Patent Document ID: 8712695
Application ID: 11246722
Patent Flag: 1

Claim One:
1. A system for scoring theoretical peptides used to identify peptides in a sample, comprising: a database that stores a plurality of known peptide sequences; a mass spectrometer that analyzes the sample by selecting a precursor ion, fragmenting the precursor ion and producing fragment ion data; and a processor in communication with the mass spectrometer and the database that a) receives the fragment ion data from the mass spectrometer, b) identifies a plurality of sequence tags from the fragment ion data, c) compares the plurality of sequence tags to one or more sequence segments of each peptide sequence of the plurality of known peptide sequences in the database, and scores each segment of the one or more sequence segments based on tag scores of sequence tags from the plurality of sequence tags included by each segment producing a plurality of scored segments, d) generates a plurality of peptide features that affect theoretical peptide generation and associates a probability with each feature that indicates a sample implied frequency of each peptide feature, wherein the plurality of peptide features include one or more of modifications, digestions, species of origin, or mutations, e) generates, for each scored segment of the plurality of scored segments, one or more theoretical peptides by, (i) calculating a feature probability threshold based on the score of the segment so that the higher the score of segment the lower the feature probability threshold, (ii) generating one or more theoretical peptides for the segment by applying each peptide feature of the plurality of peptide features that has a probability above the feature probability threshold to the segment, and (iii) selecting each theoretical peptide of the one or more generated theoretical peptides that has a mass within a mass tolerance of the mass of the precursor ion, and f) scores the one or more theoretical peptides for each scored segment by performing a comparison of each theoretical peptide with the fragment ion data.