PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR.

ABSTRACT: Background: Currently, post-translational modification (PTM) search in MS/MS data is performed using either open modification search (OMS) or closed search (CS) algorithms. The OMS method allows for the determination of many PTMs and unknown mass-shifts in one run. In contrast, closed search algorithms are more sensitive but limited in the number of PTMs that can be specified in one search. Methods: In this manuscript, we propose an optimized Python algorithm based on the IdentiPy search engine that performs an automated sequential search for each PTM based on previous annotations from public databases and customized protein lists. We also determined the sufficient size of the search space to increase the significance of false discovery rate (FDR) estimation. We modified the

SUBMITTER: Strogov YY 

PROVIDER: S-EPMC12921745 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature