title: A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.
abstract: 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 subsets of the 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 four data sets examined with the PepArML analysis, Peppy exceeded the accuracy performance of the other scoring systems. Peppy is available for download at http://geneffects.com/peppy .
authors.affiliation: Department of Biochemistry & Biophysics, UNC School of Medicine, Chapel Hill, North Carolina 27599, United States. brian@geneffects.com
authors.forename: Brian A
authors.initials: BA
authors.lastname: Risk
authors.forename: Nathan J
authors.initials: NJ
authors.lastname: Edwards
authors.forename: Morgan C
authors.initials: MC
authors.lastname: Giddings
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001798:Blood Proteins / Q000737:chemistry; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping; D020539:Sequence Analysis, Protein; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D001798:Blood Proteins; D010446:Peptide Fragments