eLife (Jul 2015)
An open-source computational and data resource to analyze digital maps of immunopeptidomes
- Etienne Caron,
- Lucia Espona,
- Daniel J Kowalewski,
- Heiko Schuster,
- Nicola Ternette,
- Adán Alpízar,
- Ralf B Schittenhelm,
- Sri H Ramarathinam,
- Cecilia S Lindestam Arlehamn,
- Ching Chiek Koh,
- Ludovic C Gillet,
- Armin Rabsteyn,
- Pedro Navarro,
- Sangtae Kim,
- Henry Lam,
- Theo Sturm,
- Miguel Marcilla,
- Alessandro Sette,
- David S Campbell,
- Eric W Deutsch,
- Robert L Moritz,
- Anthony W Purcell,
- Hans-Georg Rammensee,
- Stefan Stevanovic,
- Ruedi Aebersold
Affiliations
- Etienne Caron
- ORCiD
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
- Lucia Espona
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
- Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, Germany
- Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, Germany
- Nicola Ternette
- Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom
- Adán Alpízar
- Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain
- Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Cecilia S Lindestam Arlehamn
- La Jolla Institute for Allergy and Immunology, La Jolla, United States
- Ching Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
- Ludovic C Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
- Armin Rabsteyn
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, Germany
- Pedro Navarro
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Sangtae Kim
- Pacific Northwest National Laboratory, Richland, United States
- Henry Lam
- Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China
- Theo Sturm
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
- Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain
- Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, United States
- David S Campbell
- Institute for Systems Biology, Seattle, United States
- Eric W Deutsch
- Institute for Systems Biology, Seattle, United States
- Robert L Moritz
- Institute for Systems Biology, Seattle, United States
- Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, Germany
- Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, Germany
- Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
- DOI
- https://doi.org/10.7554/eLife.07661
- Journal volume & issue
-
Vol. 4
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.
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