a lab where the MS would every now and then be plubed to an 1100 LC system (non-routine kinda stuff for plant support group). Freddy ****************************************************************************** From: Eric van der Horst Date: 20 Feb 2004 05:45:50 -0800 Subject: sensitivity in LC-MS(/MS) dependend on guad column Organization: * During method development in our laboratory we sometimes come across a peculiar problem: The sensitivity of the Mass spectrometer (Peak heigth and total area under the chromatogram) can be dependent on whether or not we use a guard column or a fritt filter. Sensitivity has been seen to increase and decrease, depending on the compound. Not only for processed samples from a biological matrix, but also in test solutions (compound dissolved a water/organic solvent mixture)this effect occurs. The ionisation technique we use is turbo-ionspray. From ionisation theory I cannot understand what would cause the change in sensitiviy. Could someone hazard a guess for me? Thanking you in advance, Eric van der Horst ****************************************************************************** From: Chip Cody Date: 20 Feb 2004 08:00:21 -0800 Subject: Re: Question on HRMS Organization: * There are several questions pending. Here are some answers: 1. This is where that art of analytical method development comes into play. The method development for HRSIM requires careful choice of the target m/z set for each analyte. Because of the M to 2 M (or less...) limitation, you cannot always chose the most abundant peaks as you might for LRSIM. It is sometimes better to chose a closely spaced set of peaks at higher m/z, even if they are not the most abundant. For example, one might monitor M+. and [M-Cl]+, or M+. and isotope peaks for a polychlorinated species. There are established protocols (e.g. EPA protocols) for HRSIM for many compound classes. 2. Yes, I made a mistake. I intended to say that a decade is 500 to 5000. I was thinking about the M to 2M range for voltage scans. 3. I don't know about the stabilization modes on the Concept. On our machines, the Hall probe field regulation can be turned off, but this is only sometimes done at a resolving power of 30,000 or more when noise from the regulation circuit can become significant. If you do not use field stabilization, you may have cleaner peaks at very high resolution, but you must rely on the lock mass correction and temperature stability in the lab and cooling water is critical. I do not turn off field stabilization for any routine measurements that I make. Chip Cody Mudbunny wrote in message news:... } } Voltage scanning is an alternative. In this scan mode, you "park" the } } magnet at a fixed value and scan the accelerating voltage and ESA. } } Magnet hysteresis is not a problem, but the response decreases as } } voltage decreases (and m/z increases) during the scan. } } } } If our mass spectrometers are adjusted correctly, we can scan the } } voltage from M to 2M (50% of the acclerating voltage range), but the } } signal at 2M will be decreased. Lock masses from known reference } } standards are used to correct slow ppm-level drift in the magnetic } } field due to temperature fluctuations. Electric field scans are } } linear, so calibration only requires two reference points. Scanning } } from M to 2M is more-or-less the maximum possible range for a voltage } } scan. Scanning over a decade would produce no signal for the high-m/z } } ions. } } Ahhh. That'll teach me to reply before reading the whole thread. } Thanks!! } } } The same comments apply to selected ion monitoring (SIM) measurements. } } Magnet switching is used for low-resolution SIM, and voltage } } switching is used for high-resolution SIM. There are exceptions to } } everything. We have performed magnet-switching HRSIM experiments, but } } they are uncommon. } } Ahhh. Interesting. I will, in the very near future, be using the } instrument to do the quantitative high res SIM of various } nitrosamines, with pfk as the reference. So what are the advantages } and disadvantages of using the instrument in Field stabilisation mode } vs. Current stabilisation mode? In this case, sensitivity is a must, } as we will be looking at concentrations in ppt (parts per trillion) } levels. } } Marcel ****************************************************************************** From: Mudbunny Date: 20 Feb 2004 10:11:24 -0800 Subject: Re: Question on HRMS Organization: * Freddy Smith wrote in message news:... } Mudbunny wrote: } } } } So then I can tell my bosses, who want me to use the Concept to do } } quantitation of pesticides by GC-MS (m/z range of about 60 to 450) } } that it is not really going to be useful? From what I understand from } } all of the response so far (thank you!! thank you!! thank you!!!) I } } will get decent response at the low masses, but as I get higher, the } } response is going to suck, thus making it very difficult to do } } quantitative analysis of compounds in the ppb concentration range. } } } } This then will lead them to the next question that I would like to } } confirm. They are then going to ask me to do SIM analysis of the } } pesticides. How can I go from a basic MS dataset to the exact masses } } required for a SIM experiment. I have a direct probe, so is it as } } simple as putting a sample of the pesticide on the end of the probe, } } sticking it in, and then using the scope to manually look for peaks?? } } } } I am new to the MS field but am of the thought that it will be very } difficult to detect ppb components in a mix with the direct probe method. } I would have imagined that one would require pre separation with a GC } column. Even with SIM you would not be able to quantify your levels as you } would not know which species are generating those ions, with the added } problem that some of these ions might be secondary ions ?? More } experienced users might be able to comment further and correct me on this } if I am wrong ??? I think I was pretty unclear on the above. (I was typing it after a long day at work and my mind was focussed on going home and watching Survivor and CSI). Anyways, I should have said to (1)use the probe on the neat compounds to determine the exact masses (2) inject single component mixes into the GC to determine the retention time and (3) then use those determined masses/RTs in a SIM experiment to do the quantitation. Marcel ****************************************************************************** From: Mudbunny Date: 20 Feb 2004 10:14:36 -0800 Subject: Re: NewBie: Help Organization: * Elijah Bailey wrote in message news:... } I got some mass spec data of blood samples (for cancer patients) } to analyze and it is distributed in 4 directories. } } NormalControl, Benign, Malignant, Reference } } I understand Benign and Malignant stand for cancer. What might be } NormalControl and Reference? I dont know any biology, just trying } my luck here if someone could help. I am not in Biology either, but Here is what I think. NormalControl indicates, to me, that you might be doing analyses of patients undergoing some sort of therapy. The NormalControl would be bloodsamples of patients who are not undergoing the treatment, or they may be of the patient before the treatment. To establish a baseline of sorts. Reference would be reference compounds or spectra. Of the chemo drug, normal blood components and the like. Keep in mind I am not experienced at all with blood chemistry or any biology at all. Good luck. Marcel ****************************************************************************** From: phil harris Date: 20 Feb 2004 12:03:35 -0800 Subject: frac pattern and background gas Organization: * I was working with a process mass spec (quadrupole) and observed what I saw as unusual results. Any advice on explaining these. To do our quantititative work, we need to determing the fractionation pattern of the gases of interest. In general, they are similar to the NIST library but each mass spec is a bit different. To determine our methane fractionation patter, we initially used a methane balance argon cylinder. However, when we ran a mixture that had both 50 % hydrogen and 20 % CO2 in it (along with argon and methane), we got significantly different fractionation patterns (ie ion current at masses 15, 14 and 13 were several percent different than they were for the methane/argon cylinder). I am not concerned that the absolute currents were different, but rather that their ratio was different as this indicates a change in the fractionation pattern. I can understand that as I change the gas composition, I can get different amounts of gas getting through the capillary leak, but I am not sure why the fractionation pattern changed. Is this due to ion molecule reactions, and the H2+ ions reaction with neutral species from the methane ? I would have thought that about 1 - 10 microtorr, these sort of reactions would be inconsequential. Any advice or suggestions ? Regards Phil ****************************************************************************** From: TObject Date: Sun, 22 Feb 2004 20:59:28 GMT Subject: Re: Databases Organization: * On peptide-catalog.com you can search for peptides by molecular weight. http://www.peptide-catalog.com/PC/Peptides Try google, it pulls out a number of such web sites. "Maxell" wrote in message news:c0osu6$4ut$1@news-int2.gatech.edu... } } Hi! } Where can I find a good database that is searchable on molecular } weight. It should preferably be free of charge. } ****************************************************************************** From: Kendall Date: Mon, 23 Feb 2004 03:01:06 GMT Subject: Re: Tryptic digests Organization: * } To set the scene I am currently involved in a creating a new E coli } database and part of what we plan to put in this database is a large } collection of experimental data from published work. } } One problem I am having at the moment is a number of proteomic } experiments show a predicted number of tryptic fragments but the actual } numbers vary hugely between different published work. My understanding, } as a geneticist, is that trypsin cuts like a restriction enzyme after } arginine or lysine residues and therefore I would have thought that the } number of fragments would be easy to predict. The numbers for specific } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } Could you tell me if my understanding of the specificity of trypsin } digest is correct and if not what it is? If so why would the predicted } number of fragemtns vary so much in the two examples? } } Regards } } Richard Richard- While I'm not entirely clear on what your stated numbers mean, let me take a stab at your questions anyway. First off, your understanding of the specificity of Trypsin is correct, though, depending on the specific amino acid sequence, there can be additional "rules". A brief explanation of these special cases of Trypsin behavior can be found at: http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html#Tryps I must admit, however, that I do not understand what your stated numbers for each of the two protein examples means (i.e., 19 or 27 for fep A). Do you mean that one source predicts 19 peptides and another predicts 27 peptides? Or do you mean that one source reports the *detection* of 19 peptides and another reports the detection of 27? If the numbers are theoretical numbers of peptides, I cannot answer your question. However, if the numbers are from two different sets of experimental results, there are several possibilities: 1. Trypsin digestion may not go to completion if the experimental conditions are not chosen properly. For instance, some proteins, under physiological conditions, are highly resistant to protease digestion (i.e., Ribonuclease A). However, under slightly destabilizing conditions, with the addition of some heat or a chemical denaturant, the folded protein structure "breaks down" allowing digestion to proceed to completion. 2. If all of the peptides are analyzed at the same time, i.e. a MALDI experiment or an electrospray (ESI) experiment without chromatographic separation, the ionization of some peptides will suppress the ionization of other peptides present in the mixture. This ionization suppression effect is widely observed when analyzing mixtures of peptides, and for this reason many times a chromatographic separation is coupled to a mass spec. in order to lower the number of peptides that are introduced to the mass spec at the same time. 3. MALDI and ESI experiments performed on the same peptide digest will often produce non-identical, but complimentary, results. Often MALDI can "see" some peptides that are not seen by ESI, and vice versa. Hope I understood your question and some of my ramblings were helpful; if not, let me know! -Kendall ****************************************************************************** From: David Stranz Date: Mon, 23 Feb 2004 13:58:09 -0600 Subject: Re: Tryptic digests Organization: * Kendall wrote in news:c1cud3$jbp$1@news-int2.gatech.edu: } } To set the scene I am currently involved in a creating a new E } coli } database and part of what we plan to put in this database } is a large } collection of experimental data from published } work. } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but } the actual } numbers vary hugely between different published } work. My understanding, } as a geneticist, is that trypsin cuts } like a restriction enzyme after } arginine or lysine residues } and therefore I would have thought that the } number of } fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } Could you tell me if my understanding of the specificity of } trypsin } digest is correct and if not what it is? If so why } would the predicted } number of fragemtns vary so much in the } two examples? } } } Regards } } } } Richard } } } Richard- } } While I'm not entirely clear on what your stated numbers mean, } let me take a stab at your questions anyway. First off, your } understanding of the specificity of Trypsin is correct, though, } depending on the specific amino acid sequence, there can be } additional "rules". A brief explanation of these special cases } of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.h } tml#Tryps } } I must admit, however, that I do not understand what your stated } numbers for each of the two protein examples means (i.e., 19 or } 27 for fep A). Do you mean that one source predicts 19 peptides } and another predicts 27 peptides? Or do you mean that one source } reports the *detection* of 19 peptides and another reports the } detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot } answer your question. } } However, if the numbers are from two different sets of } experimental results, there are several possibilities: } 1. Trypsin digestion may not go to completion if the } experimental conditions are not chosen properly. For instance, } some proteins, under physiological conditions, are highly } resistant to protease digestion (i.e., Ribonuclease A). } However, under slightly destabilizing conditions, with the } addition of some heat or a chemical denaturant, the folded } protein structure "breaks down" allowing digestion to proceed to } completion. 2. If all of the peptides are analyzed at the same } time, i.e. a MALDI experiment or an electrospray (ESI) } experiment without chromatographic separation, the ionization of } some peptides will suppress the ionization of other peptides } present in the mixture. This ionization suppression effect is } widely observed when analyzing mixtures of peptides, and for } this reason many times a chromatographic separation is coupled } to a mass spec. in order to lower the number of peptides that } are introduced to the mass spec at the same time. } 3. MALDI and ESI experiments performed on the same peptide } digest will often produce non-identical, but complimentary, } results. Often MALDI can "see" some peptides that are not seen } by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were } helpful; if not, let me know! } } -Kendall } } } An additional complication to the above is that in many cases "identification" of a peptide is made via a database search, using one of the many software programs and databases available. Failure to "identify" a peptide could mean that a) the peptide wasn't observed experimentally (due to reasons described above), b) the selection criteria for deciding which experimental m/z values to submit for the search excluded one or more of the observed peptides (signal too weak, too many peptides already on the list, whatever), c) the database has sequence errors, resulting in calculation of an incorrect theoretical mass for the peptide and therefore a failure to match numerically, d) the database doesn't contain information about post- translational modifications, and the experimental peptide is modified (thus again, a mismatch between observed and theoretical mass based on sequence), e) in ESI in particular, the charge state on the observed peptide wasn't correctly deduced from the data, and therefore the mass presented to the search is incorrect, f) the observed peptide has an adduct (such as sodium or potassium) that isn't accounted for by the search software (which might assume everything is protonated), g) the database doesn't contain the protein from which the peptide was derived, and therefore the protein reported as the "hit" is just plain wrong, or h) any one of a number of other ways things could go awry. Hope this "helps" :-) David ****************************************************************************** From: "Horler, R" Date: Tue, 24 Feb 2004 11:34:44 +0000 Subject: Re: Tryptic digests Organization: * Kendell Many thanks for your response. It has expanded my knowledge of MS although unfortunately the numbers are the predicted number of tryptic peptides. Other data i.e. detected number, understandably are also different but that was to be expected at least now i understand why a bit better. Many thanks Richard Kendall wrote: } } To set the scene I am currently involved in a creating a new E coli } } database and part of what we plan to put in this database is a large } } collection of experimental data from published work. } } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but the actual } } numbers vary hugely between different published work. My understanding, } } as a geneticist, is that trypsin cuts like a restriction enzyme after } } arginine or lysine residues and therefore I would have thought that the } } number of fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } } Could you tell me if my understanding of the specificity of trypsin } } digest is correct and if not what it is? If so why would the predicted } } number of fragemtns vary so much in the two examples? } } } } Regards } } } } Richard } } Richard- } } While I'm not entirely clear on what your stated numbers mean, let me take a } stab at your questions anyway. First off, your understanding of the } specificity of Trypsin is correct, though, depending on the specific amino } acid sequence, there can be additional "rules". A brief explanation of } these special cases of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html#Tryps } } I must admit, however, that I do not understand what your stated numbers for } each of the two protein examples means (i.e., 19 or 27 for fep A). Do you } mean that one source predicts 19 peptides and another predicts 27 peptides? } Or do you mean that one source reports the *detection* of 19 peptides and } another reports the detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot answer your } question. } } However, if the numbers are from two different sets of experimental results, } there are several possibilities: } 1. Trypsin digestion may not go to completion if the experimental conditions } are not chosen properly. For instance, some proteins, under physiological } conditions, are highly resistant to protease digestion (i.e., Ribonuclease } A). However, under slightly destabilizing conditions, with the addition of } some heat or a chemical denaturant, the folded protein structure "breaks } down" allowing digestion to proceed to completion. } 2. If all of the peptides are analyzed at the same time, i.e. a MALDI } experiment or an electrospray (ESI) experiment without chromatographic } separation, the ionization of some peptides will suppress the ionization of } other peptides present in the mixture. This ionization suppression effect } is widely observed when analyzing mixtures of peptides, and for this reason } many times a chromatographic separation is coupled to a mass spec. in order } to lower the number of peptides that are introduced to the mass spec at the } same time. } 3. MALDI and ESI experiments performed on the same peptide digest will often } produce non-identical, but complimentary, results. Often MALDI can "see" } some peptides that are not seen by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were helpful; if } not, let me know! } } -Kendall ****************************************************************************** From: bizzwire Date: Wed, 25 Feb 2004 01:23:07 GMT Subject: Re: Tryptic digests Organization: * One reason for the discrepency *could be* that several cleavage sites could result in the same tryptic fragment. for example, for example, say the sequence -X-R-R-X (where X is any non-arg/non-lys amino acid, R=Arginine) appears twice in the primary structure. Complete digestion will result in two monopeptide arginine fragments. Do you count this as one or two fragments? Besides simply relying on the output of a computer program, you might find it instructive to take a paper and pencil, and try determining the theoretical number of peptides based on some pretty straightforward cleavage rules. } From: "Horler, R" } Organization: * } Newsgroups: sci.techniques.mass-spec } Date: Fri, 20 Feb 2004 09:35:00 +0000 } Subject: Tryptic digests } } Hello } } To set the scene I am currently involved in a creating a new E coli } database and part of what we plan to put in this database is a large } collection of experimental data from published work. } } One problem I am having at the moment is a number of proteomic } experiments show a predicted number of tryptic fragments but the actual } numbers vary hugely between different published work. My understanding, } as a geneticist, is that trypsin cuts like a restriction enzyme after } arginine or lysine residues and therefore I would have thought that the } number of fragments would be easy to predict. The numbers for specific } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } Could you tell me if my understanding of the specificity of trypsin } digest is correct and if not what it is? If so why would the predicted } number of fragemtns vary so much in the two examples? } } Regards } } Richard } } } } } ****************************************************************************** From: David Stranz Date: Mon, 23 Feb 2004 13:58:09 -0600 Subject: Re: Tryptic digests Organization: * Kendall wrote in news:c1cud3$jbp$1@news-int2.gatech.edu: } } To set the scene I am currently involved in a creating a new E } coli } database and part of what we plan to put in this database } is a large } collection of experimental data from published } work. } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but } the actual } numbers vary hugely between different published } work. My understanding, } as a geneticist, is that trypsin cuts } like a restriction enzyme after } arginine or lysine residues } and therefore I would have thought that the } number of } fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } Could you tell me if my understanding of the specificity of } trypsin } digest is correct and if not what it is? If so why } would the predicted } number of fragemtns vary so much in the } two examples? } } } Regards } } } } Richard } } } Richard- } } While I'm not entirely clear on what your stated numbers mean, } let me take a stab at your questions anyway. First off, your } understanding of the specificity of Trypsin is correct, though, } depending on the specific amino acid sequence, there can be } additional "rules". A brief explanation of these special cases } of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.h } tml#Tryps } } I must admit, however, that I do not understand what your stated } numbers for each of the two protein examples means (i.e., 19 or } 27 for fep A). Do you mean that one source predicts 19 peptides } and another predicts 27 peptides? Or do you mean that one source } reports the *detection* of 19 peptides and another reports the } detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot } answer your question. } } However, if the numbers are from two different sets of } experimental results, there are several possibilities: } 1. Trypsin digestion may not go to completion if the } experimental conditions are not chosen properly. For instance, } some proteins, under physiological conditions, are highly } resistant to protease digestion (i.e., Ribonuclease A). } However, under slightly destabilizing conditions, with the } addition of some heat or a chemical denaturant, the folded } protein structure "breaks down" allowing digestion to proceed to } completion. 2. If all of the peptides are analyzed at the same } time, i.e. a MALDI experiment or an electrospray (ESI) } experiment without chromatographic separation, the ionization of } some peptides will suppress the ionization of other peptides } present in the mixture. This ionization suppression effect is } widely observed when analyzing mixtures of peptides, and for } this reason many times a chromatographic separation is coupled } to a mass spec. in order to lower the number of peptides that } are introduced to the mass spec at the same time. } 3. MALDI and ESI experiments performed on the same peptide } digest will often produce non-identical, but complimentary, } results. Often MALDI can "see" some peptides that are not seen } by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were } helpful; if not, let me know! } } -Kendall } } } An additional complication to the above is that in many cases "identification" of a peptide is made via a database search, using one of the many software programs and databases available. Failure to "identify" a peptide could mean that a) the peptide wasn't observed experimentally (due to reasons described above), b) the selection criteria for deciding which experimental m/z values to submit for the search excluded one or more of the observed peptides (signal too weak, too many peptides already on the list, whatever), c) the database has sequence errors, resulting in calculation of an incorrect theoretical mass for the peptide and therefore a failure to match numerically, d) the database doesn't contain information about post- translational modifications, and the experimental peptide is modified (thus again, a mismatch between observed and theoretical mass based on sequence), e) in ESI in particular, the charge state on the observed peptide wasn't correctly deduced from the data, and therefore the mass presented to the search is incorrect, f) the observed peptide has an adduct (such as sodium or potassium) that isn't accounted for by the search software (which might assume everything is protonated), g) the database doesn't contain the protein from which the peptide was derived, and therefore the protein reported as the "hit" is just plain wrong, or h) any one of a number of other ways things could go awry. Hope this "helps" :-) David ****************************************************************************** From: Lisa Lavoie Date: 25 Feb 2004 13:40:24 -0800 Subject: Agilent and Thermo Ion traps Organization: * Hi: I am trying to chose between two ion trap instruments, the Agilent XCT and the Thermo LCQ Deca XP Max. Among my concerns are: 1) ruggedness (how often does one need to stop analyses for preventive maintenance, how many service calls need to be made). 2) availability of parts for both LC and MS. 3) ability to do MS to the nth degree. 4) ease of use of software. 5) ability to gather some isotopic data (understanding limitations of a trap) 6) reproducibilty of mass measurements 7) ability to do some quantittive analysis. My primary use will be to identify unknowns in very complex chromatograms. Thanks for your help, Lisa ****************************************************************************** From: Martin Steel Date: 25 Feb 2004 13:21:46 -0800 Subject: ThermoFinnigam Quantum Ultra for sale Organization: * New in the box Finnigan Quantum Ultra ESI APCI New Data System New Xcalibur software Factory Installation and warranty In stock and ready to deliver immediately Martin Steel Director, Global Trading McKinley Scientific 33-C Wilson Drive Sparta, NJ 07871, USA V: 973.579.4144 F: 973.579.4145 ****************************************************************************** From: Mudbunny Date: 26 Feb 2004 07:59:14 -0800 Subject: Re: Question on HRMS Organization: * Chip Cody wrote in message news:... } There are several questions pending. Here are some answers: } } 1. This is where that art of analytical method development comes into } play. The method development for HRSIM requires careful choice of the } target m/z set for each analyte. Because of the M to 2 M (or less...) } limitation, you cannot always chose the most abundant peaks as you } might for LRSIM. It is sometimes better to chose a closely spaced set } of peaks at higher m/z, even if they are not the most abundant. For } example, one might monitor M+. and [M-Cl]+, or M+. and isotope peaks } for a polychlorinated species. There are established protocols (e.g. } EPA protocols) for HRSIM for many compound classes. Yup. I have looked, and most of the HRSIM EPA protocols are for smaller groups of compounds (like nitrosamines). Pesticides are, most of the time, done by ECD or open scan GCMS on a quad. So my plan is to seperate the compounds into groups (sat 3 or 4 minutes long) and then try to pick M+ values that are close to each other (within the M-2M limit you mentioned) and then try to find the exact masses through the use of direct probe analysis of the neat compounds. Thanks for your help. Marcel ****************************************************************************** From: K. Murray Date: 26 Feb 2004 13:06:58 -0800 Subject: MS Terms and Definitions Project Organization: * IUPAC is sponsoring a task group for updating the standard terms and definitions for mass spectrometry. We need your input to make this project work. The web site for the project is http://www.msterms.com/ and it has links to the latest IUPAC and ASMS glossaries set up for on-line document review and there is a general discussion forum. Of course, Usenet is an excellent forum and anything discussed here will be included in the overall discussion. Also feel free to e-mail your comments. Thanks. Kermit Murray kmurray@ch335c.chem.lsu.edu ****************************************************************************** From: Joe Fredendall Date: Fri, 27 Feb 2004 08:22:30 -0500 Subject: Finnigan XSQ users: Organization: * Do you have a Finnigan TSQ or SSQ 70, 700, 710 or 7000 stuffed somewhere in a corner because the former operator either left the company or was promoted? Are you or someone you know currently struggling with ICL procedures or ICIS scripts? Do you have TSQ operators who are not proficient enough to use the instrument to the fullest capability? Does your limited budget prohibit you from paying outrageous rates for service visits and maintenance contracts? Are you reluctant to adopt a second hand TSQ instrument because you don’t know how to use it? I have 16 years experience working on Finnigan TSQ instrument and 6 years devoted to training operators how to use them. I specialize in providing custom tailored training courses on advanced TSQ system operation and maintenance. A small investment of time on your part may be all that’s necessary to unleash the full power of your Finnigan TSQ. Talk to me to find out if you could benefit by my talking to you. Joseph Fredendall Ph.D. Hunters Creek Trading Co. 7051 Hunters Creek Road South Wales, NY. 14139 Phone 866-200-7508 Fax 866-480-3046 HunterCreek@adelphia.net Linking people, products and profits worldwide [ Part 2, Text/SANITIZER-LOG (charset: ISO-8859-1 "Latin 1 (Western ] [ Europe)") 168 lines. ] [ Unable to print this part. ] ****************************************************************************** From: David Stranz Date: Mon, 23 Feb 2004 13:58:09 -0600 Subject: Re: Tryptic digests Organization: * Kendall wrote in news:c1cud3$jbp$1@news-int2.gatech.edu: } } To set the scene I am currently involved in a creating a new E } coli } database and part of what we plan to put in this database } is a large } collection of experimental data from published } work. } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but } the actual } numbers vary hugely between different published } work. My understanding, } as a geneticist, is that trypsin cuts } like a restriction enzyme after } arginine or lysine residues } and therefore I would have thought that the } number of } fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } Could you tell me if my understanding of the specificity of } trypsin } digest is correct and if not what it is? If so why } would the predicted } number of fragemtns vary so much in the } two examples? } } } Regards } } } } Richard } } } Richard- } } While I'm not entirely clear on what your stated numbers mean, } let me take a stab at your questions anyway. First off, your } understanding of the specificity of Trypsin is correct, though, } depending on the specific amino acid sequence, there can be } additional "rules". A brief explanation of these special cases } of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.h } tml#Tryps } } I must admit, however, that I do not understand what your stated } numbers for each of the two protein examples means (i.e., 19 or } 27 for fep A). Do you mean that one source predicts 19 peptides } and another predicts 27 peptides? Or do you mean that one source } reports the *detection* of 19 peptides and another reports the } detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot } answer your question. } } However, if the numbers are from two different sets of } experimental results, there are several possibilities: } 1. Trypsin digestion may not go to completion if the } experimental conditions are not chosen properly. For instance, } some proteins, under physiological conditions, are highly } resistant to protease digestion (i.e., Ribonuclease A). } However, under slightly destabilizing conditions, with the } addition of some heat or a chemical denaturant, the folded } protein structure "breaks down" allowing digestion to proceed to } completion. 2. If all of the peptides are analyzed at the same } time, i.e. a MALDI experiment or an electrospray (ESI) } experiment without chromatographic separation, the ionization of } some peptides will suppress the ionization of other peptides } present in the mixture. This ionization suppression effect is } widely observed when analyzing mixtures of peptides, and for } this reason many times a chromatographic separation is coupled } to a mass spec. in order to lower the number of peptides that } are introduced to the mass spec at the same time. } 3. MALDI and ESI experiments performed on the same peptide } digest will often produce non-identical, but complimentary, } results. Often MALDI can "see" some peptides that are not seen } by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were } helpful; if not, let me know! } } -Kendall } } } An additional complication to the above is that in many cases "identification" of a peptide is made via a database search, using one of the many software programs and databases available. Failure to "identify" a peptide could mean that a) the peptide wasn't observed experimentally (due to reasons described above), b) the selection criteria for deciding which experimental m/z values to submit for the search excluded one or more of the observed peptides (signal too weak, too many peptides already on the list, whatever), c) the database has sequence errors, resulting in calculation of an incorrect theoretical mass for the peptide and therefore a failure to match numerically, d) the database doesn't contain information about post- translational modifications, and the experimental peptide is modified (thus again, a mismatch between observed and theoretical mass based on sequence), e) in ESI in particular, the charge state on the observed peptide wasn't correctly deduced from the data, and therefore the mass presented to the search is incorrect, f) the observed peptide has an adduct (such as sodium or potassium) that isn't accounted for by the search software (which might assume everything is protonated), g) the database doesn't contain the protein from which the peptide was derived, and therefore the protein reported as the "hit" is just plain wrong, or h) any one of a number of other ways things could go awry. Hope this "helps" :-) David ****************************************************************************** From: Lee Ferguson Date: 27 Feb 2004 09:23:40 -0800 Subject: Waters CapLC problems Organization: * Hello, I've got a brand new Waters/Micromass CapLC-QTOF system, and I've been having some problems with my CapLC. Basically, it is almost impossible for me to get reproducible retention times. I am running 1 uL/min gradient from 5-95% ACN over about 50 minutes on a custom-packed C18 column. The pressure is about 3500 psi at the start of the run, so nothing really out of the ordinary. Often, the first time I run the system on any given day, nothing will elute until the middle of the run, then everything comes off as one big peak, almost as if there is a step gradient forming. After about 5 runs or so back-to-back, things start to settle down and my retention times become roughly reproducible. I have the "Micromass" version of the LC, with the gradient mixer and valve next to the ion source. I'm suspicious that my problem is caused by imbalanced small leaks in the two pumps, causing solvent A to back up past the mixer into the (long) line from pump B when the system sits for a long time at low %B (i.e. when equilibrating). However, the diagnostics leak test indicates that the leakage is "within spec" for all of the pumps. Anyone else have problems with this? Actually, I'd appreciate opinions from anyone who has experience with the CapLC system for proteomics work. Lee Ferguson University of South Carolina lee.ferguson@NOSPAM.sc.edu (remove NOSPAM to email me) ****************************************************************************** From: Tim Dorsey Date: 27 Feb 2004 08:59:51 -0800 Subject: Have rights for a old, low res, gas, magnetic ms, Organization: * Looking for help redesigning this ms for simple and cost effect production. Also own the rights to manufacturing of a atmospheric leak valve (nc to 1 x 10-9) and small quadrapole (RAMS unit). Also would like to see if anyone may have a instrument that could do what we are doing now with our model MGA 1100 gas mass spectrometer. MA Tech recently purchased this from General Electrical Medical Systems Information Technologies Services the rights of manufacturing for the servicing of the (originally Perkin Elmer) MGA 1100. This line of mass spectrometers is still widely used and respected. Their is base of over 400 units. They are getting older and nothing to replace them at this time. It is a fixed magnetic 90 degree sector 2 - 140 amu. It samples gases at 60 cc/min. These units are sampling at atmosphere pressure and up 9 gases being identified in a response time of 100ms (0 to 90 % of all readings). I have been in the the mass spec service field for 20 years and basically have been looking for mass spec's that we could oem for our own sales in the US. Over 200 customers in medical research and industrial applications. If your mass spec could replace or be adapted to do so and you have a interest please email me. I am also looking for Regards, Timothy G. Dorsey President MA TECH SERVICES, INC. 1920 SOUTH BROADWAY SAINT LOUIS, MISSOURI 63104 1-314-421-0944 Fax: 1-314-621-2077 E-mail: tim@masspec.com ****************************************************************************** From: park Date: 27 Feb 2004 13:50:20 -0800 Subject: purchase ld/ms Organization: * We are considering the purchase of a Waters ZQ LC/MS . Does anyone have experience with this instrument? Is it reliable and is it easily maintained? How is support from the company? Any information, good or bad, will help us make a decision. ****************************************************************************** From: bizzwire Date: Sat, 28 Feb 2004 02:08:09 GMT Subject: Re: purchase ld/ms Organization: * I'm an ex-Waters employee, so I'm a little hesitant to post to the forum, especiallly since I did a lot of the early evaluation work on the ZQ. However, I now work in a pharmacutical company and use equipment from a variety of vendors and feel pretty well-equipped to critique them, We have a ZQ in our lab. It is used as a walkup instrument for a large number (~30) of chemists who use it to confirm the molecular weights of their synthetic products and to monitor various reaction steps and processes. In this capacity, it has been a real workhorse, racking up thousands, if not tens of thousands of injections with a very small investment in downtime and maintenance. Most of our instrument problems are due to nasty samples and chemists doing stupid things rather than arising from the hardware itself. The instrument has a single electronics board, so whenever there is a board-level issue, a technician comes, swaps out the entire board and you're back in business. Waters service I would rate as average. We usually get someone in house within a day or two to fix the ZQ (after first jumpnig through an automated voice-mail labyrinth and waiting for a callback wich invariably happens the minute you go to the bathroom). We have some older, triple-quad instruments which are more troublesome, and sometimes getting a qualified person in takes considerably longer- however, this shouldn't be an issue with the ZQ unless you're in, say Korea or something (just kidding!!) As important as the hardware is, software is of equal importance. Waters (Micromass, really) "MassLynx" software is in my opinion, the most flexible, intuitive and powerful operating system on the market. Excalibur (Used on all Thermo systems) comes in second, IMHO (they both spring from the same roots, after all). Agilent systems are unfortunately wedded to their Chemstation software which is okay, I guess, if you plan on doing the same analysis day in and day out. For methods development or real research, however, it is a balky, cantakerous and over-engineered monstrosity, and I speak as someone who uses both in his daily work. I haven't worked with the ABI software in several years, yet the people in our company who do use it intensively are not terribly enamored of it. Shimadzu and JEOL both have several machines on the market, but I haven't any real "face-time" with them so do not feel qualified to render any verdict. That said, remember that a single quadrupole mass spectrometer is really neither fish nor fowl, and is only suited to two applications; molecular weight confirmation in an "Open Acces" environment, and as a detector/trigger for mass-directed preparative chromatography. These ar a single quad's "killer Apps." for any other application, I would suggest that you may want to think of other options. If you plan on doing any serious quantitaive work in complex biological matrices, you should by a triple quad. The ABI instruments have been and remain the gold standard for most contract labs doing high-volume quantitative work. If you want to do MS^n for, say, metabolite or degradant elucidation or protein sequencing, you should consider an ion trap or FTMS machine-Thermo has an interesting-looking machine they've recently unveiled. In addition, good old GCMS with electron-impact ionization still has a lot to commend itself and, depending on you needs, might fill the bill. Think long and hard about what your immediate and long-range experimental needs are before you decide on a particular instrument. In re-reading this post, I realize that the above screed has probably not been terribly helpful; perhaps if you gave us some more specific information on what you plan on doing we can answer more concretely. HTH Bizz } park } Subject: purchase ld/ms } } We are considering the purchase of a Waters ZQ LC/MS . Does anyone } have experience with this instrument? } } Is it reliable and is it easily maintained? How is support from the } company? Any information, good or bad, will help us make a decision. } ****************************************************************************** From: Joerg Hau Date: Sat, 28 Feb 2004 09:23:07 +0100 Subject: Re: Tryptic digests Organization: * On Monday 23 February 2004 20:58, David Stranz wrote: } An additional complication to the above is that in many cases } "identification" of a peptide is made via a database search, using } one of the many software programs and databases available. } } Failure to "identify" a peptide could mean that } } a) the peptide wasn't observed experimentally (due to reasons } described above), } } b) the selection criteria for deciding which experimental m/z } values to submit for the search excluded one or more of the } observed peptides (signal too weak, too many peptides already on } the list, whatever), } } c) the database has sequence errors, resulting in calculation of an } incorrect theoretical mass for the peptide and therefore a failure } to match numerically, } } d) the database doesn't contain information about post- } translational modifications, and the experimental peptide is } modified (thus again, a mismatch between observed and theoretical } mass based on sequence), } } e) in ESI in particular, the charge state on the observed peptide } wasn't correctly deduced from the data, and therefore the mass } presented to the search is incorrect, } } f) the observed peptide has an adduct (such as sodium or potassium) } that isn't accounted for by the search software (which might assume } everything is protonated), } } g) the database doesn't contain the protein from which the peptide } was derived, and therefore the protein reported as the "hit" is } just plain wrong, or } } h) any one of a number of other ways things could go awry. Ah, David ... you put your fingers exactly on the spot(s) that hurt ;-) To add yet two more points (that somehow blend with (c) and (g)): i) The peptide was never reported before, so you will not find it in any (at least any public) database. Anyway, someone has to be the first to do the de-novo sequencing of a peptide ... j) The database contains duplicates that are not identical, i.e. the wrong peptide is reported. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: David Stranz Date: Sat, 28 Feb 2004 17:58:17 -0600 Subject: Re: Tryptic digests Organization: * Joerg Hau wrote in news:c1q6pe$259$1@news-int.gatech.edu: } On Monday 23 February 2004 20:58, David Stranz wrote: } } } An additional complication to the above is that in many cases } } "identification" of a peptide is made via a database search, } using } one of the many software programs and databases } available. } } } Failure to "identify" a peptide could mean that } } } } a) the peptide wasn't observed experimentally (due to reasons } } described above), } } } } b) the selection criteria for deciding which experimental m/z } } values to submit for the search excluded one or more of the } } observed peptides (signal too weak, too many peptides already } on } the list, whatever), } } } } c) the database has sequence errors, resulting in calculation } of an } incorrect theoretical mass for the peptide and therefore } a failure } to match numerically, } } } } d) the database doesn't contain information about post- } } translational modifications, and the experimental peptide is } } modified (thus again, a mismatch between observed and } theoretical } mass based on sequence), } } } } e) in ESI in particular, the charge state on the observed } peptide } wasn't correctly deduced from the data, and therefore } the mass } presented to the search is incorrect, } } } } f) the observed peptide has an adduct (such as sodium or } potassium) } that isn't accounted for by the search software } (which might assume } everything is protonated), } } } } g) the database doesn't contain the protein from which the } peptide } was derived, and therefore the protein reported as the } "hit" is } just plain wrong, or } } } } h) any one of a number of other ways things could go awry. } } Ah, David ... you put your fingers exactly on the spot(s) that } hurt ;-) To add yet two more points (that somehow blend with (c) } and (g)): } } i) The peptide was never reported before, so you will not find } it in any (at least any public) database. Anyway, someone has to } be the first to do the de-novo sequencing of a peptide ... } } j) The database contains duplicates that are not identical, i.e. } the wrong peptide is reported. } } Cheers + HTH, } } - Joerg } } Hello Joerg, Having written two commercial and one prototype protein database search applications, I can comment with a little bit of authority. (The first was what grew into Micromass ProteinLynx Global Server, the second a short-lived product offered by Agilent, the third done under contract to another MS vendor and never introduced commercially). Your additional points are certainly correct. Fortunately, those who are making commercial protein database search software now are also providing statistical and other diagnostic metrics so an informed user can evaluate how good the hits really are. Unfortunately, for uninformed users the first entry on the list is always correct, and then they spend quite a bit of time wondering how a liver enzyme could have found its way into their brain tissue prep. Cheers, David ****************************************************************************** From: Michael Sherrell Date: Mon, 01 Mar 2004 16:13:26 -0800 Subject: Seqs, synths, mass specs/MALDIs, liquid handlers available Organization: * Grizzly Analytical: Sequencers, synthesizers, mass specs, MALDIs, liquid handlers, cytometers etc. for sale New engineering development, service and retail facility: 377 Oyster Pt Blvd #11, South San Francisco CA 94080 **Oligosynthesizers: Expedite 8909: $14,500. Includes M.O.S.S, rebuilt w/ new ABI valves, 90-day warranty. + $3,500/trityl. ABI 394: $14,200. Rebuilt; 90-day warranty. ABI 394: $19,900. Trityl, MAC, rebuilt: about as good as the new 3400. ABI 392: $12,200. Rebuilt; 90-day warranty. ABI 391: $11,750. Rebuilt; 90-day warranty. ABI 3948: $25,000. Rebuilt/installed w/ 90-day warranty. ABI 390Z: $11,000. Rebuilt/warranteed. (Oligosynthesis reagents, ~75% off list: Oxidizer, Cap A, Cap B, Activator, Deblock, amadites, + 8909 columns) Beckman 1000M: $11,000. Excellent condition; guaranteed. CyClone: $7,500. New-in-box; 90 day parts warranty. Similar to ABI 392. Biosearch 8700: $10,000. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. BioSearch 8750: $10,500. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. Biosearch 8700: $8,000. Rebuilt; 90-day warr. + $2K/Windows. BioSearch 8750. ~$4,000. Have 5; cheaper & faster than 394s. Cruachem PS250. <=$2,500. 6 available. *High throughput synthesizers: BLP 192: $125,000. 2 plates, 8 min. cycle time. New; incl. install + 1 yr. warr. TAGC 96: $95,000. Fast; optimized for small-scale up to 50 bases. Polygen 10. Call if interested. Polyplex Gene Machine: $89,000. Installed/warranteed. **Oligosequencers: ABI 3100: $85,000. Includes factory install, software license. ABI 310: $28,000. Mac. Includes factory install; guar. eligible for service. ABI 310: $31,000. PC. Includes factory install; guar. eligible for service. ABI 3700: $75,000. Includes factory install; guar. eligible for service. ABI 3700: $19,000. From major genome center; beautifully maintained. MegaBace 4000: Offers considered. Have three; currently under mfr. svc contract. MegaBace 1000: $22,000. Incl. installation by manufacturer. ABI 377: $15,500. 96-lane; install factory incl., eligible for service. (Also suitable for tiling.). Genescan: $5,000. Licensed software for the 377, 310 or 373. ABI 373 stretch: $9,000. Big Dye upgrade. Pharmacia ALF Express: $14,000, incl. 90-day parts & labor warr. Visible Genetics: $20,000. Unused. Have 3. LiCor 4200: $25,000. Incl. Global Upgrade; guaranteed installable. LiCor 4000LS <: $20,000. 1994 model; can have Global Upgrade. Genomyx LR: $2,500. Boots; many accessories. MJ Basestation 51. Call for pricing. No robotic loading, 2 years old, under service contract. MJ Research BaseStation: $105,000. 2 yrs old; still under svc. contract. MJ Research BaseStation: $125,000. 6 mos. old; still under svc. contract. **Real-time PCR: ABI 7900: $68,000. Installed/warranteed. ABI 7700: $34,000. Installed/warranteed. ABI 7000: $29,000. Installed/warranteed. 2002 model. BioRad iCycler: $32,000. 90-day warranty. **Peptide synthesizers: ABI 433: $33,000. Original, ABI-supportible 433. These come and go; call/email to reserve. 90-day warr. ABI 433: $24,000. Upgraded from 431. We support. Rebuilt, 90-day warr. ABI 431: $16,000. Rebuilt, 90-day warr. ABI 430: $10,500. Rebuilt, 90-day warranty. ABI 432: $15,000. Rebuilt, 90-day warranty. Capriccio 1: $65,000. New instrument. Benchtop, large scale; faster and more efficient than ACT 400. Incl. install, 1 yr svc. PerSeptive 9500: $12,750. Rebuilt w/ 90-day warranty. PerSeptive 9050: $16,000. Rebuilt w/ 90-day warranty. CS Bio 336. ~$27,000. 6 mos old; lease default. 3 peps simultaneous; .05-.25 mmol. ACT LabTech III: $15,000. 30-day warranty. Pioneer: $40,000. Includes factory install, eligible for svc. contract MPS unit for the Pioneer peptide synthesizer: $5,000. New and unused; price = 25% of new cost. ACT 396 MPS: $42,000. Factory refurb; includes 120-day warranty. PerSeptive 9600: $13,750. Rebuilt, warranteed. ACT Vantage: $79,000. Excellent condition. ACT 357-MPS. Call for pricing. CEM Discover benchtop single peptide synthesizer: ~$12,000; call. ACT 90: $16,250. Only used twice. Incl. install; guar. eligible for svc. Argonaut Quest 205: $27,000. ASW model. Argonaut Quest 210: $19,000. ASW model. **Peptide sequencers: ABI 494 HT: $75,000. Installed, guaranteed ok for service contract. ABI 494 cLc. Offers considered. ABI 492: $25,000 installed, eligible for service contract. Beckman 6300. Various prices. Have several; can rebuild or sell for parts. ABI 421: $10,000. Offers considered. ABI 477/120: $1,500. Good working order or right of return. ABI 477. Service, parts available. ABI 473/476: $15,000. Good working order; install/service available. Beckman 6300 AA: $ 8,000. Rebuilt/warranteed ABI 470A: $2,000. For parts. Many extra parts. *[Note: various other ABI, HP, Millipore, Biosearch, Beckman, etc. sequencers, synthesizers etc. available; please inquire.] **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Q-Trap: $125,000 installed, eligible for service. Sciex API 3000 upgrade: $35,000. HSID interface: higher sensitivity and s/n at high flow rates; comparable to API 4000. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 300: $49,000. NT; has 365 interface. ES only. Install included; guar. eligible for svc contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex APCI probe: $7,900. For API 150, 300, 365 or Q-Star Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $165,000. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $50,000. ES, API 2, Xcalibur software, installation and 30-day warranty. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec M: $115,000. Mag Sector; orthogonal TOF MS/MS; 4 sources, FPD and TOF included; currently working well. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. ABI 4700: Must sell; all offers considered. TOF/TOF MS/MS Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. **Liquid handlers: Biomek FX (core system): $450,000 good working order. Includes 3 meter Orca, fluorometer, incubator, more. Biomek FX: $60,000. Single arm. Biomek 2000, no side loader, $49,000. Beckman Multimek, $34,000. Zymark Sciclone: 1.5 years old; $43K. Zymark Staccato system: $250,000 and up, depending on accessories, install, warranty. XP-arm based Zymarks: $10,000 and $20,000, depending on accessories. Tecan RSP-200/8 ID Robot Sample Processor, fully equipped: call/email if interested. Hamilton MicroLab AT2 Plus robot, $38,000 Packard Multiprobe 20400 and CP20400, Packard refurbed, $16,500 for either Transgenomic WAVE system, $22,000 incl. installation, eligible for svc. Quantity discounts for up to 20 units. Tecan Genesis RSP 150, no Roma, $52,000 delivered w/ 90-day warranty. Tecan Genesis RSP 100, $41,000 delivered w/ 90-day warranty. LC Packings UltiMate NanoLC system w/ FAMOS autosampler, $37,300 Scitec robotic liquid handling system, 3-meter rail, $60,000 guaranteed working Tom-Tec Quadras, various configurations, refurbished and warrantied. Hamilton Microlab 2200: call for pricing. Gilson 215: call for price. ABI 877 Catalyst Turbo: $12,000 or best offer Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically 96-well microplate source, glass slide, microwell plate or membrane target), ~ 5 years old. **Other expensive hi-tech items: *NMRs: Varian Inova 600 NMR: $275,000 guaranteed installable; +$25K/install. Bruker Avance 500 DRX, unshielded, cryoprobe ( available for $175,000 separately) + 5 other probes, 3 channel, $325,000 installed. Optional autosampler, $25,000. Varian Inova AS 600, shielded, 5 mm broadband, 9-position autosampler, $400,000 installed w/ 90-day warr. FX90Q NMR w/ Tek-Mag, $19,500. Others available; inquire if interested. *Flow cytometers: COULTER® EPICS XL-MCL^Ù: $45,000. 4 color with Multi Carousel Loader includes rebuilt, installation and one-year warranty. Coulter Epics Elite: 9 years old but never used. Call/email if interested. COULTER® EPICS XL^ÙFlow Cytometer: $45,000.00 Currently in operation. Includes XL2, EXPO and Data Mate Software, APC UPS Back-up, factory installation, and other options. FACS Vantage SE with the DIVA option: $160,500. (2 lasers: 488nm and UV tunable). Bought in June '02 and never used. BD FACSCalibur w/ FACSLoader: $84,000. 4 color. 1998; excellent condition. BD FACScan; offers considered. 3 color w/ argon laser, FITC, PE & 7 AAD BD FACSort Cell Sorter, $39,000. 3 color, MAC G3, Cellquest, install included MoFlo Analyzer with MoSkeeto System: $99,750.00. 6-channel / 5-color detector, Carvo MSP - 9000 Auto sampler, Summit 3.1 Software, Laser. Scanning Cytometer: Microscope-based. Two-laser system. $85,000 guaranteed installable. Others available; inquire if interested. *Arrayers/spotters/readers: HP/Affymetrix GeneArray 3000 system, $120,000 installed w/ 1 yr. warr. SpotBot Personal Microarrayer, $9,750. 2002; excellent condition. HP GeneArray G2500A reader w/ laser, $22,000, including new data system but no fluidics station. Affymetrix 417 Arrayer/spotter: seller considering rather low offers; call if interested. Affymetrix 417 Arrayer/spotter: $34,500 reconditioned with 1 year warranty HP/Affymetrix GeneArray Scanner Model G2500A, unused, $49,000. CELLOMICS ScanArray HCS: 2003 model. Factory install, license discount available; offers considered. Packard ScanArray 4000: $39,250. 2000 instrument. Incl. factory install; eligible for service contract. Packard ScanArray 3000: $17,250. Incl. factory install; eligible for service contract. Genomic Solutions GeneTAC microarray Hybridization Station: $27,000. (for details see www.genomicsolutions.com/products/bio/hyb.html) Amersham Lucidea SLIDE PRO Hybridization Station: $18,500. Ciphergen ProteinChip Reader PBS II: $65,000. Current upgrades; includes factory install, 30-day warranty. *Spot pickers: Genetix QPix2 benchtop: $79,570 installed. Incl. 96-well picking head, gridding option, etc; Q-Fill optional. Genetix QBot picker/arrayer. Call/email if interested. BioRobotics BioPick automatic colony picker. Excellent condition. ~$60,000 Genomic Solutions Flexys; much less than new price; call/email if interested. *Microscopes: ZEISS Axioskop Trinocular Microscope, $24,650 For phase contrast, DIC and Epi-Flourscence Cambridge Stereoscope S90B SEM w/ Kevex EDX: $25,000. Incl. secondary and backscattering detectors, Polaroid system, some options, factory installation. Working now. Optional one year service sontracts available. Meridian ACAS 570C LSCM. Other Laser Scanning Confocal microscopes available, call or email for list. Leica Confocal TCS-4D: $51,000. NT upgrades, 2 or 3 laser w/ DMRBE microscope bought new in 1997. Includes factory installation. Various (SEM) Scanning Electron Microscopes, $9,500-$375,000. Call or email for list. Various (TEM) Transmission Electron Microscopes; call or email for list. Various (AFM) Atomic Force Microscopes: Veeco, Digital Instruments, Park Scientific, Topometrix, etc. Call or email for list.; call or email for list. Various surgical, neuro surgical microscopes, call or email for list. Various optical microscopes, call or email for list. *Truly miscellaneous: Biacore 3000: in negotiations; call/email if interested.. Molecular Devices/LJL Biosystems Criterion Analyst HT System: $35,000. Amersham Typhoon 9410 scanner: Accepting offers. 2003 system, top condition. The first large-format gel , blot and microarray imager; also optimized for protein research. Perkin Elmer 1010M Micro Densitometer: was $325,000 new. Now in Japan. Call if interested. Amersham FARCyte/Tecan Ultra fluorescence plate reader, new in box, $50,000. List: $80K. Packard 50TR flow scintillation analyzer. Call for price. Brand new, unused. Accutag Radio Frequency Reader/10k Automated Microreactor Sorting System, $80,000 Genevac's Mega 1200 ultra high throughput solvent evaporation system, 1.5 yrs old but unused, $200,000 or best offer. New Brunswick Bioflo 3000 bioreactor: $18,900. 10 liter; new probes; 90-day warr. Process Engineers 29 liter mammalian cell bioreactor, new/unused, ~$35,000 or best offer. *(other bioreactors/fermenters available; inquire if interested.) Cambridge Stereoscope S90B SEM w/ Kevex EDX: $10,000. Incl. secondary and backscattering detectors, Polaroid system, some options. Working now. **Too hard to classify: Li-Cor Odyssey: $25,000 ($40K new). Guaranteed good working order. See for specs. BioCAD 20s and 60s w/ 90-day warr. available for $10-15,000, depending on details. 700E also avail. < $25,000. ABI VISION Workstation (souped-up BioCAD; see AB website for details): offers considered. Luminex LX100 (simultaneous assay of multiple analytes): $29,000. Glycoprep 1000 automated hydrazinolysis machine: $9,000; good working order Packard Topcount 12-detector 96 well microplate scintillation counter, $35,000 Jasco FP6500 Fluorescence Spectrometer. Excellent condition. $11,500. ABI 120 HPLC, $1,500 ABI 877: have several; different configs, prices, none very expensive; call PE 9600 thermalcyclers: $3,750 w/ 90-day warranty PE 9700 96-well thermalcyclers: $5,300 w/ 90-day warranty PE 9700 384-well thermalcyclers: $5,450 w/ 1 yr. warranty PE 2400 thermalcyclers: $2,450 w/ 90-day warranty PE 480 thermalcyclers: $3,000 guaranteed working; have several Beckman P/ACE MDQ: $24,000 Beckman P/ACE 5510: $19,500. Refurbed, warranteed. MD PhosphorImager Storm 860, $30,000. MD FSI FluorImager, $15,000 **Service: We rebuild valve blocks for ABI 430, 431 and 39x @ $65/port, 90-day warranty Service and contracts on ABI 39n and PerSeptive 8909/8905s available. Service contracts on Hewlett Packard HPLCs, GCs and MSs available at a savings over HP rates **Also available: Agilent 1100 HPLCs, virtually all configurations/detectors. HPLCs, ICs, CEs, FPLCs: microbore to prep scale. A variety of other lab instruments. Call or check the website: www. grizzlyanalytical. com. Please call or email for more information or if you have items to sell. Michael Sherrell Grizzly Analytical (USA) www.grizzlyanalytical.com 707 887 2919/fax 707 887 9834 [All the items are subject to prior sale.] [If you do not wish to receive my emails, please return this with "Stop" in the subject line, and accept my apologies for the inconvenience.] ****************************************************************************** From: Chip Cody Date: 2 Mar 2004 03:31:15 -0800 Subject: Re: Question on HRMS Organization: * Marcel, A caution: please check your mass spectrometer specifications to see how wide an electric field switching range is supported. The M to 2M range is a characteristic of JEOL magnetic sectors. I am not sure whether your mass spectrometer supports this wide a range or not. Regardless, the EPA protocols specify target masses that are carefully chosen to be suitable for HRSIM on any magnetic sector in good operating condition. Also, I can offer a helpful hint: I have often used the NIST Mass Spec Interpreter (provided with the most recent versions of the library search database) to suggest fragment ion compositions that can be used to calculate exact masses. This is useful when it is not convenient to measure standards,. Like any theoretical model, it should be used with caution until you can confirm the actual m/z values for the target compound's fragment masses by measuring a standard. You can introduce the standard samples for exact mass measurement via direct probe if that is a practical means for introducing your specific analytes; otherwise, you will have to introduce them via GC/MS. Chip Cody Mudbunny wrote in message news:... } } Yup. I have looked, and most of the HRSIM EPA protocols are for } smaller groups of compounds (like nitrosamines). Pesticides are, most } of the time, done by ECD or open scan GCMS on a quad. So my plan is to } seperate the compounds into groups (sat 3 or 4 minutes long) and then } try to pick M+ values that are close to each other (within the M-2M } limit you mentioned) and then try to find the exact masses through the } use of direct probe analysis of the neat compounds. } } } } Thanks for your help. } } Marcel ****************************************************************************** From: James Barnett Date: Tue, 02 Mar 2004 20:50:35 +0000 Subject: Re: purchase ld/ms Organization: * bizzwire wrote: } thousands, if not tens of thousands of injections with a very small } investment in downtime and maintenance. Most of our instrument problems are } due to nasty samples and chemists doing stupid things rather than arising } from the hardware itself. } Oh tell me about it. They've blocked autosampler needles. Samples with snow storm amounts of solids in them. Samples made up in dichloromethane, on a MeCn/ Water reverse phase HPLC system. The best one is not leaving a sample in the autosampler, and not putting vial cap and septa on the vial!! I must have had the world record for most overloaded samples, ever. Their a messy bunch too, they never take their samples away, piles of vials left on all the equipment. Good to hear the ZQ is a work horse, the Thermo Electron MSQ Surveyor, is to be recommended to. We are up to 50K samples a year. Regards, James ****************************************************************************** From: Chris R. Lee Date: Tue, 2 Mar 2004 22:03:27 +0100 Subject: Re: Agilent and Thermo Ion traps Organization: * May I add: easy interchangeable coupling with LC and CE? Regards "Lisa Lavoie" a écrit dans le message de news: c1j5a3$i8u$1@news-int2.gatech.edu... } Hi: } I am trying to chose between two ion trap instruments, the Agilent XCT } and the Thermo LCQ Deca XP Max. Among my concerns are: } } 1) ruggedness (how often does one need to stop analyses for preventive } maintenance, how many service calls need to be made). } } 2) availability of parts for both LC and MS. } } 3) ability to do MS to the nth degree. } } 4) ease of use of software. } } 5) ability to gather some isotopic data (understanding limitations of } a trap) } } 6) reproducibilty of mass measurements } } 7) ability to do some quantittive analysis. } } } My primary use will be to identify unknowns in very complex } chromatograms. } } Thanks for your help, } Lisa } } . ****************************************************************************** From: Mike Sherrell Date: Wed, 3 Mar 2004 14:44:21 -0800 Subject: Mass specs & MALDIs available Organization: * Mass Specs, MALDIs available from Grizzly Analytical www.grizzlyanalytical.com; 707 887 2919, mike@grizzlyanalytical.com Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Q-Trap: $125,000 installed, eligible for service. Sciex API 3000 upgrade: $35,000. HSID interface: higher sensitivity and s/n at high flow rates; comparable to API 4000. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 300: $49,000. NT; has 365 interface. ES only. Install included; guar. eligible for svc contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex APCI probe: $7,900. For API 150, 300, 365 or Q-Star Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $165,000. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $50,000. ES, API 2, Xcalibur software, installation and 30-day warranty. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec M: $115,000. Mag Sector; orthogonal TOF MS/MS; 4 sources, FPD and TOF included; currently working well. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. ABI 4700: Must sell; all offers considered. TOF/TOF MS/MS Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: Elijah Bailey Date: 4 Mar 2004 21:42:57 -0800 Subject: shifts in spectra Organization: * I have a set of Mass Spectra and have observed systamatic shifts in the spectra (These were got from MALDI-TOF)... Can anyone point me to software / papers which can correct linear shifts (scaling?) in the spectra? Thanks, --Elijah ****************************************************************************** From: Jimmy Date: 5 Mar 2004 07:06:30 -0800 Subject: How to quantitate drugs in plasma in early drug discovery Organization: * We work on bioequivalency studies. For that purpose, we use both STDs and ISTDs to determine drug levels in plasms. However, there are usually no STDs available in early drug discovery. Therefore, we wouldn't be able to optimize the QqQ and would have no calibration curve. How do discovery people quantitate drugs in plasma, for which they have no STDs? Do they optimize QqQ? If not, how to determine Q1 and Q3 m/z and collision energy etc.? How to demerine the drug conc without a calibration curve? Also, what dosages to rats etc if we don't know the ADME, namely Cmax for a certain dosage? TIA! Jimmy ****************************************************************************** From: Jimmy Date: 5 Mar 2004 07:07:41 -0800 Subject: Difference between clusters and adducts Organization: * Please explain me the difference between them. TIA. Jimmy ****************************************************************************** From: Janson Date: 6 Mar 2004 17:02:14 -0800 Subject: High-Throughput Analysis Organization: * Hello, Fellow Bioanalytical LC-MS Chemists, I am new to this area. I would like a few questions. People use mainly two types of high throughput techniques: direct injection of plasma (Turbulent Flow etc) and 96 well plates. Could you please tell me the advantages and disadvantages for the both? Like throughput, LLOQ, plasma volume, column and cartridge cost, method development time etc. Thank you very much for your time and consideration. Janson ****************************************************************************** From: Janson Date: 7 Mar 2004 12:22:51 -0800 Subject: Metabolite ID, ISTD Organization: * Are there short online references on metabolite identification by MS? (less than 50 pages preferred) Also, are there short books on the subject? We usually use ISTDs for drug quantitation. Sometimes it's difficult to get a suitable one. Is it a mandatory requirement by regulatory agencies to use an ISTD for quantitation? Would it be ok if a method doesn't use an ISTD but it does meet FDA bioanalytical method validation requirements? Thanks in advance. Janson ****************************************************************************** From: Erik Holmgren Date: Wed, 10 Mar 2004 09:28:51 +0100 Subject: ESI-MS Nitrite, Nitrate Organization: * Dear MS specialists, I have a Bruker Esquire 3000+ Ion trap. I'm trying to analyse Nitrite and Nitrate on this system. Does anyone have any suggestions reg. LC system and MS conditions ? Best regards, Erik ****************************************************************************** From: Eileen Date: Wed, 10 Mar 2004 16:39:45 -0800 Subject: how to compare two MS sensitivity? Organization: * if there are two MS, one is LCQ classic, the other is LCQ deca. from the theory (or the company introduction), deca is around 10 times sensitivity than classic. how do you test it? thanks Eileen ****************************************************************************** From: Svetlin Grancharov Date: 12 Mar 2004 13:39:40 -0800 Subject: MINITAB file format Organization: * Does somebody have MTW file format specs. I have to implement MINITAB MTW files reader but I do not have any documents about this format. I will appreciate all clues you can give me. Best, Svetlin Grancharov ****************************************************************************** From: Ricksfbrsc Date: 13 Mar 2004 03:19:03 GMT Subject: Re: how to compare two MS sensitivity? Organization: * The sensitivity is compound specific, so run each system with compounds that you are interested in and determine the detection limit. Typically, that is done by estimating when the signal to noise ratio (p-p) is 3. I would optimize the conditions on each instrument, then run a standard at a fairly low level. ****************************************************************************** From: Joerg Hau Date: Sat, 13 Mar 2004 10:51:01 +0100 Subject: Re: how to compare two MS sensitivity? Organization: * Hi } if there are two MS, one is LCQ classic, the other is LCQ deca. from } the theory (or the company introduction), deca is around 10 times } sensitivity than classic. how do you test it? Generally speaking, by measuring and comparing the signal(s) that you obtain when you introduce the same amount(s) of the same compound(s) under the same conditions in the two machines. By the definition of "sensitivity", the machine with 10x higher sensitivity should yield a calibration curve that is 10x steeper. A common misunderstanding is that "10x higher sensitivity" equals to "10x improved detection limit". This _can_ be the case, but not necessarily: Sensitivity is defined as the change of signal intensity per change of amount of compound - i.e. the slope if the calibration curve. In contrast to this, detection/quantitation limits are usually defined by S/N ratio. For these tests, most manufacturers tend to use Reserpine (probably because it does not fragment easily and thus gives a nice fat [M+H]+, whatever the ion source conditions are ;-). However, if you need to buy an instrument based on sensitivity (or LOD ;-), then define your own needs with your own compounds under your own conditions, and have them measured. And fix them in the sales contract. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: ad@news1.news.xs4all.nl Date: Sun, 14 Mar 2004 15:33:45 +0100 Subject: Re: how to compare two MS sensitivity? Organization: * "Joerg Hau" wrote in message news:c31o43$qie$1@news-int.gatech.edu... } Hi } } } if there are two MS, one is LCQ classic, the other is LCQ deca. from } } the theory (or the company introduction), deca is around 10 times } } sensitivity than classic. how do you test it? } } Generally speaking, by measuring and comparing the signal(s) that you } obtain when you introduce the same amount(s) of the same compound(s) } under the same conditions in the two machines. } } By the definition of "sensitivity", the machine with 10x higher } sensitivity should yield a calibration curve that is 10x steeper. } } A common misunderstanding is that "10x higher sensitivity" equals to } "10x improved detection limit". This _can_ be the case, but not } necessarily: Sensitivity is defined as the change of signal intensity } per change of amount of compound - i.e. the slope if the calibration } curve. In contrast to this, detection/quantitation limits are usually } defined by S/N ratio. } } For these tests, most manufacturers tend to use Reserpine (probably } because it does not fragment easily and thus gives a nice fat [M+H]+, } whatever the ion source conditions are ;-). However, if you need to } buy an instrument based on sensitivity (or LOD ;-), then define your } own needs with your own compounds under your own conditions, and have } them measured. And fix them in the sales contract. } } Cheers + HTH, } } - Joerg } } } -- } joerg dot hau at swissonline dot ch * Lausanne, Switzerland } http://homepage.sunrise.ch/mysunrise/joerg.hau/ } "All standard disclaimers apply". } remove "nospam." from my address to reply } (this became necessary due to increasing SPAM) } } what do you mean by :"fix them in the sales contract"? ad ****************************************************************************** From: Chip Cody Date: 15 Mar 2004 03:56:20 -0800 Subject: Re: how to compare two MS sensitivity? Organization: * Joerg Hau wrote in message news:... } A common misunderstanding is that "10x higher sensitivity" equals to } "10x improved detection limit". This _can_ be the case, but not } necessarily: Sensitivity is defined as the change of signal intensity } per change of amount of compound - i.e. the slope if the calibration } curve. In contrast to this, detection/quantitation limits are usually } defined by S/N ratio. } Joerg makes an important distinction. A mass spectrometer can be very sensitive for a standard sample, but the detection limits may be poor for a particular analysis. It may be easy to report a high S/N for a relativley large amount of sample introduced, but it is not always easy to ahieve a proportional S/N for a smaller sample size. Detection limits depend on the ability to discriminate the analyte from chemical background, and also on the ability to introduce small amounts of analyte efficiently without losses. Common solutions to the first problem involve high resolution or MS/MS. Solutions to the second problem are highly method-specific and may relate to solvent choice, flow rates, passivation of active surfaces, injection method, separation method, etc. A comment: The "amount consumed" definition that is sometimes used for ESI measurements (especially nanoESI) can be misleading. This term reflects a higher-concentration sample measured for a short time. It is more a measure of sensitivity and measurement speed than a real measure of practical detection limits. Chip Cody ****************************************************************************** From: Mudbunny Date: 15 Mar 2004 07:35:24 -0800 Subject: Increasing S/N Organization: * I am not sure if this would be better served in a chromatography group, but this seems liek a good place to start. I am using a Kratos Concept (Now manufactured by MSI) attached to a HP 5890 GC. 5uL of a 0.1 ng/uL sample are being injected onto the column. I am using a 50:1 split ratio. The trap current is at 5, and I am using HRSIM techniques. The compound is N-nitrosodimethylamine, and the sample has an internal standard (d6-NDMA). Currently, I end up with a S/N of about 16. I need to be able to see a sanmple with a concentration of 0.001 ng/uL. Currently, I see nothing but noise. Do the wise people in this have any suggestions?? Thanks Marcel ****************************************************************************** From: David Stranz Date: Mon, 15 Mar 2004 11:17:29 -0600 Subject: Re: how to compare two MS sensitivity? Organization: * ad@news1.news.xs4all.nl wrote in news:c32fev$33k$1@news-int2.gatech.edu: } } "Joerg Hau" wrote in message } news:c31o43$qie$1@news-int.gatech.edu... } } Hi } } } } } if there are two MS, one is LCQ classic, the other is LCQ } deca. from } } the theory (or the company introduction), deca is } around 10 times } } sensitivity than classic. how do you test } it? } } } Generally speaking, by measuring and comparing the signal(s) } that you } obtain when you introduce the same amount(s) of the } same compound(s) } under the same conditions in the two } machines. } } } By the definition of "sensitivity", the machine with 10x } higher } sensitivity should yield a calibration curve that is } 10x steeper. } } } A common misunderstanding is that "10x higher sensitivity" } equals to } "10x improved detection limit". This _can_ be the } case, but not } necessarily: Sensitivity is defined as the } change of signal intensity } per change of amount of compound - } i.e. the slope if the calibration } curve. In contrast to this, } detection/quantitation limits are usually } defined by S/N } ratio. } } } For these tests, most manufacturers tend to use Reserpine } (probably } because it does not fragment easily and thus gives a } nice fat [M+H]+, } whatever the ion source conditions are ;-). } However, if you need to } buy an instrument based on sensitivity } (or LOD ;-), then define your } own needs with your own } compounds under your own conditions, and have } them measured. } And fix them in the sales contract. } } } Cheers + HTH, } } } } - Joerg } } } } } } -- } } joerg dot hau at swissonline dot ch * Lausanne, Switzerland } } http://homepage.sunrise.ch/mysunrise/joerg.hau/ } } "All standard disclaimers apply". } } remove "nospam." from my address to reply } } (this became necessary due to increasing SPAM) } } } } } } } what do you mean by :"fix them in the sales contract"? } } ad } } } I think Joerg means that once you have determined the sensitivity specifications you need for your particular analyses, and the manufacturer says that they can meet those specifications, then you need to make meeting -that- specification a condition (line item) in the sales contract. The manufacturer doesn't get paid until they meet all the terms of the sale, including meeting the specification you and the salesman agreed on. It doesn't do you any good to accept the manufacturer's standard conditions for sensitivity (eg. reserpine) if that is inappropriate for the analyses that you do. David ****************************************************************************** From: Joerg Hau Date: Mon, 15 Mar 2004 18:23:18 +0100 Subject: Re: how to compare two MS sensitivity? Organization: * On Sunday 14 March 2004 15:33, ad@news1.news.xs4all.nl wrote: [Fullquote snipped] } However, if you need to buy an instrument based on sensitivity (or } LOD ;-), then define your own needs with your own compounds under } your own conditions, and have them measured. And fix them in the } sales contract. } } what do you mean by :"fix them in the sales contract"? Your needs & specifications. Instrument purchase and installation nowadays ends up in some OQ/PV (operational qualification & performance validation) - in short, you test if it works as desired. Now, if your field of work requires that the instrument MUST be able to do something very specific - e.g. "detect x pg of compound A in z with S/N 10", then you will obviously make your instrument selection based on tests around this criterium. And to make sure that the instrument performs not only in the demo lab but also on-site, you might request inclusion of those selection criteria, e.g. in terms of (additional?) PV specifications, in the sales contract. All this within reasonable limits, of course. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: Ricksfbrsc Date: 16 Mar 2004 00:29:45 GMT Subject: Re: Increasing S/N Organization: * I can't address the trap optimization, but you can: 1. Use splitless injection-inject 1-2 ul, set the purge time to 0.75 minute, purge flow to 25 ml/min. You may have to lower the column temperature as it needs to be set at least 10 C (better 15 or 20 C) below the solvent boiling point to get good focusing. Make sure to not turn on the MS until after the solvent has eluted. This step should increase the amount injected on the column by a factor of 10 for 1 ul (and 20 by 2 ul but your system may not handle that large an injection well). 2. Do you have to use HRSIM? Generally sensitivity is much better in a low resolution mode. ****************************************************************************** From: ISABEL.CARVALHO Date: Tue, 16 Mar 2004 12:54:40 -0000 Subject: API3000 problems Organization: * Dear Sirs, Here in the LNIV - Laboratorio Nacional de Investigação Veterinária, Portugal, we have an HPLC acoplated to an API3000 detector. We are having some problems with the detection of the compounds. For example, in Nitrofurans (in poultry muscle matrix), in Nitroimidazoles (also poultry muscle matrix) and even in Cloranphenicol, after injecting 3, 4 times the same sample, the signal reduces to half or even less. In Nitrofurans it is even worse, because in the middle of an analysis, the signal simply disapears, and at the end (last 2 - 3 minutes) suddenly appears again. We have already explored all possibilities of hardware: * in the HPLC, we´ve changed the LC pumps (we used another HPLC pump), we´ve used new and freshly made solvents; * we´ve changed the autosampler and we´ve exchanged the injection needle - it could be an obstruction problem; * we opened and cleaned the mass spectrometer; * we have calibrated the mass spectrometer in positive and negative mode; * we´ve exchanged the peek tubing transfer line and the Turbo ion spray electrode, in the ESI; * we´ve changed the chromatografic columns. It is not an extraction problem, because we also have tried the direct mixture of each compound. Do you have any more ideas? Cause we can´t think of nothing else. Have you heard of anyone who had the same problem? Best regards, Rita Barbosa. ****************************************************************************** From: Mudbunny Date: 16 Mar 2004 05:18:11 -0800 Subject: Re: Increasing S/N Organization: * Ricksfbrsc wrote in message news:... } I can't address the trap optimization, but you can: } 1. Use splitless injection-inject 1-2 ul, set the purge time to 0.75 minute, } purge flow to 25 ml/min. You may have to lower the column temperature as it } needs to be set at least 10 C (better 15 or 20 C) below the solvent boiling } point to get good focusing. Make sure to not turn on the MS until after the } solvent has eluted. This step should increase the amount injected on the } column by a factor of 10 for 1 ul (and 20 by 2 ul but your system may not } handle that large an injection well). The solvent being used is dichloromethane, which boils at around 40C. The building we are in has crappy AC, so 10 C below will have to do. My worry with injecting it splitless is that the solvent tailing will cause a lot of problems and noise . } 2. Do you have to use HRSIM? Generally sensitivity is much better in a low } resolution mode. I have never used a HRMS before, so I was going off of the Ministry of the Environment and EPA methods for the analysis of NDMA by HRMS. They say that a resolution of 7000 is the minimum that their methods require. You are the second person to recommend to me that I lower my resolution, so I will be giving that (I will try a resolution of about 3000) a shot as well. Thanks Marcel ****************************************************************************** From: Mudbunny Date: 16 Mar 2004 08:13:45 -0800 Subject: Re: Increasing S/N Organization: * Ricksfbrsc wrote in message news:... } I can't address the trap optimization, but you can: } 1. Use splitless injection-inject 1-2 ul, set the purge time to 0.75 minute, } purge flow to 25 ml/min. You may have to lower the column temperature as it } needs to be set at least 10 C (better 15 or 20 C) below the solvent boiling } point to get good focusing. Make sure to not turn on the MS until after the } solvent has eluted. This step should increase the amount injected on the } column by a factor of 10 for 1 ul (and 20 by 2 ul but your system may not } handle that large an injection well). I have been playing around with your suggestions. The 25 mL/min resulted in peaks broadening too much, so I went back to about 3 mL/min. I have dropped the starting temp down to 30 C, and it seems to be working quite well. Now all I have to do is find out what kind of injecion port liner I have, an dchange it (if required) Marcel ****************************************************************************** From: "Marcom @ ChemUserWorld.com" Date: Tue, 16 Mar 2004 17:14:29 GMT Subject: MS at PittCon 2004 by ChemUserWorld.com Organization: * FREE Webinar: Pitcon 2004 Review Thursday, March 18th - 9AM-10AM (PST) Unable to attend Pitcon this year? Looking for an update? Join us for a FREE review of this years Pitcon 2004. ChemUserWorld.com President David Sparkman has just return from Chicago with all the scoop on what's hot and what's not. So, if a tight budget kept you home, this webinar is a must. To register, click here. (pre-registration is not required). ****************************************************************************** From: Vincent Date: 16 Mar 2004 14:07:40 -0800 Subject: Re: Agilent and Thermo Ion traps Organization: * With regards to the LC to CE interchange the Agilent is probably your best bet as they sell CE-MS instuments and have the software and hardware to do it. We are in the process of setting up an Agilent CE on a Applied Biosystems API2000 triple quad. We've had to design and fabricate a source for it and we will need to run the system with two computers; one for the CE and the other for the MS. Also there is a source voltage issue that you must look into for coupling the CE to the Deca and I would suggest you make sure you can control the LCQ MS start/stop using the CE. Vince Chris R. Lee wrote in message news:... } May I add: easy interchangeable coupling with LC and CE? } } Regards } } "Lisa Lavoie" a écrit dans le message de news: } c1j5a3$i8u$1@news-int2.gatech.edu... } } Hi: } } I am trying to chose between two ion trap instruments, the Agilent XCT } } and the Thermo LCQ Deca XP Max. Among my concerns are: } } } } 1) ruggedness (how often does one need to stop analyses for preventive } } maintenance, how many service calls need to be made). } } } } 2) availability of parts for both LC and MS. } } } } 3) ability to do MS to the nth degree. } } } } 4) ease of use of software. } } } } 5) ability to gather some isotopic data (understanding limitations of } } a trap) } } } } 6) reproducibilty of mass measurements } } } } 7) ability to do some quantittive analysis. } } } } } } My primary use will be to identify unknowns in very complex } } chromatograms. } } } } Thanks for your help, } } Lisa } } } } } } } . ****************************************************************************** From: bizzwire Date: Wed, 17 Mar 2004 00:30:28 GMT Subject: Re: how to compare two MS sensitivity? Organization: * } } if there are two MS, one is LCQ classic, the other is LCQ deca. from the } theory (or the company introduction), deca is around 10 times sensitivity } than classic. how do you test it? } thanks } Eileen } Several years ago (I'd rather not recall how many), the "Young Mass Spectrometrists" workgroup at ASMS put out a paper titled "How to buy a mass spectrometer" or some similar title. It discussed the pitfalls and common misunderstandings that the OP and subsequent posters have raised. I'll try to dig it out; for some reason I think it was the one in Washington D.C. ****************************************************************************** From: Jim Startin Date: Wed, 17 Mar 2004 11:21:50 +0000 Subject: API 3000 problems with nitrofurans analysis etc Organization: * On Tue, 16 Mar 2004 12:54:40 ISABEL.CARVALHO wrote: "we have an HPLC acoplated to an API3000 detector. We are having some problems with the detection of the compounds. For example, in Nitrofurans (in poultry muscle matrix), in Nitroimidazoles (also poultry muscle matrix) and even in Cloranphenicol, after injecting 3, 4 times the same sample, the signal reduces to half or even less. In Nitrofurans it is even worse, because in the middle of an analysis, the signal simply disapears, and at the end (last 2 - 3 minutes) suddenly appears again. We have already explored all possibilities of hardware........" From this description it sounds possible that you are suffering from partial or complete suppression of ionisation. I suspect that the first extract injection puts a large amount of low polarity material onto the column and this starts to elute a few injections later. This is quite a frequent problem in trace analysis of foods by electrospray. If you cannot improve the cleanup then try extending the HPLC run time and/or including a column washing step at high organic between injections. Reduce the extract concentration/injection volume to the minimum consistent with the LOD you need to achieve. A useful experiment is to infuse the analyte into the HPLC flow through a Tee-piece and run a series of blanks. ======================================================================= ****************************************************************************** From: "Parees,David M" Date: Wed, 17 Mar 2004 09:31:19 -0500 Subject: Re: Increasing S/N Organization: * Mudbunny wrote... >I am not sure if this would be better served in a chromatography >group, but this seems like a good place to start. > >I am using a Kratos Concept (Now manufactured by MSI) attached to a HP >5890 GC. 5uL of a 0.1 ng/uL sample are being injected onto the column. >I am using a 50:1 split ratio. The trap current is at 5, and I am >using HRSIM techniques. The compound is N-nitrosodimethylamine, and >the sample has an internal standard (d6-NDMA). Currently, I end up >with a S/N of about 16. I need to be able to see a sample with a >concentration of 0.001 ng/uL. Currently, I see nothing but noise. Do >the wise people in this have any suggestions?? > >Thanks > >Marcel > ***************** I'd suggest: While splitless analysis was already suggested, with warnings about injection volume (and replied to, with concerns about effects of the solvent peak), I think this needs to be examined more thoroughly. Certainly, the originally quoted split ratio of 50:1 need not be so high, although the 5 uL inj. volume is on the high end for this type of injection. Under the original conditions, assuming a linear, accurate split, only 10 pg are going to the column when a 0.1 ng/uL solution is injected. Trying to detect a concentration x100 lower without changing some conditions would be fruitless. But standard splitless analysis would also fall short, even assuming a 5 uL injection could be made without any strange effects from the dichloromethane solvent. The dimethylnitrosamine will not be eluting long enough after the solvent. One thing to consider is a large-volume injection using a column system with a significant "retention gap" capillary segment. The work of Grob and Zlatkis, among others, should be consulted. Dave ****************************************************************************** From: Ricksfbrsc Date: 18 Mar 2004 23:02:13 GMT Subject: Re: Increasing S/N Organization: * Marcel, The purge flow should be ~25 ml/min. to minimize tailing after the splitless injection. If the column flow rate is at 3 ml/min., it is on the high side, I'd drop it to 1-1.5 ml/min. ****************************************************************************** From: Doug Stevens Date: 19 Mar 2004 21:05:54 -0800 Subject: Re: API3000 problems Organization: * An approach I've used with some success in this type of problem is to first try to isolate the chromatograph from the MS. You mentioned that you have tried two different HPLC's. Do you have a non-MS (UV, PDA, ELSD, etc...) detector available for them? As an ex-MS field engineer I might be tempted to chase this as an MS charging problem but I'd recommend eliminating the LC as the source of problems first. If a non-MS detector shows the same performance then you can concentrate on the entire LC system (solvents, additives, column, autosampler, pump, injection valve, tubing type) and forget about the MS. If the non-MS detector shows good performance then troubleshooting on the MS would be warranted. Some ideas for troubleshooting the LC: 1. If the two LC's you've already tried are the same model then try the samples on a completely different vendor's HPLC. This should eliminate problem sources specific to a particular LC hardware configuration. 2. Find a non-MS detector to try the samples on. Really, it will be worth the effort. In no time you'll know whether or not the MS is suspect. 3. Double check the solubility of your analytes in the solvents you are diluting sample into. I used to reach for acetonitrile a lot of times because it was handy only to find out later that another solvent is better for a given analyte. I used to at least. Now I keep the Merck close at hand. MSDS sheets and Google searches can be helpful for solubility information as well. 4. Remove the column from the LC system. Using standards diluted in mobile phase and a non-MS detector, inject samples of increasing concentration. This removes the LC column from the equation. 5. Try a different stationary phase for the LC column if #4 looks good. Make a significant change not just C8 to C18. A cyano or phenyl-hexyl should give a different selectivity than C8 or C18 if that's whats being used now. 6. Routine maintenance on the LC. Replaced the check valves, needle seat in the AS, rotor in the sampling valve, and maybe a nitric acid passivation. 7. Try different plumbing. If you are using PEEK try fused silica. Avoid using stainless once you couple to the MS as electrospray and stainles steel don't mix. If the problem persists then it is likely that the MS is having a problem. Specifically, the problem sounds like charging. One approach to troubleshoot charging is: 8. Start an infusion at a constant low flow rate (10µL/min or so). While the infusion continues switch the system out of Operate (high voltages off) for ten seconds. After switching back into Operate make note of the signal intensity. If it is significantly higher than immediately before the high voltages were switched off but continuously decays across time then charging is likely. Charging is the result of dirty components in the MS. The dirtying of the system leads to components coated with matrix and other contaminants. This leads to a higher than usual voltages needing to be applied to the contaminated device and possibly the devices near it. Essentially the contamination acts like an insulating layer which can also have a capacitance associated with it. Taking the high voltages off the system temporarily discharges the component and leads to effective application of the applied voltage but only for a short period. Hence, the decay in signal across time. In severe cases the signal may decay right in front of your eyes. In less severe cases it may take a number of minutes. Some systems need to be switched between positive and negative ion modes to fully discharge. 9. A call to ABI tech support is definitely in order at this point. I'm sure they can provide a few additional hints about frequently encountered problems and some suggested solutions. Hope this helps. I'm a bit done in after PittCon and being on the road for another week after that so I hope this all makes sense. Good Luck! Regards, Doug Stevens Principal MS Applications Chemist Waters Corp. ISABEL.CARVALHO wrote in message news:... } Dear Sirs, } } Here in the LNIV - Laboratorio Nacional de Investigação Veterinária, } Portugal, we have an HPLC acoplated to an API3000 detector. We are having } some problems with the detection of the compounds. For example, in } Nitrofurans (in poultry muscle matrix), in Nitroimidazoles (also poultry } muscle matrix) and even in Cloranphenicol, after injecting 3, 4 times the } same sample, the signal reduces to half or even less. In Nitrofurans it is } even worse, because in the middle of an analysis, the signal simply } disapears, and at the end (last 2 - 3 minutes) suddenly appears again. } We have already explored all possibilities of hardware: } } * in the HPLC, we´ve changed the LC pumps (we used another HPLC pump), } we´ve used new and freshly made solvents; } * we´ve changed the autosampler and we´ve exchanged the injection } needle - it could be an obstruction problem; } * we opened and cleaned the mass spectrometer; } * we have calibrated the mass spectrometer in positive and negative } mode; } * we´ve exchanged the peek tubing transfer line and the Turbo ion } spray electrode, in the ESI; } * we´ve changed the chromatografic columns. } } It is not an extraction problem, because we also have tried the direct } mixture of each compound. } } Do you have any more ideas? Cause we can´t think of nothing else. Have you } heard of anyone who had the same problem? } } Best regards, } Rita Barbosa. ****************************************************************************** From: Chip Cody Date: 22 Mar 2004 12:20:17 -0800 Subject: Re: Increasing S/N Organization: * [ The following text is in the "ISO-8859-1" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] A splitless injection is definitely recommended for analysis at these levels. You are throwing away most of your analyte when you split. Also, the 5 ul injection volume is definitely too large unless you are using a large-volume injector with a programmable temperature vaporizing inlet. The problem is that the injector liner volume needs to be matched to the volume of the vaporized solvent. A 4 mm ID liner is good for 2 ul injections, but 5 ul of methylene chloride will expand to a larger volume than the injector liner can accomodate and the sample will be lost. Don't use a split injector liner for splitless injections or vice-versa (combination liners are generally OK). Chose a deactivated injector liner that matches your injection volume and method and replace septa and liners frequently. Replacing an injector liner that has a tiny spot of contamination on it with a new one can improve your detection limits by as much as 10 times. Also, high-purity solvents can make a big difference in your results for trace level analysis. It is easier to work out the method if you separate chromatography problems from mass spec problems. I suggest that you work out the chromatography and maximize the S/N for a larger injection amount (e.g. 0.1 ng/ul) at low resolving power, then gradually increase the resolving power and decrease the amount injected. Chip Cody JEOL USA, Inc. "Parees,David M" wrote in message news:... } Mudbunny wrote... } } }I am not sure if this would be better served in a chromatography } }group, but this seems like a good place to start. } } } }I am using a Kratos Concept (Now manufactured by MSI) attached to a HP } }5890 GC. 5uL of a 0.1 ng/uL sample are being injected onto the column. } }I am using a 50:1 split ratio. The trap current is at 5, and I am } }using HRSIM techniques. The compound is N-nitrosodimethylamine, and } }the sample has an internal standard (d6-NDMA). Currently, I end up } }with a S/N of about 16. I need to be able to see a sample with a } }concentration of 0.001 ng/uL. Currently, I see nothing but noise. Do } }the wise people in this have any suggestions?? } } } }Thanks } } } }Marcel } } } } ***************** } I'd suggest: } } While splitless analysis was already suggested, with warnings about injection volume (and replied to, with concerns about } effects of the solvent peak), I think this needs to be examined more thoroughly. Certainly, the originally quoted split ratio } of 50:1 need not be so high, although the 5 uL inj. volume is on the high end for this type of injection. Under the original } conditions, assuming a linear, accurate split, only 10 pg are going to the column when a 0.1 ng/uL solution is injected. } Trying to detect a concentration x100 lower without changing some conditions would be fruitless. But standard splitless } analysis would also fall short, even assuming a 5 uL injection could be made without any strange effects from the } dichloromethane solvent. The dimethylnitrosamine will not be eluting long enough after the solvent. One thing to consider is } a large-volume injection using a column system with a significant "retention gap" capillary segment. The work of Grob and } Zlatkis, among others, should be consulted. } } Dave ****************************************************************************** From: Chip Cody Date: 23 Mar 2004 10:14:33 -0800 Subject: Re: Difference between clusters and adducts Organization: * Nobody has replied to this question (difference between clusters and adducts) in quite a while, so I'll try to reestablish the thread. David Sparkman's "Mass Spec Desk Reference" defines a cluster ion as "an ion formed by the combination of an ion with one or more of another ion, atom, or molecule of a chemical species (e.g., [(H2O)nH]+ is a cluster ion)." I usually think of an adduct ion as an ion that if formed by combining an ion with a single neutral species, e.g. [M+NH4]+. If that is correct, then adducts are a subset of cluster ions. Any comments or observations (agree/disagree)from the terminology buffs reading the newsgroup? Chip Cody Jimmy wrote in message news:... } Please explain me the difference between them. } } TIA. } } Jimmy ****************************************************************************** From: Mudbunny Date: 25 Mar 2004 08:59:26 -0800 Subject: Re: Increasing S/N Organization: * Chip Cody wrote in message news:... } It is easier to work out the method if you separate chromatography } problems from mass spec problems. I suggest that you work out the } chromatography and maximize the S/N for a larger injection amount } (e.g. 0.1 ng/ul) at low resolving power, then gradually increase the } resolving power and decrease the amount injected. } Thanks Chip. That is what I decided to do. I took a fairly concentrated sample, and then di 5 or 6 injections each from 1 to 5 uL. I am using a new injection port liner, designed for volumes >2 uL. It looks like the best volume injection to use will be either 1 uL or 4 uL. I am going to be confirming this soon, and then go on to playing with the MS stuff. Electron multiplier gain, trap current, all sorts of stuff like that. Thanks Marcel ****************************************************************************** From: Richard Wall Date: Thu, 25 Mar 2004 18:21:57 -0000 Subject: FS Optic II Programmable Temperature injector and EPC Organization: * For Sale Optic II injector for Split/splitless and PTV large volume injections. Comes complete with its own EPC and program module and fits to any GC. We can provide installation in the UK http://cgi.ebay.co.uk/ws/eBayISAPI.dll?ViewItem&category=7321&item=3805542064&ssPageName=STRK:MESSE:IT Thanks Richard Wall CE Instruments Ltd 01942-733362 ****************************************************************************** From: "Hau,Joerg,LAUSANNE,NRC/BAS" Date: Fri, 26 Mar 2004 09:30:31 +0100 Subject: MAT8430 giveaway, eventually parts for sale Organization: * Dear All, We have definitively reached the point where our good old trusty MAT8430 has to be switched off and decommissioned. The instrument shall be given away "in good hands" (preferably university or similar institution). If nobody is interested of taking it as a whole, we _may_ consider selling individual parts. The instrument consists roughly of the following: - Finnigan MAT8430 (double-focusing sector field MS) - "old-style" 330 Turbo Pumps plus roughing pumps - EI/CI Ion Source - Xe FAB - Solid Probe Inlet - Mascom RMA display - GC HP 5890 with custom-made, short transfer line - TSS Shrader Data System ("old" version, Win98 based) The instrument has been operational until last month and is well maintained. Location: Lausanne, Switzerland. Legal conditions: You take care about the _complete_ logistics. No warranty. All standard disclaimers apply. If you are interested, please contact me *soon* at the e-mail address given below. If you are interested in buying parts, please make an offer (i.e. do not ask "how much do you want for it" - we will not consider such postings). Merci beaucoup, and have a nice day! - Joerg -- Dr Jörg Hau Research Scientist & IT coordinator Nestlé Research Center PO Box 44, CH-1000 Lausanne 26 Phone + 41 21 785 8069 Fax + 41 21 785 9486 e-mail: joerg.hau(at)rdls.nestle.com ****************************************************************************** From: Elijah Bailey Date: 28 Mar 2004 02:25:06 -0800 Subject: albumin removal from human serum Organization: * What is the preferred way to remove albumin from human serum before throwing it to a mass spec machine. (We are looking for biomarkers) Thanks, --Elijah ****************************************************************************** From: Bertram.Frank@epamail.epa.gov Date: Mon, 29 Mar 2004 14:02:54 -0500 Subject: Re: Increasing S/N Organization: * Marcel: I am missing some of this discussion thread, so I don't know everything that has been said, but I have a couple of comments on the GC side. If you are trying to squeeze sensitivity, the objective is to get the analyte peak out as soon as practical yet consistent with separation from other components. (incl. solvent) This gives the best peak height, in general, because of less tailing. Dave said that 50:1split is too high and I agree, unless you are trying to discriminate against very volatile compounds. Try an injection splitless. Rick said that a flow of 4mL/min. is too high, and I tend to agree there, too, unless you are using a megabore column. (I hope not.) The critical parameter for maximizing column efficiency is average velocity, not flow. As far as I know, most columns have maximum efficiency between 30 cm/sec and 60 cm/sec. I like to keep it between 35 and 45 if possible and run constant flow (not constant pressure) between about 0.7 and 1.8 mL/min. (The mass spec likes it better, too.) You can vary the temperature ramps to achieve separation between components most of the time. The advice we hear to increase flow when peak height is low is not always the best. They are trying to move up the elution without killing chromatographic resolution. Also, you may need a different column. I don't know what you are using, but a DB-35ms (or HP-35ms) MAY be better for amines. I better shutup before I get labeled a chromatographer. Frank ****************************************************************************** From: Jean Francois GAL Date: Tue, 30 Mar 2004 09:59:05 +0200 Subject: adducts, clusters and more Organization: * To Chip, Jimmy, and those interested in terminology I suggest that "cluster" could be the generic term. "Adduct" may be restricted to a "two-partner" association like NH4+ or a cation (but not the bare proton) added to a neutral species. There are special cases of adducts : proton-bound "dimers" for example. The results of these exchanges could be forwarded to ASMS or IUPAC for the current discussion forum on MS Terms and Definitions. http://www.msterms.com/ Regards, Jean-François Gal A NOTER/PLEASE NOTICE : nouveau nom de laboratoire/new lab name ----------------------------------------------------- Prof. J.-F. GAL Laboratoire de Radiochimie, Sciences Analytiques et Environnement Fac. des Sciences*Parc Valrose Univ. de Nice-Sophia Antipolis 06108 NICE Cedex 2*FRANCE Tel : (33) (0)4 92 07 61 10 Fax : (33) (0)4 92 07 61 11 E-mail : Jean-Francois.Gal@unice.fr (gal@unice.fr) http://www.unice.fr/ ----------------------------------------------------- ****************************************************************************** From: Kajjo Date: 1 Apr 2004 02:08:31 -0800 Subject: Varian SMS data file format? Organization: * Hi everyone! Does anyone know details of the SMS Varian data file format. As far as we know, old manuals contained a appendix or section describing the binary format (header, byte order etc) of the SMS files. Unfortunately, the new device came without any such description and we would like to write a program to automatically process our GC/MS data files. Any help much appreciated! Kajjo Please answer also by email to kajjo@gmx.de Thanks! ****************************************************************************** From: Harry Dijk Date: Sat, 3 Apr 2004 16:45:25 +0100 Subject: Finnigan Mass Specs available Organization: * For Sale the following Instruments. www.triplemass.nl info@triplemass.nl **Thermo Finnigan SSQ7000 with Trace or HP5890 GC **Thermo Finnigan TSQ700 with API or GC or both **Thermo Finnigan SSQ710 with HP5890 GC Please mail for further details. Triplemass BV Hazelaarlaan 10 3852JH ERMELO Netherlands Phone: +31 341 454541 Fax: +31 341 454365 ****************************************************************************** From: Mike Sherrell Date: Mon, 5 Apr 2004 15:14:02 -0700 Subject: Mass specs and MALDIs available Organization: * Grizzly Analytical mass specs & MALDIs available: **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 2000: $125,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 300: $49,000. NT; has 365 interface. ES only. Install included; guar. eligible for svc contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex API 2000 TurboIon Spray: $5,500. Interface and orifice plate. Sept. 2002. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $50,000. ES, API 2, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. MM/Waters ZMD 2000: $35,000. ESI, APCI; guaranteed good working order. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: "[ISO-8859-1] -= C ß =-" Date: Tue, 06 Apr 2004 06:20:37 GMT Subject: Perfume / Flavor Library Organization: * It is my understanding that a Perfume/Flavor library is available from NIST, but it is bundled with another larger (not relevant) library. Anyone know an FTP site that has only that library? Or the name of that library. I understand that this library ends in .MS, but I do not know the file name. FWIW, I can accept up to 9 megs of data to my e-mail box (saving 1 meg for mail = total 10megs). TIA, -= Chris ß =- _______________________________________________________ ****************************************************************************** From: David P. Enot Date: Tue, 06 Apr 2004 09:20:43 +0100 Subject: MALDI Info Organization: * Dear all, Does anybody have in mind a good recent review on MALDI techniques/applications. I am almost interested in the laser technology and the physical processes involved with this technique. Any proposition will be much appreciated. Cheers! David ****************************************************************************** From: Mudbunny Date: 7 Apr 2004 07:18:03 -0700 Subject: Re: Increasing S/N Organization: * Bertram.Frank@epamail.epa.gov wrote in message news:... } Marcel: } } I am missing some of this discussion thread, so I don't know everything } that has been said, but I have a couple of comments on the GC side. If } you are trying to squeeze sensitivity, the objective is to get the } analyte peak out as soon as practical yet consistent with separation } from other components. (incl. solvent) This gives the best peak height, } in general, because of less tailing. Dave said that 50:1split is too } high and I agree, unless you are trying to discriminate against very } volatile compounds. Try an injection splitless. Rick said that a flow of } 4mL/min. is too high, and I tend to agree there, too, unless you are } using a megabore column. (I hope not.) The critical parameter for } maximizing column efficiency is average velocity, not flow. As far as I } know, most columns have maximum efficiency between 30 cm/sec and 60 } cm/sec. I like to keep it between 35 and 45 if possible and run constant } flow (not constant pressure) between about 0.7 and 1.8 mL/min. (The mass } spec likes it better, too.) You can vary the temperature ramps to } achieve separation between components most of the time. The advice we } hear to increase flow when peak height is low is not always the best. } They are trying to move up the elution without killing chromatographic } resolution. Also, you may need a different column. I don't know what you } are using, but a DB-35ms (or HP-35ms) MAY be better for amines. I better } shutup before I get labeled a chromatographer. I have switched to a splitless injection, and it is working much better. I have a column flow of about 1 mL/min. The temperature ramps work to get seperation between the peaks so that they are far enough apart that, except for NDMA and d6-NDMA, I can have a seperate group for each compound. The column that I am using is one that is designed for nitrosamines and other similar compounds. I am quite happy with the chromatography right now. Now all I have to do is figure out how to tweak the MS signal some. That is trickier. Marcel ****************************************************************************** From: Matt Rainsberg Date: 8 Apr 2004 14:46:33 -0700 Subject: PFTBA valve Organization: * I have an HP 5985 MS with a leaky PFTBA solenoid valve. The mass spec pulls a great vacuum (10-7 torr) when the valve is closed. When we try to tune and open the valve, the pressure spikes and we lose the vacuum gauge. The restoration of the vacuum to 10-7 torr is quick (<5 minutes). We've replaced the valve, teflon tape, and actual glass calibration vial...but to no avail. Any ideas? BTW, does anyone know where I can get another glass calibration vial? matt mr210102@ohio.edu ****************************************************************************** From: Peter Harrington Date: Thu, 08 Apr 2004 22:42:07 GMT Subject: Help--Troubleshooting a leaky PFTBA solenoid Organization: * We are having difficulties with an HP 5988 GC-MS system. One of my graduate students was filling the PFTBA vial, and now when we open the solenoid, the pressure shoots up and our diffusion pumps shut off. He also broke the glass vial by dropping it, but we happened to have a spare that we replaced it with. The pressure indicates a massive leak. When the valve is off, the system holds vacuum well. Could the O-ring around the vial be bad? We have replaced PFTBA before and never encountered this problem. In troubleshooting he completely removed the solenoid without carefully checking its orientation. The two ends are labeled 1 and 2. He tells me that the end labeled 2 should be towards the vacuum. Any help would be greatly appreciated. TIA. Pete ****************************************************************************** From: Dr. Dickie Date: Fri, 09 Apr 2004 05:10:52 -0400 Subject: Re: PFTBA valve Organization: * On 8 Apr 2004 14:46:33 -0700, Matt Rainsberg wrote: }I have an HP 5985 MS with a leaky PFTBA solenoid valve. The mass spec }pulls a great vacuum (10-7 torr) when the valve is closed. When we }try to tune and open the valve, the pressure spikes and we lose the }vacuum gauge. The restoration of the vacuum to 10-7 torr is quick (<5 }minutes). We've replaced the valve, teflon tape, and actual glass }calibration vial...but to no avail. Any ideas? } }BTW, does anyone know where I can get another glass calibration vial? } }matt } }mr210102@ohio.edu } There typically is a spike upon opening the value. The method that I used was to open the valve and wait about one minute for the pressure to stabilize before tuning. However, that spike does seem a bit excessive. You should be able to get a new valve through SIS. Look here: http://www.sisweb.com/home.htm HTH Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: Dr. Dickie Date: Fri, 09 Apr 2004 05:14:37 -0400 Subject: Re: Help--Troubleshooting a leaky PFTBA solenoid Organization: * On Thu, 08 Apr 2004 22:42:07 GMT, Peter Harrington wrote: }We are having difficulties with an HP 5988 GC-MS system. One of my graduate }students was filling the PFTBA vial, and now when we open the solenoid, the }pressure shoots up and our diffusion pumps shut off. He also broke the }glass vial by dropping it, but we happened to have a spare that we replaced }it with. } }The pressure indicates a massive leak. When the valve is off, the system }holds vacuum well. } }Could the O-ring around the vial be bad? We have replaced PFTBA before and }never encountered this problem. } }In troubleshooting he completely removed the solenoid without carefully }checking its orientation. The two ends are labeled 1 and 2. He tells me }that the end labeled 2 should be towards the vacuum. } }Any help would be greatly appreciated. } }TIA. } }Pete } It is very easy to break the glass vial when tightening it back down. It is also easy to cut the seal (it is not a o-ring but a sleeve of sots--at least typically, there are a lot of set-ups used that I have seen). Another problem that crops up is that PFTBA get's in the neck of the vial and gets sucked up into the instrument when first opened; however, it does sound like you got a leak. Go to SIS and find replacement parts and good help: http://www.sisweb.com/home.htm Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: David Sparkman Date: Sun, 11 Apr 2004 13:48:37 GMT Subject: RE:Adduct vs Cluster Organization: * The following are the proposed definitions for these two terms in the next edition "Mass Spectrometry Desk Reference". The sub- and superscripts may look strange. cluster ion-a cluster is a species resulting from two or more neutral (usually molecules) that are bound together through non-covalent forces; e.g., H2O clusters, analyte multimers, analyte molecules combined with molecules of mobile phase (e.g., Analyte + MeOH, Analyte + AcCN, etc.), etc. A cluster ion is formed by the combination of an ion with one or more of another ion, atom, or molecule of a chemical species (e.g., [(H2O)nH]+ is a cluster ion). adduct ion-(a.k.a adduct) an ion that results from an ion/molecule reaction where the ion attaches itself to the molecule. A protonated molecule is a special case of an adduct ion. Ions formed in the gas phase in chemical ionization such as RC2H5+ and R C3H5+ or gas-phase ions such as RNa+ , RNH4+, RCl-, etc. produced in electrospray are adduct ions. -- O. David Sparkman Consultant-At-Large ods @ compuserve.com ****************************************************************************** From: David Bostwick Date: Mon, 12 Apr 2004 13:17:47 -0400 Subject: ADMIN - forged approvals Organization: * Several articles have recently appeared pretending to be from votenader.org. The approvals are forged, and the articles are from someone who appears to be upset with votenader, since similar articles are appearing in many other newsgroups. We're trying to block these articles. On a similar issue, the STMS submission address has been relatively free from spam, but the recent distribution of several viruses has ended that. We get 10-30 spam messages each day. Be sure that your article has a descriptive subject line, or it may be deleted by accident when the spam is removed. Thank you. David David Bostwick School of Chemistry and Biochemistry Ga. Inst. of Technology Atlanta. GA 30332-0400 Phone: 404-385-4250 FAX: 404-894-4061 ****************************************************************************** From: Filippo Rusconi Date: Mon, 12 Apr 2004 19:29:37 +0200 Subject: proofreading of a mass spec manual Organization: * Hello to all of you, I just wanted to ask if somebody would be interested in proofreading the manual of a software program (GNU polyxmass) that I'm authoring. There are a number of pages on polymer chemistry and gas-phase fragmentations that may need some expert proofreading. The manual is located at http://polyxmass.org/varia/polyxmass.pdf. By the way, the GNU polyxmass software suite is Free Software (not only Open Source, but real Free Software according to the www.gnu.org definition). It runs under GNU/Linux and MacOSX, although it might run under MS-Windows with Cygwin. It is an on-going development effort that already is usable... Feel free to try it, by downloading from www.polyxmass.org (hosted on bioinformatics.org). Comments at polyxmass-maintainer {[a t]} polyxmass ## dot ## org Cheers, Filippo ****************************************************************************** From: Chip Cody Date: 12 Apr 2004 11:04:55 -0700 Subject: Re: Adduct vs Cluster Organization: * Thanks, David! These definitions are clear and to the point, and they are consistent with what both Jean-Francois and I were thinking. David Sparkman wrote in message news:... } The following are the proposed definitions for these two terms in the next } edition "Mass Spectrometry Desk Reference". The sub- and superscripts may } look strange. } } cluster ion-a cluster is a species resulting from two or more neutral } (usually molecules) that are bound together through non-covalent forces; } e.g., H2O clusters, analyte multimers, analyte molecules combined with } molecules of mobile phase (e.g., Analyte + MeOH, Analyte + AcCN, etc.), etc. } A cluster ion is formed by the combination of an ion with one or more of } another ion, atom, or molecule of a chemical species (e.g., [(H2O)nH]+ is a } cluster ion). } } } adduct ion-(a.k.a adduct) an ion that results from an ion/molecule reaction } where the ion attaches itself to the molecule. A protonated molecule is a } special case of an adduct ion. Ions formed in the gas phase in chemical } ionization such as RC2H5+ and R C3H5+ or gas-phase ions such as RNa+ , } RNH4+, RCl-, etc. produced in electrospray are adduct ions. ****************************************************************************** From: Peter Harrington Date: Tue, 13 Apr 2004 02:33:25 GMT Subject: Low Sensitivity Organization: * Hi: Thanks for the help with the leaky pftba valve. Now, the instruments seems to scan ok, but we have horrible sensitivity. We replaced the electron multiplier. We can pick-up the m/z 69 peak, but m/z 131 is about 5% and we see no other PFTBA peaks at higher mass. We have never cleaned the quads. Could that be the problem? Tuning did not seem to help. Would a dirty source cause this type of problem, as well? We had just cleaned the source, but when we were trouble-shooting the instrument, I am worried the source may have become a bit fingered up. Another symptom is that the instrument scans, but if we shut the source off and on. The instrument (HP 5988) continues to turn itself off, once the target current rises. However, if the instrument is left off for a period of 10 minutes or longer, this problem does not arise. TIA, Pete ****************************************************************************** From: Elijah Bailey Date: 12 Apr 2004 20:30:21 -0700 Subject: Base Line Correction Organization: * What are the ways known to do base line correction? Why does it occur in Mass-Spectra? Thanks in advance for your help, --Elijah ****************************************************************************** From: Michael Sherrell Date: Tue, 13 Apr 2004 12:48:34 -0700 Subject: Seqs, synths, mass specs/MALDIs, liquid handlers available Organization: * Grizzly Analytical: Sequencers, synthesizers, mass specs, MALDIs, liquid handlers, cytometers etc. for sale For text string search in Outlook Express, use ctrl+shift+F For text string search in Outlook, use F4. **Oligosynthesizers: Expedite 8909: $14,500. Includes M.O.S.S, rebuilt w/ new ABI valves, 90-day warranty. + $3,500/trityl. ABI 394: $14,200. Rebuilt; 90-day warranty. ABI 394: $19,900. Trityl, MAC, rebuilt: about as good as the new 3400. ABI 392: $12,200. Rebuilt; 90-day warranty. ABI 391: $11,750. Rebuilt; 90-day warranty. ABI 3948: $25,000. Rebuilt/installed w/ 90-day warranty. ABI 390Z: $11,000. Rebuilt/warranteed. (Oligosynthesis reagents, ~75% off list: Oxidizer, Cap A, Cap B, Activator, Deblock, amadites, + 8909 columns) Beckman 1000M: $11,000. Excellent condition; guaranteed. CyClone: $7,500. New-in-box; 90 day parts warranty. Similar to ABI 392. Biosearch 8700: $10,000. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. BioSearch 8750: $10,500. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. Biosearch 8700: $8,000. Rebuilt; 90-day warr. + $2K/Windows. BioSearch 8750. ~$4,000. Have 5; cheaper & faster than 394s. Cruachem PS250. <=$2,500. 6 available. MacConnell MiniPrep 48 (for DNA Purification): $6,000. Used once. 48 samples/hr. Specs: www.macconnell.com/specs_48.htm *High throughput synthesizers: BLP 192: $125,000. 2 plates, 8 min. cycle time. New; incl. install + 1 yr. warr. TAGC 96: $95,000. Fast; optimized for small-scale up to 50 bases. Polygen 10. Call if interested. Polyplex Gene Machine: $89,000. Installed/warranteed. **Oligosequencers: ABI 3100: $85,000. Includes factory install. ABI 3100 Avant: $55,000.Includes factory install, $5,000 in consumables. ABI 310: $28,000. Mac. Includes factory install; guar. eligible for service. ABI 310: $31,000. PC. Includes factory install; guar. eligible for service. ABI 3700: $65,000. Includes factory install; guar. eligible for service. ABI 3700: $29,000. From major genome center; beautifully maintained. MegaBace 1000: $22,000. Incl. installation by manufacturer. ABI 377: $15,500. 96-lane; install factory incl., eligible for service. (Also suitable for tiling.). Genescan: $5,000. Licensed software for the 377, 310 or 373. ABI 373 stretch: $9,000. Big Dye upgrade. Pharmacia ALF Express: $14,000, incl. 90-day parts & labor warr. Visible Genetics: $20,000. Unused. Have 3. LiCor 4200: $25,000. Incl. Global Upgrade; guaranteed installable. LiCor 4000LS <: $20,000. 1994 model; can have Global Upgrade. Genomyx LR: $2,500. Boots; many accessories. MJ Basestation 51. Call for pricing. No robotic loading, 2 years old, under service contract. MJ Research BaseStation: $105,000. 2 yrs old; still under svc. contract. MJ Research BaseStation: $125,000. 6 mos. old; still under svc. contract. **Real-time PCR: ABI 7700: $34,000. Installed/warranteed. ABI 7000: $29,000. Installed/warranteed. 2002 model. BioRad iCycler: $32,000. 90-day warranty. **Peptide synthesizers: ABI 433: $33,000. Original, ABI-supportible 433. These come and go; call/email to reserve. 90-day warr. ABI 433: $24,000. Upgraded from 431. We support. Rebuilt, 90-day warr. ABI 431: $16,000. Rebuilt, 90-day warr. ABI 430: $10,500. Rebuilt, 90-day warranty. ABI 432: $15,000. Rebuilt, 90-day warranty. Capriccio 1: $65,000. New instrument. Benchtop, large scale; faster and more efficient than ACT 400. Incl. install, 1 yr svc. PerSeptive 9500: $12,750. Rebuilt w/ 90-day warranty. PerSeptive 9050: $16,000. Rebuilt w/ 90-day warranty. CS Bio 336. ~$27,000. 6 mos old; lease default. 3 peps simultaneous; .05-.25 mmol. ACT LabTech III: $15,000. 30-day warranty. Pioneer: $40,000. Includes factory install, eligible for svc. contract MPS unit for the Pioneer peptide synthesizer: $5,000. New and unused; price = 25% of new cost. ACT 396 MPS: $42,000. Factory refurb; includes 120-day warranty. PerSeptive 9600: $13,750. Rebuilt, warranteed. ACT Vantage: $79,000. Excellent condition. ACT 357-MPS. Call for pricing. CEM Discover benchtop single peptide synthesizer: ~$12,000; call. ACT 90: $16,250. Only used twice. Incl. install; guar. eligible for svc. Argonaut Quest 205: $27,000. ASW model. Argonaut Quest 210: $19,000. ASW model. **Peptide sequencers: ABI 494 cLc. Offers considered. ABI 494 HT: $40,000. Installed, guaranteed ok for service contract. ABI 492: $25,000 installed, eligible for service contract. Beckman 6300. Various prices. Have several; can rebuild or sell for parts. ABI 421: $10,000. Offers considered. ABI 477/120: $1,500. Good working order or right of return. ABI 477. Service, parts available. ABI 473/476: $15,000. Good working order; install/service available. Beckman 6300 AA: $ 8,000. Rebuilt/warranteed ABI 470A: $2,000. For parts. Many extra parts. *[Note: various other ABI, HP, Millipore, Biosearch, Beckman, etc. sequencers, synthesizers etc. available; please inquire.] **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 2000: $125,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 300: $49,000. NT; has 365 interface. ES only. Install included; guar. eligible for svc contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex API 2000 TurboIon Spray: $5,500. Interface and orifice plate. Sept. 2002. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $50,000. ES, API 2, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. MM/Waters ZMD 2000: $35,000. ESI, APCI; guaranteed good working order. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $110,000. API-LC/Orth. 2000 model. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. **Liquid handlers: Biomek FX (core system): $450,000 good working order. Includes 3 meter Orca, fluorometer, incubator, more. Biomek FX: $60,000. Single arm. Biomek 2000, no side loader, $49,000. Beckman Multimek, $34,000. Zymark Sciclone: 1.5 years old; $43K. Zymark Staccato system: $250,000 and up, depending on accessories, install, warranty. XP-arm based Zymarks: $10,000 and $20,000, depending on accessories. Tecan RSP-200/8 ID Robot Sample Processor, fully equipped: call/email if interested. Hamilton MicroLab AT2 Plus robot, $38,000 Packard Multiprobe 20400 and CP20400, Packard refurbed, $16,500 for either Transgenomic WAVE system, $22,000 incl. installation, eligible for svc. Tecan Genesis RSP 150, no Roma, $52,000 delivered w/ 90-day warranty. Tecan Genesis RSP 100, $41,000 delivered w/ 90-day warranty. LC Packings UltiMate NanoLC system w/ FAMOS autosampler, $37,300 Scitec robotic liquid handling system, 3-meter rail, $60,000 guaranteed working Tom-Tec Quadras, various configurations, refurbished and warrantied. Hamilton Microlab 2200: call for pricing. Gilson 215: call for price. ABI 877 Catalyst Turbo: $12,000 or best offer Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically 96-well microplate source, glass slide, microwell plate or membrane target), ~ 5 years old. **Other expensive hi-tech items: *NMRs: Varian Inova 600 NMR: $275,000 guaranteed installable; +$25K/install. Bruker Avance 500 DRX, unshielded, cryoprobe ( available for $175,000 separately) + 5 other probes, 3 channel, $425,000 installed. Optional autosampler, $25,000. FX90Q NMR w/ Tek-Mag, $19,500. Others available; inquire if interested. *Flow cytometers: FACS Vantage SE with the DIVA option: $160,500. (2 lasers: 488nm and UV tunable). Bought in June '02 and never used. BD FACSCalibur w/ FACSLoader: $84,000. 4 color. 1998; excellent condition. BD FACScan; $28,500. 3 color single laser. BD FACSort Cell Sorter, $39,000. 3 color, MAC G3, Cellquest, install included COULTER® EPICS XL-MCL^Ù: $45,000. 4 color with Multi Carousel Loader includes rebuilt, installation and one-year warranty. Coulter Epics Elite: 9 years old but never used. Call/email if interested. COULTER® EPICS XL^ÙFlow Cytometer: $45,000.00 Currently in operation. Includes XL2, EXPO and Data Mate Software, APC UPS Back-up, factory installation, and other options. MoFlo Analyzer with MoSkeeto System: $99,750.00. 6-channel / 5-color detector, Carvo MSP - 9000 Auto sampler, Summit 3.1 Software, Laser. Scanning Cytometer: Microscope-based. Two-laser system. $85,000 guaranteed installable. Others available; inquire if interested. *Arrayers/spotters/readers: Affymetrix GeneArray 3000 system, $90,000 good working order; + $30,000 /install w/ 1 yr. warr.$120,000 installed w/ 1 yr. warr. SpotBot Personal Microarrayer, $9,750. 2002; excellent condition. HP GeneArray G2500A reader w/ laser, $22,000, including new data system but no fluidics station. Affymetrix 417 Arrayer/spotter: seller considering rather low offers; call if interested. Affymetrix 417 Arrayer/spotter: $34,500 reconditioned with 1 year warranty HP/Affymetrix GeneArray Scanner Model G2500A, unused, $49,000. CELLOMICS ScanArray HCS: 2003 model. Factory install, license discount available; offers considered. Packard ScanArray 4000: $39,250. 2000 instrument. Incl. factory install; eligible for service contract. Packard ScanArray 3000: $17,250. Incl. factory install; eligible for service contract. Genomic Solutions GeneTAC microarray Hybridization Station: $27,000. (for details see www.genomicsolutions.com/products/bio/hyb.html) Amersham Lucidea SLIDE PRO Hybridization Station: $18,500. Ciphergen ProteinChip Reader PBS II: $65,000. Current upgrades; includes factory install, 30-day warranty. *Spot pickers: Genetix QPix2 benchtop: $79,570 installed. Incl. 96-well picking head, gridding option, etc; Q-Fill optional. Genetix QBot picker/arrayer. Call/email if interested. BioRobotics BioPick automatic colony picker. Excellent condition. ~$60,000 Genomic Solutions Flexys; much less than new price; call/email if interested. *Microscopes: ZEISS Axioskop Trinocular Microscope, $24,650 For phase contrast, DIC and Epi-Flourscence Cambridge Stereoscope S90B SEM w/ Kevex EDX: $25,000. Incl. secondary and backscattering detectors, Polaroid system, some options, factory installation. Working now. Optional one year service sontracts available. Meridian ACAS 570C LSCM. Other Laser Scanning Confocal microscopes available, call or email for list. Leica Confocal TCS-4D: $51,000. NT upgrades, 2 or 3 laser w/ DMRBE microscope bought new in 1997. Includes factory installation. Cambridge Stereoscope S90B SEM w/ Kevex EDX: $10,000. Incl. secondary and backscattering detectors, Polaroid system, some options. Working now. Various (SEM) Scanning Electron Microscopes, $9,500-$375,000. Call or email for list. Various (TEM) Transmission Electron Microscopes; call or email for list. Various (AFM) Atomic Force Microscopes: Veeco, Digital Instruments, Park Scientific, Topometrix, etc. Call or email for list.; call or email for list. Various surgical, neuro surgical microscopes, call or email for list. Various optical microscopes, call or email for list. *Truly miscellaneous: Thermo Kevex Omicron XRF: $45,750. Excellent condition. Includes installation. Ventana Discovery Hyb System: advanced slide staining platform for target and compount drug discovery. Check www.ventanadiscovery.com. Call/ email to discuss price. Molecular Devices/LJL Biosystems Criterion Analyst HT System: $35,000. Amersham Typhoon 9410 scanner: Accepting offers. 2003 system, top condition. The first large-format gel , blot and microarray imager; also optimized for protein research. Perkin Elmer 1010M Micro Densitometer: was $325,000 new. Now in Japan. Call if interested. Amersham FARCyte/Tecan Ultra fluorescence plate reader, new in box, $50,000. List: $80K. Packard 50TR flow scintillation analyzer. Call for price. Brand new, unused. Accutag Radio Frequency Reader/10k Automated Microreactor Sorting System, $80,000 Genevac's Mega 1200 ultra high throughput solvent evaporation system, 1.5 yrs old but unused, $200,000 or best offer. New Brunswick Bioflo 3000 bioreactor: $18,900. 10 liter; new probes; 90-day warr. Process Engineers 29 liter mammalian cell bioreactor, new/unused, ~$35,000 or best offer. *(other bioreactors/fermenters available; inquire if interested.) **Too hard to classify: Li-Cor Odyssey: $25,000 ($40K new). Guaranteed good working order. See for specs. BioCAD 20s and 60s w/ 90-day warr. available for $10-15,000, depending on details. 700E also avail. < $25,000. ABI VISION Workstation (souped-up BioCAD; see AB website for details): offers considered. Luminex LX100 (simultaneous assay of multiple analytes): $29,000. Glycoprep 1000 automated hydrazinolysis machine: $9,000; good working order Packard Topcount 12-detector 96 well microplate scintillation counter, $35,000 Jasco FP6500 Fluorescence Spectrometer. Excellent condition. $11,500. ABI 120 HPLC, $1,500 ABI 877: have several; different configs, prices, none very expensive; call PE 9600 thermalcyclers: $3,750 w/ 90-day warranty PE 9700 96-well thermalcyclers: $5,300 w/ 90-day warranty PE 9700 384-well thermalcyclers: $5,450 w/ 1 yr. warranty PE 2400 thermalcyclers: $2,450 w/ 90-day warranty PE 480 thermalcyclers: $3,000 guaranteed working; have several Beckman P/ACE MDQ: $24,000 Beckman P/ACE 5510: $19,500. Refurbed, warranteed. MD PhosphorImager Storm 860, $30,000. MD FSI FluorImager, $15,000 MD Cytosensor Microphysiometer: $9,800 w/ 90-day warr. **Service: We rebuild valve blocks for ABI 430, 431 and 39x @ $65/port, 90-day warranty Service and contracts on ABI 39n and PerSeptive 8909/8905s available. Service contracts on Hewlett Packard HPLCs, GCs and MSs available at a savings over HP rates **Also available: Agilent 1100 HPLCs, virtually all configurations/detectors. HPLCs, ICs, CEs, FPLCs: microbore to prep scale. A variety of other lab instruments. Call or check the website: www. grizzlyanalytical. com. Please call or email for more information or if you have items to sell. Michael Sherrell Grizzly Analytical (USA) www.grizzlyanalytical.com 707 887 2919/fax 707 887 9834 [All the items are subject to prior sale.] [If you do not wish to receive my emails, please return this with "Stop" in the subject line, and accept my apologies for the inconvenience.] ****************************************************************************** From: David Stranz Date: Wed, 14 Apr 2004 22:30:11 -0500 Subject: Call for Speakers - ASMS Computer Applications workshop Organization: * This year's ASMS Computer Applications Interest Group workshop will be held on Monday, May 24 from 5:30 to 7:00 pm at the ASMS annual meeting in Nashville. The topic is "Algorithms for Metabolite Identification and Characterization". I am looking for two speakers to fill out the schedule. Talks will be informal, at most 15 minutes in length with plenty of time for Q&A, and must be STRICTLY NON-COMMERCIAL in nature. There will be a total of four speakers, including the two I have already scheduled. I will consider speakers representing vendors, but the workshop is meant to be algorithm and technique-focused, not an excuse to show attendees something they can read in product marketing brochures or applications notes. If you have a novel algorithm or approach that you can describe from a technical point of view, I will consider that. If you are interested in speaking, please contact me by e-mail at david_stranz AT MassSpec DOT com (replace AT and DOT with the obvious and remove the whitespace). Please provide a title and a brief description. Keep in mind that a 15-minute talk translates to at most 7 to 10 slides... not 25. Best Regards, David Stranz Sierra Analytics, Inc. ASMS Computer Applications Interest Group Co-coordinator (with Randy Julian of Lilly) ****************************************************************************** From: Frederik Pruijn Date: Fri, 16 Apr 2004 06:53:09 +1200 Subject: Postdoctoral position available Organization: * Postdoctoral Position In HPLC/Mass Spectrometry Auckland Cancer Society Research Centre The University of Auckland, New Zealand Fixed Term 2 years UniServices is a leading edge research and consulting company fully owned by The University of Auckland. We are seeking a postdoctoral scientist to join a multidisciplinary drug discovery team directed by Professor William Wilson to assist in the preclinical development of novel hypoxia-activated anticancer prodrugs. The appointee will be responsible for the development of biomarkers of nitroindoline alkylating agents and for the identification of metabolites and DNA adducts of dinitrobenzamide nitrogen mustards. The ACSRC operates two single stage quadrupole mass spectrometers, an Agilent ion trap and has access to a TSQ Quantum triple quadrupole mass spectrometer. Applicants must have experience in mass spectrometry (preferably tandem ms) and ideally should have a strong background in bioanalysis and pharmacology. Skills in small animal models and tissue culture would be advantageous. Applicants must be a good team player, have good verbal and written communication skills and be methodical whilst assisting the research team to achieve set milestones. The salary is dependent upon background and experience and will be within the range NZ$52,000 to NZ$62,000. Further information can be obtained from Professor William Wilson, email wr.wilson@auckland.ac.nz or Dr Frederik B. Pruijn, email f.pruijn@auckland.ac.nz Please forward your application to Chris West, Human Resources Advisor, UniServices, Private Bag 92019 Auckland, New Zealand or email chris.west@auckland.ac.nz Applications close on 16 April 2004. ****************************************************************************** From: Mudbunny Date: 15 Apr 2004 12:11:45 -0700 Subject: Question on Reference books Organization: * I am trying to start a small reference library at my work on MS and high res MS. What reference books would the collective knowledge in here suggest?? Please reply to newsgroup as the e-mail addy is a spam-trap. Marcel ****************************************************************************** From: David Allen Date: Fri, 16 Apr 2004 11:44:04 GMT Subject: Re: Low Sensitivity- maybe the filament? Organization: * Peter, When I had an HP5985, I had occasional problems with the filament. It was a fiddly setup with the filament held by two hooks that needed to have sufficient tension in order to maintain electrical contact when current was passing. I am not familiar with the HP5988, but your description suggests that this is a filament problem to me. Regards, David Allen Peter Harrington wrote: } Hi: } } Thanks for the help with the leaky pftba valve. } } Now, the instruments seems to scan ok, but we have horrible sensitivity. We } replaced the electron multiplier. We can pick-up the m/z 69 peak, but m/z } 131 is about 5% and we see no other PFTBA peaks at higher mass. } } We have never cleaned the quads. Could that be the problem? } } Tuning did not seem to help. Would a dirty source cause this type of } problem, as well? We had just cleaned the source, but when we were } trouble-shooting the instrument, I am worried the source may have become a } bit fingered up. } } Another symptom is that the instrument scans, but if we shut the source off } and on. The instrument (HP 5988) continues to turn itself off, once the } target current rises. However, if the instrument is left off for a period } of 10 minutes or longer, this problem does not arise. } } TIA, } } Pete } } } } ****************************************************************************** From: Dave White Date: Sun, 18 Apr 2004 02:53:12 GMT Subject: Re: Low Sensitivity- maybe the filament? Organization: * } Peter Harrington wrote: } } We have never cleaned the quads. Could that be the problem? May be. Dirty quads can cause a loss of high mass transmission. ****************************************************************************** From: Jeff Gambera Date: Mon, 19 Apr 2004 01:29:43 GMT Subject: Quattro II service Organization: * Does anyone out there know of a third party service provider (outside of Waters), who willl service a Micromass Quattro II ? Thanks ****************************************************************************** From: Mark Graham Date: Mon, 19 Apr 2004 11:50:52 +1000 Subject: Storage of samples on MALDI plates Organization: * Is anyone aware of a way to store MALDI plates with samples spotted on them so that they can still be analysed many days after spotting with good sensitivity? I was thinking maybe something to prevent breakdown of matrix and/or sample like storage in the dark, under nitrogen, with dessicant or under vacuum. Would this help? Mark Graham ****************************************************************************** From: Elijah Bailey Date: 19 Apr 2004 00:39:19 -0700 Subject: baseline correction : NewBie Organization: * Does anyone know why baseline correction is needed for MALDI-TOF spectra? Thanks in advance for ur comments and help, --Elijah ****************************************************************************** From: Fred Mellon Date: Mon, 19 Apr 2004 09:38:38 +0100 Subject: Re: Quattro II service Organization: * If you are UK-based, try SpectroServ: http://www.SpectroServ.com regards, Fred "Jeff Gambera" wrote in message news:c5vf6f$5j3$1@news-int2.gatech.edu... } Does anyone out there know of a third party service provider (outside of } Waters), who willl service a Micromass Quattro II ? } Thanks } } } ****************************************************************************** From: Dave White Date: Mon, 19 Apr 2004 14:15:48 GMT Subject: Re: Quattro II service Organization: * "Jeff Gambera" wrote in message news:c5vf6f$5j3$1@news-int2.gatech.edu... } Does anyone out there know of a third party service provider (outside of } Waters), who willl service a Micromass Quattro II ? } Thanks If you're US based, I highly recommend Research Scientific Services at http://www.resci.com/. Their main Quattro engineer, Paul Holmes, worked out of the Micromass UK factory then Micromass US for a number of years and has a LOT of experience with these instruments. Cheaper than Waters, and more knowledgeable than most of the 'engineers' you get these days. Dave White SpectraChrom Software www.spectrachrom.com ****************************************************************************** From: Athula Attygalle Date: Mon, 19 Apr 2004 23:13:32 GMT Subject: Re: Quattro II service Organization: * "Jeff Gambera" wrote in message news:c5vf6f$5j3$1@news-int2.gatech.edu... } Does anyone out there know of a third party service provider (outside of } Waters), who willl service a Micromass Quattro II ? } Thanks } } }I strongly recommend http://www.resci.com/ Their service is excellent and charges are very reasonable Athula Attygalle/Stevens Center for Mass spectrometry ============================================= Micromass mass-spectrometry service by experts! Yearly instrument service contracts and daily service Periodic Maintenance contracts Installation, qualification and specification Moving, setup and relocation Refurbished MS sales with full-spec installation and RSS warranty WE'RE HIRING NEW SERVICE ENGINEERS! See EMPLOYMENT Page! Our team grew in these last two years ... QTOF, Quattro-Micro, Q-TOF-Micro service via new staff New used-instrument sales storage and routing facility in Dublin, Ohio. New Maryland refurbishment/repair laboratory (December 2003) NEW, EXPANDED CORPORATE OFFICE HEADQUARTERS in Maryland! General Info: info@resci.com Phone: (800) 676-1991 ****************************************************************************** From: David Stranz Date: Tue, 20 Apr 2004 04:04:06 -0500 Subject: Re: baseline correction : NewBie Organization: * Elijah Bailey wrote in news:c60gvu$5sl$1@news- int.gatech.edu: } } Does anyone know why baseline correction is needed for MALDI-TOF } spectra? } } Thanks in advance for ur comments and help, } --Elijah } } One reason: When centroiding, failure to correct for non-zero baseline will lead to systematic error in computing intensities of centroided peaks (either area or height intensities). This is true when centroiding any profile MS spectrum, not just MALDI-TOF. ****************************************************************************** From: Janson Date: 20 Apr 2004 03:39:07 -0700 Subject: How are ions generated in APCI without discharge current? Organization: * I see still some ions when I run APCI but set the discharge current to zero. How are they produced? Thanks! ****************************************************************************** From: David Stranz Date: Tue, 20 Apr 2004 04:04:06 -0500 Subject: Re: baseline correction : NewBie Organization: * Elijah Bailey wrote in news:c60gvu$5sl$1@news- int.gatech.edu: } } Does anyone know why baseline correction is needed for MALDI-TOF } spectra? } } Thanks in advance for ur comments and help, } --Elijah } } One reason: When centroiding, failure to correct for non-zero baseline will lead to systematic error in computing intensities of centroided peaks (either area or height intensities). This is true when centroiding any profile MS spectrum, not just MALDI-TOF. ****************************************************************************** From: RJ Classon Date: 20 Apr 2004 10:22:59 -0700 Subject: Re: How are ions generated in APCI without discharge current? Organization: * Janson wrote in message news:... } I see still some ions when I run APCI but set the discharge current to } zero. How are they produced? } } Thanks! Janson: It would be helpful if you provided a little more information. Is the yield of ions (signal intensity) as strong as with the corona turned on? Do you see ions with no HPLC flow rate? Do you see ions with only certain mobile phases? Do you see ions only at certain temperatures? Is the signal intensity stable or does it decrease/increase over time? What m/z are the ions you typically find with the voltage off? If you are finding your target species as an ion without any APCI voltage applied, you might want to look at the possibility that you have an alternative ionization mechanism taking place. For example, most amines will produce ions in solution if there is any acid present. Put these compounds into water, mix with a trace of acid, blow them through an APCI source, turn off the corona discharge, and you essentially are doing nebulizer assisted electrospray, and will see some ions for the amines. It might not be as strong as what you would see with elecrospray, but it is due to a similar mechanism. If you are finding ions without any liquid flow, then you probably have some contamination to trace down. APCI normally starts off by producing gas phase ions from the nebulizer gas(es) and mobile phase. These evaporate and convert additional mobile phase into superacid or superbase species in the gas phase. These can provide charge transfer to your target species. Turning off the discharge current means you won't be producing gas phase ions by electrical discharge. But you can still have ions present from a lot of other causes. For example, water by itself produces H3O+ ions at a 10-7 rate. If there is any acid present in the water, the production of protonated water molecules will be higher. These can still do charge transfer to your target, to impurities in your mobile phase, or can form cluster ions with solvent molecules depending on temperatures. If you have any salts present, these will be ionic in water was soon as they are dissolved. The heat of an APCI source can generally increase the yield of ions from a number of mechanisms even without any other electrical discharge. So you can have ions from an APCI source from a number of reasons even without any voltage applied. Bob Classon LCMS Group Shimadzu Scientific Instruments 7102 Riverwood Drive Columbia, MD 21046 ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 20 Apr 2004 21:49:47 +0200 Subject: Re: How are ions generated in APCI without discharge current? Organization: * In this case ions are produced by means of Thermospray Ionisation. Best Regards Rainer Loerwald ThermoElectron Germany Janson schrieb: } } I see still some ions when I run APCI but set the discharge current to } zero. How are they produced? } } Thanks! ****************************************************************************** From: Janson Date: 20 Apr 2004 19:03:39 -0700 Subject: Re: How are ions generated in APCI without discharge current? Organization: * Hello, Classon: Thanks a lot for your reply. I was using MP of methanol and water, APCI negative for a steroid type analyte. In the middle of the analyte optimization, I stopped discharge current and ran a positive scan from 150-800 m/z (with the same MP). Then I saw some ions of polytyrosine that had been used for calibration and tuning (TSQ Quantum). The intensity was about 1/1000 of the intensity of infusion. There are sure a lot of ions in the solutions. However, those ions stick together with ions of opposite charge. Therefore, it is not very likely that they would get to the gas phase with net charge on them. That is why spray voltage is needed for ESI. Is something wrong with my reasoning? I guess, collision in the source could induce ionization and result in net charge. How likely is it? Again, thanks for your reply. I am an LC person in nature (Ph.D. in HPLC)! Janson ****************************************************************************** From: J T Hill Date: Wed, 21 Apr 2004 10:43:56 +0100 Subject: CI Control Valve Organization: * Hello Does anyone know where I can get a gas flow controller valve for CI applications? This would be for both ammonia and methane. We had a Negretti diaphragm valve on a VG 70-SE which has gone belly up and the manufacturer has gone out of business. We substituted a precision needle valve but this is really unsatisfactory. We use CI both positive and negative extensively for air sensitive compounds. Valco manufacture a flow controller Model 202 which has a flow rate down to 0.5mL/min. We are not sure whether this will do the job on a high vacuum system and it is expensive at around $825.00 for the stainless steel version. I would appreciate any ideas. Many thanks John Hill Mass Spectrometry Facility Chemistry Dept. University College London ****************************************************************************** From: Chip Cody Date: 21 Apr 2004 05:50:49 -0700 Subject: Re: Question on Reference books Organization: * Mudbunny wrote in message news:... } I am trying to start a small reference library at my work on MS and } high res MS. What reference books would the collective knowledge in } here suggest?? } } Please reply to newsgroup as the e-mail addy is a spam-trap. } } Marcel David Sparkman's "Mass Spec Desk Reference" ($28.45, Global View Publishing: 2000, http://www.lcms.com) contains a thorough list of mass spec reference books, with comments on the major publications. (David has a copy in his library of every mass spec book ever published.) A few new reference books have been published since 2000 (I contributed to one of them...) but David's book lists the reference texts that should form the core of a mass spec library. Of course, your personal choice of reference books will depend on what your applications will be. Chip ****************************************************************************** From: Joe Kim Date: 20 Apr 2004 18:22:01 -0700 Subject: Japanese Compact Diaphragm Vacuum Pumps Organization: * Oil-free for cleanroom use Long term high reliability Designed to minimize noise generation http://www.netmotion.com/htm_files/wh_pumps.htm ****************************************************************************** From: Chip Cody Date: 21 Apr 2004 06:17:58 -0700 Subject: Re: How are ions generated in APCI without discharge current? Organization: * This phenomenon was first observed in Thermospray sources when ions were observed after the operator forgot to turn the filament on. The mechanism is not fully understood, but it is usually attributed "statistical charging". That is, when liwuid containing a conductive solute is rapidly evaporated, some droplets contain an excess charge of a given polarity*. The API interface (and analyzer) will have some positive or negative potential that will attract and analyze droplets with an excess charge of the appropriate polarity. Your sensitivity will be obviously be less than when using a corona discharge. "Friction electrification" has also been proposed as a mechanism where forces from the nebulizing gas and droplet collisions cause droplet shear, resulting in a statistical excess of charges. *Reference: Yergey, A.L.; Edmonds, C. G.; Ivor, A.S.L.; Vestal, M. L. "Liquid Chromatography/Mass Spectrometry: Techniques and Applications", Plenum Press: New York (1989) Chip Cody Janson wrote in message news:... } Hello, Classon: } } Thanks a lot for your reply. } } I was using MP of methanol and water, APCI negative for a steroid type } analyte. In the middle of the analyte optimization, I stopped } discharge current and ran a positive scan from 150-800 m/z (with the } same MP). Then I saw some ions of polytyrosine that had been used for } calibration and tuning (TSQ Quantum). The intensity was about 1/1000 } of the intensity of infusion. } } There are sure a lot of ions in the solutions. However, those ions } stick together with ions of opposite charge. Therefore, it is not very } likely that they would get to the gas phase with net charge on them. } That is why spray voltage is needed for ESI. Is something wrong with } my reasoning? } } I guess, collision in the source could induce ionization and result in } net charge. How likely is it? } } Again, thanks for your reply. I am an LC person in nature (Ph.D. in } HPLC)! } } Janson ****************************************************************************** From: RJ Classon Date: 21 Apr 2004 09:08:38 -0700 Subject: Re: How are ions generated in APCI without discharge current? Organization: * Based on the additional info about the conditions, it appears that you have some limited amount thermospray ionization going on. Before there was a APCI or 'heated nebulizer' interface, there was a gas phase ionization technique called thermospray. It was originally developed around 1980 by Marvin Vestal along with Fergusson, Blakley, Carmody and others, and can now be thought of as a form of APCI without electrode discharge. The original concept sprayed mobile phase through a heated tube into a reduced pressure region prior to the MS. It needs some ions in the mobile phase in order to do charge transfer and thus works well when there is some heat, some easil ionized additives and some aqueous mobile phase present. In essence the first step of the ionization is basically an ion evaporation similar to electrospray until the liquid gets heated and vaporized, then it becomes a gas phase process similar to APCI. Thermospray is still used, but is not very common. Being so energetic a process, it often causes thermal decomposition. The chemistry of the additives can also be a bit tricky to master. Some users analyzed steroids by thermospray back a few years. You may want to look up these references. Regards, Bob Classon LCMS Group Shimadzu Scientific Instruments 7201 Riverwood Dr. Columbia, MD 21046 Janson wrote in message news:... } Hello, Classon: } } Thanks a lot for your reply. } } I was using MP of methanol and water, APCI negative for a steroid type } analyte. In the middle of the analyte optimization, I stopped } discharge current and ran a positive scan from 150-800 m/z (with the } same MP). Then I saw some ions of polytyrosine that had been used for } calibration and tuning (TSQ Quantum). The intensity was about 1/1000 } of the intensity of infusion. } } There are sure a lot of ions in the solutions. However, those ions } stick together with ions of opposite charge. Therefore, it is not very } likely that they would get to the gas phase with net charge on them. } That is why spray voltage is needed for ESI. Is something wrong with } my reasoning? } } I guess, collision in the source could induce ionization and result in } net charge. How likely is it? } } Again, thanks for your reply. I am an LC person in nature (Ph.D. in } HPLC)! } } Janson ****************************************************************************** From: Mudbunny Date: 21 Apr 2004 08:33:40 -0700 Subject: What type of filter to use Organization: * I have another question for the collective wisdom out there. The Concept HRMS that I am working on allows you to choose your noise filter frequency. It has a fairly wide range, from 30 kHz, down to 1 Hz. What is the ideal frequency to use in order to eliminate most of the noise in my spectrum, yet also leave as much of the signal present? Is the best bet to use the automatic value that it picks (which is usually 30 Hz)? or choose my own value? I know that as you loer the frequency, you also lose signal intensity, how does this affect your sample?? Marcel ****************************************************************************** From: Joerg Hau Date: Wed, 21 Apr 2004 20:23:21 +0200 Subject: Re: What type of filter to use Organization: * Hi Mudbunny, euh, Marcel, } The Concept HRMS that I am working on allows you to choose your } noise filter frequency. It has a fairly wide range, from 30 kHz, } down to 1 Hz. What is the ideal frequency to use in order to } eliminate most of the noise in my spectrum, yet also leave as much } of the signal present? It depends ;-) If you use the MS in SIM mode (i.e. you are essentially recording mass chromatograms), you will want to adapt the filter to the "sampling speed" that you use - usually in the some-Hz region. If you use the MS in "real" scanning mode, 30 Hz would be way too low. In that case, the filter width will depend on the combination of resolution and scan rate that you use (i.e. the sampling rate). I can dig out the formula if needed, but under "usual" conditions the filter will be in the several-10-kHz-range. } Is the best bet to use the automatic value that it picks (which } is usually 30 Hz)? Is that a data system option, or a hardware button? (I've never worked with the Kratos Concept, but the CH5, CH7, VG7070 and MAT8430 all had hardware filters ;-) } I know that as you loer the frequency, you also lose signal } intensity, how does this affect your sample?? Essentially these filters are low-pass filters, i.e. they filter out the higher-frequency components (noise, spikes). The lower the filter cutoff frequency, the broader the signal gets. You don't want that ... better record at a higher sampling rate and use software processing to smooth afterwards, if needed. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: "Parees,David M." Date: Wed, 21 Apr 2004 15:26:47 -0400 Subject: Re: Storage of samples on MALDI plates Organization: * In response to the query below: It does depend on your choice of matrix and what type of samples you are analyzing. Using 2,5-DHB as the matrix, I find that some materials are stable on the plate in the lab for periods of weeks, while others are not good after a couple of days. With dithranol, I'd expect fewer problems. I think that storage in vacuum, overall, is not a good idea. Many matrices are not particularly large molecules and have some volatility. I think you will lose your matrix fairly rapidly (overnight?). Storage in the dark...under nitrogen...and especially in a refrigerator or freezer might help. Dave Air Products and Chemicals, Inc. Mark Graham wrote... } }Is anyone aware of a way to store MALDI plates with samples spotted on them }so that they can still be analysed many days after spotting with good }sensitivity? } }I was thinking maybe something to prevent breakdown of matrix and/or sample }like storage in the dark, under nitrogen, with dessicant or under vacuum. }Would this help? } }Mark Graham ****************************************************************************** From: "Volker Grau, Ph.D." Date: 21 Apr 2004 14:26:23 -0700 Subject: Re: CI Control Valve Organization: * J T Hill wrote in message news:... } Hello } } Does anyone know where I can get a gas flow controller valve for CI } applications? This would be for both ammonia and methane. } We had a Negretti diaphragm valve on a VG 70-SE which has gone belly up and } the manufacturer has gone out of business. } We substituted a precision needle valve but this is really unsatisfactory. } We use CI both positive and negative extensively for air sensitive compounds. } Valco manufacture a flow controller Model 202 which has a flow rate down to } 0.5mL/min. We are not sure whether this will do the job on a high vacuum } system and it is expensive at around $825.00 for the stainless steel version. } } I would appreciate any ideas. } } Many thanks } } John Hill } Mass Spectrometry Facility } Chemistry Dept. } University College London Hello John, we have still some Negretti diaphrama ci valves, one is factory refurbished, others are not used at all, because they were fitted to dioxin mass spectrometers. On some mass spec´s like TRIO, MD800 and others the more simple M-Valve were used, made by Negretti. They are as well out of production but we can repair them. Regards Volker Grau Service für Massenspektrometrie GmbH Idstein ****************************************************************************** From: Scott Rando Date: Wed, 21 Apr 2004 22:06:13 -0400 Subject: Re: What type of filter to use Organization: * Bandwidth to select is dependant on mass resolution and scan speed (s/d) Examples: 1 s/d at 2000 resolution=3 kHz 3 s/d at 2000 resolution=1 kHz ...and for 3 s/d at 5000 resolution it would be 3 kHz, These are rough estimates..but higher the scan speed or resolution, then the higher the bandwidth. Good Luck! Scott "Mudbunny" wrote in message news:c6681n$e0b$1@news-int2.gatech.edu... } I have another question for the collective wisdom out there. } } The Concept HRMS that I am working on allows you to choose your noise } filter frequency. It has a fairly wide range, from 30 kHz, down to 1 } Hz. What is the ideal frequency to use in order to eliminate most of } the noise in my spectrum, yet also leave as much of the signal } present? Is the best bet to use the automatic value that it picks } (which is usually 30 Hz)? or choose my own value? I know that as you } loer the frequency, you also lose signal intensity, how does this } affect your sample?? } } Marcel } ****************************************************************************** From: Elijah Bailey Date: 22 Apr 2004 07:20:37 -0700 Subject: Re: baseline correction : NewBie Organization: * Thanks David. But what I dont understand is why MALDI-TOF or other Mass-Spec machines make an error that needs baseline correction? What is the physical device/reason that this phenomenon occurs in the result? Thanks, --Elijah David Stranz wrote in message news:... } Elijah Bailey wrote in news:c60gvu$5sl$1@news- } int.gatech.edu: } } } } } Does anyone know why baseline correction is needed for MALDI-TOF } } spectra? } } } } Thanks in advance for ur comments and help, } } --Elijah } } } } } } One reason: } } When centroiding, failure to correct for non-zero baseline will lead } to systematic error in computing intensities of centroided peaks } (either area or height intensities). This is true when centroiding } any profile MS spectrum, not just MALDI-TOF. ****************************************************************************** From: Mudbunny Date: 22 Apr 2004 10:01:38 -0700 Subject: Re: Question on Reference books Organization: * Chip Cody wrote in message news:... } Mudbunny wrote in message news:... } } I am trying to start a small reference library at my work on MS and } } high res MS. What reference books would the collective knowledge in } } here suggest?? } } } } Please reply to newsgroup as the e-mail addy is a spam-trap. } } } } Marcel } } David Sparkman's "Mass Spec Desk Reference" ($28.45, Global View } Publishing: 2000, http://www.lcms.com) contains a thorough list of } mass spec reference books, with comments on the major publications. } (David has a copy in his library of every mass spec book ever } published.) A few new reference books have been published since 2000 } (I contributed to one of them...) but David's book lists the reference } texts that should form the core of a mass spec library. Thanks, I have decided to order that one, Intro to Mass Spectrometry (JT Watson) and Mass Spectrometry:Principles and Applications (de Hoffmann and Stroobant). Marcel ****************************************************************************** From: Michael_P_Balogh@waters.com Date: Thu, 22 Apr 2004 14:21:31 -0400 Subject: Conference on Small Molecule Science open for registration Organization: * The Conference on Small Molecule Science (CoSMoS, www.cosmos2004.org) being held August 8-14, 2004 is a not-for-profit venue created for small molecule science topics and related interests. As a research style conference, every effort is made to keep the quality of the proceedings and the "take home" message foremost. The program committee has been selected from some of the recognized leading practitioners in industry including: Dr. Luke Miller (GlaxoSmithKline, Research Triangle Park, NC) Dr. Kathleen Cox (Schering Plough, Kenilworth, NJ) Dr. Jeffery Gilbert (Dow AgroScience, Indianapolis, IN) Dr. Guy Carter (Wyeth Research, Pearl River, NY) Dr. Uwe Neue (Waters Corporation, MA) Dr. Cornelis Hop (Pfizer Research, Groton, CT). Attendance is limited to ensure a high degree of interaction and focus. The campus of Roger Williams University, Bristol, Rhode Island (www.rwu.edu) was chosen since it offers up-to-date lecture facilities as well as social gathering opportunities. The summer on the ocean setting also offers the Newport Jazz Festival 20 minutes away in Newport along with its famous mansions, dining and other resort enjoyment in the Narragansett bay area. Attendees are encouraged at the very reasonable conference housing cost to consider bringing their families. Provisions are made to extend their stay at either of the two housing sites (one an air conditioned suite arrangement dorm on campus, the other a hotel just across the bridge from campus) for the days immediately before and after the conference. CoSMoS2004 opens on Monday evening August 9 following pre-conference events with two-and-a-half days featuring two sessions each morning followed by a free afternoon and evening on Tuesday and workshops and a conference dinner event on Wednesday. Abstracts and registrations (until the maximum attendee limit is reached) can be submitted on line. =========================================================== The information in this email is confidential, and is intended solely for the addressee(s). Access to this email by anyone else is unauthorized and therefore prohibited. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful. =========================================================== ****************************************************************************** From: Mudbunny Date: 22 Apr 2004 12:37:41 -0700 Subject: Re: baseline correction : NewBie Organization: * Elijah Bailey wrote in message news:... } Thanks David. But what I dont understand is why MALDI-TOF } or other Mass-Spec machines make an error that needs baseline } correction? What is the physical device/reason that this } phenomenon occurs in the result? Pretty much anything that causes your baseline to drift over the course of a run will result in needing baseline correction. If you are running it through a GC first, you may have crud coming off of your column that affects your baseline. It may drift up or may drift down over the course of the run. For example, if it is a new column, and you didn't condition it enough, your TIC trace will be sloping down. Depending on how your data analysis program determines peak start and stop, you may end up with a significant variation between what it reports and what it actually is. Remember, you want the base of the "triangle" that defines the peak to follow the baseline. Another possibility is that you may have electronic noise that is affecting the collector. In my old lab, we ended up with a GC-MS and a glove-box on the same circuit. Whenever the pump would kick in, there would be a noticeable wobble in the MS trace due to the surge of juice that it pulls in. It was enough to get through the filter and affect the TIC. We ended up having to get the university electricians in to rewire the lab. Marcel ****************************************************************************** From: Mudbunny Date: 22 Apr 2004 12:45:39 -0700 Subject: Re: Low Sensitivity- maybe the filament? Organization: * I couldn't get to the original post, so I am piggybacking on this one. } } Peter Harrington wrote: } } Tuning did not seem to help. Would a dirty source cause this type of } } problem, as well? We had just cleaned the source, but when we were } } trouble-shooting the instrument, I am worried the source may have become a } } bit fingered up. When I was learning how to clean the source on my high-res machine, I was told that although the convention is to wear gloves when handling source parts, it is not really necessary. As long as you get your grad students to wash off the Doritos crumbs/McDonalds sweet and sour dipping sauce/hot wing sauce off their hands, it isn't much of a problem. After it has been at temperature for half an hour or so, all of the skin oils are pretty much gone. } } Another symptom is that the instrument scans, but if we shut the source off } } and on. The instrument (HP 5988) continues to turn itself off, once the } } target current rises. However, if the instrument is left off for a period } } of 10 minutes or longer, this problem does not arise. I don't understand this question. Marcel ****************************************************************************** From: Mudbunny Date: 22 Apr 2004 13:26:26 -0700 Subject: Re: Base Line Correction Organization: * Elijah Bailey wrote in message news:... } What are the ways known to do base line correction? There are two ways (that I know of) to do baseline correction. Manual and automatic. Manually is very simple. With your mouse, you use the cursor to pick a number of points (>2) that you set as the baseline. It will then drop the trace, following the points you specified, down to the bottom of your trace window, parallel with the bottom of the window. Note, you have to be careful doing this that you don't a) artificially emphasize peaks or b) make them disappear. Automatically is a bit easier but also a bit more complex. In this case, the computer does it for you. However, it is important to make sure that you know how it determines the baseline. the ones that I have seen use a mathematical formula that fits the closest to what *it* determines is the baseline. Sometimes you have control over what order polynomial it applies, sometimes you don't. Again, you want to make sure that the computer is not artificially emphasizing or shrinking peaks. Baseline correction shouldn't actually change the size of the peaks. What it will do is make your trace prettier and make determining the size of the peaks less difficult. } Why does it occur in Mass-Spectra? See my answer in the other message you posted. Marcel Note, I am by no means an expert. I *think* I know what I am talking about, but it is always a good idea to confirm what I have written with your local MS guru. ****************************************************************************** From: Claude Chenier Date: Thu, 22 Apr 2004 16:02:36 -0600 Subject: LC-ESI-MS (QTOF) impurities in acetontrile/water/TFA mobile phase Organization: * We are using an acetonitrile/water(with 0.1% Trifluoroacidic acid) mobile phase for LC-ESI-MS. We have a background that appears to contain two significant compounds with elemental formulae of C12H20O4 (MW 228.136) and C10H16O4 (MW 200.105). MH+ ions were observed. Does anyone have any knowledge of these apparent impurities? Claude Chenier DRDC Suffield Claude.Chenier@drdc-rddc.gc.ca ****************************************************************************** From: usedlabequip Date: 23 Apr 2004 11:02:19 -0700 Subject: Refurbished Analytical Equipment Available Organization: * !!!!FOR SALE!!!! 1. Applied BioSystems Prism 7900HT Real Time PCR 2. PerSeptive-ABI Mariner (ESI-TOF) Biospectrometry Workstation 3.) Cohesive Technologies model turboflow 2300 HTLC/HPLC system complete with HP 1100 # G1322A Degasser, # G1311A Quat. Pump, & # G1312 Binary Pump 4.) Perspective BioSystems VOYAGER-DE STR MALDI-TOF. 5.) Hewlett Packard 1100 isocratic pumps 6.) Micromass Q-TOF II 7.) Thermo Finnigan TSQ 7000 with API II LC/MS/MS 8.) Thermo Finnigan LCQ Classic LC/MS/MS 9.) Micromass ZMD 2000 LC/MS 10.) Micromass Quattro Ultima LC/MS/MS 11.) Varian Unity Inova 300 MHz NMR 12.) Varian Mercury MVX 300 MHz NMR 13.) Bruker AC300 MHz Plus NMR 14.) Varian Unity Plus 400 MHz NMR 15.) Varian Unity 500 MHz NMR 16.) Bruker Avance 500 MHz LC/NMR 17.) Varian Inova 600 MHz LC/NMR 18.) Bruker Avance 700 MHz NMR 19.) Genomics Solutions GeneTAC Hybstation 20.) Beckman Coulter LS200 21.) Neslab Chiller 22.) Bruker MicroCryoProbe 500 with chiller *Please call for further details. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 ****************************************************************************** From: David Sparkman Date: Fri, 23 Apr 2004 11:04:51 -0700 Subject: Re: Question on Reference books Organization: * Marcel, There is a new book just out. "Mass Spectrometry: A Textbook" by Jurgen H. Gross, Springer-Verlag, ISBN: 3-540-40739-1. I have just started to review this book, but I like it enough that I am adopting it for my course this fall. I will post the reference to the review that I do for this book. Regards; David "Mudbunny" wrote in message news:c5mtar$ibj$1@news-int2.gatech.edu... } I am trying to start a small reference library at my work on MS and } high res MS. What reference books would the collective knowledge in } here suggest?? } } Please reply to newsgroup as the e-mail addy is a spam-trap. } } Marcel } ****************************************************************************** From: Mudbunny Date: 23 Apr 2004 12:02:00 -0700 Subject: Re: What type of filter to use Organization: * Joerg Hau wrote in message news:... } Hi Mudbunny, euh, Marcel, } } } The Concept HRMS that I am working on allows you to choose your } } noise filter frequency. It has a fairly wide range, from 30 kHz, } } down to 1 Hz. What is the ideal frequency to use in order to } } eliminate most of the noise in my spectrum, yet also leave as much } } of the signal present? } } It depends ;-) } } If you use the MS in SIM mode (i.e. you are essentially recording mass } chromatograms), you will want to adapt the filter to the "sampling } speed" that you use - usually in the some-Hz region. I figured as much. SO I am in the process of going through all of the settings, running 4 or 5 injections and moving on to the next. So far I have gone from 30 kHz and am now at 100 Hz. No improvement as of yet in the noise filtering. I guess that this is Murphy's laws in action. Seeing as how I started at the high end, the right setting is at the low end. I am sure that if I had started at the low end, we would be in a universe where everything is reversed. } If you use the MS in "real" scanning mode, 30 Hz would be way too low. } In that case, the filter width will depend on the combination of } resolution and scan rate that you use (i.e. the sampling rate). I can } dig out the formula if needed, but under "usual" conditions the } filter will be in the several-10-kHz-range. Nahh, don't bother. I think I have managed to convince my bosses that scanning over any extended range on this thing is counter-productive and loses a lot of sensitivity. } } Is the best bet to use the automatic value that it picks (which } } is usually 30 Hz)? } } Is that a data system option, or a hardware button? (I've never worked } with the Kratos Concept, but the CH5, CH7, VG7070 and MAT8430 all had } hardware filters ;-) It is a data-system option. Or at least the way to choose it is through the software that controls the collector. (In the same window, you also choose whether to use an internal or external standard, what type of data to record (nominal, raw, exact, or time) and a couple of others that I don't recall at the moment. 30 kHz, 10 kHz, 3 kHz, 1 kHz, 300 Hz, 100 Hz, 30 Hz, 10 Hz, 3 Hz, and 1 Hz are the available settings. } } I know that as you loer the frequency, you also lose signal } } intensity, how does this affect your sample?? } } Essentially these filters are low-pass filters, i.e. they filter out } the higher-frequency components (noise, spikes). The lower the filter } cutoff frequency, the broader the signal gets. You don't want } that ... better record at a higher sampling rate and use software } processing to smooth afterwards, if needed. OK, that makes sense. Now I just have to figure out if there is any software available that will do external data process for this and, if so, how to extract the data. Thanks Marcel ****************************************************************************** From: Joerg Hau Date: Sun, 25 Apr 2004 09:19:59 +0200 Subject: Re: What type of filter to use Organization: * Hi Marcel, { noise filter frequency } } } If you use the MS in SIM mode (i.e. you are essentially recording } mass } chromatograms), you will want to adapt the filter to the } "sampling } speed" that you use - usually in the some-Hz region. } } I figured as much. SO I am in the process of going through all of } the settings, running 4 or 5 injections and moving on to the next. } So far I have gone from 30 kHz and am now at 100 Hz. No improvement } as of yet in the noise filtering. From memory, 100 Hz filter would mean that you acquire SIM data with your sector field MS at a rate of roughly 10...30 Hz (!). I guess that a value about 1 order of magnitude lower might be more appropriate ;-) } that scanning over any extended range on this thing is } counter-productive and loses a lot of sensitivity. Again, it depends on what you want to do. Trace quantitation will require SIM, while "simple" will identification probably require scanning ... yet both at a repetition rate that is compatible with your chromatographic system. As soon as you are scanning, most type of MS (not only your dinosaur, but also any quadrupole etc.) will have the problem that sensitivity and scan range go into opposite directions. With the exception of MS that work with a "bulk" of ions, such as ToF. But then again, these tend to suffer from an insufficient dynamic range for "true" quan work ... BTW, the MAT8430 handbook contains some nice explanation of the formulae for filter calculation. For those interested, here is a short summary: During a scan, the frequency "band" that you need depend on the scan mode, speed, and resolution. In an *exponential* scan (used only with real mass spectrometers ;-), scan speed is given in "seconds per decade", e.g. the time needed to scan from m/z 50 to m/z 500. The time spent for scanning the width of a peak is then t_per_peak = T_per_decade / (2.3 * Resolution) ... the factor 2.3 is the usual conversion factor from "ln" to "log10", and "ln" is there because it's exponential ;-) As an example, with 1 s/dec and R=2000, time per peak is 0.2 ms. Note that time-per-peak time is independant from mass. "Experience shows" that peak distortion is below 10% if the time constant of the data system (in this case: the filter) is less than approx. 10% of the time-per-peak. The relationship between time constant and frequency is freq = 1 / (2 * pi * t) ... so that (with the 0.2 ms-peak-width-example above), the preferred time constant is 0.02 ms or shorter, equivalent to a filter setting of ca. 8 kHz or higher. Cheers & HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: JC Date: 25 Apr 2004 20:26:42 -0700 Subject: Re: Question on Reference books Organization: * David Sparkman wrote in message news:... } Marcel, } } There is a new book just out. "Mass Spectrometry: A Textbook" by Jurgen H. } Gross, Springer-Verlag, ISBN: 3-540-40739-1. I have just started to review } this book, but I like it enough that I am adopting it for my course this } fall. I will post the reference to the review that I do for this book. } } Regards; } David } } } "Mudbunny" wrote in message } news:c5mtar$ibj$1@news-int2.gatech.edu... } } I am trying to start a small reference library at my work on MS and } } high res MS. What reference books would the collective knowledge in } } here suggest?? } } } } Please reply to newsgroup as the e-mail addy is a spam-trap. } } } } Marcel } } "Partical aspects of Gas Chromatography / Mass spectrometry" by Gordon M Message is also a good reference to start with. Regards, Jacky ****************************************************************************** From: Mudbunny Date: 26 Apr 2004 06:57:31 -0700 Subject: Re: What type of filter to use Organization: * Joerg Hau wrote in message news:... } Hi Marcel, } } { noise filter frequency } } } } } If you use the MS in SIM mode (i.e. you are essentially recording } } mass } chromatograms), you will want to adapt the filter to the } } "sampling } speed" that you use - usually in the some-Hz region. } } } } I figured as much. SO I am in the process of going through all of } } the settings, running 4 or 5 injections and moving on to the next. } } So far I have gone from 30 kHz and am now at 100 Hz. No improvement } } as of yet in the noise filtering. } } From memory, 100 Hz filter would mean that you acquire SIM data with } your sector field MS at a rate of roughly 10...30 Hz (!). I guess } that a value about 1 order of magnitude lower might be more } appropriate ;-) Well, I tried a 30 Hz Filter this morning, and didn't even try an injection. The resulting trace on the scope was crap and incredibly wide. So I gave up and am using a filter of 100 Hz. I am not sure what you mena by your comment about acquiring SIM data at a rate of 10-30 Hz?? Are you talking about the cycle time for SIM acquisition?? If so, I have it at 1 second. If it should be 1 order of magnitude lower, then should it be at about 0.1 seconds?? } } that scanning over any extended range on this thing is } } counter-productive and loses a lot of sensitivity. } } Again, it depends on what you want to do. Trace quantitation will } require SIM, while "simple" will identification probably require } scanning ... yet both at a repetition rate that is compatible with } your chromatographic system. We will only be doing trace quantition on this instrument. Thanks Marcel ****************************************************************************** From: "Neal E Craft, PhD" Date: Tue, 27 Apr 2004 12:41:47 -0400 Subject: LC-MS Organization: * Dear Users Group, We are in the process of looking for a good used LC-MS. We would like a workhorse that is easy to maintain and parts are readily available. While we would tend to use it mainly for monitoring a single ion, a triple quad would allow us to follow metabolites in biological samples. The compounds that we are interested in are nutritional and include carotenoids, bioflavonoids, and antioxidants. Since these are in plasma and urine, the concentrations tend to be low so sensitivity is a key issue. Due to the cost, we will probably be looking at a previous generation/used MS. Please provide feedback on the positives and negatives of the instruments and software available. It is impossible to get unbiased oppions from the manufacturers. Are there any real "lemons" out there to avoid? How substantial was the improvement in sensitivity from the API2 source to the Z-spray (or other equivalents)? Any help would be appreciated. Thanks, Neal Neal E. Craft, PhD President Craft Technologies, Inc. 4344 Frank Price Church Rd. Wilson, NC 27893 Phone: 252-206-7071 Fax: 252-206-1305 www.crafttechnologies.com ****************************************************************************** From: "Engel, Marc" Subject: ICP MS Date: Wed, 28 Apr 2004 08:37:03 -0400 Organization: * Does anyone know of a good reference book for ICP MS? I am especially interested in one that would pesticide analysis and other environmental applications. Thanks Marc Marc Engel Food Laboratory, Food Safety, FDACS 3125 Connor Blvd # 9 Tallahassee Fl 32304 850 414 0409 If I do not respond to your email please contact me by phone. Our firewall may have prevented your email from coming through ****************************************************************************** From: dawe Date: 28 Apr 2004 06:59:57 -0700 Subject: wiff files Organization: * Hello everybody, we are trying to develop some algorithms to analyze mass-spec data saved in wiff format. The only way we can do it is exporting them to a Jcamp format (text files) but this means working with files up to 500 Mb big! A lot of time is spent in exporting and analyzing. Does anybody know if there is a way to work with analyst binary wiff files? Thanks dawe ****************************************************************************** From: David Stranz Date: Wed, 28 Apr 2004 11:55:09 -0500 Subject: Re: wiff files Organization: * dawe wrote in news:c6oict$qkd$1@news-int.gatech.edu: } Hello everybody, } we are trying to develop some algorithms to analyze mass-spec } data saved in wiff format. The only way we can do it is } exporting them to a Jcamp format (text files) but this means } working with files up to 500 Mb big! A lot of time is spent in } exporting and analyzing. Does anybody know if there is a way to } work with analyst binary wiff files? } } Thanks } dawe } } You should contact your MDS Sciex / Applied Biosystems support person and ask for a copy of the Analyst Cookbook. It is a programmer's manual that describes how to access the Analyst system (including wiff files) through the Analyst ActiveX/COM interface. Be advised that writing code to do this is not easy. David ****************************************************************************** From: Justin Withers Date: Wed, 28 Apr 2004 12:08:53 -0500 Subject: Re: wiff files Organization: * Dave, if you would like we, the vendor, can help, Post a question at faqs.appliedbiosystems.com and we'll get it to the right people, Justin Withers AB dawe wrote: } Hello everybody, } we are trying to develop some algorithms to analyze mass-spec data } saved in wiff format. The only way we can do it is exporting them to a } Jcamp format (text files) but this means working with files up to 500 } Mb big! A lot of time is spent in exporting and analyzing. } Does anybody know if there is a way to work with analyst binary wiff } files? } } Thanks } dawe } ****************************************************************************** From: Joerg Hau Date: Thu, 29 Apr 2004 22:12:27 +0200 Subject: Re: What type of filter to use Organization: * Hi Mudbunny { This is a re-post - it seems that my previous msg got lost } } { noise filter frequency } }} }} I figured as much. SO I am in the process of going through all }} of the settings, running 4 or 5 injections and moving on to the }} next. So far I have gone from 30 kHz and am now at 100 Hz. No }} improvement as of yet in the noise filtering. }} }} From memory, 100 Hz filter would mean that you acquire SIM data }} with your sector field MS at a rate of roughly 10...30 Hz (!). I }} guess that a value about 1 order of magnitude lower might be more }} appropriate ;-) } } Well, I tried a 30 Hz Filter this morning, and didn't even try an } injection. The resulting trace on the scope was crap and incredibly } wide. That's natural: The scope view is taken during a fast voltage scan; in this mode, using a "slow" filter will considerably distort the peak shape ... however, if you are running SIM acquisition you want a slow filter. } So I gave up and am using a filter of 100 Hz. Dommage ... you've tried 30 kHz down to 100 Hz, and stopped the series just before it got interesting ;-) } I am not sure what you mena by your comment about acquiring SIM } data at a rate of 10-30 Hz?? Are you talking about the cycle time } for SIM acquisition?? Yes. } If so, I have it at 1 second. If it should be 1 order of magnitude } lower, then should it be at about 0.1 seconds?? 1 s cycle time is fine. In this case, the filter should have a time constant of less than 0.1 s. I'd try with 10 and 30 Hz and see which trace looks more realistic ;-) Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: Davide Cittaro Date: Fri, 30 Apr 2004 21:35:03 GMT Subject: Re: wiff files Organization: * } You should contact your MDS Sciex / Applied Biosystems support person } and ask for a copy of the Analyst Cookbook. It is a programmer's } manual that describes how to access the Analyst system (including } wiff files) through the Analyst ActiveX/COM interface. Be advised } that writing code to do this is not easy. } Thanks, we've contacted the support for that ****************************************************************************** From: K. Murray Date: 2 May 2004 19:29:17 -0700 Subject: Call for Speakers: MS Terms and Definitions Workshop Organization: * There will be a workshop on "Mass Spectrometry Terms and Definitions" at this year's ASMS meeting in Nashville. The workshop will be held on Tuesday, May 25 from 5:30 to 7:00 pm. If you are interested in giving a 10 to 15 minute presentation at the workshop, please send a title and brief description to kmurray@ch335c.chem.lsu.edu. One of the main goals of the workshop is to bring together the ASMS Measurements and Standards Committee and the IUPAC Task Group on "Standard Definitions of Terms Relating to Mass Spectrometry," which was established earlier this year. For more information on the IUPAC project, see http://www.msterms.com/ and http://www.iupac.org/projects/2003/2003-056-2-500.html. See you in Nashville! Kermit Murray http://ch335c.chem.lsu.edu/ ****************************************************************************** From: Richard Date: 3 May 2004 05:21:49 -0700 Subject: Dynasoap for ion source cleaning Organization: * Has anyone ever used Dynasoap to clean their ion source? A service engineer says that's all he uses and gets wonderful results. He gave me a couple of ounces of his stash. Dynasoap, a phosphoric acid based ultrasonic cleaner, apparently is no longer available. I can't find much of anything about it on the internet. The listed manufacturer no longer mentions it on their website. It has me curious. The engineer appears to be very competent and knowledgable. This does sound too good to be true. Strangly enough the magic potion has disappeared. Richard ****************************************************************************** From: Jimmy Date: 6 May 2004 09:45:25 -0700 Subject: Sciex Analyst 1.4 software Organization: * We use Analyst 1.3 and consider to upgrade to Analyst 1.4. Does anyone out there have any good or bad experiences with the Analyst 1.4 software for SCIEX MS instruments? Thanks in advance! Jimmy ****************************************************************************** From: Davide Cittaro Date: Thu, 06 May 2004 20:26:35 GMT Subject: Re: Sciex Analyst 1.4 software Organization: * Mmm, that's not probably what you want to hear about... We use Analyst QS and I've found a lot of bugs, maybe dued to the .NET environment. dawe ****************************************************************************** From: Jimmy Date: 7 May 2004 10:42:13 -0700 Subject: Arcing Organization: * Could someone please explain me What is arcing? How do we know from mass spectra that there is arcing? What causes arcing in ESI or APCI? How to minimize or reduce arcing (namely factors affecting arcing, like spray voltage or discharge current, MP conductivity and flow rate, solvent type e.g. hexane or water)? Thanks! Jimmy ****************************************************************************** From: Jim Madsen Date: Sun, 09 May 2004 17:15:21 -0600 Subject: Re: Dynasoap for ion source cleaning Organization: * One of our service engineers recommends "Barkeeper's Friend". (Never tried it). Jim Richard wrote: } Has anyone ever used Dynasoap to clean their ion source? A service } engineer says that's all he uses and gets wonderful results. } } He gave me a couple of ounces of his stash. Dynasoap, a phosphoric } acid based ultrasonic cleaner, apparently is no longer available. I } can't find much of anything about it on the internet. The listed } manufacturer no longer mentions it on their website. } } It has me curious. The engineer appears to be very competent and } knowledgable. This does sound too good to be true. Strangly enough the } magic potion has disappeared. } } Richard } ****************************************************************************** From: bizzwire Date: Mon, 10 May 2004 02:36:37 GMT Subject: Re: Dynasoap for ion source cleaning Organization: * } Richard wrote: } } } Has anyone ever used Dynasoap to clean their ion source? A service } engineer says that's all he uses and gets wonderful results. } snip } } It has me curious. The engineer appears to be very competent and } knowledgable. This does sound too good to be true. Strangly enough the } magic potion has disappeared. } } Richard } Quick question: are we talking about an EI source or an ESI source? Electrospray sources, to me, are like cast-iron frying pans. They're pretty when they're new and shiny, but for best results, you want one that's well "seasoned." I've found that, especially for quantitation, while a sparkling clean source will give you the highest signal, as it "burns in" the response will drop , usually fairly quickly, and then tend to stabilize. I never clean my source unless there is significant signal loss or instability. If it aint fixed..... ****************************************************************************** From: Mike Sherrell Date: Mon, 10 May 2004 12:04:29 -0700 Subject: Mass specs, MALDIs available Organization: * Grizzly Analytical mass specs, MALDIs, etc. for sale **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $125,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex API 2000 TurboIon Spray: $5,500. Interface and orifice plate. Sept. 2002. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $50,000. ES, API 2, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass Quattro Micro: $135,000. Call/email for details. License not incl. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $110,000. API-LC/Orth. 2000 model. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: Richard Date: 10 May 2004 14:20:26 -0700 Subject: Re: Dynasoap for ion source cleaning Organization: * bizzwire wrote in message news:... } } Richard } } } Quick question: are we talking about an EI source or an ESI source? } Electrospray sources, to me, are like cast-iron frying pans. They're pretty } when they're new and shiny, but for best results, you want one that's well } "seasoned." I've found that, especially for quantitation, while a sparkling } clean source will give you the highest signal, as it "burns in" the } response will drop , usually fairly quickly, and then tend to stabilize. } I never clean my source unless there is significant signal loss or } instability. If it aint fixed..... Gee, I didn't think anybody was going to respond which sort of surprised me. The source in question is an EI source from an Agilent 5973. Yes, my test compounds (DFTPP, endrin and p,p'-DDT were breaking down. Cleaning the source did improve the breakdown. This engineer works on our LC/MS. He says he never uses anything but Dynasoap. Strangly enough nearly all references to it have disappeared from the internet though I found a number of hits last year. The last manufacturer, Misonix, no longer has a reference I can find on their website. I found that a paste of the white abrasive powder (sorry, my mind just went blank) with about 5% dynasoap solution cleaned the black burned areas faster than anything I have used previously. I was wondering why nobody uses it if this stuff is supposed to be so good. I imagine people who read this digest have tried just about everything there is to clean their sources. Richard ****************************************************************************** From: Philip Date: 11 May 2004 08:16:48 -0700 Subject: Drifting Area under Curve Organization: * I am using a Finnigan Trace in split mode with EPC and if I inject the same sample 10 times the Area under the curve for the relevent M/z drifts down from 31385777 29899287 28819125 27314319 25890797 24608734 23235077 21860872 20443938 19073173 Any ideas what could be causing this? Thanks Philip ****************************************************************************** From: Tobias Kind Date: 11 May 2004 10:24:34 -0700 Subject: Re: LC-ESI-MS (QTOF) impurities in acetontrile/water/TFA mobile Organization: * Claude Chenier wrote in message news:... } We are using an acetonitrile/water(with 0.1% Trifluoroacidic acid) mobile } phase for LC-ESI-MS. We have a background that appears to contain two } significant compounds with elemental formulae of C12H20O4 (MW 228.136) and } C10H16O4 (MW 200.105). } } MH+ ions were observed. Does anyone have any knowledge of these apparent } impurities? } Dear Claude, go the typical way, change the pH stepwise, try with MeOH if possible, ions still there? Go4 ultrapure water (that one you would never drink, because its too expensive :), avoid TFA if possible, use a low activity RP column (if you are using RP). Avoid using plasticware, only use glass and bake out all your glassware and deactivate it. Check the purity of your solvents with GC. Most impurities come from the solvents. So even if your MW prediction is right (no pseudo molecular ion, no adduct formation etc.) there is still not enough information about your experiment. Screen the usual suspects, I had ~200 compounds for C12H20O4 and ~300 compounds for C10H16O4 in my MS database, not that much. Better than 212.351.054 calculated molecules for C10H16O4 or some 4.479.136.654 molecules for C12H20O4. Good time for a structure elucidation :-) With kind regards Tobias Kind www.amdis.net ****************************************************************************** From: Joel Bondurant Date: 11 May 2004 15:42:54 -0700 Subject: Derivative Spectra Peak Fitting with PeakFit Organization: * Using PeakFit software (www.seasolve.com / www.systat.com), you can easily fit derivative spectra without programming. Since PeakFit is a general nonlinear fitting engine, you can load your data and fit it with a user defined function that is the derivative of the underlying peak lineshape. PeakFit will compute the derivative of the peak in the user defined menu. I would suggest not going this route initially in your analysis since PeakFit is best at looking for peaks, not derivatives of peaks. I suggest entering the calculation Y=Y-YMEAN under the data menu, and then looking at the cumulative area under the data menu. This will get you back one derivative and then you can fit your peaks normally. Repeat the process to get back one more derivative. Once you have the peaks fitted, you can check by taking the derivative of the fitted functions (mathematica/maple/tables) and fitting your original data. Anyone who is more experienced and knowledgeable please chime in. ****************************************************************************** From: Joel Bondurant Date: 11 May 2004 15:21:22 -0700 Subject: Peak Fitting / Deconvolution Organization: * PeakFit 4.12 helps you separate overlapping peaks by statistically fitting numerous peak functions to one data set, which can help you find even the most obscure patterns in your data. The background can be fit as a separate polynomial, exponential, logarithmic, hyperbolic or power model. This fitted baseline is then subtracted before peak characterization data (such as areas) is calculated, which gives much more accurate results. And any noise (like you get with electrophoretic gels or Raman spectra) that might bias raw data calculations is filtered simply by the nonlinear curve fitting process. Nonlinear curve fitting is essential for accurate peak analysis and accurate research. http://www.seasolve.com/products/peakfit/index.html Systat Software, Inc. has recently re-acquired PeakFit software! Joel Bondurant Scientific & Engineering Account Manager SYSTAT Software, Inc 501 Canal Blvd, Suite C Richmond, CA. 94804 ph. 510-231-0968 fx. 510-231-4789 www.systat.com ****************************************************************************** From: David Sparkman Date: Wed, 12 May 2004 08:34:36 -0700 Subject: Re: Drifting Area under Curve Organization: * Philip, Are you using autosampler? Whether you are doing an autosampler injection or a manual injection, are you using a sandwich technique and are you doing fast or slow injections? When was the last time you change your septum? After an hour of rest, does the first injection in a second series give the original first or last value from the previous series? What is your scan range and speed? What is happening with relative peak areas to an internal standard? I have more questions than answers, but by looking at these questions, you should be on your way to an answer. If you still have problems, post the answers and I'll try to be more helpful. Regards; David "Philip" wrote in message news:c7qtth$kkv$1@news-int.gatech.edu... } I am using a Finnigan Trace in split mode with EPC and if I inject the } same sample 10 times the Area under the curve for the relevent M/z } drifts down from } } 31385777 } 29899287 } 28819125 } 27314319 } 25890797 } 24608734 } 23235077 } 21860872 } 20443938 } 19073173 } } Any ideas what could be causing this? } } Thanks } } Philip } ****************************************************************************** From: grober Date: Wed, 12 May 2004 19:40:40 +0100 Subject: Re: Dynasoap for ion source cleaning Organization: * My HP engineer used to use German "AUTOSOL" METAL POLISH www.autosol.de which you can buy in Halfords. Great for getting into those nooks and crannies in an MS ENGINE SOURCE with a cotton bud. You had to ultrasonic in Dichloromethane afterwards to remove any silicones followed by acetone/ di-ethyl ether. Seems to work well with no residue effects. "Richard" wrote in message news:c75edg$8mq$1@news-int.gatech.edu... } } Has anyone ever used Dynasoap to clean their ion source? A service } engineer says that's all he uses and gets wonderful results. } } He gave me a couple of ounces of his stash. Dynasoap, a phosphoric } acid based ultrasonic cleaner, apparently is no longer available. I } can't find much of anything about it on the internet. The listed } manufacturer no longer mentions it on their website. } } It has me curious. The engineer appears to be very competent and } knowledgable. This does sound too good to be true. Strangly enough the } magic potion has disappeared. } } Richard } ****************************************************************************** From: Rich Yelton Date: Thu, 13 May 2004 21:23:00 GMT Subject: Re: Dynasoap for ion source cleaning Organization: * Hello Richard, Occasionally i will use a paste made of the common laboratory glass cleaner which goes by the name of "Alconox" . It is readily available and should give similar results to the Dynasoap. Meticulous rinsing in hot water is required as to not leave a residue which can become charged and defect ions.If you want to use something that is fast and leaves no harmfull residues, try Agilent "green" abrasive paper >= 400 grit alum/ox > . Another good trick to clean ion burn and discoloration is to use a "bundled fiberglass pencil. These used to be available from Finnigan but I have also seen them in art supply stores. Best of Luck ! -- Richard O. Yelton Spectratek Mass Spectrometry Services www.massspecrepair.com ryelton@massspecrepair.com 859-341-6599 "Richard" wrote in message news:c75edg$8mq$1@news-int.gatech.edu... } } Has anyone ever used Dynasoap to clean their ion source? A service } engineer says that's all he uses and gets wonderful results. } } He gave me a couple of ounces of his stash. Dynasoap, a phosphoric } acid based ultrasonic cleaner, apparently is no longer available. I } can't find much of anything about it on the internet. The listed } manufacturer no longer mentions it on their website. } } It has me curious. The engineer appears to be very competent and } knowledgable. This does sound too good to be true. Strangly enough the } magic potion has disappeared. } } Richard } ****************************************************************************** From: "Haig, Terrence" Date: Fri, 14 May 2004 13:51:41 +1000 Subject: Cleaning TFA contamination from LC/MS Organization: * Request for help from experienced LC/MS users: from: Terry Haig Analytical Labs Charles Sturt University Australia Having had some cause previously to try a few percent trifluoroacetic acid (TFA) in one of our trial mobile phases for some LC/MS quadrupole work on a C-18 column using our Navigator aQa system, we now find lingering contamination from this compound (especially at m/z 113) spoiling our sensitivity as it once was before TFA use. We would be grateful for any experienced suggestions as to effective ways of removing this contamination from our system, as we have only had limited success with all cleaning methods so far. Regards and thanks for suggestions. Terry Haig. ======================= School of Science & Technology Charles Sturt University, NSW, Australia EMAIL> thaig@csu.edu.au Phone: +61 (0)2-69332502 FAX: +61 (0)2-69332737 ****************************************************************************** From: Mudbunny Date: 14 May 2004 07:34:07 -0700 Subject: Re: Dynasoap for ion source cleaning Organization: * Richard wrote in message news:... } Has anyone ever used Dynasoap to clean their ion source? A service } engineer says that's all he uses and gets wonderful results. } } He gave me a couple of ounces of his stash. Dynasoap, a phosphoric } acid based ultrasonic cleaner, apparently is no longer available. I } can't find much of anything about it on the internet. The listed } manufacturer no longer mentions it on their website. } } It has me curious. The engineer appears to be very competent and } knowledgable. This does sound too good to be true. Strangly enough the } magic potion has disappeared. What was suggested to me for my high res mass specs was to buy a miniature sandblaster, along with some aluminum oxide blasting powder. Note this is not recommended for aanything with a coating or anything like that. Marcel ****************************************************************************** From: dawe Date: 14 May 2004 07:42:47 -0700 Subject: molecular diagnosis position Organization: * One in ten women in the Western world get breast cancer; half die from it. How tumours look tells oncologists little about which ones might spread. We want to use mass spectrometry to investigate the composition of blood serum to find markers that allow to diagnose early the onset of this malignant disease and to distinguish different forms to allow tailored treatment. Our group is composed of nearly ten people combining biochemistry, molecular biology, mass spectrometry, chemistry, and programming. We have state-of-the-art instrumentation and have just finished the creation of software that allows extracting peaks from complex mass spectrometric data sets. This forms the foundation of a statistics project to find significant changes in data sets from patients when compared to controls. The ideal candidate would already have or strongly desire knowledge in statistical methods such as Bayesian theory, Principal Component Analysis, Genetic Algorithms, Neural networks and of statistical software like R. or Weka. Samples and medical expertise are obtained through close collaboration with the IEO, Italy's largest private cancer hospital, and INT, Italy's largest public cancer hospital, both situated nearby and having together over 25.000 patients per year. We are a very motivated and mostly young, mixed gender group and would like to encourage applications from women and from out-side Italy. Knowledge of English is expected; Italian is not required. Depending on the experience of the applicant the position can yield into a Ph.D. degree (17.000 Euro/year) or postdoctoral appointment (20.000-27.000 Euro/year). Taxation is 20%; health insurance is included (public). Applications should be in English and contain as PDF or RTF a curriculum vitae, a motivation letter including experience in the field, and the contact details of two references. Application deadline is May 28th, 2004. The data is waiting, so we would like to fill the position as soon as possible. Contact: Dr. Juri Rappsilber, email: rappsilber@ifom-firc.it, Further information on the group www.ifom-firc.it/proteomics/, institute www.ifom-ieo-campus.it/, and hospitals: www.ieo.it/inglese/Welcome.html, www.istitutotumori.mi.it/int/default.asp ****************************************************************************** From: Rinus Luijmes Date: Sun, 16 May 2004 19:06:03 +0200 Subject: Cetac ASX510 autosampler: can it be programmed for custom-made Organization: * In two weeks our new Agilent 7500ce ICP-MS will arrive at our lab. It comes with an Cetac ASX510 autosampler. We don't use sampletubes for our samples on our autosamplers but custom-made blocks made of PETP with 200 holes in them to hold the samples (click on the white block on this page to view: http://www.xs4all.nl/~digirini/contents/icp-ms.html#liquidhandling). This is because we analyse a large amount of samples. Can the Cetac ASX510 be programmed to go to position x, y, z in millimeters? If so, I can make a custom table with all the sample positons at the right places in the right order. Greetings, Rinus Luijmes. ****************************************************************************** From: Michael_P_Balogh@waters.com Date: Mon, 17 May 2004 08:16:34 -0400 Subject: LCMS Workshop at ASMS Organization: * LC/MS Evening Workshop Discussion of Novel Approaches to LCMS Practice: Do they solve problems? Tuesday, 25 May 2004 5:30 - 7:00 Michael P. Balogh, Waters Corporation, Organizer for LCMS Interests Katrina Rogers, MDS Pharma Services, Bothell, WA The LC/MS and Related Topics interest group has traditionally focused on specific issues and enhancements in the field, which have an impact on LC/MS as a practice. The practical aspects of how novel technologies are employed by early adopters have taken over increasingly from the original invention itself. This workshop reflects those changes and provides an opportunity to examine techniques typically associated with LCMS, which might have a dramatic impact on how many practitioners address problem solving. EMPLOYING NOVEL TECHNOLOGIES USING AN ION FILTERING DEVICE TO ELIMINATE METABOLITE INTERFERENCE IN DRUG QUANTITATION BY LC-MS/MS Mohammed Jemal, Drug Disposition and Bioanalytical Sciences, Bristol-Myers Squibb Ion mobility based filtering (specifically FAIMS) has been a topic of interest recently. This talk presents some insight to its practical application removing metabolite interference and thereby improving drug quantitation. A "MULTIMODE" ION SOURCE FOR SIMULTANEOUS ELECTROSPRAY AND ATMOSPHERIC PRESSURE CHEMICAL IONIZATION Steve Fischer, Agilent Technologies A brief description of the physical challenges to simultaneous APCI and ESI ion formation and the technology used to overcome those physical challenges. To demonstrate simultaneous APCI/ESI operation of this source, several compounds and mixtures of compounds were analyzed. The multimode source produced results in a single analytical run that were comparable to those for the individual compounds ionized using standard single-mode ion sources. Other test results indicate the multimode source produces comparable spectra to and has essentially equivalent sensitivity to a single mode ion source. QUANTITATING PEPTIDES THE PITFALLS OF PEPTIDE QUANTITATION Peter Stoffolano, P&G The pain points in developing quantitative assays for peptides can be different from challenges associated with other small molecule method development. These challenges can potentially impact the overall performance and reliability of a method. Variables such as analyte solubility, adsorption, peptide stability in the matrix and extract are basic issues that often require different optimization due to small differences in peptide sequences. The discussion focuses on these variables and how we have optimized experimental conditions, in contrast to small molecule assay development. QUANTITATING PEG PEPTIDES Craig Marshall, Amgen PEG conjugated peptides typically do not lend themselves to LC/MS detection and quantitation. The PEG-peptide investigated produces a broad continuous gaussian charge distribution when scanning in a single quadrupole mode. On fragmentation, smaller PEG segments are observed as fragments using Q3 in triple quadrupole mass spectrometers. Two different mass spectrometer methods were employed. One method monitored the precursor ions of the PEG fragment, while the other, an SRM method, monitored a window set in a range of the charge envelope with a transition to the desired fragment. This LC-MS/MS method benefits by much lower variability and a 15 fold lower limit of detection over the immunoassay. Although this technique measures the delivered â^À^Üwar headâ^À^Ý indirectly through the PEG portion of the molecule, the science behind the parent drug purification, a very stable linking structure, and PEG metabolism indicates that the method would be valid. ENHANCING METABOLIC STUDIES AN "ORGANIC CHEMISTRY" BASED METHOD FOR PREDICTING METABOLITE STRUCTURES FROM MS/MS DATA. Heather Desaire, University of Kansas Metabolite analysis typically involves rapid identification of the chemical composition of the metabolite by automated HPLC-MS methods, followed by the laborious process of identifying the structure of the metabolite. Structural identification can be cumbersome because interpretation of MS/MS data may not readily provide enough information. We have begun to develop predictive rules that describe how compounds dissociate under low-energy collision-induced dissociation (CID) conditions. The rules are based on a mechanistic understanding of reaction pathways. We apply general principles of physical organic chemistry to predict fragmentation of unknowns: This is useful in determining structures of unknowns from MS/MS data. CHARACTERIZING METABOLITES AND CHEMICALLY MODIFIED METABOLITES: ENHANCING SENSITIVITY AND COVERAGE WITH DERIVITIZATION Sunia Afzaal Trauger, The Scripps Center for Mass Spectrometry The fundamental reality of MS analysis is that the analyte must be ionizable. Important biomolecules such as steroids, carbohydrates, and lipids often do not ionize efficiently. Two derivatizing methods were developed for detecting metabolites in both positive and negative ion modes. The reagents include a mono-(dimethylaminoethyl) succinate imidazolide reagent, which covalently attaches an amine for enhanced positive ion signal, and a sulfur trioxide/pyridine reagent, which attaches a sulfate for improved negative ion signal. These modification reactions were performed on simple solutions containing cholesterol and more complex human serum samples. The results demonstrate the effectiveness of chemical modification in increasing the sensitivity of MS analysis in both simple and complex systems as well as the potential for identifying previously unobserved metabolites. =========================================================== The information in this email is confidential, and is intended solely for the addressee(s). Access to this email by anyone else is unauthorized and therefore prohibited. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful. =========================================================== ****************************************************************************** From: Chip Cody Date: 17 May 2004 10:40:39 -0700 Subject: Re: LC-ESI-MS (QTOF) impurities in acetontrile/water/TFA mobile Organization: * Tobias Kind wrote in message news:... } Claude Chenier wrote in message news:... } } We are using an acetonitrile/water(with 0.1% Trifluoroacidic acid) mobile } } phase for LC-ESI-MS. We have a background that appears to contain two } } significant compounds with elemental formulae of C12H20O4 (MW 228.136) and } } C10H16O4 (MW 200.105). } } } } MH+ ions were observed. Does anyone have any knowledge of these apparent } } impurities? } } Candidate compounds are dipropyl and dibutyl maleate (DBM). The latter is a common additive to plastics, pigments, etc. Finding and eliminating the source could be challenging. Over the years, I have found plasticizers and additives in everything from solvents to containers to gas lines. Good luck! Chip Cody (JEOL) ****************************************************************************** From: Rich Date: 18 May 2004 02:50:47 -0700 Subject: Micromass Q-Tof Masslynx problem (unable to open commlist.acq) Organization: * Dear All, Don't know if someone can help with this one: I am getting the following error message 'unable to open COMMLIST.ACQ' when trying to acquire data. The problem arose whilst trying to calibrate the Q-Tof. The Q-Tof is a mkII running Masslynx version 3.4 I was running an acquisition, stopped the acquisition, moved a couple of .raw files into the E drive (which contained a .cal file), tried to acquire again but the error message appeared. I've tried moving the file back, rebooting, running engcon, checked the epc with hyperterm etc to no avail. Help - the boss is about to reach for the nut-hammer..... R ****************************************************************************** From: Eric van der Meulen Date: 18 May 2004 04:54:20 -0700 Subject: Re: Drifting Area under Curve Organization: * We had similar problems with our TSQ GCMS in 1998, equipped with the 7000 ion source (which is, I believe, similar to the Trace source). It appeared that the source temperature was too low and could not be set higher. Our solution was to change to the old source design. So: check your source temperature! Eric van der Meulen ****************************************************************************** From: "Alvarez, Melissa" Date: Tue, 18 May 2004 13:56:22 -0700 Subject: vendor recommendation for formic acid Organization: * Hi All, Can anyone recommend a good vendor for formic acid? Melissa Alvarez Protein Design Labs, Inc. 34801 Campus Drive Fremont, CA 94555 Phone: (510) 742-2047 ****************************************************************************** From: Mad Scientist Date: Tue, 18 May 2004 16:19:45 -0700 Subject: Mass Spec Database Organization: * Hi, We have an ion-trap mass spectrometer, which we use for mainly metabolite identification. The software used to operate this instrument is Xcalibur from Thermo-finnigan. As you all know that one injection on the MS can generate a lot of data. Over few years, we have collected a lot of data. We would like to create a database, which will help us in analyzing the raw data by doing e.g. base-peak analysis for a particular m/z, look for a MS Spectrum. Does anyone know of any such tool (commercially available) that will help us organize the data? Any input is appreciated. Purvi ****************************************************************************** From: dawe Date: 19 May 2004 04:37:03 -0700 Subject: Re: Mass Spec Database Organization: * I'm interested in this too, but I know that such a software doesn't exist. In our lab we are planning to implement our own database for interpreted spectra, but this will probably take a lot of time! dawe ****************************************************************************** From: Dennis FalkenstrXm Date: Thu, 20 May 2004 09:13:14 +0200 Subject: Re: Mass Spec Database Organization: * On Tue, 18 May 2004 16:19:45 -0700, Mad Scientist wrote: }a MS Spectrum. Does anyone know of any such tool (commercially }available) that will help us organize the data? Any input is Have you taken a look at the ACD/MS Manager? We are just starting to build our own database that sound similar to yours by using ACD/MS Manager. So far we are just in the planning phase but are already impressed about the software ability to import spectra from different vendors like Micromass 3Q, QTOF and Agilent 1Q and iontrap. Besides the database it has an impressive tool to compare LCMS data that I am sure you would like if you look for small amounts of metabolite in a complex matrix. You can find more about ACD/MS Manager at: http://www.acdlabs.com/products/spec_lab/exp_spectra/ms/ Best regards Dennis Falkenstrøm ****************************************************************************** From: Victor Benham Date: Thu, 20 May 2004 23:14:29 -0400 Subject: 2004 SAS/SSC Tour Speaker Dinner Presentation. Organization: * Dear friends and colleagues: It is our pleasure to host this year^Òs SAS/SSC Tour Speaker, Professor Robert G. Michel, from the University of Connecticut, and President of the Society of Applied Spectroscopy SAS, in a dinner-presentation meeting to be held in the National Research Council, on Tuesday June 8. The lecture is entitled, Resonant laser ablation of metals detected by atomic emission in a microwave plasma, and by inductively coupled plasma mass spectrometry. For more details, please the actual announcement pates at the bottom of this page. Please do join us to listen to a vibrant and state-of-the-art presentation, and to renew the acquaintances and friendships. We would appreciate of your intent so that we can prepare sufficient dinner and drinks to serve you better. At the same time, we would very much like to receive your suggestions and ideas as they will be given a serious consideration, and discussed in the local section and national meetings. Please note that we require volunteers in every position at the local executive level. If you would like to offer your services, we would VERY MUCH like to hear from you! In the meantime, please plan on attending the Tour Speaker Lecture presented by Professor Robert G. Michel, and post this announcement to the attention of your colleagues. Thank you, and looking forward to see you there. Best regards. Dr. Victor Benham, SSC-International Liaison The Ottawa Valley Section. """""""""""""""""""""""""""""""""""""""""""" 2004 SAS TOUR SPEAKER DINNER MEETING FEATURING Prof. Robert G. Michel President of the Society of Applied Spectroscopy, SAS Department of Chemistry, University of Connecticut Storrs, Connecticut, 06269 - 3060, U.S.A. PRESENTING Resonant laser ablation of metals detected by atomic emission in a microwave plasma, and by inductively coupled plasma mass spectrometry. DATE & TIME Tuesday June 8 2004, cash bar (6:00-7:00) pm. Dinner served at 7:00 pm sharp. Presentation scheduled to commence between (8:15-8:30) pm LOCATION National Research Council of Canada, Institute for Molecular Sciences, 100 Sussex Drive, Ottawa, Canada. K1A 0R6, about two blocks east of the Royal Canadian Mint, Cafeteria/bar (basement), Presentation (room 3001), PARKING Parking is free! Please make sure to register your name and affiliation at the commissionaire's desk. MENU Appetizer: Garden salad with dressing, Main dish: Chicken Rosemary, fresh asparagus and rice pilaf, Dessert: Blueberry cheesecake, and coffee/tea. RATES Students: free, Members: $5.00, Non-members: $10.00. Payment will be collected at the event. This event is subsidized by the society. ABSTRACT: Laser ablation refers to the explosive process by which a solid sample is vaporized though a violent laser-material interaction resulting in a plume of atoms, ions, molecules, and clusters. These species can be detected in a variety of ways in order to achieve a quantitative elemental analysis. It is widely accepted that it is ideal for the laser ablation process to produce a low-density gaseous plume of material with the same stoichiometric ratios of constituents as found in the bulk material. However, it has been shown that an increase in sensitivity and selectivity of detection of an analyte can be achieved by tuning the laser wavelength to match that of a resonant gas phase transition of that analyte. Tuning the ablation laser to such a wavelength has been termed Resonant Laser Ablation (RLA), but only a few papers have studied the phenomenon in a fundamental way, and still fewer have attempted to evaluate the analytical utility of RLA. The data presented here illustrate the resonant enhancement effect in pure copper and aluminum samples, chromium oxide thin films, and for trace molybdenum in stainless steel samples. There are two main characteristics of the phenomenon. The first is that there is an increase in the number of atoms ablated from the surface. The second is that the spectral resolution of the effect is of the order of 1 nm although, here, a laser with about 5 pm spectral bandwidth was used. The effect was found to be virtually identical whether the atoms were detected by use of a microwave induced plasma with atomic emission detection, by an inductively coupled plasma with mass spectrometric detection, or by observation of the number of laser pulses required to penetrate through thin films. This presentation will show data that illustrate the enhancement, and review some of the conceptual framework that indicates why this enhancement occurs. RESERVATION Must be made NO later than Tuesday MORNING, June 8, 2004. Please contact: Ana H. Delgado, ph. 613-993-3719, fax. 613-954-5984 Email: ana.delgado@ncr.ca (no later than Friday June 3) Conrad Gregoire, ph. 613-995-4213, fax. 613-943-1286 Email: gregoire@nrn1.nrcan.gc.ca and Victor Benham Email: Victor_Benham@Canada.com ****************************************************************************** From: Robert Mistrik Date: 21 May 2004 00:56:08 -0700 Subject: Re: Mass Spec Database Organization: * }a MS Spectrum. Does anyone know of any such tool (commercially }available) that will help us organize the data? Any input is At the ASMS will be launched Mass Frontier 4.0 (distributed by Thermo Electron) that does exactly what you need. Mass Frontier is able to read Finnigan raw data. A unique feature of Mass Frontier is the ability to create searchable libraries of data reduced chromatographic data. Retention times and TIC profiles, as well as selected scans or detected component mass spectra or MS/MS spectral trees can be exported to user libraries and searched using various criteria. This feature allows you to search a particular spectrum in a series of GC/LC/MSn library records (target analysis), or you can perform cross matching of all scans or components in a chromatogram against spectral data of other chromatographic records (dereplication). Chromatograms are organized in a similar manner to spectral libraries, with the difference that a single library entry represents a data reduced chromatogram rather than a simple spectrum or tree. Mass Frontier runs professional SQL relational database for spectra and chromatograms. Mass Frontier incorporates a novel automated system for detecting chromatographic components in complex GC/MS or LC/MS or GC/LC/MS^n runs and extracting mass spectral signals from closely coeluting components (deconvolution). Mass Spectra or spectral trees obtained after deconvolution can be searched in libraries or classified using Principal Component Analysis, Neural Networks or Fuzzy clustering. Robert Mistrik HighChem, Ltd. ****************************************************************************** From: duck Date: Sat, 22 May 2004 15:58:52 GMT Subject: Re: Dynasoap for ion source cleaning Organization: * 1. Do not use aluminum oxide powder for source cleaning!!! Aluminum oxide will cut rather than clean. Use #9 glass beads from S.S. White. We have been using these for > 20 years in one of their Airbrasive machines (see www.airbrasive.com). Do not use any sandblaster on thin metal foils used for electron entrance holes, beam restrictors or focusing plates. The force of the beads will cause rapid heating of thin foils and they will warp. Aluminum oxide should be used only on surfaces where you want a rough surface or to cut metal or other materials. 2. There are Micro-Mesh brand polishing sheets and sticks available in various grits from corse to fine. We have used these for polishing ESI cones, focusing plates and even MALDI targets. A Micromass engineer told me that they didnt like using these on Quad rod assemblies becasue they left a residue that was difficult to rinse away on the rods when assembled in a set. 3. 3M makes Imperial Lapping sheets in various grits. These are Mylar sheets with abrasive attached. The Micromass engineer told me that this is what they were using for Quad rods because any residue would rinse away. Richard Milberg University of Illinois Urbana, IL "Mudbunny" wrote in message news:c82m5k$1nt$1@news-int2.gatech.edu... } Richard wrote in message news:... } } Has anyone ever used Dynasoap to clean their ion source? A service } } engineer says that's all he uses and gets wonderful results. } } } } He gave me a couple of ounces of his stash. Dynasoap, a phosphoric } } acid based ultrasonic cleaner, apparently is no longer available. I } } can't find much of anything about it on the internet. The listed } } manufacturer no longer mentions it on their website. } } } } It has me curious. The engineer appears to be very competent and } } knowledgable. This does sound too good to be true. Strangly enough the } } magic potion has disappeared. } } } What was suggested to me for my high res mass specs was to buy a } miniature sandblaster, along with some aluminum oxide blasting powder. } Note this is not recommended for aanything with a coating or anything } like that. } } Marcel } } ****************************************************************************** From: Chris R. Lee Date: Mon, 24 May 2004 21:43:28 +0200 Subject: Re: vendor recommendation for formic acid Organization: * Try Fluka. They provide typical specifications in their catalogue, which gives some indication that the purification procedure is under control. Nowadays you don't often see 76% grade in the catalogues. This is the azeotrope, which according to something I read a long time ago is more stable than the pure acid (which, after all, is an aldehyde). One solution is to distill the azeotrope yourself about once a year. Use all-glass apparatus with some kind of simple column. Store small portions in glass vessels in the fridge. Regards "Alvarez, Melissa" a écrit dans le message de news: c8du0d$ofv$1@news-int2.gatech.edu... } Hi All, } Can anyone recommend a good vendor for formic acid? } } Melissa Alvarez } Protein Design Labs, Inc. } 34801 Campus Drive } Fremont, CA 94555 } Phone: (510) 742-2047 } } . ****************************************************************************** From: Michael Sherrell Date: Mon, 24 May 2004 14:43:28 -0700 Subject: Seqs, synths, mass specs/MALDIs, liquid handlers etc. available Organization: * Grizzly Analytical: Sequencers, synthesizers, mass specs, MALDIs, liquid handlers, cytometers etc. for sale For text string search in Outlook Express, use ctrl+shift+F For text string search in Outlook, use F4. **Oligosynthesizers: Expedite 8909: $14,500. Includes M.O.S.S, rebuilt w/ new ABI valves, 90-day warranty. + $3,500/trityl. ABI 394: $14,200. Rebuilt; 90-day warranty. ABI 394: $19,900. Trityl, MAC, rebuilt: about as good as the new 3400. ABI 392: $12,200. Rebuilt; 90-day warranty. ABI 391: $11,750. Rebuilt; 90-day warranty. ABI 3948: $25,000. Rebuilt/installed w/ 90-day warranty. ABI 390Z: $11,000. Rebuilt/warranteed. (Oligosynthesis reagents, ~75% off list: Oxidizer, Cap A, Cap B, Activator, Deblock, amadites, + 8909 columns) Beckman 1000M: $11,000. Excellent condition; guaranteed. CyClone: $7,500. New-in-box; 90 day parts warranty. Similar to ABI 392. Biosearch 8700: $10,000. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. BioSearch 8750: $10,500. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. Biosearch 8700: $8,000. Rebuilt; 90-day warr. + $2K/Windows. BioSearch 8750. ~$4,000. Have 5; cheaper & faster than 394s. Cruachem PS250. <=$2,500. 6 available. MacConnell MiniPrep 48 (for DNA Purification): $6,000. Used once. 48 samples/hr. Specs: www.macconnell.com/specs_48.htm *High throughput synthesizers: BLP 192: $125,000. 2 plates, 8 min. cycle time. New; incl. install + 1 yr. warr. TAGC 96: $95,000. Fast; optimized for small-scale up to 50 bases. Polygen 10. Call if interested. Polyplex Gene Machine: $89,000. Installed/warranteed. **Oligosequencers: ABI 3100: $85,000. Includes factory install. ABI 3100 Avant: $55,000.Includes factory install, $5,000 in consumables. ABI 310: $28,000. Mac. Includes factory install; guar. eligible for service. ABI 310: $31,000. PC. Includes factory install; guar. eligible for service. ABI 3700: $65,000. Includes factory install; guar. eligible for service. ABI 3700: $29,000. From major genome center; beautifully maintained. ABI 3700: $7,000. Complete; was working when deinstalled. MegaBace 1000: $22,000. Incl. installation by manufacturer. ABI 377: $15,500. 96-lane; factory install incl., eligible for service. (Also suitable for tiling.). Genescan: $5,000. Licensed software for the 377, 310 or 373. ABI 373 stretch: $9,000. Big Dye upgrade. Pharmacia ALF Express: $14,000, incl. 90-day parts & labor warr. Visible Genetics: $20,000. Unused. Have 3. LiCor 4200: $25,000. Incl. Global Upgrade; guaranteed installable. LiCor 4000LS <: $20,000. 1994 model; can have Global Upgrade. Genomyx LR: $2,500. Boots; many accessories. MJ Basestation 51. Call for pricing. No robotic loading, 2 years old, under service contract. MJ Research BaseStation: $105,000. 2 yrs old; still under svc. contract. MJ Research BaseStation: $125,000. 6 mos. old; still under svc. contract. **Real-time PCR: ABI 7900: $75,000. < 1 yr. old. Installed/warranteed. ABI 7700: $27,000. Installed/warranteed. ABI 7000: $29,000. Installed/warranteed. 2002 model. BioRad iCycler: $32,000. 90-day warranty. **Peptide synthesizers: ABI 433: $44,500. Original, ABI-supportible 433. These come and go; call/email to reserve. 90-day warr. ABI 433: $31,000. Upgraded from 431. We support. Rebuilt, 90-day warr. ABI 431: $16,000. Rebuilt, 90-day warr. ABI 430: $10,500. Rebuilt, 90-day warranty. Rainin Symphony: $65,000. Rebuilt, 6 mo. warranty. ABI 432: $15,000. Rebuilt, 90-day warranty. Capriccio 1: $65,000. New instrument. Benchtop, large scale; faster and more efficient than ACT 400. Incl. install, 1 yr svc. PerSeptive 9500: $12,750. Rebuilt w/ 90-day warranty. PerSeptive 9050: $16,000. Rebuilt w/ 90-day warranty. CS Bio 336. ~$27,000. 6 mos old; lease default. 3 peps simultaneous; .05-.25 mmol. ACT LabTech III: $15,000. 30-day warranty. Pioneer: $40,000. Includes factory install, eligible for svc. contract MPS unit for the Pioneer peptide synthesizer: $5,000. New and unused; price = 25% of new cost. ACT 396 MPS: $42,000. Factory refurb; includes 120-day warranty. PerSeptive 9600: $13,750. Rebuilt, warranteed. ACT Vantage: $79,000. Excellent condition. ACT 357-MPS. Call for pricing. CEM Discover benchtop single peptide synthesizer: $16,000. ACT 90: $16,250. Only used twice. Incl. install; guar. eligible for svc. Argonaut Quest 205: $27,000. ASW model. Argonaut Quest 210: $19,000. ASW model. **Peptide sequencers: ABI 494 cLc. Offers considered. ABI 494 HT: $40,000. Installed, guaranteed ok for service contract. ABI 492: $25,000 installed, eligible for service contract. Beckman 6300. Various prices. Have several; can rebuild or sell for parts. ABI 421: $10,000. Offers considered. ABI 477/120: $1,500. Good working order or right of return. ABI 477. Service, parts available. ABI 473/476: $15,000. Good working order; install/service available. Beckman 6300 AA: $ 8,000. Rebuilt/warranteed ABI 470A: $2,000. For parts. Many extra parts. *[Note: various other ABI, HP, Millipore, Biosearch, Beckman, etc. sequencers, synthesizers etc. available; please inquire.] **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $125,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex API 2000 TurboIon Spray: $5,500. Interface and orifice plate. Sept. 2002. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass Quattro Micro: $135,000. Call/email for details. License not incl. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $110,000. API-LC/Orth. 2000 model. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. **Liquid handlers: MDS Sciex NanoLC systems: more useful for proteomics than LC Packings Nanomate. Call for info. Biomek FX (core system): $450,000 good working order. Includes 3 meter Orca, fluorometer, incubator, more. Biomek FX: $60,000. Single arm. Biomek 2000, no side loader, $49,000. Beckman Multimek, $34,000. Zymark Sciclone: 1.5 years old; $43K. Zymark Staccato system: Subsantial discount; price depends on accessories, install, warranty. XP-arm based Zymarks: $10,000 and $20,000, depending on accessories. Tecan RSP-200/8 ID Robot Sample Processor, fully equipped: call/email if interested. Hamilton MicroLab AT2 Plus robot, $38,000 Packard Multiprobe 20400 and CP20400, Packard refurbed, $16,500 for either Transgenomic WAVE system, $30,000 incl. installation, eligible for svc. Tecan Genesis RSP 150, no Roma, $52,000 delivered w/ 90-day warranty. Tecan Genesis RSP 100, $41,000 delivered w/ 90-day warranty. LC Packings UltiMate NanoLC system w/ FAMOS autosampler, $37,300 Scitec robotic liquid handling system, 3-meter rail, $60,000 guaranteed working Tom-Tec Quadras, various configurations, refurbished and warrantied. Hamilton Microlab 2200: call for pricing. Gilson 215: call for price. ABI 877 Catalyst Turbo: $12,000 or best offer Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically 96-well microplate source, glass slide, microwell plate or membrane target), ~ 5 years old. **Other expensive hi-tech items: *NMRs: Varian Inova 600 NMR: $275,000 guaranteed installable; +$25K/install. Bruker Avance 500 DRX, unshielded, cryoprobe ( available for $175,000 separately) + 5 other probes, 3 channel, $425,000 installed. Optional autosampler, $25,000. FX90Q NMR w/ Tek-Mag, $19,500. Others available; inquire if interested. *Flow cytometers: FACS Vantage SE with the DIVA option: $160,500. (2 lasers: 488nm and UV tunable). Bought in June '02 and never used. BD FACSCalibur w/ FACSLoader: $84,000. 4 color. 1998; excellent condition. BD FACScan; $28,500. 3 color single laser. BD FACSort Cell Sorter, $39,000. 3 color, MAC G3, Cellquest, install included COULTER® EPICS XL-MCL^Ù: $45,000. 4 color with Multi Carousel Loader includes rebuilt, installation and one-year warranty. Coulter Epics Elite: 9 years old but never used. Call/email if interested. COULTER® EPICS XL^ÙFlow Cytometer: $45,000.00 Currently in operation. Includes XL2, EXPO and Data Mate Software, APC UPS Back-up, factory installation, and other options. MoFlo Analyzer with MoSkeeto System: $99,750.00. 6-channel / 5-color detector, Carvo MSP - 9000 Auto sampler, Summit 3.1 Software, Laser. Scanning Cytometer: Microscope-based. Two-laser system. $85,000 guaranteed installable. Others available; inquire if interested. *Arrayers/spotters/readers: SpotBot Personal Microarrayer, $9,750. 2002; excellent condition. HP GeneArray G2500A reader w/ laser, $22,000, including new data system but no fluidics station. Affymetrix 417 Arrayer/spotter: seller considering rather low offers; call if interested. Affymetrix 417 Arrayer/spotter: $34,500 reconditioned with 1 year warranty HP/Affymetrix GeneArray Scanner Model G2500A, unused, $49,000. CELLOMICS ScanArray HCS: 2003 model. Factory install, license discount available; offers considered. Packard ScanArray 4000: $39,250. 2000 instrument. Incl. factory install; eligible for service contract. Packard ScanArray 3000: $17,250. Incl. factory install; eligible for service contract. Genomic Solutions GeneTAC microarray Hybridization Station: $27,000. (for details see www.genomicsolutions.com/products/bio/hyb.html) Amersham Lucidea SLIDE PRO Hybridization Station: $18,500. Ciphergen ProteinChip Reader PBS II: $65,000. Current upgrades; includes factory install, 30-day warranty. *Spot pickers: Genomic Solutions Pro-Pic, new 10/01, model FLX 51001. Must sell; price half of new. Genetix QPix2 benchtop: $79,570 installed. Incl. 96-well picking head, gridding option, etc; Q-Fill optional. Genetix QBot picker/arrayer. Call/email if interested. BioRobotics BioPick automatic colony picker. Excellent condition. ~$60,000 Genomic Solutions Flexys; much less than new price; call/email if interested. *Microscopes: ZEISS Axioskop Trinocular Microscope, $24,650 For phase contrast, DIC and Epi-Flourscence Cambridge Stereoscope S90B SEM w/ Kevex EDX: $25,000. Incl. secondary and backscattering detectors, Polaroid system, some options, factory installation. Working now. Optional one year service sontracts available. Meridian ACAS 570C LSCM. Other Laser Scanning Confocal microscopes available, call or email for list. Cambridge Stereoscope S90B SEM w/ Kevex EDX: $10,000. Incl. secondary and backscattering detectors, Polaroid system, some options. Working now. Various (SEM) Scanning Electron Microscopes, $9,500-$375,000. Call or email for list. Various (TEM) Transmission Electron Microscopes; call or email for list. Various (AFM) Atomic Force Microscopes: Veeco, Digital Instruments, Park Scientific, Topometrix, etc. Call or email for list.; call or email for list. Various surgical, neuro surgical microscopes, call or email for list. Various optical microscopes, call or email for list. *Truly miscellaneous: Spectrumedix Reveal 9610 Capillary TGCE mutation discovery system: $150,000. 1.5 yrs. old; still under extended warranty. New price: $231,000. Thermo Kevex Omicron XRF: $45,750. Excellent condition. Includes installation. Ventana Discovery Hyb System: advanced slide staining platform for target and compount drug discovery. Check www.ventanadiscovery.com. Call/ email to discuss price. Molecular Devices/LJL Biosystems Criterion Analyst HT System: $35,000. Amersham Typhoon 8600 scanner: Accepting offers. Perkin Elmer 1010M Micro Densitometer: was $325,000 new. Now in Japan. Call if interested. Amersham FARCyte/Tecan Ultra fluorescence plate reader, new in box, $50,000. List: $80K. Packard 50TR flow scintillation analyzer. Call for price. Brand new, unused. Accutag Radio Frequency Reader/10k Automated Microreactor Sorting System, $80,000 Genevac's Mega 1200 ultra high throughput solvent evaporation system, 1.5 yrs old but unused, $200,000 or best offer. New Brunswick Bioflo 3000 bioreactor: $18,900. 10 liter; new probes; 90-day warr. Process Engineers 29 liter mammalian cell bioreactor, new/unused, ~$35,000 or best offer. *(other bioreactors/fermenters available; inquire if interested.) **Too hard to classify: Li-Cor Odyssey: $25,000 ($40K new). Guaranteed good working order. See for specs. BioCAD 20s and 60s w/ 90-day warr. available for $10-15,000, depending on details. 700E also avail. < $25,000. ABI VISION Workstation (souped-up BioCAD; see AB website for details): offers considered. Luminex LX100 (simultaneous assay of multiple analytes): $29,000. Glycoprep 1000 automated hydrazinolysis machine: $9,000; good working order Packard Topcount 12-detector 96 well microplate scintillation counter, $35,000 ABI 120 HPLC, $1,500 ABI 877: have several; different configs, prices, none very expensive; call PE 9600 thermalcyclers: $3,750 w/ 90-day warranty PE 9700 96-well thermalcyclers: $5,300 w/ 90-day warranty PE 9700 384-well thermalcyclers: $5,450 w/ 1 yr. warranty PE 2400 thermalcyclers: $2,450 w/ 90-day warranty PE 480 thermalcyclers: $3,000 guaranteed working; have several Beckman P/ACE MDQ: $24,000 Beckman P/ACE 5510: $19,500. Refurbed, warranteed. MD PhosphorImager Storm 860, $30,000. MD FSI FluorImager, $15,000 MD Cytosensor Microphysiometer: $9,800 w/ 90-day warr. **Service: We rebuild valve blocks for ABI 430, 431 and 39x @ $65/port, 90-day warranty Service and contracts on ABI 39n and PerSeptive 8909/8905s available. Service contracts on Hewlett Packard HPLCs, GCs and MSs available at a savings over HP rates **Also available: Agilent 1100 HPLCs, virtually all configurations/detectors. HPLCs, ICs, CEs, FPLCs: microbore to prep scale. A variety of other lab instruments. Call or check the website: www. grizzlyanalytical. com. Please call or email for more information or if you have items to sell. Michael Sherrell Grizzly Analytical (USA) www.grizzlyanalytical.com 707 887 2919/fax 707 887 9834 [All the items are subject to prior sale.] [If you do not wish to receive my emails, please return this with "Stop" in the subject line, and accept my apologies for the inconvenience.] ****************************************************************************** From: Rich Date: 25 May 2004 02:54:34 -0700 Subject: Re: Micromass Q-Tof Masslynx problem (unable to open commlist.acq) Organization: * Dear All, Bit the bullet and went for a re-install. Everything worked without problems. Cheers, R ****************************************************************************** From: "Little, James - Eastman" Date: Thu, 27 May 2004 15:08:56 -0400 Subject: Identification of Surfactants by Electrospray LCMS Organization: * We have developed some useful new approaches for the identification of unknown surfactants. The method employs electrospray LCMS (positive/negative ion, in-source CID or MSMS) for analyses. Then excel-based databases and MSMS library searches are used to identify the unknowns. Information can be found at: "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle Surfactant Link at bottom of web page. If you find any additional surfactants not in my databases, please let me know. I will add to the list for others to use. Other topics on the webpage include: accurate mass information (dead time in TOF, typical magnetic errors), library search software, EI multipy charged ions, building simple CI manifold; TSCA and CAS database for identification of unknows by LCMS and GCMS, diazomethane by-products/reactions, silylation by-products/reactions, characterization of polyesters, etc. [Problems Printing Report? Sometimes using Adobe Acrobat, you'll get a partial page when printing, be sure to go to file/print and check "fit to page" and "print as image" options boxes!] James Little Tel. No. 423-229-8685 office Tel. No. 423-229-8022 lab Tel. No. 423-367-0914 Cell "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ "Twenty years from now you will be more disappointed by the things you didn't do than by the ones you did. So throw off the bowlines, sail away from the safe harbor. Catch the trade winds in your sails. Explore. Dream. Discover." ****************************************************************************** From: Rich Yelton Date: Fri, 28 May 2004 19:43:20 GMT Subject: Re: Cleaning TFA contamination from LC/MS Organization: * Looks like you may have contaminated the tubing and filters in your mobile phase reservoir system. I would consider replacing the filters and then reevaluate the situation.You may be more successful by using tenths of a percent TFA. "Haig, Terrence" wrote in message news:c82ccp$s53$1@news-int2.gatech.edu... } } Request for help from experienced LC/MS users: } } from: Terry Haig } Analytical Labs } Charles Sturt University } Australia } } Having had some cause previously to try a few percent trifluoroacetic } acid (TFA) in one of our trial mobile phases for some LC/MS quadrupole work } on a C-18 column using our Navigator aQa system, we now find } lingering contamination from this compound (especially at m/z 113) } spoiling our sensitivity as it once was before TFA use. } } We would be grateful for any experienced suggestions as to effective ways } of removing this contamination from our system, as we have only had limited } success with all cleaning methods so far. } } Regards and thanks for suggestions. } } } Terry Haig. } ======================= } School of Science & Technology } Charles Sturt University, NSW, Australia } EMAIL> thaig@csu.edu.au } Phone: +61 (0)2-69332502 } FAX: +61 (0)2-69332737 } } ****************************************************************************** From: Simon Date: 1 Jun 2004 02:17:40 -0700 Subject: HELP: problems with LCQtune software Organization: * HELP: problems with LCQtune software Hy, I am a researcher working in mass spectrometry field and I have a problem with the LCQtune software for the LCQdecaXP instrument. I have recently realized a new ionization source name "Surface Activated Chemical Ionization - (SACI)" by Simone Cristoni, Luigi Rossi Bernardi, Ida Biunno, Michela Tubaro, Federico Guidugli Rapid Commun. Mass Spectrom. 2003, 17(17), 1973-1981. Now, I would like to modify the software LCQ Tune to permit to set the parameters of this new ionization source. Do you know if it is possible? Do exist some free API that permit to change and personalize the LCQtune program? If not do you know if I can contact some person of ThermFinnigan that can help me? Please reply me both to this newsgroup and to my E-MAIL address (dtoycr@tin.it). Thank you very much for your help. Sincerely yours Simone ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 01 Jun 2004 21:30:53 +0200 Subject: Re: HELP: problems with LCQtune software Organization: * Simon, as far as I know there is no way to modify the tune program or its API. Also all the procedures that run inside the instrument are encrypted and not even readable. Contact your local Thermo office for assistance to contact the factory in San Jose,CA. Best Regards Rainer Loerwald Thermo Electron Corp. Germany Simon schrieb: } } HELP: problems with LCQtune software } } Hy, } } I am a researcher working in mass spectrometry field and I have a } problem with the LCQtune software for the LCQdecaXP instrument. I have } recently realized a new ionization source name "Surface Activated } Chemical Ionization - (SACI)" by Simone Cristoni, Luigi Rossi } Bernardi, Ida Biunno, Michela Tubaro, Federico Guidugli Rapid Commun. } Mass Spectrom. 2003, 17(17), 1973-1981. } Now, I would like to modify the software LCQ Tune to permit to set the } parameters of this new ionization source. Do you know if it is } possible? Do exist some free API that permit to change and personalize } the LCQtune program? If not do you know if I can contact some person } of ThermFinnigan that can help me? } } Please reply me both to this newsgroup and to my E-MAIL address } (dtoycr@tin.it). } } Thank you very much for your help. } } Sincerely yours } } Simone ****************************************************************************** From: Andrew Peters Date: Wed, 02 Jun 2004 11:51:00 -0300 Subject: Enhanced Data Analysis in ChemStation Organization: * Hi MS users, I have a seemingly simple problem with ChemStation. I am performing SIM analysis on 2 compounds, monitoring 2 ions for each and I need peak areas for each ion. I can get this info by manually extracting SIM signals and integrating but I would like to get the data in a summary report as this would make data handling more rapid and simpler to transfer to spreadsheet. I have set up a calibration method but the output only supplies the RT and response of the quantitation ion. Is there a simple way to get the report to include peak areas for both the quantitation AND the qualifier ion? I am using ChemStation G1701BA v. B.01.00, with Enhanced Data Analysis. Thanks in advance for any help. Andrew Peters ====================================== Dr. Andrew J. Peters Associate Research Scientist Bermuda Biological Station for Research Ferry Reach, St. George's GE01, Bermuda Tel: 441-297-1880 ext. 240 Fax: 441-297-8143 e-mail: apeters"at"bbsr.edu web: http://www.bbsr.edu ====================================== ****************************************************************************** From: Ray Siegener Date: 2 Jun 2004 09:41:29 -0700 Subject: HP 5890 II EPC Problem Organization: * Hi all, I have a 5890 series II GC with EPC connected to a 5971 MS. A 30m RTX-5 column is installed. I am observing erratic EPC pressure readings at sttings below 10 PSI (I need 6.8 psi to get 1ml/min at 35C starting temp). When I turn the purge valve off, the pressure reaches 6.8 and holds steady. There also seems to be a temperature component to this in that the EPC will remain steady at < 100C but fluctuates over 100 C. I have already installed a new mass flow controller, new proportional valve, cleaned the split and septum purge lines, and swapped out the solenoid for one from a working instrument. Any additional suggestions will be appreciated. rs ****************************************************************************** From: ChemUserWorld Date: Wed, 02 Jun 2004 21:18:15 GMT Subject: Re: HP 5890 II EPC Problem Organization: * Ray, You should ask this question to Dr. ChemUser at http://www.ChemUserWorld.com. ChemUserWorld.com "Ray Siegener" wrote in message news:c9l0hd$5e4$1@news-int2.gatech.edu... } Hi all, } I have a 5890 series II GC with EPC connected to a 5971 MS. A 30m } RTX-5 column is installed. I am observing erratic EPC pressure } readings at sttings below 10 PSI (I need 6.8 psi to get 1ml/min at 35C } starting temp). When I turn the purge valve off, the pressure reaches } 6.8 and holds steady. There also seems to be a temperature component } to this in that the EPC will remain steady at < 100C but fluctuates } over 100 C. I have already installed a new mass flow controller, new } proportional valve, cleaned the split and septum purge lines, and } swapped out the solenoid for one from a working instrument. Any } additional suggestions will be appreciated. } rs } ****************************************************************************** From: ChemUserWorld Date: Wed, 02 Jun 2004 21:16:01 GMT Subject: Re: Enhanced Data Analysis in ChemStation Organization: * Andrew, You should ask this question to Dr. ChemUser at http://www.ChemUserWorld.com. ChemUserWorld.com "Andrew Peters" wrote in message news:c9kq4e$q36$1@news-int.gatech.edu... } Hi MS users, } } I have a seemingly simple problem with ChemStation. I am performing SIM } analysis on 2 compounds, monitoring 2 ions for each and I need peak areas } for each ion. I can get this info by manually extracting SIM signals and } integrating but I would like to get the data in a summary report as this } would make data handling more rapid and simpler to transfer to } spreadsheet. I have set up a calibration method but the output only } supplies the RT and response of the quantitation ion. Is there a simple } way to get the report to include peak areas for both the quantitation AND } the qualifier ion? I am using ChemStation G1701BA v. B.01.00, with } Enhanced Data Analysis. } } Thanks in advance for any help. } } Andrew Peters } } ====================================== } Dr. Andrew J. Peters } Associate Research Scientist } Bermuda Biological Station for Research } Ferry Reach, St. George's GE01, Bermuda } Tel: 441-297-1880 ext. 240 Fax: 441-297-8143 } e-mail: apeters"at"bbsr.edu } web: http://www.bbsr.edu } ====================================== } } } ****************************************************************************** From: Mike Sherrell Date: Wed, 2 Jun 2004 13:26:40 -0700 Subject: Grizzly Analytical Mass Specs, MALDIs, etc. available Organization: * Grizzly Analytical Mass Specs, MALDIs, etc. available **Mass specs: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000: $150,000 installed/warranteed. Sciex API 3000: $190,000 W/ upgrade to ~ API 4000 sensitivity and S/N. API 3000 upgrade: $38,500. Increases sensitivity and (S/N) Ratio at high flow rates to ~ that of an API 4000. Install incl. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $125,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex API 2000 TurboIon Spray: $5,500. Interface and orifice plate. Sept. 2002. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass Quattro Micro: $135,000. Call/email for details. License not incl. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $60,000. European install included; available in US. MM Autospec V: $70,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $105,000. API-LC/Orth. 2000 model. Manufacturer-certified. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Also available: oligo- and peptide synthesizers and sequencers, sample prep gear, etc. Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: JC Date: 2 Jun 2004 17:47:02 -0700 Subject: Re: Sciex Analyst 1.4 software Organization: * If you're running in WinNT, then Analyst 1.3 is ok. Davide Cittaro wrote in message news:... } Mmm, that's not probably what you want to hear about... We use Analyst } QS and I've found a lot of bugs, maybe dued to the .NET environment. } } dawe ****************************************************************************** From: Drew Spencer Date: Thu, 03 Jun 2004 02:18:40 GMT Subject: Re: HP 5890 II EPC Problem Organization: * Ray, You don't mention this, but have you leak checked everything? Also, how erratic is erratic? More than 0.01 ml/min flow? When I've experienced this in the past (flows that bounce around) and found it mostly related to pressure leakage at the ferrules connecting the column to the transfer line or inlet. We had the same symptoms as the components expanded during the run causing things to seal up more completely than when cold. The ferrule/nut at the ms transfer line has proven to be the culprit for us in most cases. I've also seen leaks either at the weldment shell (liner o-ring or septum) or the inlet ferrule after repeated heating and cooling. We recently replaced the standard xfer line nut with one of Restek's no-vent setups and have been very pleased with how well it keeps things sealed not to mention the convenience of being able to switch columns without having to fully vent. There could be something flaky with the EPC controller card on the GC but I'd look there last. Good Luck, Drew Spencer Ray Siegener wrote: } Hi all, } I have a 5890 series II GC with EPC connected to a 5971 MS. A 30m } RTX-5 column is installed. I am observing erratic EPC pressure } readings at sttings below 10 PSI (I need 6.8 psi to get 1ml/min at 35C } starting temp). When I turn the purge valve off, the pressure reaches } 6.8 and holds steady. There also seems to be a temperature component } to this in that the EPC will remain steady at < 100C but fluctuates } over 100 C. I have already installed a new mass flow controller, new } proportional valve, cleaned the split and septum purge lines, and } swapped out the solenoid for one from a working instrument. Any } additional suggestions will be appreciated. } rs } ****************************************************************************** From: Hubert Tang Date: Fri, 04 Jun 2004 00:25:13 +0000 Subject: Two LC pumps by Xcalibur Organization: * Dear all, Wondering if anyone has experience in configuring two Agilent 1100 LC pumps (Binary and quaternary) and controlled by Xcalibur 1.4 software. Finnigan's engineer told me that the driver does not support simultaneous control of two pumps with this software. Any modification required? Please advise. Hubert ________________________________________________________________________________ Use MSN Messenger to chat with friends and family. ****************************************************************************** From: grober Date: Fri, 4 Jun 2004 09:45:51 +0100 Subject: Re: HP 5890 II EPC Problem Organization: * I always found great problems sealing the column into the injector port if I used graphitised vespel ferrules. This often recommended for GC/MS rather than pure graphite ferrules. While I would recommend graphitised vespel at the mass spec end of the column I found that pure graphite ferrules gave the most reliable seal at the inlet end. Just use care when installing the column and break off a short length ~3 cms after you have threaded the end of the column thro the new ferrule- you should use a new ferrule every install! good luck. ****************************************************************************** From: David Naugler Date: 4 Jun 2004 09:43:47 -0700 Subject: Software for Shimadzu and Waters Organization: * Hi, I'm relatively new to mass spec. I'm mostly an NMR spectroscopist. In the NMR world there are a number of free software packages for off-line analysis if NMR data, e.g. NMRpipe/NMRDraw in the Linux world and MestRe-C in the MS Windows world. Let me describe the systems I've been using: LC-MS: Waters 2690 Separations module, 996 Photodiode array detector, Micromass ZQ and MassLynx V3.5 software. GC-MS: Shimadzu GCMS-QP5050A, Class 5000 software. My question is whether there is good free software available that can be used for the off-line analysis of Waters and Shimadzu data sets? Thanks. dgn ****************************************************************************** From: Bizzwire Date: Sat, 05 Jun 2004 00:20:38 GMT Subject: Re: Software for Shimadzu and Waters Organization: * David Naugler wrote... } } Hi, } } I'm relatively new to mass spec. I'm mostly an NMR spectroscopist. In } the NMR world there are a number of free software packages for } off-line analysis if NMR data, e.g. NMRpipe/NMRDraw in the Linux world } and MestRe-C in the MS Windows world. } } Let me describe the systems I've been using: } } LC-MS: Waters 2690 Separations module, 996 Photodiode array detector, } Micromass ZQ and MassLynx V3.5 software. I can't speak for the Shimadzu/GC-MS setup, but why do you feel the need for "off-line" data analysis.? What, exactly do you plan on doing? chramotgram/spectrum manipulation and display? Quantitation? MassLynx is pretty robust and I never had any problem doing any of these things while acquiring. Additionally, it probably has a lot more firepower and is a lot better arranged/more intuitive than any freeware you'll find. You *do* realize that you can do a non-acquisition installation of the software, don't you? (I'm pretty sure this won't violate any licensing issues, but you should check with your sales-person) You *could* run into problems if you want to do some heavy number-crunching like MaxENt or large-scal statistical calculations, but if you are as new to MS as you say, I kind of doubt that these are your intentions. I say fire away. I'd be willing to bet that you have this hang-up ingrained from years of Chemstation use. MassLynx is a very different animal. (DISCLAIMER: Ex-Waters employee) ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Sat, 05 Jun 2004 23:27:13 +0200 Subject: Re: Two LC pumps by Xcalibur Organization: * Hubert, dual pump is only possible with Surveyor MS pumps with one configured as "MS pump" and the other as "Sample pump". Currently no other configurations are supported. Best Regards Rainer Loerwald Thermo Electron Corp. Germany Hubert Tang schrieb: } } Dear all, } } Wondering if anyone has experience in configuring two Agilent 1100 LC } pumps (Binary and quaternary) and controlled by Xcalibur 1.4 software. } Finnigan's engineer told me that the driver does not support simultaneous } control of two pumps with this software. Any modification required? } Please advise. } } Hubert } } ________________________________________________________________________________ } Use MSN Messenger to chat with friends and family. ****************************************************************************** From: Phil Date: Sun, 6 Jun 2004 11:16:23 +0200 Subject: Re: Enhanced Data Analysis in ChemStation Organization: * Hi Andrew, A simple macro can definitely achieve this. You can even generate a CSV output file so that you can trigger Excel automatically at the end of this macro. If you don't have any macro experience, let me know and send me one of your datafiles at lesgothics@free.fr and I'll see if I can do something quick for you Rgds Phil "Andrew Peters" a écrit dans le message de news:c9kq4e$q36$1@news-int.gatech.edu... } Hi MS users, } } I have a seemingly simple problem with ChemStation. I am performing SIM } analysis on 2 compounds, monitoring 2 ions for each and I need peak areas } for each ion. I can get this info by manually extracting SIM signals and } integrating but I would like to get the data in a summary report as this } would make data handling more rapid and simpler to transfer to } spreadsheet. I have set up a calibration method but the output only } supplies the RT and response of the quantitation ion. Is there a simple } way to get the report to include peak areas for both the quantitation AND } the qualifier ion? I am using ChemStation G1701BA v. B.01.00, with } Enhanced Data Analysis. } } Thanks in advance for any help. } } Andrew Peters } } ====================================== } Dr. Andrew J. Peters } Associate Research Scientist } Bermuda Biological Station for Research } Ferry Reach, St. George's GE01, Bermuda } Tel: 441-297-1880 ext. 240 Fax: 441-297-8143 } e-mail: apeters"at"bbsr.edu } web: http://www.bbsr.edu } ====================================== } } } ****************************************************************************** From: Ain Date: Mon, 07 Jun 2004 13:30:34 -0400 Subject: Re: HP 5890 II EPC Problem Organization: * Ray Siegener wrote... } }Hi all, }I have a 5890 series II GC with EPC connected to a 5971 MS. A 30m }RTX-5 column is installed. I am observing erratic EPC pressure }readings at sttings below 10 PSI (I need 6.8 psi to get 1ml/min at 35C }starting temp). When I turn the purge valve off, the pressure reaches }6.8 and holds steady. There also seems to be a temperature component }to this in that the EPC will remain steady at < 100C but fluctuates }over 100 C. I have already installed a new mass flow controller, new }proportional valve, cleaned the split and septum purge lines, and }swapped out the solenoid for one from a working instrument. Any }additional suggestions will be appreciated. }rs Hi All According to my handy Hewlett-Packard flow/pressure calculator (FlowCalc2.07), a 30 m column with a carrier gas (He assumed) flow of 1 ml/min at 35 C and 6.8 psi head pressure and vacuum at outlet would have an ID of 0.25mm. Is this correct? A couple of clues: higher flow with purge valve on and >100 C both cause instability problems. EPC's have some limitations to complement their benefits. They can need 10-20 psi pressure differential to regulate properly . At 100 C you would need 10-11 psi column head pressure to obtain 1ml/min carrier flow. This means that you may need up to 30 psi to your EPC. Is your purge valve flow reducing the available pressure to the EPC? Excessive purge flow or massive leak or insufficient EPC pressure (is the EPC line plugged?) may cause these problems. Some EPC's also do not work at very low column head pressures (1-3 + psi). "When I turn the purge valve off, the pressure reaches 6.8 and holds steady" Are you suggesting the pressure buildup is gradual? Is this a new problem? Has the instrument ever worked in this configuration? Ain Raitsakas Senior Analyst Instrumentation Laboratory Lakehead University Thunder Bay, ON Canada P7B 5E1 ****************************************************************************** From: jin Date: 7 Jun 2004 15:32:57 -0700 Subject: Excess Volume in Full Loop Injection Organization: * hi, there, In the full loop injection of Thermo Finnigan Ion Trap, the total volume of sample drawn by the syringe, according to the definition, is: Total Volume = 3 x Injection Volume + Excess Volume What does this excess volume mean? It also said that for all injection volumes the excess volume is 41ul. Also, in partial loop injection: Total Volume = Injection Volume + Excess Volume, And for all injection volumes of partial loop injection, the excess volume is 10ul. What does this excess volume mean? Why the values of Excess Volume in full loop and partial loop are different? thanks so much!!! jin ****************************************************************************** From: Ray Siegener Date: 8 Jun 2004 10:51:39 -0700 Subject: Re: HP 5890 II EPC Problem Organization: * Ray Siegener wrote in message news:... } Hi all, } I have a 5890 series II GC with EPC connected to a 5971 MS. A 30m } RTX-5 column is installed. I am observing erratic EPC pressure } readings at sttings below 10 PSI (I need 6.8 psi to get 1ml/min at 35C } starting temp). When I turn the purge valve off, the pressure reaches } 6.8 and holds steady. There also seems to be a temperature component } to this in that the EPC will remain steady at < 100C but fluctuates } over 100 C. I have already installed a new mass flow controller, new } proportional valve, cleaned the split and septum purge lines, and } swapped out the solenoid for one from a working instrument. Any } additional suggestions will be appreciated. } rs Apparently this problem was caused by a bad injection port; it may be either due to bad seal between the injection port and the large column reducing nut, or some sort of problem with the weldment on the injection port itself. Anyway, after replacing every valve in the inlet system, as well as swapping out an entire EPC assembly with that from a different instrument, I decidied to replace the injection port. As suggested by Andy Yakuboff (THanks Andy!) there must have been some problem with the old shell as the pressure has behaved appropriately since then, and we are back to running samples. It is interesting to note that the instrument DID Pass a pressure test (Twice!)with the old shell, which confounded the troubleshooting prossess. Thanks again to Andy and everyone else who responded. rs ****************************************************************************** From: bizzwire Date: Tue, 08 Jun 2004 22:55:58 GMT Subject: Re: Excess Volume in Full Loop Injection Organization: * } From: jin } } hi, there, } } In the full loop injection of Thermo Finnigan Ion Trap, the total } volume of sample drawn by the syringe, according to the definition, } is: } } Total Volume = 3 x Injection Volume + Excess Volume } } What does this excess volume mean? } snip.............. } } What does this excess volume mean? } } } } } Why the values of Excess Volume in full loop and partial loop are } different? } } thanks so much!!! } } jin Go here for a detailed explanation: http://www.rheodyne.com/pdfs/tech_note_5.pdf This is done to ensure the best injection-to-injection reproducibility (i.e., precision) . The flow when filling the loop is not so much a "plug", but is rather a parabola. Material close to the inner wall of the loop moves much slower than in the center. Anyway, I am going to guess that this is a default setting which you can change (I don't have Excalibur to hand). If you're willing to trade quantitative precision for sample conservation (and let's face it: not many people use a trap for quantitation), then by all means, change this "Overfill factor" if you can. However, doesn't the sample volume specified in the sample list overide any other volume settings? ****************************************************************************** From: J T Hill Date: Wed, 09 Jun 2004 16:22:27 +0100 Subject: NCI List & Ion Trap Organization: * Helen Hello Two questions I would like to ask: 1. Does anyone have or know of a reference mass list for negative CI that extends down to 100-200 mass range? Heptacosa and PFK are not much use. We are getting goods results for the small molecule samples we run by NCI but they all want accurate mass on the molecular ion. If anyone has a table to hand perhaps they could somehow send me a copy, thanks. 2. On a different project, we are about to buy an automated LC-MS ion trap system for high sample throughput. We need to detect small molecules in complex biological mixtures using MS/MS techniques. We have evaluated the ion traps from both Thermo, Bruker, Agilent and Applied Bio for a Q-Trap. If anyone has any comments for this type of application and any preference for the type of systems to use I would appreciate them. This could be for either 3 dimensional or linear ion traps. Regards John Hill Chemistry Dept. Mass Spectrometry Facility University College London ****************************************************************************** From: Joerg Hau Date: Wed, 09 Jun 2004 21:13:22 +0200 Subject: Re: Software for Shimadzu and Waters Organization: * Hi All, On Saturday 05 June 2004 02:20, Bizzwire wrote: } why do you feel the need for "off-line" data analysis.? I can't answer that, but at my workplace we do most of our data processing as post-acquisition processing. I presume David is looking for some software that allows to manipulate the data from several different data systems elsewhere than just on the acquisition PCs (which are often located in a noisy lab). } What,exactly do you plan on doing? chramotgram/spectrum } manipulation and display? Quantitation? Indeed this would be nice to know ... and onb which platform. } MassLynx is pretty robust and I never had any problem doing any of } these things while acquiring. ... yet there are many things that ML cannot do. Try do print e.g. always the same few mass traces from a series of data files that were acquired in full-scan mode ... it has never (?) been possible in MassLynx. We've been requesting this "feature" for years, and the request has been ignored for quite the same time - so I can fully understand if David is looking for "something else". And, btw, he is not the only one ;-) } Additionally, it probably has a lot more firepower and is a lot } better arranged/more intuitive than any freeware you'll find. Uhm ... he spoke about Free Software, not freeware. Among others, "Free Software" means that the source code is available freely. This allows to fit the software to your needs, instead of limiting your "needs" to the capabilities of the software. } you can do a non-acquisition installation of the software, } don't you? (I'm pretty sure this won't violate any licensing } issues, but you should check with your sales-person) Uhm ... usually this _will_ violate the license. AFAIK you have to buy every single license from Waters, unless your salesperson has made a promise in a well-chosen moment ;-) @David: (1) There are a number of more-or-less free software packages around (for GCMS, AMDIS comes to mind) but their usefulness depends on what you need - so, what exactly are you looking for? (2) Most of these packages cannot read the native data formats directly, as the MS manufacturers seem to consider this a secret of defense. You will probably have to export the raw data to an intermediate format such as netCDF (ANDI-MS) and then read those. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: Dave White Date: Thu, 10 Jun 2004 15:17:21 GMT Subject: Re: Software for Shimadzu and Waters Organization: * "Joerg Hau" wrote in message news:ca7r6b$soc$1@news-int2.gatech.edu... } @David: (1) There are a number of more-or-less free software packages } around (for GCMS, AMDIS comes to mind) but their usefulness depends on } what you need - so, what exactly are you looking for? (2) Most of } these packages cannot read the native data formats directly, as the } MS manufacturers seem to consider this a secret of defense. You will } probably have to export the raw data to an intermediate format such } as netCDF (ANDI-MS) and then read those. } We have the ability to read a number of native data formats, including MassLynx, and can create solutions to meet just about any end users need. Not free, but very cost effective. Dave White SpectraChrom Software www.softwareformassspec.com info< AT >spectrachrom.com replace < AT > with @ for valid e-mail ****************************************************************************** From: Chip Cody Date: 10 Jun 2004 15:35:35 -0700 Subject: Re: NCI List Organization: * J T Hill wrote in message news:... } } 1. Does anyone have or know of a reference mass list for negative CI that } extends down to 100-200 mass range? Heptacosa and PFK are not much use. We } are getting goods results for the small molecule samples we run by NCI but } they all want accurate mass on the molecular ion. If anyone has a table to } hand perhaps they could somehow send me a copy, thanks. } As you point out, PFK does not produce abundant low-m/z ions in negative ion mode. For our work with the electron monochromator, I often add trace levels of hexafluorobenzene (C6F6-. at m/z 185.990418). The fragment [M-F]- (m/z 166.992015) appears at a different resonance energy than the M-., but you may see both with a conventional negative ion source. You may also consider adding a trace of nitrobenzene (C6H5NO2 at m/z 123.032029). However, be aware that nitrobenzene is "sticky" and hard to get rid of. Nitrobenzene also produces abundant NO2- at m/z 45.992904. Some people add chloroform or other small chlorocarbons for negative-ion calibration. For what it's worth, the exact masses for PFK negative ions are listed on our web site: http://www.jeol.com/ms/docs/PFKneg.html This includes several low-abundance peaks at low m/z, some of which are impurities (Cl or I) and therefore will not show up in all cases. Chip Cody (JEOL) ****************************************************************************** From: David Smith Date: Thu, 10 Jun 2004 20:06:42 -0500 Subject: Re: Excess Volume in Full Loop Injection Organization: * } SNIP: We are thinking about purchasing a trap ? Consequently your comment on "not many people use a trap for quantitation" is disturbing ??? please explain ?? D. } } quantitative precision for sample conservation (and let's face it: not many } people use a trap for quantitation), then by all means, change this } "Overfill factor" if you can. } } However, doesn't the sample volume specified in the sample list overide any } other volume settings? ****************************************************************************** From: David Smith Date: Thu, 10 Jun 2004 20:20:28 -0500 Subject: Mass spec courses ?? Organization: * Any one know of any good mass spec courses coming up that; (1) Go over more advanced concepts in GC-MS (2) Cover LC-MS (3) Are Agient inclined?? (Chemstation ) Thank you, D ****************************************************************************** From: Kendall Date: Fri, 11 Jun 2004 01:31:05 GMT Subject: Re: NCI List & Ion Trap Organization: * } 2. On a different project, we are about to buy an automated LC-MS ion trap } system for high sample throughput. We need to detect small molecules in } complex biological mixtures using MS/MS techniques. } We have evaluated the ion traps from both Thermo, Bruker, Agilent and } Applied Bio for a Q-Trap. If anyone has any comments for this type of } application and any preference for the type of systems to use I would } appreciate them. This could be for either 3 dimensional or linear ion traps. } } Regards } } John Hill } Chemistry Dept. } Mass Spectrometry Facility } University College London John- I can't answer your 1st question ... sorry. However, I have had hands on experience with both Agilent's trap and one of Thermo's older traps (LCQ Deca). Both are nice, and each have some features which are slightly better than the other. To be honest, I never really had any serious problems with either instrument. The major complaint I had with the LCQ Deca I used was the "up the kilt" spray design on the electrospray source - Thermo has since moved to off axis spraying with their newer line of ESI sources. I read a bit about Thermo's new linear trap and was pretty intrigued by it - apparently it's got a dual detector setup that effectively doubles your limit of detection. Also, from what I understand, the Agilent trap and the Bruker trap are basically the same machine. And the software packages for the Bruker and the Agilent are *exactly* the same. I've become quite familiar with the Bruker/Agilent acquisition and data analysis software and like it quite a bit. The data analysis package is a little intimidating at first (lots, and lots, and lots of buttons) but it is very flexible. I've never used an Applied trap - only their MALDIs and their (now discontinued) ESI-TOF (Mariner). Don't know if that helps or not - but there you go! -Kendall ****************************************************************************** From: David Sparkman Date: Fri, 11 Jun 2004 04:10:28 -0700 Subject: Re: Mass spec courses ?? Organization: * David, The ACS (http://www.acs.org/shortcourses) Mass Spectrometry/Chromatography: Principles and Practice" does all that and more. Various instrument manufacturers provide instruments for the course. You get the opportunity to see a lot of different LC-MS and GC-MS instruments. The course is in Stockton, CA at the University of the Pacific August 2 -- 6. A block of hotel rooms has been arranged participants. The course is limited to 24 people. This course has been taught for over 15 years. Go to the above site and download the brochure in PDF format. This is not an operators-training course for a specific instument; it is a cource that allows you to learn how to use both LC/MS and GC/MS. David Sparkman Consultant-At-Large "David Smith" wrote in message news:cab3h6$63u$1@news-int2.gatech.edu... } Any one know of any good mass spec courses coming up that; } } (1) Go over more advanced concepts in GC-MS } (2) Cover LC-MS } (3) Are Agient inclined?? (Chemstation ) } } Thank you, } D } } } ****************************************************************************** From: bizzwire Date: Fri, 11 Jun 2004 11:58:12 GMT Subject: Re: Excess Volume in Full Loop Injection Organization: * } From: David Smith } } We are thinking about purchasing a trap ? Consequently your comment on "not } many people use a trap for quantitation" is disturbing ??? please explain ?? } The current wisdom (which may no longer be true) is that a trap can only hold so many ions,. The number of ions trapped will depend on the ion flux and the filling time. If you use a fixed time for filling the trap, you can get space-charge effects when the ion flux is high (too many ions in the trap). If you use "automatic gain control," (which fills the trap with a pre-set number of ions) you get varying cycle time from scan to scan, leading to varying numbers of data points across a chromatographic peak. At least this used to be the case with the first generation of traps. Manufacturers claim that linear traps can hold many more ions which can mitigate this issue. Don't get me wrong: you *can* use a trap for quantitation, often with good results. However, the proof is in the pudding, and if you did a survey of labs doing serious quantitaion (bioanalytical CROs, for example), you would find that they use triple quadrupoles almost exclusively. ****************************************************************************** From: Chip Cody Date: 11 Jun 2004 13:58:36 -0700 Subject: Re: Mass spec courses ?? Organization: * I can always recommend the ACS course "Chromatography Principles and Practice". The course is held only once this year at University of the Pacific (Stockton, CA) on Aug. 2-6, 2004. I have sent several people to this course over the years. This is a classroom and laboratory class, with several different LC/MS and GC/MS systems available for hand-on experience. The instructors will keep you busy, but you'll get your money's worth... Chip Cody (JEOL) ****************************************************************************** From: Chip Cody Date: 11 Jun 2004 14:28:08 -0700 Subject: Re: Mass spec courses ?? Organization: * Here is the web link for the ACS course that I mentioned in my last posting: http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=education\professional\sccr20.html Chip Cody (JEOL) ****************************************************************************** From: leanne chen Date: Sat, 12 Jun 2004 08:57:05 -0700 (PDT) Subject: carry-over problem on GC/MS Organization: * Hi, All, We use GC/MS to determine gas Acetone. First, we heat the material (which have been soaked in Acetone and dried) for several minutes at 200C, then inject the gas into the GC. The problem is that we still can see the Acetone peak at second injection (room air, not sample). We have tried to pull and push the plunger in the syringe many times (>50 times) at a fume hood/different room before making room air injection. We have thought that to use different syringe for different sample, it would work for a few samples. How are about for a number of samples? Could anyone please give us advice on how to clean the syringe after injecting gas Acetone and make sure that there is no gas Acetone carry-over? Many thanks in advance. Leanne __________________________________ Do you Yahoo!? Friends. Fun. Try the all-new Yahoo! Messenger. http://messenger.yahoo.com/ ****************************************************************************** From: David Smith Date: Sat, 12 Jun 2004 16:06:56 -0500 Subject: Re: Excess Volume in Full Loop Injection Organization: * Can one merely think of "too high a flux" in essence as the same as the concept of saturating a detector ?? And if so merely dilute the system for quantitation. Additionally, (maybe someone might know this) at what percent of your "average" High energy dynode saturation concentration will the trap be aomprimized ??? Also why don't triple quads suffer a similar drawback ??? Presumably it could be imagined that the flux through a quad would also get so high as to space charge effects ?? Just a thought ?? Thankin you, D. bizzwire wrote: } The current wisdom (which may no longer be true) is that a trap can only } hold so many ions,. The number of ions trapped will depend on the ion flux } and the filling time. If you use a fixed time for filling the trap, you can } get space-charge effects when the ion flux is high (too many ions in the } trap). If you use "automatic gain control," (which fills the trap with a } pre-set number of ions) you get varying cycle time from scan to scan, } leading to varying numbers of data points across a chromatographic peak. } } At least this used to be the case with the first generation of traps. } Manufacturers claim that linear traps can hold many more ions which can } mitigate this issue. } } Don't get me wrong: you *can* use a trap for quantitation, often with good } results. However, the proof is in the pudding, and if you did a survey of } labs doing serious quantitaion (bioanalytical CROs, for example), you would } find that they use triple quadrupoles almost exclusively. ****************************************************************************** From: David Smith Date: Sat, 12 Jun 2004 16:11:06 -0500 Subject: Re: carry-over problem on GC/MS Organization: * It's quite possible that you are saturating your split lines and getting carry over in that manner. Possibly thay are partially blocked and need cleaning ?? D. leanne chen wrote: } Hi, All, } } We use GC/MS to determine gas Acetone. First, we heat } the material (which have been soaked in Acetone and } dried) for several minutes at 200C, then inject the } gas into the GC. The problem is that we still can see } the Acetone peak at second injection (room air, not } sample). We have tried to pull and push the plunger in } the syringe many times (>50 times) at a fume } hood/different room before making room air injection. } We have thought that to use different syringe for } different sample, it would work for a few samples. How } are about for a number of samples? Could anyone please } give us advice on how to clean the syringe after } injecting gas Acetone and make sure that there is no } gas Acetone carry-over? } } Many thanks in advance. } } Leanne } } } } __________________________________ } Do you Yahoo!? } Friends. Fun. Try the all-new Yahoo! Messenger. } http://messenger.yahoo.com/ ****************************************************************************** From: Dr. Dickie Date: Sun, 13 Jun 2004 05:22:09 -0400 Subject: Re: carry-over problem on GC/MS Organization: * On Sat, 12 Jun 2004 08:57:05 -0700 (PDT), leanne chen wrote: }Hi, All, } }We use GC/MS to determine gas Acetone. First, we heat }the material (which have been soaked in Acetone and }dried) for several minutes at 200C, then inject the }gas into the GC. The problem is that we still can see }the Acetone peak at second injection (room air, not }sample). We have tried to pull and push the plunger in }the syringe many times (>50 times) at a fume }hood/different room before making room air injection. }We have thought that to use different syringe for }different sample, it would work for a few samples. How }are about for a number of samples? Could anyone please }give us advice on how to clean the syringe after }injecting gas Acetone and make sure that there is no }gas Acetone carry-over? } }Many thanks in advance. } }Leanne } } } } }__________________________________ }Do you Yahoo!? }Friends. Fun. Try the all-new Yahoo! Messenger. }http://messenger.yahoo.com/ I would probably vote for saturated split lines, like David said; however, if you want to clean the syringe (and you should), what I have used that works is taking a vacuum filtration flask attached to vacuum source with a single hole rubber stopper. Into the hole in the stopper insert a needle that will fit the syringe (or simply make the hole the proper diameter so the syringe front just fits in the hole). After injection, and multiple solvent rinses, pull the plunger out of the syringe and insert it into the rubber stopper such that the vacuum pulls air through the syringe until next injection. I hope that is clear, it is difficult to explain, and simple to do and show. Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: bizzwire Date: Sun, 13 Jun 2004 14:22:17 GMT Subject: Re: Excess Volume in Full Loop Injection Organization: * } From: David Smith } } Can one merely think of "too high a flux" in essence as the same as the } concept of saturating a detector ?? And if so merely dilute the system for quantitation. Not the same concept, but the same result, anyway- a decrease linear range. } Additionally, (maybe someone might know this) at what percent of your } "average" High energy dynode saturation concentration will the trap be aomprimized ??? couldn't tell you. } Also why don't triple quads suffer a similar drawback ??? Presumably it could } be imagined that the flux through a quad would also get so high as to space } charge effects ?? Good question. which I leave it to my betters to address this- This has David Sparkman's name all over it. ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Sun, 13 Jun 2004 23:21:47 +0200 Subject: Re: carry-over problem on GC/MS Organization: * Leanne, to distiguish between a syringe and a GC problem, simply start a second run without injection. ;-) Rainer leanne chen schrieb: } } Hi, All, } } We use GC/MS to determine gas Acetone. First, we heat } the material (which have been soaked in Acetone and } dried) for several minutes at 200C, then inject the } gas into the GC. The problem is that we still can see } the Acetone peak at second injection (room air, not } sample). We have tried to pull and push the plunger in } the syringe many times (>50 times) at a fume } hood/different room before making room air injection. } We have thought that to use different syringe for } different sample, it would work for a few samples. How } are about for a number of samples? Could anyone please } give us advice on how to clean the syringe after } injecting gas Acetone and make sure that there is no } gas Acetone carry-over? } } Many thanks in advance. } } Leanne } } } } __________________________________ } Do you Yahoo!? } Friends. Fun. Try the all-new Yahoo! Messenger. } http://messenger.yahoo.com/ ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 15 Jun 2004 00:09:19 +0200 Subject: LCQ Deca XP Max Organization: * Hello All, someone sent me a question regarding problems with a Deca XP Max today but the mail got lost (I don´t know how). Please send again. Rainer ****************************************************************************** From: grober Date: Tue, 15 Jun 2004 00:42:06 +0100 Subject: Re: carry-over problem on GC/MS Organization: * Are you temperature programming the gc column. What type of column are you using - porous polymer plot?? Try a quick ramp up to column max between injections to flush the column out. Try baking out your syringe in an oven to clean it. You might have to use two and swap them! Is air water vapour mobilising acetone residue in injector/column on second injection? you dont say what the acetone concentration in your sample is and what concentration do you detect in the blank run?? A bit more info on your analytical conditions might help! "leanne chen" wrote in message news:cafqdi$oqp$1@news-int2.gatech.edu... } Hi, All, } } We use GC/MS to determine gas Acetone. First, we heat } the material (which have been soaked in Acetone and } dried) for several minutes at 200C, then inject the } gas into the GC. The problem is that we still can see } the Acetone peak at second injection (room air, not } sample). We have tried to pull and push the plunger in } the syringe many times (>50 times) at a fume } hood/different room before making room air injection. } We have thought that to use different syringe for } different sample, it would work for a few samples. How } are about for a number of samples? Could anyone please } give us advice on how to clean the syringe after } injecting gas Acetone and make sure that there is no } gas Acetone carry-over? } } Many thanks in advance. } } Leanne } } } } } __________________________________ } Do you Yahoo!? } Friends. Fun. Try the all-new Yahoo! Messenger. } http://messenger.yahoo.com/ } ****************************************************************************** From: Matt Rainsberg Date: 16 Jun 2004 08:25:54 -0700 Subject: Re: carry-over problem on GC/MS Organization: * If the syringe is dirty, Hamilton makes nifty syringe cleaning tool that has really helped in our lab. You can get it from Fisher at: https://www1.fishersci.com/Coupon?gid=183652&cid=1328 matt leanne chen wrote in message news:... } Hi, All, } } We use GC/MS to determine gas Acetone. First, we heat } the material (which have been soaked in Acetone and } dried) for several minutes at 200C, then inject the } gas into the GC. The problem is that we still can see } the Acetone peak at second injection (room air, not } sample). We have tried to pull and push the plunger in } the syringe many times (>50 times) at a fume } hood/different room before making room air injection. } We have thought that to use different syringe for } different sample, it would work for a few samples. How } are about for a number of samples? Could anyone please } give us advice on how to clean the syringe after } injecting gas Acetone and make sure that there is no } gas Acetone carry-over? } } Many thanks in advance. } } Leanne } } } } } __________________________________ } Do you Yahoo!? } Friends. Fun. Try the all-new Yahoo! Messenger. } http://messenger.yahoo.com/ ****************************************************************************** From: Martin Steel Date: Wed, 16 Jun 2004 15:29:25 +0000 (UTC) Subject: Mass specs and HPLC Organization: * Instrumentation - June 2004 USED SCIEX API 4000 Available in 2005 with ESI, APCI, Analyst data system. Register for pre-notification at http://www.mckscientific.com/4000.php Available: ThermoFinnigan DECA XP+ New in 2001, with ESI and APCI and Xcalibur software and Data System. Professionally de-installed by Thermo. Micromass Quattro-LC: Benchtop MS with Zspray API interface and both APCI and ESI sources. Computer and Masslynx software. 2 - 4000 Da. Neslab Recirculating chiller. Professionally de-installed and packed. Finnigan TSQ 7000: Triple Quadrupole with ESI and APCI, complete with upgraded API 2. This instrument has been meticulousy refurbished with many boards upgraded and replaced by Thermo. Short term rental available! Finnigan LCQ Classic: Classic Ion Trap mass spectrometer with ESI and high performance APCI, Xcalibur data system and software. Instrument is available with installation and warranty. Excellent MS/MS capability for any lab. Walk-Up Micromass LCT: LCT API-oa TOF with ES coaxial probe (ZLC-API2), APCI probe (ZLC-EP4), Harvard 22 basic microprocessor syringe, Neslab CFT-25D recirculating chiller, computer with OpenLynx Open Access software for LC/MS. Micromass Q-TOF Ultima: Global Hybrid Quadrupole/Orthogonal Time of Flight Mass Spectrometer with Megaflow-Z, Nanoflow-Z, Pico-tip. Year 2002 model. Excellent condition. HP 1100: configured with G1315A DAD, G1316A Column Heating , G1312A Binary pump, G1322A Degasser + computer and Chemstation. NEW CTC PAL HTS: New in the box, complete with fast wash station, 6 port valve and control terminal. Requires PAL TraySet or PAL Stack. Tecan Genesis 200/8: 8 tip with the RoMa Arm option, Gemini 4.0 software and data system. Miscellaneous 2 x Zymed ST5050 Immunostainers Peltier kit for PE 200 Autosampler New ThermoFinnigan Surveyor PDA Sciex Turboionspray source Spark Holland Endurance Autosampler Microtech UltraPLUS II HPLC Waters 996 HPLC System WANT TO BUY: Instrumentation. Please email us with your availability ---------------------------------------------------------------- Martin Steel Director, Global Trading McKinley Scientific 33-C Wilson Drive Sparta, NJ 07871, USA V: 973.579.4144 F: 973.579.4145 -- Posted via Mailgate.ORG Server - http://www.Mailgate.ORG ****************************************************************************** From: "Parees,David M." Date: Wed, 16 Jun 2004 11:56:25 -0400 Subject: Mass spectra of esoteric compounds Organization: * I am looking for reference EI spectra of the following two compounds: 1. F5S-O-O-SF5 (bis(pentafluorosulfur) peroxide) 2. XeF2 (xenon difluoride) I have a 1989 set of the Wiley books and I searched on the NIST site. It is possible that these compounds are among the hundreds of thousands added to Wiley since my old edition. If anyone can direct me to reference spectra for these compounds, or can provide ion lists and intensities (there sure isn't going to be much for XeF2!), I'd appreciate it. thanks, Dave Parees Air Products and Chemicals, Inc. 7201 Hamilton Blvd. Allentown, PA 18195 610-481-5794 + ****************************************************************************** From: David Sparkman Date: Wed, 16 Jun 2004 23:10:37 GMT Subject: Re: Excess Volume in Full Loop Injection Organization: * "Mass Spectrometry Forum: Space Charge in Mass Spectrometry" Kenneth L. Busch, Spectroscopy, vol. 19, no. 6, Jun 2004, 35-38. Good Luck!! -- O. David Sparkman Consultant-At-Large ods at compuserve dot com "bizzwire" wrote in message news:caj2ks$jt4$1@news-int.gatech.edu... } } } } From: David Smith } } } } Can one merely think of "too high a flux" in essence as the same as the } } concept of saturating a detector ?? And if so merely dilute the system for } quantitation. } } Not the same concept, but the same result, anyway- a decrease linear range. } } } Additionally, (maybe someone might know this) at what percent of your } } "average" High energy dynode saturation concentration will the trap be } aomprimized ??? } } couldn't tell you. } } } Also why don't triple quads suffer a similar drawback ??? Presumably it could } } be imagined that the flux through a quad would also get so high as to space } } charge effects ?? } } Good question. which I leave it to my betters to address this- This has } David Sparkman's name all over it. } } ****************************************************************************** From: David Sparkman Date: Fri, 18 Jun 2004 14:29:26 GMT Subject: AMDIS Ver 2.6 (May 2004) Organization: * AMDIS (Automated Mass spectral Deconvolution and Identification System) Version 2.6 (May 2004) is now available for download at http://chemdata.nist.gov/mass-spc/amdis/ or by selecting AMDIS Download Page at http://chemdata.nist.gov. Anyone currently using AMDIS should download this new version. If you are not already using AMDIS, you can download this program. It is available at no charge. The program can read most chromatography mass spectral data file formats. Regards David -- O. David Sparkman Consultant-At-Large odsatcompuservedotcom ****************************************************************************** From: Dr. Detlev Hochmuth Date: Fri, 18 Jun 2004 20:24:32 +0200 Subject: Essential Oils / Flavour database Organization: * Dear Sir/Madam, with regards to your recent news group inquiry, please allow us to draw your attention to our new GC/MS interpretation software and unique essential oil mass spectral library "Terpenoids and Related Constituents of Essential Oils". You may find further details at www.massfinder.com Please do not hesitate to contact me in case of any further questions. Best regards, Detlev Hochmuth --- Dr. Detlev Hochmuth Störtebekerweg 48 21149 Hamburg Germany hochmuth@web.de support@massfinder.com www.massfinder.com ****************************************************************************** From: Doug Stevens Date: 21 Jun 2004 20:22:01 -0700 Subject: Re: NCI List Organization: * I've had good luck calibrating for accurate mass measurement work in NCI using PFTBA with a dash of DCM added (just a wet needle) in as a low mass calibration point. I've actually got both points, for the 35Cl and 37Cl, in a reference file compatible with MassLynx if you're interested. The file is a simple tab delimited Notepad format and should be easily transfered to other platforms. I'm at home just now and so don't have it handy. Let me know if you'd like it forwarded. Regards, Doug Stevens Principal MS Applications Specialist Waters Corp. Chip Cody wrote in message news:... } J T Hill wrote in message news:... } } } } } 1. Does anyone have or know of a reference mass list for negative CI that } } extends down to 100-200 mass range? Heptacosa and PFK are not much use. We } } are getting goods results for the small molecule samples we run by NCI but } } they all want accurate mass on the molecular ion. If anyone has a table to } } hand perhaps they could somehow send me a copy, thanks. } } } } As you point out, PFK does not produce abundant low-m/z ions in } negative ion mode. For our work with the electron monochromator, I } often add trace levels of hexafluorobenzene (C6F6-. at m/z } 185.990418). The fragment [M-F]- (m/z 166.992015) appears at a } different resonance energy than the M-., but you may see both with a } conventional negative ion source. You may also consider adding a trace } of nitrobenzene (C6H5NO2 at m/z 123.032029). However, be aware that } nitrobenzene is "sticky" and hard to get rid of. Nitrobenzene also } produces abundant NO2- at m/z 45.992904. } } Some people add chloroform or other small chlorocarbons for } negative-ion calibration. } } For what it's worth, the exact masses for PFK negative ions are listed } on our web site: } } http://www.jeol.com/ms/docs/PFKneg.html } } This includes several low-abundance peaks at low m/z, some of which } are impurities (Cl or I) and therefore will not show up in all cases. } } Chip Cody (JEOL) ****************************************************************************** From: Doug Stevens Date: 21 Jun 2004 20:22:01 -0700 Subject: Re: NCI List Organization: * I've had good luck calibrating for accurate mass measurement work in NCI using PFTBA with a dash of DCM added (just a wet needle) in as a low mass calibration point. I've actually got both points, for the 35Cl and 37Cl, in a reference file compatible with MassLynx if you're interested. The file is a simple tab delimited Notepad format and should be easily transfered to other platforms. I'm at home just now and so don't have it handy. Let me know if you'd like it forwarded. Regards, Doug Stevens Principal MS Applications Specialist Waters Corp. Chip Cody wrote in message news:... } J T Hill wrote in message news:... } } } } } 1. Does anyone have or know of a reference mass list for negative CI that } } extends down to 100-200 mass range? Heptacosa and PFK are not much use. We } } are getting goods results for the small molecule samples we run by NCI but } } they all want accurate mass on the molecular ion. If anyone has a table to } } hand perhaps they could somehow send me a copy, thanks. } } } } As you point out, PFK does not produce abundant low-m/z ions in } negative ion mode. For our work with the electron monochromator, I } often add trace levels of hexafluorobenzene (C6F6-. at m/z } 185.990418). The fragment [M-F]- (m/z 166.992015) appears at a } different resonance energy than the M-., but you may see both with a } conventional negative ion source. You may also consider adding a trace } of nitrobenzene (C6H5NO2 at m/z 123.032029). However, be aware that } nitrobenzene is "sticky" and hard to get rid of. Nitrobenzene also } produces abundant NO2- at m/z 45.992904. } } Some people add chloroform or other small chlorocarbons for } negative-ion calibration. } } For what it's worth, the exact masses for PFK negative ions are listed } on our web site: } } http://www.jeol.com/ms/docs/PFKneg.html } } This includes several low-abundance peaks at low m/z, some of which } are impurities (Cl or I) and therefore will not show up in all cases. } } Chip Cody (JEOL) ****************************************************************************** From: Evil PockY Date: 22 Jun 2004 08:12:18 -0700 Subject: Where to sell lab equipment? Organization: * Hi people, I have a brand new Tecan Genesis 200 for sale, but I have no idea where to start. I thought about eBay, but it doesn't seem like the right place. Is there any website that's specialized in lab equipment trading? Any helpe would be greatly appreciated. PockY ****************************************************************************** From: Tom Crabtree Date: Tue, 22 Jun 2004 14:26:03 -0700 Subject: Re: Where to sell lab equipment? Organization: * http://www.labx.com TomC Evil PockY wrote: } Hi people, } } I have a brand new Tecan Genesis 200 for sale, but I have no idea } where to start. I thought about eBay, but it doesn't seem like the } right place. Is there any website that's specialized in lab equipment } trading? Any helpe would be greatly appreciated. } } PockY } ****************************************************************************** From: Evil PockY Date: 22 Jun 2004 19:15:08 -0700 Subject: Re: Where to sell lab equipment? Organization: * Cool, thanks! Tom Crabtree wrote in message news:... } http://www.labx.com } } TomC } } Evil PockY wrote: } } Hi people, } } } } I have a brand new Tecan Genesis 200 for sale, but I have no idea } } where to start. I thought about eBay, but it doesn't seem like the } } right place. Is there any website that's specialized in lab equipment } } trading? Any helpe would be greatly appreciated. } } } } PockY } } ****************************************************************************** From: Tom Crabtree Date: Tue, 22 Jun 2004 21:09:03 -0700 Subject: Re: Where to sell lab equipment? Organization: * You're quite welcome. TomC Evil PockY wrote: } Cool, thanks! } } Tom Crabtree wrote in message news:... } } http://www.labx.com } } } } TomC } } } } Evil PockY wrote: } } } Hi people, } } } } } } I have a brand new Tecan Genesis 200 for sale, but I have no idea } } } where to start. I thought about eBay, but it doesn't seem like the } } } right place. Is there any website that's specialized in lab equipment } } } trading? Any helpe would be greatly appreciated. } } } } } } PockY } } } } ****************************************************************************** From: jin Date: 23 Jun 2004 11:20:06 -0700 Subject: could anyone tell me the accuracy of the quantitation by ion trap Organization: * As title, thanks so much! jin ****************************************************************************** From: usedlabequip Date: 23 Jun 2004 14:22:06 -0700 Subject: Cohesive 2300 HTLC with CTC HTS Pal Organization: * Cohesive Technologies 2300 HTLC TurboFlow System complete with CTC Analytics HTS Pal with stack. $49,500.00. Please contact for further details regarding specifications, warranty, and installation. Labx.com Ad Number: 214818 Direct URL for picture: http://www.labx.com/aref.cfm?ad=214818 Cohesive system information from manufacturer: http://www.cohesivetech.com/liquidchromatography/turbo.shtml CTC Pal system information from manufacturer: http://www.ctc.ch/misc/HTSPAL.pdf Thank you! International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 sales@ietltd.com CK ****************************************************************************** From: David Stranz Date: Wed, 23 Jun 2004 22:33:54 -0500 Subject: Re: could anyone tell me the accuracy of the quantitation by ion Organization: * jin wrote in news:cbcins$nc1$1@news- int2.gatech.edu: } } As title, thanks so much! jin } The answer to your question, the way you asked it, is "No". Accuracy in any MS measurement on any instrument depends on the analyte, its matrix, the source, source conditions, inherent ionizability of the analyte, absolute concentration of the analyte and concentration relative to other species in the sample, interferences due to isobaric species, distribution of the analyte signal over multiple charge states and/or multiple adducts, quantity injected, and on and on. ****************************************************************************** From: Ludwig Gruber Date: Fri, 25 Jun 2004 10:07:38 +0200 Subject: Re: could anyone tell me the accuracy of the quantitation by ion Organization: * [ The following text is in the "ISO-8859-1" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] In our experience ion trap mass specs are not as reliable for quantitation as comparable quadrupole and double focussing instruments. This is mainly caused by mechanisms like AGC (automatic gain control), which is used to prevent space-charge effects in the trap . In general ion traps are more capable in the fields of identification (full scan), most of them you can use them for MS-MS or MS n experiments. But this is only a general experience. The reliability of quantitation is also influenced by a number of other factors, so you will need to consider the approbriate instrument for every single analytical method. Regards Ludwig Gruber ****************************************************************************** From: Carole Date: 29 Jun 2004 03:27:14 -0700 Subject: Re: AMDIS Ver 2.6 (May 2004) Organization: * I use AMDIS recently and I do not manage to make a comparison of spectra. The software stop in postanalyse: compare dated file. The processing window starts but remains blocked. The number of component is very higt (about 5000-6000) before threschold. Could we change that ? Do you know sofware which can comparate chromato/mass spectra ? Thanks Best rgds -------------------------------------------------------------------------------- ****************************************************************************** From: David Sparkman Date: Wed, 30 Jun 2004 13:42:06 GMT Subject: Re: AMDIS Ver 2.6 (May 2004) Organization: * Carole, I sent your post to the people at NIST. This was their reply: There are several things that you can do to reduce the problem. First of all you can look at only a portion of the file, but from the description of the data it is possible that the data file is too complex for simple analysis. To start with lower the sensitivity - set to very low - this will dramatically reduce the number of components. Check to see that you have the correct type of data file - if for example you are trying to process an ion trap file as if were a quadrapole you may get too many components. If you do truly have 6000+ components in the file, it may require a different approach to analysis. -- O. David Sparkman Consultant-At-Large odsatcompuservedotcom "Carole" wrote in message news:cbrr77$ase$1@news-int.gatech.edu... } I use AMDIS recently and I do not manage to make a comparison of } spectra. The software stop in postanalyse: compare dated file. The } processing window starts but remains blocked. } The number of component is very higt (about 5000-6000) before } threschold. Could we change that ? } Do you know sofware which can comparate chromato/mass spectra ? } Thanks } Best rgds } -------------------------------------------------------------------------- ------ } ****************************************************************************** From: Joerg Hau Date: Wed, 30 Jun 2004 22:44:11 +0200 Subject: Software to compare mass chromatograms & mass spectra (was: AMDIS Organization: * Hi, } Do you know sofware which can comparate chromato/mass spectra ? Taking your request literally - i.e. without any relation to AMDIS -, you may want to have a look at COMSPARI. It's a software that was written to facilitate the analysis of "paired" samples, i.e. samples that are "almost" identical yet present some subtle difference. Website: . COMSPARI is Free Software (not in the sense of "free beer", but "freedom to use and to modify"), published unter the GPL. Lit.: J. E. Katz, J. Hau, D. S. Dumlao, and S. Clarke: "A New Technique (COMSPARI) to Facilitate the Identification of Minor Compounds in Complex Mixtures by GC/MS and LC/MS: Tools for the Visualisation of Matched Datasets". J. Amer. Soc. Mass Spectrom. 15 (2004), 580-584. DOI: Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: duck Date: Wed, 30 Jun 2004 23:18:10 GMT Subject: ABI 140B Syringe Pump Seals Organization: * Anybody have an alternative supply source for the high pressure and low pressure seals for an ABI 140B pump with 10 mL syringes? They are no longer available from ABI or Bodman. Please reply to rmilberg@uiuc.edu Richard Milberg Univ. of Illinois SCS Mass Spec Lab Urbana, IL 217-333-2545 ****************************************************************************** From: duck Date: Wed, 30 Jun 2004 23:26:15 GMT Subject: Re: ABI 140B Syringe Pump Seals Organization: * I just discovered that Perkin Elmer still supplies some parts for the 140B as well as other older pumps. The seals are back-ordered until the end of August though. They have a down-loadedable pdf catalog: http://las.perkinelmer.com/content/download/LC.pdf Richard Milberg Unive. of Illinois ****************************************************************************** From: David Stranz Date: Wed, 30 Jun 2004 22:42:32 -0500 Subject: Re: ABI 140B Syringe Pump Seals Organization: * duck wrote in news:cbvn7f$kde$1@news-int.gatech.edu: } I just discovered that Perkin Elmer still supplies some parts } for the 140B as well as other older pumps. } } The seals are back-ordered until the end of August though. } } } They have a down-loadedable pdf catalog: } } http://las.perkinelmer.com/content/download/LC.pdf } } Richard Milberg } Unive. of Illinois } } duck? ****************************************************************************** From: Sue Date: 1 Jul 2004 10:36:22 -0700 Subject: Recent Experiences - Thermal Desorption Equipment Organization: * Needing to upgrade automated thermal desorption equipment. Application - air sampling from environmental chambers onto sorbent tubes, thermally desorbing volatile organics captured on tubes into Agilent GC/MS. Looking for comments on recent experience with thermal desorption equipment. Considering SIS Short-path, Gerstel, Dynatherm, Marks. If you were buying today, what would you purchase? Thanks for any input. ****************************************************************************** From: John Bartmess Date: Tue, 06 Jul 2004 10:58:29 -0400 Subject: Altered re-mailing of the newsgroup Organization: * For those of you who have been receiving this newsgroup in the semi-weekly remailings, there's going to be a trial alteration in how that's done. Due to a 10 day absence from the Net on my part, and to new software at the remailing site (U. of Tennessee), I'm setting things up so that every post that appears on the newsgroup gets remailed automatically to those subscribed to the remailing list, rather than my doing a compilation semi-weekly with a header, etc. You should thus be getting postiongs more quickly, but more of them. John Bartmess ****************************************************************************** From: bizzwire Date: Tue, 06 Jul 2004 22:19:59 GMT Subject: Re: Altered re-mailing of the newsgroup Organization: * I have neglected for too long to say this: Thanks, John!!! We all really appreciate the work you put into this group. } From: John Bartmess } Organization: * } Newsgroups: sci.techniques.mass-spec } Date: Tue, 06 Jul 2004 10:58:29 -0400 } Subject: Altered re-mailing of the newsgroup } } For those of you who have been receiving this newsgroup in the semi-weekly } remailings, there's going to be a trial alteration in how that's done. Due to } a 10 day absence from the Net on my part, and to new software at the remailing } site (U. of Tennessee), } I'm setting things up so that every post that appears on the newsgroup gets } remailed automatically to those subscribed to the remailing list, rather than } my doing a compilation semi-weekly with a header, etc. You should thus be } getting postiongs more } quickly, but more of them. } } John Bartmess } } ****************************************************************************** From: Paola Date: Thu, 8 Jul 2004 15:59:05 +0200 Subject: Lowering of total ion counting (ion trap MS) Organization: * Dear all, We use our ion trap instruments (Saturn 2000) quite intensively, analysing a sample each 30 mins in a semiauthomatic way in order to obtain semi-continuous data. Our goal is to verify the ability of the instruments to work as monitoring devices in non supervised areas (where no daily tuning is possible). The instruments experienced a progressive lowering of the RIC value (for example, RIC value decreased from 4900 to 2300 during a week period) and, consequently, data obtained by quantification of standard solutions resulted lower than expected. Is this due to the lack of tuning or could it be ascribed to other instrumental problems (ageing of filament or of electromultiplier)? Could you suggest a solution alternative to the instrumental tuning? Thank you very much for your kind help! Best Regards, Paola ****************************************************************************** From: Katya Tsaioun Date: Thu, 8 Jul 2004 12:31:47 -0400 Subject: Negative ionization Organization: * Hi, Could anyone please help me expand on the number of tricks we could add to our bag for not well ionizing compounds identification and quantification? Or even listing a few things would be helpful. We have an ABI Qtrap machine, a few months old. Thankfully, Katya ktsaioun@surfacelogix.com ****************************************************************************** From: David Sparkman Date: Thu, 08 Jul 2004 22:41:40 GMT Subject: Re: Lowering of total ion counting (ion trap MS) Organization: * Paola, I do not recall what is the meaning of RIC in the Saturn data system. I believe it is the total ion current for a given spectrum. If a chromatogram is displayed, the RIC is ion current for the spectrum that is the apex of the chromatographic base peak. I think what you are saying is that for the injection of a given amount of sample the signal strength is decreasing over time. This can happen because the multiplier is aging or the system is building a background that results in shorter ionization times for your analyte. Short of doing another tune be bring the instrument back to its original sensitivity (and this may not work if the cause is increasing contamination resulting in reduced ionization times) the best you can do is have a standard of a know concentration injected. Use the observed mass chromatographic peak area vs that for the same time to correct the result of your calibration curve. This technique is sometimes called the continuing calibration. This is not the best way to do quntitation, but it may help with your problem. -- O. David Sparkman Consultant-At-Large ods-at-compuserve-dot-com "Paola" wrote in message news:ccjkgd$9re$1@news-int.gatech.edu... } Dear all, } We use our ion trap instruments (Saturn 2000) quite intensively, analysing } a sample each 30 mins in a semiauthomatic way in order to obtain } semi-continuous data. Our goal is to verify the ability of the instruments } to work as monitoring devices in non supervised areas (where no daily tuning } is possible). The instruments experienced a progressive lowering of the RIC } value (for example, RIC value decreased from 4900 to 2300 during a week } period) and, consequently, data obtained by quantification of standard } solutions resulted lower than expected. } Is this due to the lack of tuning or could it be ascribed to other } instrumental problems (ageing of filament or of electromultiplier)? } Could you suggest a solution alternative to the instrumental tuning? } Thank you very much for your kind help! } Best Regards, } Paola } } } ****************************************************************************** From: carl braybrook Date: 8 Jul 2004 23:47:37 -0700 Subject: Schematics Organization: * Hi has anyone got some copies of schematics for a Kratos Kompact MALDI tof. Thanks Carl ****************************************************************************** From: Jeff Gambera Date: Sat, 10 Jul 2004 01:16:59 GMT Subject: mass-ent software Organization: * Hello: Our organization recently had donated to us a Quattro II with electrospray/APCI running mass-lynx 3.3 Does anyone out there have a copy of Mass-Ent 1 or Mass-Ent 3 or protein lynx that will run under this older version of the software? Thanks Bill H. (415) 884-0221 ****************************************************************************** From: bizzwire Date: Sat, 10 Jul 2004 12:44:06 GMT Subject: Re: mass-ent software Organization: * } From: Jeff Gambera } Hello: } Our organization recently had donated to us a Quattro II with } electrospray/APCI running mass-lynx 3.3 } Does anyone out there have a copy of Mass-Ent 1 or Mass-Ent 3 or protein } lynx that will run under this older version of the software? } Thanks Don't want to rain on your parade, but it may not be as simple as this. Besides the issue of copyright infringement, MaxEnt has an added wrinkle to it. In order to run MaxEnt, you must first install the "Transform" option. This additional software carries with it a license to use the deconvolution algorithm owned by (I believe) by Fenn and/or Whitehouse. MaxEnt cannot be loaded/run without the transform option. The proper (and legal) thing to do would be to purchase both options from Waters. Also, a word of warning- the results you get from MaxEnt are very dependent on the quality of the raw data and the program parameter settings. Read the program documentation to ensure you are using it properly or else you run the risk of generating very real-looking artefacts. There may be aternative freeware/shareware options out there. I'm sure that others on this board can point them out (I'd be interested in learning of other programs myself) Bizz ****************************************************************************** From: Martin Steel Date: Mon, 12 Jul 2004 20:42:12 +0000 (UTC) Subject: Mass Specs and more Organization: * McKinley Scientific Instrumentation - July 2004 Micromass Q-TOF Ultima: Global Hybrid Quadrupole/Orthogonal Time of Flight Mass Spectrometer with Megaflow-Z, Nanoflow-Z, Pico-tip. Originally purchased in 2002 Micromass Quattro-LC: Benchtop MS with Zspray API interface and both APCI and ESI sources. Computer and Masslynx software. 2 - 4000 Da. Neslab Recirculating chiller. Professionally de-installed and packed. Walk-Up Micromass LCT: LCT API-oa TOF with ES coaxial probe (ZLC-API2), APCI probe (ZLC-EP4), Harvard 22 basic microprocessor syringe, Neslab CFT-25D recirculating chiller, computer with OpenLynx Open Access software for LC/MS. ThermoFinnigan DECA XP+: New in 2001, with ESI and APCI and Xcalibur software and Data System. Professionally de- installed by Thermo. Latest Technology Ion Trap from Thermo. Finnigan LCQ Classic: Classic Ion Trap mass spectrometer with ESI and high performance APCI, Xcalibur data system and software. Instrument is available with installation and warranty. Excellent MS/MS capability for any lab. Finnigan TSQ 7000: Triple Quadrupole with ESI and APCI, complete with upgraded API 2. This instrument has been meticulousy refurbished with many boards upgraded and replaced by Thermo. Short term rental available! Excellent value for a triple quad. Tecan Genesis 200/8: 8 tip with the RoMa Arm option, Gemini 4.0 software and data system. This unit is in excellent physical and cosmetic condition. CyberLab C240PC: 2001 Gilson Cyberlab C240 Protein Crystallization Robotic Workstation, compete with Gripper, Flipper, 96 and 8 Channel, Computer and software. Waters Alliance 2965: complete Waters Alliance 2695 with 2996 Photo Diode Array, Column heater and Empower software and computer. Miscellaneous: New ThermoFinnigan Surveyor PDA Spark Holland Endurance Autosampler Zymed ST5050 Immunostainer Peltier kit for PE 200 Autosampler Microtech UltraPLUS II HPLC Waters 996 Photodiode Array Detector Waters 717 Plus Autosampler ThermoQuest Trace 2000 GC Waters 486 Tunable Absorbance Detector New CTC PAL HTS Wanterd: Surplus instrumentation! Please email us with anything you have available. Contact: info@mckscientific.com To unsubscribe, send a blank email to remove@mckscientific.com Copyright © 2004 McKinley Scientific, LLC - All Rights Reserved -- Posted via Mailgate.ORG Server - http://www.Mailgate.ORG ****************************************************************************** From: Paola Date: Tue, 13 Jul 2004 10:20:07 +0200 Subject: Re: Lowering of total ion counting (ion trap MS) Organization: * Dear David, your answer to my question was of great help. I think the background increasing could be the explanation of the signal lowering. We are now implementing a method to "clean" the trap between analysys by using pure helium. I hope it will work; the continuous calibration method seems a bit to complex to be used in a system which must be located in non supervised areas. Thank you very much for your help! Best regards, Paola "David Sparkman" ha scritto nel messaggio news:ccm3np$6fb$1@news-int.gatech.edu... } Paola, } } I do not recall what is the meaning of RIC in the Saturn data system. I } believe it is the total ion current for a given spectrum. If a chromatogram } is displayed, the RIC is ion current for the spectrum that is the apex of } the chromatographic base peak. } } I think what you are saying is that for the injection of a given amount of } sample the signal strength is decreasing over time. This can happen because } the multiplier is aging or the system is building a background that results } in shorter ionization times for your analyte. } } Short of doing another tune be bring the instrument back to its original } sensitivity (and this may not work if the cause is increasing contamination } resulting in reduced ionization times) the best you can do is have a } standard of a know concentration injected. Use the observed mass } chromatographic peak area vs that for the same time to correct the result of } your calibration curve. This technique is sometimes called the continuing } calibration. This is not the best way to do quntitation, but it may help } with your problem. } } } -- } O. David Sparkman } Consultant-At-Large } ods-at-compuserve-dot-com } "Paola" wrote in message } news:ccjkgd$9re$1@news-int.gatech.edu... } } Dear all, } } We use our ion trap instruments (Saturn 2000) quite intensively, } analysing } } a sample each 30 mins in a semiauthomatic way in order to obtain } } semi-continuous data. Our goal is to verify the ability of the instruments } } to work as monitoring devices in non supervised areas (where no daily } tuning } } is possible). The instruments experienced a progressive lowering of the } RIC } } value (for example, RIC value decreased from 4900 to 2300 during a week } } period) and, consequently, data obtained by quantification of standard } } solutions resulted lower than expected. } } Is this due to the lack of tuning or could it be ascribed to other } } instrumental problems (ageing of filament or of electromultiplier)? } } Could you suggest a solution alternative to the instrumental tuning? } } Thank you very much for your kind help! } } Best Regards, } } Paola } } } } } } } } } ****************************************************************************** From: usedlabequip Date: 16 Jul 2004 13:24:54 -0700 Subject: Refurbished Analytical Instruments Available Organization: * !!!!FOR SALE!!!! 1. Applied BioSystems Prism 7900HT Real Time PCR 2. PerSeptive-ABI Mariner (ESI-TOF) Biospectrometry Workstation 3.) Cohesive Technologies model turboflow 2300 HTLC/HPLC system complete with HP 1100 # G1322A Degasser, # G1311A Quat. Pump, & # G1312 Binary Pump 4.) Perspective BioSystems VOYAGER-DE STR MALDI-TOF. 5.) Hewlett Packard 1100 isocratic pumps 6.) Micromass Q-TOF II 7.) Thermo Finnigan TSQ 7000 with API II LC/MS/MS 8.) Thermo Finnigan LCQ Classic LC/MS/MS 9.) Micromass ZMD 2000 LC/MS 10.) Micromass Quattro Ultima LC/MS/MS 11.) Varian Unity Inova 300 MHz NMR 12.) Varian Mercury MVX 300 MHz NMR 13.) Bruker AC300 MHz Plus NMR 14.) Varian Unity Plus 400 MHz NMR 15.) Varian Unity 500 MHz NMR 16.) Bruker Avance 500 MHz LC/NMR 17.) Varian Inova 600 MHz LC/NMR 18.) Bruker Avance 700 MHz NMR 19.) Genomics Solutions GeneTAC Hybstation 20.) Beckman Coulter LS200 21.) Neslab Chiller 22.) Bruker MicroCryoProbe 500 with chiller *Please call for further details. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 ****************************************************************************** From: Agn?s Date: 20 Jul 2004 01:33:31 -0700 Subject: Re: AMDIS Ver 2.6 (May 2004) Organization: * Recently using AMDIS 32 to compare some chromato/mass spectra, I manage neither to print the list of retention times (and the information list) nor to export it to a spreadsheet such as EXCEL (or to any other file that could be printed). Do you know a way to do that? Thanks. Best regards ****************************************************************************** From: David Sparkman Date: Tue, 20 Jul 2004 14:54:19 GMT Subject: Re: AMDIS Ver 2.6 (May 2004) Organization: * Angus, I do not understand your question. AMDIS prints RT of target compound matches. Please explain what you are trying to do. Are you using a target compound library? Are you trying to get a list of RTs for all components, regardless of whether or not they represent target compounds? Regards; David -- O. David Sparkman Consultant-At-Large ods @ compuserve.com "Agn?s" wrote in message news:cdj9je$sro$1@news-int2.gatech.edu... } Recently using AMDIS 32 to compare some chromato/mass spectra, I } manage neither to print the list of retention times (and the } information list) nor to export it to a spreadsheet such as EXCEL (or } to any other file that could be printed). } } Do you know a way to do that? } } Thanks. Best regards } ****************************************************************************** From: Carole Date: 21 Jul 2004 00:24:17 -0700 Subject: Re: AMDIS Ver 2.6 (May 2004) Organization: * Dear, I'm working with Agnes and we are trying to get a list of RTs for components which are unique/signifiant. When we compare too chromat we would like to extract only the different peaks between them and their RTs. We find that if we do "save component MS" we can open the file under "bloc note" and can read the file RTs but it's not really easy because of the format of the bloc note, excel should be better. Do you know a way to do that ? Thanks for your help. Rgds. ****************************************************************************** From: Reinhard Stroh Date: Mon, 26 Jul 2004 13:29:07 +0200 Subject: Re: Sciex Analyst 1.4 software Organization: * Jimmy wrote: } We use Analyst 1.3 and consider to upgrade to Analyst 1.4. } } Does anyone out there have any good or bad experiences with the } Analyst 1.4 software for SCIEX MS instruments? } } Thanks in advance! } } Jimmy } Do not upgrade. Analyst 1.4 is veeeeeery slow. regards Reinhard Stroh ****************************************************************************** From: Greg Byam Date: 26 Jul 2004 14:07:34 -0700 Subject: Analytical Laboratory Exposition -- Virtual Seminars Organization: * There's an upcoming virtual seminar on Chromatography, Spectroscopy and Microscopy technologies and applications. It will feature several highly regarded keynote speakers on October 27 & 27. You can interact via business card exchange, instant messaging, etc...It's like being at an exhibition or conference. Here's the url of the registration page: http://www.laboratoryequipment.com/scripts/analyticalLabExpo.asp ****************************************************************************** From: Kenneth H.N. Chan Date: Tue, 27 Jul 2004 14:45:49 -0400 Subject: MCP for QStar Organization: * Hello ionizers, Has anyone try to replace the MCP on their QStar? If not does anyone know the size of the MCPs? We would like to order it before we break vacuum... KC ****************************************************************************** From: Matthias Heinemann Date: 28 Jul 2004 00:11:06 -0700 Subject: Detection of amoles? Organization: * Dear all, I am looking for an instrument/device which is capable of detecting (and quantification) of amole quantities. Is there any technique/system capable of doing this? Any hints are greatly appreciated! Best regards, Matthias ****************************************************************************** From: David Smith Date: 28 Jul 2004 07:05:17 -0700 Subject: Finding Contamination sources (Coomassie?) Organization: * I'm an intern in a mollecular biology lab for the summer. I'm running MALDI-TOF MS on trypsinized proteins from Coomassie stained bands. The bands were washed with 50%ACN,25mM ammonium bicarbonate until almost all blue was gone. I extracted w/ 50% ACN,0.1% TFA. The matrix I'm using is alpha-cyano matrix. I have repeatedly seen a very strong peak at 855. I have been unable to identify this peak as keratin or trypsin. Is it Coomassie? The proteins are extracted from Arabidopsis, are there any likely culprits that someone can point me to. Thanks, David Smith ****************************************************************************** From: Joerg Hau Date: Wed, 28 Jul 2004 22:32:41 +0200 Subject: Re: Detection of amoles? Organization: * Hi } I am looking for an instrument/device which is capable of detecting } (and quantification) of amole quantities. Is there any } technique/system capable of doing this? Sure. Any recent mass spectrometer can do this. The count of ions that arrive at the detector may correspond to even lower amounts, but this still fulfills your requirement of "detecting amol quantities" ;-) More seriously, it might eventually turn out to be be useful if you would tell us *what* you want to detect, and certainly *where* (or "in what") you want to do this. Are you looking for a pesticide residue in water, or is it more like metabolites in a whole organism? Reproducible and accurate detection of minute amounts has very few to do with a particular mass spectrometer. It's more about classical analytical chemistry - think sampling, cleanup, enrichment. And _please_ do not forget the reproducibility of the overall process. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: David McLeod Date: Thu, 29 Jul 2004 09:48:58 -0400 Subject: Re: Finding Contamination sources (Coomassie?) Organization: * David Smith wrote: } I'm an intern in a mollecular biology lab for the summer. I'm running } MALDI-TOF MS on trypsinized proteins from Coomassie stained bands. } The bands were washed with 50%ACN,25mM ammonium bicarbonate until } almost all blue was gone. I extracted w/ 50% ACN,0.1% TFA. The matrix } I'm using is alpha-cyano matrix. } } I have repeatedly seen a very strong peak at 855. I have been unable } to identify this peak as keratin or trypsin. Is it Coomassie? The } proteins are extracted from Arabidopsis, are there any likely culprits } that someone can point me to. } } Thanks, } David Smith } David If you are using alpha cyano as your matrix then a m/z of 855.0720 corresponds to a trimer of alpha. Try adding 1-10mM of ammonium citrate to your matrix prep to reduce the intensity of multimeric forms of the alpha matrix Regards Dave McLeod ****************************************************************************** From: Brian Arbogast Date: Thu, 29 Jul 2004 09:15:39 -0700 Subject: Kratos MS-50TC Organization: * We're taking apart and sending to surplus our MS50 in a couple weeks. If on the slight chance anyone would be interested in parts, power supplies, sources, circuit boards, etc., let me know. Brian Arbogast Oregon State University Anyone besides us still have a working MS50??? ****************************************************************************** From: irojdest@hotmail.com Date: 1 Aug 2004 00:46:35 -0700 Subject: A newbie question regarding TIMS technique Organization: * Hello. We have received the results of analysis of our sample with ThermoFinnigan MAT262 spectrometer by another lab. In the course of analysis the lab did panoramics spectrum. The samples in the form of 200 mkm thick foil strips were placed directly onto the heating filament and then heated with short "pulses" to investigate only the surface layer about 1 mkm thick. When we asked around, however, people from other labs using MAT262 said that such experimental routine is inadequate, and normally the sample should be chemically dissolved and analysed afterwards. My questions are: 1)Does anyone use the same direct sample heating technique? 2) What are potential problems in direct heating? Thanks in advance Sincerely, Igor ****************************************************************************** From: Matthias Heinemann Date: 1 Aug 2004 23:06:18 -0700 Subject: Re: Detection of amoles? Organization: * Hi Joerg! The sample (a few 100 femtolitres) will contain ions (K+, Cl-, Ca2+ ..) and the molecules to quantify are metabolites. We will only have roughly 100.000 molecules of each metabolite. The error in quantification should be less than 5% and Replicates won't be possible. Is there still a chance to do this? Best regards, Matthias Joerg Hau wrote in message news:... } Hi } } } I am looking for an instrument/device which is capable of detecting } } (and quantification) of amole quantities. Is there any } } technique/system capable of doing this? } } Sure. Any recent mass spectrometer can do this. The count of ions that } arrive at the detector may correspond to even lower amounts, but this } still fulfills your requirement of "detecting amol quantities" ;-) } } More seriously, it might eventually turn out to be be useful if you } would tell us *what* you want to detect, and certainly *where* (or } "in what") you want to do this. Are you looking for a pesticide } residue in water, or is it more like metabolites in a whole organism? } } Reproducible and accurate detection of minute amounts has very few to } do with a particular mass spectrometer. It's more about classical } analytical chemistry - think sampling, cleanup, enrichment. And } _please_ do not forget the reproducibility of the overall process. } } Cheers + HTH, } } - Joerg ****************************************************************************** From: JC Date: 2 Aug 2004 03:23:13 -0700 Subject: Re: Sciex Analyst 1.4 software Organization: * Reinhard Stroh wrote in message news:... } Jimmy wrote: } } We use Analyst 1.3 and consider to upgrade to Analyst 1.4. } } } } Does anyone out there have any good or bad experiences with the } } Analyst 1.4 software for SCIEX MS instruments? } } } } Thanks in advance! } } } } Jimmy } } } Do not upgrade. } Analyst 1.4 is veeeeeery slow. } regards } Reinhard Stroh Hi Reinhard, Oh Thanks !! By the way, what's the configuration of your PC ? Since I'd like to change my PC. One of the offers included the upgrade of Analyst. Since they can't find WinNT anymore, and the only option is Win 2000 !! JC ****************************************************************************** From: JC Date: 2 Aug 2004 03:33:29 -0700 Subject: Re: Detection of amoles? Organization: * Joerg Hau wrote in message news:... } Hi } } } I am looking for an instrument/device which is capable of detecting } } (and quantification) of amole quantities. Is there any } } technique/system capable of doing this? } } Sure. Any recent mass spectrometer can do this. The count of ions that } arrive at the detector may correspond to even lower amounts, but this } still fulfills your requirement of "detecting amol quantities" ;-) } } More seriously, it might eventually turn out to be be useful if you } would tell us *what* you want to detect, and certainly *where* (or } "in what") you want to do this. Are you looking for a pesticide } residue in water, or is it more like metabolites in a whole organism? } } Reproducible and accurate detection of minute amounts has very few to } do with a particular mass spectrometer. It's more about classical } analytical chemistry - think sampling, cleanup, enrichment. And } _please_ do not forget the reproducibility of the overall process. } } Cheers + HTH, } } - Joerg Hey Joerg, It's hard to say that the MS can do amole level or not. Since most of the recent MS can have such level of detection. But the sensitivity should be defined on what compound you are going to detect. E.g. A MS can detect amole of reserpine which does not mean the MS can detect amole level of your compounds. The best way is to prepare samples of your compounds in your amole level and send to the suppliers. Remember, the results of your compounds is the best indicator ! JC ****************************************************************************** From: Joerg Hau Date: Mon, 02 Aug 2004 20:25:13 +0200 Subject: Re: Detection of amoles? Organization: * Hi Matthias, } The sample (a few 100 femtolitres) will contain ions (K+, Cl-, Ca2+ } ..) and the molecules to quantify are metabolites. We will only have } roughly 100.000 molecules of each metabolite. Thanks for this additional information. } The error in quantification should be less than 5% So that's quantifying 100'000 molecules with 5% accuracy. In general, working at the trace level, you can estimate yourself happy if you reach 20% ... yet in theory (!) your 5% should be possible. If I remember correctly from my lessons in micro- and trace analysis, "for statistical reasons" you need 10'000 detected molecules to achieve about 1% accuracy. In other words, you need about 10% of your minuscule sample well ionised, and just in front of the detector. Using MS, the problem is now that you need to get at least 10% of the molecules (a) ionised and (b) to the detector. Conventional MS have transmission rates (= the fraction of ions that gets trough from source to detector) of about 1E-5, if you are lucky perhaps 1E-4. This means that only 10...100 out of the 100'000 molecules will make it to the detector. (btw, anyone here with transmission data for recent traps and ToF instruments ?). This is just numbers yet, not counting any losses during sample preparation, handling etc., which can account for quite some loss: just shaking an Eppendorf vial that contains your sample may mean that all molecules are gone, absorbed to the wall :-( } and Replicates won't be possible Oops. Here's a real problem. Serious quantitative work requires that you do replicates. If you cannot do a sufficient number of replicates, you have no statistics. If you do not have statistics, no serious journal will (... should?) accept the data. Can't you use another, maybe non-destructive technique? Fluorescence, dye labelling, whatever ... ? Best regards & HTH,   - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply ****************************************************************************** From: Matthias Heinemann Date: 3 Aug 2004 08:12:42 -0700 Subject: Re: Detection of amoles? Organization: * Hi Joerg, thanks a lot for your detailed answer. My last question: Would an FTICR-MS be of any help in that problem? Thanks a lot in advance! Matthias Joerg Hau wrote in message news:... } Hi Matthias, } } } The sample (a few 100 femtolitres) will contain ions (K+, Cl-, Ca2+ } } ..) and the molecules to quantify are metabolites. We will only have } } roughly 100.000 molecules of each metabolite. } } Thanks for this additional information. } } } The error in quantification should be less than 5% } } So that's quantifying 100'000 molecules with 5% accuracy. } } In general, working at the trace level, you can estimate yourself } happy if you reach 20% ... yet in theory (!) your 5% should be } possible. If I remember correctly from my lessons in micro- and trace } analysis, "for statistical reasons" you need 10'000 detected } molecules to achieve about 1% accuracy. } } In other words, you need about 10% of your minuscule sample well } ionised, and just in front of the detector. } } Using MS, the problem is now that you need to get at least 10% of the } molecules (a) ionised and (b) to the detector. Conventional MS have } transmission rates (= the fraction of ions that gets trough from } source to detector) of about 1E-5, if you are lucky perhaps 1E-4. } This means that only 10...100 out of the 100'000 molecules will make } it to the detector. (btw, anyone here with transmission data for } recent traps and ToF instruments ?). } } This is just numbers yet, not counting any losses during sample } preparation, handling etc., which can account for quite some loss: } just shaking an Eppendorf vial that contains your sample may mean } that all molecules are gone, absorbed to the wall :-( } } } and Replicates won't be possible } } Oops. Here's a real problem. } } Serious quantitative work requires that you do replicates. If you } cannot do a sufficient number of replicates, you have no statistics. } If you do not have statistics, no serious journal will (... should?) } accept the data. } } Can't you use another, maybe non-destructive technique? Fluorescence, } dye labelling, whatever ... ? } } Best regards & HTH, }   } - Joerg ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 03 Aug 2004 22:44:28 +0200 Subject: Re: Detection of amoles? Organization: * Hi Matthias, FTICR-MS gives you high resolution (=specific) data, but not the real sensitivity. A linear Ion Trap has a higher sensitivity due to the fact, that nearly all ions trapped will be detected. Another thing Joerg did not mention are effects from the presence of ions forming adducts and reducing the total number of unique ions of the same mass. What about other compounds in the matrix? No solvent is 100 % clean ;-) Best regards Rainer Loerwald ThermoElectron Corp. Germany Matthias Heinemann schrieb: } } Hi Joerg, } } thanks a lot for your detailed answer. } } My last question: Would an FTICR-MS be of any help in that problem? } } Thanks a lot in advance! } Matthias } } Joerg Hau wrote in message news:... } } Hi Matthias, } } } } } The sample (a few 100 femtolitres) will contain ions (K+, Cl-, Ca2+ } } } ..) and the molecules to quantify are metabolites. We will only have } } } roughly 100.000 molecules of each metabolite. } } } } Thanks for this additional information. } } } } } The error in quantification should be less than 5% } } } } So that's quantifying 100'000 molecules with 5% accuracy. } } } } In general, working at the trace level, you can estimate yourself } } happy if you reach 20% ... yet in theory (!) your 5% should be } } possible. If I remember correctly from my lessons in micro- and trace } } analysis, "for statistical reasons" you need 10'000 detected } } molecules to achieve about 1% accuracy. } } } } In other words, you need about 10% of your minuscule sample well } } ionised, and just in front of the detector. } } } } Using MS, the problem is now that you need to get at least 10% of the } } molecules (a) ionised and (b) to the detector. Conventional MS have } } transmission rates (= the fraction of ions that gets trough from } } source to detector) of about 1E-5, if you are lucky perhaps 1E-4. } } This means that only 10...100 out of the 100'000 molecules will make } } it to the detector. (btw, anyone here with transmission data for } } recent traps and ToF instruments ?). } } } } This is just numbers yet, not counting any losses during sample } } preparation, handling etc., which can account for quite some loss: } } just shaking an Eppendorf vial that contains your sample may mean } } that all molecules are gone, absorbed to the wall :-( } } } } } and Replicates won't be possible } } } } Oops. Here's a real problem. } } } } Serious quantitative work requires that you do replicates. If you } } cannot do a sufficient number of replicates, you have no statistics. } } If you do not have statistics, no serious journal will (... should?) } } accept the data. } } } } Can't you use another, maybe non-destructive technique? Fluorescence, } } dye labelling, whatever ... ? } } } } Best regards & HTH, } } } } - Joerg ****************************************************************************** From: bizzwire Date: Tue, 03 Aug 2004 21:25:02 GMT Subject: Re: Detection of amoles? Organization: * }Matthias Heinemann } } Hi Joerg, } } thanks a lot for your detailed answer. } } My last question: Would an FTICR-MS be of any help in that problem? High mass accuracy does not automatically equate to high sensitivity. Most (if not all) of the sampling inefficiencies described by Joerg happen at the front of the machine, so putting a trap in the back won't help. True, you can collect ions over an extended period of time, but you could also do this in a regular ion trap instrument. This will help your detection limits, but it will bite you in the ass if you're thinking of doing any sort of chromatographic separation- it's hard to collect ions for a minute or two when your peak width is six seconds. ****************************************************************************** From: Joy Flash Date: 4 Aug 2004 08:57:49 -0700 Subject: Anybody know MALDI-TOF, bruker? Organization: * One of my friend uses it and want to know if any third-party software can analysis its output file? Any ideas? Deeply appreciate! ****************************************************************************** From: Joerg Hau Date: Thu, 05 Aug 2004 18:34:14 +0200 Subject: Bruker MALDI-ToF data format, was: Anybody know MALDI-TOF, bruker? Organization: * Hi [ Bruker MALDI-ToF ] } any third-party software can analysis its output file? What do you mean by "analyse its output file" ? If you need a way to read the raw data file - so that you can process its content with something else -, I recommend to ask Bruker support for the data format. They are usually pretty helpful; as long as your goal is not the development of a concurrent software product, I dare to say that your chances of getting this information are fair. Once you have the description of the data format, a decent programmer can write the necessary software to access the file contents within a day. Almost all of the XMASS format is pretty straightforward (except for the calibration ;-). Cheers + HTH, - Joerg PS. No, I cannot share it. Ask Bruker, please. -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". ****************************************************************************** From: Mike Sherrell Date: Fri, 6 Aug 2004 07:43:53 -0700 Subject: Grizzly Analytical Mass Specs, MALDIs, etc. available Organization: * **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000: $150,000 installed/warranteed. Sciex API 3000: $190,000 W/ upgrade to ~ API 4000 sensitivity and S/N. API 3000 upgrade: $38,500. Increases sensitivity and (S/N) Ratio at high flow rates to ~ that of an API 4000. Install incl. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $120,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase; incl. install, warr. Sciex API 365: $65,000. NT, turboionspray. Installed, warranteed. Sciex 365 w/ EP10+: $149,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Hitachi M 8000: $82,000. Ion trap. 1999; excellent condition; incl. LC. Micromass Quattro Micro: $135,000. Call/email for details. License not incl. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro LCZ: $131,500. Includes installation, warranty. Micromass Quattro IIZ: $149,000. Z-Spray. Includes install, warranty. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $60,000. European install included; available in US. MM Autospec V: $70,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Voyager Elite XL: offers considered. incl. Vestec Multi-gauge, Advantec fraction collector Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $90,000. 2000 model; Nanoflow-Z CapElectrophoresis electrospray. Guaranteed installable. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $90,000. API-LC/Orth. 2000 model. Manufacturer-certified. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **GC/Other MS: Micromass VG70 SE: $45,000. Hi resolution GC/MS MSI Autoconcept: $380,000. New; multiramp temp; Agilent GC and Agilent or CTC autosampler. Includes install, 1 yr. warranty. Thermoquest GCQ: $30,000. GC/MS/MS; EI/CI; rebuilt; 90-day warranty. Agilent 5973/6890: $65,000. EI/CI/NCI; one year warranty. HP 5890 II/5970B: Offers considered. SmartCard II, software incl. HP 5989 MS engine: $28,500. 2000 amu mass range, pos/neg CI, APCI. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: Werner Spahl Date: Fri, 6 Aug 2004 09:47:26 +0200 Subject: Re: Bruker MALDI-ToF data format, was: Anybody know MALDI-TOF, bruker? Organization: * Hallo Joerg, On Thu, 5 Aug 2004, Joerg Hau wrote: } Almost all of the XMASS format is pretty straightforward (except } for the calibration ;-). ich wusste garnicht, dass ihr auch Bruker Geraete habt. Wir haben hier gerade ein Autoflex II installiert bekommen und ich wollte dich einfach mal fragen, ob ihr mit sowas Erfahrungen habt. Mir geht es vor allem um die Massenfeinbestimmung von kleinen Molekuelen (<2000 u), die mir zwar machbar, angesichts der verschiedenen Kalibrierungs- und Peakdetektions- algorithmen aber noch recht willkuerlich erscheint. Ausserdem bin ich auf der Suche nach einer guten Nicht-Saeure Matrix, was nehmt ihr denn da so? Ansonsten bin ich von der Software ziemlich enttaeuscht, obwohl ich als Vergleich nur die gute alte ICIS II kenne. Alleine das Datenformat selbst mit all diesen Unterverzeichnissen ist doch ein Witz und vom NMR geklaut! -- Werner Spahl (spahl@cup.uni-muenchen.de) Freedom for "The meaning of my life is to make me crazy" Vorlonships ****************************************************************************** From: Hubert Tang Date: Mon, 09 Aug 2004 09:21:35 +0000 Subject: Interference in LCMSMS Organization: * Dear all, Recenly I observe a huge interferring m/z from 239>198 and 199>158 using LC-triple quad MS. The source of contamination seems to be in LC part. Mobile phase solvents used are 0.1% formic acid, acetonitrile, MilliQ water. LC pump is Agilent 1100 binary pump and all connections use PEEK tubings. Does anyone has any clue? Kind regards, Hubert Tang ________________________________________________________________________________ Linguaphone : Learning English? Get Japanese lessons for FREE ****************************************************************************** From: kj Date: Tue, 10 Aug 2004 18:48:52 +0000 (UTC) Subject: 2 Qs on computing tryptic peptides w/ miscleavages Organization: * Hi! I have a couple of questions both having to do with the concept of miscleavages. I'm trying to figure out what exactly people *usually* mean when they talk about "allowing a maximum of n miscleavages" when computing the expected tryptic peptides from an input sequence. First, does "allowing a maximum of n miscleavages" refer to the maximum number of miscleavages allowed in the *whole* input sequence, or the maximum number of miscleavages allowed within any one run (not followed by P) of consecutive K/R residues in this sequence? If the latter is the case, does it include "runs" of a single K/R ? OK, if my understanding is correct, if I have a stretch of sequence of the form ...@RKR$... (where @ stands for any non-[KR] amino acid, $ stands for any non-[KRP] amino acid, and the ... indicate continuation) , and allow a maximum of n = 0, 1, or 2 miscleavage, then the expected peptides resulting from this stretch for these three cases will be n = 0 ...@R K R $... n = 1 all those for the case n = 0, plus ...@RK KR R$... n = 2 all those for the case n = 1, plus ...@RKR KR$... Did I get this right? Thanks! kj -- NOTE: In my address everything before the first period is backwards; and the last period, and everything after it, should be discarded. ****************************************************************************** From: Philippe FRANCOIS Date: 10 Aug 2004 23:52:23 -0700 Subject: Header in Masslynx 4.0 Organization: * Hello does anyone know how to insert the "filename" in the header with MassLynx 4.0. In Masslynx 3.5 (as for Masslab) it used to be possible via the header command "systemlist, DATA, 3" but that particular feature seems to have disapeared. ****************************************************************************** From: bizzwire Date: Wed, 11 Aug 2004 16:23:28 GMT Subject: Re: Header in Masslynx 4.0 Organization: * } Philippe FRANCOIS writes } Hello } } does anyone know how to insert the "filename" in the header with } MassLynx 4.0. In Masslynx 3.5 (as for Masslab) it used to be possible } via the header command "systemlist, DATA, 3" but that particular } feature seems to have disapeared. } If you mean display the filename in either the spectrum or chromatogram, it's very simple. The only problem is that I don't have MassLynx to hand at the moment, so I'm going ny memory. In, either the spectrum or chromatogram window, go to the toolbar and click on "Display." click on the "View" menu item which will pull up a dialog box. You should see a button marked "Header." Click on this and you will see a drop down box on the left (showing the available fields you can put into the header) and a cryptic, yet non-intuitive set of boxes to the right (which represent where the fields will be displayed. in the upper drop-down box select "Raw file...uh, something, something." The lower drop-down menu should have a field named "filename" or something similar. click on it to select. Now, on the right-hand thingie, click on where in the header you want this to appear. Now click on the "Add" button in the middle. It's just that simple!!!! ****************************************************************************** From: Steve.z.Cepa Date: 16 Aug 2004 08:56:52 -0700 Subject: Re: Interference in LCMSMS Organization: * Since the two neutral losses are both 41, which is almost certainly due to acetonitrile, that leaves you with 158, which is puzzling. But then working up, consider [2DMSO + 2ACN + H]+ at m/z 239 If DMSO was a solvent used during injection, it may be taking a long time to bleed off. Consider also, preparing fresh mobile phase and see if it disappears. Hubert Tang wrote in message news:... } Dear all, } } Recenly I observe a huge interferring m/z from 239>198 and 199>158 using } LC-triple quad MS. The source of contamination seems to be in LC part. } Mobile phase solvents used are 0.1% formic acid, acetonitrile, MilliQ } water. LC pump is Agilent 1100 binary pump and all connections use PEEK } tubings. Does anyone has any clue? } Kind regards, } Hubert Tang } ****************************************************************************** From: "Palome, Elaine" Date: Mon, 16 Aug 2004 16:52:54 -0400 Subject: Analytical chemistry opening Organization: * Opening in Analytical Chemistry at ArQule, Woburn, MA ArQule, Inc. (Nasdaq: ARQL) is a biotechnology company engaged in research and development of small-molecule cancer therapeutics based on its innovative Activated Checkpoint TherapySM (ACTSM) platform to produce next-generation drugs that are intended to improve the way cancer patients are treated. Compounds resulting from the ACTSM platform are intended to selectively kill cancer cells and spare normal cells by restoring and activating cellular checkpoints that are defective in cancer cells. ArQule’s combined strengths in small-molecule chemistry, intelligent drug design and molecular biology for target identification/validation, form a promising drug discovery and development platform that has the potential to deliver clinical candidates with improved activity and reduced toxicity over other molecular approaches and traditional therapies. At the heart of this platform lies a unique approach to anti-cancer therapies: the ACTSM platform and a novel method for producing compounds with the best balance of drug-like properties (Optimal Chemical EntityTM or OCETM compounds). Brief Purpose of the job: Provide analytical support as part of the integrated combinatorial chemistry platform within the Chemical Technologies business. Have a thorough understanding of the role of the analytical department within the Chemical Technologies business and high throughput organic synthesis field. Job Responsibilities: Work with team of analytical chemists who perform analysis of library compounds to support chemistry and production departments. Perform LC and MS method development for high throughput applications. Represent the Analytical Department on multi-disciplinary teams across the company and co-ordinate activities with other senior staff members of the department. Review data and interact with other groups to determine future actions based on analytical results. Support and enhance team structure by acting as an expert resource for training and mentoring. Perform QA audits of data as required. Have a detailed understanding of the functions and processes of other departments in the Chemical Technologies business, and understand the impact of operational changes across Chemical Technologies. Have a broad understanding of the Early Discovery process within the Pharmaceutical industry, and ArQule’s role in this process. Identify issues, present solutions and escalate to management when appropriate. Identify, research and implement enhancements in processes and techniques to continuously improve the analytical department’s productivity and capability. Present results informally and formally at internal and external meetings Education: Ph.D. Analytical Chemistry, Organic Chemistry or equivalent scientific discipline with >2 years industrial experience. Technical Competencies: Experience in separation science, especially RP-HPLC, is required. Additional experience in method development, preparative HPLC, SFC, CE, and/or chiral separations a plus. Experience in mass spectroscopy, preferably LC-MS, is required. Additional experience in method development and NMR a plus. Experience in supervision and/or team leadership is highly desired Solid understanding of organic and physical chemistry. Experience in writing software applications or HT-techniques and automation a plus Work Habits: Excellent team player, able to work effectively in multi-disciplinary groups; ability to work on multiple projects and deliver against tight timelines is essential. Track Record: Proven track record in LC-MS, minimum 2 years experience in a LC-MS laboratory. Industry experience strongly preferred. To apply for this position and to learn more about ArQule, please visit www.arqule.com Elaine M. Palome Director of Employment ArQule, Inc. epalome@arqule.com 781.994.0480 (office) 781.264.2559 (mobile) www.arqule.com "Surround yourself with the best people you can find, delegate authority, and don't interfere." Ronald Reagan-Address to the nation ****************************************************************************** From: Richard M. Irwin Date: Tue, 17 Aug 2004 00:40:40 -0400 Subject: Old MALDI-TOF Parts Organization: * Anyone have a line on control boards for old Vestec RBT-2 Malti TOF? Drop me a line (remove "nospam")! Rich rmirwin2nospam@aug.com ****************************************************************************** From: Richard B. Opsal Date: 18 Aug 2004 12:31:20 -0700 Subject: New ITS40, Magnum, and Saturn I acquisition system Organization: * A new acquisition system is available for users of Finnigan ITS40, Magnum, and Varian Saturn I ion traps. The Vx Acquisition System replaces the MS-DOS based system with one based on Windows 2000 and Windows XP. Information on Vx can be found at: http://www.adronsystems.com/products_vx.htm Further, a working "demo" of the Vx program is available from: http://www.adronsystems.com/downloads.htm Vx integrates easily with HP and Agilent ChemStation while bringing in all the advantages of Windows 2000 and Windows XP. These advantages include: }} Strong networking and printer access. }} Data archival through DVD, CD, tape or Windows backup server. }} Easy installation, instrument configuration and operation. For further information, please contact: Richard Opsal Tel: (218) 266-3455 Fax: (218) 266-3472 http://www.adronsystems.com/ ****************************************************************************** From: ICDD Webmaster Date: 18 Aug 2004 12:51:24 -0700 Subject: Ludo Frevel Crystallography 2005 Scholarship Awards Organization: * Ludo Frevel Crystallography 2005 Scholarship Awards Application deadline is 1 November 2004 Sponsored by the International Centre for Diffraction Data If you will be pursuing an advanced degree in crystallography or related discipline in 2005, then we encourage you to apply for this scholarship. For more information on how to apply visit http://www.icdd.com/resources/awards/frevel.htm or contact Leah Mooney at mooney@icdd.com or Tel: +610-325-9814. ****************************************************************************** From: Jeff Gambera Date: Thu, 19 Aug 2004 03:38:32 GMT Subject: Quattro triple quad Organization: * Is anyone familliar with the source control circuitry of the quattro 1 or 2 ? we cannot get the electron energy to readback over 55 or the emission to readback over 60 regardless of the setpoint. Source has been completely rebuilt with new filament and ceramics. Looking at the skematic, can't quite determine how electron energy is set and from where the setpoint is derived. Can anyone help. (Micromass/Waters will NOT answer questions at this level) Thanks Bill Heriot NIAID ****************************************************************************** From: Jimmy Date: 19 Aug 2004 04:30:39 -0700 Subject: How to reduce Na adducts Organization: * There are both H and Na adducts with my analyte. Is there anyway to reduce Na adduct amounts so that there is mainly H adduct? Thanks! ****************************************************************************** From: Doug Stevens Date: 20 Aug 2004 08:01:40 -0700 Subject: Re: Quattro triple quad Organization: * Jeff Gambera wrote in message news:... } Is anyone familliar with the source control circuitry of the quattro 1 or 2 } ? we cannot get the electron energy to readback over 55 or the emission to } readback over 60 regardless of the setpoint. Source has been completely } rebuilt with new filament and ceramics. Looking at the skematic, can't quite } determine how electron energy is set and from where the setpoint is derived. } Can anyone help. } (Micromass/Waters will NOT answer questions at this level) } Thanks } Bill Heriot } NIAID I used to be a demo chemist on QII and had this problem crop up on one of our demo instruments. Replacing the filament control unit was the fix in that case. Hope this helps. ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Fri, 20 Aug 2004 21:21:46 +0200 Subject: Re: Quattro triple quad Organization: * Bill, I tried to send you an email, but the address wasn´t ok. Rainer Jeff Gambera schrieb: } } Is anyone familliar with the source control circuitry of the quattro 1 or 2 } ? we cannot get the electron energy to readback over 55 or the emission to } readback over 60 regardless of the setpoint. Source has been completely } rebuilt with new filament and ceramics. Looking at the skematic, can't quite } determine how electron energy is set and from where the setpoint is derived. } Can anyone help. } (Micromass/Waters will NOT answer questions at this level) } Thanks } Bill Heriot } NIAID ****************************************************************************** From: Chip Cody Date: 21 Aug 2004 10:47:44 -0700 Subject: Re: How to reduce Na adducts Organization: * There is no simple answer. It is common to see a variety of adducts ([M+H]+, [M+Na]+, [M+NH4]+ etc.) when using ESI. This can be a real problem when dealing with unknowns. I don't trust a molecular weight assignment for a total unknown unless I can find a readily assignable pair of adducts (positive or negative). Sometimes you can force a shift of the adduct by adding a source of potassium or ammonium. If the compound can be ionized by APCI, you may be able to get preferential formation of [M+H]+. Otherwise, it depends on the source of Na. Solvents are often the culprit. We found that bottled "HPLC-grade" water was unsuitable for our work and we purchased a water purifier that delivers 18.3 megohm water when fed HPLC-grade water. Alkali metal cations can be leached out of glass containers, so plastic containers may help. However, plastic containers present a different set of problems (adsorption of hydrophilic compounds, contamination with plasticizers, etc.). If the sodium is in the sample, you will have to chose a suitable desalting procedure. LC or equivalent (such as "Ziptips") will be helpful. The alkali metal cation problem is particularly vexing for nucleotides and people have developed a wide range of desalting procedures. If you can provide more information about your analyte type, perhaps someone can provide specific suggestions. Good luck! Chip Jimmy wrote in message news:... } There are both H and Na adducts with my analyte. Is there anyway to } reduce Na adduct amounts so that there is mainly H adduct? } } Thanks! ****************************************************************************** From: Werner Spahl Date: Mon, 23 Aug 2004 15:15:18 +0200 Subject: CMASS reference file for m-nitrobenzyl alcohol Organization: * Hi, has anyone here using a Finnigan MAT90/95/900 a CMASS reference file for pos/neg m-nitrobenzyl alcohol which they could email to me? Thanks! -- Werner Spahl (spahl@cup.uni-muenchen.de) Freedom for "The meaning of my life is to make me crazy" Vorlonships ****************************************************************************** From: Sandra Benge 203-925-1500 Date: 23 Aug 2004 12:38:50 -0700 Subject: Mass Spec Specialist in New Haven County, CT 203-925-1500 Sandra Benge Organization: * Mass Spec. Specialist -- New Haven County, Connecticut. This biotech start-up offers a relaxed and friendly atmosphere with accessible, visionary management. Their scientists utilize the latest in development tools. They have secured over $34 million in their third round of funding. Most people who interview here jump at the opportunity. This Research Associate will be a member of a rapidly expanding drug discovery team and will provide in vitro ADME support, especially bioanalytical support for the lead discovery and optimization programs. Expertise in LC-MS/MS is sought and candidates with Finnigan mass spectrometry operating software (Xcalibur) will be given special consideration. They seek someone who has at least three years industrial experience in LC/MS with a BS or MS in Organic Chemistry. They boast an excellent benefits package along with three weeks vacation first year, stock options, and a superior relocation package. Salary is competitive $50,000 to $80,000 a year dependent upon experience. I can be reached at 203-925-1500 or via email at bengeks@connix.com. Should your email be "bounced-back" to you, please email me at my hotmail account sandrabenge@hotmail.com Thank you. Sincerely yours, --- Sandy Sandra Benge, Recruiter KirklandSEARCH 203 925-1500 www.kirklandsearch.com bengeks@connix.com sandrabenge@hotmail.com ****************************************************************************** From: Andrew Peters Date: Tue, 24 Aug 2004 10:52:08 -0300 Subject: HP 5992/5970 MS filaments available. Organization: * Hi, During a lab clean-out I found 8 unused filaments for a HP 5992/5970 MS, bought from SIS (SIS part # HPF4, corresponding HP part # 05990-60084). We currently have an Agilent 5973 and these parts are therefore redundant. Anyone interested in having them? Any offers? They currently retail for $110 each. Regards, Andrew ****************************************************************************** From: Dave Kaleta Date: 24 Aug 2004 14:47:23 -0700 Subject: Leybold turbo pump reliability Organization: * I'd like comments from the community regarding the longevity and reliability of Leybold turbomolecular pumps. We have an ABI QStar XL and have experienced 3 failures in 2 years of ownership. The current failure is a TW700 pump, the other pump still operating is a 701 (not sure what the previous models to fail were). We're understandably concerned about the potential of further failures; earlier pumps were under warranty, but no more, and we have no service contract. It would appear the it is the controller that failed (in this integrated unit, requiring pump replacement). Are the pumps not up to the task, was there an inherent design flaw with the 700's that (hopefully) was rectified with the 701, etc? I've noted failures posted here and particularly the incorporation of an axial bearing dampener in late models (perhaps the hoped-for fix?). thanks, Dave Kaleta U Tennessee Knoxville ****************************************************************************** From: Kent Kirkland Date: Wed, 25 Aug 2004 15:14:05 +0000 Subject: JobOpen- Research Assoc. Biopharmaceutical analysis LC-MS/MS -CT, Organization: * A biopharmaceutical company in Greater New Haven, CT seeks a Research Associate with a background in pharmaceutical analysis and metabolite identification. This startup biotech outfit has an untraditional, relaxed atmosphere, accessible, visionary management, the latest development tools, and millions in the bank for drug discovery. They have secured a third round of funding in a tight venture capital environment, so there must be some good science going on here. The Research Associate will be a member of a rapidly expanding drug discovery team providing in vitro ADME support, especially bioanalytical support for lead discovery and optimization programs using LC-MS/MS. Requires at least three years of pharmaceutical or biotech experience using LC/MS for analysis and metabolite identification, coupled with a BS or MS in Chemistry. Exp. with Finnigan mass spectrometry operating software (Xcalibur) preferred. No PhDs on this one. $60,000 to $80,000. Benefits include stock options and three weeks vacation the first year. We will present candidates on salaries up to $10,000 more. For further details, contact Kent Kirkland, C.P.C., at KirklandSEARCH,(203) 925-1500, kentkcpc@hotmail.com, www.kirklandsearch.com _________________________________________________________________ On the road to retirement? Check out MSN Life Events for advice on how to get there! http://lifeevents.msn.com/category.aspx?cid=Retirement ****************************************************************************** From: John Sherratt Date: 25 Aug 2004 09:31:24 -0700 Subject: Opening for LC-MS/MS Bioanalysts Organization: * Upstate NY Excellent package + benefits Outstanding opportunity to join a highly innovative and successful provider of LC-MS/MS bioanalytical services. Working in close knit teams in an excellent environment, you will operate and troubleshoot advanced LC-MS/MS systems in support of diverse drug development programmes. You will have high levels of responsibility for your own studies, including regular sponsor contact. Candidates will be of graduate calibre with 2-10 years experience of LC-MS/MS and ideally bioanalysis, in commercial laboratories. You will be confident and effective communicators able to seamlessly fit into a dynamic team environment. The willingness and ability to relocate to Upstate New York, USA is essential! Full relocation expenses and visa/greencard paperwork will be provided. Call VRS for further information. VRS Tel: +44 (0) 161 976 4000 Fax: +44 (0) 161 976 2561 ms@vrs-uk.net www.vrs-uk.net Vantage House, 26a. Northenden Road, Sale, Cheshire, M33 3BR, UK VRS are Europe's first Recruitment Consultancy specialising in Mass Spectrometry, all types of Analyses supported by Mass Spectrometry and the associated Separation/Extraction techniques. VRS was formed by Mass Spectrometry and recruitment professionals to provide a focussed and quality service. ****************************************************************************** From: emilio.pastori Date: Wed, 25 Aug 2004 21:37:41 +0200 Subject: Re: Sciex Analyst 1.4 software Organization: * Dear Jimmy, I've installed analyst 1.4 last week, I'm tryng it and I'm quite satisfied. I notice that is just a little bit slower than 1.2 that I have installed before. I Work in GLP and I think that this version (I have added HotFix 1, 3 and 5) is better that the previous one's. Kind Regards Federico "Jimmy" ha scritto nel messaggio news:c7dvrk$24d$1@news-int2.gatech.edu... } We use Analyst 1.3 and consider to upgrade to Analyst 1.4. } } Does anyone out there have any good or bad experiences with the } Analyst 1.4 software for SCIEX MS instruments? } } Thanks in advance! } } Jimmy } ****************************************************************************** From: David Sparkman Date: Tue, 31 Aug 2004 13:49:05 GMT Subject: ACS MS Interpretation on the Web Organization: * The American Chemical Society will be offering a course in mass spectral interpretation on the Web this Fall (Begining September 14). This is a six-week, 12-section (each session 1.5 hours) course with interactive sessions and off-line assignments which will be marked and returned. This is the fifth time this popular course has been offered in the last two years. For complete details, go to: http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=education\professional\wcsp06.html If the above url fails, go to http://www.acs.org/shortcourses and follow the links to Web Courses Regards; David -- O. David Sparkman Consultant-At-Large ods spam @ no compuserve.com ****************************************************************************** From: fcarrera@almirall.es Date: Tue, 31 Aug 2004 16:07:39 +0200 Subject: Electrospray spectra of silyl derivatives Organization: * Hello MS people! I am fighting with the electrospray MS spectrum of a molecule. MW=353, and it has only 2 functional groups: - carbamate with a trimethylsilyl: N-CO-O-CH2CH2-Si(CH3)3 - a tetramethyl dioxaborolane: -B-O-C(CH3)2 (5 members ring: 1B, 2O and 2 C) ! ! O - C(CH3)2 There is not (M+H)+ but some (2M+H)+=707 The base peak is 326 (M-27) and 342 (M- 11) is also abundant. Mobile phase: ammonium formate (pH=3), methanol and acetonitrile. Could someone tell me what ions are 326 and 342 ? Francesc Carrera i Carrera Mass Spectrometry System Manager Analysis R&D Department Research Center ALMIRALL PRODESFARMA S.A. Barcelona e-mail: fcarrera@almirall.es ___________________________________________________________________________________________________ The information contained in this facsimile/electronic message is proprietary and confidential and is only and exclusively addressed to the named recipient(s). We have to advise you that any use, copying or distribution of the above referred information by any unintended recipient may be illicit and result in damage, harm and loss to the sender and/or to the intended recipient(s). If you have received this message in error, please immediately notify us. ___________________________________________________________________________________________________ ****************************************************************************** From: jin Date: 31 Aug 2004 15:09:40 -0700 Subject: Ion Signal Suppression Problems Organization: * hi, there, I am confused about one ion suppression problem related with Finnigan Ion Trap. I described that in the following: The original concentration of sample is 100uM. 10ul injected onto the column with HPLC gradient and the MS was in full scan mode , no ion suppression found, good chromatogram achieved. Then, the same amount of 10ul was injected onto the same column with the same gradient, everything is the same except the MS was in SRM mode this time. Very strong ion signal suppression was met. I got aweful chromatogram. Could anyone be kindly enough to tell me the reason behind this? Thanks so much! jin ****************************************************************************** From: "Hau,Joerg,LAUSANNE,NRC/BAS" Date: Wed, 1 Sep 2004 14:45:12 +0200 Subject: Display problem with ICIS2 on AlphaStation Organization: * Dear All, We have a display problem with the Finnigan ICIS2 software. We are running Finnigan's ICIS2 under Digital Unix 4.0 on an AlphaStation 200 4/100. A while back, the terminal window of the 'tsq700' started to have vertical stripes. - Only the 'tsq700' window is concerned. All other windows (spec, chro, other X applications, ...) appear normal. - The stripes do _not_ disappear if you change the monitor. - They _do_ disappear if you control the instrument over another X terminal, such as a Linux PC. The local Finnigan service could not really help ("suggest to re-install everything and see if it goes away" ... hey, this isn't MS Windows ;-). These stripes take the color of the window decoration, so a workaround is to set this color to black. I'm pretty much convinced that the solution must be somewhere in the configuration of the terminal settings for that particular X window when it is used on the AlphaStation. Has anyone else observed this? Any ideas? Thanks for any help, - Joerg Dr Jörg Hau Dept. of Bioanalytical Science Nestlé Research Center PO Box 44, CH-1000 Lausanne 26 Phone + 41 21 785 8069 Fax + 41 21 785 9486 e-mail: joerg.hau(at)rdls.nestle.com ****************************************************************************** From: Eric van der Meulen Date: 1 Sep 2004 08:20:50 -0700 Subject: Re: Electrospray spectra of silyl derivatives Organization: * My best guess is that m/z=326 is formed by loss of HCN from your molecule: usually a loss of 27 amu is HCN. Suppose m/z=707 is not [2M+H]+ but a sodium adduct of mass 684, then m/z=342 (actually 342.5) could be [707-Na+2H]2+ , a doubly charged ion. You should check if m/z=342 is doubly charged. Look at the mass difference between the C12 and C13 isotope. If this mass difference is 1, the peak is singly charged. If it is 0.5, the peak is doubly charged. That is all I can think of for the moment..... Greetings, Eric van der Meulen ****************************************************************************** From: Chip Cody Date: 1 Sep 2004 11:27:05 -0700 Subject: Re: Electrospray spectra of silyl derivatives Organization: * Unfortunately, I don't have any answers for you, only a few comments and questions. I would certainly not expect boron loss from a molecular ion or a protonated molecule, so I don't think that the (M-11) peak is a fragment from one of these species. The m/z 326 and 342 species differ by 15, usually indicating a methyl group loss. These may be fragments from the proton-bound dimer. Does the abundance of these peaks change if you vary the cone voltage? Dimer formation should be favored at high sample concentration or low cone voltage. Maybe if you raise the cone voltage or lower the concentration you will see a difference. If you have exact mass measurements, that would really help you make assignments. Even if not, the silicon and boron isotope peaks should help. For example, it should be evident whether you have one, two, or zero borons in these peaks. Was this compound silylated for GC/MS analysis (it does not look like that is the case...? We usually prefer the underivatized compounds for ESI analysis. Good luck! Chip Cody fcarrera@almirall.es wrote in message news:... } Hello MS people! } } I am fighting with the electrospray MS spectrum of a molecule. } } MW=353, and it has only 2 functional groups: } } - carbamate with a trimethylsilyl: N-CO-O-CH2CH2-Si(CH3)3 } } - a tetramethyl dioxaborolane: -B-O-C(CH3)2 (5 members } ring: 1B, 2O and 2 C) } ! ! } O - C(CH3)2 } } } There is not (M+H)+ but some (2M+H)+=707 } } The base peak is 326 (M-27) and 342 (M- 11) is also abundant. } } Mobile phase: ammonium formate (pH=3), methanol and acetonitrile. } } Could someone tell me what ions are 326 and 342 ? } } Francesc Carrera i Carrera } Mass Spectrometry System Manager } Analysis R&D Department } Research Center } ALMIRALL PRODESFARMA S.A. } Barcelona } e-mail: fcarrera@almirall.es } } } ___________________________________________________________________________________________________ } } The information contained in this facsimile/electronic message is proprietary and } confidential and is only and exclusively addressed to the named recipient(s). We have } to advise you that any use, copying or distribution of the above referred information } by any unintended recipient may be illicit and result in damage, harm and loss to the } sender and/or to the intended recipient(s). If you have received this message in error, } please immediately notify us. } ___________________________________________________________________________________________________ ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Wed, 01 Sep 2004 21:35:34 +0200 Subject: Re: Display problem with ICIS2 on AlphaStation Organization: * Hi Joerg, remember that the instrument display is generated inside the MS, not on the station. It is then sent to the station (on the early 70 instruments a KEL-terminal was connected to the display control FSBC directly). What the station does is an emulation of the KEL. So the problem should be related to your graphics card or to the display control FSBC. I would suspect the graphics card first, then swap the display-controller with instrument- or Unix-controller (if you need help to do that contact me directly, there are several jumpers and chips to be changed). Hope this helps. Cheers Rainer "Hau,Joerg,LAUSANNE,NRC/BAS" schrieb: } } Dear All, } } We have a display problem with the Finnigan ICIS2 software. } } We are running Finnigan's ICIS2 under Digital Unix 4.0 on an AlphaStation } 200 4/100. A while back, the terminal window of the 'tsq700' started to } have vertical stripes. } } - Only the 'tsq700' window is concerned. All other windows (spec, } chro, other X applications, ...) appear normal. } } - The stripes do _not_ disappear if you change the monitor. } } - They _do_ disappear if you control the instrument over another X } terminal, such as a Linux PC. } } The local Finnigan service could not really help ("suggest to re-install } everything and see if it goes away" ... hey, this isn't MS Windows ;-). } } These stripes take the color of the window decoration, so a workaround } is to set this color to black. } } I'm pretty much convinced that the solution must be somewhere in the } configuration of the terminal settings for that particular X window } when it is used on the AlphaStation. } } Has anyone else observed this? Any ideas? } } Thanks for any help, } } - Joerg } } Dr Jörg Hau } Dept. of Bioanalytical Science } Nestlé Research Center } PO Box 44, CH-1000 Lausanne 26 } Phone + 41 21 785 8069 } Fax + 41 21 785 9486 } e-mail: joerg.hau(at)rdls.nestle.com ****************************************************************************** From: bizzwire Date: Thu, 02 Sep 2004 11:44:19 GMT Subject: Re: Electrospray spectra of silyl derivatives Organization: * Eric van der Meulen wrote } Suppose m/z=707 is not [2M+H]+ but a sodium adduct of mass 684, then } m/z=342 (actually 342.5) could be [707-Na+2H]2+ , a doubly charged } ion. Check your math: 707 +23 +H (I think "2H" was a typo)=731 731/2=365.5, not 342.5 Assuming you meant [684+Na+H]++, the answer is still wrong (354) Bizz ****************************************************************************** From: bizzwire Date: Thu, 02 Sep 2004 12:13:10 GMT Subject: Re: Electrospray spectra of silyl derivatives Organization: * } } I am fighting with the electrospray MS spectrum of a molecule. } } MW=353, and it has only 2 functional groups: } } - carbamate with a trimethylsilyl: N-CO-O-CH2CH2-Si(CH3)3 } } - a tetramethyl dioxaborolane: -B-O-C(CH3)2 (5 members } ring: 1B, 2O and 2 C) } ! ! } O - C(CH3)2 } } } There is not (M+H)+ but some (2M+H)+=707 } } The base peak is 326 (M-27) and 342 (M- 11) is also abundant. } } Mobile phase: ammonium formate (pH=3), methanol and acetonitrile. } } Could someone tell me what ions are 326 and 342 ? } } Francesc Carrera i Carrera } Are you doing this by infusion or LC? If the former, you could have contaminant/ion suppression issues and/or you could be trying to interpret the superposition of multiple spectra- before wearing yourself out chasing red herrings, try doing LC/MS. Also, check your source voltages- you could be generating clusters/inducing front-end CID. Are you doing this on a trap? You could be seeing ion/molecule reactions. Cut back on the the concentration and/or trapping time. Again, try LC/MS introduction instead of infusion. If you have access, try repeating the experiment on a quadrupole instrument (or vice-versa). Also, have you tried doing negative ionization? Negative ionization GOOD. This might clear things up. Or not. Lastly, double-check your math. Loss of a naked Boron atom (M-11) doesn't sound kosher. Doble-check your logic. Just because you think the molecular weight *should* be 353 doesn't mean it has to be. We'll need to know more of the history of the sample to avoid making false assumptions. You should try/consider all of the above before asking for help; I think the problem lies with what you are doing (or not doing) rather than with the molecule. ****************************************************************************** From: bizzwire Date: 2 Sep 2004 12:39:26 -0700 Subject: Re: Electrospray spectra of silyl derivatives Organization: * } } I am fighting with the electrospray MS spectrum of a molecule. } } MW=353, and it has only 2 functional groups: } } - carbamate with a trimethylsilyl: N-CO-O-CH2CH2-Si(CH3)3 } } - a tetramethyl dioxaborolane: -B-O-C(CH3)2 (5 members } ring: 1B, 2O and 2 C) } ! ! } O - C(CH3)2 } } } There is not (M+H)+ but some (2M+H)+=707 } } The base peak is 326 (M-27) and 342 (M- 11) is also abundant. } } Mobile phase: ammonium formate (pH=3), methanol and acetonitrile. } } Could someone tell me what ions are 326 and 342 ? Some compounds are very ionophoric. How about this? The true M.W. is 303. 326=[M+NA]+ 342=[M+K]+ 707? I don't know, unless you meant 607, which is the [2M+H]+ ****************************************************************************** From: bizzwire Date: 2 Sep 2004 12:45:46 -0700 Subject: Re: Ion Signal Suppression Problems Organization: * jin wrote in message news:... } hi, there, } } I am confused about one ion suppression problem related with } Finnigan Ion Trap. I described that in the following: } } The original concentration of sample is 100uM. } } 10ul injected onto the column with HPLC gradient and the MS was in } full scan mode , no ion suppression found, good chromatogram achieved. } } Then, the same amount of 10ul was injected onto the same column } with the same gradient, everything is the same except the MS was in } SRM mode this time. Very strong ion signal suppression was met. I got } aweful chromatogram. } } Could anyone be kindly enough to tell me the reason behind this? } } Thanks so much! uh....you do realize that in SRM, you monitor the *Fragment* ion from an MS/MS experiment. If you are monitoring the parent, you wont see anything, because you've busted it up. ****************************************************************************** From: Ricksfbrsc Date: 02 Sep 2004 23:39:53 GMT Subject: Re: Electrospray spectra of silyl derivatives Organization: * Boron has a very distinctive isotope pattern: 25% B-10 and 100% B-11. If this molecule has one B, then it will have a (M-1) of 25% of M. If there is a dimer, then there should be 6.2% (M-2), 49% (M-1), and 100% M. This, of course, doesn't take the other isotopes into account. Use the Sheffield Isotope calculator if you want the whole pattern. At least you should be able to tell if Boron is there! Rick ****************************************************************************** From: jenndawnw Date: 2 Sep 2004 16:58:38 -0700 Subject: seldi or other technique for protein id/quantification of cell Organization: * heard mixed reviews of SELDI...does anyone have any good suggestions for mass spec quantification without using tandem mass spec? We could do 2d gel or proteome lab, followed by ESI-TOF or MALDI, but our samples cannot be labeled with nitrogen...they are coming off the facs machine and are flourescently labeled...so the quantification side of things could be tricky...i'm worried about SELDI because i've heard that it's low sensitivity is a problem...also we need to see glycosylation/phosphorylation/methylation state of proteins...as you can tell i'm a newbie to this so any advise is greatly appreciated!! ****************************************************************************** From: L FRIEDMAN Date: Sat, 04 Sep 2004 11:48:08 GMT Subject: ICIS Organization: * If you are still using ICIS and would like to upgrade, I have what you want. Computers from $100 to $2000. Desk tops and towers. CPU Speeds to 667. Hard drives to 18 GIG. Internal & external Tape drives. Internal & external Maxoptix MO RW drives. Software doesn't have to stop at Digital UNIX 4.0D or E. I have units running Tru64 F & G. Upgrades to Tru64 UNIX 5.0, 5.0A, 5.1, 5.1A, & even the last release 5.1B. Alpha 3000/400 $100 Alpha 200 4/233 $500 Alpha Tower 400 $600 Alphastation 255/233 $900 Alphastation 500. depends on CPU speed. $1000 to $2000. Compaq Tower PWS XP1000 500 cpu. $1500 Microway 533MHz with removable drive trays. $750. All are available now except the XP1000 at 667 CPU. This one would take a few weeks and would cost $3000. Prices are dependent on drive size, memory, software version, accessories, etc. All will have ICIS service pack II. Lloyd -- http://lloyds-masspeconsulting.com/ Lloyd Friedman POB 111 Whiting, NJ 08759 Ph: 732-849-0674 Cell: 908-600-5354 service@lloyds-masspeconsulting.com ****************************************************************************** From: David Smith Date: Tue, 07 Sep 2004 22:39:08 -0500 Subject: Column inlet to MS detector Organization: * Does anybody know th potential problems of hooking up an on column inlet to a MS detector (5973N in particular) ?? Contamination etc ... Thanking you ****************************************************************************** From: Ricksfbrsc Date: 08 Sep 2004 22:14:02 GMT Subject: Re: Column inlet to MS detector Organization: * I'm not sure what you're suggesting, but a MS runs in a vacuum and an inlet runs at greater than atmospheric pressure. If this is what you're suggesting, then there is going to be problems unless you use a narrow bore transfer line. ****************************************************************************** From: Gunter Kuhnle Date: 9 Sep 2004 16:58:31 GMT Subject: Strange calibration line behaviour Organization: * Hallo, I have a problem which puzzles me a bit as I kind think of any explanation. We are quantifying a set of compounds whith a LC/MS method using 13C3-labelled internal standards. Using labelled standards, I expected the IS to behave in a very similar way to the TA - unfortunately, something unexpected happened: each calibration line (which is injected from low to high concentration) is perfectly linear, but has a different slope. Furthermore, there seems to be no trend in the slope, i.e. the slope is not always getting lower. Looking at the area of the peaks indicates that something is happening with the IS which is not happening to the TA - however, I cannot think of anything which would only affect a labelled compound (this behaviour happens with pure standards, so any kind of matrix interference could be exclude). Does anyone has an idea what may cause this behaviour? Thank you! Best wishes, Gunter ****************************************************************************** From: David Smith Date: Thu, 09 Sep 2004 22:00:08 -0500 Subject: Re: Column inlet to MS detector Organization: * To rephrase: What are the implications of hooking up a column (with on-column inlet) to a MS detector ..ie. vacuum surges?..contamination ??...overloading ?? Thanking you Ricksfbrsc wrote: } I'm not sure what you're suggesting, but a MS runs in a vacuum and an inlet } runs at greater than atmospheric pressure. If this is what you're suggesting, } then there is going to be problems unless you use a narrow bore transfer line. ****************************************************************************** From: Mike Sherrell Date: Fri, 10 Sep 2004 09:33:01 -0700 Subject: Grizzly Analytical Mass Specs, MALDIs, etc. available Organization: * Grizzly Analytical Mass Specs, MALDIs, etc. available **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000: $150,000 installed/warranteed. Sciex API 3000: $190,000 W/ upgrade to ~ API 4000 sensitivity and S/N. API 3000 upgrade: $38,500. Increases sensitivity and (S/N) Ratio at high flow rates to ~ that of an API 4000. Install incl. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $120,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase; incl. install, warr. Sciex API 365: $65,000. NT, turboionspray. Installed, warranteed. Sciex 365 w/ EP10+: $149,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. Finnigan LCQ DECA: $67,500. ESI, Xcalibur 1.2, install, warranty incl. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Hitachi M 8000: $82,000. Ion trap. 1999; excellent condition; incl. LC. Micromass Quattro micro API: $150,000; Complete 2000. On factory service contract when deinstalled. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro LCZ: $131,500. Includes installation, warranty. Micromass Quattro IIZ: $149,000. Z-Spray. Includes install, warranty. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $60,000. European install included; available in US. MM Autospec V: $70,000. European install included; available in US. Mass spec sample introduction systems listed under liquid handlers, below. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. Voyager Elite XL: offers considered. incl. Vestec Multi-gauge, Advantec fraction collector Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $90,000. 2000 model; Nanoflow-Z CapElectrophoresis electrospray. Guaranteed installable. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $90,000. API-LC/Orth. 2000 model. Manufacturer-certified. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **GC/Other MS: Micromass VG70 SE: $45,000. Hi resolution GC/MS MSI Autoconcept: $380,000. New; multiramp temp; Agilent GC and Agilent or CTC autosampler. Includes install, 1 yr. warranty. Thermoquest GCQ: $30,000. GC/MS/MS; EI/CI; rebuilt; 90-day warranty. Agilent 5973/6890: $65,000. EI/CI/NCI; one year warranty. HP 5890 II/5970B: Offers considered. SmartCard II, software incl. HP 5989 MS engine: $28,500. 2000 amu mass range, pos/neg CI, APCI. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. **Also available: HPLCs, sequencers, synthesizers, etc: www.grizzlyanalytical.com. Regards, Michael Sherrell mike@grizzlyanalytical.com Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: "uccajth@ucl.ac.uk" Date: Fri, 10 Sep 2004 17:50:21 -0400 Subject: Ion Traps Organization: * Hello All A few months back I wrote to the mass spec news group asking for their advice on the purchase of an ion trap to look at small molecules in complex biological mixtures using MS/MS techniques. This is actually a bio-chemical engineering project and the compounds concerned are ketodioles and aminodioles in very small concentrations. One person replied, thank you Kendall. We need to make a decision by next Tuesday (14th Sept) at the latest. The situation is that Thermo have now offered a linear ion trap the LTQ, which is bit more expensive but with superior performance. The committee set up to decide is now split between the LTQ and the Bruker HCT (or the Agilent equivalent). In all cases an Agilent 1100 HPLC connected to whatever trap, is preferable. We need to ask users of the LTQ about reliability and service support during the warranty period. Do people think 3D traps will eventually be replaced in the long run by 2D linear traps which scan faster, are more sensitive and upgrade able to the FTMS? What about users of the HCT/XCT traps, are these pretty reliable? I also need to ask about the reproducibility of MS/MS spectra between a 3D trap compared to 2D linear ion traps when used to search user or commercial libraries. I would appreciate any response, many thanks. Regards John Hill Mass Spectrometry Facility University College London Chemistry Department -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . ****************************************************************************** From: Ricksfbrsc Date: 11 Sep 2004 11:25:41 GMT Subject: Re: Column inlet to MS detector Organization: * There aren't any special considerations. I do on-column routinely for GC/MS of high boiling compounds. It is also good for more labile compounds. The normal solvent delay where the MS is off might need to be extended a little bit due to amount of solvent on column, but it is really the same as splitless. The column will "filter" any dirt, so it can get contaminated easier, so the MS should be ok, although your column may not. On-column is trickier to do, but once you get everything set, is pretty standard. On the Agilent GC's, the autosampler works fine for doing the injection. ****************************************************************************** From: David Smith Date: Sat, 11 Sep 2004 14:10:31 -0500 Subject: Re: Column inlet to MS detector Organization: * Thanks !!! Ricksfbrsc wrote: } There aren't any special considerations. I do on-column routinely for GC/MS of } high boiling compounds. It is also good for more labile compounds. } } The normal solvent delay where the MS is off might need to be extended a little } bit due to amount of solvent on column, but it is really the same as splitless. } The column will "filter" any dirt, so it can get contaminated easier, so the } MS should be ok, although your column may not. } } On-column is trickier to do, but once you get everything set, is pretty } standard. On the Agilent GC's, the autosampler works fine for doing the } injection. ****************************************************************************** From: John Sherratt Date: 13 Sep 2004 03:02:47 -0700 Subject: UK opportunity for: LC-MS Bioanalytical Applications Specialist Organization: * Urgent requirement for a Senior Bioanalytical Scientist with extensive knowledge and experience with LC-MS/MS and HPLC. The role involves developing complex bioanalytical methods for the extraction, clean up and analysis of small mol. compounds from various biological samples. Working closely with new and existing clients, you will define analytical requirements and develop methods to enable achievement of objectives. This is a key and high profile role; the successful applicant will significantly contribute to the company’s continued growth in Europe. An exciting and rare opportunity – contact VRS to discuss further. ****************************************************************************** From: lailiang Date: Mon, 13 Sep 2004 16:22:27 -0600 Subject: saturn manual Organization: * I am looking for Saturn II GC-MS system operator manual. I have tried Varian and they informed me that this manual is no longer available from them. Does anyone have this manual that I may be able to borrow and make copy or for purchase? Any helps would be greatly appreciated! ****************************************************************************** From: Peter Date: Tue, 14 Sep 2004 07:46:24 +0200 Subject: Re: saturn manual Organization: * "lailiang" wrote in message news:ci5fuf$ph5$1@news-int.gatech.edu... } I am looking for Saturn II GC-MS system operator manual. I have tried } Varian and they informed me that this manual is no longer available from them. } Does anyone have this manual that I may be able to borrow and make copy or for } purchase? Any helps would be greatly appreciated! } Hello: I might be able to help. If you can point out your specific needs I can copy the pages. We can't borrow the manual, but may be able to make copies. It is a huge amount of pages though. regards -- Peter M. van Galen - Research Assistant Mass Spectrometry Organic Chemistry Department, Radboud University Nijmegen Toernooiveld 1, 6525 ED Nijmegen, Netherlands V: +31(0)24 3653269/2095/2362 F: +31(0)24 3652929/3393 mailto:pvang@science.ru.nl http://oase.uci.kun.nl/~massspec == All sent mail is scanned with NAV2003 (auto-updated) == ****************************************************************************** From: lailiang Date: Tue, 14 Sep 2004 10:47:06 -0600 Subject: Re: saturn manual Organization: * Thanks for your response, I am a graduate student at Brigham Young University, I have no other means to obtain this manual. we would be very happy to pay for having a copy of the manual made for our use. I believe Kinkos can do this. Thank you very much in advance for your help. "Peter" wrote in message news:ci6sbr$b0h$1@news-int2.gatech.edu... } } "lailiang" wrote in message } news:ci5fuf$ph5$1@news-int.gatech.edu... } } I am looking for Saturn II GC-MS system operator manual. I have tried } } Varian and they informed me that this manual is no longer available from } them. } } Does anyone have this manual that I may be able to borrow and make copy } or for } } purchase? Any helps would be greatly appreciated! } } } } Hello: } } I might be able to help. If you can point out your specific needs I can } copy } the pages. We can't borrow the manual, but may be able to make copies. It } is } a huge amount of pages though. } } regards } } } -- } Peter M. van Galen - Research Assistant Mass Spectrometry } Organic Chemistry Department, Radboud University Nijmegen } Toernooiveld 1, 6525 ED Nijmegen, Netherlands } V: +31(0)24 3653269/2095/2362 F: +31(0)24 3652929/3393 } mailto:pvang@science.ru.nl http://oase.uci.kun.nl/~massspec } } == All sent mail is scanned with NAV2003 (auto-updated) == } } } ****************************************************************************** From: lailiang Date: Tue, 14 Sep 2004 22:48:09 -0600 Subject: PROMs for saturn II GC-MS Organization: * Mr. Yelton from Spectratek helped me to make saturn II GC-MS running, unfortunately the PROMs (the firmware we have is specially for CI, we want to do EI instead) doesn't fit for the software we have (Version 1.1 and 5.2), does anyone have such PROM that I may be able to buy or give me an offer? Thanks in advance for help and any response would be greatly appreciated! ****************************************************************************** From: Martin Steel Date: Wed, 15 Sep 2004 14:12:27 +0000 (UTC) Subject: Equipment for sale Organization: * M i s c e l l a n e o u s Fisher Marathon 10K Benchtop GCI Icewagon DH60WCLT Blue M Gravity Oven 0V-18A Napco Autoclave 8000-DSE C h r o m a t o g r a p h y Waters 626 HPLC System Spark Holland Endurance 920 Waters Tunable Absorbance Detector 486 Micro-Tech Scientific UltraPlus II Ternary Gradient HPLC Waters Photodiode Array Detector 996 Waters Controller and Pump 600S 626 Thermo Surveyor PDA PhotoDiode Array Detector R o b o t i c s Gilson Cyberlab C240PC Protein Crystallography Qiagen Biorobot 8000 Tecan Genesis 200/8 Qiagen Biorobot 9600 Beckman Multimek 96 Channel Tecan Proteam 150/8 D N A - R N A - P r o t e i n ABI Procise 494 N-Terminal Sequencer ABI Sequence Detection System 7700 GeneMachines Oligo Synthesizer PolyPlex Amersham Biosciences MegaBACE 1000 ABI Geneamp 5700 M a s s S p e c t r o m e t r y Finnigan LCQ Classic Finnigan TSQ 7000 Finnigan LCQ DECA Shimadzu/Proteome Systems Xcise Axima CFR PLUS Finnigan DECA XP Plus Micromass QTOF Ultima M i c r o a r r a y Techne Oven HB-2D Genomic Solutions Flexys Colony Picker GeneMachines Microarraying Robot Omnigrid 100 Tecan LS 400 Tecan Hybridization Station HS 4800 Molecular Dynamics Generation III Microarray System N M R Varian Inova 600Mhz -- Posted via Mailgate.ORG Server - http://www.Mailgate.ORG ****************************************************************************** From: Kajjo Date: 16 Sep 2004 02:00:19 -0700 Subject: NIST GC/MS data file format (Thermo XCalibur) Organization: * Hi folks, does anyone know the structure of the NIST GC/MS data file format (not the library format), usually with the extension *.raw? I'd like to bulk process those GC/MS runs and therefore need to read them directly. I gather this NIST format is identical to that used by Thermo-Finnigan XCalibur software. Many thanks, Kajjo ****************************************************************************** From: John Sherratt Date: 16 Sep 2004 02:24:28 -0700 Subject: UK opportunity for: LC-MS/MS Bioanalytical Method Developer Organization: * Outstanding opportunity to join a highly specialised team involved in the research and development of LC-MS/MS bioanalytical methods. With a mainly pharmaceutical focus, you will be developing methods to identify and quantify parent compounds and metabolites in complex biological matrices. This will include very low level (pg/mL) and technically difficult assays that will stretch you knowledge to its limits. The ideal candidate will have significant knowledge and experience of LC-MS/MS and bioanlytical method development combined with a strong understanding of the underlying chemistry. A background in DMPK with a pharma, CRO, instrument supplier or other type of research group would be ideal. You will be capable of working accurately under pressure and taking initiative and leading projects with minimal supervision. This is a technically challenging, diverse and very non-routine role – call VRS for further details. +44 (0) 161 976 4000 www.vrs-uk.net ****************************************************************************** From: David Sparkman Date: Thu, 16 Sep 2004 20:19:46 GMT Subject: Re: NIST GC/MS data file format (Thermo XCalibur) Organization: * Kajjo, There is no such thing as an NIST GC/MS data file and therefore, there can be no file format. The Thermo Electron Finnigan Xcalibur, Waters Micromass, and P&E systems produce chromatography/mass spectrometry data files that have a raw extension. The default mass spectral search engine used by the Xcalibur and P&E systems is the NIST MS Search program's. The NIST MS Search Program reads data files that are in a text format and have the extension .msp. I can supply you with this format. NIST has developed a program for the analysis of chromatographic/mass spectrometry data called AMDIS (Automated Mass spectral Deconvolution and Identification System) which reads the data file formats from most of the commercial C/MS system. AMDIS does not have a proprietary file format either. AMDIS can only read the Xcalibur files when Xcalibur has been installed on the same computer that AMDIS is installed on. Go to http://chemdata.nist.gov for more information about the NIST MS Search Program and AMDIS. Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "Kajjo" wrote in message news:cic0j1$7b9$1@news-int.gatech.edu... } } Hi folks, } does anyone know the structure of the NIST GC/MS data file format (not } the library format), usually with the extension *.raw? I'd like to } bulk process those GC/MS runs and therefore need to read them } directly. I gather this NIST format is identical to that used by } Thermo-Finnigan XCalibur software. } Many thanks, } Kajjo } } ****************************************************************************** From: RichY Date: Thu, 16 Sep 2004 22:06:38 GMT Subject: Re: PROMs for saturn II GC-MS Organization: * The issue here is that the SAP board is outfitted with eproms labeled CI option revision XXX and the software they are currently running gives the ERROR: INVALID PRom REVISION . The software revision does not seem to support any CI option and causes other problems with diagnostics and data acquisition. The question is what software revision for the Saturn 1 or 2 will support the CI option firmware? Another possiblility is to replace the CI option eproms with standard Eproms . Any help in locating any of these would be appreciated by the grad students at BYU "lailiang" wrote in message inews:ci9ig8$q58$1@news-int.gatech.edu... } Mr. Yelton from Spectratek helped me to make saturn II GC-MS running, } unfortunately the PROMs (the firmware we have is specially for CI, we want } to do EI instead) doesn't fit for the software we have (Version 1.1 and } 5.2), does anyone have such PROM that I may be able to buy or give me an } offer? Thanks in advance for help and any response would be greatly } appreciated! } } } ****************************************************************************** From: Michael Gehm Date: 17 Sep 2004 07:16:29 -0700 Subject: Looking for mass spectra of two petroleum fuels Organization: * Hi, I'm looking for the mass spectra of two relatively similar petroleum fuels (gasolene and kerosene, preferably, but I'm flexible), in a tabular, text-based form. This is for a simulation I'm writing. I'm unlikely to ever need any other mass-spectra, so purchasing a library is out of the question. Does anyone have any pointers to a location where I can get free MS of these two materials? Thanks, -M ****************************************************************************** From: lailiang Date: Fri, 17 Sep 2004 14:10:17 -0600 Subject: Re: PROMs for saturn II GC-MS Organization: * Thank you for your help, Richard. "RichY" wrote in message news:cid2v7$p9j$1@news-int.gatech.edu... } The issue here is that the SAP board is outfitted with eproms labeled CI } option revision XXX and the software they are currently running gives the } ERROR: INVALID PRom REVISION . The software revision does not seem to } support any CI option and causes other problems with diagnostics and data } acquisition. The question is what software revision for the Saturn 1 or 2 } will support the CI option firmware? Another possiblility is to replace } the } CI option eproms with standard Eproms . Any help in locating any of these } would be appreciated by the grad students at BYU } } "lailiang" wrote in message } inews:ci9ig8$q58$1@news-int.gatech.edu... } } Mr. Yelton from Spectratek helped me to make saturn II GC-MS running, } } unfortunately the PROMs (the firmware we have is specially for CI, we } want } } to do EI instead) doesn't fit for the software we have (Version 1.1 and } } 5.2), does anyone have such PROM that I may be able to buy or give me an } } offer? Thanks in advance for help and any response would be greatly } } appreciated! } } } } } } } } ****************************************************************************** From: lailiang Date: Fri, 17 Sep 2004 14:08:59 -0600 Subject: ePROMs board Organization: * We are looking for replacement ePROMs board for our Saturn I ion trap mass spectrometer. Does anyone have Saturn I or II which is out of service that we can purchase? By the way, I was told that the part number of the ePROMs board from Varian is X392054400 (SAP board). Thanks in advance for helps! ****************************************************************************** From: David Sparkman Date: Sun, 19 Sep 2004 12:11:08 GMT Subject: Re: Looking for mass spectra of two petroleum fuels Organization: * M, As I am sure you are aware, both gasoline and kerosene are mixtures of hundreds of different compound, if not thousands. A mass spectrum of either of these substances would be the mass spectrum of a mixture of compounds that have different boiling points. Introduction of such a sample into the mass spectrometer would be difficult be cause of fractionation that would take place in the vacuum system and during a data acquisition. Getting a characteristic spectrum of either of these materials presents a challenge. People in forensic have looked at obtain an average spectrum from a GC/MS analysis of fire debris for characterization of such mixtures, but other than that, I am not aware of A mass spectrum of either gasoline or kerosene. Spectra of neither of these two substances can be found in any of the commercial mass spectral database, because the databases are of pure compounds. What are you trying to accomplish? Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "Michael Gehm" wrote in message news:cievfh$3cg$1@news-int.gatech.edu... } } Hi, } } I'm looking for the mass spectra of two relatively similar petroleum } fuels (gasolene and kerosene, preferably, but I'm flexible), in a } tabular, text-based form. } } This is for a simulation I'm writing. I'm unlikely to ever need any } other mass-spectra, so purchasing a library is out of the question. } Does anyone have any pointers to a location where I can get free MS of } these two materials? } } Thanks, } } -M } ****************************************************************************** From: Kajjo Date: 19 Sep 2004 09:10:57 -0700 Subject: Thermo XCalibur RAW data file format Organization: * Dear David, thanks for the reply, which somewhat clarified the situation a little bit. I know now, that I am just looking for the binary structure and GC/MS data file format of Themo Finnigan XCalibur RAW files. Anyway, I need to bulk process and read XCalibur RAW files and would appreciate any clues on how to natively, directly read those RAW files, at least in case of simple one-dimensional GC/MS data. By the way, I feel that reading ones own data files to process them in a different way than provided by standard acquisition software should be nothing to be blocked from by GC/MS companies. Best regards, Kajjo David Sparkman wrote in message news:... } Kajjo, } } There is no such thing as an NIST GC/MS data file and therefore, there can } be no file format. The Thermo Electron Finnigan Xcalibur, Waters Micromass, } and P&E systems produce chromatography/mass spectrometry data files that } have a raw extension. The default mass spectral search engine used by the } Xcalibur and P&E systems is the NIST MS Search program's. The NIST MS } Search Program reads data files that are in a text format and have the } extension .msp. I can supply you with this format. } } NIST has developed a program for the analysis of chromatographic/mass } spectrometry data called AMDIS (Automated Mass spectral Deconvolution and } Identification System) which reads the data file formats from most of the } commercial C/MS system. AMDIS does not have a proprietary file format } either. } } AMDIS can only read the Xcalibur files when Xcalibur has been installed on } the same computer that AMDIS is installed on. } } Go to http://chemdata.nist.gov for more information about the NIST MS Search } Program and AMDIS. } } Regards; } David } } -- } O. David Sparkman } Consultant-At-Large } ods no @ spam compuserve.com } "Kajjo" wrote in message } } } } Hi folks, } } does anyone know the structure of the NIST GC/MS data file format (not } } the library format), usually with the extension *.raw? I'd like to } } bulk process those GC/MS runs and therefore need to read them } } directly. I gather this NIST format is identical to that used by } } Thermo-Finnigan XCalibur software. } } Many thanks, } } Kajjo } } } } ****************************************************************************** From: David Sparkman Date: Mon, 20 Sep 2004 03:25:28 GMT Subject: Re: Thermo XCalibur RAW data file format Organization: * Kojjo, This is something you will have to take up with Thermo. They supply NIST with an application that will allow you to read the information in their data file, not the file format. If you have the ability to create the Excalibur files, this application should serve your purposes. The application will only work on systems where Xcalibur is installed. Remember, that I am the "messenger", this is not my policy. The issue is with Thermo, not me. Good Luck!! Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "Kajjo" wrote in message news:cile6v$s54$1@news-int.gatech.edu... } } Dear David, } thanks for the reply, which somewhat clarified the situation a little } bit. I know now, that I am just looking for the binary structure and } GC/MS data file format of Themo Finnigan XCalibur RAW files. } } Anyway, I need to bulk process and read XCalibur RAW files and would } appreciate any clues on how to natively, directly read those RAW } files, at least in case of simple one-dimensional GC/MS data. } } By the way, I feel that reading ones own data files to process them in } a different way than provided by standard acquisition software should } be nothing to be blocked from by GC/MS companies. } } Best regards, } Kajjo } } } David Sparkman wrote in message news:... } } Kajjo, } } } } There is no such thing as an NIST GC/MS data file and therefore, there can } } be no file format. The Thermo Electron Finnigan Xcalibur, Waters Micromass, } } and P&E systems produce chromatography/mass spectrometry data files that } } have a raw extension. The default mass spectral search engine used by the } } Xcalibur and P&E systems is the NIST MS Search program's. The NIST MS } } Search Program reads data files that are in a text format and have the } } extension .msp. I can supply you with this format. } } } } NIST has developed a program for the analysis of chromatographic/mass } } spectrometry data called AMDIS (Automated Mass spectral Deconvolution and } } Identification System) which reads the data file formats from most of the } } commercial C/MS system. AMDIS does not have a proprietary file format } } either. } } } } AMDIS can only read the Xcalibur files when Xcalibur has been installed on } } the same computer that AMDIS is installed on. } } } } Go to http://chemdata.nist.gov for more information about the NIST MS Search } } Program and AMDIS. } } } } Regards; } } David } } } } -- } } O. David Sparkman } } Consultant-At-Large } } ods no @ spam compuserve.com } } "Kajjo" wrote in message } } } } } } Hi folks, } } } does anyone know the structure of the NIST GC/MS data file format (not } } } the library format), usually with the extension *.raw? I'd like to } } } bulk process those GC/MS runs and therefore need to read them } } } directly. I gather this NIST format is identical to that used by } } } Thermo-Finnigan XCalibur software. } } } Many thanks, } } } Kajjo } } } } } } } ****************************************************************************** From: Richard Wall Date: Mon, 20 Sep 2004 09:01:56 +0100 Subject: Re: Thermo XCalibur RAW data file format Organization: * Dear Kajjo The MS companies including Thermo have been forced to encrypt their RAW data files by the Pharmaceutical industry and the decision to do so makes a lot of sense. For security of data it is necessary that users cannot without specialist knowledge gain access to the raw data and edit it as to do so could enable falsification of results. From what you are saying in that you only wish to look at one (surely you mean two) dimensional data you should be looking at an exported file format as the raw file provides three dimensional data and complete audit trail and acquisition data ? Good luck Regards Richard "Kajjo" wrote in message news:cile6v$s54$1@news-int.gatech.edu... } } Dear David, } thanks for the reply, which somewhat clarified the situation a little } bit. I know now, that I am just looking for the binary structure and } GC/MS data file format of Themo Finnigan XCalibur RAW files. } } Anyway, I need to bulk process and read XCalibur RAW files and would } appreciate any clues on how to natively, directly read those RAW } files, at least in case of simple one-dimensional GC/MS data. } } By the way, I feel that reading ones own data files to process them in } a different way than provided by standard acquisition software should } be nothing to be blocked from by GC/MS companies. } } Best regards, } Kajjo } } } David Sparkman wrote in message } news:... } } Kajjo, } } } } There is no such thing as an NIST GC/MS data file and therefore, there } can } } be no file format. The Thermo Electron Finnigan Xcalibur, Waters } Micromass, } } and P&E systems produce chromatography/mass spectrometry data files that } } have a raw extension. The default mass spectral search engine used by } the } } Xcalibur and P&E systems is the NIST MS Search program's. The NIST MS } } Search Program reads data files that are in a text format and have the } } extension .msp. I can supply you with this format. } } } } NIST has developed a program for the analysis of chromatographic/mass } } spectrometry data called AMDIS (Automated Mass spectral Deconvolution } and } } Identification System) which reads the data file formats from most of } the } } commercial C/MS system. AMDIS does not have a proprietary file format } } either. } } } } AMDIS can only read the Xcalibur files when Xcalibur has been installed } on } } the same computer that AMDIS is installed on. } } } } Go to http://chemdata.nist.gov for more information about the NIST MS } Search } } Program and AMDIS. } } } } Regards; } } David } } } } -- } } O. David Sparkman } } Consultant-At-Large } } ods no @ spam compuserve.com } } "Kajjo" wrote in message } } } } } } Hi folks, } } } does anyone know the structure of the NIST GC/MS data file format (not } } } the library format), usually with the extension *.raw? I'd like to } } } bulk process those GC/MS runs and therefore need to read them } } } directly. I gather this NIST format is identical to that used by } } } Thermo-Finnigan XCalibur software. } } } Many thanks, } } } Kajjo } } } } } } } ****************************************************************************** From: Joerg Hau Date: Mon, 20 Sep 2004 11:39:30 +0200 Subject: Re: Thermo XCalibur RAW data file format Organization: * Hi } I know now, that I am just looking for the binary structure and } GC/MS data file format of Themo Finnigan XCalibur RAW files. } } Anyway, I need to bulk process and read XCalibur RAW files and would } appreciate any clues on how to natively, directly read those RAW } files, at least in case of simple one-dimensional GC/MS data. As far as I'm aware, the Xcalibur CD contains a SDK (not installed by default), which should allow you to do this. The ".raw" files are supposed to be accessed via some COM/OCX interface, which implies that you are bound to M$ Windows :-( As for the native format: according to the answer I got from Thermo regarding a very similar request, their data data format is not "available" in any way. Not even by signing a NDA. I know, however, that a few people are working on reverse-engineering these files (and that of other manufacturers). Due to the complete lack of manufacturer support, this still bears the risk of some "false readings", but IMHO it is better that nothing.    } By the way, I feel that reading ones own data files to process them } in a different way than provided by standard acquisition software } should be nothing to be blocked from by GC/MS companies. I wholeheartily agree. After all, these data are yours, not Thermo's. Footnote: I don't know what you are planning to do, but you may eventually export the data in netCDF format and work with that. It's far from being fast (due to the CDF data file structure, which is not a random access file), but at least the read/write routines are publicly available ... and they work on any platform. Cheers + HTH,   - Joerg   -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove the obvious from my address to reply ****************************************************************************** From: Richard B. Opsal Date: 20 Sep 2004 06:30:04 -0700 Subject: Re: Thermo XCalibur RAW data file format Organization: * Kajjo, I believe the only Thermo supported method for obtaining MS spectra out of the XCalibur data files is to use Thermo's XDK (XCalibur Development Kit). You need to install the XDK when installing XCalibur. I don't know of any Thermo released document describing their XCalibur file format. I also believe you need to be a Visual Basic or Visual C++ program to access the XDK routines. Richard ****************************************************************************** From: Michael Coleman Date: Mon, 20 Sep 2004 10:59:01 -0500 Subject: Re: Thermo XCalibur RAW data file format Organization: * Richard Wall writes: } The MS companies including Thermo have been forced to encrypt their } RAW data files by the Pharmaceutical industry and the decision to do } so makes a lot of sense. For security of data it is necessary that } users cannot without specialist knowledge gain access to the raw } data and edit it as to do so could enable falsification of results. This would be such an absurd rationale that I have a hard time believing it could possibly be true. (Do they also forbid scientists to load and run their own gels, for fear that they'll cheat on them as well?) Do you have a reference on this? I thought that the reason for this (otherwise ridiculous) requirement was to allow Thermo and friends to sell more licenses for this very expensive conversion software. (There's also a tendency in the Windows world to prefer API's over standard file formats and protocols, even though the latter are almost always the superior engineering solution.) Regards, Mike ****************************************************************************** From: David Sparkman Date: Tue, 21 Sep 2004 12:11:09 GMT Subject: The Nitrogen Rule Organization: * Can anyone tell of the first use of the term "nitrogen rule" in the literature? Even if the term was used in an article. I have found the term in John Bynon's 1960 book, again in the book he wrote with Saunders and Williams (The Mass Spectra of Organic Molecules, 1968), in McLaffery's Interpretation of Mass Spectra, 2nd ed. (but not in the 1st edition), and, of course, in wide use after 1973. Is this term widely used in early organic chemistry? If so, what are some citations? Any help will be greatly appreciated. Please post your answers on this site. Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com ****************************************************************************** From: David Stranz Date: Tue, 21 Sep 2004 10:49:41 -0500 Subject: Re: Thermo XCalibur RAW data file format Organization: * Michael Coleman wrote in news:cin5on$atk$1@news-int2.gatech.edu: } Richard Wall writes: } } The MS companies including Thermo have been forced to encrypt } their } RAW data files by the Pharmaceutical industry and the } decision to do } so makes a lot of sense. For security of data } it is necessary that } users cannot without specialist knowledge } gain access to the raw } data and edit it as to do so could } enable falsification of results. } } This would be such an absurd rationale that I have a hard time } believing it could possibly be true. (Do they also forbid } scientists to load and run their own gels, for fear that they'll } cheat on them as well?) Do you have a reference on this? } } I thought that the reason for this (otherwise ridiculous) } requirement was to allow Thermo and friends to sell more } licenses for this very expensive conversion software. (There's } also a tendency in the Windows world to prefer API's over } standard file formats and protocols, even though the latter are } almost always the superior engineering solution.) } } Regards, } Mike } } Mike, Perhaps you aren't in the pharmaceutical industry, which has the FDA and 21 CFR 11 rules to contend with. The rationale for not allowing end users to >>>modify<<< data is very sound and very valid under these operating conditions. I don't know that the files are encrypted; I do know that they are in a binary format that has not been made public. Except for Agilent's ChemStation, most vendors have the same policy with respect to their file formats. They want to be free to change them at will to support new instruments or new experiments, to ensure that when a pharmaceutical company conducts an FDA audit that they can assure them that raw data is secure, and basically to protect their heavy IP investments in designing and implementing secure and efficient data storage formats and access mechanisms. The Xcalibur XDK, as others have said, allows >>read only<< access to all of the data stored during an Xcalibur acquisition. This development kit allows ANYONE to write software to read Xcalibur files, as we and others have done in writing our applications. If you want to write such a file reader and get rich off the income, Thermo have given you the tools to do it. As a professional mass spectrometry software developer, I much prefer published, documented APIs over published file formats. I don't want to have to reimplement my software to read MS files every time a vendor changes formats. I don't want to have to spend my resources writing such software in the first place. Far better for me that the vendor writes and supports this API, ensures that I am insulated from changes in their underlying file formats, and lets me focus on writing applications of use to mass spectrometrists instead of wasting time keeping up with the vendors and their file formats. I really don't care how the data are stored; I'm merely interested in being able to read it, and nearly all the vendors have provided a means to do so. And sorry, Joerg, but the MS data system world is almost totally an MS Windows world. Business, not necessarily technical, reasons have driven this decision. The vast majority of MS users prefer a Windows-based platform, not because it's the best there is, but because they are familiar with it and because every other computer they use in their business and at home is also Windows-based. The IT department and the company executives like it, too. None of us who develop software like it much, but if you want to develop commercially viable products, you're stuck with it. Best regards, David ****************************************************************************** From: David Stranz Date: Tue, 21 Sep 2004 10:49:41 -0500 Subject: Re: Thermo XCalibur RAW data file format Organization: * Michael Coleman wrote in news:cin5on$atk$1@news-int2.gatech.edu: } Richard Wall writes: } } The MS companies including Thermo have been forced to encrypt } their } RAW data files by the Pharmaceutical industry and the } decision to do } so makes a lot of sense. For security of data } it is necessary that } users cannot without specialist knowledge } gain access to the raw } data and edit it as to do so could } enable falsification of results. } } This would be such an absurd rationale that I have a hard time } believing it could possibly be true. (Do they also forbid } scientists to load and run their own gels, for fear that they'll } cheat on them as well?) Do you have a reference on this? } } I thought that the reason for this (otherwise ridiculous) } requirement was to allow Thermo and friends to sell more } licenses for this very expensive conversion software. (There's } also a tendency in the Windows world to prefer API's over } standard file formats and protocols, even though the latter are } almost always the superior engineering solution.) } } Regards, } Mike } } Mike, Perhaps you aren't in the pharmaceutical industry, which has the FDA and 21 CFR 11 rules to contend with. The rationale for not allowing end users to >>>modify<<< data is very sound and very valid under these operating conditions. I don't know that the files are encrypted; I do know that they are in a binary format that has not been made public. Except for Agilent's ChemStation, most vendors have the same policy with respect to their file formats. They want to be free to change them at will to support new instruments or new experiments, to ensure that when a pharmaceutical company conducts an FDA audit that they can assure them that raw data is secure, and basically to protect their heavy IP investments in designing and implementing secure and efficient data storage formats and access mechanisms. The Xcalibur XDK, as others have said, allows >>read only<< access to all of the data stored during an Xcalibur acquisition. This development kit allows ANYONE to write software to read Xcalibur files, as we and others have done in writing our applications. If you want to write such a file reader and get rich off the income, Thermo have given you the tools to do it. As a professional mass spectrometry software developer, I much prefer published, documented APIs over published file formats. I don't want to have to reimplement my software to read MS files every time a vendor changes formats. I don't want to have to spend my resources writing such software in the first place. Far better for me that the vendor writes and supports this API, ensures that I am insulated from changes in their underlying file formats, and lets me focus on writing applications of use to mass spectrometrists instead of wasting time keeping up with the vendors and their file formats. I really don't care how the data are stored; I'm merely interested in being able to read it, and nearly all the vendors have provided a means to do so. And sorry, Joerg, but the MS data system world is almost totally an MS Windows world. Business, not necessarily technical, reasons have driven this decision. The vast majority of MS users prefer a Windows-based platform, not because it's the best there is, but because they are familiar with it and because every other computer they use in their business and at home is also Windows-based. The IT department and the company executives like it, too. None of us who develop software like it much, but if you want to develop commercially viable products, you're stuck with it. Best regards, David ****************************************************************************** From: Beverley Earl Date: Wed, 22 Sep 2004 10:08:37 +0100 (BST) Subject: Diffusion Pumps Organization: * Dear List Members We have a HP 5989 MS Engine and it has developed a problem whereby after trying to restart the instrument after a full shut down the diffusion pumps didn^Òt appear to come on. The manifold pressure did not fall below 4x10-2, hence the thought that these pumps did not come on, there was also a distinct lack of heat and the MS fault light came on. Unfortunately there is also a problem with the chiller which is stuck at 9oC; this is below the minimum recommended in the manual which may have caused the thermal cut out switch preventing the pumps coming on. However the chiller has been problematic for a while and has reached this temperature and lower before, there is another possibility that there is a problem with the power distribution board as the MS fault light came on. Please advise as to the solution to the problem and which is the more likely option for the fault? For example how easy are the boards to change as we have a spare instrument but no service contract? Many thanks Beverley Earl ****************************************************************************** From: Tom Crabtree Date: Wed, 22 Sep 2004 10:51:56 -0700 Subject: Re: Diffusion Pumps Organization: * The first step is to verify that the mechanical pumps are providing enough vacuum for the diffusion pumps to turn on. Make sure the system is leak free. Providing that the mechanical pumps are operational the next thing to check is that there is voltage to heater element on the diffusion pump. If there is no voltage to the heater element then the problem is likely in the electronics. If you have voltage then check continuity of heater element. If you still are not getting heating, check the continuity of the thermal trip device on diffusion pump. Although the chiller is running a little cold it should not cause any problems with operation of diffusion pump. It will however cause all kinds of problems with condensate dripping from over cold cooling pipes quite possibly into delicate electronics, but that's hopefully another issue entirely. Good luck! TomC Beverley Earl wrote: } Dear List Members } } We have a HP 5989 MS Engine and it has developed a problem whereby after } trying to restart the instrument after a full shut down the diffusion } pumps didn^Òt appear to come on. } } The manifold pressure did not fall below 4x10-2, hence the thought that } these pumps did not come on, there was also a distinct lack of heat and } the MS fault light came on. } } Unfortunately there is also a problem with the chiller which is stuck at } 9oC; this is below the minimum recommended in the manual which may have } caused the thermal cut out switch preventing the pumps coming on. However } the chiller has been problematic for a while and has reached this } temperature and lower before, there is another possibility that there is } a problem with the power distribution board as the MS fault light came } on. Please advise as to the solution to the problem and which is the more } likely option for the fault? For example how easy are the boards to } change as we have a spare instrument but no service contract? } } Many thanks } } Beverley Earl } } } ****************************************************************************** From: Steve Date: Wed, 22 Sep 2004 16:08:58 -0400 Subject: Re: Diffusion Pumps Organization: * Also check your fuses. I seem to remember our diff pumps failed because a fuse blew on the 5989. Our other major problem was that although the pumps started ok they overheated and then shut down, and that was due to blocked cooling lines. The cooler was running but not actually circulating through the system. Then all we would see is poor vacuum and cold pumps....but there are error lights on the back board behind the pumps to show you whether the diff pumps are actually starting or not. ------------------------------------------------ Dr. Stephen J. Eyles Director, Mass Spectrometry Facility University of Massachusetts - Amherst Polymer Science & Engineering A-528 Conte Building 120 Governors Drive Amherst, MA 01003, USA eyles@polysci.umass.edu Tel: (413) 577-1528 Fax: (413) 545-0082 ------------------------------------------------ ****************************************************************************** From: nick Date: Thu, 23 Sep 2004 10:51:48 -0400 Subject: Micromass Quattro Micro Organization: * Hey All, I have a Micromass Quattro Micro that I am looking to find a home for. If you are interested call me at 617-332-4790. -Nick ****************************************************************************** From: Chip Cody Date: 23 Sep 2004 09:49:42 -0700 Subject: Re: Thermo XCalibur RAW data file format Organization: * I can't speak for any other vendors, but we can't blame 21 CFR Part 11 for proprietary databases. All of our customers who must comply with 21 CFR Part 11 regulations have either 3rd party commercial (e.g. Nugenesis or equivalent) or proprietary archival software that blocks write access to a datafile. Therefore it doesn't matter if someone knows _how_ to edit a datafile -- they are not permitted write access to the original datafile. The data format for the Shrader software that we use on our GCmates has a fully documented data format, yet we have customers operating in 21CFR.11 - compliant facilities. That being said, it is often more practical to provide a documented function library that allows the used to extract data from a proprietary data format. It is often more portable, reliable and practical for the 3rd-party programmer to use the library functions than to reinvent the wheel and try to access the proprietary data format. This is easier for the vendor to support through format revisions and it ensures that the data format is read correctly by the 3rd party programmer. The decision about what data access method is provided depends on the complexity of the data format, frequency of format changes, and a lot of other factors. TSome tools are publicly available. The andi-MS (netCDF) data format was designed to provide a common data interchange format. Most vendors provide andi_MS data import and export. It is still a useful standard, but growing data file sizes and the development of new data formats to describe innovative experiments means that the common data format has lagged behind the state of the art. There are also commercial data exchange programs such as MassTransit from Palisades and ChromView from ChemSW that provide data interchange functions. Chip Cody } Michael Coleman wrote in } news:cin5on$atk$1@news-int2.gatech.edu: } } } Richard Wall writes: } } } The MS companies including Thermo have been forced to encrypt } } their } RAW data files by the Pharmaceutical industry and the } } decision to do } so makes a lot of sense. For security of data } } it is necessary that } users cannot without specialist knowledge } } gain access to the raw } data and edit it as to do so could } } enable falsification of results. } } } } This would be such an absurd rationale that I have a hard time } } believing it could possibly be true. (Do they also forbid } } scientists to load and run their own gels, for fear that they'll } } cheat on them as well?) Do you have a reference on this? ****************************************************************************** From: Joerg Hau Date: Fri, 24 Sep 2004 10:51:01 +0200 Subject: Accessibility of data file formats (was: Re: Thermo XCalibur RAW Organization: * Hi David et al., } I don't know that the files are encrypted; I do know that they are } in a binary format that has not been made public. Except for } Agilent's ChemStation, most vendors have the same policy with } respect to their file formats. They want to be free to change them } at will to support new instruments or new experiments, to ensure } that when a pharmaceutical company conducts an FDA audit that they } can assure them that raw data is secure, and basically to protect } their heavy IP investments in designing and implementing secure and } efficient data storage formats and access mechanisms. ... yet disclosing a file format does not exclude future extension nor backward-compatibility. One example of a commercial, widespread, proprietary, yet publicly disclosed and available "data format" is Adobe's PDF: Adobe alone defines it, it has already undergone a number of extensions and changes, yet there are many non-proprietary applications (including libraries/APIs for almost all operating systems and hardware platforms) that allow reading/writing PDF files. } I really don't care how the data are stored; I'm merely interested } in being able to read it, Thanks for pointing this out, and yes: Full ACK :-) } And sorry, Joerg, but the MS data system world is almost totally an } MS Windows world. Business, not necessarily technical, reasons } have driven this decision. I know. Especially for the business part. Yet ... while most data acquisition and desktop data processing systems are being built and run under Microsoft Windows, most of the "number-crunching" applications (in particular those related to "omics") are developed and run on Linux or other "-ix" systems. And this is one of the reasons why I have a need to access MS data files "generated on a Windows PC" from Linux. I really wish the MS manufacturers would bother to provide some means of accessing data _across_ platforms. The API/libaries you mention are usually MS-Windows-only and/or limited to a given programming language (usually Microsoft Visual Basic). Thus, when switching to another platform, I would have to reinvent the wheel and work directly off the binary data format (if it were available). This is the reason why I currently prefer to work off an an independent data exchange format such as netCDF, albeit it does not support "all" extensions (such as MS/MS mixed with MS scans), and its implementation is often somewhat buggy (ChemStation). Just my (very personal) 2 cts ... Cheers & best regards, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove the obvious from my address to reply ****************************************************************************** From: ILya A Mikhasenko Date: 24 Sep 2004 02:26:22 -0700 Subject: LC/MSD API-ES Capillary and Chamber Current params unstable Organization: * Hello there dear colleagues, I'm using Agilent 1100 LC and G1946C MSD with API-ES source for drugs detection in blood plasma. So there is a trouble occurs: MSD error and run stop in random time after analysis had started. There is a record in a logbook: «SprayChamber/Capillary voltage cannot be maintained" There is a capillary voltage splash to 1500 nA before the error, some times this parameter oscillates in 0-16 nA range. In previous successful runs Capillary voltage was in 40-90 nA range. Chamber current is generally about 1.4 uA. But some time also goes to 10 uA, and then returns back, but no error occurs. So my question is what is that capillary and chamber current parameters, what does it show, and what are they depend on? May be you faced such things before. Thank you. ****************************************************************************** From: Jeff Gambera Date: Sun, 26 Sep 2004 17:59:26 GMT Subject: Re: Diffusion pumps Organization: * These diffusion pumps have a low temp cutout switch as well as a high temp cutout. It seems that the low temp cutout has tripped preventing the diff pumps from heating. Keel the cooling water within limits. Bill Heriot NIAID (415) 884-0221 ****************************************************************************** From: Phil Date: Sun, 26 Sep 2004 22:54:25 +0200 Subject: Re: Thermo XCalibur RAW data file format Organization: * Hi Joerg and others, } } As far as I'm aware, the Xcalibur CD contains a SDK (not installed by } default), which should allow you to do this. The ".raw" files are } supposed to be accessed via some COM/OCX interface, which implies } that you are bound to M$ Windows :-( } Yes! There is an SDK called XDK which gives you ANY read access you want to Xcalibur datafiles Yes, you are bound to Windows but it works... } As for the native format: according to the answer I got from Thermo } regarding a very similar request, their data data format is not } "available" in any way. Not even by signing a NDA. } True! } I know, however, that a few people are working on reverse-engineering } these files (and that of other manufacturers). Due to the complete } lack of manufacturer support, this still bears the risk of some } "false readings", but IMHO it is better that nothing. This won't give you much 21 CFR compliance!!! } } } By the way, I feel that reading ones own data files to process them } } in a different way than provided by standard acquisition software } } should be nothing to be blocked from by GC/MS companies. } } I wholeheartily agree. After all, these data are yours, not } Thermo's. } Noone prevents you write your own reading utility. If you need one I have a whole bunch of these! } Footnote: I don't know what you are planning to do, but you may } eventually export the data in netCDF format and work with that. It's } far from being fast (due to the CDF data file structure, which is not } a random access file), but at least the read/write routines are } publicly available ... and they work on any platform. True! Philippe Levi Thermo Electron France ****************************************************************************** From: Phil Date: Sun, 26 Sep 2004 22:58:48 +0200 Subject: Re: Thermo XCalibur RAW data file format Organization: * Michael, } This would be such an absurd rationale that I have a hard time } believing it could possibly be true. (Do they also forbid scientists } to load and run their own gels, for fear that they'll cheat on them as } well?) Do you have a reference on this? See the 21CFR documents about CRC validation and electronic signature } } I thought that the reason for this (otherwise ridiculous) requirement } was to allow Thermo and friends to sell more licenses for this very } expensive conversion software. (There's also a tendency in the } Windows world to prefer API's over standard file formats and } protocols, even though the latter are almost always the superior } engineering solution.) } Nope... Phil ****************************************************************************** From: Phil Date: Sun, 26 Sep 2004 23:03:59 +0200 Subject: Re: Thermo XCalibur RAW data file format Organization: * Hi Dave and all, } } Mike, } } Perhaps you aren't in the pharmaceutical industry, which has the } FDA and 21 CFR 11 rules to contend with. The rationale for not } allowing end users to >>>modify<<< data is very sound and very } valid under these operating conditions. Totally agreed } } I don't know that the files are encrypted; I do know that they are } in a binary format that has not been made public. Except for } Agilent's ChemStation, most vendors have the same policy with } respect to their file formats. They want to be free to change them } at will to support new instruments or new experiments, to ensure } that when a pharmaceutical company conducts an FDA audit that they } can assure them that raw data is secure, and basically to protect } their heavy IP investments in designing and implementing secure and } efficient data storage formats and access mechanisms. As you said, the datafiles are not encrypted but in a binary format. Maybe Mike is not aware of the difference. } } The Xcalibur XDK, as others have said, allows >>read only<< access } to all of the data stored during an Xcalibur acquisition. This } development kit allows ANYONE to write software to read Xcalibur } files, as we and others have done in writing our applications. If } you want to write such a file reader and get rich off the income, } Thermo have given you the tools to do it. } } As a professional mass spectrometry software developer, I much } prefer published, documented APIs over published file formats. I } don't want to have to reimplement my software to read MS files } every time a vendor changes formats. I don't want to have to spend } my resources writing such software in the first place. Far better } for me that the vendor writes and supports this API, ensures that I } am insulated from changes in their underlying file formats, and } lets me focus on writing applications of use to mass } spectrometrists instead of wasting time keeping up with the vendors } and their file formats. I really don't care how the data are } stored; I'm merely interested in being able to read it, and nearly } all the vendors have provided a means to do so. } I totally agree with Dave on this! If you call "Rawfile.Detector.Chromatogram.Data" or else to access the chromatogram itself, it is 1000 times better than counting bytes in a weird hope to get to the beginning of the chromatogram! } And sorry, Joerg, but the MS data system world is almost totally an } MS Windows world. Business, not necessarily technical, reasons } have driven this decision. The vast majority of MS users prefer a } Windows-based platform, not because it's the best there is, but } because they are familiar with it and because every other computer } they use in their business and at home is also Windows-based. The } IT department and the company executives like it, too. } True! Phil ****************************************************************************** From: Fred Mellon Date: Wed, 29 Sep 2004 11:57:01 +0100 Subject: Re: LC/MSD API-ES Capillary and Chamber Current params unstable Organization: * A colleague of mine had a similar experience with an Agilent MSD. The problem occurred when running gradients with high water content and was basically a condensation problem, exacerbated by build-up of solid material in the spray chamber and ion source (which acted as nucleation centres for condensation). The problem was solved by increasing the drying gas flow and the nebuliser pressure and also by cleaning the source and spray chamber (the spray chamber can be cleaned quite easily by wiping out with 50% isopropanol). You may need to clean once a week if the instrument is used heavily (and with high aqueous solvents). regards, Fred Mellon "ILya A Mikhasenko" wrote in message news:cj13b7$knv$1@news-int2.gatech.edu... } } Hello there dear colleagues, I'm using Agilent 1100 LC and G1946C MSD } with API-ES source for drugs detection in blood plasma. So there is a } trouble occurs: MSD error and run stop in random time after analysis } had started. There is a record in a logbook: «SprayChamber/Capillary } voltage cannot be maintained" There is a capillary voltage splash to } 1500 nA before the error, some times this parameter oscillates in 0-16 } nA range. In previous successful runs Capillary voltage was in 40-90 } nA range. } Chamber current is generally about 1.4 uA. But some time also goes to } 10 uA, and then returns back, but no error occurs. } So my question is what is that capillary and chamber current } parameters, what does it show, and what are they depend on? May be you } faced such things before. Thank you. } ****************************************************************************** From: user@domain.invalid Date: Wed, 29 Sep 2004 13:33:51 +0200 Subject: Carlo Erba GC8000 Organization: * Hi I need specific information about how to control the GC instrument (Carlo Erba GC 8000 Series) by its RS232 interface. The manual does not give any information. I would like to control the instrument by a self written software. Can anyone help? ****************************************************************************** From: Kenneth H.N. Chan Date: Wed, 29 Sep 2004 08:35:28 -0400 Subject: Re: Thermo XCalibur RAW data file format Organization: * Hello All, If you are interested in getting a hold of your data in an XML format, try: http://sashimi.sourceforge.net/index.html Since I'm not a Xcalibur user, I can not tell you if it works, But It does work for Masslynx data. They have ports to both windows and Linux And there are tools to export the XMLmz format to other formats like txt, pkl, mfg, dta. and they have parser (in C) so you don't have to do all the leg work. It is not for the faint of heart, you might have to compile from source... KC "Phil" wrote in message news:cj7svv$f84$1@news-int.gatech.edu... } Hi Joerg and others, } } } } As far as I'm aware, the Xcalibur CD contains a SDK (not installed by } } default), which should allow you to do this. The ".raw" files are } } supposed to be accessed via some COM/OCX interface, which implies } } that you are bound to M$ Windows :-( } } } } Yes! There is an SDK called XDK which gives you ANY read access you want to } Xcalibur datafiles } Yes, you are bound to Windows but it works... } } } As for the native format: according to the answer I got from Thermo } } regarding a very similar request, their data data format is not } } "available" in any way. Not even by signing a NDA. } } } } True! } } } I know, however, that a few people are working on reverse-engineering } } these files (and that of other manufacturers). Due to the complete } } lack of manufacturer support, this still bears the risk of some } } "false readings", but IMHO it is better that nothing. } } This won't give you much 21 CFR compliance!!! } } } } } } By the way, I feel that reading ones own data files to process them } } } in a different way than provided by standard acquisition software } } } should be nothing to be blocked from by GC/MS companies. } } } } I wholeheartily agree. After all, these data are yours, not } } Thermo's. } } } } Noone prevents you write your own reading utility. If you need one I have a } whole bunch of these! } } } Footnote: I don't know what you are planning to do, but you may } } eventually export the data in netCDF format and work with that. It's } } far from being fast (due to the CDF data file structure, which is not } } a random access file), but at least the read/write routines are } } publicly available ... and they work on any platform. } } True! } } Philippe Levi } Thermo Electron France } } } } ****************************************************************************** From: Richard Wall Date: Wed, 29 Sep 2004 19:10:12 +0100 Subject: Re: Carlo Erba GC8000 Organization: * Dear ? The GC8000 series can in theory be controlled via its rs232 connection and instructions for this and how to control via an integrator such as the DP700. Why do you want to do this when a free software control that runs it in windows is available from your local agent and from the factory download site ? As a UK supplier we are happy to deal with UK customers, if abroad you should contact your local agents, details on www.thermo.com or go to the factory web site http://www.ceinstruments.it/ and request a download password. Regards Richard Wall CE Instruments Ltd www.ceinstruments.co.uk wrote in message news:cje9pf$d70$1@news-int2.gatech.edu... } Hi } } I need specific information about how to control the GC instrument } (Carlo Erba GC 8000 Series) by its RS232 interface. The manual does not } give any information. I would like to control the instrument by a self } written software. } Can anyone help? } } ****************************************************************************** From: Harry Dijk Date: Thu, 30 Sep 2004 22:52:40 +0100 Subject: Thermo Instruments Organization: * The following used instruments are now available. Finnigan LCQ classic Finnigan TSQ700 Finnigan SSQ710 Finnigan SSQ7000 Please contact us for further details. www.triplemass.nl ****************************************************************************** From: Sharon C Date: 30 Sep 2004 15:29:45 -0700 Subject: lactose on ESI-mass spec Organization: * When I analyze lactose by ESI-mass spec in positive ion mode, the most intense ion peak is 685.5. The molecular weight of lactose is 342. I have searched the literature and have not been able to find any mention of dimer formation of disaccharides, or any phenomenon that may cause the molecular mass to double. I am fairly certain that this is not a contaminant because I see this phenomenon with other disaccharides (i.e. observe the 2M+H mass). Has anyone else observed this before? Or does anyone know what this molecule may be? Also, if anyone knows of any references that may help me solve this question, I would also appreciate hearing about it/them. ****************************************************************************** From: David Stranz Date: Fri, 01 Oct 2004 16:47:20 -0500 Subject: Re: Thermo XCalibur RAW data file format Organization: * Kenneth H.N. Chan wrote in news:cjee7b$iin$1@news-int.gatech.edu: } Hello All, } } If you are interested in getting a hold of your data in an XML } format, try: } } http://sashimi.sourceforge.net/index.html } } Since I'm not a Xcalibur user, I can not tell you if it works, } But It does work for Masslynx data. } They have ports to both windows and Linux } And there are tools to export the XMLmz format to other formats } like txt, pkl, mfg, dta. and they have parser (in C) so you } don't have to do all the leg work. } } It is not for the faint of heart, you might have to compile from } source... } } KC } I'm almost certain that sashimi also uses the Xcalibur XDK, so now you're another step farther away from the actual raw data. And any intermediate format, no matter if it is andiMS (netCDF) or sashimi (XML) or something else, will involve a loss of information content. Unfortunately, there are no really good solutions yet, and nothing that is truly platform independent. (netCDF and XML -are- platform independent, but the means to get the original data into those formats aren't - you are still stuck with an initial conversion step that can only be done on the source platform). David ****************************************************************************** From: David Stranz Date: Fri, 01 Oct 2004 16:47:20 -0500 Subject: Re: Thermo XCalibur RAW data file format Organization: * Kenneth H.N. Chan wrote in news:cjee7b$iin$1@news-int.gatech.edu: } Hello All, } } If you are interested in getting a hold of your data in an XML } format, try: } } http://sashimi.sourceforge.net/index.html } } Since I'm not a Xcalibur user, I can not tell you if it works, } But It does work for Masslynx data. } They have ports to both windows and Linux } And there are tools to export the XMLmz format to other formats } like txt, pkl, mfg, dta. and they have parser (in C) so you } don't have to do all the leg work. } } It is not for the faint of heart, you might have to compile from } source... } } KC } I'm almost certain that sashimi also uses the Xcalibur XDK, so now you're another step farther away from the actual raw data. And any intermediate format, no matter if it is andiMS (netCDF) or sashimi (XML) or something else, will involve a loss of information content. Unfortunately, there are no really good solutions yet, and nothing that is truly platform independent. (netCDF and XML -are- platform independent, but the means to get the original data into those formats aren't - you are still stuck with an initial conversion step that can only be done on the source platform). David ****************************************************************************** From: Joerg Hau Date: Mon, 04 Oct 2004 18:40:30 +0200 Subject: sashimi (was: Re: Thermo XCalibur RAW data file format) Organization: * Hi }} If you are interested in getting a hold of your data in an XML }} format, try: }} }} http://sashimi.sourceforge.net/index.html Indeed. That was the one I was referring to in an earlier post. } I'm almost certain that sashimi also uses the Xcalibur XDK, It doesn't. It is quite some time ago that I have been in contact with the sashimi team, but if they used the XDK (a pure MS-Windows product), how would they provide their Linux port? } Unfortunately, there are no really good solutions yet, and nothing } that is truly platform independent. (netCDF and XML -are- platform } independent, but the means to get the original data into those } formats aren't - you are still stuck with an initial conversion step } that can only be done on the source platform). ... because manufacturers do not provide any platform-independant routines, nor any information to write this by yourself (we're back to the starting point ;-) They provide at best a means to do the conversion on _the_ platform where their instrument software runs. Perfectly understandable from a commercial point of view, but as an "end user" I perceive this sometimes as quite annoying. Especially if you want to do things that the original software cannot do. The bad thing is that even these conversion routines are too frequently uncomplete or broken ... as an example, CDF from Waters' MassLynx 4 still pretends to be manufactured by VG (!) and running under MS-DOS. And CDF from Agilent/Chemstation always contain negative masses. Cheers! - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove the obvious from my address to reply ****************************************************************************** From: Bila Date: 5 Oct 2004 08:42:55 -0700 Subject: (ESI)MS/MS: variable fragment pattern? Organization: * My question is related to (ESI)MS/MS fragmentation. The MS/MS product ions of the same compound (M+H)+ was found different measured within an interval of several weeks. The product ions were totally different. Does anybody have an explanation for this behaviour? Thanks! KB ****************************************************************************** From: Mike Sherrell Date: Tue, 5 Oct 2004 13:16:36 -0700 Subject: Grizzly Analytical Mass Specs, MALDIs, etc. available Organization: * Grizzly Analytical Mass Specs, MALDIs, etc. available Mike Sherrell mike@grizzlyanalytical.com 707 887 2919 www.grizzlyanalytical.com **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000: $150,000 installed/warranteed. Sciex API 3000: $190,000 W/ upgrade to ~ API 4000 sensitivity and S/N. API 3000 upgrade: $38,500. Increases sensitivity and (S/N) Ratio at high flow rates to ~ that of an API 4000. Install incl. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $120,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase; incl. install, warr. Sciex API 365: $65,000. NT, turboionspray. Installed, warranteed. Sciex 365 w/ EP10+: $149,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $109,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex Turboionspray source (aka ESI) for API 150, 356 or 3000: $6,250. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $45,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Agilent 1100 VL LC/MSD: offers considered. 2004 system. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. Finnigan LCQ DECA: $67,500. ESI, Xcalibur 1.2, install, warranty incl. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan TSQ 7000 GC/MS: $65,000. GC and LC-capable; Xcalibur. Install, warr. avail. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Bruker Esquire: $85,000. Ion trap. Incl. install, guaranteed. Hitachi M 8000: $82,000. Ion trap. 1999; excellent condition; incl. LC. Micromass Quattro micro API: $150,000; Complete 2000. On factory service contract when deinstalled. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro LCZ: $131,500. Includes installation, warranty. Micromass Quattro IIZ: $149,000. Z-Spray. Includes install, warranty. Micromass Quattro Ultima: Accepting offers; call/email if interested. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $60,000. European install included; available in US. MM Autospec V: $70,000. European install included; available in US. Mass spec sample introduction systems listed under liquid handlers, below. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $67,000. Extensively refurbished. Voyager RP: $44,000. Incl. install; service contracts avail. Will QC peptides; continuous extraction. Voyager Elite XL: offers considered. incl. Vestec Multi-gauge, Advantec fraction collector Voyager MALDI lasers: rebuilt; full warrantee; ~2/3 price of new; install available. Call for info. Mariner ESI-TOF: $45,000. Installed/guar. ok for factory service. MicroMass TOF 2e-Spec: call/email to discuss price. 1999; many options; good working order. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $90,000. 2000 model; Nanoflow-Z CapElectrophoresis electrospray. Guaranteed installable. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $90,000. API-LC/Orth. 2000 model. Manufacturer-certified. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **GC/Other MS: Micromass VG70 SE: $45,000. Hi resolution GC/MS MSI Autoconcept: $380,000. New; multiramp temp; Agilent GC and Agilent or CTC autosampler. Includes install, 1 yr. warranty. Thermoquest GCQ: $30,000. GC/MS/MS; EI/CI; rebuilt; 90-day warranty. Agilent 5973/6890: $65,000. EI/CI/NCI; one year warranty. HP 5890 II/5970B: Offers considered. SmartCard II, software incl. HP 5989 MS engine: $28,500. 2000 amu mass range, pos/neg CI, APCI. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: RichYelton Date: Wed, 06 Oct 2004 16:58:40 GMT Subject: Re: lactose on ESI-mass spec Organization: * Reduce your Lactose sample concentration by 75% and reanalyze to see if it decreases dimer formation. "Sharon C" wrote in message news:cji6gf$g27$1@news-int.gatech.edu... } } When I analyze lactose by ESI-mass spec in positive ion mode, the most } intense ion peak is 685.5. The molecular weight of lactose is 342. I } have searched the literature and have not been able to find any } mention of dimer formation of disaccharides, or any phenomenon that } may cause the molecular mass to double. I am fairly certain that this } is not a contaminant because I see this phenomenon with other } disaccharides (i.e. observe the 2M+H mass). Has anyone else observed } this before? Or does anyone know what this molecule may be? Also, if } anyone knows of any references that may help me solve this question, I } would also appreciate hearing about it/them. } ****************************************************************************** From: RichYelton Date: Wed, 06 Oct 2004 17:04:05 GMT Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Something has changed, check your spray parameters as well as your mobile phase concentration , PH etc.and pump pressure, check to see if the sample decomposes and requires fresh preparation "Bila" wrote in message news:cjul5e$221$1@news-int.gatech.edu... } My question is related to (ESI)MS/MS fragmentation. } The MS/MS product ions of the same compound (M+H)+ was found different } measured within an interval of several weeks. The product ions were } totally different. Does anybody have an explanation for this } behaviour? } } Thanks! } KB } ****************************************************************************** From: Bizzwire Date: Wed, 06 Oct 2004 21:23:56 GMT Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * } Bila wrote } } My question is related to (ESI)MS/MS fragmentation. } The MS/MS product ions of the same compound (M+H)+ was found different } measured within an interval of several weeks. The product ions were } totally different. Does anybody have an explanation for this } behaviour? } } Thanks! } KB } Question1: Is this the first time you've compared MS/MS fragments, or has it been your experience that you always get the kind of reproducible Fragmentation spectra from ESI that you would expect from EI spectra? Question 2: Is this on a trap or a triple., or what? Question 3: Are we talking about gross differences in the spectra (such as ions in one spectrum which are absent in the other), or are we splitting hairs (in one spectrum, ion X is 4.6% of the base peak, but in the other spectrum, it's 5.2%)? Question 4: Have you ever seen a commercial library ofESI MS/MS spectra? Ever wonder why not? I think that there's nothing wrong with your sample or your instrument. The problem lies with your expectations. ****************************************************************************** From: Bila Date: 7 Oct 2004 05:17:43 -0700 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * I will try to describe the situation more detailed. To Q1: I compared the MS/MS spectra run on the same instrument using the same conditions of LC and MS (that means from ESI). To Q2: Measurements were performed on a triple quad (Quantum). To Q3: The differences were heavy (ions in one spectrum were absent in the other); for example, starting from the same parent ion the most abundant fragment ions were the first time 327 and 182 while several weeks later 305 and 488. To Q4: There are several attempts to develop libraries of ESI MS/MS spectra using standardised conditions. } Question1: Is this the first time you've compared MS/MS fragments, or has } it been your experience that you always get the kind of reproducible } Fragmentation spectra from ESI that you would expect from EI spectra? } } Question 2: Is this on a trap or a triple., or what? } } Question 3: Are we talking about gross differences in the spectra (such as } ions in one spectrum which are absent in the other), or are we splitting } hairs (in one spectrum, ion X is 4.6% of the base peak, but in the other } spectrum, it's 5.2%)? } } Question 4: Have you ever seen a commercial library ofESI MS/MS spectra? } Ever wonder why not? } } I think that there's nothing wrong with your sample or your instrument. The } problem lies with your expectations. ****************************************************************************** From: Bila Date: 7 Oct 2004 05:36:35 -0700 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * I agree, something has changed. I took into account the unknowns you mentioned, since I used every time the same LC and MS parameters (Retention time is the same but the fragment spectrum is different; for example: most abundant doughter ions at 305 and 488, and previously at 327 and a minor at 182). The shift of 22Da (305 to 327, most intensive fragments) may suggest to a natrium adduct. Is that possible, since the filtered paren ion was the same? Thanks! RichYelton wrote in message news:... } Something has changed, check your spray parameters as well as your mobile } phase concentration , PH etc.and pump pressure, check to see if the sample } decomposes and requires fresh preparation ****************************************************************************** From: Michael Coleman 0wnRy3zgJosv6 Date: Fri, 08 Oct 2004 18:12:54 -0500 Subject: Re: Thermo XCalibur RAW data file format Organization: * David Stranz writes: } Perhaps you aren't in the pharmaceutical industry, which has the } FDA and 21 CFR 11 rules to contend with. The rationale for not } allowing end users to >>>modify<<< data is very sound and very } valid under these operating conditions. I disagree. It's not necessary to obfuscate the data in order to have proof that it hasn't been modified after leaving the instrument. If that's really the goal, then the instruments could cryptographically sign the data (which would still allow everyone to read and interpret it). This, together with a good archiving system (as mentioned by another poster), would be pretty solid. Counting on an undocumented binary file format to prevent changes is just "security by obscurity" (i.e., fairly worthless or worse). } [Vendors] want to be free to change [file formats] at will to } support new instruments or new experiments, to ensure that when a } pharmaceutical company conducts an FDA audit that they can assure } them that raw data is secure, and basically to protect their heavy } IP investments in designing and implementing secure and efficient } data storage formats and access mechanisms. Changing file formats is something that needs to be planned for, but it's certainly not impossible. A well-designed (perhaps XML-based) file format could be just as extensible as an API. As above, I don't see how the current "secret" formats provide any real security at all. } The Xcalibur XDK, as others have said, allows >>read only<< access } to all of the data stored during an Xcalibur acquisition. This } development kit allows ANYONE to write software to read Xcalibur } files, as we and others have done in writing our applications. If } you want to write such a file reader and get rich off the income, } Thermo have given you the tools to do it. AFAIK, the XDK is only for Windows, and costs money. This seems a lot less desirable than a documented file format, which everyone could write to. Note that it is possible to have both. I'm not trying to deny anyone their API--I'd just like to have access to the raw file. I don't want to have to deal with bugs and security holes in closed-source vendor software if I don't have to, and I don't want to have my platform options needlessly foreclosed. Mike ****************************************************************************** From: JC Date: 8 Oct 2004 18:37:20 -0700 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Bila wrote in message news:... } I will try to describe the situation more detailed. } } To Q1: I compared the MS/MS spectra run on the same instrument using } the same conditions of LC and MS (that means from ESI). } } To Q2: Measurements were performed on a triple quad (Quantum). } } To Q3: The differences were heavy (ions in one spectrum were absent in } the other); for example, starting from the same parent ion the most } abundant fragment ions were the first time 327 and 182 while several } weeks later 305 and 488. } } To Q4: There are several attempts to develop libraries of ESI MS/MS } spectra using standardised conditions. } } } } Question1: Is this the first time you've compared MS/MS fragments, or has } } it been your experience that you always get the kind of reproducible } } Fragmentation spectra from ESI that you would expect from EI spectra? } } } } Question 2: Is this on a trap or a triple., or what? } } } } Question 3: Are we talking about gross differences in the spectra (such as } } ions in one spectrum which are absent in the other), or are we splitting } } hairs (in one spectrum, ion X is 4.6% of the base peak, but in the other } } spectrum, it's 5.2%)? } } } } Question 4: Have you ever seen a commercial library ofESI MS/MS spectra? } } Ever wonder why not? } } } } I think that there's nothing wrong with your sample or your instrument. The } } problem lies with your expectations. Further to your questions, please check: 1- Is this "change" on fragments also the same when using freshly prepared standard of the same compound while the conditions, mobile phase etc are the same ? If the freshly prepared compound found normal, then try to spike an significant amount of the normal compound to your previous sample and do the analysis. Let's see if you can found both in the analysis, if not, try to check your make up solvent. 2- Do you have a record on the product ion scan pattern of your compound when it was normal. And try to get the current "changed" product ion scan spectrum, is the whole spectrum changed ? 3- What is the resolution you set in Q1, Q2 in your TSQ ? I wonder if there is any slightly shift on the mass axis, which will give you totally different spectrum although the chance is slim except there are some ion with similar m/z and RT with your compound. You may verify that by Q1 scan. I have experienced this before and which can be solved by using different HPLC program or different HPLC column. ****************************************************************************** From: Phil Date: Sat, 9 Oct 2004 22:19:38 +0200 Subject: Re: Thermo XCalibur RAW data file format Organization: * Mike, } } The Xcalibur XDK, as others have said, allows >>read only<< access } } to all of the data stored during an Xcalibur acquisition. This } } development kit allows ANYONE to write software to read Xcalibur } } files, as we and others have done in writing our applications. If } } you want to write such a file reader and get rich off the income, } } Thermo have given you the tools to do it. } } AFAIK, the XDK is only for Windows, and costs money. This seems a lot } less desirable than a documented file format, which everyone could } write to. You don't know well! The XDK is STANDARD with EVERY copy of Xcalibur and yes, it is only for Windows!!! } } Note that it is possible to have both. I'm not trying to deny anyone } their API--I'd just like to have access to the raw file. I don't want } to have to deal with bugs and security holes in closed-source vendor } software if I don't have to, and I don't want to have my platform } options needlessly foreclosed. } There are no bugs that I know of dealing with reading rawfiles and, believe me, I have used it extensively!! Which security holes? This is no mission critical stuff!! } Mike Phil ****************************************************************************** From: Mike Coleman Date: 10 Oct 2004 00:21:56 -0400 Subject: Re: Thermo XCalibur RAW data file format Organization: * Phil writes: } } AFAIK, the XDK is only for Windows, and costs money. This seems a lot } } less desirable than a documented file format, which everyone could } } write to. } } You don't know well! The XDK is STANDARD with EVERY copy of Xcalibur and } yes, it is only for Windows!!! Well, Xcalibur costs a lot of money, right? So, one cannot use the XDK without paying a substantial fee. Or am I missing something? } } Note that it is possible to have both. I'm not trying to deny anyone } } their API--I'd just like to have access to the raw file. I don't want } } to have to deal with bugs and security holes in closed-source vendor } } software if I don't have to, and I don't want to have my platform } } options needlessly foreclosed. } There are no bugs that I know of dealing with reading rawfiles and, believe } me, I have used it extensively!! } Which security holes? This is no mission critical stuff!! The point is that without access to the source code, there's no way for us to determine this. You may think of the API-plus-vendor-DLL as a benefit, but realistically it is also a liability. Providing direct access to a (well-designed) raw file would remove this liability. Mike ****************************************************************************** From: Phil Date: Sun, 10 Oct 2004 18:21:38 +0200 Subject: Re: Thermo XCalibur RAW data file format Organization: * } Well, Xcalibur costs a lot of money, right? So, one cannot use the XDK } without paying a substantial fee. Or am I missing something? } If you use a Thermo MS you have Xcalibur + the XDK anyway, don't you? If you don't it obviously is another story. You can always get the xcalibur file converted to CDF or any other format... Phil ****************************************************************************** From: Rich Yelton Date: Tue, 12 Oct 2004 05:23:03 GMT Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Perhaps the increase in mass is due to a sodium adduct. "Bila" wrote in message news:ck3gsk$j1s$1@news-int2.gatech.edu... } I agree, something has changed. } I took into account the unknowns you mentioned, since I used every } time the same LC and MS parameters (Retention time is the same but the } fragment spectrum is different; for example: most abundant doughter } ions at 305 and 488, and previously at 327 and a minor at 182). The } shift of 22Da (305 to 327, most intensive fragments) may suggest to a } natrium adduct. Is that possible, since the filtered paren ion was the } same? } } Thanks! } } } RichYelton wrote in message news:... } }} Something has changed, check your spray parameters as well as your mobile }} phase concentration , PH etc.and pump pressure, check to see if the sample }} decomposes and requires fresh preparation } ****************************************************************************** From: David Stranz Date: Tue, 12 Oct 2004 15:48:02 -0500 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Rich Yelton wrote in news:ckgmkn$afo$1@news-int.gatech.edu: } Perhaps the increase in mass is due to a sodium adduct. } How could that be, if he is selecting on the same precursor ion m/z? This could only happen if he coincidentally had another species in solution that was isobaric when sodiated with his original protonated species. And then, the product ion spectrum should be a mixture of fragments from both species. ****************************************************************************** From: fluorosenor Date: 13 Oct 2004 00:08:37 -0700 Subject: ionization in mass spec Organization: * does anyone know the answers to the following questions or can anyone please give me references for the following questions: (1) how does ionization occur in UV-based MALDI? (2) what is electron capture ionization in mass spectrometry? any help would be greatly appreciated...thanks ****************************************************************************** From: craig3201 Date: 13 Oct 2004 22:49:54 -0700 Subject: Any comments on TOF systems (Bruker vs Leco)? Organization: * Hello All My department is considering the purchase of an LCMS system. Our shortlist has been narrowed to two TOF systems - the Bruker MicroTOF and the Leco UniqueTOF. I would be interested in receiving general comments from anyone using either of these systems with regard to: user-friendliness of both hardware and software, the use of the "accurate mass"-to-formula software in the mass range 200-600 amu (compounds isolated from botanical extracts), any problems associated with installation or general use (resolved or not). General comments are also most welcome. Many thanks, Craig. ****************************************************************************** From: David Sparkman Date: Thu, 14 Oct 2004 12:34:34 GMT Subject: Re: Any comments on TOF systems (Bruker vs Leco)? Organization: * Craig, I would be interested in know what were the knockout factors for the JEOL, Agilent, and Waters LC TOF instruments. Regards; David -- O. David Sparkman Consultant-At-Large ods@compuserve.com "craig3201" wrote in message news:cklodp$q6t$1@news-int2.gatech.edu... } } Hello All } } My department is considering the purchase of an LCMS system. Our } shortlist has been narrowed to two TOF systems - the Bruker MicroTOF } and the Leco UniqueTOF. I would be interested in receiving general } comments from anyone using either of these systems with regard to: } user-friendliness of both hardware and software, the use of the } "accurate mass"-to-formula software in the mass range 200-600 amu } (compounds isolated from botanical extracts), any problems associated } with installation or general use (resolved or not). General comments } are also most welcome. } } Many thanks, } Craig. } ****************************************************************************** From: David Sparkman Date: Thu, 14 Oct 2004 08:39:48 -0400 Subject: What Happened to My Post Organization: * Why was my response to "ionization in mass spec" not posted? RESPONSE This sounds just like homework questions I assigned last week. If this was not covered in class, look at your text book. If you do not have a text book, go to the library and find a copy of Watson's book on Mass Spectrometry. If the library has burned down (I hear this one at least once a week), go to Google and search the topics. If you still can't answer the questions, drop out of school, change your name, dye your hair, and take a bus to another town. Regards; David -- O. David Sparkman Consultant-At-Large osparkma no @ spam uop.edu ****************************************************************************** From: Steen Pontoppidan Date: Thu, 14 Oct 2004 16:04:08 +0200 Subject: JEOL AX 505 W Organization: * A Jeol AX 505 W high resolution mass spectrometer located in Denmark can puchased for a small amount of money. The instrument is equipped with FAB,CI,Negative ion,GC Interface. The 13 year old instrument is used on daily basis and it meets all installation specification. For further information contact Steen Pontoppidan at sp@msvision.dk or +45 40404501 ****************************************************************************** From: Kajjo Date: 14 Oct 2004 11:35:26 -0700 Subject: Re: Thermo XCalibur RAW data file format Organization: * Dear everyone, since I posted my initial message a lot of replies accumulated in the last weeks. However, unfortunately there appears to be no possibility to directly access the XCalibur data files. *sigh* Using the XDK is no solution at all -- whoever might have tried knows very well how painstakingly slow the data extraction executes. Since the XCalibur main program itself is able to load data much faster, it appears they do not even use their own XDK routines. Native reading of data files is by far faster and much more convenient for the user. Bulk processing and routine usage of RAW files in 3rd party programs is something many users require und most users could profit from. I still figure that preventing me from reading my own data is somewhat unbelievable. Whatever pharmaceutical companies might like -- they certainly have much better authentication procedures than just preventing experienced programmers from reading data files. Anyway, such important companies like Agilent or Perkin Elmer do not have any problems with opening their formats with an NDA. So, as far as I understand this situation is just political rather then rational. Customers shouldn't be treated like this. It would be an option to be able to decide inside XCalibur to alternatively or additionally directly write to a popular format like JCAMP, which would conserve the secrecy about RAW and still open up data for further evaluation. Last comment to some suggestions: CDF is the worst GC/MS format ever invented... complicated, slow, tedious, bulky. Thanks again for your comments anyway. Kajjo ****************************************************************************** From: usedlabequip Date: 14 Oct 2004 14:08:59 -0700 Subject: Refurbished Analytical Instrument Worldwide Organization: * ....................................................... IET Ltd. is an authorized Thermo Finnigan Reseller ^ÅTHERMO FINNIGAN NEW ARRIVALS^Å Thermo Finnigan DECA XP PLUS LC/MS/MS Thermo Finnigan DECA LC/MS/MS Thermo Finnigan Quantum LC/MS/MS Thermo Finnigan AQA LC/MS Thermo Finnigan LCQ Classic LC/MS/MS Thermo Finnigan TSQ 7000 LC/MS/MS with API I More IET MASS SPECTROMETERS Micromass Quattro Ultima LC/MS/MS Micromass Q-TOF USA Applied Biosystems Sciex API 2000 LC/MS/MS Applied Biosystems Sciex API 150 MCA LC/MS Shimadzu LCMS 2010 BIOTECHNOLOGY Applied Biosystems Prism 7900 HT Real Time PCR Cohesive 2303 HTLC with CTC HTS Pal Perceptive Biosystems Voyager-DE STR Hewlett Packard 1100 isocratic pumps Beckman Coulter LS 200 particle size analyzer Genomics Solutions GeneTAC Hybridization Station NMR Varian Mercury MVX 300 MHz NMR Varian Unity 500 MHz NMR Bruker AC Plus 300 MHz NMR Bruker Avance DMX 300 MHz NMR Bruker 3mm NMR MicroCryoProbe (500 MHz) For a complete list of our current inventory, please visit us on the web at http://www.ietltd.com or give us a call at 001.847.913.0777 or 1.800.438.4522. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 sales@ietltd.com ........................................................... ****************************************************************************** From: Kendall Date: Fri, 15 Oct 2004 01:07:34 GMT Subject: Re: Any comments on TOF systems (Bruker vs Leco)? Organization: * } My department is considering the purchase of an LCMS system. Our } shortlist has been narrowed to two TOF systems - the Bruker MicroTOF } and the Leco UniqueTOF. I would be interested in receiving general } comments from anyone using either of these systems with regard to: . I am the primary user of my company's two Bruker microTOF instruments - I love 'em. I can't really comment on Leco's system as I've never used it. More specifically, to address your issues: } user-friendliness of both hardware and software, The engineering behind these machines is very impressive. I've found the microTOF to be extremely rugged (we run quite nasty biological samples into them). The mass accuracy over time has minimal drift (due to a temperature compensation feature), the source does *not* require frequent cleaning, I've never had any trouble with the quality of the electrospray, the resolution is phenomenal, etc, etc. *Most* of the control software is really good. The mass spec control software is good, and the data analysis software is very nice - I've had a bit of trouble with Bruker's HyStar software, however (basically their version of Chemstation, which controls the LC as well as the MS). Occasional glitches with this software have, however, always been met with a quick response from their people in Billerica. } the use of the } "accurate mass"-to-formula software in the mass range 200-600 amu } (compounds isolated from botanical extracts), I haven't used their software for this purpose - we have an in house program that does this for us. By the way, we also use the instrument for small molecule analysis (less than 1000 Da). } any problems associated } with installation or general use (resolved or not). General comments } are also most welcome All things considered, I'd definitely recommend this machine. Good luck! -Kendall (for e-mail, replace both "zz" s with "LL" s - spam proofed) ****************************************************************************** From: Kendall Date: Fri, 15 Oct 2004 01:13:13 GMT Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * [snip] } 3- What is the resolution you set in Q1, Q2 in your TSQ ? I wonder if } there is any slightly shift on the mass axis, which will give you } totally different spectrum although the chance is slim except there } are some ion with similar m/z and RT with your compound. You may } verify that by Q1 scan. I have experienced this before and which can } be solved by using different HPLC program or different HPLC column. How can you attribute gas phase fragmentation differences in the MS to some sort of change in the LC column? ****************************************************************************** From: Kendall Date: Fri, 15 Oct 2004 01:18:33 GMT Subject: Re: lactose on ESI-mass spec Organization: * "Sharon C" wrote in message news:cji6gf$g27$1@news-int.gatech.edu... } } When I analyze lactose by ESI-mass spec in positive ion mode, the most } intense ion peak is 685.5. The molecular weight of lactose is 342. I } have searched the literature and have not been able to find any } mention of dimer formation of disaccharides, or any phenomenon that } may cause the molecular mass to double. I am fairly certain that this } is not a contaminant because I see this phenomenon with other } disaccharides (i.e. observe the 2M+H mass). Has anyone else observed } this before? Or does anyone know what this molecule may be? Also, if } anyone knows of any references that may help me solve this question, I } would also appreciate hearing about it/them. dimer formation is very common in ESI - your intuition was right on. try rich's suggestion of lowring the concentration of your analyte - that should favor M+H over M+M+H formation. -Kendall ****************************************************************************** From: Joerg Hau Date: Fri, 15 Oct 2004 22:08:50 +0200 Subject: JCAMP & netCDF (was: Re: Thermo XCalibur RAW data file format) Organization: * Hi, } It would be an option to be able to decide inside XCalibur to } alternatively or additionally directly write to a popular format } like JCAMP, which would conserve the secrecy about RAW and still } open up data for further evaluation. I fully agree to this idea, but JCAMP is a moving target... the draft for JCAMP 6 for MS exists, but is still far from optimal. } CDF is the worst GC/MS format ever invented... complicated, slow, } tedious, bulky. Slow and bulky, yes. Yet ... it is the only format that is publicly available _and_ somewhat supported by (almost) all vendors _and_ available on all platforms! I use CDF in a "two-step conversion" to bring data into the format that I need (e.g. raw -> cdf -> ASCII or whatever) ... and this task can be automated easily. Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove the obvious from my address to reply ****************************************************************************** From: Maria Jose Date: 15 Oct 2004 17:28:02 -0700 Subject: Help with mass spectrometer Organization: * Hello everybody, I am working with a HP 5988A mass spectrometer in the UAMS in Arkansas. Yesterday, suddenly the source manifold pressure changed from 10-6 to 10-4 and the filament light in the gauge controller turned off. First I changed the plug from the filament tube in front to the filament tube behind, and nothing happened. From then to now, every time I try to turn the switch for the gauge controller filament on the indicator led lights for one second and then turns off, and pressure goes from 10-4 to 10-6 for one second and then comes back to 10-4. I cannot also turn the filament on. The filament turns only on when the degas switch is on but then the pressure remains unchanged. I have also checked the column and it hasn't been leaking. Could you please help me? Does anybody have any suggestions? Can it be due to a bad connection or to any defective internal plug in the mass spectrometer???? Thank you in advance for your comments. ****************************************************************************** From: Dr. Dickie Date: Sat, 16 Oct 2004 05:18:46 -0400 Subject: Re: ionization in mass spec Organization: * On 13 Oct 2004 00:08:37 -0700, fluorosenor wrote: } }does anyone know the answers to the following questions or can anyone }please give me references for the following questions: } }(1) how does ionization occur in UV-based MALDI? } Last time I looked into this (about 5 years ago), the census was that it was a variety of processes (depending on analyte, matrix, and other conditions). Some pre-formed in matrix, others formed in plume, possibly others simply by laser interaction. You have quite a bit of homework to do! There was a good book, by Verdes (sp? not sure of the spelling, right now my books are packed in boxes as the wife has ordered an office re-do) covering laser based ionization. You should be able to get enough papers to bury you on the subject. Look into Franz Hillenkamp (again, not sure of spelling. He is the father of current MALDI--I don't care what the Nobel Prize committee says) }(2) what is electron capture ionization in mass spectrometry? } If the name alone does not give you enough information to do your homework, then you are lost. } } }any help would be greatly appreciated...thanks Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: Kent Electronics Date: Sat, 16 Oct 2004 17:49:21 +0100 Subject: VG Bits Organization: * Hello We are clearing out our premises in the UK and have a number of electronics units for Micromass VG ZAB and 70-S sector instruments plus FAB guns and sources etc. There are also electronic units for the Micromass Autospec an including interface unit. We also have an ICS (Flowcool) water chiller type IC20 (3 phase 230V) used for cooling 70-SE. Some old Finnigan spares also availble. All these items must go by November. Many thanks John Hill Kent Electronics ****************************************************************************** From: Ricksfbrsc Date: 18 Oct 2004 00:14:40 GMT Subject: Re: Help with mass spectrometer Organization: * Maria, The behavior you describe is consistent with a leak. 1. Check to make sure that the column nut on the interface is tight (in fact I'd replace the ferrule on general principles if you haven't for a while as they tend to get compressed and don't seal after a while). 2. check that there isn't a break in the column somewhere. The easiest way to do this after a visual scan is to remove the column and seal off the interface (use a solid piece of wire that will snugly fit a ferrule or a solid ferrule). Another advantage of this is that it will isolate the system into two big pieces (MS and GC). If it won't pump down, then the leak is on the MS side. If it pumps down, then the problem is on the GC side. Almost all the time it's either a leaky ferrule or a broken column, especially since it was sudden. Good luck in your hunt. Rick "Maria Jose" <> wrote in message news:... } } Hello everybody, } I am working with a HP 5988A mass spectrometer in the UAMS in } Arkansas. Yesterday, suddenly the source manifold pressure changed } from 10-6 to 10-4 and the filament light in the gauge controller } turned off. First I changed the plug from the filament tube in front } to the filament tube behind, and nothing happened. From then to now, } every time I try to turn the switch for the gauge controller filament } on the indicator led lights for one second and then turns off, and } pressure goes from 10-4 to 10-6 for one second and then comes back to } 10-4. I cannot also turn the filament on. The filament turns only on } when the degas switch is on but then the pressure remains unchanged. I } have also checked the column and it hasn't been leaking. Could you } please help me? Does anybody have any suggestions? Can it be due to a } bad connection or to any defective internal plug in the mass } spectrometer???? } Thank you in advance for your comments. } ****************************************************************************** From: JC Date: 17 Oct 2004 22:27:25 -0700 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Hi Kendall, Yes, the LC column will not affect the fragmentation of a compound. But,I wonder he has picked a wrong parent compound which with very similar molecular mass to his target analyte. That's why I asked him about the resolution and mass axis shift in his system. Remember, the unit resolution is only 0.7 amu at full width at half height. Taking account into the resolution and the mass shift, it may be a chance that the system pick a compound with very similar molecular mass and very similar retention time in the run. If this is being the case, a totally different fragmentation pattern observed is expected. That may be his case. However, such case can be verified by using different HPLC col. if he is picking a wrong parent peak. JC Kendall wrote in message news:... } [snip] } } } 3- What is the resolution you set in Q1, Q2 in your TSQ ? I wonder if } } there is any slightly shift on the mass axis, which will give you } } totally different spectrum although the chance is slim except there } } are some ion with similar m/z and RT with your compound. You may } } verify that by Q1 scan. I have experienced this before and which can } } be solved by using different HPLC program or different HPLC column. } } } How can you attribute gas phase fragmentation differences in the MS to some } sort of change in the LC column? ****************************************************************************** From: David Sparkman Date: Mon, 18 Oct 2004 11:53:53 GMT Subject: Re: ionization in mass spec Organization: * Dr. Dickie, I just read your post in response to "ionization in mass spec" on sci.technique.mass-spec. I am interested in the book you mentioned. I am building a mass spectrometry library that will eventually go to the Chemical Heritage Foundation. I know of one book edited by Kent Voorhees (Analytical Pyrolysis, Techniques and Applications). There is a book edited by David Lubman "Lasers and Mass Spectrometry, but the book you refer to is unknown to me. Any additional information you can provide will be greatly appreciated. BTW, I agree with you about Hillenkamp and Karas. Regards; David O. David Sparkman Consultant-At-Large -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "Dr. Dickie" wrote in message news:ckrbp0$g3t$1@news-int.gatech.edu... } On 13 Oct 2004 00:08:37 -0700, fluorosenor wrote: } } } } }does anyone know the answers to the following questions or can anyone } }please give me references for the following questions: } } } }(1) how does ionization occur in UV-based MALDI? } } } } Last time I looked into this (about 5 years ago), the census was that } it was a variety of processes (depending on analyte, matrix, and other } conditions). Some pre-formed in matrix, others formed in plume, } possibly others simply by laser interaction. You have quite a bit of } homework to do! There was a good book, by Verdes (sp? not sure of the } spelling, right now my books are packed in boxes as the wife has } ordered an office re-do) covering laser based ionization. You should } be able to get enough papers to bury you on the subject. Look into } Franz Hillenkamp (again, not sure of spelling. He is the father of } current MALDI--I don't care what the Nobel Prize committee says) } } }(2) what is electron capture ionization in mass spectrometry? } } } If the name alone does not give you enough information to do your } homework, then you are lost. } } } } } }any help would be greatly appreciated...thanks } } } Dr. Dickie } Skepticult member in good standing #394-00596-438 } Poking kooks with a pointy stick } ==================================== } "Let be be finale of seem. } The only emperor is the emperor of ice-cream" } Wallace Stevens-1923 } ===================================== } ****************************************************************************** From: Olivier Plaut Date: Mon, 18 Oct 2004 18:13:59 +0200 Subject: Re: Help with mass spectrometer Organization: * In addition to what Rick wrote (and was correct) - you should take advantage you have a 5988: it allows you to replace the column by a no-hole ferrule without stopping the pumps. - if the pressure is too high, the gauge will turn off, this is normal.If the gauge turns off, it disconnects the diffusion pump. - your MS is probably in a "vent state" -> you'll have to push the white "pumpdown" button in order initiate the diffusion pump. After 15 minutes you should be able to turn the gauge on and then, after another 15 minutes to release the pumpdown button. Olivier Maria Jose a écrit : } Hello everybody, } I am working with a HP 5988A mass spectrometer in the UAMS in } Arkansas. Yesterday, suddenly the source manifold pressure changed } from 10-6 to 10-4 and the filament light in the gauge controller } turned off. First I changed the plug from the filament tube in front } to the filament tube behind, and nothing happened. From then to now, } every time I try to turn the switch for the gauge controller filament } on the indicator led lights for one second and then turns off, and } pressure goes from 10-4 to 10-6 for one second and then comes back to } 10-4. I cannot also turn the filament on. The filament turns only on } when the degas switch is on but then the pressure remains unchanged. I } have also checked the column and it hasn't been leaking. Could you } please help me? Does anybody have any suggestions? Can it be due to a } bad connection or to any defective internal plug in the mass } spectrometer???? } Thank you in advance for your comments. ****************************************************************************** From: Olivier Plaut Date: Mon, 18 Oct 2004 18:19:36 +0200 Subject: Ions ratio 219/69 inversed in autotune Organization: * Hi everybody, On an Agilent 5973, after cleaning the source, all parameters are normal, except that we have now, for PFTBA, a 219/69 ratio of 130%, instead of 50-70% normally. This means that the base peak of PFTBA is now 219. Has anyone already seen this? Thanks Olivier ****************************************************************************** From: Dr. Dickie Date: Mon, 18 Oct 2004 15:16:46 -0400 Subject: Re: Re: ionization in mass spec Organization: * On Mon, 18 Oct 2004 11:53:53 GMT, David Sparkman wrote: }Dr. Dickie, }I just read your post in response to "ionization in mass spec" on }sci.technique.mass-spec. I am interested in the book you mentioned. I am }building a mass spectrometry library that will eventually go to the Chemical }Heritage Foundation. I know of one book edited by Kent Voorhees (Analytical }Pyrolysis, Techniques and Applications). There is a book edited by David }Lubman "Lasers and Mass Spectrometry, but the book you refer to is unknown }to me. Any additional information you can provide will be greatly }appreciated. } }BTW, I agree with you about Hillenkamp and Karas. } }Regards; }David }O. David Sparkman }Consultant-At-Large Laser Ionization Mass Analysis (Chemical Analysis) by Akos Vertes, et al I just looked in up on Amazon. It is listed as out of print. That is a shame. Perhaps the data was old, but this was invaluable when I was writing my dissertation. Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: lailiang Date: Mon, 18 Oct 2004 14:01:53 -0600 Subject: Fisons 8000 GC series FID detector Organization: * We have a Fisons 8000 series GC , unfortunately the FID detector is out of order, is there anyone who knows where we can get the replacement? This product is not supported by its manufacturer. Thank you in advance for your help! ****************************************************************************** From: reh Date: 18 Oct 2004 12:59:13 -0700 Subject: Re: ionization in mass spec Organization: * Could this be the book: Laser Ionization Mass Analysis Author: Akos Vertes, Fred Adams, Renaat Gijbels Format: Hardcover Published: April 1993 ISBN: 0471536733 List Price: $175.00 Pages: 560 Publisher: John Wiley & Sons Inc Type: Illustrated Synopsis Redefines laser ionization's place in analytical chemistry along with the discovery of several new techniques and their promising applications including laser-solid interaction which is used in diamond synthesis, high temperature superconductor preparation, desorption of large biomolecules and sampling of solids for chemical analysis. Concentrates on the pulsed laser now viewed as a tool of depositing a tunable amount of energy into a chosen degree of material rather than as a fast local surface heating device. ****************************************************************************** From: Ricksfbrsc Date: 18 Oct 2004 22:06:01 GMT Subject: Re: Ions ratio 219/69 inversed in autotune Organization: * all the time. If you want to force the ratio the other way, use the tune designed to do this (I'm at home and don't remember it's name). Basically it adjusts the lens to throw away abundance so that it mets the EPA criteria. This is a historic accident based upon magnetic sector MS getting written into EPA methods before they discovered that they discriminate against higher mass ions. I generally use the eisens tune as it optimizes all the lenses for sensitivity. ****************************************************************************** From: L FRIEDMAN Date: Mon, 18 Oct 2004 23:32:21 GMT Subject: Re: Ions ratio 219/69 inversed in autotune Organization: * Yes many times. On a quad system, the offset, collision, and rf power voltages will affect the low end. Of course, you need to look at the resolution of both these peaks. If 69 is under resolved and or 219 is under resolved, it would look this way. "Olivier Plaut" wrote in message news:cl0sb3$j0l$1@news-int.gatech.edu... } Hi everybody, } } On an Agilent 5973, after cleaning the source, all parameters are } normal, except that we have now, for PFTBA, a 219/69 ratio of 130%, } instead of 50-70% normally. This means that the base peak of PFTBA is } now 219. } } Has anyone already seen this? } } Thanks } Olivier } } ****************************************************************************** From: Richard Wall Date: Mon, 18 Oct 2004 23:50:15 +0100 Subject: Re: Fisons 8000 GC series FID detector Organization: * Strange. The GC8000 series is now out of it's serviceability lifetime having been last manufactured over ten years ago however the detector and amplifier were available with the Tops GC that is still supported in Europe. You should be able to get new replacements from your local Thermo Electron GC supplier as it is still available in Europe. Regards Richard www.ceinstruments.co.uk "lailiang" wrote in message news:cl1b6q$8sf$1@news-int2.gatech.edu... } We have a Fisons 8000 series GC , unfortunately the FID detector is out of } order, is there anyone who knows where we can get the replacement? This } product is not supported by its manufacturer. } } Thank you in advance for your help! } } } } ****************************************************************************** From: Bila Date: 19 Oct 2004 01:18:47 -0700 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Hi JC, it remains still misterious, since the effect was observed not only for one compound (viz 2 compounds with different RT). However, a shift of the mass axis might be a reason. Bila JC wrote in message news:... } Hi Kendall, } } Yes, the LC column will not affect the fragmentation of a compound. } But,I wonder he has picked a wrong parent compound which with very } similar molecular mass to his target analyte. That's why I asked him } about the resolution and mass axis shift in his system. Remember, the } unit resolution is only 0.7 amu at full width at half height. Taking } account into the resolution and the mass shift, it may be a chance } that the system pick a compound with very similar molecular mass and } very similar retention time in the run. If this is being the case, a } totally different fragmentation pattern observed is expected. That may } be his case. However, such case can be verified by using different } HPLC col. if he is picking a wrong parent peak. } JC ****************************************************************************** From: David Sparkman Date: Tue, 19 Oct 2004 08:37:26 -0400 Subject: Re: Ions ratio 219/69 inversed in autotune Organization: * Olivier, Check to see what version of the software you are using. The Autotune may be a maximum senstivity tune. This will cause 219 to become the base peak. Use the Standard Spectrum tune. When Agilent went from G1701B to G1701C what had been enhanced sensitivity tune became auto tune. This is why cocanine had a base peak of 82 on older instruments and 182 on instruments that used the newer versions of software. BTW, Ricksfbrsc, you got it backwards. It was the early quads that discriminated against the high m/z value ions, not the magnetic sectors. The so-called "mass discrimination" was a result of the quads' DC fringe field effects at the filter's entrance and the variable momentum of ions of different m/z values resulting from low velocities (as compared to mag sector instruments) due to the quads' low ion accelerating voltages as ions struck the detector. The problem with fringe fields was corrected using either the Brubaker RF only prefilter or the Turner-Kruger entrance-lens. The ion momentum problem has been addressed with the use of high-energy dynodes at the exit of the quad. The EPA wrote-in the tune that matched the early Finnigan instruments. This caused the current manufactures of quads at the time (including Finnigan) to have to detune their instruments to meet the EPA requirements. The only GC/MS that does not have 69 as the base peak for PFTBA, that I know of, is the Thermo Electron Finnigan Polaris Q. Regards; David O. David Sparkman Consultant-At-Large osparkma no @ spam uop.edu ****************************************************************************** From: "Khristine Anderson, Recruiter" Date: Tue, 19 Oct 2004 09:58:57 -0700 Subject: Analytical Chemist/Mass Spectrometrist - Houston, TX Organization: * Analytical Chemist/Mass Spectrometrist - Houston, TX I am assisting to recruit a Analytical Chemist/Mass Spectrometrist for a pharmaceutical company located in Houston, TX. COMPANY: They are a pharmaceutical company that discovers, develops and commercializes small molecule drugs aimed at cardiovascular and inflammatory diseases. REQUIREMENTS: Requires a Ph. D. degree in an analytical chemistry discipline and minimum 3 years experience in a pharmaceutical company or Master's degree with equivalent experience in a pharmaceutical company. Experience with pharmacokinetic analysis of small molecules highly desirable. The ideal candidate should be proficient in bioanalytical methods development using HPLC and MS instrumentation. The successful candidate will be working and collaborating with other analytical chemistry group members as well as medicinal chemists, biologists, and project teams to provide information that will help in the evaluation of small molecules. Experience on a Finnigan ion trap and/or Micromass QTOF essential with experience on Waters HPLC instruments and associated software would be desirable. Familiarity with other techniques such as IR, UV, and NMR and interpretation of results would be helpful. Must be experienced in the extraction of drugs and metabolites from biological matrices and able to develop HPLC and LC/MS methods from scratch to analyze these small molecules. We require a highly motivated individual who can work with minimum supervision while maintaining work of high quality. Must also have excellent oral and written skills with strong presentation abilities and capable of defending data obtained. Prior supervisory experience would be beneficial. Apply: If you are interested in applying for one of these positions, please forward your Word formatted resume, cover note and salary requirement to resumes@workwondersstaffing.net. Please include the specific position to which you are applying in the subject line of your email. This will ensure your resume is routed to the correct recruiter as quickly as possible. Please note, only qualified candidates will be contacted for interviews. Receipt of your resume will be confirmed if it is sent as an attachment. Referrals: If you are not interested in the opportunity for yourself, please consider referring a colleague or friend. We do have a generous referral program. More details are available here: http://www.workwondersstaffing.net/CandidateResources/Referrals.html Thank you for your time - have a great day! Senior Recruiter Work Wonders Staffing http://www.workwondersstaffing.net Please note, your email address has not been added to any mailing list or database. It is unlikely that you will receive any additional email from Work Wonders Staffing. If you like, please just reply with a note asking us to not contact you again and we will comply. Also, just FYI, this email does not contain falsified routing information and is not being sent with the intent to disrupt the normal operation or use of a computer, Internet site, or e-mail address. ****************************************************************************** From: JC Date: 19 Oct 2004 19:21:19 -0700 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * Hi Bila, For example, if the m/z of the target compound is 250.0 with RT 3.20 min, and another compound in the matrix having m/z 250.5 and RT 3.15 min. Also the mass cal. and the resolution cal. of the system is not well adjusted. This may be a reason, although not a high chance.... Anyway I got experience on this. During tuning and method development, it gave me a pretty good peak. However, when injecting the samples with matrix, SIM mode had shown a large peak, but MRM gave very weak signal. What I had done was re-cal the system, retune the compound, then a little bit improvement in MRM observed but the SIM was still very large. But when using another col., two SIM signal found, one with my expected MRM, another not. JC Bila wrote in message news:... } Hi JC, } } it remains still misterious, since the effect was observed not only } for one compound (viz 2 compounds with different RT). However, a shift } of the mass axis might be a reason. } Bila } } JC wrote in message news:... } } Hi Kendall, } } } } Yes, the LC column will not affect the fragmentation of a compound. } } But,I wonder he has picked a wrong parent compound which with very } } similar molecular mass to his target analyte. That's why I asked him } } about the resolution and mass axis shift in his system. Remember, the } } unit resolution is only 0.7 amu at full width at half height. Taking } } account into the resolution and the mass shift, it may be a chance } } that the system pick a compound with very similar molecular mass and } } very similar retention time in the run. If this is being the case, a } } totally different fragmentation pattern observed is expected. That may } } be his case. However, such case can be verified by using different } } HPLC col. if he is picking a wrong parent peak. } } JC ****************************************************************************** From: Boy_italia Date: Wed, 20 Oct 2004 20:35:44 GMT Subject: Re: Ions ratio 219/69 inversed in autotune Organization: * .. } The only GC/MS that does not have 69 as the base peak for PFTBA, that I } know of, is the Thermo Electron Finnigan Polaris Q. } Yes but it's another history ! Finnigan PolarisQ it's an ion trap analyzer and as ALL THE ION TRAP ANALYZER like Varian Saturn 2000 has a little different path of fragmentation. bye cus ****************************************************************************** From: Graeme Robertson Date: Thu, 21 Oct 2004 12:24:07 +0100 Subject: Re: Fisons 8000 GC series FID detector Organization: * This GC was made by Carlo Erba in Italy and marketed under the Fisons name. I think most Carlo Erba detectors of that vintage are interchangeable so you might try the manufacturers web site customer.support@ceinstruments.it or cannibalise an old carlo erba unit. good luck "lailiang" wrote in message news:cl1b6q$8sf$1@news-int2.gatech.edu... } We have a Fisons 8000 series GC , unfortunately the FID detector is out of } order, is there anyone who knows where we can get the replacement? This } product is not supported by its manufacturer. } } Thank you in advance for your help! } } } } ****************************************************************************** From: craig3201 Date: 21 Oct 2004 05:55:14 -0700 Subject: Re: Any comments on TOF systems (Bruker vs Leco)? Organization: * Hello David As far as I am aware, Jeol doesn't have any representation in South Africa. Agilent equipment is available but they also seem to keep a very low profile. The Waters system has not been rejected but moved to the bottom of the list because the provisional offer price is about 20% more expensive than the Bruker or Leco systems. I was approached yesterday by Shimadzu/Kratos and I will be meeting with Varian tomorrow to discuss any of their systems which will serve our intended application - a resonably robust system to provide "accurate" mass determination of natural products in the 200-600 amu range. We could still consider systems other than TOF, provided that they meet these requirements at an academically-affordable cost; suggestions are most welcome. Regards, Craig. }David Sparkman wrote in message >news:... } Craig, } } I would be interested in know what were the knockout factors for the JEOL, } Agilent, and Waters LC TOF instruments. } } Regards; } David } } -- } O. David Sparkman } Consultant-At-Large } ods@compuserve.com } "craig3201" wrote in message } news:cklodp$q6t$1@news-int2.gatech.edu... } } } } Hello All } } } } My department is considering the purchase of an LCMS system. Our } } shortlist has been narrowed to two TOF systems - the Bruker MicroTOF } } and the Leco UniqueTOF. I would be interested in receiving general } } comments from anyone using either of these systems with regard to: } } user-friendliness of both hardware and software, the use of the } } "accurate mass"-to-formula software in the mass range 200-600 amu } } (compounds isolated from botanical extracts), any problems associated } } with installation or general use (resolved or not). General comments } } are also most welcome. } } } } Many thanks, } } Craig. } } ****************************************************************************** From: Davide Cittaro Date: Thu, 21 Oct 2004 20:22:42 GMT Subject: spectra conformation Organization: * Hi folks, I'm looking for some information about how MS/MS spectra are. In particular I would like to know if there are some studies and statistics about how often one can find certain ion types or combinations (that is, for example, couples of a/b ions). Thanks Davide ****************************************************************************** From: lailiang Date: Mon, 25 Oct 2004 14:30:30 -0600 Subject: Re: Fisons 8000 GC series FID detector Organization: * Thank you for your help, we will try and say if they still support this kind of detector. Lailiang "Graeme Robertson" wrote in message news:cl8c97$88e$1@news-int2.gatech.edu... } This GC was made by Carlo Erba in Italy and marketed under the Fisons } name. } I think most Carlo Erba detectors of that vintage are interchangeable so } you } might try the manufacturers web site customer.support@ceinstruments.it or } cannibalise an old carlo erba unit. good luck } } } "lailiang" wrote in message } news:cl1b6q$8sf$1@news-int2.gatech.edu... } } We have a Fisons 8000 series GC , unfortunately the FID detector is out } of } } order, is there anyone who knows where we can get the replacement? This } } product is not supported by its manufacturer. } } } } Thank you in advance for your help! } } } } } } } } } } } } ****************************************************************************** From: Gregor Kos Date: Mon, 25 Oct 2004 21:14:33 GMT Subject: msp file export from chemstation Organization: * hi, i am using hp chemstation software and NIST 2.0 for collecting and analyzing gc-ms data. after an upgrade from nist 1.6 to 2.0 a couple of weeks ago, everything was working fine. recently, export of the *.msp file stopped working (i.e. no file is written to the chemstation data directory or anywhere else). we have several people with different skill-levels working on the machine and despite asking around, i do not know, what happened. i have installed the chemstation macros again, but no success. the chemstation software does not give an error message, but the export looks alright, but no file is created. reinstalling the nist 2.0 upgrade did not help either. the nist program itself is working well and so is the chemstation. my computer configuration is: Chemstation G1701BA, Version B.01.00 WinNT 4.0, SP 3 NIST 2.0 AMIDS 2.6 any suggestions? many thanks in advance! greg -- Gregor Kos McGill University Atmospheric and Oceanic Sciences Montreal, QC Canada gregor(dot)kos(at)mcgill(dot)ca ****************************************************************************** From: David Sparkman Date: Tue, 26 Oct 2004 12:51:56 GMT Subject: Re: msp file export from chemstation Organization: * Gregor The new macros from the NIST download site now write the file TempSpec.msd in the \hpchem folder along with another file (hpnist.txt). The older versions write msp files in the folder that is the data file and had the same name as the data file. This change was made to solve a problem with processing data from read-only devices. Do, the following: 1. Do you have all the menu items for the NIST Search Program on the Spectrum menu? PBM Quick Search NIST Search Multiple Lib PBM Search Set Default Search Engine NIST Output AMDIS If you do not have theses items, go to http://chemdata.nist.gov and click on the NIST MS Search program upgrade. Look at the bottom of the page to go to the ChemStation information. Download the V2 macros and install them. If this does not fix the problem, look in the folder with the NIST MS Search Program and see if there is a file with the name AUTOIMP.msd. Open this file with Note Pad. It should have a single line that reads c:\hpchem\hpnist.txt, assuming that your CS software is on the c: drive and in the hpchem folder. If it does not edit it. If you are still having problems, please feel free to contact me. You can also take your ChemStation Questions to http://www.ChemUserWorld.com Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "Gregor Kos" wrote in message news:clk491$bka$1@news-int2.gatech.edu... } } hi, } } i am using hp chemstation software and NIST 2.0 for collecting and } analyzing gc-ms data. after an upgrade from nist 1.6 to 2.0 a couple of } weeks ago, everything was working fine. } } recently, export of the *.msp file stopped working (i.e. no file is } written to the chemstation data directory or anywhere else). we have } several people with different skill-levels working on the machine and } despite asking around, i do not know, what happened. } } i have installed the chemstation macros again, but no success. the } chemstation software does not give an error message, but the export } looks alright, but no file is created. reinstalling the nist 2.0 upgrade } did not help either. the nist program itself is working well and so is } the chemstation. } } my computer configuration is: } Chemstation G1701BA, Version B.01.00 } WinNT 4.0, SP 3 } NIST 2.0 } AMIDS 2.6 } } any suggestions? } many thanks in advance! } } greg } -- } Gregor Kos } McGill University } Atmospheric and Oceanic Sciences } Montreal, QC } Canada } gregor(dot)kos(at)mcgill(dot)ca } ****************************************************************************** From: John Sherratt Date: 26 Oct 2004 07:55:33 -0700 Subject: UK requirement for LC-MS Mass Spectrometrist Organization: * Opportunity for a mass spectrometrist with proven LC-MS skills to take a lead role developing methods for the high throughput analysis new chemical entities. The analyses will be in support of formulations for diverse studies such as toxicology and pharmacology; the compounds will be mainly small molecules, for pharma and agrochem products, and some large mols. The ideal candidate will have proven method development skills, at least 2 years LC-MS experience, knowledge of GC-MS and ideally experience supporting formulation chemistry at any stage of the discovery or development process. Call VRS for further information! +44 (0) 161 976 4000 www.vrs-uk.net ****************************************************************************** From: Graeme Robertson Date: Tue, 26 Oct 2004 18:01:56 +0100 Subject: Re: Fisons 8000 GC series FID detector Organization: * This GC was made by Carlo Erba in Italy and marketed under the Fisons name. I think most Carlo Erba detectors of that vintage are interchangeable so you might try the manufacturers web site customer.support@ceinstruments.it or cannibalise an old carlo erba unit. good luck ****************************************************************************** From: Jeff Gambera Date: Tue, 26 Oct 2004 22:48:11 GMT Subject: MassLynx Organization: * we are having a problem with MassLynx 3.3 or 3.5 while trying to process data with MaxEnt. The program freezes upon submission of the request and MassLynx must be shut down and restarted to recover. Transform works OK. Any suggestions? Thanks ****************************************************************************** From: lijun chen Date: Tue, 26 Oct 2004 17:31:26 -0700 (PDT) Subject: About MW Organization: * Hi, I have a sample (peptide fragments or peptide related small molecule), the MW is 1871. ESI positive got peaks: 936.2(19%), 624.8(62%), 542.1(100%) by using LCQ Deca. I have questions about these peaks: If 936.2 is a +2 charge ion, the MW is supposed to be (936x2)-2=1870, there is 1 less than the real MW. If 624.8 is a +3 charge ion, the MW is supposed to be (625x3)-3=1872, there is 1 more than the real MW. I do not know how to explain them. Could anyone give me some advises? Thanks in advance. Lijun __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ****************************************************************************** From: Fred Mellon Date: Wed, 27 Oct 2004 09:20:38 +0100 Subject: Source of Diene derivatisation reagent for enhanced ESI? Organization: * Hi All, I need to find a supplier of the diene derivatisation reagent DMEQTAD (Cookson-type reagent, 4-[2-(6,7-dimethoxy-4-methyl-3-oxo-3,4-dihydroquinoxalyl)ethyl]-1,2,4-triazo line-3,5-dione). I intend to use this to enhance the ESI MS response of vitamin D and its metabolites (see Higashi et al, J. Pharm. Biomed. Anal., 2002, vol 29, 947-955). The Wako Pure Chemical Co (Osaka, Japan) appears to be the only supplier. Does anyone either have a web address for this company, or can give me the name/address of their UK/European agents? (I'm also investigating the use of an alternative derivatisation reagent, 4-phenyl urazole, but already have potential suppliers of this). regards, Fred Dr Fred A Mellon Head of Mass Spectrometry Team Institute of Food Research Norwich Research Park Norwich NR4 7UA UK tel. +44 (0)1603 255299 fax +44 (0)1603 255038 email: fred(dot)mellon(at)bbsrc(dot)ac(dot)uk ****************************************************************************** From: bizzwire Date: Wed, 27 Oct 2004 12:31:25 GMT Subject: Re: MassLynx Organization: * } From: Jeff Gambera } } we are having a problem with MassLynx 3.3 or 3.5 while trying to process } data with MaxEnt. The program freezes upon submission of the request and } MassLynx must be shut down and restarted to recover. Transform works OK. Any } suggestions? } Thanks Are you sure your computer is freezing? MaxEnt is a number-crunching hog, and will certainly slow things down, especially if you're working with a lot of data points. In addition, it is VERY dependant on your settings, so if you have specified a very wide mass window and very small resolution settings and are working with a spectrum from 100-3000 amu, each iteration could be so slow as to appear that the computer has frozen-up. Try setting the MaxEnt mass range to a window +/- a couple of thousand amu around the expected mass (assuming you know what that is). Set the resolution to 1 or 2 amu, and the maximum number of iterations to something small, say 5-10. Also, zoom the spectrum window to cover just a couple of the charge states, and let 'er rip. This probably wont get you a very precise or accurate result, but will tell you if MaxEnt is working as it should, more or less. PS. There are several flavors of MaxEnt, meant for different applications. Make sure that you are using the right one (i.e. MaxEnt I, rather than MaxEnt III). ****************************************************************************** From: Fred Mellon Date: Wed, 27 Oct 2004 14:20:18 +0100 Subject: Re: MassLynx Organization: * Jeff, Has your PC OS been upgraded recently? Older versions of MassLynx, and probably embedded progs like MaxEnt, are only guaranteed to work (as far as I am aware) with Windows NT up to and including service pack 4. We had to revert to SP4 after an IT upgrade to SP6 caused problems with Masslynx 3.5. regards, Fred "Jeff Gambera" wrote in message news:clmobr$no3$1@news-int.gatech.edu... } we are having a problem with MassLynx 3.3 or 3.5 while trying to process } data with MaxEnt. The program freezes upon submission of the request and } MassLynx must be shut down and restarted to recover. Transform works OK. Any } suggestions? } Thanks } } ****************************************************************************** From: Chip Cody Date: 27 Oct 2004 10:36:17 -0700 Subject: Re: About MW Organization: * You need to include the fractional m/z values. Assuming that the m/z 542.1 peak is unrelated, then the calculated molecular weight from two adjacent charge states at m/z 936.2 and m/z 624.8 would be 1870.88. That is the average estimate from two charge states, neither of which is necessarily an exact m/z value. If the actual MW is really 1870.9, then the exact m/z values would be 936.4 and 624.3. lijun chen wrote in message news:... } Hi, } } I have a sample (peptide fragments or peptide related } small molecule), the MW is 1871. ESI positive got } peaks: 936.2(19%), 624.8(62%), 542.1(100%) by using } LCQ Deca. } } I have questions about these peaks: } } If 936.2 is a +2 charge ion, the MW is supposed to be } (936x2)-2=1870, there is 1 less than the real MW. } } If 624.8 is a +3 charge ion, the MW is supposed to be } (625x3)-3=1872, there is 1 more than the real MW. } } I do not know how to explain them. Could anyone give } me some advises? Thanks in advance. } } Lijun } } } } __________________________________________________ } Do You Yahoo!? } Tired of spam? Yahoo! Mail has the best spam protection around } http://mail.yahoo.com ****************************************************************************** From: Kendall Date: Thu, 28 Oct 2004 00:22:55 GMT Subject: Off axis ESI source for LCQ DECA? Organization: * Hi all- I was wondering if anyone has an off axis electrospray source that will fit Finnigan's LCQ DECA ion trap mass spec. that they might be interested in selling. I currently have the "down the throat" ESI source which is, well, lets say less than ideal. Thanks, Kendall P.S. For email responses replace "ZZ" in address to "LL" (spam protection, you know). ****************************************************************************** From: Indium Date: Thu, 28 Oct 2004 00:58:14 GMT Subject: Quantitation in LC/MS or LC/MS/MS Organization: * For good precision and accuracy is it a requirement that an isotopically labeled internal standard be used that resembles the structure of the analyte? What kind of precision and accuracy can be expected with a triple quad for a simple matrix without an isotopically labeled internal standard? What about numerous analytes of unknown structure in a simple matrix, so an isotope cannot be used? I am a novice so go easy on me. ****************************************************************************** From: Simon Date: 28 Oct 2004 03:23:38 -0700 Subject: HELP - Applied Biosystems SAMPLE PLATE for Membrane Gels Organization: * Hello, I am an Italian resercher. It has been recenly bought, in my laboratory, a MALDI (Voyager DE-STR 2). I am writing you becase I have a problems with a MALDI plate and in particular with the plates "VOY SAMPLE PLATE FOR MEMBRANE GELS, P/N:V700698". As far as I know, it should be possible to analyze, with this MALDI plate, the membrane gels. The only problem is that it doesn't exhist the instructions on how to use it. I have also tried to search on internet with google and other search engines without results. Does anyone know how to use these MALDY PLATE? Alternativelly could anyone send me documentations on how to use these plates? Could anyone tell me where I can find the documantation to use this plate (e.g. some site on internet)? Please, reply me both on this newsgroup and by E-MAIL at the follow E-MAIL address: dtoycr@tin.it I would like to thank you very much for your help. Sincerely yours Simone ****************************************************************************** From: Chris R. Lee Date: Thu, 28 Oct 2004 22:25:05 +0200 Subject: Re: Quantitation in LC/MS or LC/MS/MS Organization: * There are 2 things to think about here. 1. The ion yield of a mass spectrometer will vary, even during a day, and may or may not be a linear function of amount, depending on such things as ultra-trace impurities in your mobile phase. If you don't have a labelled standard the thing to do is to run a calibration curve every day, so you know where you stand. The curve is often straight, but it may also be concave (most usual) or convex. 2. Co-eluted components in your mixture may inhibit or enhance ionisation. There's plenty of literature on this. One solution is to add a low concentration of the target analyte post-column and see if its signal is constant. The other way is to use standard additions - that means with every sample if the samples are different. To get a reasonable estimate of confidence limits by inverse regression analysis, you usually need 6 additions (including zero), because there are only N-2 degrees of freedom. In a practical well-controlled situation you may just use one standard addition. By the way, most injectors can do the standard additions automatically, so it's not a big problem if the analysis time isn't too long. Precision in terms of repeatability depends on the situation, but often you get between, say, 1 & 5% RSD if the peak height to noise ratio is not too close to the detection limit. An important source of variance is response drift, which is never taken into account by validation protocols... Finally, I should mention that a triple quad has the advantage compared to simgle quads of eliminating most of the noise due to mobile phase clusters and impurities - it isn't only a question of selectivity with respect to components of your mixture. An alternative is medium-resolution MS (TOF or magnetic sector), which is highly selective at low m/z, and gives the accurate mass (hence the molecular formula) of your analytes. Regards "Indium" a écrit dans le message de news: clpjfr$5na$1@news-int.gatech.edu... } } For good precision and accuracy is it a requirement that an isotopically } labeled internal standard be used that resembles the structure of the } analyte? What kind of precision and accuracy can be expected with a } triple quad for a simple matrix without an isotopically labeled internal } standard? What about numerous analytes of unknown structure in a simple } matrix, so an isotope cannot be used? I am a novice so go easy on me. } ****************************************************************************** From: Andor J Kiss Date: Fri, 29 Oct 2004 12:49:52 -0500 Subject: Convert *.dat file to *.pkl format Organization: * Hello, I have some Voyager SE DTR MALDI TOF files. I wish to save the peaks list in a Micromass PEAK TABLE LIST (*.PKL) format such that I can upload the *.PKL file into our stand-alone version of MASCOT. The ultimate aim is to used MASCOT to perform peptide fingerprinting using a proprietary protein database. Does anyone know of a *FREE* file converter that will convert either a *.DAT or *.PKT file into a *.PKL file? Thanks, Andor ****************************************************************************** From: Maxell Date: 30 Oct 2004 01:19:36 -0700 Subject: Adducts in negative ion mode Organization: * Fairly often I observe M+31 (probably [M-H+32] ions in negative ions mode (ESI). Does anyone know what type of adduct ion this is? ****************************************************************************** From: Tony Lam Date: 30 Oct 2004 01:20:45 -0700 Subject: Question about Mass range of single quadrpole GC-MS / LC-MS Organization: * Recently I was heard that the mass range of a Shimadzu GC-MS system can reach 1024 m/z I would like to ask whether any other single quad MS have range that can cover to 1024 m/z or even higher?? Thanks very much ****************************************************************************** From: Phil Date: Sat, 30 Oct 2004 19:14:30 +0200 Subject: Re: Question about Mass range of single quadrpole GC-MS / LC-MS Organization: * Hi Tony, The PE Clarus goes also up to 1024 or so and the DSQ from Thermo Electron goes to 1050... Phil ****************************************************************************** From: L FRIEDMAN Date: Sat, 30 Oct 2004 20:07:02 GMT Subject: Re: Question about Mass range of single quadrpole GC-MS / LC-MS Organization: * There are SSQ7X0 that go to 4000 and SSQ7000 that go slightly above that in the high mass range. No all Finnigan SSQ's can go to the high mass range. The low mass range on the 700 is 2000amu & the 7000 low mass range will go to a minimum of 2500amu. Depending on the PLL frequency that the rods dip in, I have seen well over 2600. "Tony Lam" wrote in message news:cm07qg$6mv$1@news-int.gatech.edu... } } Recently I was heard that the mass range of a Shimadzu GC-MS system } can reach 1024 m/z } } I would like to ask whether any other single quad MS have range that } can cover to 1024 m/z or even higher?? } } Thanks very much } ****************************************************************************** From: David Sparkman Date: Sat, 30 Oct 2004 20:54:51 GMT Subject: Re: Adducts in negative ion mode Organization: * Maxwell, What is the number 32, besides the age of my girl friend? It is 17 plus 15. What is the number 17 besides the age of my dog in human years? It is 16 plus 1, which is the mass of 1 O atom plus 1 H atom. What is the number 15 besides the age of my favorite single-malt whisky in years? It is 12 plus 3 which is the mass of 1 C atom and 3 hydrogen atoms. Add then all together, you get CH3OH, which is the alcohol you do not want to drink, no matter how old it is. Is metanol a component in your mobil phase? Regards; David -- O. David Sparkman Consultant-At-Large osparkma no @ spam uop.edu "Maxell" wrote in message news:cm07pu$g1r$1@news-int2.gatech.edu... } } Fairly often I observe M+31 (probably [M-H+32] ions in negative ions } mode (ESI). Does anyone know what type of adduct ion this is? } } ****************************************************************************** From: David Sparkman Date: Sat, 30 Oct 2004 21:07:57 GMT Subject: Re: Question about Mass range of single quadrpole GC-MS / LC-MS Organization: * Tony, The Finnigan Trace DSQ from Thermo Electron has an advertised m/z range of 1 -1,050 amu [sic] (when will they ever learn?). Many older model GC/MS products like the RIBER R 1010 had an m/z range to 1,000 or above. I believe you wanted to say, "I was told ..." or "I heard ..." Regards; David -- O. David Sparkman Consultant-At-Large osparkma no @ spam uop.edu "Tony Lam" wrote in message news:cm07qg$6mv$1@news-int.gatech.edu... } } Recently I was heard that the mass range of a Shimadzu GC-MS system } can reach 1024 m/z } } I would like to ask whether any other single quad MS have range that } can cover to 1024 m/z or even higher?? } } Thanks very much } ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Sat, 30 Oct 2004 23:16:35 +0200 Subject: Re: Adducts in negative ion mode Organization: * Which solvent do you use? Rainer Maxell schrieb: } } Fairly often I observe M+31 (probably [M-H+32] ions in negative ions } mode (ESI). Does anyone know what type of adduct ion this is? ****************************************************************************** From: someone@aol.com Date: Sat, 30 Oct 2004 22:21:36 GMT Subject: ESI Positive Charge Origins Organization: * I am not very familliar with the types of positive ion species that are permissible in positive ion mode ESI. Are radical cations typically formed during fragamentation of the MH+ ion? Are any species with a positive charge possible, e.g. radical cation? I have seen fragment ions similar to piperidine with a double bond between the nitrogen and the adjacent carbon with a positive charge on the nitrogen - this to me implies a loss of hydride which I am sure is not occurring. It would make more sense if the nitrogen was a radical cation that would imply loss of a hydrogen radical. What about fragments containing carbonium ions - are they possible? ****************************************************************************** From: Maxell Date: 31 Oct 2004 02:36:16 -0800 Subject: Re: Adducts in negative ion mode Organization: * It happens in acetonitril/water system. I never use methanol. In msms operation the loss is 32. Cheers, Maxell David Sparkman wrote in message news:... } Maxwell, } } What is the number 32, besides the age of my girl friend? It is 17 plus 15. } What is the number 17 besides the age of my dog in human years? It is 16 } plus 1, which is the mass of 1 O atom plus 1 H atom. What is the number 15 } besides the age of my favorite single-malt whisky in years? It is 12 plus 3 } which is the mass of 1 C atom and 3 hydrogen atoms. Add then all together, } you get CH3OH, which is the alcohol you do not want to drink, no matter how } old it is. } } Is metanol a component in your mobil phase? } } Regards; } David } } -- } O. David Sparkman } Consultant-At-Large } osparkma no @ spam uop.edu } } "Maxell" wrote in message } news:cm07pu$g1r$1@news-int2.gatech.edu... } } } } Fairly often I observe M+31 (probably [M-H+32] ions in negative ions } } mode (ESI). Does anyone know what type of adduct ion this is? } } } } ****************************************************************************** From: David Sparkman Date: Sun, 31 Oct 2004 08:51:58 -0500 Subject: GC/MS m/z Range Organization: * Group, In a recent post, it was asked what GC/MS instruments have an m/z range greater than 1,000. I am curious to know if anyone is analyzing anything by GC/MS that approaches a mass of 1,000 Da. I know that some perflournated derivatives can get up there, but what is the practicality of an instrument that will go this high? Regards; David -- O. David Sparkman Consultant-At-Large osparkma no @ spam uop.edu Antioch, CA 94531 1-925-754-5003 M ****************************************************************************** From: L FRIEDMAN Date: Sun, 31 Oct 2004 15:12:32 GMT Subject: Re: Question about Mass range of single quadrpole GC-MS / LC-MS Organization: * I don't know about the DSQ, but I was always able to tune the TSQ & SSQ GCMS's to see Helium. Even though the specs were 10-2000. On the LKB GCMS, I was always able to see hydrogen. 14 is doubly charges nitrogen. A good indication of a massive leak. 32 is oxygen. 40 is argon. If you have a massive leak (i.e. 28 is 4 or more times bigger then 18) you will get a pseudo CI at 41. ****************************************************************************** From: Rich Milberg Date: Sun, 31 Oct 2004 20:49:13 GMT Subject: Re: GC/MS m/z Range Organization: * Dave: Back in 1990 when we got our first VG/Fisons/Micromass/Waters 70-VSE I ran silicon cage compounds that were sufficiently volatile to pass through a J&W 15 meter by 0.25 mm ID normal film ticknessDB-1 capillary well below 300 deg C. Best of all these compounds required operation at 6 kV since they produced numerous EI+ ions in excess of 3,000 Da. Richard Milberg Univ. of Illinois Urbana, IL "David Sparkman" wrote in message news:cm2src$a1r$1@news-int.gatech.edu... } } Group, } } In a recent post, it was asked what GC/MS instruments have an m/z range } greater than 1,000. I am curious to know if anyone is analyzing anything } by } GC/MS that approaches a mass of 1,000 Da. I know that some perflournated } derivatives can get up there, but what is the practicality of an instrument } that will go this high? } } Regards; } David } } -- } O. David Sparkman } Consultant-At-Large } osparkma no @ spam uop.edu } } } Antioch, CA 94531 } 1-925-754-5003 } } M } ****************************************************************************** From: Rich Milberg Date: Sun, 31 Oct 2004 20:52:50 GMT Subject: Re: Question about Mass range of single quadrpole GC-MS / LC-MS Organization: * Anybody look at manufacturers' literature lately? The Waters ZQ single has a standard mass range of >2000 Da and is available with >4000 Da as an option. R. Milberg Univ. of Illinois Urbana, IL "Tony Lam" wrote in message news:cm07qg$6mv$1@news-int.gatech.edu... } } Recently I was heard that the mass range of a Shimadzu GC-MS system } can reach 1024 m/z } } I would like to ask whether any other single quad MS have range that } can cover to 1024 m/z or even higher?? } } Thanks very much } ****************************************************************************** From: Phil Date: Mon, 1 Nov 2004 10:29:42 +0100 Subject: Re: GC/MS m/z Range Organization: * David, Probably noone's going that far in GCMS, but some do go beyond 1000 when using DIP/DEP.... FWIW Phil ****************************************************************************** From: Tony Lam Date: 1 Nov 2004 06:08:06 -0800 Subject: Re: GC/MS m/z Range Organization: * David Sparkman wrote in message news:... } Group, } } In a recent post, it was asked what GC/MS instruments have an m/z range } greater than 1,000. I am curious to know if anyone is analyzing anything } by } GC/MS that approaches a mass of 1,000 Da. I know that some perflournated } derivatives can get up there, but what is the practicality of an instrument } that will go this high? } } Regards; } David } } -- } O. David Sparkman } Consultant-At-Large } osparkma no @ spam uop.edu } } } Antioch, CA 94531 } 1-925-754-5003 } } M Actually in my lab we are using GC-MS system to analyze compounds that very close to 1000Da. I just wonder what are the avaiable systems that can handle routine qualitative and quantative analysis of ~ 1000Da (or M+); but having similar price to that of GC6890-MS5973 agilent / Shimadzu QP2010 ? For routine consideration, if a compound can elute from GC, then why use LC ? The detection should not be limited by the mass range limit of MSD. ****************************************************************************** From: Simon Grist Date: Mon, 01 Nov 2004 16:49:08 +0000 Subject: Re: HELP - Applied Biosystems SAMPLE PLATE for Membrane Gels Organization: * Hi Simon, Have you tried the Applied Biosystems website? If you have the p/n for the plate, they should have some info available on how to use it - or at least have a contact number to talk to someone about it. Good luck Simon Simon wrote: } Hello, I am an Italian resercher. It has been recenly bought, in my } laboratory, a MALDI (Voyager DE-STR 2). I am writing you becase I have } a problems with a MALDI plate and in particular with the plates "VOY } SAMPLE PLATE FOR MEMBRANE GELS, P/N:V700698". As far as I know, it } should be possible to analyze, with this MALDI plate, the membrane } gels. The only problem is that it doesn't exhist the instructions on } how to use it. I have also tried to search on internet with google and } other search engines without results. Does anyone know how to use } these MALDY PLATE? Alternativelly could anyone send me documentations } on how to use these plates? Could anyone tell me where I can find the } documantation to use this plate (e.g. some site on internet)? } } Please, reply me both on this newsgroup and by E-MAIL at the follow } E-MAIL address: dtoycr@tin.it } } I would like to thank you very much for your help. } } Sincerely yours } } Simone ****************************************************************************** From: "Olivier Philippe" Subject: Protomics software announcement Date: Mon, 1 Nov 2004 14:11:50 +0100 Organization: * Genebio has recently released a new software platform for proteomics MS data analysis called Phenyx. ( www.phenyx-ms.com ) In conjunction with the Swiss Institute of Bioinformatics and incorporating the true probabilistic and flexible scoring system OLAV developed at GeneProt Inc., this new search engine enables the identification and characterization of proteins and peptides from mass spectrometry data. Genebio offers a public version of the Phenyx Calculation Engine after registration at http://www.phenyx-ms.com/downloads/downloads.html. Best regards, Olivier ****************************************************************************** From: Chris R. Lee Date: Mon, 1 Nov 2004 21:58:04 +0100 Subject: Re: GC/MS m/z Range Organization: * A very long time ago when our VG/Fisons/Micromass/Waters 70-70 (to copy an earlier reply) was limited to m/z 700 at full accelerating voltage, suppliers of quadrupoles took great pleasure in telling us what we were missing. Phil has a good point: since GC/MS uses EI/CI, many purchasers buy one or more of the available direct insertion probe options. Some of us would also buy the particle beam interface if it were available. The PB ionises compounds API doesn't reach, and it is also great for self-service MS. You connect a capillary restrictor to the interface, and the user just dips it into his solution. Regards "Phil" a écrit dans le message de news: cm565u$b1n$1@news-int.gatech.edu... } David, } } Probably noone's going that far in GCMS, but some do go beyond 1000 when } using DIP/DEP.... } } FWIW } } Phil } } } ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 02 Nov 2004 01:37:33 +0100 Subject: Re: Adducts in negative ion mode Organization: * And the sample has never seen Methanol in any way? What about the sample itself, which functional groups are in the molecule? Rainer Maxell schrieb: } } It happens in acetonitril/water system. I never use methanol. } In msms operation the loss is 32. } } Cheers, } Maxell } } David Sparkman wrote in message news:... } } Maxwell, } } } } What is the number 32, besides the age of my girl friend? It is 17 plus 15. } } What is the number 17 besides the age of my dog in human years? It is 16 } } plus 1, which is the mass of 1 O atom plus 1 H atom. What is the number 15 } } besides the age of my favorite single-malt whisky in years? It is 12 plus 3 } } which is the mass of 1 C atom and 3 hydrogen atoms. Add then all together, } } you get CH3OH, which is the alcohol you do not want to drink, no matter how } } old it is. } } } } Is metanol a component in your mobil phase? } } } } Regards; } } David } } } } -- } } O. David Sparkman } } Consultant-At-Large } } osparkma no @ spam uop.edu } } } } "Maxell" wrote in message } } news:cm07pu$g1r$1@news-int2.gatech.edu... } } } } } } Fairly often I observe M+31 (probably [M-H+32] ions in negative ions } } } mode (ESI). Does anyone know what type of adduct ion this is? } } } } } } ****************************************************************************** From: Carole Date: 2 Nov 2004 01:19:39 -0800 Subject: CI-MS Ammonia Organization: * I look for profiles of ammoniac in positive chemical ionisation and negative (the peaks that I obtained were 11, 19, 29, 40...) this is strange ?. The first data were peaks to 18 and 35 that seems more logical. Has someone an idea about this ? Thanks to help me .... ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 02 Nov 2004 21:33:27 +0100 Subject: Re: CI-MS Ammonia Organization: * I agree, 18 and 35 are o.k. Are there any parts of your ammonia-supply that are not stable to the gas (gaskets etc). All materials should be stainless steel. Next, close the main valve of the ammonia bottle, evacuate the line and pressure regulator and check for leaks. HTH Rainer Carole schrieb: } } I look for profiles of ammoniac in positive chemical ionisation and } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } strange ?. The first data were peaks to 18 and 35 that seems more } logical. } Has someone an idea about this ? } Thanks to help me .... ****************************************************************************** From: Ricksfbrsc Date: 02 Nov 2004 21:44:22 GMT Subject: Re: GC/MS m/z Range Organization: * I have analyzed some ethoxylated surfactants and PEGs up to about 1400 Da by derivitizing the end groups, cold on-column injection, J&W DB-5HT column on a HP (or if you prefer, AT) 5989MS. Also, some stabilizers like Irganox 3114 or 1010 (I can't remember which) that has a molecular weight around 1000. ****************************************************************************** From: Dave White Date: Wed, 03 Nov 2004 01:18:30 GMT Subject: Re: GC/MS m/z Range Organization: * We analyze brominated diphenyl ethers (used in flame retardents, etc.). The labeled deca compounds require analyzing mass 973. It gets a bit hairy up there, but it is doable. Dave White SpectraChrom Software www.spectrachrom.com ****************************************************************************** From: Jason Dunsmore Date: 2 Nov 2004 16:41:07 -0800 Subject: New proteomics forum, http://forums.deltastat.org/ Organization: * A new proteomics forum is available at: http://forums.deltastat.org/ Please come and discuss any topic related to proteomics (wet lab or informatics). Advertisements are prohibited. Jason Dunsmore ****************************************************************************** From: Eric van der Meulen Date: 3 Nov 2004 07:33:18 -0800 Subject: Re: CI-MS Ammonia Organization: * I agree with Rainer on 18 and 35 for ammonia, but what you are seeing now seems like methane in positive mode: 19 for H3O+, 29 for C2H5 and 40 (should be 41?) for C3H5+ .... I don't know what 11 could be. Are you sure your reactant gas is ammonia? If it really is ammonia, it's impossible to see methane peaks: even the smallest amount of ammonia will quench them. With respect to the stainless steel parts: I don't remember having seen any signals because of that, but I have seen brass parts of the roughing pumps turning bright blue as a result of ammonia. So Rainer is right on making sure to use stainless steel parts. Regards, Eric "rainer [iso-8859-2] lörwald" wrote in message news:... } I agree, } } 18 and 35 are o.k. Are there any parts of your ammonia-supply that are } not stable to the gas (gaskets etc). All materials should be stainless } steel. Next, close the main valve of the ammonia bottle, evacuate the } line and pressure regulator and check for leaks. } } HTH } Rainer } } } Carole schrieb: } } } } I look for profiles of ammoniac in positive chemical ionisation and } } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } } strange ?. The first data were peaks to 18 and 35 that seems more } } logical. } } Has someone an idea about this ? } } Thanks to help me .... ****************************************************************************** From: Chip Cody Date: 3 Nov 2004 10:01:10 -0800 Subject: Re: CI-MS Ammonia Organization: * The masses that you report ARE strange. m/z 11 could only be boron, and then you should expect to see both boron 10 and boron 11 isotopes. Normally, you should see m/z 18,35,52... A reagent-ion mass spectrum for ammonia chemical ionization is posted on our website at: http://www.jeol.com/ms/docs/ammonia.jpg Chip Cody (JEOL USA, Inc.) Carole wrote in message news:... } I look for profiles of ammoniac in positive chemical ionisation and } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } strange ?. The first data were peaks to 18 and 35 that seems more } logical. } Has someone an idea about this ? } Thanks to help me .... ****************************************************************************** From: Mike Sherrell Date: Wed, 3 Nov 2004 11:55:52 -0800 Subject: Grizzly Analytical MS, MALDIs, etc. available Organization: * **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000: $150,000 installed/warranteed. Sciex API 3000: $190,000 W/ upgrade to ~ API 4000 sensitivity and S/N. API 3000 upgrade: $38,500. Increases sensitivity and (S/N) Ratio at high flow rates to ~ that of an API 4000. Install incl. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $120,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase; incl. install, warr. Sciex API 365: $65,000. NT, turboionspray. Installed, warranteed. Sciex 365 w/ EP10+: $149,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $109,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $48,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex Turboionspray source (aka ESI) for API 150, 365 or 3000: $6,250. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $45,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Agilent 1100 VL LC/MSD: offers considered. 2004 system. Finnigan Quantum: $160,000. ESI only (APCI available); factory refurbed; guaranteed installable. Install/warranty avail. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. Finnigan LCQ DECA: $67,500. ESI, Xcalibur 1.2, install, warranty incl. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan TSQ 7000 GC/MS: $65,000. GC and LC-capable; Xcalibur. Install, warr. avail. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Bruker Esquire: $85,000. Ion trap. Incl. install, guaranteed. Hitachi M 8000: $82,000. Ion trap. 1999; excellent condition; incl. LC. Micromass Quattro micro API: $150,000; Complete 2000. On factory service contract when deinstalled. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro LCZ: $131,500. Includes installation, warranty. Micromass Quattro IIZ: $149,000. Z-Spray. Includes install, warranty. Micromass Quattro Ultima: $125,000. VE. Z-Spray, APCI-Z, new MassLynx workstation. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. Mag sector/TOF hybrid. 1997 model. Good working order. Micromass Autospec M: $179,000. Mag sector/TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new) Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $60,000. European install included; available in US. MM Autospec V: $70,000. European install included; available in US. Mass spec sample introduction systems available; inquire. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR: $138,500. Includes install; guaranteed eligible for svc contract. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $67,000. Extensively refurbished. Voyager RP: $44,000. Incl. install; service contracts avail. Will QC peptides; continuous extraction. Voyager Elite XL: offers considered. incl. Vestec Multi-gauge, Advantec fraction collector Voyager MALDI lasers: rebuilt; full warrantee; ~2/3 price of new; install available. Call for info. Micromass M@LDI LR: $79,000. 2002 linear + reflection benchtop; determine intact protein mass and mPMF. Install included. Mariner ESI-TOF: $45,000. Installed/guar. ok for factory service. MicroMass TOF 2e-Spec: call/email to discuss price. 1999; many options; good working order. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $90,000. 2000 model; Nanoflow-Z CapElectrophoresis electrospray. Guaranteed installable. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $90,000. API-LC/Orth. 2000 model. Manufacturer-certified. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Sequenom MassARRAY: offers considered. 7K system (2002), for genotyping. Current software. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker OmniFlex: $69,750. 2000 model; all hardware upgrades; factory install, warranty included. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. Bruker Biflex III: various systems available; call or email to discuss Bruker Proflex III: offers considered. Excellent condition. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **GC/Other MS: Micromass VG70 SE: $45,000. Hi resolution GC/MS MSI Autoconcept: $380,000. New; multiramp temp; Agilent GC and Agilent or CTC autosampler. Includes install, 1 yr. warranty. Thermoquest GCQ: $30,000. GC/MS/MS; EI/CI; rebuilt; 90-day warranty. Agilent 5973/6890: $65,000. EI/CI/NCI; one year warranty. HP 5890 II/5970B: Offers considered. SmartCard II, software incl. HP 5989 MS engine: $28,500. 2000 amu mass range, pos/neg CI, APCI. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Wed, 03 Nov 2004 23:37:00 +0100 Subject: Re: CI-MS Ammonia Organization: * Just one more... regarding the plumbing, often solenoids are used to switch the gas flow. Common seal material is Viton, which is decomposed by ammonia (but this takes some time...). Before these seals harden, they swell and don´t let any gas pass through them regardless if they are on or off. If you use a tree for supplying different gases, the ammonia input might be closed and what you see is the methane leaking in from another port....This would correspond to the masses observed (see Eric´s answer) except mass 11 which is still a mystery. A solution is to replace all Viton by Kalrez, but be sure Kalrez is not in long time contact with fluorinated compounds like FC-43 or PFK, as these damage Kalrez (similia similibus solvuntur). Good luck! Rainer Carole schrieb: } } I look for profiles of ammoniac in positive chemical ionisation and } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } strange ?. The first data were peaks to 18 and 35 that seems more } logical. } Has someone an idea about this ? } Thanks to help me .... ****************************************************************************** From: Carole Date: 4 Nov 2004 00:14:36 -0800 Subject: Re: CI-MS Ammonia Organization: * Hello , We solved the problem while reconsidering the impact electronic, we have remake a tune then we passed by again in CI and there the peaks are correct...! Gauging is good and profile them waited are good (18 (100 %),35 (10 % max)°. We think that the tune was "wron" by deduction ... Thank you for your advice ****************************************************************************** From: Doug Stevens Date: 4 Nov 2004 03:22:28 -0800 Subject: Re: GC/MS m/z Range Organization: * I have been analyzing PDMS this week by GC/MS using CI and FI and getting peaks as high as 1480Da. That's just the highest mass. There are, of course, a series of peaks in the 1000 to 1500Da range as well. In the past I have seen analytes in the 1000 to 1500Da range but not very often. If memory serves one was a set of perfluorinated compounds and the other was a set of silicon containing analytes. Regards, Doug Stevens MS Applications Specialist Waters Corp. Dave White wrote in message news:... } We analyze brominated diphenyl ethers (used in flame retardents, etc.). The } labeled deca compounds require analyzing mass 973. It gets a bit hairy up } there, but it is doable. } } Dave White } SpectraChrom Software } www.spectrachrom.com ****************************************************************************** From: Bila Date: 4 Nov 2004 05:14:48 -0800 Subject: Loss of 22 Da from parent ion Organization: * Performing LC-MS/MS (triple quad) fairly often I get fragments 22 Da lower than the [M+H]+. To my knowledge a loss of 22 Da is not common. Does anybody know what's the reason for? Thanks! ****************************************************************************** From: Eric van der Meulen Date: 4 Nov 2004 15:58:55 -0800 Subject: Re: Loss of 22 Da from parent ion Organization: * The only thing that I can think of is, that what you think is your [M+H]+, is, in fact, the [M+Na]+. Loss of 22 amu would mean that Na is exchanged for H in your MSMS experiment. Does this make sense? Best regards, Eric Bila wrote in message news:... } Performing LC-MS/MS (triple quad) fairly often I get fragments 22 Da } lower than the [M+H]+. To my knowledge a loss of 22 Da is not common. } Does anybody know what's the reason for? } Thanks! ****************************************************************************** From: Victor Benham Date: Thu, 04 Nov 2004 21:09:51 -0500 Subject: ICP-AES and ICP-MS Sample Preparation Workshop - Ottawa - November 16, 1st Announcement. Organization: * SPECTROSCOPY SOCIETY OF CANADA Notice of Workshop - Ottawa - November 16 Subject: Sample Preparation Workshop - Ottawa - November 16 Dear Colleagues, The Spectroscopy Society of Canada has arranged for a seminar on sample preparation for Tuesday, November 16, 2004. The seminar will be conducted by Dr. Joe Brenner of Ben Gurion University in Israel. He will be giving a modified version of his popular ACS course. Dr. Brenner is widely acknowledged as one of the World's leading experts on sample preparation with nearly 100 publications on the subject. Please see the attachment for more details or contact Conrad Gregoire at 613-995-4213 or gregoire@nrcan.gc.ca. Regards, Victor Benham. SAMPLE PREPARATION STRATEGIES AND THEIR IMPACT ON ICP-AES AND ICP-MS RESULTS Join the Spectroscopy Society of Canada on Tuesday, November 16, 2004, for a sample preparation workshop conducted by Dr. Joe (Isaac) Brenner. One of the world's leading authorities on sample preparation, Dr. Brenner will deliver a version of his regular ACS sample preparation course. Sample solution integrity and reliability of preparation protocols dictate whether results are valid. Errors in sample preparation are the main source of uncertainty in the entire analytical process. This short course will address the status, requirements, and challenges of sample preparation for a wide range of analytical tasks and materials using ICP-AES and MS. The advantages and disadvantages of various procedures will be critically evaluated using conventional figures of merit such as LODs, contamination, multielement capability, recovery of labile and refractory elements, convenience of operation, automation, cost, sample size, and sample throughput. Among techniques discussed will be fusions, sinters, mixed acid routines in closed vessels and microwave ovens, and partial digestion for mode of analyte occurrence. The uniqueness of this session is the impact of sample preparation on the measurement system - on interferences in the aerosol generation and transport systems, in the plasma and in the ICP-MS interface. Sample preparation therefore is not a stand-alone part of the analysis but critically effects sample introduction and detection. Several selected applications for analysis of environmental, geological, biological, metallurgical, petrochemical and energy-based materials such as fly ash and coal, crude oils and multiphase bituminous sludges will be described. In particular, routines employed in trace element analysis of environmental and waste materials (Standard Methods, EPA 200.7, 200.8, SW846 6010 and 6020 and the 3000 series) will be detailed. Aspects of laboratory accreditation will be highlighted. Agenda: 8:00 AM Registration: Coffee and light refreshments will be served. 8:30 AM Decomposition Strategies: - Advantages of solution techniques, calibration and validation. - Strategies. Acid decomposition, fusions, sinters, open dish, pressurized containers, microwave digestion. - Partial decomposition and extraction for determining mode of occurrence of elements and species - Advantages and disadvantages of the strategies in terms of chemical resistance of refractory samples, loss of volatiles, poor recovery, reagent cost, contamination and sample throughput. - Instrumentation 10:30 AM Applications: Preparation of geological, environmental, biological and energy-based samples such as fly ash, coal, crude oil and multiphase bituminous sludge: - Open dish and closed containers, microwave dissolution and fusion procedures for selected materials be described in detail. - The procedures will be evaluated using conventional figures of merit such as limits of detection, recovery, sample throughput, and contamination. - Sample preparation for compliant analysis of waters, wastewaters, and solid wastes (EPA 200.7, 200.8, SW-846 6010B, 6020A and the 3000 series) will be highlighted. - Partial extractions using species selective reagents Effect of sample preparation on the plasma and sample introduction systems: - Salt and acid interferences, memory effects. Easily ionized element effects, salt clogging in torch injectors and in ICP-MS cones. 12:00 PM Lunch: An opportunity to meet with other analysts and exchange views. 1:00 PM Applications (continued): - Compensation of interference effects: Review of approaches to overcoming sample-preparation related interference effects in ICP-AES and MS. - Low consumption nebulizers, robust ICPs, internal standards, and reaction and collision cells. - Axial vs. radial ICP-AES considerations Discussion: - Comparison of open and closed vessels with microwave-assisted digestion. - Problem solving in sample preparation. - Is direct solids analysis using laser and spark ablation and slurry nebulization alternatives to sample preparation. 2:30 PM Finish. Location: Travelodge Ottawa West - Imperial Room 1376 Carling Avenue Ottawa, Ontario, K1Z 7L5 Tel: (613) 722-7600 Map: http://www.travelodge.com/Travelodge/control/Booking/map;jsessionid=BHB9CJtg7vTGN1jH6fNklFmWnxpVw2gCgkjZtKzhgmajIQTGRChH!-5558277!-1559074007?pid=11311&brandInfo=TL&MQZoom=5&brand_selected= Cost: $100 for members (SSC and AOAC) and $120 for non-members (cheques preferred). Registration: Please e-mail Conrad Gregoire (gregoire@nrcan.gc.ca) or call (613-995-4213) to reserve your place. ****************************************************************************** From: Chris R. Lee Date: Fri, 5 Nov 2004 21:48:34 +0100 Subject: Re: CI-MS Ammonia Organization: * Carole has solve her problem, but her posts provide a reminder that ammonia is a disaster in contact with anything other than stainless steeel and fluoropolymers. Can anyone advise on the choice of ammonia-compatible flow regulators; the options seem to be a needle valve, a pressure regulator upstream of a restrictor, and a relatively expensive electronic mass flow controller. Regards "rainer [iso-8859-2] lörwald" a écrit dans le message de news: cmbt0v$res$1@news-int2.gatech.edu... } } Just one more... } } regarding the plumbing, often solenoids are used to switch the gas flow. } Common seal material is Viton, which is decomposed by ammonia (but this } takes some time...). Before these seals harden, they swell and don´t let } any gas pass through them regardless if they are on or off. If you use a } tree for supplying different gases, the ammonia input might be closed } and what you see is the methane leaking in from another port....This } would correspond to the masses observed (see Eric´s answer) except mass } 11 which is still a mystery. A solution is to replace all Viton by } Kalrez, but be sure Kalrez is not in long time contact with fluorinated } compounds like FC-43 or PFK, as these damage Kalrez (similia similibus } solvuntur). } } Good luck! } Rainer } } } Carole schrieb: } } } } I look for profiles of ammoniac in positive chemical ionisation and } } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } } strange ?. The first data were peaks to 18 and 35 that seems more } } logical. } } Has someone an idea about this ? } } Thanks to help me .... } ****************************************************************************** From: Tony Lam Date: 5 Nov 2004 18:14:41 -0800 Subject: Re: GC/MS m/z Range Organization: * Dave White wrote in message news:... } We analyze brominated diphenyl ethers (used in flame retardents, etc.). The } labeled deca compounds require analyzing mass 973. It gets a bit hairy up } there, but it is doable. } } Dave White } SpectraChrom Software } www.spectrachrom.com Dear Dave, Brominated diphenyl ethers is troublesome... Just yesterday, one of the GC-MS gave GC-chromatograms with correct retention time region at the deca-isomer/congener, giving the correct ion ratio at three qualifier-fragment ions, ...but the indiviudal MS chromatogram within the the peak is very noisy and shows no "visual" character of deca.... Have you or anyone have encounter such strange problem? Why such problem exist?? Besides, I am very interested where I can find the deca-BDE congener at m/z 973 ****************************************************************************** From: Tony Lam Date: 5 Nov 2004 21:37:26 -0800 Subject: under water MS Organization: * Just surfing the web and find this interesting article: http://cot.marine.usf.edu/hems/underwater/TrAC%20Reprint%20Wenner.pdf although just having 200amu mass range... ****************************************************************************** From: Chip Cody Date: 8 Nov 2004 10:30:09 -0800 Subject: Re: CI-MS Ammonia Organization: * We use piezoelectric valves that seem to be NH3-resistant. I don't know the manufacturer offhand. However, I should point out that 1-5% ammonia in methane is generally a better CI gas. This was shown by Rudewicz and Munson in the 80's Later Dorn, Grade and Ligon used percent levels of 50% 15-N-labelled ammonia in methane. The problem is that analyte ions produced by ammonia CI can back-react with neutral ammonia causing loss of analyte signal. I reported an investigation of this by FTICR in 1989 (Analytical Chemistry). Ammonia in methane produces NH4+, but the neutral background is primarily methane, and signal loss is attenuated. A nice side benefit is that your gas plumbing is exposed to less ammonia. Chip Cody Chris R. Lee wrote in message news:... } Carole has solve her problem, but her posts provide a reminder that ammonia } is a disaster in contact with anything other than stainless steeel and } fluoropolymers. } } Can anyone advise on the choice of ammonia-compatible flow regulators; the } options seem to be a needle valve, a pressure regulator upstream of a } restrictor, and a relatively expensive electronic mass flow controller. } } Regards } ****************************************************************************** From: americanlaboratory@earthlink.net Date: 08 Nov 2004 15:23:03 -0800 Subject: American Laboratory News Organization: * Following are the themes to be featured in AL: * September Advances in Laboratory Software; Robotics, LIMS and Data Management; Gas Chromatography Focus * October Bioanalytical Techniques; Environmental Analysis; EAS Preview; Elemental Spectroscopy * November Microscopy, Optics, and Image Analysis; Microchemical Analysis; Sample Preparation; Micro LC Focus * December Pharmaceutical Analysis; Molecular Spectroscopy; Separation Science Dear Colleague, Please accept my invitation to receive a free subscription to our journal, American Laboratory. American Laboratory covers the disciplines of analytical and bio-analytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. [img1.jpg] For your FREE subscription to American Laboratory please click here to update your account. If you cannot see the above link, please copy and paste the following into your browser: http://203.197.214.171/americanlab/ I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor ________________________________________________________________________________ **If this email has reached you in error or you would like to be removed from future email offers, please reply to this email with "remove" in the subject line.** 12280 Saratoga-Sunnyvale Rd., Suite - 105, Saratoga, CA, 95070 americanlaboratory@earthlink.net ________________________________________________________________________________ ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Tue, 09 Nov 2004 00:57:47 +0100 Subject: Re: CI-MS Ammonia Organization: * My choice would be a simple needle valve with compatible seals. Keep the forepressure as low as needed and adjust the CI gas pressure in the source to a ratio of about 10:1 for M+H/M+. Exception is i-Butane which should have a maximum intensity on 57 with lowest possible intensity of 43. HTH Rainer "Chris R. Lee" schrieb: } } Carole has solve her problem, but her posts provide a reminder that ammonia } is a disaster in contact with anything other than stainless steeel and } fluoropolymers. } } Can anyone advise on the choice of ammonia-compatible flow regulators; the } options seem to be a needle valve, a pressure regulator upstream of a } restrictor, and a relatively expensive electronic mass flow controller. } } Regards } } "rainer [iso-8859-2] lörwald" a écrit dans le } message de news: cmbt0v$res$1@news-int2.gatech.edu... } } } } Just one more... } } } } regarding the plumbing, often solenoids are used to switch the gas flow. } } Common seal material is Viton, which is decomposed by ammonia (but this } } takes some time...). Before these seals harden, they swell and don´t let } } any gas pass through them regardless if they are on or off. If you use a } } tree for supplying different gases, the ammonia input might be closed } } and what you see is the methane leaking in from another port....This } } would correspond to the masses observed (see Eric´s answer) except mass } } 11 which is still a mystery. A solution is to replace all Viton by } } Kalrez, but be sure Kalrez is not in long time contact with fluorinated } } compounds like FC-43 or PFK, as these damage Kalrez (similia similibus } } solvuntur). } } } } Good luck! } } Rainer } } } } } } Carole schrieb: } } } } } } I look for profiles of ammoniac in positive chemical ionisation and } } } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } } } strange ?. The first data were peaks to 18 and 35 that seems more } } } logical. } } } Has someone an idea about this ? } } } Thanks to help me .... } } ****************************************************************************** From: carl braybrook Date: 9 Nov 2004 21:25:21 -0800 Subject: Re: MassLynx Organization: * Jeff Gambera wrote in message news:... } we are having a problem with MassLynx 3.3 or 3.5 while trying to process } data with MaxEnt. The program freezes upon submission of the request and } MassLynx must be shut down and restarted to recover. Transform works OK. Any } suggestions? } Thanks I have found that if you do a survey scan, stop before it refines when happy and change the parameters, then this is most often the outcome. You either have to save it or discard it and start again with new parameters, then I have no problems, or should I say far less. ****************************************************************************** From: carl braybrook Date: 9 Nov 2004 21:39:25 -0800 Subject: biodiesel Organization: * I was wondering if anyone could help me with some basic questions on testing biodiesel. I have been asked to measure the total free methyl ester content, and also free and total glycerine in 100% biodiesel. This particular Biodiesel is produced from used cooking oil, and the current method employed may be giving low amounts of methyl ester. Any comment or suggestions would be much appreciated. ****************************************************************************** From: Bila Date: 10 Nov 2004 05:42:46 -0800 Subject: Re: Loss of 22 Da from parent ion Organization: * Hello Eric, in this case I'm sure to have filtered the [M+H]+ in the Q1, since I knew the structure of the compound. Best regards, Bila Eric van der Meulen wrote in message news:... } The only thing that I can think of is, that what you think is your } [M+H]+, is, in fact, the [M+Na]+. Loss of 22 amu would mean that Na is } exchanged for H in your MSMS experiment. Does this make sense? } } Best regards, } } Eric } } Bila wrote in message news:... } } Performing LC-MS/MS (triple quad) fairly often I get fragments 22 Da } } lower than the [M+H]+. To my knowledge a loss of 22 Da is not common. } } Does anybody know what's the reason for? } } Thanks! ****************************************************************************** From: Joris Beld Date: 10 Nov 2004 08:27:12 -0800 Subject: LCQdeca vacuum problem Organization: * Dear all, Has anybody a good suggestion where to start looking when our LCQdeca LCMS (ESI) system starts to lose vacuum all the time as soon as the source is closed and the MS is switched on? We already checked all the connections for leaks, let Edwards perform maintenance on our two vacuum pumps but unfortunately without any succes. To be more precise: system is in standby mode, tuneplus window opened, closing the source and switching 'on' the ion gauge: it reminds us that the turbopump is running fine but one sees that the ion gauge pressure is increasing (from 1x10-5 Torr to > 4x10-5 Torr) and the convectron pressure stays pretty much constant at 2-3 Torr upon closing the source. Than switching the MS detector 'on' gives rise to a dramatic effect on the ion gauge pressure, it goes directly off scale up to 8x10-5 Torr and the MS detector switches back to standby mode (and one cannot even switch the ion gauge 'on' since vacuum disappeared). We are open for any suggestions?! Thanks in advance. Kind regards, Joris Beld ****************************************************************************** From: David Shteynberg Date: 10 Nov 2004 11:50:02 -0800 Subject: Proteomics Informatics at ISB - Next Course Jan. 2005 Organization: * The Seattle Proteome Center at the Institute for Systems Biology is offering a course on Proteomics Informatics. The objective of this course is to instruct active proteomics researchers in the use of a suite of software tools designed for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments using the ICAT reagent labeling method, multi-dimensional chromatography and tandem mass spectrometry. Through daily lectures and hands-on exercises, each course participant should become proficient in the use of the tools. For more information and for Application Materials please visit: http://www.proteomecenter.org/course.php You can read more about the software and even download the tools covered in the course at: http://tools.proteomecenter.org/software.php To visit the Seattle Proteome Center website point your browser to: http://www.proteomecenter.org/ Thanks and we hope to see you there! ****************************************************************************** From: Richard B. Opsal Date: 10 Nov 2004 13:33:16 -0800 Subject: Teknivent and ProLab Users - Vector/2 and EnviroLink Windows Organization: * Vector/2 and EnviroLink users, a Windows 2000, Windows XP upgrade is now available for these OS/2 based systems. Adron Systems owns the Vector/2 and EnviroLink product lines, formerly from ProLab Resources, Inc. and Teknivent Corporation. The Vx Acquisition System runs natively on Windows 2000 and Windows XP. Gone is the use of OS/2. For screen shots and further information on Vx, refer to the following site: http://www.adronsystems.com/products_vx.htm A working demo version of the Vx Acquisition System is available from the following site: http://www.adronsystems.com/downloads.htm You can use the demo version to tune and calibrate your instrument. The demo allows for data acquisition runs upto 10 minutes long. If you'd like to try the demo out on an actual instrument, you'll need a National Instruments PCI-GPIB card. If your mass spectrometer isn't listed when configuring an instrument, contact Adron Systems for an "instrument definition file." For the next few months, Adron Systems is offering introductory pricing for Vector/2 and EnviroLink upgrades. Richard Opsal Adron Systems http://adronsystems.com (218) 266-3455 ****************************************************************************** From: BMF7908 Date: 11 Nov 2004 00:55:15 GMT Subject: Re: LCQdeca vacuum problem Organization: * Don't know if this helps, but I had a similar issue on a TSQ Quantum Ultra. It was rumored that a bad batch of ion gauges made it out into the field with behavior you described. Also, since the outgas filament is not used, sometimes it takes a good overnight of pumping in the "on" position to get the ion gauge stable. In my case, it was replacing the ion source board (if I remember right!) that finally resolved it. Hope this helps, Brian ****************************************************************************** From: Joris Beld Date: 11 Nov 2004 03:50:36 -0800 Subject: Re: LCQdeca vacuum problem Organization: * Thanks a lot! Also someone else proposed already to replace the ion gauge. But after playing around with the machine a lot, the problem seems to be a little bit different. When the MS is standby, with the ion gauge 'on' (overnight), the ion gauge pressure is around 1.5x10-5 Torr and the Convector gauge pressure 0.7 Torr. When we switch 'on' the stream of the LC towards the MS (divert valve), the pressure goes slowly up. In 5-10 minutes, the ion gauge pressure is around 3.2x10-5 Torr and the Convector gauge pressure around 3 Torr. Most of the time than a peak occurs in the ion gauge pressure and the MS switches itself to standby mode. In 5-10 minutes the vacuum is back to its starting point. If I look at the turbopump I see the rotational speed being constant but the power usage increase (from 40 Watt to 73 Watt just before the collapse). Since both ion gauge as convector gauge show an increase in pressure, I think it a bit strange that both are broken or faulty?! So a technician suggested that there could be a leak in the seal of the heated capillary?! Any suggestions welcome! Thanks! Kind regards, Joris Beld ETH Hönggerberg Zürich, Switzerland ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Thu, 11 Nov 2004 23:58:55 +0100 Subject: Re: LCQdeca vacuum problem Organization: * Hello Joris, 0.7 Torr for the convectron is a litle low for an open capillary. Seal the capillary with a simple GC septum. You should reach 0.03-0.06 Torr on the convectron pressure. If it is higher, replace the Kalrez O-ring sealing the capillary to the spray shield. If in doubt, also replace the PEEK parts in front and behind it. Check the temperature of the heated capillary with an external meter. It appears that desolvation doesn´t take place correctly causing a lot of solvent to enter the second and third vacuum stage which forces the breakdown of the vacuum system. If vacuum remains stable without LC flow, this should be the reason for the problem. HTH Rainer Joris Beld schrieb: } } Thanks a lot! Also someone else proposed already to replace the ion } gauge. } } But after playing around with the machine a lot, the problem seems to } be a little bit different. } } When the MS is standby, with the ion gauge 'on' (overnight), the ion } gauge pressure is around 1.5x10-5 Torr and the Convector gauge } pressure 0.7 Torr. When we switch 'on' the stream of the LC towards } the MS (divert valve), the pressure goes slowly up. In 5-10 minutes, } the ion gauge pressure is around 3.2x10-5 Torr and the Convector gauge } pressure around 3 Torr. Most of the time than a peak occurs in the ion } gauge pressure and the MS switches itself to standby mode. In 5-10 } minutes the vacuum is back to its starting point. } } If I look at the turbopump I see the rotational speed being constant } but the power usage increase (from 40 Watt to 73 Watt just before the } collapse). } } Since both ion gauge as convector gauge show an increase in pressure, } I think it a bit strange that both are broken or faulty?! So a } technician suggested that there could be a leak in the seal of the } heated capillary?! } } Any suggestions welcome! Thanks! } Kind regards, } } Joris Beld } ETH Hönggerberg } Zürich, Switzerland ****************************************************************************** From: Bizzwire Date: Fri, 12 Nov 2004 00:10:21 GMT Subject: Re: LCQdeca vacuum problem Organization: * } Dear all, } } Has anybody a good suggestion where to start looking when our LCQdeca } LCMS (ESI) system starts to lose vacuum all the time as soon as the } source is closed and the MS is switched on? We already checked all the ..... . } We are open for any suggestions?! . First thing that comes to mind is, "have you recently rebuilt/cleaned the source or opened the machine up for any reason prior to this problem arising? ****************************************************************************** From: BMF7908 Date: 12 Nov 2004 01:55:41 GMT Subject: Re: LCQdeca vacuum problem Organization: * In addition to the other good suggestions posted by others, make sure your capillary heater is working as expected and is set for the flow you are using. You probably already checked this, but just in case. Brian }Subject: Re: LCQdeca vacuum problem }From: Joris Beld beld@org.chem.ethz.ch }Date: 11/11/2004 6:50 AM Eastern Standard Time }Message-id: } } }Thanks a lot! Also someone else proposed already to replace the ion }gauge. } }But after playing around with the machine a lot, the problem seems to }be a little bit different. } }When the MS is standby, with the ion gauge 'on' (overnight), the ion }gauge pressure is around 1.5x10-5 Torr and the Convector gauge }pressure 0.7 Torr. When we switch 'on' the stream of the LC towards }the MS (divert valve), the pressure goes slowly up. In 5-10 minutes, }the ion gauge pressure is around 3.2x10-5 Torr and the Convector gauge }pressure around 3 Torr. Most of the time than a peak occurs in the ion }gauge pressure and the MS switches itself to standby mode. In 5-10 }minutes the vacuum is back to its starting point. } }If I look at the turbopump I see the rotational speed being constant }but the power usage increase (from 40 Watt to 73 Watt just before the }collapse). } }Since both ion gauge as convector gauge show an increase in pressure, }I think it a bit strange that both are broken or faulty?! So a }technician suggested that there could be a leak in the seal of the }heated capillary?! } }Any suggestions welcome! Thanks! }Kind regards, } }Joris Beld }ETH Hönggerberg }Zürich, Switzerland } } } } } } } ****************************************************************************** From: Andrew Peters Date: Fri, 12 Nov 2004 14:02:47 -0400 Subject: HP 5992/5970 MS filaments available. Organization: * Hi, I am reposting this message as I have not been receiving any of the STMS re-mails for the past few months and so I don't know if anyone responded. Thanks to John B. for sorting out the problem! During a lab clean-out I found 8 unused filaments for a HP 5992/5970 MS, bought from SIS (SIS part # HPF4, corresponding HP part # 05990-60084). We currently have an Agilent 5973 and these parts are therefore redundant. Anyone interested in having them? Any offers? They currently retail for $110 each. Regards, Andrew ****************************************************************************** From: "Parees,David M." Date: Fri, 12 Nov 2004 13:19:48 -0500 Subject: GC/MS above m/z 1,000 Organization: * David Sparkman wrote in message news:... } Group, } } In a recent post, it was asked what GC/MS instruments have an m/z range } greater than 1,000. I am curious to know if anyone is analyzing } anything by GC/MS that approaches a mass of 1,000 Da. I know that } some perfluorinated } derivatives can get up there, but what is the } practicality of an instrument } that will go this high? } } Regards; } David } } -- } O. David Sparkman } Consultant-At-Large } osparkma no @ spam uop.edu } } } Antioch, CA 94531 } 1-925-754-5003 We analyze two grous of compounds by GC/MS that take us well above m/z 1,000. The first is species that are highly fluorinated and the second is a group of compounds that have quite a few (up to 12!) hydroxy groups. After trimethylsilylation, compounds in this group can have molecular weights well above 1,500 Da, and molecular ions are frequently observed. Chromatographic behavior is also excellent. We have analyzed fluorinated species above 2,000 Da by GC/MS. Yes, indeed, there is value in having a GC/MS instrument that is capable of analyzing species with molecular weights above 1,000 Da. As has been noted by others, highly brominated species can also have molecular weights pushing up into this range and yet be successfully analyzed by GC. We have experienced that as well. Dave Parees Air Products and Chemicals, Inc. 7201 Hamilton Blvd. Allentown, PA 18095 610-481-5794 ****************************************************************************** From: "Parees,David M." Date: Fri, 12 Nov 2004 16:27:31 -0500 Subject: possible problem with ion maps Organization: * In response to the posted note (below) about anomalous ion maps for poly-brominated species, one possible reason is that these species are significantly mass deficient. That is, the exact mass for the C-12/H-1/Br-79 species (and whatever other elements are present) is quite a bit below the integer mass. If you put in the integer mass for the ion map, even with a +/- 0.5 Da window, you might be missing a lot of signal intensity. Label the spectrum from your analysis, and add the 0.1 digit. E. g. if it is 966.5, then put that mass in for the ion map. Dave Parees Air Products and Chemicals, Inc. 7201 Hamilton Blvd. Allentown, PA 18195 610-481-5794 Dave White wrote in message news:... } We analyze brominated diphenyl ethers (used in flame retardants, } etc.). The labeled deca compounds require analyzing mass 973. It gets } a bit hairy up there, but it is doable. } } Dave White } SpectraChrom Software } www.spectrachrom.com Dear Dave, Brominated diphenyl ethers is troublesome... Just yesterday, one of the GC-MS gave GC-chromatograms with correct retention time region at the deca-isomer/congener, giving the correct ion ratio at three qualifier-fragment ions, ...but the individual MS chromatogram within the peak is very noisy and shows no "visual" character of deca.... Have you or anyone have encounter such strange problem? Why such problem exist?? Besides, I am very interested where I can find the deca-BDE congener at m/z 973 ****************************************************************************** From: Rich Milberg Date: Fri, 12 Nov 2004 23:15:42 GMT Subject: Re: LCQdeca vacuum problem Organization: * Did you take the ion gauge out and replace or re-install? Someone did on one of the ones here and forgot to clean the junkola inside the top of the analyzer housing where it makes it's vacuum seal. The LCQ wouldnt pump down to roughing pressure. Rich Milberg UI-UC Urbana, IL "rainer [iso-8859-2] lörwald" wrote in message news:cn13oj$k1d$1@news-int.gatech.edu... } Hello Joris, } } 0.7 Torr for the convectron is a litle low for an open capillary. Seal } the capillary with a simple GC septum. You should reach 0.03-0.06 Torr } on the convectron pressure. If it is higher, replace the Kalrez O-ring } sealing the capillary to the spray shield. If in doubt, also replace the } PEEK parts in front and behind it. Check the temperature of the heated } capillary with an external meter. It appears that desolvation doesn´t } take place correctly causing a lot of solvent to enter the second and } third vacuum stage which forces the breakdown of the vacuum system. If } vacuum remains stable without LC flow, this should be the reason for the } problem. } } HTH } Rainer } } } Joris Beld schrieb: } } } } Thanks a lot! Also someone else proposed already to replace the ion } } gauge. } } } } But after playing around with the machine a lot, the problem seems to } } be a little bit different. } } } } When the MS is standby, with the ion gauge 'on' (overnight), the ion } } gauge pressure is around 1.5x10-5 Torr and the Convector gauge } } pressure 0.7 Torr. When we switch 'on' the stream of the LC towards } } the MS (divert valve), the pressure goes slowly up. In 5-10 minutes, } } the ion gauge pressure is around 3.2x10-5 Torr and the Convector gauge } } pressure around 3 Torr. Most of the time than a peak occurs in the ion } } gauge pressure and the MS switches itself to standby mode. In 5-10 } } minutes the vacuum is back to its starting point. } } } } If I look at the turbopump I see the rotational speed being constant } } but the power usage increase (from 40 Watt to 73 Watt just before the } } collapse). } } } } Since both ion gauge as convector gauge show an increase in pressure, } } I think it a bit strange that both are broken or faulty?! So a } } technician suggested that there could be a leak in the seal of the } } heated capillary?! } } } } Any suggestions welcome! Thanks! } } Kind regards, } } } } Joris Beld } } ETH Hönggerberg } } Zürich, Switzerland } } ****************************************************************************** From: James Little Date: 12 Nov 2004 19:37:15 -0800 Subject: Re: CI-MS Ammonia Organization: * We had a lot problem with the standard chemical ionization on our Finnigan TSQ70. I built a versatile manifold for using gases and gas mixtures. Also, general info is available for using and selecting CI Gases. See http://users.chartertn.net/slittle for details Site also includes information on MS and EI databases, identification of unknowns, characterization of surfactants, etc. "rainer [iso-8859-2] lörwald" wrote in message news:... } My choice would be a simple needle valve with compatible seals. Keep the } forepressure as low as needed and adjust the CI gas pressure in the } source to a ratio of about 10:1 for M+H/M+. Exception is i-Butane which } should have a maximum intensity on 57 with lowest possible intensity of } 43. } HTH } Rainer } } } "Chris R. Lee" schrieb: } } } } Carole has solve her problem, but her posts provide a reminder that ammonia } } is a disaster in contact with anything other than stainless steeel and } } fluoropolymers. } } } } Can anyone advise on the choice of ammonia-compatible flow regulators; the } } options seem to be a needle valve, a pressure regulator upstream of a } } restrictor, and a relatively expensive electronic mass flow controller. } } } } Regards } } } } "rainer [iso-8859-2] lörwald" a écrit dans le } } message de news: cmbt0v$res$1@news-int2.gatech.edu... } } } } } } Just one more... } } } } } } regarding the plumbing, often solenoids are used to switch the gas flow. } } } Common seal material is Viton, which is decomposed by ammonia (but this } } } takes some time...). Before these seals harden, they swell and don´t let } } } any gas pass through them regardless if they are on or off. If you use a } } } tree for supplying different gases, the ammonia input might be closed } } } and what you see is the methane leaking in from another port....This } } } would correspond to the masses observed (see Eric´s answer) except mass } } } 11 which is still a mystery. A solution is to replace all Viton by } } } Kalrez, but be sure Kalrez is not in long time contact with fluorinated } } } compounds like FC-43 or PFK, as these damage Kalrez (similia similibus } } } solvuntur). } } } } } } Good luck! } } } Rainer } } } } } } } } } Carole schrieb: } } } } } } } } I look for profiles of ammoniac in positive chemical ionisation and } } } } negative (the peaks that I obtained were 11, 19, 29, 40...) this is } } } } strange ?. The first data were peaks to 18 and 35 that seems more } } } } logical. } } } } Has someone an idea about this ? } } } } Thanks to help me .... } } } ****************************************************************************** From: Joris Beld Date: 13 Nov 2004 02:28:29 -0800 Subject: Re: LCQdeca vacuum problem Organization: * Dear all, Thanks for all the help! I took out the API Stack, cleaned all the parts, replaced the Kalrez O-ring and re-assembled the API Stack. Now the vacuum is stable (ion gauge around 1x10-5 Torr and convector gauge around 0.08 Torr)! Since the machine was out-of-order for a couple of months I tried to do the calibration again but for some reason it fails a lot of the calibration checks. I have to redo that. Anyway, even without new calibration injecting samples of small peptides gives nice results. Best wishes, Joris ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Sat, 13 Nov 2004 22:49:31 +0100 Subject: Re: possible problem with ion maps Organization: * See http://www.bfr2004.com/Individual%20Papers/BFR2004%20Abstract%20078%20Krumwiede.pdf for info about BDE´s Rainer "Parees,David M." schrieb: } } In response to the posted note (below) about anomalous ion maps for } poly-brominated species, one possible reason is that these species are } significantly mass deficient. That is, the exact mass for the } C-12/H-1/Br-79 species (and whatever other elements are present) is quite } a bit below the integer mass. If you put in the integer mass for the ion } map, even with a +/- 0.5 Da window, you might be missing a lot of signal } intensity. Label the spectrum from your analysis, and add the 0.1 } digit. E. g. if it is 966.5, then put that mass in for the ion map. } } Dave Parees } Air Products and Chemicals, Inc. } 7201 Hamilton Blvd. } Allentown, PA 18195 } 610-481-5794 } } Dave White wrote in message } news:... } } } We analyze brominated diphenyl ethers (used in flame retardants, } } etc.). The labeled deca compounds require analyzing mass 973. It gets } } a bit hairy up there, but it is doable. } } } } Dave White } } SpectraChrom Software } } www.spectrachrom.com } } Dear Dave, } } Brominated diphenyl ethers is troublesome... Just yesterday, one of the } GC-MS gave GC-chromatograms with correct retention time region at the } deca-isomer/congener, giving the correct ion ratio at three } qualifier-fragment ions, ...but the individual MS chromatogram within the } peak is very noisy and shows no "visual" character of deca.... } } Have you or anyone have encounter such strange problem? Why such problem } exist?? } } Besides, I am very interested where I can find the deca-BDE congener at } m/z 973 ****************************************************************************** From: James Little Date: 14 Nov 2004 06:22:36 -0800 Subject: Re: GC/MS above m/z 1,000 Organization: * [ The following text is in the "ISO-8859-1" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] We too have run many compounds over the years with MW's greater than 1000 by GC/MS. Most of them are trimethylsilyl derivatives or fluorinated compounds. There can be some problems searching these in our corporate library because the mass sufficiency or deficiency will be increased below or above nominal mass. For example, something that one would expect to have a MW of 1100 by calculating with C12, H 1, N 14, O16 would have an indicated MW of 1100.7. When this is added to most EI libraries, the m/z will be entered as 1101. The NIST library search allows one to correct the masses to correct all masses for this problem when importing. We usually add the entry to the library with and without correction because some people would not realize there was a problem when searching the database. "Parees,David M." wrote in message news:... } David Sparkman wrote in message } news:... } } } Group, } } } } In a recent post, it was asked what GC/MS instruments have an m/z range } } greater than 1,000. I am curious to know if anyone is analyzing } } anything by GC/MS that approaches a mass of 1,000 Da. I know that } } some perfluorinated } derivatives can get up there, but what is the } } practicality of an instrument } that will go this high? } } } } Regards; } } David } } } } -- } } O. David Sparkman } } Consultant-At-Large } } osparkma no @ spam uop.edu } } } } } } Antioch, CA 94531 } } 1-925-754-5003 } } We analyze two grous of compounds by GC/MS that take us well above m/z } 1,000. The first is species that are highly fluorinated and the second } is a group of compounds that have quite a few (up to 12!) hydroxy } groups. After trimethylsilylation, compounds in this group can have } molecular weights well above 1,500 Da, and molecular ions are frequently } observed. Chromatographic behavior is also excellent. We have analyzed } fluorinated species above 2,000 Da by GC/MS. Yes, indeed, there is value } in having a GC/MS instrument that is capable of analyzing species with } molecular weights above 1,000 Da. As has been noted by others, highly } brominated species can also have molecular weights pushing up into this } range and yet be successfully analyzed by GC. We have experienced that } as well. } } Dave Parees } Air Products and Chemicals, Inc. } 7201 Hamilton Blvd. } Allentown, PA 18095 } 610-481-5794 ****************************************************************************** From: Katya Tsaioun Date: Mon, 15 Nov 2004 10:56:27 -0500 Subject: Qtrap and Analyst 1.4 problems Organization: * Does anyone on this list have Applied Biosystem's QTrap 2000 with Analyst 1.4 software? We are having a number of problems and I'd like to see if it is common with this particular configuration of hardware/software or is unique to us. Thanks! Katya Tsaioun, Ph.D. Sr. Research Investigator Analytical Chemistry Surface Logix, Inc. 50 Soldiers Field Place Brighton, MA 02135 tel: 617-746-8564 fax: 617-746-8595 e-mail: ktsaioun@surfacelogix.com ****************************************************************************** From: americanlaboratory@earthlink.net Date: 15 Nov 2004 11:35:35 -0800 Subject: American Laboratory News Organization: * Following are the themes to be featured in AL: * September Advances in Laboratory Software; Robotics, LIMS and Data Management; Gas Chromatography Focus * October Bioanalytical Techniques; Environmental Analysis; EAS Preview; Elemental Spectroscopy * November Microscopy, Optics, and Image Analysis; Microchemical Analysis; Sample Preparation; Micro LC Focus * December Pharmaceutical Analysis; Molecular Spectroscopy; Separation Science Dear Colleague, Please accept my invitation to receive a free subscription to our journal, American Laboratory. American Laboratory covers the disciplines of analytical and bio-analytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. For your FREE subscription to American Laboratory please click here to update your account. If you cannot see the above link, please copy and paste the following into your browser: http://203.197.214.171/americanlab/ I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor ________________________________________________________________________________ **If this email has reached you in error or you would like to be removed from future email offers, please reply to this email with "remove" in the subject line.** 12280 Saratoga-Sunnyvale Rd., Suite - 105, Saratoga, CA, 95070 americanlaboratory@earthlink.net ________________________________________________________________________________ ****************************************************************************** From: Jason Dunsmore Date: 16 Nov 2004 08:43:12 -0800 Subject: New proteomics forum, http://forums.deltastat.org/ Organization: * A new proteomics forum is available at: http://forums.deltastat.org/ Please come and discuss any topic related to proteomics (wet lab or informatics). Commercial advertisements are prohibited. Jason Dunsmore ****************************************************************************** From: Gregor Kos Date: Tue, 16 Nov 2004 17:03:43 GMT Subject: peak area display in amids 2.61 Organization: * hi, is there a way to calculate and display the peak area of an analysed peak in amdis 2.61? my data format is hp chemstation and i would like to know the peak area without using the chemstation software. i do not always have access to the chemstation computer. any help is appreciated! thanks. regards, greg -- gregor kos dept. of atmospheric and oceanic scienes mcgill university, montreal, canada gregor(dot)kos(at)mcgill(dot)ca ****************************************************************************** From: James Little Date: 20 Nov 2004 16:42:07 -0800 Subject: Re: peak area display in amids 2.61 Organization: * Don't know how to do in AMDIS, but Wsearch, found on web, can process HP files and do area. Also can send to NIST Ver 2 search, see http://www.wsearch.com.au/ Gregor Kos wrote in message news:... } hi, } } is there a way to calculate and display the peak area of an analysed } peak in amdis 2.61? } } my data format is hp chemstation and i would like to know the peak area } without using the chemstation software. i do not always have access to } the chemstation computer. } } any help is appreciated! thanks. } } regards, } greg ****************************************************************************** From: Marc Rosen Date: 20 Nov 2004 19:18:58 -0800 Subject: Re: Qtrap and Analyst 1.4 problems Organization: * Hello Katya, I don't have a Q-Trap (API 3000 TIS)but it took an entire week to upgrade from Analyst1.3.1 (on an NT platform ) to 1.4 (using XP SP1. Note do not use SP2 with Analyst 1.4!). Our ADC using driver 6.9.3 was not responding. All other peripherals worked but there was no way to use the absorbance detector. Finally after 5 days a technician arrived (there was a training conference in Florida and all the service techs were there.) I think we solved the problem by loading an earlier driver that was included in 1.3 but I don't have the driver number with me at home - can check Monday Katya Tsaioun wrote in message news:... } Does anyone on this list have Applied Biosystem's QTrap 2000 with Analyst } 1.4 software? We are having a number of problems and I'd like to see if } it is common with this particular configuration of hardware/software or } is unique to us. Thanks! } } Katya Tsaioun, Ph.D. } Sr. Research Investigator } Analytical Chemistry } } Surface Logix, Inc. } 50 Soldiers Field Place } Brighton, MA 02135 } tel: 617-746-8564 } fax: 617-746-8595 } e-mail: ktsaioun@surfacelogix.com ****************************************************************************** From: Richard Wall Date: Mon, 22 Nov 2004 16:46:57 -0000 Subject: FS Thermo Finnigan Voyager GC/MS EI CI +/ -ve Ion Organization: * For sale in UK Voyager GC/MS, running Masslab 1.4V NIST library Fitted with GC Tops with DPFC (EPC) AS800 Autosampler MS has 250 l/s Turbo EI/CI 2-1023 AMU mass range Three complete sources, EI, CI + and CI -/ve £15000 plus VAT info@ceinstruments.co.uk www.ceinstruments.co.uk ****************************************************************************** From: standrewsmarketing@earthlink.net Date: 23 Nov 2004 02:05:29 -0800 Subject: Invitation from Manufacturers of Spectrometers and Organization: * SPECTROMETERS AND SPECTROPHOTOMETERS ________________________________________________________________________________ St. Andrews Marketing Associates New York / New York Glasgow / Scotland Dear Colleague, St. Andrews Marketing Associates, on behalf of American Laboratory and American Biotechnology Laboratory, is conducting a study on the use of Spectrometers and Spectrophotometers. This study will help determine how we can best serve your needs and those of your peers. If you use or are planning to use Spectrometers and Spectrophotometers, please take a few minutes to fill out our survey by Clicking Here. If you cannot see the above link, please copy and paste the following link into your browser: http://203.197.214.171/iscsurvey/index.asp?email=mass.spec@gatech.edu&id=2 We appreciate your time and participation in helping us serve you better. Not a subscriber to American Laboratory / International Laboratory News? Please accept my invitation to receive a free subscription to our journal. American Laboratory / International Laboratory News covers the disciplines of analytical and bio-analytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology. For your FREE subscription to American Laboratory / International Laboratory News please click here. If you cannot see the above link, please copy and paste the following into your browser: http://203.197.214.171/almenu/ I am confident that you will enjoy our journal and find it to be of significant professional value. I look forward to hearing from you. Sincerely yours, Brian Howard, Ph.D. Editor ________________________________________________________________________________ **If this email has reached you in error or you would like to be removed from future email offers, please reply to this email with "remove" in the subject line.** St. Andrews Marketing Associates P.O.Box 5180 Milford, CT 06460-9747 standrewsmarketing@earthlink.net ________________________________________________________________________________ ****************************************************************************** From: David Sparkman Date: Wed, 1 Dec 2004 16:40:47 -0800 Subject: Re: peak area display in amids 2.61 Organization: * Greg After doing an analysis with a target library, a Results Window appears on the Right of the AMDIS display. The top part of this Results Window contain the names of the compounds identified. The lower left part (Component) has a scroll down list. A number of factors are reported in this list for the compound that is highlighted in the above part of the diplay. One is the peak area for the deconvoluted target compound. If there is no Area listing, put the Mouse pointer on the list in the Component pane and click the Right Mouse button. Select View Options from the displayed menu. This will open the View Options dialog box. Find Area in the left pane and put it in the right pane. Then click on Apply and then on Close. Now you can view the Area for any deconvolute target compound. When you select File from the Main Menu Bar and select Generate a Report, a tab delineated file that can be imported int (or opened if the XLS extension is used) Excel. Look at the various possibilities. If you still have questions, you can contact me. Rgards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "Gregor Kos" wrote in message news:cndhju$249$1@news-int2.gatech.edu... } hi, } } is there a way to calculate and display the peak area of an analysed } peak in amdis 2.61? } } my data format is hp chemstation and i would like to know the peak area } without using the chemstation software. i do not always have access to } the chemstation computer. } } any help is appreciated! thanks. } } regards, } greg } -- } gregor kos } dept. of atmospheric and oceanic scienes } mcgill university, montreal, canada } gregor(dot)kos(at)mcgill(dot)ca } ****************************************************************************** From: GCasi Date: 6 Dec 2004 06:18:42 -0800 Subject: RP-HPLC column regeneration Organization: * Hello everyone, I have a problem with RP-HPLC purification of oligonucleotides, and even though this is a group specialized on mass spec, maybe someone of you could help me; here is my problem. I am using a three moths old 250/4.6 Nucleosil 300-5 C18 column to purify oligonucleotides with triethylammonium acetate / Acetonitrile buffer system, and I wanted to regenerate the column. In a first attempt I reversed the flow on the column and applied a 1 mL/min flow with the following solvents: Acetonitrile, MeOH, THF, MeOH and back to acetonitrile. Every wash lasted 25 minutes. The result was that I eluted a lot of material from the column; the separation quality increased, but the back-pressure at 5% acetonitrile in TEAA buffer at 40°C, raised from 120 bars to 160 bars. In a second attempt I used 0.4 mL/min and only Acetonitrile,THF and back to acetonitrile, and this time the pressure raised evem more to 180 bars. I tried to flush the column also with water, but did not help. I don't know what I am doing wrong. Does anybody of you know how I could wash the column and still maintain moderatly-high pressure? Do you think I will be able to recover the column, or should I trash it? Thank you for your help Best regards, Giulio ****************************************************************************** From: ad Date: Mon, 6 Dec 2004 16:54:26 +0100 Subject: Re: RP-HPLC column regeneration Organization: * maybe a better place for this question: http://www.chromforum.com "GCasi" wrote in message news:cp1rfi$8u6$1@news-int.gatech.edu... } Hello everyone, } } I have a problem with RP-HPLC purification of oligonucleotides, and } even though this is a group specialized on mass spec, maybe someone of } you could help me; here is my problem. } } I am using a three moths old 250/4.6 Nucleosil 300-5 C18 column to } purify oligonucleotides with triethylammonium acetate / Acetonitrile } buffer system, and I wanted to regenerate the column. } } In a first attempt I reversed the flow on the column and applied a 1 } mL/min flow with the following solvents: Acetonitrile, MeOH, THF, MeOH } and back to acetonitrile. Every wash lasted 25 minutes. The result was } that I eluted a lot of material from the column; the separation } quality increased, but the back-pressure at 5% acetonitrile in TEAA } buffer at 40°C, raised from 120 bars to 160 } bars. } } In a second attempt I used 0.4 mL/min and only Acetonitrile,THF and } back to acetonitrile, and this time the pressure raised evem more to } 180 bars. } } I tried to flush the column also with water, but did not help. } } I don't know what I am doing wrong. } } Does anybody of you know how I could wash the column and still } maintain moderatly-high pressure? Do you think I will be able to } recover the column, or should I trash it? } Thank you for your help } } Best regards, } Giulio } ****************************************************************************** From: Joerg Hau Date: Mon, 06 Dec 2004 17:28:35 +0100 Subject: Re: RP-HPLC column regeneration Organization: * Hi } I am using a three moths old 250/4.6 Nucleosil 300-5 C18 column to } purify oligonucleotides with triethylammonium acetate / Acetonitrile } buffer system, and I wanted to regenerate the column. } } In a first attempt I reversed the flow on the column and applied a 1 } mL/min flow with the following solvents: Acetonitrile, MeOH, THF, } MeOH and back to acetonitrile. In this case, compounds such as inorganic buffer salts did not have a real chance to get off the column. They may have precipitated in the column, which could explain the pressure increase you observe. Always start with some acqueous solvent, then slowly move to the hard stuff. If we have to switch solvents on a system, we even do a flush with Isopropanol which is a nice "intermediate" solvent. } Every wash lasted 25 minutes. BTW, it's not the time that counts but the volume hat goes through the column. Same effect can be achieved in 12 min at ~2 ml/min. } Does anybody of you know how I could wash the column and still } maintain moderatly-high pressure? Do you think I will be able to } recover the column, or should I trash it? Depends on the number of injections and on the workplace. First of all, I would switch to a new column so that work can continue. If it's a rather new column (in terms of # of injections), maybe contact the manufacturer and ask for advice. If it has already a few hundred injections, just dump it - the time you spend "fixing" this is usually more expensive than a new column. Even at ETHZ ;-) As a general technique, I try to avoid accumulation of "late-eluting" material on the column by running the gradient up to 95+ percent of organic phase - it takes a bit longer, but our columns usually survive hundreds of injections this way. Cheers & HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove the obvious from my address to reply ****************************************************************************** From: Dave Kaleta Date: 7 Dec 2004 07:03:07 -0800 Subject: Re: RP-HPLC column regeneration Organization: * Anoher good source for this kind of questions is http://www.abrf.org/ ****************************************************************************** From: Dave Kaleta Date: 7 Dec 2004 10:12:08 -0800 Subject: peak fitting/deconvolution Organization: * I'm using PeakFit to fit peak functions to peak envelopes from spectra obtained on a Micromass QuattroII in HDX experiments. My question(s) revolve around the basis of peak fitting, best practices, etc. I get a real "black box" feel to performing the anaylsis, setting parameters, and I'd like to have more confidence that I'm not producing peaks out of thin air. I have spectra of the fully deuterated peptide (my problem spectra are partially deuterated) and my thought is to utilize the peak shape & width of these isolated, well defined, peaks to lock the peak shape function parameters for the peak fitting of the multiple peak envelope. Smoothing is another major concern. We've typically smoothed the data prior to importation to PeakFit, but this, of course, can affect the result. Difficult to evaluate the fit without a smoothed data set, on the other hand. I have some feelers out to Applied Math people as to the basics, figuring that's my best bet. thanks for any suggestions, I've found precious little while searching... Dave ****************************************************************************** From: David Stranz Date: Tue, 07 Dec 2004 19:27:43 -0600 Subject: Re: peak fitting/deconvolution Organization: * Dave Kaleta wrote in news:cp51hn$n9t$1@news-int.gatech.edu: } I'm using PeakFit to fit peak functions to peak envelopes from } spectra obtained on a Micromass QuattroII in HDX experiments. } My question(s) revolve around the basis of peak fitting, best } practices, etc. } I get a real "black box" feel to performing the anaylsis, } setting parameters, and I'd like to have more confidence that } I'm not producing peaks out of thin air. } } I have spectra of the fully deuterated peptide (my problem } spectra are partially deuterated) and my thought is to utilize } the peak shape & width of these isolated, well defined, peaks to } lock the peak shape function parameters for the peak fitting of } the multiple peak envelope. Smoothing is another major concern. } We've typically smoothed the data prior to importation to } PeakFit, but this, of course, can affect the result. Difficult } to evaluate the fit without a smoothed data set, on the other } hand. } } I have some feelers out to Applied Math people as to the basics, } figuring that's my best bet. } } thanks for any suggestions, I've found precious little while } searching... } } Dave } } } You might want to consider a different approach. Realize that the partially deuterated isotope cluster envelope is actually a superposition of envelopes of various deuteration states, all the way from 0 (i.e. nondeuterated) to full (perdeutero). If your deuteration kinetics are unimodal, you can model the deuteration level as a discrete probability distribution over the available states, and reduce the problem of fitting to one of determining the center and width of a probability function, like a Gaussian. The computed cluster resulting from such a probability-based fit is actually quite good. ****************************************************************************** From: David Stranz Date: Tue, 07 Dec 2004 19:27:43 -0600 Subject: Re: peak fitting/deconvolution Organization: * Dave Kaleta wrote in news:cp51hn$n9t$1@news-int.gatech.edu: } I'm using PeakFit to fit peak functions to peak envelopes from } spectra obtained on a Micromass QuattroII in HDX experiments. } My question(s) revolve around the basis of peak fitting, best } practices, etc. } I get a real "black box" feel to performing the anaylsis, } setting parameters, and I'd like to have more confidence that } I'm not producing peaks out of thin air. } } I have spectra of the fully deuterated peptide (my problem } spectra are partially deuterated) and my thought is to utilize } the peak shape & width of these isolated, well defined, peaks to } lock the peak shape function parameters for the peak fitting of } the multiple peak envelope. Smoothing is another major concern. } We've typically smoothed the data prior to importation to } PeakFit, but this, of course, can affect the result. Difficult } to evaluate the fit without a smoothed data set, on the other } hand. } } I have some feelers out to Applied Math people as to the basics, } figuring that's my best bet. } } thanks for any suggestions, I've found precious little while } searching... } } Dave } } } You might want to consider a different approach. Realize that the partially deuterated isotope cluster envelope is actually a superposition of envelopes of various deuteration states, all the way from 0 (i.e. nondeuterated) to full (perdeutero). If your deuteration kinetics are unimodal, you can model the deuteration level as a discrete probability distribution over the available states, and reduce the problem of fitting to one of determining the center and width of a probability function, like a Gaussian. The computed cluster resulting from such a probability-based fit is actually quite good. ****************************************************************************** From: David Stranz Date: Tue, 07 Dec 2004 19:27:43 -0600 Subject: Re: peak fitting/deconvolution Organization: * Dave Kaleta wrote in news:cp51hn$n9t$1@news-int.gatech.edu: } I'm using PeakFit to fit peak functions to peak envelopes from } spectra obtained on a Micromass QuattroII in HDX experiments. } My question(s) revolve around the basis of peak fitting, best } practices, etc. } I get a real "black box" feel to performing the anaylsis, } setting parameters, and I'd like to have more confidence that } I'm not producing peaks out of thin air. } } I have spectra of the fully deuterated peptide (my problem } spectra are partially deuterated) and my thought is to utilize } the peak shape & width of these isolated, well defined, peaks to } lock the peak shape function parameters for the peak fitting of } the multiple peak envelope. Smoothing is another major concern. } We've typically smoothed the data prior to importation to } PeakFit, but this, of course, can affect the result. Difficult } to evaluate the fit without a smoothed data set, on the other } hand. } } I have some feelers out to Applied Math people as to the basics, } figuring that's my best bet. } } thanks for any suggestions, I've found precious little while } searching... } } Dave } } } You might want to consider a different approach. Realize that the partially deuterated isotope cluster envelope is actually a superposition of envelopes of various deuteration states, all the way from 0 (i.e. nondeuterated) to full (perdeutero). If your deuteration kinetics are unimodal, you can model the deuteration level as a discrete probability distribution over the available states, and reduce the problem of fitting to one of determining the center and width of a probability function, like a Gaussian. The computed cluster resulting from such a probability-based fit is actually quite good. ****************************************************************************** From: Mike Sherrell Date: Wed, 8 Dec 2004 16:18:23 -0800 Subject: Mass specs, MALDIs available Organization: * Grizzly Analytical mass specs, MALDIs available 707 887 2919/mike@grizzlyanalytical.com **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. API 3000 upgrade: $38,500. Increases sensitivity and (S/N) Ratio at high flow rates to ~ that of an API 4000. Install incl. Sciex API 2000: $95,000 installed and warranteed. Sciex API 2000: $120,000: Incl. EPQ3 upgrade to ~ API 3000 sensitivity, install & Warranty. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase; incl. install, warr. Sciex API 365: $65,000. NT, turboionspray. Installed, warranteed. Sciex 365 w/ EP10+: $149,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $109,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $48,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex Turboionspray source (aka ESI) for API 150, 365 or 3000: $6,250. Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $45,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Agilent 1100 VL LC/MSD: offers considered. 2004 system. Finnigan Quantum: $160,000. ESI only (APCI available); factory refurbed; guaranteed installable. Install/warranty avail. Finnigan Deca XP+: $150,500. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. Finnigan LCQ DECA: $67,500. ESI, Xcalibur 1.2, install, warranty incl. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $29,500. Single quad. Installed, 30-day warr. Finnigan TSQ 7000: $50,000. ES, Xcalibur software, installation and 30-day warranty. Workhorse triple quad. Finnigan TSQ 7000 GC/MS: $65,000. GC and LC-capable; Xcalibur. Install, warr. avail. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Bruker Esquire: $85,000. Ion trap. Incl. install, guaranteed. Hitachi M 8000: $82,000. Ion trap. 1999; excellent condition; incl. LC. Micromass Quattro micro API: $150,000; Complete 2000. On factory service contract when deinstalled. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro LCZ: $131,500. Includes installation, warranty. Micromass Quattro IIZ: $149,000. Z-Spray. Includes install, warranty. Micromass Quattro Ultima: $125,000. VE. Z-Spray, APCI-Z, new MassLynx workstation. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Micromass ZQ: $105,000. 2002; incl. HP 1100; Z-Spray. MM/Waters ZMD 4000: $49,000. ESI, APCI. +$10K/factory install. Micromass ZABSpec Ultima OA TOF: $89,000. Mag sector/TOF hybrid. 1997 model. Good working order. Micromass Autospec M: $179,000. Mag sector/TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new) Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. Finnigan MAT 90: $16,000. All parts intact, plus spares included. MM Autospec: call if interested. Mag Sector. TOF, MSMS, ESI, MALDI, EI/CI. MM Autospec S: $60,000. European install included; available in US. MM Autospec V: $70,000. European install included; available in US. Mass spec sample introduction systems listed under liquid handlers, below. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: $45,000. Installed, guaranteed. Voyager DE STR: $138,500. Includes install; guaranteed eligible for svc contract. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $67,000. Extensively refurbished. Voyager RP: $44,000. Incl. install; service contracts avail. Will QC peptides; continuous extraction. Voyager Elite XL: offers considered. incl. Vestec Multi-gauge, Advantec fraction collector Voyager MALDI lasers: rebuilt; full warrantee; ~2/3 price of new; install available. Call for info. Micromass M@LDI LR: $79,000. 2002 linear + reflection benchtop; determine intact protein mass and mPMF. Install included. Mariner ESI-TOF: $45,000. Installed/guar. ok for factory service. MicroMass TOF 2e-Spec: call/email to discuss price. 1999; many options; good working order. MicroMass Q-TOF API-US: call/email to discuss price. 2002; includes CapLC. MicroMass Q-Tof Ultima: call/email to discuss price. Complete 2002 system. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $90,000. 2000 model; Nanoflow-Z CapElectrophoresis electrospray. Guaranteed installable. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. MicroMass LC-TOF: $90,000. API-LC/Orth. 2000 model. Manufacturer-certified. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Sequenom MassARRAY: offers considered. 7K system (2002), for genotyping. Current software. Bruker Ultraflex: call/email to discuss price. Working perfectly in lab Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker OmniFlex: $69,750. 2000 model; all hardware upgrades; factory install, warranty included. Bruker Reflex III: $89,000. 1999 model; includes chiller, standalone AS-90. Bruker Biflex III: various systems available; call or email to discuss Bruker Proflex III: offers considered. Excellent condition. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. Waters MALDI prep device. Offers considered. Used only once. Includes plates and kits. *Also available: service/contracts on Voyager DE, DE RP and PRO. **GC/Other MS: Micromass VG70 SE: $45,000. Hi resolution GC/MS MSI Autoconcept: $380,000. New; multiramp temp; Agilent GC and Agilent or CTC autosampler. Includes install, 1 yr. warranty. Thermoquest GCQ: $30,000. GC/MS/MS; EI/CI; rebuilt; 90-day warranty. Agilent 5973/6890: $65,000. EI/CI/NCI; one year warranty. HP 5890 II/5970B: Offers considered. SmartCard II, software incl. HP 5989 MS engine: $28,500. 2000 amu mass range, pos/neg CI, APCI. Finnigan Trace 2000: offers considered. 1998. EI/CI, autosampler, NIST library, Xcalibur Finnigan Magnum GC/MS Ion trap: $7,500. Incl. GC. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: Ramon Barnes Date: Sun, 12 Dec 2004 13:48:33 -0500 Subject: Call for Papers Asia-Pacific Winter Conference Organization: * 2005 Asia-Pacific Winter Conference on Plasma Spectrochemistry Chiang Mai, Thailand, April 25^Ö30, 2005 Call for Papers The first biennial Asia-Pacific Winter Conference will be held in April 2005 at the Lotus Hotel Pang Suan Kaew (www.lotuspskhotel.com) in Chiang Mai, Thailand (www.tourismthailand.org). More than 300 scientists are expected, and over 200 papers on modern plasma spectrochemistry will be presented. Six plenary lectures and 22 invited speakers will highlight critical topics in 12 symposia. Abstracts of contributed papers are now solicited. Symposium Features ^Õ Elemental speciation and sample preparation ^Õ Excitation mechanisms and plasma phenomena ^Õ Flow injection and flow processing spectrochemical analysis ^Õ Glow discharge atomic and mass spectrometry ^Õ Inductively coupled plasma atomic and mass spectrometry ^Õ Laser ablation and breakdown spectrometry ^Õ Microwave atomic and mass spectrometry ^Õ Plasma chromatographic detectors ^Õ Plasma instrumentation, microplasmas, automation, and software innovations ^Õ Sample introduction and transport phenomena ^Õ Sample preparation, treatment, and automation; high-purity materials ^Õ Spectrochemical chemometrics, expert systems, and software ^Õ Spectroscopic standards and reference materials, databases ^Õ Radionuclide and Stable isotope analyses and applications Also ^Õ Continuing Education Short Courses, Saturday - Sunday, April 23-24 ^Õ Manufacturer's Seminars, Saturday - Sunday, April 23-24 ^Õ Spectroscopy Instrumentation Exhibition, Monday - Thursday, April 25-28 ^Õ Provocative Panel Discussions, Daily ^Õ Workshop on New Plasma Instrumentation, Tuesday - Thursday, April 26-28 ^Õ Conference Excursion, Thursday, April 28, and Dinner, Friday, April 29 Information For program, registration, hotel, and transportation details, visit the Conference website at http://www-unix.oit.umass.edu/~wc2005, or contact Ramon Barnes, ICP Information Newsletter, Inc., P.O. Box 666, Hadley, MA 01003-0666, telephone: 413-256-8942, fax 413-256-3746, e-mail wc2005@chem.umass.edu. 2005 Asia Pacific Winter Conference on Plasma Spectrochemistry Monday - Saturday, April 25-30, 2005, Chiang Mai, Thailand Schedule of Activities Call for Papers, Abstracts Due; Early Bird Registration Monday, January 3, 2005 Exhibitor Booth Reservation and Pre-Registration Due Monday, January 3, 2005 Final Abstracts for All Papers Due Friday, January 28, 2005 Exhibitor Reservation Deadline Friday, January 28, 2005 Conference Pre-Registration Friday, January 28, 2005 HotelPre-Reservation Friday, March 25, 2005 Late Pre-Registration Deadline Friday, March 25, 2005 Winter Conference Short Courses Saturday ^Ö Sunday, April 23 ^Ö 24, 2005 Manufacturers^Ò Seminars Saturday ^Ö Sunday, April 23 ^Ö 24, 2005 Winter Conference on Plasma Spectrochemistry Monday ^Ö Saturday, April 25 ^Ö 30, 2005 Workshop on New Plasma Instrumentation Tuesday ^Ö Thursday, April 26 ^Ö 28, 2005 InstrumentExhibition Monday ^Ö Thursday, April 25 ^Ö 28, 2005 Conference Dinner Friday, April 29, 2005 Conference Manuscripts Final Deadline Thursday, June 30, 2005 Tentative Program Monday, April 25, 2005 08:00 Opening and Welcome 08:10 PL01 Plenary Lecture 1 09:10 IL01 Invited Lecture 1 09:40 IL02 Invited Lecture 2 10:10 Break 10:30 IL03 Invited Lecture 3 11:00 CL01 Contributed Lecture 1 11:30 CL02 Contributed Lecture 2 12:00 Lunch and Exhibition Opening Afternoon Parallel Sessions: Plasma Spectrochemistry and Non-plasma Atomic Spectrometry Exhibition and Poster Session Tuesday, April 26, 2005 08:00 PL02 Plenary Lecture 2 09:00 IL04 Invited Lecture 4 09:30 IL05 Invited Lecture 5 10:00 Break 10:30 IL06 Invited Lecture 6 11:00 CL03 Contributed Lecture 3 11:30 CL04 Contributed Lecture 4 12:00 Lunch Afternoon Parallel Sessions: Plasma Spectrochemistry and Non-plasma Atomic Spectrometry Poster Session and Exhibition Wednesday, April 27, 2005 08:00 PL03 Plenary Lecture 3 09:00 IL07 Invited Lecture 7 09:30 IL08 Invited Lecture 8 10:00 Break 10:30 IL09 Invited Lecture 9 11:00 IL10 Invited Lecture 10 11:30 IL11 Invited Lecture 11 12:00 Lunch Afternoon Parallel Sessions: Plasma Spectrochemistry and Non-plasma Atomic Spectrometry Poster Session and Exhibition Thursday, April 28, 2005 08:00 PL04 Plenary Lecture 4 09:00 IL12 Invited Lecture 12 09:30 IL13 Invited Lecture 13 10:00 Break 10:30 IL14 Invited Lecture 14 11:00 CL05 Contributed Lecture 5 11:30 CL06 Contributed Lecture 6 12:00 Lunch Exhibition Closes Afternoon Excursion Friday, April 29, 2005 08:00 PL05 Plenary Lecture 5 09:00 IL15 Invited Lecture 15 09:30 IL16 Invited Lecture 16 10:00 Break 10:30 IL17 Invited Lecture 17 11:00 CL07 Contributed Lecture 7 11:30 CL08 Contributed Lecture 8 12:00 Lunch Afternoon Parallel Sessions: Plasma Spectrochemistry and Non-plasma Atomic Spectrometry Poster Session Conference Dinner Saturday, April 30, 2005 08:00 PL06 Plenary Lecture 6 09:00 IL18 Invited Lecture 18 09:30 IL19 Invited Lecture 19 10:00 Break 10:30 IL20 Invited Lecture 20 11:00 IL21 Invited Lecture 21 11:30 IL22 Invited Lecture 22 12:00 Closing and Lunch ****************************************************************************** From: SMh Date: Mon, 13 Dec 2004 10:40:02 GMT Subject: Matrix Nondissolution Organization: * I seem to be having trouble re-dissolving alpha-cyano-4-hydroxycinnamic acid (CHCA). I washed and recrystallized using what I thought was a standard technique: 1. 100 mg CHCA resuspended in 10 ml water 2. Dropwise addition of ammonium hydroxide (26%) until dissolved 3. Supernatant transferred to new tube 4. Precipitation with dropwise addition of hydrochloric acid (concd) 5. Washing of precipitate with 2 x 10 ml 0.1 N HCl 6. Dissolution of precipitate in minimal volume of acetonitrile (MeCN) 7. Aliquotting about CHCA in MeCN for about 10 mg CHCA in each storage tube 8. Evaporation of acetonitrile in a 70 degree C oven...crystals seen in tube. 9. Stored in dark at room temperature I have tried to redissolve the CHCA crystals in MeCN, and even used ultrasonic bath and hot water. I have even put in more MeCN than they had originally, and using water/MeCN proportions does not help either. I am guessing the heat of the oven caused some sort of crosslinking and formation of insoluble products. Is CHCA that reactive/sensitive to temperature? What's the best or better way to recrystallize CHCA and sinapinic acid? ****************************************************************************** From: Beverley Earl Date: Mon, 13 Dec 2004 22:19:14 -0000 Subject: HP Engine Organization: * In September I had a problem where I thought the diffusion pumps on the HP5989A were not coming on. The instrument had been off for some time and when I started it up the pressure on the manifold read 4x10-2. I blocked off the column and the pressure reduced to 2x10-2 still a significant leak. Since then I have: - replaced the manifold window seal - blocked off both sides (separately) of the analyser e.g. interface and probe port and replaced the O ring at each side. - checked the oil level and replaced the O rings on the diffusion pumps - added ptfe tape to the vent plug at the back which lets the air in when venting - tightened the nuts on the CI and other valves attached to the interface - checked the level of calibration liquid in the calibration valve. - checked that the rough pump lever is closed properly All were done separately and had no effect on the pressure as it remains at 2x10-2 with the column blocked off and the problem is that the more I do the more likely it is that I am introducing another problem! Initially I thought the diffusion pumps were not coming on as the pressure remains constant when they are turned off to vent the instrument i.e. 2x10-2. The pressure does not change when the pumps are switched off to cool but they do heat up. This implies to me that the rough pumps are achieving the pressure without the diffusion pumps. The back diffusion pump oil was slightly more yellow and the O rings more difficult to remove but there wasn't any particulate matter and the oil levels were ok. With the diffusion pumps off and the rough pumps on I put up the baffles which are manually operated but the pressure did not change if this helps at all? We do not have a maintenance contract and I need to exhaust every option before we can consider paying for an engineer. Since then I realised that they are heating up and any further advice you can offer would be welcome. Thanks Beverley ****************************************************************************** From: Tom Knight Date: 13 Dec 2004 22:12:23 -0500 Subject: Re: HP Engine Organization: * Beverley Earl writes: } With the diffusion pumps off and the rough pumps on I put up the baffles } which are manually operated but the pressure did not change if this helps } at all? } } We do not have a maintenance contract and I need to exhaust every option } before we can consider paying for an engineer. } } Since then I realised that they are heating up and any further advice you } can offer would be welcome. Have you eliminated the possibility that the gauge is failing and that you really have good vacuum? ****************************************************************************** From: Richard Wall Date: Tue, 14 Dec 2004 15:41:40 -0000 Subject: Re: HP Engine Organization: * Dear Beverley At what cost does your company value your time ? Eight weeks down, not running samples is the machine costed in hours ? Service engineers are expensive, however a good engineer should be able to exactly pinpoint problems much faster than you. There must be third party MS service companies with Engine experience available at a lower price than an Aigilent engineer. It is good that users check simple good procedures with systems but you should consider when your time starts to outweigh the cost of an engineer. Have you even called an engineer yet ? Most will advise the most common solution F.O.C before asking for a p/o to visit and fix. Perhaps they might even be able to offer a fixed price fix ? Regards Richard "Beverley Earl" wrote in message news:cpl55k$4s9$1@news-int2.gatech.edu... } } In September I had a problem where I thought the diffusion pumps on the } HP5989A were not coming on. The instrument had been off for some time and } when I started it up the pressure on the manifold read 4x10-2. I blocked } off the column and the pressure reduced to 2x10-2 still a significant } leak. Since then I have: } } - replaced the manifold window seal } } - blocked off both sides (separately) of the analyser e.g. interface and } probe port and replaced the O ring at each side. } } - checked the oil level and replaced the O rings on the diffusion pumps } } - added ptfe tape to the vent plug at the back which lets the air in when } venting } } - tightened the nuts on the CI and other valves attached to the interface } } - checked the level of calibration liquid in the calibration valve. } } - checked that the rough pump lever is closed properly } } All were done separately and had no effect on the pressure as it remains } at 2x10-2 with the column blocked off and the problem is that the more I } do the more likely it is that I am introducing another problem! } } Initially I thought the diffusion pumps were not coming on as the } pressure remains constant when they are turned off to vent the instrument } i.e. 2x10-2. The pressure does not change when the pumps are switched off } to cool but they do heat up. This implies to me that the rough pumps are } achieving the pressure without the diffusion pumps. The back diffusion } pump oil was slightly more yellow and the O rings more difficult to } remove but there wasn't any particulate matter and the oil levels were } ok. } } With the diffusion pumps off and the rough pumps on I put up the baffles } which are manually operated but the pressure did not change if this helps } at all? } } We do not have a maintenance contract and I need to exhaust every option } before we can consider paying for an engineer. } } Since then I realised that they are heating up and any further advice you } can offer would be welcome. } } Thanks } } Beverley } } ****************************************************************************** From: Allis Chien Date: Tue, 14 Dec 2004 08:34:02 -0800 Subject: MS: EI on solids Organization: * Hi all, Does anyone know of a facility to which I can refer a student who needs to get a mass spec on an extremely insoluble compound? In the past, similar compounds have been analyzed by EI using a solids probe, but we don't have this capability in our lab. Thanks, Allis Stanford University Mass Spectrometry http://mass-spec.stanford.edu allis@stanford.edu ****************************************************************************** From: More Cowbell Date: Tue, 14 Dec 2004 15:21:24 -0800 Subject: MS/MS classes anywhere? Organization: * Is anyone aware of mass-spec classes that teach fundamentals in MS/MS? Either in the San Francisco Bay Area or anywhere else? -- Mike Northrop ****************************************************************************** From: Graeme Robertson Date: Wed, 15 Dec 2004 00:31:35 -0000 Subject: Re: HP Engine Organization: * Have you got waterflow thro the diff pumps. Unused water pipes can block up preventing water cooling causing the thermal trips on the pumps to switch them off and on thus never reaching operating temp/effective pumping. Otherwise my money is on some ion gauge fault /leak. Are they glass like the units on the HP5989B ? Good luck ****************************************************************************** From: Giganews Date: Tue, 14 Dec 2004 23:03:41 -0600 Subject: Re: MS/MS classes anywhere? Organization: * Mike; The American Society for Mass Spectrometry offers several two day short courses on the saturday and sunday preceeding the annual meeting. Take a look at: MS/MS: Fundamentals and Applications Instructors: Vicki Wysocki, Arpad Somogyi, George Tsaprailis, Linda Breci, and Paul Haynes "More Cowbell" wrote in message news:cpoe5i$a1u$1@news-int2.gatech.edu... } Is anyone aware of mass-spec classes that teach fundamentals in MS/MS? } Either in the San Francisco Bay Area or anywhere else? } } -- } Mike Northrop } } } } ****************************************************************************** From: David Stranz Date: Wed, 15 Dec 2004 08:22:14 -0600 Subject: Re: MS: EI on solids Organization: * Allis Chien wrote in news:cpn4v5$pa5$1@news-int2.gatech.edu: } Hi all, } } Does anyone know of a facility to which I can refer a student } who needs to get a mass spec on an extremely insoluble compound? } In the past, similar compounds have been analyzed by EI using a } solids probe, but we don't have this capability in our lab. } } Thanks, } Allis } } Stanford University Mass Spectrometry } http://mass-spec.stanford.edu } allis@stanford.edu } } } } Hi Allis, You might try talking to Fred Fago, who runs the MS lab in the geology department at Stanford. They have a Micromass Autospec, and I'd be surprised if they didn't have some type of solids probe. Otherwise, maybe talk to Axel Ehmann at Mass-Search in Modesto. He has a 4-sector ZAB which I believe has a solids probe. Regards, David ****************************************************************************** From: "Ligon, Woodfin V (Research)" Date: Wed, 15 Dec 2004 11:06:10 -0500 Subject: Manual for HP 5995 Organization: * Is there any chance at all that someone has kept the manuals (operation and/or service) for an HP 5995. I would be willing to buy them or copy them... Please contact Woody Ligon wligon@nycap.rr.com ****************************************************************************** From: Eric van der Meulen Date: 15 Dec 2004 12:21:17 -0800 Subject: Re: HP engine Organization: * Dear Beverly, I was thinking the same as Tom Knight did: do your ion gauges still work? Remember that there are two of them one the MS Engine, one above the front diff pump, and one at the rear of the analyzer manifold, wich can be monitored separately using the switch on the readout. The gauges are not easy to reach: to get to the rear one, you should remove the back part of the cover (the grey cover, not the black rear part). Another thing is that there is not much space in the machine, so you should have a colleague with very small hands handle it. The reason why I suspect the rear ion gauge is that you mentioned that the oil in the rear diff pump was more yellow than the oil in the front one. In my view it should be the other way around and it could have been caused by a vacuum problem in the analyzer, causing a high gas load in the rear pump. I would tighten the gauge port or replace the O-ring (maybe it was damnged the last time the gauge was changed?), or, even better, change the ion gauge : it is possible to accidently bend the metal feedthroughs on the ion gauge when attaching the readout plug, or bumping into them (as I said there is not much space in the machine). This bending of the metal feedthroughs can cause small cracks in the glass, giving rise to a leak (I've seen it myself....or actually, to be honest, caused it myself). For troubleshooting purposes you could even plug the back port and use the front gauge for vacuum readout. But to be honest, considering all the things you have already done and the huge amount of down time, I tend to agree with Richard Wall: Try and find a service engineer, because you have already done more than the average user would ever do. Greetings and good luck, Eric ****************************************************************************** Date: Wed, 15 Dec 2004 18:21:08 -0500 Subject: Re: Matrix Nondissolution ( Recrystallizing CHCA matrix) Organization: * We have used this protocol for re-crystallization of CHCA with no subsequent solubilization problems: 1. Dissolve CHCA in warm ethanol (60-70°C usually seems to work fine). 2. Centrifuge and filter precipitate. 3. Add two volumes of ice-cold deionized water to the filtrate (most CHCA will precipitate out immediately). 4. (to increase your recovery somewhat, you can leave the mixture in the refrigerator overnight). 5. Filter precipitate and wash with cold water. 6. Dry matrix in air, covered with foil to keep from light, and then store at 0° C (in the dark). (We usually pre-weigh amounts in the range of 1-2 mg into a bunch of 1.5 ml tubes, marking the exact weight in each tube on the outside, and then just pull a single tube out of the freezer and use the weight marked on that tube to calculate the amount of Acetonitrile, water, and TFA needed to make the matrix up that day at whatever concentration we need - saves waiting for a whole bottle of recrystallized CHCA to get up to room temperature to avoid condensation. When we get tired of pre-weighing CHCA into tubes or it's time for lunch, we put the rest into a larger glass scintillation vial, which we pull out only the next time we need to aliquot a bunch of tubes or when we are making up larger quantities to put into our ProBot. You can easily prepare enough re-crystallized material for a year or more with the procedure above, and the recrystallized material seems to be stable for at least that long (at least by color, we haven't done any rigorous testing)). We did try sonicating the ethanol mix one time (same crude starting material), and the resulting material didn't seem to perform as well, nor did it look the same as the "standard method". So perhaps there is some kind of heat reaction at higher temps or after longer sonication? But your 70° oven (unless it wasn't really at 70°) isn't any higher than the ethanol solutions we use, so...? --Bruce ************************************************* Bruce A. Stanley, Ph.D. Director, Proteomics/Mass Spectrometry Facility Director, Scientific Programs Section of Research Resources H093 Office Tele: (717) 531-5329 FAX: (717) 531-0239 ************************************************* *****E-Mail Confidentiality Notice***** This message (including any attachments) contains information intended for a specific individual(s) and purpos e that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. SMh wrote: }I seem to be having trouble re-dissolving alpha-cyano-4-hydroxycinnamic }acid (CHCA). }I washed and recrystallized using what I thought was a standard technique: }1. 100 mg CHCA resuspended in 10 ml water }2. Dropwise addition of ammonium hydroxide (26%) until dissolved }3. Supernatant transferred to new tube }4. Precipitation with dropwise addition of hydrochloric acid (concd) }5. Washing of precipitate with 2 x 10 ml 0.1 N HCl }6. Dissolution of precipitate in minimal volume of acetonitrile (MeCN) }7. Aliquotting about CHCA in MeCN for about 10 mg CHCA in each storage tube }8. Evaporation of acetonitrile in a 70 degree C oven...crystals seen in tube. }9. Stored in dark at room temperature } } }I have tried to redissolve the CHCA crystals in MeCN, and even used }ultrasonic bath and hot water. I have even put in more MeCN than they had }originally, and using water/MeCN proportions does not help either. } }I am guessing the heat of the oven caused some sort of crosslinking and }formation of insoluble products. Is CHCA that reactive/sensitive to }temperature? } }What's the best or better way to recrystallize CHCA and sinapinic acid? ****************************************************************************** From: Bruce Stanley Date: Wed, 15 Dec 2004 18:21:08 -0500 Subject: Recrystallizing CHCA matrix Organization: * We have used this protocol for re-crystallization of CHCA with no subsequent solubilization problems: 1. Dissolve CHCA in warm ethanol (60-70°C usually seems to work fine). 2. Centrifuge and filter precipitate. 3. Add two volumes of ice-cold deionized water to the filtrate (most CHCA will precipitate out immediately). 4. (to increase your recovery somewhat, you can leave the mixture in the refrigerator overnight). 5. Filter precipitate and wash with cold water. 6. Dry matrix in air, covered with foil to keep from light, and then store at 0° C (in the dark). (We usually pre-weigh amounts in the range of 1-2 mg into a bunch of 1.5 ml tubes, marking the exact weight in each tube on the outside, and then just pull a single tube out of the freezer and use the weight marked on that tube to calculate the amount of Acetonitrile, water, and TFA needed to make the matrix up that day at whatever concentration we need - saves waiting for a whole bottle of recrystallized CHCA to get up to room temperature to avoid condensation. When we get tired of pre-weighing CHCA into tubes or it's time for lunch, we put the rest into a larger glass scintillation vial, which we pull out only the next time we need to aliquot a bunch of tubes or when we are making up larger quantities to put into our ProBot. You can easily prepare enough re-crystallized material for a year or more with the procedure above, and the recrystallized material seems to be stable for at least that long (at least by color, we haven't done any rigorous testing)). We did try sonicating the ethanol mix one time (same crude starting material), and the resulting material didn't seem to perform as well, nor did it look the same as the "standard method". So perhaps there is some kind of heat reaction at higher temps or after longer sonication? But your 70° oven (unless it wasn't really at 70°) isn't any higher than the ethanol solutions we use, so...? --Bruce ************************************************* Bruce A. Stanley, Ph.D. Director, Proteomics/Mass Spectrometry Facility Director, Scientific Programs Section of Research Resources H093 Office Tele: (717) 531-5329 FAX: (717) 531-0239 ************************************************* *****E-Mail Confidentiality Notice***** This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. SMh wrote >I seem to be having trouble re-dissolving alpha-cyano-4-hydroxycinnamic >acid (CHCA). > >I washed and recrystallized using what I thought was a standard technique: > >1. 100 mg CHCA resuspended in 10 ml water >2. Dropwise addition of ammonium hydroxide (26%) until dissolved >3. Supernatant transferred to new tube >4. Precipitation with dropwise addition of hydrochloric acid (concd) >5. Washing of precipitate with 2 x 10 ml 0.1 N HCl >6. Dissolution of precipitate in minimal volume of acetonitrile (MeCN) >7. Aliquotting about CHCA in MeCN for about 10 mg CHCA in each storage tube >8. Evaporation of acetonitrile in a 70 degree C oven...crystals seen in >tube. >9. Stored in dark at room temperature > > >I have tried to redissolve the CHCA crystals in MeCN, and even used >ultrasonic bath and hot water. I have even put in more MeCN than they had >originally, and using water/MeCN proportions does not help either. > >I am guessing the heat of the oven caused some sort of crosslinking and >formation of insoluble products. Is CHCA that reactive/sensitive to >temperature? > >What's the best or better way to recrystallize CHCA and sinapinic acid? > ****************************************************************************** From: rsiegener@metaenv.com Date: 16 Dec 2004 08:44:52 -0800 Subject: Electron multiplier Organization: * HI all, I am looking to replace the electron multiplier in our HP 5971. Amyone have any recommendations between the DeTech 2300, Burle 5900 magnum, or Agilent replacement. Thanks Ray ****************************************************************************** From: Drew Spencer Date: Fri, 17 Dec 2004 05:29:18 GMT Subject: Re: Electron multiplier Organization: * Hi Ray, We recently replaced the failing Burle in our 5971 with an ETP and have been very happy with the results thus far. Check out this link for details: http://www.etpsci.com/htm/etp/tech_info/product_data_sheets.asp I ended up getting a deal on mine through a local vendor who is an SGE reseller. Their tech support was very good when we had problems originally mounting the multiplier to the quad due to interface differences. After the initial install issues were resolved, we've been very happy with the results and would highly recommend this as an option to the Burle and others. I have no affiliation with SGE/ETP other than being a satisfied customer. Drew rsiegener@metaenv.com wrote: } HI all, } I am looking to replace the electron multiplier in our HP 5971. Amyone } have any recommendations between the DeTech 2300, Burle 5900 magnum, or } Agilent replacement. } Thanks } Ray } } ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Fri, 17 Dec 2004 20:17:52 +0100 Subject: Re: Electron multiplier Organization: * Ray, have you tried K&M? They also deliver mounting hardware for the first time conversion. http://kandm.com/cem.asp Rainer rsiegener@metaenv.com schrieb: } } HI all, } I am looking to replace the electron multiplier in our HP 5971. Amyone } have any recommendations between the DeTech 2300, Burle 5900 magnum, or } Agilent replacement. } Thanks } Ray ****************************************************************************** From: nuin Date: 17 Dec 2004 12:08:20 -0800 Subject: GASP: GC/MS Analysis Software Package Organization: * GASP is a cross-platform software developed in C++ with wxWidgets as GUI framework, that allows the comparison of GC/MS runs, in order to determine differences in composition of samples. The program reads output files from Xcalibur, HP Chemstation and AMDIS, converts and align these files in order to make the comparisons. GASP has a direct link with R to generate statistical analysis of the alignments. GASP is available free of charge for universities and non-profit organizations. A complete help file is available to download also. If you want to learn more about GASP capabilities before using it, get the help file and check the program's features. The software is available at: http://evol.mcmaster.ca/paulo/gasp.php GASP was developed to analysis of metabolomics data, such as plant composition comparison, cell composition comparison, etc. It is cross-platform and runs with no change in Linux and Windows. GASP is not a analytical chemistry software, its main use as said is metabolomics where at first the determination of the right compound is secondary to the determination of differences in sample compositions. Cheers Paulo Nuin Dept of Biology McMaster University ****************************************************************************** From: David Sparkman Date: Sun, 19 Dec 2004 05:55:11 -0800 Subject: MS Interprtation Course Organization: * The American Chemical Society will offer a Web Based interactive course in the Interpretation of Mass Spectra beginning January 6, 2005. The course meets twice a week for 6 weeks for 1.5 hours each time. For more details, go to: http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=education\professional\wcsp06.html Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com ****************************************************************************** From: David Sparkman Date: Sun, 19 Dec 2004 05:58:22 -0800 Subject: Looking for a Book Organization: * I am looking to purchase a copy of: Mass Spectrometry: Principles and Applications, 2nd Ed. McGraw-Hill, NY; 1981, ISBN: 007030575 HB or 0070705690 paper by I. Howe, D. Williams, and R.D. Bowen. I have looked at abebooks.com To contact me, remove the no spam from my address. -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com ****************************************************************************** From: John Dulak Date: Mon, 20 Dec 2004 18:55:24 -0500 Subject: Re: Looking for a Book Organization: * David Sparkman wrote: } } I am looking to purchase a copy of: } Mass Spectrometry: Principles and Applications, 2nd Ed. McGraw-Hill, NY; } 1981, ISBN: 007030575 HB or 0070705690 paper by I. Howe, D. Williams, and } R.D. Bowen. } } I have looked at abebooks.com } } To contact me, remove the no spam from my address. } } -- } O. David Sparkman } Consultant-At-Large } ods no @ spam compuserve.com David: This site: http://www.bibliofind.com/ Seems to have what you want. (Watch out for word wrap on links) http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y03Y0547269Y7694666/104-9302392-9612737 http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y01Y6744558Y9808547/104-9302392-9612737 http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y02Y2851889Y8437409/104-9302392-9612737 http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y01Y4545758Y6550789/104-9302392-9612737 HTH & GL John -- \\\\\// "Don't take life so seriously... | | ...it's only a temporary condition." (.) (.) ========================================oOO==(_)==OOo== _____________________________________________ | John G. Dulak | | Gnomeway Services | /)| E-mail me from my home page at: |(\ / )| http://users.telerama.com/~jdulak/email.htm |( \ ( (|____________________________________________ |) )_ ((( \ \ > /_) ( \ < / / ))) (\\\ \ \_/ / \ \_/ / ///) \ / \ / \ _/ \_ / / / \ \ ****************************************************************************** From: David Sparkman Date: Mon, 20 Dec 2004 18:25:58 -0800 Subject: Re: Looking for a Book Organization: * John, Thanks very much but these are the correct title, but wrong authors. These are the 2nd edition by de Hoffmann and Stroobant (2001). I am looking for the book by Howe, Williams, and Bowen, 1981. I'm still looking. Regards; David -- O. David Sparkman Consultant-At-Large ods no @ spam compuserve.com "John Dulak" wrote in message news:cq80i6$1l0$1@news-int.gatech.edu... } David Sparkman wrote: } } } } I am looking to purchase a copy of: } } Mass Spectrometry: Principles and Applications, 2nd Ed. McGraw-Hill, NY; } } 1981, ISBN: 007030575 HB or 0070705690 paper by I. Howe, D. Williams, and } } R.D. Bowen. } } } } I have looked at abebooks.com } } } } To contact me, remove the no spam from my address. } } } } -- } } O. David Sparkman } } Consultant-At-Large } } ods no @ spam compuserve.com } } David: } } This site: } } http://www.bibliofind.com/ } } Seems to have what you want. (Watch out for word wrap on links) } } http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y03Y0547269Y7694666/104-9302392-9612737 } } http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y01Y6744558Y9808547/104-9302392-9612737 } } http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y02Y2851889Y8437409/104-9302392-9612737 } } http://s1.amazon.com/exec/varzea/ts/exchange-glance/Y01Y4545758Y6550789/104-9302392-9612737 } } } HTH & GL } } John } -- } \\\\\// } "Don't take life so seriously... | | } ...it's only a temporary condition." (.) (.) } ========================================oOO==(_)==OOo== } _____________________________________________ } | John G. Dulak | } | Gnomeway Services | } /)| E-mail me from my home page at: |(\ } / )| http://users.telerama.com/~jdulak/email.htm |( \ } ( (|____________________________________________ |) )_ } ((( \ \ > /_) ( \ < / / ))) } (\\\ \ \_/ / \ \_/ / ///) } \ / \ / } \ _/ \_ / } / / \ \ } } ****************************************************************************** From: John Dulak Date: Mon, 20 Dec 2004 22:14:32 -0500 Subject: Re: Looking for a Book Organization: * David: Sorry I got the title right but the author is wrong. John -- \\\\\// "Don't take life so seriously... | | ...it's only a temporary condition." (.) (.) ========================================oOO==(_)==OOo== _____________________________________________ | John G. Dulak | | Gnomeway Services | /)| E-mail me from my home page at: |(\ / )| http://users.telerama.com/~jdulak/email.htm |( \ ( (|____________________________________________ |) )_ ((( \ \ > /_) ( \ < / / ))) (\\\ \ \_/ / \ \_/ / ///) \ / \ / \ _/ \_ / / / \ \ ****************************************************************************** From: Dana Reed Date: Wed, 22 Dec 2004 14:10:41 -0600 Subject: Free VG7070 HF (you pay shipping) Organization: * Hi, We have a VG7070-HF that we'd be using for FAB for the past several years. We don't do FAB anymore and We've moved our MSS data system to a VG 70SE that we're using to do EI/CI/GCMS. If anyone needs or wants a VG 70 either for spare parts, or for analysis, let me know. It was recently turned off (3 months ago) since we didn't have room to set it up in our new facility. It doesn't have a data system but there are 3rd party systems available for these machines. There is a picture on our web site at: http://www.chem.umn.edu/services/massspec/ I'd just hate to throw out a working instrument, so I hope someone takes me up on this offer. Thanks, Dana ****************************************************************************** From: Rich Trubey Date: 23 Dec 2004 09:05:35 -0800 Subject: Ionization Suppression Under Air Peak (Agilent 5973 MSD)?? Organization: * I am trying to detect various light gases using a DB-1 column directed to an MSD. For target analytes that elute under the air peak (my injections contain small amount of air), has anyone ever seen suppression of analyte ionization due to simultaneous ionization of air gases? Target analytes are at ppm levels. Injections are 1 mL volume (sometimes split, sometimes s/less) via a GasTight syringe. I know that typically a PLOT column would be better but that is not necessarily an option for me. I've heard rumors of this effect but not anything well documented. Thanks! ****************************************************************************** From: Christopher R. Lee Date: Thu, 23 Dec 2004 21:46:00 +0100 Subject: Re: Electron multiplier Organization: * I have also had good results with ETPs. Once though, an MS Engine autotune failed because it couldn't cope with the high gain of a new multiplier. An advantage of this type of multiplier is that it dies slowly and gracefully, whereas continuous dynode types tend to crash so rapidly that you can't be sure the problem is with the multiplier. Regards "Drew Spencer" a écrit dans le message de news: cpulh4$dei$1@news-int2.gatech.edu... } Hi Ray, } } We recently replaced the failing Burle in our 5971 with an ETP and have } been very happy with the results thus far. Check out this link for } details: } } http://www.etpsci.com/htm/etp/tech_info/product_data_sheets.asp } } I ended up getting a deal on mine through a local vendor who is an SGE } reseller. Their tech support was very good when we had problems } originally mounting the multiplier to the quad due to interface } differences. After the initial install issues were resolved, we've been } very happy with the results and would highly recommend this as an option } to the Burle and others. } } I have no affiliation with SGE/ETP other than being a satisfied customer. } } Drew } } rsiegener@metaenv.com wrote: } } HI all, } } I am looking to replace the electron multiplier in our HP 5971. Amyone } } have any recommendations between the DeTech 2300, Burle 5900 magnum, or } } Agilent replacement. } } Thanks } } Ray } } } } } ****************************************************************************** From: tk2003deja@amdis.net Date: 23 Dec 2004 23:42:51 -0800 Subject: Re: Looking for a Book Organization: * Hi David, } } } I am looking to purchase a copy of: } } } Mass Spectrometry: Principles and Applications, 2nd Ed. McGraw-Hill, NY; } } } 1981, ISBN: 007030575 HB or 0070705690 paper by I. Howe, D. Williams, try one of the better book-engines: http://www.sfb.at/ Enter the title and then filter for year 1981 - will give 5 direct results. IF you enter the ISBN only 3 results. ($120-$288) Go directly here and save 20 bucks: http://www.zubalbooks.com/ its 100 dollar and still available :-) ...and a Happy New Year! Tobias Kind www.amdis.net PS: http://news.google.com/news?q=Somerville+Massachusetts+%22merry+christmas%22 ****************************************************************************** From: JLshen2000@yahoo.ca Date: 26 Dec 2004 19:47:20 -0800 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * I have seen cases in which the analytes showed diffrenet ratios of M+H/M+Na in dirty ion sources. Of course, this happened before Q1. If Q2 were contaminated, I would suspect that there were conversion of M+H or/and fragments to the corresponding sodiated forms in Q2. Possible? Regards, Jimmy ****************************************************************************** From: Don Date: Wed, 29 Dec 2004 19:44:54 GMT Subject: Re: Ionization Suppression Under Air Peak (Agilent 5973 MSD)?? Organization: * "Rich Trubey" wrote in message news:cqf21g$lnr$1@news-int2.gatech.edu... } I am trying to detect various light gases using a DB-1 column directed } to an MSD. For target analytes that elute under the air peak (my } injections contain small amount of air), has anyone ever seen } suppression of analyte ionization due to simultaneous ionization of air } gases? Target analytes are at ppm levels. Injections are 1 mL volume } (sometimes split, sometimes s/less) via a GasTight syringe. } } I know that typically a PLOT column would be better but that is not } necessarily an option for me. } } I've heard rumors of this effect but not anything well documented. } Thanks! } If you don't need quantification and the gases are appropriate, one trick I've used many times is to run a loop of the column just after the injector through a dewar of liquid N2. You can inject a slowly as you like and wait until the unretained air (and lighter gases) have eluted and then run the trapped residual. ****************************************************************************** From: Don Date: Wed, 29 Dec 2004 19:44:54 GMT Subject: Re: Ionization Suppression Under Air Peak (Agilent 5973 MSD)?? Organization: * "Rich Trubey" wrote in message news:cqf21g$lnr$1@news-int2.gatech.edu... } I am trying to detect various light gases using a DB-1 column directed } to an MSD. For target analytes that elute under the air peak (my } injections contain small amount of air), has anyone ever seen } suppression of analyte ionization due to simultaneous ionization of air } gases? Target analytes are at ppm levels. Injections are 1 mL volume } (sometimes split, sometimes s/less) via a GasTight syringe. } } I know that typically a PLOT column would be better but that is not } necessarily an option for me. } } I've heard rumors of this effect but not anything well documented. } Thanks! } If you don't need quantification and the gases are appropriate, one trick I've used many times is to run a loop of the column just after the injector through a dewar of liquid N2. You can inject a slowly as you like and wait until the unretained air (and lighter gases) have eluted and then run the trapped residual. ****************************************************************************** From: IET Ltd Date: 29 Dec 2004 19:49:50 -0800 Subject: Micromass LCT API-LC / Orthogonal TOF Mass Spectrometer Available Organization: * Micromass LCT API-LC / Orthogonal TOF Mass Spectrometer, with Gilson 215 Liquid Handler, Compaq PC, cables, etc. The price is $69,000.00 plus the cost of installation. Please contact for further information. Please contact: Sara Schell, Sales Manager International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 ph: 847-913-0777 fax: 847-913-0785 sales@ietltd.com http://www.ietltd.com ****************************************************************************** From: oookhc@hotmail.com Date: 29 Dec 2004 21:13:23 -0800 Subject: Re: Mass Spectrometer Wanted Organization: * You might check the following link http://www.ScienceOxygen.com/apparatus/62.html It does not sell anything over there -- it is just a collection of links about Mass Spectrometer. Probably you can get the information you need there... ****************************************************************************** From: Kent Electronics Date: Thu, 30 Dec 2004 12:55:05 -0000 Subject: Autospec Bits Organization: * Hi All We are moving out of our premises after 15 years. We still have a box full of Micromass Autospec electronic units plus a few ion source bits for disposal, last chance. We will donate them to any university providing the freight and packing charges are paid for. Many thanks Regards John Hill Kent Electronics ****************************************************************************** From: Giacomo56 Date: Thu, 30 Dec 2004 10:51:59 -0600 Subject: Re: Mass Spectrometer Wanted Organization: * What kind of Mass Spec are you looking for? Details please.... Thanks wrote in message news:cr0vro$8ej$1@news-int.gatech.edu... } You might check the following link } } http://www.ScienceOxygen.com/apparatus/62.html } } It does not sell anything over there -- it is just a collection } of links about Mass Spectrometer. Probably you can get } the information you need there... } } } ****************************************************************************** From: kieserbn@rogers.com Date: 30 Dec 2004 18:42:31 -0800 Subject: Re: MS/MS classes anywhere? Organization: * More Cowbell wrote: } Is anyone aware of mass-spec classes that teach fundamentals in MS/MS? } Either in the San Francisco Bay Area or anywhere else? } } -- } Mike Northrop If it is LC/MS you're interested in, Applied Biosystems offers practical MS courses at its facility in Foster City. Here's the link: http://www.appliedbiosystems.com/service/training/course.cfm?productID=1001&submit=Get+Courses regards, BK ****************************************************************************** From: jameslittle@eastman.com Date: 31 Dec 2004 05:06:58 -0800 Subject: Re: (ESI)MS/MS: variable fragment pattern? Organization: * We do a lot of in-source fragmentation for substructural information on a variety of instruments using ammonium acetate added post-column or part of the buffer system. We have noted by flow injection that the M+H, M+NH4, and M+Na ions optimize at different in-source collision values. In general the ratio of the M+Na/M+NH4 increase as the in-source (cone, declustering potential, whatever the manufacturer calls it) voltage employed increases. Often very handy when your not sure if you have a M+H or M+NH4, or M+Na ion when only one of the ions are noted. On the Micromass LCT TOF at an in-source (cone voltage) of 75 volts, normally just the M+Na ion is left while all the M+H and M+NH4 ions have yielded substructural fragments. JLshen2000@yahoo.ca wrote: } I have seen cases in which the analytes showed diffrenet ratios of } M+H/M+Na in dirty ion sources. Of course, this happened before Q1. If } Q2 were contaminated, I would suspect that there were conversion of M+H } or/and fragments to the corresponding sodiated forms in Q2. Possible? } Regards, } } } Jimmy