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Pedrioli, Patrick G A
Vizcaíno, Juan A
Arlehamn, Cecilia S L
Ottenhoff, Tom H M
Meijgaarden, Krista E
Kaufmann, Stefan H E
Castle, John C
Nesvizhskii, Alexey I
Deutsch, Eric W
Campbell, David S
Moritz, Robert L
Zubarev, Roman A
Ytterberg, Anders Jimmy
Purcell, Anthony W
Costello, Catherine E
van Veelen, Peter A
van Els, Cécile A C M
Heck, Albert J R
de Souza, Gustavo A
Sollid, Ludvig M
MetadataShow full item record
TitleThe SysteMHC Atlas project.
Published inNucleic Acids Res 2018; 46(D1):1237-47
PubliekssamenvattingMass 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.
- The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses.
- Authors: Shao W, Caron E, Pedrioli P, Aebersold R
- Issue date: 2020
- A tissue-based draft map of the murine MHC class I immunopeptidome.
- Authors: Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E
- Issue date: 2018 Aug 7
- Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry.
- Authors: Freudenmann LK, Marcu A, Stevanović S
- Issue date: 2018 Jul
- The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases.
- Authors: Vizcaíno JA, Kubiniok P, Kovalchik KA, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E
- Issue date: 2020 Jan
- An open-source computational and data resource to analyze digital maps of immunopeptidomes.
- Authors: Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R
- Issue date: 2015 Jul 8