{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Scheid J"],"funding":["CHIST-ERA","Deutsche Forschungsgemeinschaft","Fonds Wetenschappelijk Onderzoek,Belgium","HORIZON EUROPE Project BAXERNA 2.0","Invest BW Innovation grant","Deutsche Krebshilfe","Else Kröner-Fresenius-Stiftung"],"pagination":["290"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12455830"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["26(1)"],"pubmed_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 MS<sup>2</sup>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<sub>MHCquant2</sub> dataset (n = 92) and expands the benign human immunopeptidome by ove"],"journal":["Genome biology"],"pubmed_title":["MHCquant2 refines immunopeptidomics tumor antigen discovery."],"pmcid":["PMC12455830"],"funding_grant_id":["2022_EKSE.79","EXC2180-390900677","BW1_4064/03/TruVac","70114948","ODEEP-EU","101080544","12B7123N, G010023N, G028821N, 1SE3724N"],"pubmed_authors":["Martens L","Lemke S","Sachsenberg T","Declerq A","Hoenisch-Gravel N","Wacker M","Gabriels R","Bichmann L","Dubbelaar ML","Bauer J","Scheid J","Dengler A","Nahnsen S","Walz JS"],"additional_accession":[]},"is_claimable":false,"name":"MHCquant2 refines immunopeptidomics tumor antigen discovery.","description":"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<sup>2</sup>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<sub>MHCquant2</sub> dataset (n = 92) and expands the benign human immunopeptidome by ove","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Sep","modification":"2026-06-03T19:40:25.585Z","creation":"2026-05-01T03:10:19.253Z"},"accession":"S-EPMC12455830","cross_references":{"pubmed":["40983925"],"doi":["10.1186/s13059-025-03763-8"]}}