PXD013831

PXD013831 is an original dataset announced via ProteomeXchange.

Title	the landscape of phosphorylated HLA-I ligands
Description	The identification and prediction of HLA-I–peptide interactions play an important role in our understanding of antigen recognition in infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. In this study, we collected in-depth phosphorylated HLA-I peptidomics data (1,920 unique phosphorylated peptides) from several studies covering 67 HLA-I alleles and expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands for several alleles. In addition to the previously observed preferences for phosphorylation at P4, for proline next to the phosphosite and for arginine at P1, we could detect a clear enrichment of phosphorylated peptides among HLA-C ligands and among longer peptides. Binding assays were used to validate and interpret these observations. We then used these data to develop the first predictor of HLA-I– phosphorylated peptide interactions and demonstrated that combining phosphorylated and unmodified HLA-I ligands in the training of the predictor led to highest accuracy.
HostingRepository	PRIDE
AnnounceDate	2019-12-18
AnnouncementXML	Submission_2020-01-10_02:00:26.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	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-14 00:29:37	ID requested
1	2019-12-18 15:12:48	announced
⏵ 2	2020-01-10 02:00:28	announced	2020-01-10: Updated publication reference for PubMed record(s): 31848261.

Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, M, ü, ller M, Coukos G, Bassani-Sternberg M, Gfeller D, Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. Mol Cell Proteomics, 19(2):390-404(2020) [pubmed]

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

curator keyword: Biological, Biomedical

submitter keyword: Immunopeptidomics, HLA binding peptides, Phosphorylations

Michal Bassani-Sternberg
contact affiliation	Department of oncology UNIL CHUV Ludwig Institute for Cancer Research 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/2019/12/PXD013831

PRIDE project URI

• PRIDE
  1. PXD013831
     1. Label: PRIDE project
     2. Name: the landscape of phosphorylated HLA-I ligands