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. Author manuscript; available in PMC: 2010 Jul 8.
Published in final edited form as: Proteomics. 2009 Mar;9(5):1220–1229. doi: 10.1002/pmic.200800473
False positives (FP) = 2 * decoy hits
True positives (TP) = All targets above threshold - FP
False discovery rate (FDR) = FP / FP + TP

Example for 1000 identifications, 20 decoy identifications.

FDR = 40 / 1000 = 4%