PXD017839

PXD017839 is an original dataset announced via ProteomeXchange.

Title	Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and design of immunotherapeutics
Description	The features of peptide antigens that contribute to their immunogenicity are poorly understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a novel method which provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra- and inter-allelic differences in pMHC stability and reveals broader profiles of stability than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improved the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:15:51.960.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emma Jappe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-03 01:42:27	ID requested
1	2020-11-30 00:20:12	announced
2	2020-12-15 22:26:27	announced	2020-12-16: Updated publication reference for PubMed record(s): 33298915.
⏵ 3	2024-10-22 05:15:54	announced	2024-10-22: Updated project metadata.

Jappe EC, Garde C, Ramarathinam SH, Passantino E, Illing PT, Mifsud NA, Trolle T, Kringelum JV, Croft NP, Purcell AW, Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design. Nat Commun, 11(1):6305(2020) [pubmed]

10.1093/nar/gky1106;

submitter keyword: MHC, thermostability, immunopeptidome

Anthony Wayne Purcell
contact affiliation	Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
contact email	anthony.purcell@monash.edu
lab head
Emma Jappe
contact affiliation	Evaxion Biotech, Technical University of Denmark
contact email	emja@evaxion-biotech.com
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/2020/11/PXD017839

PRIDE project URI

• PRIDE
  1. PXD017839
     1. Label: PRIDE project
     2. Name: Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and design of immunotherapeutics