MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.

ABSTRACT: Liquid chromatography-mass spectrometry based proteomics, particularly in the bottom-up approach, relies on the digestion of proteins into peptides for subsequent separation and analysis. The most prevalent method for identifying peptides from data-dependent acquisition mass spectrometry data is database search. Traditional tools typically focus on identifying a single peptide per tandem mass spectrum, often neglecting the frequent occurrence of peptide co-fragmentations leading to chimeric spectra. Here, we introduce MSFragger-DDA+, a database search algorithm that enhances peptide identification by detecting co-fragmented peptides with high sensitivity and speed. Utilizing MSFragger's fragment ion indexing algorithm, MSFragger-DDA+ performs a comprehensive search within the full isolatio

SUBMITTER: Yu F 

PROVIDER: S-EPMC11978857 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature