MS²Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates.

ABSTRACT: Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented peptides on almost all cells that can be used in anti-cancer vaccine development. However, existing immunopeptidomics data analysis pipelines suffer from the nontryptic nature of immunopeptides, complicating their identification. Previously, peak intensity predictions by MS²PIP and retention time predictions by DeepLC have been shown to improve tryptic peptide identifications when rescoring peptide-spectrum matches with Percolator. However, as MS²PIP was tailored toward tryptic peptides, we have here retrained MS²PIP to include nontryptic peptides. Interestingly, the new models not only greatly improve predictions for immunopeptides but also yield further improvements for tr

SUBMITTER: Declercq A 

PROVIDER: S-EPMC9411678 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature