Identification of 113 new histone marks by CHiMA, a tailored database search strategy.

ABSTRACT: Shotgun proteomics has been widely used to identify histone marks. Conventional database search methods rely on the "target-decoy" strategy to calculate the false discovery rate (FDR) and distinguish true peptide-spectrum matches (PSMs) from false ones. This strategy has a caveat of inaccurate FDR caused by the small data size of histone marks. To address this challenge, we developed a tailored database search strategy, named "Comprehensive Histone Mark Analysis (CHiMA)." Instead of target-decoy-based FDR, this method uses "50% matched fragment ions" as the key criterion to identify high-confidence PSMs. CHiMA identified twice as many histone modification sites as the conventional method in benchmark datasets. Reanalysis of our previous proteomics data using CHiMA led to the identification

SUBMITTER: Gao J 

PROVIDER: S-EPMC10075957 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature