Comment on Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies

Everett et al. recently reported on a statistical bias that arises in the target-decoy approach to false discovery rate estimation in two-pass protcomics search strategies as exemplified by X!Tandem. This bias can cause serious underestimation of the false discovery rate. We argue here that the unbiased solution proposed by Everett et al., however, is also biased and under certain circumstances can also result in a serious underestimate of the FDR, especially at the protein level.