TY  - JOUR
AU  - Scheid, Jonas
AU  - Lemke, Steffen
AU  - Hoenisch-Gravel, Naomi
AU  - Dengler, Anna
AU  - Sachsenberg, Timo
AU  - Declerq, Arthur
AU  - Gabriels, Ralf
AU  - Bauer, Jens
AU  - Wacker, Marcel
AU  - Bichmann, Leon
AU  - Martens, Lennart
AU  - Dubbelaar, Marissa L
AU  - Nahnsen, Sven
AU  - Walz, Juliane
TI  - MHCquant2 refines immunopeptidomics tumor antigen discovery.
JO  - Genome biology
VL  - 26
IS  - 1
SN  - 1465-6906
CY  - London
PB  - BioMed Central
M1  - DKFZ-2025-01945
SP  - 290
PY  - 2025
AB  - 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
KW  - Humans
KW  - Antigens, Neoplasm: immunology
KW  - Peptides: immunology
KW  - HLA Antigens: immunology
KW  - Software
KW  - Neoplasms: immunology
KW  - Proteomics: methods
KW  - HLA (Other)
KW  - Immunopeptidomics (Other)
KW  - Immunotherapy (Other)
KW  - Mass spectrometry (Other)
KW  - Nextflow (Other)
KW  - Nf-core (Other)
KW  - Open-source (Other)
KW  - Pipeline (Other)
KW  - Antigens, Neoplasm (NLM Chemicals)
KW  - Peptides (NLM Chemicals)
KW  - HLA Antigens (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:40983925
C2  - pmc:PMC12455830
DO  - DOI:10.1186/s13059-025-03763-8
UR  - https://inrepo02.dkfz.de/record/304839
ER  -