PXD033106-1
PXD033106 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery |
| Description | Strazar M, Park J, Abelin JG, Taylor HB, Pedersen TK, Plichta DR, Brown EM, Eraslan B, Ortiz K, Clauser KR, Carr SA, Xavier RJ, Graham DB. 2022. T cell responses are exquisitely antigen-specific and directed against peptide epitopes displayed by human leukocyte antigen (HLA) on the surface of presenting cells. In particular, class II HLA (HLA-II) is remarkably polymorphic, which allows for presentation of diverse peptide antigens to T cells, but also forms the basis for genetic associations with diverse immunopathologies across the spectrum of infectious disease and autoimmunity. Here, we employ monoallelic immunopeptidomics to retrieve over 200,000 unique peptides presented by 41 HLA-II heterodimers covering major alleles across diverse ancestries. We leveraged this expansive dataset to develop computational models that predict peptide antigens based on HLA-II binding properties and infer informative features of the protein antigens from which these peptides derive. Combining both peptide and (contextual) protein features, we develop Context Aware Predictor of T cell Antigens (CAPTAn) to discover novel T cell epitopes from prokaryotes in the human microbiome and the viral pandemic pathogen SARS-CoV-2. |
| HostingRepository | MassIVE |
| AnnounceDate | 2023-04-28 |
| AnnouncementXML | Submission_2023-04-28_05:54:35.517.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Karl Clauser |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Veillonella parvula; NCBI TaxID: 29466; scientific name: Akkermansia muciniphila; NCBI TaxID: 239935; scientific name: Bacteroides thetaiotaomicron; NCBI TaxID: 818; scientific name: Bifidobacterium longum; NCBI TaxID: 216816; scientific name: Ruminococcus gnavus ATCC 29149; NCBI TaxID: 411470; scientific name: Clostridium clostridioforme 90A1; NCBI TaxID: 999403; |
| ModificationList | unknown modification; unknown modification; unknown modification; unknown modification; unknown modification; unknown modification |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2022-04-08 06:04:13 | ID requested | |
| ⏵ 1 | 2023-04-28 05:54:35 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: immunopeptidomics, HLA-II |
Contact List
| Steven A. Carr | |
|---|---|
| contact affiliation | Broad Institute of MIT and Harvard |
| contact email | scarr@broadinstitute.org |
| lab head | |
| Karl Clauser | |
| contact affiliation | Broad Institute of MIT and Harvard |
| contact email | clauser@broadinstitute.org |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000089225/ |
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