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Related Experiment Video

Updated: Jan 17, 2026

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
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MHCquant2 refines immunopeptidomics tumor antigen discovery.

Jonas Scheid1,2,3,4,5, Steffen Lemke1,2,3,4,5, Naomi Hoenisch-Gravel1,2

  • 1Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.

Genome Biology
|September 22, 2025
PubMed
Summary

MHCquant2 is a new Nextflow pipeline for immunopeptidomics that improves the identification of human leukocyte antigen (HLA)-presented peptides. This robust workflow enhances cancer immunotherapy research by identifying over 160,000 unique HLA peptides.

Keywords:
HLAImmunopeptidomicsImmunotherapyMass spectrometryNextflowNf-coreOpen-sourcePipeline

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Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate identification of human leukocyte antigen (HLA)-presented peptides is essential for developing effective cancer immunotherapies.
  • Current immunopeptidomics workflows can be limited in scalability, reproducibility, and portability.

Purpose of the Study:

  • To develop and present MHCquant2, a scalable, modular, and standardized Nextflow pipeline for immunopeptidomics.
  • To improve the identification of HLA-presented peptides for advancing cancer immunotherapy research.

Main Methods:

  • Integration of MHCquant2 into the nf-core community framework for enhanced reproducibility and portability.
  • Utilized open-source tools including OpenMS, DeepLC, and MS 2PIP within the pipeline.
  • Validated performance on a novel benign dataset (n=92) and compared across diverse mass spectrometry (MS) platforms.

Main Results:

  • MHCquant2 demonstrated improved peptide identifications by up to 27% across various MS platforms.
  • The pipeline effectively enriched low-abundant peptides.
  • Expanded the benign human immunopeptidome by identifying over 160,000 unique naturally presented HLA peptides.

Conclusions:

  • MHCquant2 provides a robust, community-driven solution for high-throughput immunopeptidomics analyses.
  • The pipeline offers state-of-the-art performance and enhances the discovery of naturally presented HLA peptides.
  • Facilitates advancements in cancer immunotherapy by providing a standardized and scalable analysis workflow.