title: Comment on "Unbiased statistical analysis for multi-stage proteomic search strategies".
abstract: Everett et al. recently reported on a statistical bias that arises in the target-decoy approach to false discovery rate estimation in two-pass proteomics 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.
authors.affiliation: Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304, USA. bern@parc.com
authors.forename: Marshall
authors.initials: M
authors.lastname: Bern
authors.forename: Yong J
authors.initials: YJ
authors.lastname: Kil
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data*; D057386:Search Engine; D012984:Software / Q000706:statistics & numerical data*; D053719:Tandem Mass Spectrometry
chemical_list: D011506:Proteins