PXD006939

PXD006939 is an original dataset announced via ProteomeXchange.

Title	High-throughput MS-based immunopeptidomics
Description	Comprehensive knowledge of the HLA class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their extraction for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential extraction of HLA-I and -II peptides from up to 96 samples in a plate format from cell lines or tissues. Our methodology drastically reduces sample-handling and can be completed within six hours. We report identification and quantification of thousands of peptides with excellent reproducibility (Pearson correlations reaching 0.98 and 0.97, class I and II, respectively). Due to improved sensitivity, as many as 1,846 HLA-I and 2,633 HLA-II peptides were accurately identified from only 107 B-cells. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma. This straightforward method is applicable for basic and clinical applications.
HostingRepository	PRIDE
AnnounceDate	2017-12-15
AnnouncementXML	Submission_2018-05-23_07:11:36.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	2017-07-11 07:33:42	ID requested
1	2017-12-15 04:49:47	announced
⏵ 2	2018-05-23 07:11:38	announced	Updated publication reference for PubMed record(s): 29242379.

Chong C, Marino F, Pak H, Racle J, Daniel RT, M, ü, ller M, Gfeller D, Coukos G, Bassani-Sternberg M, -Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics, 17(3):533-548(2018) [pubmed]

submitter keyword: HLA peptides, HLA-I, HLA-II, affinity purification, LC-MS/MS

Michal Bassani-Sternberg
contact affiliation	Head / Immunopeptidomics unit Department of Oncology,CHUV Ludwig Cancer Research Center
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/2017/12/PXD006939

PRIDE project URI

• PRIDE
  1. PXD006939
     1. Label: PRIDE project
     2. Name: High-throughput MS-based immunopeptidomics