Mass Spectrometry Quick Links

Caveat: The following list is illustrative, not inclusive. Please do not take offense if we have left out a site. If you feel a site should be added, a link has changed or is in error, please let us know. This work is always in progress.

General Mass Spectrometry Links:

The American Society for Mass Spectrometry (ASMS)
SpectroscopyNOW - Gateway to John Wiley's "BasePeak" listing of mass spectrometry sites, resources, etc.
ISOGEOCHEM the stable isotope geochemistry web page

NIST Chemistry WebBook
Integrated Spectral Data Base System for Organic Compounds (SDBS) for mass spec and NMR data of organic compounds from the Natl Inst of Advanced Industrial Science and Technology in Japan
Mass Spec Tools - SIS: Scientific Instrument Services
Mass Spec Tips - SIS
Chemputer including an isotopic abundance calculator from the Dept. of Chemistry, University of Sheffield, UK
Quick reference guide - IonSource.Com
Introductory tutorial of EI mass spectra and compound identification from the Univ. of Arizona

Proteomics Links:

ExPASy Molecular Biology Server - software for proteomics from the Swiss Institute of Bioinformatics (SIB) and see also Genebio (creators of Phenyx)
- including ExPASy proteomics tool sets
- and UniProt protein databases
Protein Prospector - UCSF Mass Spectrometry Facility
Skyline from the MaCoss laboratory
PNNL Proteomics Research Center for Integrative Biology software suite downloads
Proteome Central a repository of proteomics data, part of the ProteomeXchange Consortium
ProteomicsDB
Human protein reference database from the Pandey Lab and the Institute of Bioinformatics

Mascot - mass spectral identification software for protein sequencing from Matrix Science
ProteinProphet^TM - open access software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST and Xpress that calculates the relative abundance of proteins from LCMS/MS data obtained from ICAT and other labeled reagent experiments - both from the Institute for Systems Biology
PROWL - protein software from Rockefeller University

Metabolomics Links:

Human Metabolome Database (HMDB)
PubChem from the NCBI
ChemSpider a free chemical structure database from the Royal Society of Chemistry
MassBank a public repository of mass spectral data from Japan
MetaboLights - a database for metabolomics experiments and derived information from EMBL-EBI
KEGG - the Kyoto Encyclopedia of Genes and Genomes
Virtual Metabolic Human (VMH) with the human metabolic reconstruction (RECON2) database and the gut microbiome
Scripps Center for Metabolomics from the Siuzdak lab with links to metabolite databases, analysis tools, and more
MAVEN - Downloadable open-source software metabolomics data analyser. The software provides an intitute interface for exploring and validating metabolomics data. The program features multi-file chromatographic aligner, peak-feature detector, isotope and adduct calculator, formula predictor, pathway visualizer, and isotopic flux animator.
MetaboAnalyst for processing and statistical analysis of metabolomics data and functional analyses such as metabolite set enrichment analysis (MSEA) and metabolic pathway analysis. From the Xia Lab at McGill.
MZmine2 - Downloadable open-source software for LCMS data processing, based on the original MZmine toolbox, but completely redesigned.
The metaP server from the Helmholtz Zentrum München

Journals, etc.:

Suppliers of Stable Isotopically Labeled Compounds:

Cambridge Isotope Laboratories (CIL) (Andover, MA)
Sigma Aldrich (formerly Isotec)
C/D/N Isotopes (Pointe-Claire, Quebec, Canada)
Martek (Olney, MD)
Medical Isotopes (Pelham, NH)

Useful Mass Spectrometry Tools:

Tables in PDF format listing amino acids, their chemical composition, their major fragments and their exact weights for common ions measured by GCMS. The amino acid derivatives and ionization modes presented are:
- t-butyldimethylsilyl (TBDMS) by electron impact ionization (EI)
- N-heptafluorobutyryl n-propyl (HFBP) by EI
- HFBP by negative chemical ionization (NCI)
- N-acetyl n-propyl (NAP) by EI
Tables in PDF format listing the theoretical abundances of the [M+1], [M+2], [M+3], ... ions relative to the M ion for common amino acid derivatives and GCMS ionization modes shown above.

Site updated by DE Matthews

from Dwight E. Matthews' Group:

Useful Sites for Mass Spectrometry & Stable Isotopes