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

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.

Authors:
ORCiD logo [1];  [1];  [2];  [2];  [3];  [4];  [5];  [5];  [6];  [1];  [1];  [2];  [7];  [8];  [9];  [1];  [4];  [6];  [10];  [10] more »;  [10];  [5];  [2];  [2];  [11] « less
+ Show Author Affiliations
  1. Institute of Molecular Systems Biology, Zurich (Switzerland)
  2. Univ. of Tubingen, Tubingen (Germany); German Cancer Consortium, Tubingen (Germany)
  3. Univ. of Oxford, Oxford (United Kingdom)
  4. Spanish National Biotechnology Centre, Madrid (Spain)
  5. Monash Univ., Clayton (Australia)
  6. La Jolla Institute for Allergy and Immunology, La Jolla, CA (United States)
  7. Univ. Medical Center of the Johannes Gutenberg, Univ. Mainz, Mainz (Germany)
  8. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
  9. Hong Kong Univ. of Science and Technology, Hong Kong (China)
  10. Institute for Systems Biology, Seattle, WA (United States)
  11. Institute of Molecular Systems Biology, Zurich (Switzerland); Univ. of Zurich, Zurich (Switzerland)
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1211538
Grant/Contract Number:  
1022509 and 1085017; HHSN272201200010C and HHSN272200900044C; ERC-2008-AdG_20080422; 3100A0-688 107679; AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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, and Aebersold, Ruedi. An open-source computational and data resource to analyze digital maps of immunopeptidomes. United States: N. p., 2015. Web. doi:10.7554/eLife.07661.
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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. An open-source computational and data resource to analyze digital maps of immunopeptidomes. United States. https://doi.org/10.7554/eLife.07661
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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, and Aebersold, Ruedi. Wed . "An open-source computational and data resource to analyze digital maps of immunopeptidomes". United States. https://doi.org/10.7554/eLife.07661. https://www.osti.gov/servlets/purl/1211538.
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@article{osti_1211538,
title = {An open-source computational and data resource to analyze digital maps of immunopeptidomes},
author = {Caron, Etienne and Espona, Lucia and Kowalewski, Daniel J. and Schuster, Heiko and Ternette, Nicola and Alpízar, Adán and Schittenhelm, Ralf B. and Ramarathinam, Sri H. and Lindestam Arlehamn, Cecilia S. and Chiek Koh, Ching and Gillet, Ludovic C. and Rabsteyn, Armin and Navarro, Pedro and Kim, Sangtae and Lam, Henry and Sturm, Theo and Marcilla, Miguel and Sette, Alessandro and Campbell, David S. and Deutsch, Eric W. and Moritz, Robert L. and Purcell, Anthony W. and Rammensee, Hans -Georg and Stevanovic, Stefan and Aebersold, Ruedi},
abstractNote = {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.},
doi = {10.7554/eLife.07661},
journal = {eLife},
number = ,
volume = 4,
place = {United States},
year = {Wed Jul 08 00:00:00 EDT 2015},
month = {Wed Jul 08 00:00:00 EDT 2015}
}
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Publisher's Version of Record
https://doi.org/10.7554/eLife.07661
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