Journal Article

DKFZ-2025-01945

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png MHCquant2 refines immunopeptidomics tumor antigen discovery.

Scheid, J. ; Lemke, S. ; Hoenisch-Gravel, N. ; Dengler, A. ; Sachsenberg, T. ; Declerq, A. ; Gabriels, R. ; Bauer, J.DKFZ* ; Wacker, M. ; Bichmann, L. ; Martens, L. ; Dubbelaar, M. L. ; Nahnsen, S. ; Walz, J.DKFZ*

2025
BioMed Central London

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Please use a persistent id in citations: doi:10.1186/s13059-025-03763-8

Abstract: Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable, and standardized workflow for immunopeptidomics. This integration allows a community-driven, robust solution for high-throughput analyses across operating systems and cloud infrastructures. MHCquant2 integrates open-source tools including OpenMS, DeepLC, and MS2PIP, improving peptide identifications by up to 27% across diverse MS platforms, particularly enriching low-abundant peptides. MHCquant2 demonstrates state-of-the-art performance on our novel benignMHCquant2 dataset (n = 92) and expands the benign human immunopeptidome by over 160,000 unique naturally presented HLA peptides.

Keyword(s): Humans (MeSH) ; Antigens, Neoplasm: immunology (MeSH) ; Peptides: immunology (MeSH) ; HLA Antigens: immunology (MeSH) ; Software (MeSH) ; Neoplasms: immunology (MeSH) ; Proteomics: methods (MeSH) ; HLA ; Immunopeptidomics ; Immunotherapy ; Mass spectrometry ; Nextflow ; Nf-core ; Open-source ; Pipeline ; Antigens, Neoplasm ; Peptides ; HLA Antigens

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Contributing Institute(s):

1. DKTK Koordinierungsstelle Tübingen (TU01)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Appears in the scientific report 2025

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