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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...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
eLife Sciences Publications, Ltd
2015
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| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507788/ https://www.ncbi.nlm.nih.gov/pubmed/26154972 http://dx.doi.org/10.7554/eLife.07661 |
| _version_ | 1782381851016429568 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Caron, Etienne |
| collection | PubMed |
| description | 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. DOI: http://dx.doi.org/10.7554/eLife.07661.001 |
| format | Online Article Text |
| id | pubmed-4507788 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2015 |
| publisher | eLife Sciences Publications, Ltd |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-45077882015-07-21 An open-source computational and data resource to analyze digital maps of immunopeptidomes 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 eLife Computational and Systems Biology 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. DOI: http://dx.doi.org/10.7554/eLife.07661.001 eLife Sciences Publications, Ltd 2015-07-08 /pmc/articles/PMC4507788/ /pubmed/26154972 http://dx.doi.org/10.7554/eLife.07661 Text en © 2015, Caron et al http://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
| spellingShingle | Computational and Systems Biology 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 An open-source computational and data resource to analyze digital maps of immunopeptidomes |
| title | An open-source computational and data resource to analyze digital maps of immunopeptidomes |
| title_full | An open-source computational and data resource to analyze digital maps of immunopeptidomes |
| title_fullStr | An open-source computational and data resource to analyze digital maps of immunopeptidomes |
| title_full_unstemmed | An open-source computational and data resource to analyze digital maps of immunopeptidomes |
| title_short | An open-source computational and data resource to analyze digital maps of immunopeptidomes |
| title_sort | open-source computational and data resource to analyze digital maps of immunopeptidomes |
| topic | Computational and Systems Biology |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507788/ https://www.ncbi.nlm.nih.gov/pubmed/26154972 http://dx.doi.org/10.7554/eLife.07661 |
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