A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.

ABSTRACT: Conventional database search methods for proteomics struggle when tasked to identify dozens or hundreds of modifications simultaneously. Open or error-tolerant searches can address this limitation, but at the cost of increased difficulty in downstream interpretation of the results and quantification. We and others have previously described "mass offset" or multi-notch searches that sit in between closed and open searches, allowing simultaneous search for hundreds of modifications with more straightforward downstream interpretation than open search. The original mass offset searches were closer to open search, lacking the ability to restrict modifications to specific amino acids. Here, we describe a new "detailed" mass offset (DMO) search implemented in the MSFragger search engine, which al

SUBMITTER: Ramirez CR 

PROVIDER: S-EPMC12324293 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature