PXD009925

PXD009925 is an original dataset announced via ProteomeXchange.

Title	HLA-I peptidomics od Meningioma tissues - Peptide length distribution and multiple specificity in naturally presented HLA-I ligands
Description	HLA-I molecules bind short peptides and present them to CD8+ T cells for TCR recognition. The length of HLA-I ligands typically ranges from 8 to 12 amino acids, but high variability is observed between different alleles. Here we used recent HLA peptidomics data to analyze in an unbiased way peptide length distributions over 85 different HLA-I alleles. Our results revealed clear clustering of HLA-I alleles with distinct peptide length distributions, which enabled us to unravel some of the molecular basis of peptide length distributions and predict peptide length distributions based on HLA-I sequences only. We further took advantage of our collection of curated HLA peptidomics studies to investigate multiple specificity in HLA-I molecules and validated these observations with binding assays. Explicitly modeling peptide length distributions and multiple specificity significantly improved predictions of naturally presented HLA-I ligands, as demonstrated in an independent benchmarking based on ten newly generated HLA peptidomics datasets from meningioma samples.
HostingRepository	PRIDE
AnnounceDate	2019-07-31
AnnouncementXML	Submission_2019-07-31_09:23:19.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	carbamoylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-28 01:23:39	ID requested
⏵ 1	2019-07-31 09:23:20	announced

Dataset with its publication pending

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

curator keyword: Biomedical

submitter keyword: HLA class I peptides, meningioma, HLA binding motifs

Michal Bassani-Sternberg
contact affiliation	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/2019/07/PXD009925

PRIDE project URI

• PRIDE
  1. PXD009925
     1. Label: PRIDE project
     2. Name: HLA-I peptidomics od Meningioma tissues - Peptide length distribution and multiple specificity in naturally presented HLA-I ligands