MHCquant2 refines immunopeptidomics tumor antigen discovery

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 integr...

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Podrobná bibliografie
Vydáno v:	Genome Biology Ročník 26; číslo 1; s. 290 - 17
Hlavní autoři:	Scheid, Jonas, Lemke, Steffen, Hoenisch-Gravel, Naomi, Dengler, Anna, Sachsenberg, Timo, Declerq, Arthur, Gabriels, Ralf, Bauer, Jens, Wacker, Marcel, Bichmann, Leon, Martens, Lennart, Dubbelaar, Marissa L., Nahnsen, Sven, Walz, Juliane S.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London BioMed Central 22.09.2025 Springer Nature B.V BMC
Témata:	Animal Genetics and Genomics Antigens Antigens, Neoplasm - immunology Bioinformatics Biomedical and Life Sciences Cancer Cancer immunotherapy Data processing Datasets Evolutionary Biology High performance computing Histocompatibility antigen HLA HLA HLA Antigens - immunology Human Genetics Humans Identification Immunopeptidomics Immunotherapy Life Sciences Mass spectrometry Microbial Genetics and Genomics Neoplasms - immunology Nextflow Nf-core Peptides Peptides - immunology Pipeline Plant Genetics and Genomics Proteomics - methods Search engines Software Open-source Immunopeptidomics Immunotherapy Nextflow Nf-core HLA Mass spectrometry Pipeline
ISSN:	1474-760X, 1474-7596, 1474-760X
On-line přístup:	Získat plný text
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Popis
Shrnutí:	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 MS 2 PIP, 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 benign MHCquant2 dataset ( n = 92) and expands the benign human immunopeptidome by over 160,000 unique naturally presented HLA peptides.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-025-03763-8