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Elife. 2015 Jul 8;4. doi: 10.7554/eLife.07661.

An open-source computational and data resource to analyze digital maps of immunopeptidomes.

Author information

  • 1Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
  • 2Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
  • 3Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom.
  • 4Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain.
  • 5Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
  • 6La Jolla Institute for Allergy and Immunology, La Jolla, United States.
  • 7Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
  • 8Pacific Northwest National Laboratory, Richland, United States.
  • 9Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China.
  • 10Institute for Systems Biology, Seattle, United States.


We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.


DIA; SWATH-MS; computational biology; human; human leukocytes antigen; immunology; immunopeptidome; systems biology; targeted mass spectrometry

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