PXD013649-2

PXD013649 is an original dataset announced via ProteomeXchange.

Title	non-canonical HLA peptides in cancer
Description	Efforts to precisely identify tumor human leukocyte antigen presented peptides (HLAp) capable of mediating T cell based tumor rejection still face important challenges. Recent reports suggest that non-canonical cancer HLAp could be immunogenic but their identification requires highly sensitive and accurate mass-spectrometry (MS)-based proteogenomics approaches. Here, we present a novel MS-based analytical pipeline that can precisely characterize the non-canonical HLAp repertoire, incorporating whole exome sequencing, bulk and single cell transcriptomics, ribosome profiling, and a combination of two MS/MS search tools. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLAp. Albeit often at low levels and in distinct subpopulations of cells, numerous non-canonical HLAp are shared across tumors. This analytical platform holds great promise for the discovery of novel cancer antigens for cancer immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:21.650.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	2019-04-26 04:09:26	ID requested
1	2019-11-27 09:08:43	announced
⏵ 2	2024-10-22 05:01:29	announced	2024-10-22: Updated project metadata.

Chong C, M, ü, ller M, Pak H, Harnett D, Huber F, Grun D, Leleu M, Auger A, Arnaud M, Stevenson BJ, Michaux J, Bilic I, Hirsekorn A, Calviello L, Sim, ó, -Riudalbas L, Planet E, Lubi, ń, ski J, Bry, ś, kiewicz M, Wiznerowicz M, Xenarios I, Zhang L, Trono D, Harari A, Ohler U, Coukos G, Bassani-Sternberg M, Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nat Commun, 11(1):1293(2020) [pubmed]

10.1038/s41467-020-14968-9;

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

curator keyword: Biomedical

submitter keyword: non-canonical translation products, mass spectrometry,cancer immunotherapy, immunopeptidomics, antigen discovery

Michal Bassani-Sternberg
contact affiliation	Department of Oncology, University Hospital of Lausanne, Ludwig Institute for Cancer Research, Lausanne, Switzerland.
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/2020/03/PXD013649

PRIDE project URI

• PRIDE
  1. PXD013649
     1. Label: PRIDE project
     2. Name: non-canonical HLA peptides in cancer