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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-07-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/07661 |
| _version_ | 1828195331913809920 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Etienne Caron |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-12T09:41:51Z |
| format | Article |
| id | doaj.art-0e99e90a2fc84f9e8fae2ad0ee1ea415 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T09:41:51Z |
| publishDate | 2015-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-0e99e90a2fc84f9e8fae2ad0ee1ea4152022-12-22T03:38:03ZengeLife Sciences Publications LtdeLife2050-084X2015-07-01410.7554/eLife.07661An open-source computational and data resource to analyze digital maps of immunopeptidomesEtienne Caron0https://orcid.org/0000-0003-2770-6970Lucia Espona1Daniel J Kowalewski2Heiko Schuster3Nicola Ternette4Adán Alpízar5Ralf B Schittenhelm6Sri H Ramarathinam7Cecilia S Lindestam Arlehamn8Ching Chiek Koh9Ludovic C Gillet10Armin Rabsteyn11Pedro Navarro12Sangtae Kim13Henry Lam14Theo Sturm15Miguel Marcilla16Alessandro Sette17David S Campbell18Eric W Deutsch19Robert L Moritz20Anthony W Purcell21Hans-Georg Rammensee22Stefan Stevanovic23Ruedi Aebersold24Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, SwitzerlandDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, SwitzerlandDepartment of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, GermanyDepartment of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, GermanyTarget Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United KingdomProteomics Unit, Spanish National Biotechnology Centre, Madrid, SpainDepartment of Biochemistry and Molecular Biology, Monash University, Clayton, AustraliaDepartment of Biochemistry and Molecular Biology, Monash University, Clayton, AustraliaLa Jolla Institute for Allergy and Immunology, La Jolla, United StatesDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, SwitzerlandDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, SwitzerlandDepartment of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, GermanyInstitute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, GermanyPacific Northwest National Laboratory, Richland, United StatesDivision of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, ChinaDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, SwitzerlandProteomics Unit, Spanish National Biotechnology Centre, Madrid, SpainLa Jolla Institute for Allergy and Immunology, La Jolla, United StatesInstitute for Systems Biology, Seattle, United StatesInstitute for Systems Biology, Seattle, United StatesInstitute for Systems Biology, Seattle, United StatesDepartment of Biochemistry and Molecular Biology, Monash University, Clayton, AustraliaDepartment of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, GermanyDepartment of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany; DKFZ partner site Tübingen, German Cancer Consortium, Tübingen, GermanyDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, SwitzerlandWe 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.https://elifesciences.org/articles/07661human leukocytes antigenimmunopeptidometargeted mass spectrometrySWATH-MSDIA |
| spellingShingle | 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 An open-source computational and data resource to analyze digital maps of immunopeptidomes eLife human leukocytes antigen immunopeptidome targeted mass spectrometry SWATH-MS DIA |
| 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 | human leukocytes antigen immunopeptidome targeted mass spectrometry SWATH-MS DIA |
| url | https://elifesciences.org/articles/07661 |
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