The American Society for Mass Spectrometry (

General use/info



Web tools

Data analysis and useful databases

There are several sites on the Internet to get useful programs and information for those doing protein mass spectrometry.

  • Protein identification from tryptic peptide fingerprint data from a MALDI-TOF analysis, or peptide mass and fragmentation data from a triple quadrupole instrument, a Q-tof or an Orbitrap, the best sites are: (the MASCOT program) (ProteinProspector)
  • A procedure for the in-gel digestion of proteins separated by 1D SDS-PAGE analysis or 2D-IEF/SDS-PAGE is well described at
  • For those who use this procedure or have carried out digestion with proteolytic enzymes in solution, the resulting peptides can be identified using UCSF MS Fit
  • Once a potential match has been made, MS Digest can be used to predict all potential peptides including user-specified posttranslational modifications. UCSF MS Digest
  • 2D-proteomics databases are available for many cell types and organs/tissues from several species as well as subcellular fractions. These are frequently annotated with regard to spot identification. The EXPASY site contains links to these databases as well as other useful programs and software for mass spectrometry


Other useful sites