  Large numbers of MS/MS peptide spectra generated in proteomics experiments
require efficient, sensitive and specific algorithms for peptide
identification. In the Open Mass Spectrometry Search Algorithm [OMSSA],
specificity is calculated by a classic probability score using an explicit
model for matching experimental spectra to sequences. At default thresholds,
OMSSA matches more spectra from a standard protein cocktail than a comparable
algorithm. OMSSA is designed to be faster than published algorithms in
searching large MS/MS datasets.
