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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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DIA, SWATH-MS, computational biology, human, human leukocytes antigen, immunology, immunopeptidome, systems biology, targeted mass spectrometry, Antigen Presentation, Antigens, Computational Biology, Databases, Factual, HLA Antigens, High-Throughput Screening Assays, Mass Spectrometry, Peptides