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

Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; Schuster, Heiko; Ternette, Nicola; Alpízar, Adán; Schittenhelm, Ralf B.; Ramarathinam, Sri H.; Lindestam Arlehamn, Cecilia S.; Chiek Koh, Ching; Gillet, Ludovic C.; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Purcell, Anthony W.; Rammensee, Hans -Georg; Stevanovic, Stefan; Aebersold, Ruedi

doi:10.7554/eLife.07661

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

Journal Article · Wed Jul 08 00:00:00 EDT 2015 · eLife

DOI: https://doi.org/10.7554/eLife.07661 · OSTI ID:1211538

^[1]; Espona, Lucia ^[1]; Kowalewski, Daniel J. ^[2]; Schuster, Heiko ^[2]; Ternette, Nicola ^[3]; Alpízar, Adán ^[4]; Schittenhelm, Ralf B. ^[5]; Ramarathinam, Sri H. ^[5]; Lindestam Arlehamn, Cecilia S. ^[6]; Chiek Koh, Ching ^[1]; Gillet, Ludovic C. ^[1]; Rabsteyn, Armin ^[2]; Navarro, Pedro ^[7]; Kim, Sangtae ^[8]; Lam, Henry ^[9]; Sturm, Theo ^[1]; Marcilla, Miguel ^[4]; Sette, Alessandro ^[6]; Campbell, David S. ^[10]; Deutsch, Eric W. ^[10] more »

Institute of Molecular Systems Biology, Zurich (Switzerland)
Univ. of Tubingen, Tubingen (Germany); German Cancer Consortium, Tubingen (Germany)
Univ. of Oxford, Oxford (United Kingdom)
Spanish National Biotechnology Centre, Madrid (Spain)
Monash Univ., Clayton (Australia)
La Jolla Institute for Allergy and Immunology, La Jolla, CA (United States)
Univ. Medical Center of the Johannes Gutenberg, Univ. Mainz, Mainz (Germany)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Hong Kong Univ. of Science and Technology, Hong Kong (China)
Institute for Systems Biology, Seattle, WA (United States)
Institute of Molecular Systems Biology, Zurich (Switzerland); Univ. of Zurich, Zurich (Switzerland)

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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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1211538

Journal Information:: eLife, Journal Name: eLife Vol. 4; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

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