Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups.

ABSTRACT: Estimating false discovery rates (FDRs) of protein identification continues to be an important topic in mass spectrometry-based proteomics, particularly when analyzing very large datasets. One performant method for this purpose is the Picked Protein FDR approach which is based on a target-decoy competition strategy on the protein level that ensures that FDRs scale to large datasets. Here, we present an extension to this method that can also deal with protein groups, that is, proteins that share common peptides such as protein isoforms of the same gene. To obtain well-calibrated FDR estimates that preserve protein identification sensitivity, we introduce two novel ideas. First, the picked group target-decoy and second, the rescued subset grouping strategies. Using entrapment searches and si

SUBMITTER: The M 

PROVIDER: S-EPMC9718969 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature