PXD056001

PXD056001 is an original dataset announced via ProteomeXchange.

Title	N-glycoproteome profiling of rice
Description	Metabolic glycan labeling (MGL) is a technique that utilizes bioorthogonal chemical reporters to investigate protein glycosylation. While this method has been widely used for glycoproteomic profiling in animals, its application in N-glycoproteomic research in crops remains limited and requires further development. In this study, we employed N-azidoacetylgalactosamine (GalNAz), a click-compatible sugar, to conduct a large-scale analysis of the N-glycoproteome in rice. Using this approach, we successfully identified 426 N-glycosylation sites and 680 N-glycosylated proteins involved in various important biological processes such as metabolism and stress response. A subset of randomly selected proteins identified by mass spectrometry were validated and confirmed to be N-glycosylated, supporting the reliability of the MGL-based method for N-glycosylation identification in rice. Moreover, by combining mass spectrometry data with biochemical validation, we discovered that the core components of the ERAD-L machinery undergo N-glycosylation. Importantly, this N-glycan modification of the ERAD-L machinery is conserved across both plants and animals. Functional studies revealed the crucial role of N-glycosylation in proper protein degradation within the ERAD-L machinery. Overall, our research significantly expanded the database of N-glycoproteins in rice and presented a highly efficient and practical approach for large-scale identification of N-glycosylated proteins, which holds potential applications for identifying N-glycosylated proteins in other crops.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_02:50:37.433.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xilong Li
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	deamidated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-18 21:39:12	ID requested
⏵ 1	2025-05-07 02:50:38	announced

10.1016/j.mcpro.2024.100883;

Lei C, Li X, Li W, Chen Z, Liu S, Cheng B, Hu Y, Song Q, Qiu Y, Zhou Y, Meng X, Yu H, Zhou W, Chen X, Li J, Chemical Glycoproteomic Profiling in Rice Seedlings Reveals N-glycosylation in the ERAD-L Machinery. Mol Cell Proteomics, 24(2):100883(2025) [pubmed]

submitter keyword: Metabolic glycan labeling (MGL), N-glycosylation,Rice

Xilong Li
contact affiliation	Yazhouwan National Laboratory, Sanya 572024, China
contact email	lixilong@yzwlab.cn
lab head
Xilong Li
contact affiliation	Yazhouwan National Laboratory, Sanya, China
contact email	xilongli@genetics.ac.cn
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/2025/05/PXD056001

PRIDE project URI

• PRIDE
  1. PXD056001
     1. Label: PRIDE project
     2. Name: N-glycoproteome profiling of rice