Spectral Probabilities and Generating Functions of Tandem Mass Spectra: a Strike Against Decoy Databases

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2008 Jul 4

PMID 18597511

Citations 240

Authors

Sangtae Kim

Nitin Gupta

Pavel A Pevzner

Affiliations

Soon will be listed here.

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.

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