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

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

Author information

1
Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
2
Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
3
Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom.
4
Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain.
5
Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
6
La Jolla Institute for Allergy and Immunology, La Jolla, United States.
7
Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
8
Pacific Northwest National Laboratory, Richland, United States.
9
Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China.
10
Institute for Systems Biology, Seattle, 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.

KEYWORDS:

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

PMID:
26154972
PMCID:
PMC4507788
DOI:
10.7554/eLife.07661
[Indexed for MEDLINE]
Free PMC Article

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