PXD046543

PXD046543 is an original dataset announced via ProteomeXchange.

Title	Thunder-DDA-PASEF boosted by MS2rescore enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCoV-2 spike protein epitopes
Description	Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). The optimized method, Thunder-DDA-PASEF, semi-selectively fragments HLAIps based on their IMS and m/z, thus increasing the coverage of immunopeptidomics analyses. Thunder-DDA-PASEF includes singly-charged peptides, which contribute to more than 35% of the HLAIp identifications. Combined with MS2Rescore, Thunder-DDA-PASEF improved ligandome coverage by 150% compared to the Standard-DDA-PASEF method, and enabled in-depth profiling of HLAIps from two human cell lines, JY and Raji, transfected to express the SARS-CoV-2 spike protein. We identified 16 spike protein HLAIps, thirteen of which had been reported to elicit immune responses in human patients.
HostingRepository	PRIDE
AnnounceDate	2024-03-19
AnnouncementXML	Submission_2024-03-19_12:59:10.726.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeewan Babu Rijal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-31 10:43:11	ID requested
⏵ 1	2024-03-19 12:59:11	announced

10.1038/S41467-024-46380-Y;

submitter keyword: MS2Rescore,Immunopeptidomics, Thunder-DDA-PASEF, timsTOF pro

Christine Carapito
contact affiliation	BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS
contact email	ccarapito@unistra.fr
lab head
Jeewan Babu Rijal
contact affiliation	BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS
contact email	jeewan-babu.rijal@etu.unistra.fr
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/2024/03/PXD046543

PRIDE project URI

• PRIDE
  1. PXD046543
     1. Label: PRIDE project
     2. Name: Thunder-DDA-PASEF boosted by MS2rescore enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCoV-2 spike protein epitopes