ProFound
ProFound is a tool for searching a protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map.

ProteinInfo
ProteinInfo is a collection of tools for retrieval and analysis of protein sequences. The capabilities of the analysis tools include peptide mapping, mass spectrometric fragmentation analysis, disulfide mapping, etc.

PeptideMap
PeptideMap is a tool for finding modifications on polypeptide sequences. The modifications can be affecting single amino acids (e.g. phoshorylation or oxidation) or cross-linking two amino acids (e.g. disulfide bonds or chemical cross-linking reagents).

PepFrag
PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.

X! Tandem
X! Tandem is a tool for identifying proteins from a collection of peptide sequences that matches tandem mass spectra.

GPMDB
GPMDB is a database of tandem mass spectra and their assigned peptide sequences. It is designed to aid in the difficult process of validating peptide MS/MS spectra.