title: Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.
abstract: Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics experiment requires a valid and accurate procedure for assigning statistical confidence estimates to identified tandem mass spectra. Despite the crucial role such procedures play in most high-throughput proteomics experiments, the scientific literature has not reached a consensus about the best confidence estimation methodology. In this work, we evaluate, using theoretical and empirical analysis, four previously proposed protocols for estimating the false discovery rate (FDR) associated with a set of identified tandem mass spectra: two variants of the target-decoy competition protocol (TDC) of Elias and Gygi and two variants of the separate target-decoy search protocol of Käll et al. Our analysis reveals significant biases in the two separate target-decoy search protocols. Moreover, the one TDC protocol that provides an unbiased FDR estimate among the target PSMs does so at the cost of forfeiting a random subset of high-scoring spectrum identifications. We therefore propose the mix-max procedure to provide unbiased, accurate FDR estimates in the presence of well-calibrated scores. The method avoids biases associated with the two separate target-decoy search protocols and also avoids the propensity for target-decoy competition to discard a random subset of high-scoring target identifications.
authors.affiliation: †School of Mathematics and Statistics F07, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Uri
authors.initials: U
authors.lastname: Keich
authors.affiliation: ‡Department of Genome Sciences, University of Washington, Foege Building S220B, 3720 15th Avenue North East, Seattle, Washington 98195-5065, United States.
authors.forename: Attila
authors.initials: A
authors.lastname: Kertesz-Farkas
authors.affiliation: ‡Department of Genome Sciences, University of Washington, Foege Building S220B, 3720 15th Avenue North East, Seattle, Washington 98195-5065, United States.|§Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195-5065, United States.
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D005189:False Positive Reactions; D010455:Peptides / Q000378:metabolism*; D010963:Plasmodium falciparum / Q000378:metabolism; D040901:Proteomics / Q000379:methods* / Q000592:standards; D015800:Protozoan Proteins / Q000378:metabolism; D015203:Reproducibility of Results; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D053719:Tandem Mass Spectrometry / Q000379:methods* / Q000592:standards
chemical_list: D029742:Caenorhabditis elegans Proteins; D010455:Peptides; D015800:Protozoan Proteins; D029701:Saccharomyces cerevisiae Proteins
keywords: false discovery rate; mass spectrometry; spectrum identification