Assigning significance to peptides identified by tandem mass spectrometry using decoy databases - PubMed (original) (raw)
Review
doi: 10.1021/pr700600n. Epub 2007 Dec 8.
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- PMID: 18067246
- DOI: 10.1021/pr700600n
Review
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
Lukas Käll et al. J Proteome Res. 2008 Jan.
Abstract
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.
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