Conditional Fragment Ion Probabilities Improve Database Searching for Nonmonoisotopic Precursors.

ABSTRACT: Stochastic, intensity-based precursor isolation can result in isotopically enriched fragment ions. This problem is exacerbated for large peptides and stable isotope labeling experiments using deuterium or ¹⁵N. For stable isotope labeling experiments, incomplete and ubiquitous labeling strategies result in the isolation of peptide ions composed of many distinct structural isomers. Unfortunately, existing proteomics search algorithms do not account for this variability in isotopic incorporation, and thus often yield poor peptide and protein identification rates. We sought to resolve this shortcoming by deriving the expected isotopic distributions of each fragment ion and incorporating them into the theoretical mass spectra used for peptide-spectrum-matching. We adapted the Comet s

SUBMITTER: O'Brien JJ 

PROVIDER: S-EPMC9903324 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature