PXD019901

PXD019901 is an original dataset announced via ProteomeXchange.

Title	Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases
Description	Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed inside the cell to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of 315 overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes for the generation ofthat generate antigenic peptides, namely intracellular aminopeptidases ERAP1, ERAP2 and IRAP. Each All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with marked differences corresponding to distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 was largely highly destructive and greatly reduced limited peptides the variability of peptide sequences availableproduced for HLA-binding. Less than 710% of computationally predicted epitopes were found to be produced by enzymatic trimming experimentally, suggesting that proteolytic aminopeptidase processing may constitute a significant filter to successful epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness of predicting for viral antigenic epitopes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:30:27.665.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martina Samiotaki
SpeciesList	scientific name: SARS bat coronavirus; NCBI TaxID: 1431340;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-19 03:06:27	ID requested
1	2021-11-25 07:37:39	announced
⏵ 2	2024-10-22 05:30:28	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

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

submitter keyword: Immune system, Peptide,Enzyme, SARS, Aminopeptidase, Major Histocompatibility Molecules, Antigen, Antigen processing and presentation, Epitope, Adaptive immunity, LC-MS/MS

Efstratios Stratikos
contact affiliation	National Centre for Scientific Research Demokritos, Agia Paraskevi, Attica, Greece
contact email	stratos@rrp.demokritos.gr
lab head
Martina Samiotaki
contact affiliation	Protein Analysis Laboratory B.S.R.C. "Alexander Fleming", Alexander Fleming Street 34 16672, Vari, Greece
contact email	samiotaki@fleming.gr
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/2021/11/PXD019901

PRIDE project URI

• PRIDE
  1. PXD019901
     1. Label: PRIDE project
     2. Name: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases