The Open Mass Spectrometry Search Algorithm (OMSSA) (55) analyzes MS/MS peptide spectra by searching libraries of known protein sequences, assigning significant hits an E-value computed in the same way as the E-value of BLAST. The web interface to OMSSA allows up to 2000 spectra to be analyzed in a single session using either BLAST nr, RefSeq or Swiss-Prot sequence libraries for comparison. Standalone versions of OMSSA that accept larger batches of spectra and allow searches of custom sequence libraries can be downloaded at pubchem.ncbi.nlm.nih.gov/omssa/download.htm.
