Journal
JOURNAL OF PROTEOME RESEARCH
Volume 7, Issue 9, Pages 3661-3667Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr070492f
Keywords
decoy database; false discovery rate; instantaneous error rate; nonlinear fitting; local false discovery rate
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False discovery rate (FDR) analyses of protein and peptide identification results using decoy database searching conventionally report aggregate or global FDRS for a whole set of identifications, which are often not very informative about the error rates of individual members in the set. We describe a nonlinear curve fitting method for calculating the local FDR, which estimates the chance that an individual protein (or peptide) is incorrect, and present a simple tool that implements this analysis. The goal of this method is to offer a simple extension to the now commonplace decoy database searching, providing additional valuable information.
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