The SysteMHC Atlas project

Wenguang Shao, Patrick G.A. Pedrioli, Witold Wolski, Cristian Scurtescu, Emanuel Schmid, Juan A. Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S.L. Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H.M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H.E. Kaufmann, Ralph Schlapbach, John C. CastleAlexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. Van Veelen, Cécile A.C.M. Van Els, Albert J.R. Heck, Gustavo A. De Souza, Ludvig M. Sollid, Arie Admon, Stefan Stevanovic, Hans Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron

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39 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)D1237-D1247
Number of pages11
JournalNucleic Acids Research
Volume46
Issue numberD1
DOIs
Publication statusPublished - 1 Jan 2018

Cite this

Shao, W., Pedrioli, P. G. A., Wolski, W., Scurtescu, C., Schmid, E., Vizcaíno, J. A., Courcelles, M., Schuster, H., Kowalewski, D., Marino, F., Arlehamn, C. S. L., Vaughan, K., Peters, B., Sette, A., Ottenhoff, T. H. M., Meijgaarden, K. E., Nieuwenhuizen, N., Kaufmann, S. H. E., Schlapbach, R., ... Caron, E. (2018). The SysteMHC Atlas project. Nucleic Acids Research, 46(D1), D1237-D1247. https://doi.org/10.1093/nar/gkx664