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

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Abstract
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.
Funding Information
  • National Health and Medical Research Council (NHMRC) (1022509 and 1085017)
  • National Institutes of Health (NIH) (HHSN272201200010C and HHSN272200900044C)
  • European Research Council (ERC) (ERC-2008-AdG_20080422)
  • Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung (3100A0-688 107679)
  • European Commission (EC) (SysteMtb, 241587)
  • German Cancer Consortium (DKTK)
  • Bundesministerium für Bildung und Forschung (e:Bio Express2Present, 0316179C)
  • Forschungszentrum Immuntherapie (FZI) (of the Johannes Gutenberg University Mainz)
  • Ministerio de Economía y Competitividad (Carlos III Health Institute (ISCIII) (ProteoRed-PRB2, PT13/0001))
  • European Commission (EC) (Marie Curie Intra-European Fellowship)
  • Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Postdoc Mobility Fellowship)
  • National Institute of General Medical Sciences (NIGMS) (R01GM087221 and 2P50 GM076547/Center for Systems Biology)