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

Abstract

We present a novel proteomics-based workflow and an open source data and computational resource for reproducibly identifying and quantifying HLA-associated peptides at high-throughput. The provided 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 by SWATH mass spectrometry (MS). This is the first community-based study towards the development of a robust platform for the reproducible and quantitative measurement of HLA peptidomes, an essential step towards the design of efficient immunotherapies.

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1221455
Report Number(s):
PNNL-SA-108494
48680; 400412000
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
eLife, 4:Article No. e07661
Additional Journal Information:
Journal Name: eLife, 4:Article No. e07661
Country of Publication:
United States
Language:
English
Subject:
human leukocytes antigen / immunopeptidome / targeted / SWATH-MS / DIA; Environmental Molecular Sciences Laboratory

Citation Formats

Caron, Etienne, Espona, Lucia, Kowalewski, Daniel J., Schuster, Heiko, Ternette, Nicola, Alpizar, Adan, Schittenhelm, Ralf B., Ramarathinam, Sri Harsha, Lindestam-Arlehamn, Cecilia S., Koh, Ching Chiek, Gillet, Ludovic, Rabsteyn, Armin, Navarro, Pedro, Kim, Sangtae, Lam, Henry, Sturm, Theo, Marcilla, Miguel, Sette, Alessandro, Campbell, David, Deutsch, Eric W., Moritz, Robert L., Purcell, Anthony, Rammensee, Hans-Georg, Stevanovic, Stevan, 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.
Caron, Etienne, Espona, Lucia, Kowalewski, Daniel J., Schuster, Heiko, Ternette, Nicola, Alpizar, Adan, Schittenhelm, Ralf B., Ramarathinam, Sri Harsha, Lindestam-Arlehamn, Cecilia S., Koh, Ching Chiek, Gillet, Ludovic, Rabsteyn, Armin, Navarro, Pedro, Kim, Sangtae, Lam, Henry, Sturm, Theo, Marcilla, Miguel, Sette, Alessandro, Campbell, David, Deutsch, Eric W., Moritz, Robert L., Purcell, Anthony, Rammensee, Hans-Georg, Stevanovic, Stevan, & Aebersold, Ruedi. An open-source computational and data resource to analyze digital maps of immunopeptidomes. United States. doi:10.7554/eLife.07661.
Caron, Etienne, Espona, Lucia, Kowalewski, Daniel J., Schuster, Heiko, Ternette, Nicola, Alpizar, Adan, Schittenhelm, Ralf B., Ramarathinam, Sri Harsha, Lindestam-Arlehamn, Cecilia S., Koh, Ching Chiek, Gillet, Ludovic, Rabsteyn, Armin, Navarro, Pedro, Kim, Sangtae, Lam, Henry, Sturm, Theo, Marcilla, Miguel, Sette, Alessandro, Campbell, David, Deutsch, Eric W., Moritz, Robert L., Purcell, Anthony, Rammensee, Hans-Georg, Stevanovic, Stevan, and Aebersold, Ruedi. Wed . "An open-source computational and data resource to analyze digital maps of immunopeptidomes". United States. doi:10.7554/eLife.07661.
@article{osti_1221455,
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 Alpizar, Adan and Schittenhelm, Ralf B. and Ramarathinam, Sri Harsha and Lindestam-Arlehamn, Cecilia S. and Koh, Ching Chiek and Gillet, Ludovic and Rabsteyn, Armin and Navarro, Pedro and Kim, Sangtae and Lam, Henry and Sturm, Theo and Marcilla, Miguel and Sette, Alessandro and Campbell, David and Deutsch, Eric W. and Moritz, Robert L. and Purcell, Anthony and Rammensee, Hans-Georg and Stevanovic, Stevan and Aebersold, Ruedi},
abstractNote = {We present a novel proteomics-based workflow and an open source data and computational resource for reproducibly identifying and quantifying HLA-associated peptides at high-throughput. The provided 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 by SWATH mass spectrometry (MS). This is the first community-based study towards the development of a robust platform for the reproducible and quantitative measurement of HLA peptidomes, an essential step towards the design of efficient immunotherapies.},
doi = {10.7554/eLife.07661},
journal = {eLife, 4:Article No. e07661},
number = ,
volume = ,
place = {United States},
year = {2015},
month = {7}
}