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

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.
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  1. Institute of Molecular Systems Biology, Zurich (Switzerland)
  2. Univ. of Tubingen, Tubingen (Germany); German Cancer Consortium, Tubingen (Germany)
  3. Univ. of Oxford, Oxford (United Kingdom)
  4. Spanish National Biotechnology Centre, Madrid (Spain)
  5. Monash Univ., Clayton (Australia)
  6. La Jolla Institute for Allergy and Immunology, La Jolla, CA (United States)
  7. Univ. Medical Center of the Johannes Gutenberg, Univ. Mainz, Mainz (Germany)
  8. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
  9. Hong Kong Univ. of Science and Technology, Hong Kong (China)
  10. Institute for Systems Biology, Seattle, WA (United States)
  11. Institute of Molecular Systems Biology, Zurich (Switzerland); Univ. of Zurich, Zurich (Switzerland)
Publication Date:
OSTI Identifier:
Grant/Contract Number:
1022509 and 1085017; HHSN272201200010C and HHSN272200900044C; ERC-2008-AdG_20080422; 3100A0-688 107679; AC05-76RL01830
Accepted Manuscript
Journal Name:
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2050-084X
eLife Sciences Publications, Ltd.
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
Country of Publication:
United States