Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.

ABSTRACT: Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the main method for high-throughput identification and quantification of peptides and inferred proteins. Within this field, data-independent acquisition (DIA) combined with peptide-centric scoring, as exemplified by the technique SWATH-MS, has emerged as a scalable method to achieve deep and consistent proteome coverage across large-scale data sets. We demonstrate that statistical concepts developed for discovery proteomics based on spectrum-centric scoring can be adapted to large-scale DIA experiments that have been analyzed with peptide-centric scoring strategies, and we provide guidance on their application. We show that optimal tradeoffs between sensitivity and specificity require careful considerations of the rela

SUBMITTER: Rosenberger G 

PROVIDER: S-EPMC5581544 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature