PXD063995-1

PXD063995 is an original dataset announced via ProteomeXchange.

Title	Comprehensive evaluation of cleavable bioorthogonal probes for site-specific O-GlcNAc proteomics
Description	O-linked β-N-acetylglucosamine (O-GlcNAc) modification (i.e., O-GlcNAcylation) on proteins is an essential modification in physiology and pathology. Although O-GlcNAcylation is functionally critical, its analysis has never been an easy task. Despite the existence of a number of methods developed in the past years, which one(s) might have the best performance is largely unclear. To that end, we proposed to conduct rigorous comparison of several cleavable bioorthogonal biotin-alkyne probes which showed promise for sensitive O-GlcNAc proteomics. In brief, we developed chemoenzymatic labeling/click chemistry-based analytical workflows for O-GlcNAc proteomics, by utilizing four cleavable bioorthogonal probes including photocleavabe-biotin-alkyne (PC-biotin-alkyne), dialkoxydiphenylsilane-biotin-alkyne (DADPS-biotin-alkyne); 1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl-biotin-alkyne (Dde-biotin-alkyne), and diazobenzene-biotin-alkyne (Diazo-biotin-alkyne). The analytical performance of the probes was evaluated with synthetic O-GlcNAc peptides and then benchmarked by mouse brain lysates for O-GlcNAc proteomics. Besides providing valuable technical insights to O-GlcNAc proteomics methods, our work yielded an unprecedented O-GlcNAc proteome depth of mouse brain. In total, 2,906 O-GlcNAc sites were unambiguously assigned on 878 proteins. Among them, 1,611 sites were newly identified, including 138 O-GlcNAcylated tyrosine residues. Our work will not only help guide selection/development of O-GlcNAc proteomics methods for future studies but also provide an invaluable resource for functional elucidation of protein O-GlcNAcylation in brain biology as well as critical insights into tyrosine O-GlcNAcylation.
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-19_18:59:30.009.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD063995
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Chunyan Hou
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-15 14:48:55	ID requested
⏵ 1	2025-10-19 18:59:31	announced

Hou C, Zhang H, Deng J, Wang X, Byers S, Levi M, Pak DTS, Moremen KW, Pei H, Hart GW, Ma J, Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics. Mol Cell Proteomics, 24(10):101064(2025) [pubmed]

10.1016/j.mcpro.2025.101064;

10.6019/PXD063995;

submitter keyword: mouse brain, O-GlcNAc, click chemistry, LC-MS/MS

Junfeng Ma
contact affiliation	Georgetown University Medical Center
contact email	Junfeng.Ma@georgetown.edu
lab head
Chunyan Hou
contact affiliation	Georgetown University
contact email	ch1363@georgetown.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/2025/10/PXD063995

PRIDE project URI

• PRIDE
  1. PXD063995
     1. Label: PRIDE project
     2. Name: Comprehensive evaluation of cleavable bioorthogonal probes for site-specific O-GlcNAc proteomics