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.