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 DeutschRobert L Moritz, Anthony Wayne Purcell, Hans-Georg Rammensee, Stefan Stevanovic, Ruedi Aebersold

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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., Schittenhelm, R. B., Ramarathinam, S., Arlehamn, C. S. L., Koh, C. C. G., Gillet, L. C., Rabsteyn, A., Navarro, P., Kim, S., Lam, H. H. N., 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. https://doi.org/10.7554/eLife.07661