PXD034773 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes |
Description | CD4+ T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on MHC-II molecules. The high polymorphism of MHC-II genes represents an important hurdle towards accurate predictions of CD4+ T-cell epitopes in different individuals and different species. Here we generated and curated a dataset of 627,013 unique MHC-II ligands identified by mass spectrometry. This enabled us to determine the binding motifs of 88 MHC-II alleles across human, mouse, cattle and chicken. Analysis of these binding specificities combined with X-ray crystallography refined our understanding of the molecular determinants of MHC-II motifs and revealed a widespread reverse binding mode in MHC-II ligands. We then developed a machine learning framework to accurately predict binding specificities and ligands of any MHC-II allele. This tool improves and expands predictions of CD4+ T-cell epitopes, as demonstrated by the identification of several viral and bacterial epitopes following the aforementioned reverse binding mode. |
HostingRepository | PRIDE |
AnnounceDate | 2023-04-07 |
AnnouncementXML | Submission_2023-04-07_10:24:40.272.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | MichalBassani-Sternberg |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-06-21 01:52:27 | ID requested | |
⏵ 1 | 2023-04-07 10:24:40 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP) (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project |
submitter keyword: HLA-II binding motifs, machine learning predictions, HLA-II peptides |
Contact List
MichalBassani-Sternberg |
contact affiliation | Ludwig Institute for Cancer Research Lausanne Centre de recherche Agora Rue du Bugnon 25A CH-1011 Lausanne |
contact email | michal.bassani@chuv.ch |
lab head | |
MichalBassani-Sternberg |
contact affiliation | UNIL/CHUV |
contact email | michal.bassani@chuv.ch |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD034773
- Label: PRIDE project
- Name: Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes