PepQueryMHC: rapid and comprehensive tumor antigen prioritization from immunopeptidomics data.

ABSTRACT: Determining tumor-specificity of MHC-bound peptides is crucial for cancer immunotherapy development, yet current methods struggle with class II peptides and non-reference sequences. We introduce PepQueryMHC, an ultra-fast tool that integrates MHC-bound peptide sequences with translated RNA-seq reads for efficient tumor antigen prioritization. We demonstrate its versatility in prioritizing class I and II tumor antigens, mapping the cellular origins of presented peptides, and resolving uncertainties surrounding the prevalence of proteasome-spliced peptides.

SUBMITTER: Choi S 

PROVIDER: S-EPMC12723928 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature