Matrix Science (Mascot) – web site for Mascot database searches. Useful information about how the databases searches are done and help with interpretation and understanding database search results.

Expasy – a web site with many useful protein tools and links

Protein Prospector – a web site from UCSF with useful protein search tools and links

ABRF – a web site for shared proteomics information

Delta Mass (ABRF) – a useful web site for identification of protein and peptide modifications based on net mass change observed in mass spectra.

ISB (Institute for Systems Biology) Proteomics Tools

Fred Hutchinson Cancer Center
Proteome Commons