Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics

Target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control in bottom-up discovery proteomics. Despite unquestionable statistical foundations, we unveil a so far unknown weakness of TDC: its intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinterpreted. This work pinpoints evidence that TDC will become less reliable along with improved accuracies of modern mass spectrometers. We therefore propose to replace TDC by a totally different method to control the FDR at spectrum, peptide and protein levels, while benefiting from the theoretical guarantees of Benjamini-Hochberg framework. This method being simpler to use, faster to compute and more stable than TDC, we argue that it is more adapted to the standardization and throughput constraints of nowadays proteomic platforms.