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

Elife. 2015 Jul 8:4:e07661. doi: 10.7554/eLife.07661.


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.

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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigen Presentation
  • Antigens / chemistry*
  • Antigens / immunology*
  • Computational Biology / methods*
  • Databases, Factual*
  • HLA Antigens / metabolism
  • High-Throughput Screening Assays / methods
  • Mass Spectrometry / methods
  • Peptides / chemistry*
  • Peptides / immunology*


  • Antigens
  • HLA Antigens
  • Peptides