%0 Journal Article
%A Scheid, Jonas
%A Lemke, Steffen
%A Hoenisch-Gravel, Naomi
%A Dengler, Anna
%A Sachsenberg, Timo
%A Declerq, Arthur
%A Gabriels, Ralf
%A Bauer, Jens
%A Wacker, Marcel
%A Bichmann, Leon
%A Martens, Lennart
%A Dubbelaar, Marissa L
%A Nahnsen, Sven
%A Walz, Juliane
%T MHCquant2 refines immunopeptidomics tumor antigen discovery.
%J Genome biology
%V 26
%N 1
%@ 1465-6906
%C London
%I BioMed Central
%M DKFZ-2025-01945
%P 290
%D 2025
%X 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
%K Humans
%K Antigens, Neoplasm: immunology
%K Peptides: immunology
%K HLA Antigens: immunology
%K Software
%K Neoplasms: immunology
%K Proteomics: methods
%K HLA (Other)
%K Immunopeptidomics (Other)
%K Immunotherapy (Other)
%K Mass spectrometry (Other)
%K Nextflow (Other)
%K Nf-core (Other)
%K Open-source (Other)
%K Pipeline (Other)
%K Antigens, Neoplasm (NLM Chemicals)
%K Peptides (NLM Chemicals)
%K HLA Antigens (NLM Chemicals)
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:40983925
%2 pmc:PMC12455830
%R 10.1186/s13059-025-03763-8
%U https://inrepo02.dkfz.de/record/304839