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<p>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 (<i>n</i> = 92) and expands the benign human immunopeptidome by over 160,000 unique naturally presented HLA peptides.</p>

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MHCquant2 refines immunopeptidomics tumor antigen discovery

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年9月22日

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  • Jonas Scheid,
  • Steffen Lemke,
  • Naomi Hoenisch-Gravel,
  • Anna Dengler,
  • Timo Sachsenberg,
  • Arthur Declerq,
  • Ralf Gabriels,
  • Jens Bauer,
  • Marcel Wacker,
  • Leon Bichmann,
  • Lennart Martens,
  • Marissa L. Dubbelaar,
  • Sven Nahnsen,
  • Juliane S. Walz

摘要

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% across diverse MS platforms, particularly enriching low-abundant peptides. MHCquant2 demonstrates state-of-the-art performance on our novel benignMHCquant2 dataset (n = 92) and expands the benign human immunopeptidome by over 160,000 unique naturally presented HLA peptides.