PXD014713-2

PXD014713 is an original dataset announced via ProteomeXchange.

Title	Chemical labeling for fine mapping of IgG N-glycosylation by ETD-MS
Description	Immunoglobulin G (IgG), which contains four subclasses (IgG1-4), is one of the most important class of glycoproteins in immune system. Because of its importance in immune system, a steady increase of interest in developing IgG as biomarker or biotherapeutic agents for the treatment of diseases has been seen, as most therapeutic mAbs were IgG-based. N-glycosylation of IgG is crucial for its effector function and makes the IgG highly heterogeneous both in structure and function, although all four subclasses of IgG contain only a single N-glycosylation site in the Fc region with highly similar amino acid sequence. Therefore, fine mapping the IgG glycosylation is necessary for understanding the IgG function and avoiding aberrant glycosylation in mAbs. However, site-specific and comprehensive N-glycosylation analysis of IgG subclasses still cannot be achieved by MS alone due to the partial sequence coverage and loss of connections among glycosylation on protein sequence. We report here a chemical labeling strategy to improve the electron transfer dissociation efficiency in mass spectrometry analysis, which enable a 100% peptide sequence coverage of N-glycopeptides in all subclasses of IgG. Combining with high-energy collisional dissociation for the fragmentation of glycans, fine mapping of N-glycosylation profile of IgG is achieved. This comprehensive glycosylation analysis strategy for the first time allows the discrimination of IgG3 and IgG4 intact N-glycopeptides with high similarity in sequence without the antibody-based pre-separation. Using this strategy, aberrant serum IgG N-glycosylation for four IgG subclasses associated with cirrhosis and hepatocellular carcinoma were revealed. Moreover, this method identifies 5 times more intact glycopeptides from human serum than native-ETD method, implying that the approach can also accommodate for large-scale site-specific profiling of glycoproteomics.
HostingRepository	PRIDE
AnnounceDate	2019-12-13
AnnouncementXML	Submission_2019-12-13_04:24:13.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	zhang lei
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-23 05:50:23	ID requested
1	2019-08-26 00:58:41	announced
⏵ 2	2019-12-13 04:24:14	announced	2019-12-13: Updated publication reference for DOI(s): 10.1039/c9sc02491c.
3	2023-11-14 08:50:23	announced	2023-11-14: Updated project metadata.

10.1039/c9sc02491c;

submitter keyword: Glycosylation, Glycopeptides, Chemical labeling, Electron transfer dissociation (ETD) mass spectrometry, IgG

haojie lu
contact affiliation	Fudan University
contact email	luhaojie@fudan.edu.cn
lab head
zhang lei
contact affiliation	fudan university
contact email	zhanglei123@fudan.edu.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/2019/08/PXD014713

PRIDE project URI

• PRIDE
  1. PXD014713
     1. Label: PRIDE project
     2. Name: Chemical labeling for fine mapping of IgG N-glycosylation by ETD-MS