{
  "abstract": "The human leukocyte antigen (HLA)-presented peptide repertoire, termed immunopeptidome, plays a crucial role for T-cell mediated immune reactions. Previously, the human immunopeptidome of non-malignant tissues has been mapped in a large-scale study, the HLA Ligand Atlas, via high-resolution data-dependent acquisition (DDA) mass spectrometry. This publicly available and user-friendly web interface (https://hla-ligand-atlas.org) is frequently used as a benign tissue reference in antigen discovery, especially for immunotherapy of cancer. Here, we extend the HLA Ligand Atlas resource with paired data-independent acquisition (DIA) runs for all tissue-subject combinations. This novel dataset comprises 946 DIA HLA class I and II immunopeptidomic runs from 242 non-malignant human samples across 18 subjects and 29 distinct tissues. Together with the published DDA runs, this extends the range and depth of analyses performed on the HLA Ligand Atlas dataset. In a concise analysis, we showcase advantages of DIA over DDA concerning spectral sampling and sensitivity. These findings are attributed to the increased dynamic range in DIA, enabling the identification of peptide transitions with low signal intensities. Moreover, we demonstrate the superior sensitivity by applying an HLA-A*02:01 allotype-specific spectral library search to identify and quantify HLA-presented peptides. We encourage reanalysis of the provided DDA and DIA data in combination as a reference for future research concerning human immunology.",
  "authors": [
    {
      "affiliations": [
        "Center for Systems and Engineering Immunology, Yale University, New Haven, Connecticut, USA",
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Leon Bichmann"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany",
        "Genentech, San Francisco, California, USA"
      ],
      "name": "Ana Marcu"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Daniel Johannes Kowalewski"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Lena Katharina Freudenmann"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Linus Backert"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany",
        "Department of Peptide-based Immunotherapy, University Hospital Tübingen, Baden-Württemberg, Germany"
      ],
      "name": "Lena Mühlenbruch"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Maren Lübke"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany",
        "Obstetrics and Gynecology, University Hospital of Tübingen, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Philipp Wagner"
    },
    {
      "affiliations": [
        "Obstetrics and Gynecology, University Hospital of Tübingen, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Tobias Engler"
    },
    {
      "affiliations": [
        "Obstetrics and Gynecology, University Hospital of Tübingen, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Sabine Matovina"
    },
    {
      "affiliations": [
        "Pediatric Stem Cell Transplantation, University Children’s Hospital Zurich, University Hospital Zurich, Zurich, Switzerland"
      ],
      "name": "Mathias Hauri-Hohl"
    },
    {
      "affiliations": [
        "Neuroimmunology and MS Research, Institute of Experimental Immunology, University of Zurich, Zürich, ZH, Switzerland"
      ],
      "name": "Roland Martin"
    },
    {
      "affiliations": [
        "Pathology, University Hospital Zurich, Zurich, Switzerland"
      ],
      "name": "Holger Moch"
    },
    {
      "affiliations": [
        "Clinical Neuroscience Center and Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland",
        "Neuroscience Center Zurich (ZNZ), University of Zurich, Zürich, Switzerland"
      ],
      "name": "Luca Regli"
    },
    {
      "affiliations": [
        "Neuroscience Center Zurich (ZNZ), University of Zurich, Zürich, Switzerland",
        "Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital Zurich, Zürich, Switzerland"
      ],
      "name": "Michael Weller"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany",
        "Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany"
      ],
      "name": "Markus W Löffler"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany",
        "Department of Peptide-based Immunotherapy, University Hospital Tübingen, Baden-Württemberg, Germany"
      ],
      "name": "Juliane S Walz"
    },
    {
      "affiliations": [
        "Applied Bioinformatics, University of Tübingen, Tübingen, Germany",
        "Institute for Bioinformatics and Medical Informatics, University Hospitals Tubingen, Tübingen, Germany"
      ],
      "name": "Oliver Kohlbacher"
    },
    {
      "affiliations": [
        "Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada"
      ],
      "name": "Hannes Röst"
    },
    {
      "affiliations": [
        "Interfaculty Institute for Cell Biology and Immunology, University of Tübingen, Tübingen, Germany"
      ],
      "name": "Hans-Georg Rammensee"
    },
    {
      "affiliations": [
        "Neuroscience Center Zurich (ZNZ), University of Zurich, Zürich, Switzerland",
        "Department of Neurosurgery, Cantonal Hospital St.Gallen, HOCH Health Ostschweiz, St. Gallen, SG, Switzerland"
      ],
      "name": "Marian C Neidert"
    }
  ],
  "title": "HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry",
  "uid": "4b391d4a-c4ec-579b-a52f-62fe89e78c4f"
}