A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities

Le résumé fourni par la source

Peppy, the proteogenomic/proteomic search software, employs a novel method for assessing the match quality between an MS/MS spectrum and a theorized peptide sequence. The scoring system uses three score factors calculated with binomial probabilities: the probability that a fragment ion will randomly align with a peptide ion; the probability that the aligning ions will be selected from the set of most intense peaks; and the probability that the intensities of fragment ions identified as y-ions are greater than those of their counterpart b-ions. The scores produced by the method act as global confidence scores, which facilitate the accurate comparison of results and the estimation of false discovery rates. Peppy has been integrated into the meta-search engine PepArML to produce meaningful comparisons with Mascot, MSGF+, OMSSA, X!Tandem, k-Score and s-Score. For two of the three the data sets examined with the PepArML analysis, Peppy exceeded the accuracy performance of the other scoring systems; for the third set Peppy was outperformed only by MSGF+.

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