An open-source computational and data resource to analyze digital maps of immunopeptidomes
- ETH Zürich, Switzerland
- University of Tübingen, Germany
- University of Oxford, United Kingdom
- Spanish National Biotechnology Centre, Spain
- Monash University, Australia
- Monash University, United States
- La Jolla Institute for Allergy and Immunology, United States
- University Medical Center of the Johannes Gutenberg University Mainz, Germany
- Pacific Northwest National Laboratory, United States
- Hong Kong University of Science and Technology, China
- Institute for Systems Biology, United States
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.
Article and author information
Author details
Reviewing Editor
- Arup K Chakraborty, Massachusetts Institute of Technology, United States
Ethics
Human subjects: Informed consent was obtained in accordance with the Declaration of Helsinki protocol. The study was performed according to the guidelines of the local ethics committee (University of Tubingen, Germany).
Version history
- Received: March 23, 2015
- Accepted: July 7, 2015
- Accepted Manuscript published: July 8, 2015 (version 1)
- Version of Record published: July 20, 2015 (version 2)
Copyright
© 2015, Caron et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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An open-source computational and data resource to analyze digital maps of immunopeptidomes
eLife 4:e07661.
https://doi.org/10.7554/eLife.07661
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