Two-dimensional target decoy strategy for shotgun proteomics

Abstract

The target-decoy approach to estimating and controlling false discovery rate has become a de facto standard in shotgun proteomics. The usual implementation, however, does not consider protein identity, one of the primary clues to correctness, and previous attempts to incorporate this information have led to biased methods that underestimate the false discovery rate. Here we propose a simple variation of the standard target-decoy approach that incorporates protein identity without biasing the false discovery rate estimate.