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

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 consen...

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Bibliographic Details
Published in:eLife 2015-07, Vol.4
Main Authors: 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
Format: Article
Language:English
Subjects:
Amino acids
Antigen Presentation
Antigens
Antigens - chemistry
Antigens - immunology
BASIC BIOLOGICAL SCIENCES
Biology
Cancer
Computational and Systems Biology
Computational Biology - methods
Computer applications
Data analysis
Data processing
Databases, Factual
DIA
High-Throughput Screening Assays - methods
Histocompatibility antigen HLA
HLA Antigens - metabolism
human leukocytes antigen
Immunology
immunopeptidome
Immunotherapy
Laboratories
Lymphocytes
Mass spectrometry
Mass Spectrometry - methods
Mass spectroscopy
Peptides
Peptides - chemistry
Peptides - immunology
Scientific imaging
SWATH-MS
targeted mass spectrometry
Tools and Resources
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Description
Summary: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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.07661