<<< Full experiment listing

PXD034773

PXD034773 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMachine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
DescriptionCD4+ 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.
HostingRepositoryPRIDE
AnnounceDate2023-04-07
AnnouncementXMLSubmission_2023-04-07_10:24:40.272.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMichalBassani-Sternberg
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-06-21 01:52:27ID requested
12023-04-07 10:24:40announced
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 affiliationLudwig Institute for Cancer Research Lausanne Centre de recherche Agora Rue du Bugnon 25A CH-1011 Lausanne
contact emailmichal.bassani@chuv.ch
lab head
MichalBassani-Sternberg
contact affiliationUNIL/CHUV
contact emailmichal.bassani@chuv.ch
dataset submitter
Full Dataset Link List
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://ftp.pride.ebi.ac.uk/pride/data/archive/2023/04/PXD034773
PRIDE project URI
Repository Record List
[ + ]