MassIVE MSV000096403

Complete Public PXD057852

Characterization of site-specific O- and N-glycopeptides from recombinant spike and ACE2 glycoproteins using LC-MS/MS analysis

Subscribe Comment Reanalyze Spectra Compare Results Add Reanalysis

Description

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of infections and deaths globally. Although vaccination campaigns are mitigating the pandemic, emerging viral variants continue to pose challenges. The spike (S) protein of SARS-CoV-2 plays a critical role in viral entry by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, making both proteins essential targets for therapeutic and vaccine development. Glycosylation of these proteins influences their structure and function, underscoring the need for detailed site-specific glycoproteomic analysis. In this study, we characterized the N- or O-glycosylation profiles of recombinant receptor-binding domain (RBD) of spike protein and ACE2 proteins expressed from HEK293 cells, as well as S2 subunit of spike protein expressed in plants cells. Using a high-resolution Orbitrap Eclipse Tribrid mass spectrometer integrated with the Ultimate 3000 RSLCnano and IQ-GPA (Identification and Quantification of GlycoProteome Analyzer), 148 N- and 28 O-glycopeptides from RBD, 71 N-glycopeptides from the S2 subunit, and 139 N-glycopeptides from ACE2 were characterized. Additionally, we report novel post-translational modifications (PTMs) in RBD glycopeptides, including mannose-6-phosphate (M6P) and GlcNAc-1-phosphate-6-O-mannose of N-glycan, and O-acetylation of O-glycan, identified for the first time. These findings provide valuable insights into the glycosylation patterns that influence protein function and immunogenicity, offering new perspectives for the development of vaccines and antibody-based therapies against COVID-19. [doi:10.25345/C5891232M] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Spike glycoprotein ; Reaction Binding Domain ; Recombinant proteins ; site-specific glycopeptides ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Ju Yeon Lee, Korea Basic Science Institute, Republic of Korea
Submitting User: juyeon4444

Publications

Song JH, Jang S, Choi JW, Hwang S, Kim KH, Kim HY, Park SC, Lee W, Lee JY.
Characterization of Site-Specific N- and O-Glycopeptides from Recombinant Spike and ACE2 Glycoproteins Using LC-MS/MS Analysis.
Int J Mol Sci. Epub 2024 Dec 20.

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files Browse Results
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.