The SysteMHC Atlas project.
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-sca...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Oxford University Press
2017
|
| _version_ | 1797084115236814848 |
|---|---|
| author | Shao, W Pedrioli, P Wolski, W Scurtescu, C Schmid, E Vizcaíno, J Courcelles, M Schuster, H Kowalewski, D Marino, F Arlehamn, C Vaughan, K Peters, B Sette, A Ottenhoff, T Meijgaarden, K Nieuwenhuizen, N Kaufmann, S Schlapbach, R Castle, J Nesvizhskii, A Nielsen, M Deutsch, E Campbell, D Moritz, R Zubarev, R Ytterberg, A Purcell, A Marcilla, M Paradela, A Wang, Q Costello, C Ternette, N van Veelen, P van Els, C Heck, A de Souza, G Sollid, L Admon, A Stevanovic, S Rammensee, H Thibault, P Perreault, C Bassani-Sternberg, M Aebersold, R Caron, E |
| author_facet | Shao, W Pedrioli, P Wolski, W Scurtescu, C Schmid, E Vizcaíno, J Courcelles, M Schuster, H Kowalewski, D Marino, F Arlehamn, C Vaughan, K Peters, B Sette, A Ottenhoff, T Meijgaarden, K Nieuwenhuizen, N Kaufmann, S Schlapbach, R Castle, J Nesvizhskii, A Nielsen, M Deutsch, E Campbell, D Moritz, R Zubarev, R Ytterberg, A Purcell, A Marcilla, M Paradela, A Wang, Q Costello, C Ternette, N van Veelen, P van Els, C Heck, A de Souza, G Sollid, L Admon, A Stevanovic, S Rammensee, H Thibault, P Perreault, C Bassani-Sternberg, M Aebersold, R Caron, E |
| author_sort | Shao, W |
| collection | OXFORD |
| description | Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts. |
| first_indexed | 2024-03-07T01:50:54Z |
| format | Journal article |
| id | oxford-uuid:9a0d3e18-68a3-4e34-9c44-5fc5e4f3e5d1 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T01:50:54Z |
| publishDate | 2017 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:9a0d3e18-68a3-4e34-9c44-5fc5e4f3e5d12022-03-27T00:18:54ZThe SysteMHC Atlas project.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:9a0d3e18-68a3-4e34-9c44-5fc5e4f3e5d1EnglishSymplectic Elements at OxfordOxford University Press2017Shao, WPedrioli, PWolski, WScurtescu, CSchmid, EVizcaíno, JCourcelles, MSchuster, HKowalewski, DMarino, FArlehamn, CVaughan, KPeters, BSette, AOttenhoff, TMeijgaarden, KNieuwenhuizen, NKaufmann, SSchlapbach, RCastle, JNesvizhskii, ANielsen, MDeutsch, ECampbell, DMoritz, RZubarev, RYtterberg, APurcell, AMarcilla, MParadela, AWang, QCostello, CTernette, Nvan Veelen, Pvan Els, CHeck, Ade Souza, GSollid, LAdmon, AStevanovic, SRammensee, HThibault, PPerreault, CBassani-Sternberg, MAebersold, RCaron, EMass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts. |
| spellingShingle | Shao, W Pedrioli, P Wolski, W Scurtescu, C Schmid, E Vizcaíno, J Courcelles, M Schuster, H Kowalewski, D Marino, F Arlehamn, C Vaughan, K Peters, B Sette, A Ottenhoff, T Meijgaarden, K Nieuwenhuizen, N Kaufmann, S Schlapbach, R Castle, J Nesvizhskii, A Nielsen, M Deutsch, E Campbell, D Moritz, R Zubarev, R Ytterberg, A Purcell, A Marcilla, M Paradela, A Wang, Q Costello, C Ternette, N van Veelen, P van Els, C Heck, A de Souza, G Sollid, L Admon, A Stevanovic, S Rammensee, H Thibault, P Perreault, C Bassani-Sternberg, M Aebersold, R Caron, E The SysteMHC Atlas project. |
| title | The SysteMHC Atlas project. |
| title_full | The SysteMHC Atlas project. |
| title_fullStr | The SysteMHC Atlas project. |
| title_full_unstemmed | The SysteMHC Atlas project. |
| title_short | The SysteMHC Atlas project. |
| title_sort | systemhc atlas project |
| work_keys_str_mv | AT shaow thesystemhcatlasproject AT pedriolip thesystemhcatlasproject AT wolskiw thesystemhcatlasproject AT scurtescuc thesystemhcatlasproject AT schmide thesystemhcatlasproject AT vizcainoj thesystemhcatlasproject AT courcellesm thesystemhcatlasproject AT schusterh thesystemhcatlasproject AT kowalewskid thesystemhcatlasproject AT marinof thesystemhcatlasproject AT arlehamnc thesystemhcatlasproject AT vaughank thesystemhcatlasproject AT petersb thesystemhcatlasproject AT settea thesystemhcatlasproject AT ottenhofft thesystemhcatlasproject AT meijgaardenk thesystemhcatlasproject AT nieuwenhuizenn thesystemhcatlasproject AT kaufmanns thesystemhcatlasproject AT schlapbachr thesystemhcatlasproject AT castlej thesystemhcatlasproject AT nesvizhskiia thesystemhcatlasproject AT nielsenm thesystemhcatlasproject AT deutsche thesystemhcatlasproject AT campbelld thesystemhcatlasproject AT moritzr thesystemhcatlasproject AT zubarevr thesystemhcatlasproject AT ytterberga thesystemhcatlasproject AT purcella thesystemhcatlasproject AT marcillam thesystemhcatlasproject AT paradelaa thesystemhcatlasproject AT wangq thesystemhcatlasproject AT costelloc thesystemhcatlasproject AT ternetten thesystemhcatlasproject AT vanveelenp thesystemhcatlasproject AT vanelsc thesystemhcatlasproject AT hecka thesystemhcatlasproject AT desouzag thesystemhcatlasproject AT sollidl thesystemhcatlasproject AT admona thesystemhcatlasproject AT stevanovics thesystemhcatlasproject AT rammenseeh thesystemhcatlasproject AT thibaultp thesystemhcatlasproject AT perreaultc thesystemhcatlasproject AT bassanisternbergm thesystemhcatlasproject AT aebersoldr thesystemhcatlasproject AT carone thesystemhcatlasproject AT shaow systemhcatlasproject AT pedriolip systemhcatlasproject AT wolskiw systemhcatlasproject AT scurtescuc systemhcatlasproject AT schmide systemhcatlasproject AT vizcainoj systemhcatlasproject AT courcellesm systemhcatlasproject AT schusterh systemhcatlasproject AT kowalewskid systemhcatlasproject AT marinof systemhcatlasproject AT arlehamnc systemhcatlasproject AT vaughank systemhcatlasproject AT petersb systemhcatlasproject AT settea systemhcatlasproject AT ottenhofft systemhcatlasproject AT meijgaardenk systemhcatlasproject AT nieuwenhuizenn systemhcatlasproject AT kaufmanns systemhcatlasproject AT schlapbachr systemhcatlasproject AT castlej systemhcatlasproject AT nesvizhskiia systemhcatlasproject AT nielsenm systemhcatlasproject AT deutsche systemhcatlasproject AT campbelld systemhcatlasproject AT moritzr systemhcatlasproject AT zubarevr systemhcatlasproject AT ytterberga systemhcatlasproject AT purcella systemhcatlasproject AT marcillam systemhcatlasproject AT paradelaa systemhcatlasproject AT wangq systemhcatlasproject AT costelloc systemhcatlasproject AT ternetten systemhcatlasproject AT vanveelenp systemhcatlasproject AT vanelsc systemhcatlasproject AT hecka systemhcatlasproject AT desouzag systemhcatlasproject AT sollidl systemhcatlasproject AT admona systemhcatlasproject AT stevanovics systemhcatlasproject AT rammenseeh systemhcatlasproject AT thibaultp systemhcatlasproject AT perreaultc systemhcatlasproject AT bassanisternbergm systemhcatlasproject AT aebersoldr systemhcatlasproject AT carone systemhcatlasproject |