PXD036939

PXD036939 is an original dataset announced via ProteomeXchange.

Title	MHC-IP MS of EpiScan A02 SARS-CoV-2 library
Description	Identification of CD8+ T-cell epitopes is critical for the development of immunotherapeutics. Existing methods for MHC-I ligand discovery are time-intensive, specialized and unable to interrogate specific proteins on a large scale. Here we present EpiScan, which uses surface MHC-I levels as a readout for whether a genetically encoded peptide is an MHC-I ligand. Oligonucleotide synthesis permits facile screening for MHC-I ligands amongst predetermined starting pools comprising >100,000 peptides. We exploit this programmability of EpiScan to uncover an unappreciated role for cysteine that increases the number of predicted ligands by 12-21%, reveal affinity hierarchies by analysis of biased-anchor peptide libraries, and screen viral proteomes for MHC-I ligands. Using these data, we generate and iteratively refine peptide binding prediction predictions to create EpiScan Predictor, or ESP. ESP performed comparably to other state-of-the-art MHC-I peptide binding prediction algorithms while not suffering from underrepresentation of cysteine-containing peptides. Thus, targeted immunopeptidomics using EpiScan will accelerate CD8+ T-cell epitope discovery towards the goal of patient-specific immunotherapeutics.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:40:13.713.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Bruno
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-22 00:12:33	ID requested
1	2022-10-13 06:05:34	announced
⏵ 2	2024-10-22 05:40:14	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: EpiScan MHC-IP SARS-CoV-2 HLA-A*02:01

Stephen Elledge
contact affiliation	Division of Genetics, Department of Medicine, Brigham and Women's Hospital
contact email	selledge@genetics.med.harvard.edu
lab head
Peter Bruno
contact affiliation	Brigham and Women's Hospital
contact email	pbruno@bwh.harvard.edu
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/2022/10/PXD036939

PRIDE project URI

• PRIDE
  1. PXD036939
     1. Label: PRIDE project
     2. Name: MHC-IP MS of EpiScan A02 SARS-CoV-2 library