Query Mix-Max Method for FDR Estimation Supported by Entrapment Queries.

ABSTRACT: Estimating the false discovery rate (FDR) is one of the key steps in ensuring appropriate error control in the analysis of shotgun proteomics data. Traditional estimation methods typically rely on decoy sequence databases or spectral libraries, which may not always provide satisfactory results due to limitations of decoy construction methods. This study introduces the query mix-max (QMM) method, a decoy-free alternative for FDR estimation in proteomics. The QMM framework builds upon the existing mix-max procedure but replaces decoy matches with entrapment queries to estimate the number of false positive discoveries. Through simulations and real data set analyses, the QMM method was demonstrated to provide reasonably accurate FDR estimation across various scenarios, particularly when smalle

SUBMITTER: Madej D 

PROVIDER: S-EPMC11894652 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature