Bias in False Discovery Rate Estimation in Mass-Spectrometry-Based Peptide Identification

Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an important but often neglected assumption that incorrect spectrum annotations are equally likely to receive either target or decoy peptides. Here we argue that this assumption is often violated in practice, even by popular methods. Preference can be given to target peptides by biased scoring functions, which result in liberal FDR estimations, or to decoy peptides by correlated spectra, which result in conservative estimations.