PXD056361-1

PXD056361 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Enabling Epitope Analysis of Glycoproteins via HDX-MS Using Antigens with Uni-formed N-linked Glycans
Description	Hydrogen deuterium exchange mass spectrometry (HDX-MS) is widely used for epitope analysis of the antibod-ies. However, epitope analysis of glycoproteins is challenging because of the heterogeneity of attached N-linked glycans. Recent studies have reported methods where N-linked glycans were removed at low pH follow-ing hydrogen deuterium exchange reactions, but the methods for glycoproteins remain controversial. Here, we demonstrate the utility of using antigens with uniformed N-linked glycans in glycoprotein epitope analysis by HDX-MS. By treating HEK293 cells with kifunensine, we were able to prepare antigens mainly with N-linked high-mannose-type glycans. Analysis of epitopes of a monoclonal antibody S309 using antigens prepared with this method allowed us to identify an epitope that included the previously reported N-linked glycan attachment sites for this antibody. We propose that using antigens with uniformed glycans should be effective for epitope analysis of glycoproteins, such as virus spike proteins covered by glycan shields. Moreover, we believe that this approach accelerates research on vaccines and neutralizing antibodies against viruses that escape host immunity through glycan shields or mutations.
HostingRepository	jPOST
AnnounceDate	2025-09-27
AnnouncementXML	Submission_2025-09-26_08:00:04.487.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Masahiro Takayama
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	unknown modification; unknown modification
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-29 17:26:38	ID requested
⏵ 1	2025-09-26 08:00:04	announced

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: Hydrogen deuterium exchange mass spectrometry, HDX-MS, glycoprotein, SARS-CoV-2

submitter keyword: Hydrogen deuterium exchange mass spectrometry, HDX-MS, glycoprotein, SARS-CoV-2

Contact List

Takeshi Ota
lab head
Masahiro Takayama
contact affiliation	Shionogi & Co., Ltd.
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST dataset URI

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.jpostdb.org/JPST003389/