MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search.

ABSTRACT: Liquid chromatography-mass spectrometry (LC-MS) 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 (DDA) mass spectrometry data is database search. Traditional tools typically focus on identifying a single peptide per tandem mass spectrum (MS2), often neglecting the frequent occurrence of peptide co-fragmentations leading to chimeric spectra. Here, we introduce MSFragger-DDA+, a novel 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 searc

SUBMITTER: Yu F 

PROVIDER: S-EPMC11507693 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature