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

Significance Statement

Researchers from ETH Zürich have developed a new technology enabling the reproducible measurement of antigens (or peptides) presented to the immune system by major histocompatibility complex (MHC) molecules. This technology – known as SWATH mass spectrometry – could be used in the future to reproducibly detect and quantify immunogenic antigens and could therefore greatly help in the design of personalized immune-based therapies against infectious diseases and cancers.


An open-source computational and data resource to analyze digital maps immunopeptidomes. Global Medical Discovery









 Journal Reference

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

Caron E1, Espona L1, Kowalewski DJ2, Schuster H2, Ternette N3, Alpízar A4, Schittenhelm RB5, Ramarathinam SH5, Lindestam Arlehamn CS6, Chiek Koh C1,Gillet LC1, Rabsteyn A2, Navarro P7, Kim S8, Lam H9, Sturm T1, Marcilla M4, Sette A6, Campbell DS10, Deutsch EW10, Moritz RL10, Purcell AW5, Rammensee HG2, Stevanovic S2, Aebersold R1.

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1Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.

2Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.

3Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom.

4Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain.

5Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.

6La Jolla Institute for Allergy and Immunology, La Jolla, United States.

7Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.

8Pacific Northwest National Laboratory, Richland, United States.

9Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China.

10Institute for Systems Biology, Seattle, United States.[/expand]


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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About the author

Etienne Caron was born in Canada. He did a Ph.D. in Systems Immunology at the University of Montreal where he worked on the analysis of the cellular immunopeptidomes. In 2013, he received a Marie Curie Intra-European Fellowship to carry out research in the group of Ruedi Aebersold in Switzerland. In 2015, he launched the HIPP (Human ImmunoPeptidomes Project) initiative as part of the Human Proteome Project. His current research focuses on how cutting edge technologies in mass spectrometry can be applied to identify and quantify MHC-associated peptides. Research on this topic will have an impact on the development of vaccines against infectious diseases and cancers.




Research on Immunopeptidomes featured on Global Medical Discovery the World’s leading source of medical research news