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The SysteMHC Atlas project.


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.

SUBMITTER: Shao W 

PROVIDER: S-EPMC5753376 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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The SysteMHC Atlas project.

Shao Wenguang W   Pedrioli Patrick G A PGA   Wolski Witold W   Scurtescu Cristian C   Schmid Emanuel E   Vizcaíno Juan A JA   Courcelles Mathieu M   Schuster Heiko H   Kowalewski Daniel D   Marino Fabio F   Arlehamn Cecilia S L CSL   Vaughan Kerrie K   Peters Bjoern B   Sette Alessandro A   Ottenhoff Tom H M THM   Meijgaarden Krista E KE   Nieuwenhuizen Natalie N   Kaufmann Stefan H E SHE   Schlapbach Ralph R   Castle John C JC   Nesvizhskii Alexey I AI   Nielsen Morten M   Deutsch Eric W EW   Campbell David S DS   Moritz Robert L RL   Zubarev Roman A RA   Ytterberg Anders Jimmy AJ   Purcell Anthony W AW   Marcilla Miguel M   Paradela Alberto A   Wang Qi Q   Costello Catherine E CE   Ternette Nicola N   van Veelen Peter A PA   van Els Cécile A C M CACM   Heck Albert J R AJR   de Souza Gustavo A GA   Sollid Ludvig M LM   Admon Arie A   Stevanovic Stefan S   Rammensee Hans-Georg HG   Thibault Pierre P   Perreault Claude C   Bassani-Sternberg Michal M   Aebersold Ruedi R   Caron Etienne E  

Nucleic acids research 20180101 D1


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 i  ...[more]

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