PXD012308-2

PXD012308 is an original dataset announced via ProteomeXchange.

Title	Deep motif deconvolution of HLA-II peptidomes
Description	CD4 T cells are key for priming and regulating immune recognition of infected and cancer cells, but predictions of class II epitopes have limited accuracy. We profiled over 100’000 HLA-II ligands by Mass Spectrometry and developed a novel motif deconvolution algorithm to analyze these data. Our work demonstrates substantial improvements in the definition of HLA-II binding motifs and enhanced accuracy in HLA-II ligand and class II epitope predictions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:52:02.423.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Bassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-11 05:24:02	ID requested
1	2019-10-16 03:04:12	announced
⏵ 2	2024-10-22 04:52:08	announced	2024-10-22: Updated project metadata.

Racle J, Michaux J, Rockinger GA, Arnaud M, Bobisse S, Chong C, Guillaume P, Coukos G, Harari A, Jandus C, Bassani-Sternberg M, Gfeller D, Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. Nat Biotechnol, 37(11):1283-1286(2019) [pubmed]

10.1038/s41587-019-0289-6;

ProteomeXchange project tag: benchmarking, Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project, machine learning

curator keyword: Biological, Biomedical

submitter keyword: Immunopeptidomics, Ligand predictions, Mass spectrometry, HLA class II, Neoantigens

Michal Bassani-Sternberg
contact affiliation	Dr Michal BASSANI-STERNBERG ¬ Group leader Laboratory Hi-TIDe: Immunopeptidomics Head of clinical Mass spectrometry unit Center of experimental therapeutics Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Biopôle 3 Chemin des Boveresses 155, CH-1066 Lausanne
contact email	michal.bassani@chuv.ch
lab head
Michal Bassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.ch
dataset submitter

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/2019/10/PXD012308

PRIDE project URI

• PRIDE
  1. PXD012308
     1. Label: PRIDE project
     2. Name: Deep motif deconvolution of HLA-II peptidomes