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Motivation: Target-decoy search (TDS) is currently the most popular strategyfor estimating and controlling the false discovery rate (FDR) of peptideidentifications in mass spectrometry-based shotgun proteomics. While thisstrategy is very useful in practice and has been intensively studiedempirically, its theoretical foundation has not yet been well established.Result: In this work, we systematically analyze the TDS strategy in a rigorousstatistical sense. We prove that the commonly used concatenated TDS provides aconservative estimate of the FDR for any given score threshold, but it cannotrigorously control the FDR. We prove that with a slight modification to thecommonly used formula for FDR estimation, the peptide-level FDR can berigorously controlled based on the concatenated TDS. We show that thespectrum-level FDR control is difficult. We verify the theoretical conclusionswith real mass spectrometry data.

A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics