Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.

TitleSpectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.
Publication TypeJournal Article
Year of Publication2008
AuthorsKim S, Gupta N, Pevzner PA
JournalJ Proteome Res
Volume7
Issue8
Pagination3354-63
Date Published2008 Aug
ISSN1535-3893
KeywordsBacterial Proteins, Data Interpretation, Statistical, Databases, Factual, Peptides, Probability, Proteomics, Shewanella, Tandem Mass Spectrometry
Abstract

A key problem in computational proteomics is distinguishing between correct and false peptide identifications. We argue that evaluating the error rates of peptide identifications is not unlike computing generating functions in combinatorics. We show that the generating functions and their derivatives ( spectral energy and spectral probability) represent new features of tandem mass spectra that, similarly to Delta-scores, significantly improve peptide identifications. Furthermore, the spectral probability provides a rigorous solution to the problem of computing statistical significance of spectral identifications. The spectral energy/probability approach improves the sensitivity-specificity tradeoff of existing MS/MS search tools, addresses the notoriously difficult problem of "one-hit-wonders" in mass spectrometry, and often eliminates the need for decoy database searches. We therefore argue that the generating function approach has the potential to increase the number of peptide identifications in MS/MS searches.

DOI10.1021/pr8001244
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18597511?dopt=Abstract
PMCPMC2689316
Alternate JournalJ. Proteome Res.
PubMed ID18597511