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 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 over 160,000 unique naturally presented HLA peptides.

Authors

Institutions

Publication Details

Journal
Genome biology
Published
2025-09-22
DOI
https://doi.org/10.1186/s13059-025-03763-8
Citations
2
Primary Topic
vaccines and immunoinformatics approaches
Type
article
Field-Weighted Citation Impact
1.61

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

MHCquant2 refines immunopeptidomics tumor antigen discovery

Arthur Declercq, Sven Nahnsen, Lennart Martens, Marcel Wacker et al.
2 citations
Genome biology
vaccines and immunoinformatics approaches
1.61
article

MHCquant2 refines immunopeptidomics tumor antigen discovery

Arthur Declercq, Sven Nahnsen, Lennart Martens, Marcel Wacker, Marissa L. Dubbelaar, Ralf Gabriels, Timo T. Sachsenberg, Leon Bichmann, Steffen Lemke, Naomi Hoenisch Gravel, Jonas Scheid, Anna Dengler, Jens Bauer, Juliane S. Walz
article en
2 citations

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 over 160,000 unique naturally presented HLA peptides.

Genome biologyVol. 26(1)
Centre National de la Recherche Scientifique (FR), German Cancer Research Center (DE), Ghent University (BE), Yale University (US), University Children's Hospital Tübingen (DE), VIB-UGent Center for Medical Biotechnology (BE), Université de Strasbourg (FR), University of Tübingen (DE)
Eberhard Karls Universität Tübingen, Forschungszentrum Jülich, German Network for Bioinformatics Infrastructure
Openalex Percentile: Top 15%
vaccines and immunoinformatics approaches
1.61
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.