[Biochemistry Q/A |Calibration and High Resolution Q/A | Chemical Ionization Q/A |
Computer Q/A |Electronics Q/A |Electrospray Q/A |GC-MS Q/A
|ICP Q/A |Ion Trap Q/A | MALDI Q/A |Miscellaneous Q/A |MS Parts and Supplies Q/A |Quadrupoles Q/A |

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More MS troubleshooting guides

Biochemistry Topics

.FASTA protein databases
Aflatoxin analysis by GC-MS?
CID spectrum of epicatechin (flavenoids)
Tandem MS of amino acids?
Aminoacid analysis by GC-MS
Ethylchloroformate for amino acid derivative
LC-MS determination of FMOC-derivatized amino acids
MS/MS references for carbohydrates and metal ions
Derivitization of neurotransmitters
Carotenoid analysis by ESI or MALDI
GC-MS determination of cysteine-derivatives
Silyl Derivatives of Monosaccharides for GC-MS
Polysulfated saccharide sodium salts in ESI neg.ion mode
Desalt a protein digest
Chaps detergent references
Peptide sequencing software
Peptide calculation software
SEQUEST software
Peptide Mass Calculations (avg. vs. monoisotopic)
MS/MS protein database search programs
Mass accuracy and peptide mass fingerprint results
Peptides sequencing
Post-translational Modifications of Proteins?
Triglycerides in MS
Triglyceride Molecular Ion and Adducts
Method to differenciate Glutamic Acid and Glutamine
Method for distinguishing Leucine and Isoleucine
3-hydroxy-palmitic acid references
MALDI trypsin map against a database
Trypsin Autolysis Peak references
Protein identification software from protease-digested mass spectra
Covalent modification of histidine
Electrospray of cobalamine with sodium contamination
Lipid molecules in blood plasma
LC-MS problems with drug analysis in plasma
Analysis of proteins from 2D gels
MALDI on silver-stained 2D gels
Database Mining in the Human Genome Initiative link
Should Eppendorf tubes be silanized?
PEGylated protein discussion links
48 Dalton increase in MALDI-TOF spectra

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Calibration and High Resolution

Accurate Mass, Exact Mass, and Peak Match Discussion
Accurate mass, Exact Mass, and Peak Match Discussion, Part II
Accurate mass precision and accuracy
Definition of Mass resolution
Calibrations for MS
Perfluorotributylamine FC-43
Spectra of Calibration gases
Useful compounds for checking resolution in EI mode
Calibration Standard for Negative Chemical Ionization
Accurate mass data in ammonia CI
Resolution and Resolving Power
FAB-High Resolution Analysis?
Polymer with mass difference of 44 other than PEG
ESI Calibration Compounds
Water cluster calibration in ESI
Negative ESI-HR Reference Compounds
LCQ custom calibration reference files
Suppliers of PFK (perfluorokerosene)
Ultramark 1600F Calibration standard source

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Chemical Ionization

CI background peaks
3% ammonia in methane reagent gas for CI
Ammonia C.I. - Pressure Regulators
NH3 as reagent gas for positive ion CI
References for Mixed CI Reagent Gases
Problem with Chemical Ionization
Self-Chemical Ionization Explanation
n-Butane as a C.I. Reagent Gas
Methane gas quality
Electron Capture-Negative Ion C.I. MS of PCBs
Methylamine Chemical Ionization / Manifold for Multiple CI gases
Negative ion C.I. on Ion trap
Accurate mass data in ammonia C.I.

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Computer Topics

Data Format Conversions

Converting Chemstation and Masslynx files
File conversion from masslab to masslib or opus
Excalibur files converted to Masslynx
Xcalibur data file converstion with ACD/MS Manager
Old Incos data files to PC
Finnegan format (.ms) to HP format (.d)
Converting msengine data files into windows files
RTE-V1 files to MSDOS Chemstation
Old HP MSD computer problem
MSD Upgrade and Smartcard
Converting HP Chem software chromatograms to ASCII
Raw time-abundance data pairs from HP Chemstation data files
Graphics in Chemstation
Data format conversion with HP Chemstation and API 300's MAC
Data conversion of LCQ data files
Converting GC-MS Workstation datafiles to DOS/Window
Spectra in Chemstation vs. Norton Utilities
HP Chemstation (Pascal) files copy/conversion to PC
HP MS-Chemstation 3.X (Pascal Software) Users
HP MSD Datasystem and MS Chemstation data export
HP Chemstation macros
Agilent/HP Chemstation Macros repository
Macro use for Agilent's Chemstation
SSQ data converted to HP Chemstation format
VG Fisons Labbase Data File Format
HP Andi AIA Support
Reading netCDF (ANDI)files
TOF MS file format(.cdf and ANDI)
Exporting MassLynx spectra
Conversion of Finnegan ITD data (.dta)to GCQ (.ms)
.ms data format
Converting .ms files to .cdf format
Exporting MALDI data into a graphics program
Saturn data file conversion to Chemstation
Converting Saturn data format to HP format
Mass spectral display for internet or email (.wmf to .html format)
IUPAC's JCAMP-DX web site link


Data Systems for sector field MS
MS-Data System for Finnigan 4500 searched
HP5971A Data System Upgrade
HP5989A GC-MS:HP-UX data system
PC Computer Upgrade for HP 5985 System
Upgrading Quattro with non-DEC PC
Question about Updating from PDP11/24
Questions about VG 7070E (PDP 11/24 upgrade)
Data System for sector MS
Replacing PRIAM disk on NOVA 4 system
Computer Upgrade for Finnegan ITD 700
Upgrade of Quattro-I computer with Windows 98 or NT
Running Saturn or Finnegan Magnum software on Win95
TRIO 1000 PC upgrade problems
Updating TRIO1 and MSD data systems
HP diskdrive web sites
Info needed for upgrading from VG MassLab
Balzer MS QMG420 software
Finnegan ITDS software


GC-MS acquisition software for all brands
Comparison of free online chemical databases
HP GC-MS date problems
HELP:Display 132000 points
HP MS Chemstation Data Tricks
Chemstation Automation Question
Finnegan MAT/Technivent Software
Data Acquisition Software for self-built ToF
Computer Analysis algorithms of MS
Algorithms to deconvolute multiply charged ions
Mass Spectral Libraries
Proper Searching of Multiple Libraries with HP Data Systems
Using Wsearch program with NIST library searches
Drug spectral libraries link
Best backup procedure on QTOF
CD ROM Backup of Data


Software connection problems in API 365
Finnegan MassLab communication problem
HP 9133D disc drive
HP 59970 Chemstation Floppy Disk Drive
Chemstation Printing Problem
PDP8 problem
VG Masslab printing problems
Printing problems with DOS Chemstation

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Electronic Topics

5970's Turbo Pump controller
High voltage resistor dividers?
Software to receive data from a mass spectrometer through a serial interface
High voltage switch
4.5 volt mercury batteries
Uninterruptible power supply (UPS)
Electrical power for MS (UPS or not?)
Uninterruptible Power Supply
Question on ToF data acquisition electronics
HP filament circuitry
Electron energy distributions of filaments
Accelerating Voltage on Finnigan MAT 8200
Laser Shot Counter
Repairs on an HP7673B Autosampler
G1701BA, HP5972, sequence terminates abnormally
HP 5971 MSD tuning problems
ESI repair on VG Platform
VG Trio-2000 troubleshooting
Ion Trap RF power supplies
2N6259 Power Transistors for Magnet Power Supply
VG-70S Energy Filter
ETP electron multipliers
ETP electron multipliers II
TSQ700 + HP1050 Relay Contacts

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Electrospray Topics

Electrospray Book and Article References
ESI Mechanism References
ESI-MS/MS references
LC/MS books
Capillary HPLC references
ESI droplet size and theory plus nanoESI
ESI Calibration Compounds
API 3000 tuning
APCI of air sensitives
Unknown artifact in protein ES-MS spectrum
ESI background contaminants
Electrospray adducts of 96 mass units
Doubly-charged or dimer ESI question
Dimer Formation in ESI
ESI adducts [M+15]+ AND [M+29]+
ESI adducts [M+63]
Electrospray adduct: M+63
Mechanism of Na+ adduct formation under APcI
Desalting primer before electrospray mass spectrometry
ESI of Cobalamine with sodium contamination
Zinc-protein analysis
Electrospray MS interpretation
Generic LC-MS Method
LC/MS/MS quantification problems
Non-linearity in API calibration curve (LC-MS/MS)
LC-MS purification system (fraction collector-MS interface)
Question on HPLC-MS
High LC/MS background
LC system for triple quad MS
HPLC effluent split between ES-MS and UV-VIS
Post column acidification
LC coupling to MS (lower flowrates vs. splitting)
Purification of mobile phase components for LC-MS (API)
ES-MS of anabolic steroids
LC-MS problems with drug analysis in plasma
LC-ESI Enhancement effect on Soil Samples
ESI-MS of membrane proteins
Protein in ESI (neg.ion mode)
Help on LC-Electrospray of corticosteroids with SPE
ESI of fagopyrine
Analysis of amprolium using LC-MS
ESI of amiodarone
ESI of nucleotides
LC-MS on flavonoids
API-MS on long chain alcohols
Peptide/Protein Ionization?Ion Pair Reagents
Boosting sensitivity in LC-MS
Problems with a 60,000 MW immunoglobulin protein
Negative Ion Electrospray Calibration
Negative ESI-HR reference compounds
Rat poison analysis by LC-MS
Sulphonic acid dyes by LC-MS
ESI analysis of naphthalenedisulfonates
LC-MS of sulfonylurea pesticides
Volatile ion pairing reagent
PEEK tubing and ion pairing reagent contamination
Anion exchange chromatography with ESI-MS
Oxygen-free ESI analysis
Cold infusion in ESI
High Resolution Spectrum on an ESMS peak
Electrohydrodynamic Ionization
Copper-amino acid chelate references
Background Problems in negative electrospray mode
Unstable Baseline in postive ESI
Non-linear standard curves in negative ESI
Internal std. considerations for LC-MS/MS
Electrospray Source Cleaning
ESI spray current problems
LCQ spray currents
Platform's pepperpot and cross-flow electrode interface
Roughing pump maintenance with APCI
Turbo pump crashes on API systems
CE-ESI-MS electrical connections
CE-ESI MS references
Umbelliferone coumarin by ESP+ analysis
Normal phase LC-ESMS or LC-APCI-MS
LC-system flushing after phosphate buffer use
Rapid noise increase in LCQ ion trap (nanospray interface)
Clusters during API
Water clusters in ESI spectra
Water cluster calibration in ESI
Water cluster ESI-MS spectrum of LCQ Ion Trap
Advice on purchase of LC-MS

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GC-MS Topics

GC-MS: Which system recommended for environmental analysis?
Using HP 6890/5973 for EPA 8270 analysis
Can GC-MS analyze H2 and O2 quantitatively
GC-MS problem with analyzing water samples
Different standards for GC-MS sensitivity
Finnigan GCQ Inlet Problem -Jade Valves
GC-MS volatiles analysis
Purge and Trap GC-MS Recommendations
Selected ion monitoring (SIM) vs. Extracted Ion
Sample-reference match criteria
SRM locks up on TSQ 700
Triazine and Arylureas analysis in Water and Soil by GC-MS
GC/LC/MS on algae toxins
GC-MS determination of thiophene and other sulfur cmpds.
GC-MS analysis of dioxin in milk
Fatty acid methyl ester (FAME) alternative derivitizing methods
Hydrolysis and derivitization of esters for GC-MS
Formation of nitriles during silylation
Essential Oil library database for SATURN II GC/MS
Online NIST spectral database
Pesticide database for GC/MS
Software to interpret GC-MS spectra from first principles
Non-vented GC-MS interfaces
MS No vent add-on devices
Graphite vs. Vespel Ferrules for GC-MS
Problem with losing GC column pressure
High Carrier Gasflow in MSD
Massive Helium Carrier Gas Leak
Electronic pressure control programming with GC/MS
HP GC-MS Chemstation Software Library Search questions
Proper searching of multiple libraries with HP data systems
Using Wsearch program with NIST library searches
Library searching of Multiple Databases with HP software
Recommendations for LC-GC MS/MS mass spectrometer
Parent and Daughter ions in GC-MS-MS
Background mass 40 in GC-MS
Questions about VG 7070E GC-MS (ordering gases)
Quantitative Multicomponent Analysis on RGA-MS (gases)
Interference in VOA GC-MS analysis
GC-MS Problem in VOA analysis
Purgeable organic methods by GC-MS
HP 7673 ALS Syringe Motors for Autosamplers
Large Volume injectors
GC-MS Source Cleaning Frequency
MS source correct cleaning procedure
Drifting Ion Ratios with HP5970 MSD
GCQ Ion Volume Performance/Cleaning
Determination of sulfur compounds by GC-MS
Phenol analysis by GC-MS
PAH analysis (internal std. areas problem)
Liquid Natural Gas analysis by GC-MS
Active carbon for dioxins/furans analysis
p,p'-DDT analysis by GC-MS
Deuterium Isotope Effect on Elution order
Water and DMSO solvent effects in GC-MS
Hydrogen vs. Helium as a Carrier Gas
GC-MS books
Tuning HP 5970
HP5970 Standard Autotune
HP 5971 MSD tuning problems
Sick MSD
Autotuning problems on HP5970 MSD
Negative baseline on HP 5970 MSD

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ICP-MS Topics

How to overcome space charge effect
Stability of ICP-MS
Iodine Analysis via ICP-MS
Isotopic fractionation for Zn isotopes
Laser Probe on Plasma Quad II
Plasmachem-L's ICP-MS listserver
ELAN 6000 ICP-MS' roughing pump troubleshooting
Metal analysis in soils by ICP-MS

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Ion Trap Topics

Ion traps vs. Quadrupoles
Trap vs. Quad in structural analysis (MS/MS)
Triple Quads vs. Ion traps
Ion trap vs. QqQ
Triple Quad vs. Ion trap vs. QTOF
Ion Trap
Saturn or GCQ purchase? Quads vs. Traps
Help on MS selection: LCQ vs. LECO plus ion trap theory
Ion trap literature and opinions
Fundamentals in Ion Trap Theory
Varian Saturn III, Ion Trap Instrument (troubleshooting)
GC/MS/MS on Saturn 4D Ion Trap
Screen Capture from Varian Saturn or Finnegan ITD
Essential Oil library database for SATURN II GC/MS
Inert Surface on Ion Traps
Chloromethane spectrum in the ion trap
Ion Trap RF powers supplies
Trapping-delay time and other ion transit questions
Rapid increase in ion trap noise (LCQ nanospray interface)
Teflon spacer contamination
Wide mass range tuning on a ESQUIRE ion trap
Parent ion scans possible by trap's MS/MS

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MALDI Topics

MALDI-TOF matrices
Basic pH MALDI matrices reference
Neutral MALDI matrices
MALDI of poly-lysine
MALDI matrix for polyimine analysis
MALDI of lipids
MALDI reviews for polymer analysis
Latex analysis
Disulfide bonds and MALDI-MS
Web Resources for laser desorption and MALDI-ToF
General Laser Desorption questions
Time of Flight References
Development of TOF
MALDI links
MALDI reference
MALDI-MS adducts
MALDI on a polyethylene-imine polymer
Opinions on Micromass Q-TOF
MALDI trypsin map against a database
MALDI dimers and trimers
MALDI matrix for large negative ion protein
MALDI on silver-stained 2D gels

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Miscellaneous Topics

Structural elucidation of natural products
C6+ m/z=72 in MS of C6Cl6
MS analysis of polymers
Sulfur analysis
Fluorine analysis by EI
FAB gun questions
Low Energy CID of M+H vs. M+Na
Collision gas for CID experiments
MS-MS fragment interpretation
In source fragmentation vs. MS/MS spectra
WWW page for isotope ratio monitoring -GCMS
Concentration dependency of stable isotope tracers in leucine
M+ Peak intensification in E.I. mode
Continuous flow isotope ratio MS troubleshooting
CE-MS peak broadening
Theoretical peak shapes
Isotope pattern software
Program to match isotopic ratios to molecular formula
Isotope Calculator software
Public Mass spectral databases
Isotopomer definition
Missing posts from the newsgroup
Sample-reference match criteria
Presentation of spectra in time series(3-D plots)
Multi-charge ions?
Mass-to-charge ratio units
MacSimion status?

SIMION 3D version 6.0
SIMION Time of Flight Modeling
SIMION6 with Windows 4.0 problem
Thermal Analysis-MS
Residual Gas Analyzers
Portable mass spectrometer
Portable GC-MS
Effect of NMR field on nearby Mass Spectrometer
Online NIST spectral database
Recent good books for GC-MS, LC-MS/MS
Recommended MS books
Mass Spec Survival Guide information
Basic information on getting started in MS
Selection criteria for purchasing a MS
Advice on good walkup MS system for synthetic chemists
Academic MS Service lab charge structure link
Mass spectral learning exercises
Interactive Mass spec learning web sites

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MS Parts/Supplies

Automated sample preparation station recommendations
Graphite vs. Vespel Ferrules for GC-MS
Large volume injectors
Cleaning an Ion Source
MS source correct cleaning procedure
How to clean an electron multiplier (channeltron)
Where to find rhenium wires for filaments
Tungsten spot weld on filament posts
Mesh or Grid sources
Metal tubing < 50 micron
Diffusion Pumps vs. Turbo Pumps: Vacuum Pump Discussion
Edwards Foreline Pump Troubleshooting
Explanation of Pumping Speed and Pumping Capacity
Roughing Pump maintenance with APCI
Mass Spectrometer manufacturers'web pages listing
Jet separator tips
Nitrogen gas generators
Membrane Nitrogen gas generators
In-house nitrogen purification for LC/MS
Nitrogen gas consumption and nitrogen generators
N2 generators for lc/ms

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Quadrupole Topics

Help!Inexplicable background problem
Field portable GC-MS
Finnegan GCQ with a different GC problem
Increased Sensitivity of the HP MSD
Quadrupole Analyser Geometry
Operating principle of quadrupoles
RF tubes for old quad?
Ion Traps vs. Quadrupoles : Recommendations
Triple Quads vs. Ion Traps
Triple Quad vs. Ion Trap vs. QTOF
Table of sensibility factors

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