MS/MS and database searching has emerged as a valuable technology for rapidly
analyzing protein expression, localization, and post-translational modifications. The
probability-based search engine Mascot has found widespread use as a tool to correlate
tandem mass spectra with peptides in a sequence database. Although the Mascot scoring
algorithm provides a probability-based model for peptide identification, the independent
peptide scores do not correlate with the significance of the proteins to which they match …