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Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
(Department of Genome Sciences, University of Washington, Seattle)ORCID iD: 0000-0001-5689-9797
2008 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 7, no 1, 29-34 p.Article in journal (Refereed) Published
Abstract [en]

Automated methods for assigning peptides to observed tandem mass spectra typically return a list of peptide-spectrum matches, ranked according to an arbitrary score. In this article, we describe methods for converting these arbitrary scores into more useful statistical significance measures. These methods employ a decoy sequence database as a model of the null hypothesis, and use false discovery rate (FDR) analysis to correct for multiple testing. We first describe a simple FDR inference method and then describe how estimating and taking into account the percentage of incorrectly identified spectra in the entire data set can lead to increased statistical power.

Place, publisher, year, edition, pages
2008. Vol. 7, no 1, 29-34 p.
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-48854DOI: 10.1021/pr700600nISI: 000252154200002PubMedID: 18067246OAI: diva2:458746
QC 20111124Available from: 2011-11-23 Created: 2011-11-23 Last updated: 2011-11-24Bibliographically approved

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Käll, Lukas
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