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PXD033106

PXD033106 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery
DescriptionStrazar 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.
HostingRepositoryMassIVE
AnnounceDate2023-04-28
AnnouncementXMLSubmission_2023-04-28_05:54:35.517.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKarl 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;
ModificationListunknown modification; unknown modification; unknown modification; unknown modification; unknown modification; unknown modification
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-04-08 06:04:13ID requested
12023-04-28 05:54:35announced
Publication List
no publication
Keyword List
submitter keyword: immunopeptidomics, HLA-II
Contact List
Steven A. Carr
contact affiliationBroad Institute of MIT and Harvard
contact emailscarr@broadinstitute.org
lab head
Karl Clauser
contact affiliationBroad Institute of MIT and Harvard
contact emailclauser@broadinstitute.org
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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