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Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.

The SysteMHC Atlas project.

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Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.
Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland.
Scientific IT Services (SIS), ETH Zurich, Zurich 8093, Switzerland.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada.
Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.
German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany.
Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne 1011, Switzerland.
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, The Netherlands.
Netherlands Proteomics Centre, Utrecht, 3584 CH, The Netherlands.
La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
Department of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands.
Department of Immunology, Max Planck Institute for Infection Biology, Berlin 10117, Germany.
Vaccine Research and Translational Medicine, Agenus Switzerland Inc., 4157 Basel, Switzerland.
Department of Pathology, BRCF Metabolomics Core, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, 1650, Argentina.
Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
Institute for Systems Biology, Seattle, WA 98109, USA.
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-171 77, Sweden.
Rheumatology Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, SE-171 77, Sweden.
Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia.
Proteomics Unit, Spanish National Biotechnology Centre, Madrid 28049, Spain.
Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, OX3 7FZ, UK.
Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands.
Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3720 BA, The Netherlands.
Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway.
The Brain Institute, Universidade Federal do Rio Grande do Norte, 59056-450, Natal-RN, Brazil.
Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel.
Faculty of Science, University of Zurich, 8006 Zurich, Switzerland.


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 (, 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.

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