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 revea

SUBMITTER: Keich U 

PROVIDER: S-EPMC4533616 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature