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

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

doi:10.7554/eLife.07661

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

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

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86 Citations (Scopus)

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 language	English
Article number	e07661
Pages (from-to)	1-17
Number of pages	17
Journal	eLife
Volume	4
Issue number	JULY 2015
DOIs	https://doi.org/10.7554/eLife.07661
Publication status	Published - 8 Jun 2015
Externally published	Yes

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10.7554/eLife.07661

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Caron, E., Espona, L., Kowalewski, D. J., Schuster, H., Ternette, N., Alpízar, A., Schittenhelm, R. B., Ramarathinam, S. H., Arlehamn, C. S. L., Koh, C. C., Gillet, L. C., Rabsteyn, A., Navarro, P., Kim, S., Lam, H., Sturm, T., Marcilla, M., Sette, A., Campbell, D. S., ... Aebersold, R. (2015). An open-source computational and data resource to analyze digital maps of immunopeptidomes. eLife, 4(JULY 2015), 1-17. Article e07661. https://doi.org/10.7554/eLife.07661

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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 Ad{\'a}n Alp{\'i}zar and Schittenhelm, {Ralf B.} and Ramarathinam, {Sri H.} and Arlehamn, {Cecilia S.Lindestam} and Koh, {Ching Chiek} and Gillet, {Ludovic C.} and Armin Rabsteyn and Pedro Navarro and Sangtae Kim and Henry Lam and Theo Sturm and Miguel Marcilla and Alessandro Sette and Campbell, {David S.} and Deutsch, {Eric W.} and Moritz, {Robert L.} and Purcell, {Anthony W.} and Rammensee, {Hans Georg} and Stefan Stevanovic and Ruedi Aebersold",

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year = "2015",

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doi = "10.7554/eLife.07661",

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Caron, E, Espona, L, Kowalewski, DJ, Schuster, H, Ternette, N, Alpízar, A, Schittenhelm, RB, Ramarathinam, SH, Arlehamn, CSL, Koh, CC, Gillet, LC, Rabsteyn, A, Navarro, P, Kim, S, Lam, H, Sturm, T, Marcilla, M, Sette, A, Campbell, DS, Deutsch, EW, Moritz, RL, Purcell, AW, Rammensee, HG, Stevanovic, S & Aebersold, R 2015, 'An open-source computational and data resource to analyze digital maps of immunopeptidomes', eLife, vol. 4, no. JULY 2015, e07661, pp. 1-17. https://doi.org/10.7554/eLife.07661

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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 - Alpízar, Adán

AU - Schittenhelm, Ralf B.

AU - Ramarathinam, Sri H.

AU - Arlehamn, Cecilia S.Lindestam

AU - Koh, Ching Chiek

AU - Gillet, Ludovic C.

AU - Rabsteyn, Armin

AU - Navarro, Pedro

AU - Kim, Sangtae

AU - Lam, Henry

AU - Sturm, Theo

AU - Marcilla, Miguel

AU - Sette, Alessandro

AU - Campbell, David S.

AU - Deutsch, Eric W.

AU - Moritz, Robert L.

AU - Purcell, Anthony W.

AU - Rammensee, Hans Georg

AU - Stevanovic, Stefan

AU - Aebersold, Ruedi

PY - 2015/6/8

Y1 - 2015/6/8

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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.

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EP - 17

JO - eLife

JF - eLife

IS - JULY 2015

M1 - e07661

ER -

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

Abstract

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