title: Computing exact p-values for a cross-correlation shotgun proteomics score function.
abstract: The core of every protein mass spectrometry analysis pipeline is a function that assesses the quality of a match between an observed spectrum and a candidate peptide. We describe a procedure for computing exact p-values for the oldest and still widely used score function, SEQUEST XCorr. The procedure uses dynamic programming to enumerate efficiently the full distribution of scores for all possible peptides whose masses are close to that of the spectrum precursor mass. Ranking identified spectra by p-value rather than XCorr significantly reduces variance because of spectrum-specific effects on the score. In combination with the Percolator postprocessor, the XCorr p-value yields more spectrum and peptide identifications at a fixed false discovery rate than Mascot, X!Tandem, Comet, and MS-GF+ across a variety of data sets.
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington;
authors.forename: J Jeffry
authors.initials: JJ
authors.lastname: Howbert
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington; §Department of Computer Science and Engineering, University of Washington, Seattle, Washington william-noble@uw.edu.
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000465:Algorithms; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D030562:Databases, Protein; D006801:Humans; D009206:Myocardium / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000706:statistics & numerical data*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D029742:Caenorhabditis elegans Proteins; D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins