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

Etienne Caron, Lucia Espona, Daniel J Kowalewski, Heiko Schuster, Nicola Ternette, Adan Alpizar, Ralf Bernd Schittenhelm, Sri Ramarathinam, Cecilia S Lindestam Arlehamn, Ching C G Koh, Ludovic C Gillet, Armin Rabsteyn, Pedro Navarro, Sangtae Kim, Henry H N Lam, Theo Sturm, Miguel Marcilla, Alessandro Sette, David S Campbell, Eric W Deutsch & 5 others Robert L Moritz, Anthony Wayne Purcell, Hans-Georg Rammensee, Stefan Stevanovic, Ruedi Aebersold

Research output: Contribution to journalArticleResearchpeer-review

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.
Original languageEnglish
Pages (from-to)1 - 17
Number of pages17
JournaleLife
Volume4
Issue numberJuly 2015
DOIs
Publication statusPublished - 2015

Cite this

Caron, E., Espona, L., Kowalewski, D. J., Schuster, H., Ternette, N., Alpizar, A., ... Aebersold, R. (2015). An open-source computational and data resource to analyze digital maps of immunopeptidomes. eLife, 4(July 2015), 1 - 17. https://doi.org/10.7554/eLife.07661
Caron, Etienne ; Espona, Lucia ; Kowalewski, Daniel J ; Schuster, Heiko ; Ternette, Nicola ; Alpizar, Adan ; Schittenhelm, Ralf Bernd ; Ramarathinam, Sri ; Arlehamn, Cecilia S Lindestam ; Koh, Ching C G ; Gillet, Ludovic C ; Rabsteyn, Armin ; Navarro, Pedro ; Kim, Sangtae ; Lam, Henry H N ; Sturm, Theo ; Marcilla, Miguel ; Sette, Alessandro ; Campbell, David S ; Deutsch, Eric W ; Moritz, Robert L ; Purcell, Anthony Wayne ; Rammensee, Hans-Georg ; Stevanovic, Stefan ; Aebersold, Ruedi. / An open-source computational and data resource to analyze digital maps of immunopeptidomes. In: eLife. 2015 ; Vol. 4, No. July 2015. pp. 1 - 17.
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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.",
author = "Etienne Caron and Lucia Espona and Kowalewski, {Daniel J} and Heiko Schuster and Nicola Ternette and Adan Alpizar and Schittenhelm, {Ralf Bernd} and Sri Ramarathinam and Arlehamn, {Cecilia S Lindestam} and Koh, {Ching C G} and Gillet, {Ludovic C} and Armin Rabsteyn and Pedro Navarro and Sangtae Kim and Lam, {Henry H N} and Theo Sturm and Miguel Marcilla and Alessandro Sette and Campbell, {David S} and Deutsch, {Eric W} and Moritz, {Robert L} and Purcell, {Anthony Wayne} and Hans-Georg Rammensee and Stefan Stevanovic and Ruedi Aebersold",
year = "2015",
doi = "10.7554/eLife.07661",
language = "English",
volume = "4",
pages = "1 -- 17",
journal = "eLife",
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Caron, E, Espona, L, Kowalewski, DJ, Schuster, H, Ternette, N, Alpizar, A, Schittenhelm, RB, Ramarathinam, S, Arlehamn, CSL, Koh, CCG, Gillet, LC, Rabsteyn, A, Navarro, P, Kim, S, Lam, HHN, Sturm, T, Marcilla, M, Sette, A, Campbell, DS, Deutsch, EW, Moritz, RL, Purcell, AW, Rammensee, H-G, Stevanovic, S & Aebersold, R 2015, 'An open-source computational and data resource to analyze digital maps of immunopeptidomes', eLife, vol. 4, no. July 2015, pp. 1 - 17. https://doi.org/10.7554/eLife.07661

An open-source computational and data resource to analyze digital maps of immunopeptidomes. / Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J; Schuster, Heiko; Ternette, Nicola; Alpizar, Adan; Schittenhelm, Ralf Bernd; Ramarathinam, Sri; Arlehamn, Cecilia S Lindestam; Koh, Ching C G; Gillet, Ludovic C; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry H N; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S; Deutsch, Eric W; Moritz, Robert L; Purcell, Anthony Wayne; Rammensee, Hans-Georg; Stevanovic, Stefan; Aebersold, Ruedi.

In: eLife, Vol. 4, No. July 2015, 2015, p. 1 - 17.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - An open-source computational and data resource to analyze digital maps of immunopeptidomes

AU - Caron, Etienne

AU - Espona, Lucia

AU - Kowalewski, Daniel J

AU - Schuster, Heiko

AU - Ternette, Nicola

AU - Alpizar, Adan

AU - Schittenhelm, Ralf Bernd

AU - Ramarathinam, Sri

AU - Arlehamn, Cecilia S Lindestam

AU - Koh, Ching C G

AU - Gillet, Ludovic C

AU - Rabsteyn, Armin

AU - Navarro, Pedro

AU - Kim, Sangtae

AU - Lam, Henry H N

AU - Sturm, Theo

AU - Marcilla, Miguel

AU - Sette, Alessandro

AU - Campbell, David S

AU - Deutsch, Eric W

AU - Moritz, Robert L

AU - Purcell, Anthony Wayne

AU - Rammensee, Hans-Georg

AU - Stevanovic, Stefan

AU - Aebersold, Ruedi

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

UR - http://www.ncbi.nlm.nih.gov/pubmed/26154972

U2 - 10.7554/eLife.07661

DO - 10.7554/eLife.07661

M3 - Article

VL - 4

SP - 1

EP - 17

JO - eLife

JF - eLife

SN - 2050-084X

IS - July 2015

ER -

Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpizar A et al. An open-source computational and data resource to analyze digital maps of immunopeptidomes. eLife. 2015;4(July 2015):1 - 17. https://doi.org/10.7554/eLife.07661