PXD027174

PXD027174 is an original dataset announced via ProteomeXchange.

Title	Systems analysis of plasma IgG intact N-glycopeptides from pa-tients with chronic kidney diseases via combined electron-transfer/higher-energy collisional dissociation and stepped colli-sion energy/higher-energy collisional dissociation mass spectrom-etry within half an hour
Description	Immunoglobulin G (IgG) molecules modulate an immune response. However, site-specific N-glycosylation signatures of plasma IgG in patients with chronic kidney disease (CKD) remain unclear. This study aimed to propose a novel method to explore the N-glycosylation pattern of IgG and to compare it with reported methods. We separated human plasma IgG from 58 healthy controls (HC) and 111 patients with CKD. Purified IgG molecules were digested by trypsin. Tryptic peptides with-out enrichment were analyzed using a combination of electron-transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) mass spectrometry (EThcD-sceHCD-MS/MS). This resulted in higher spectral quality, more informative fragment ions, higher Byonic score, and nearly twice the depth of intact N-glycopeptide identification than sceHCD or EThcD alone. Site-specific N-glycosylation mapping revealed that intact N-glycopeptides were differentially expressed in HC and CKD patients; thus, it can be a diagnostic tool. This study provides a method for the determination of glycosylation patterns in CKD and a framework for understanding the role of IgG in the pathophysiology of CKD.
HostingRepository	PRIDE
AnnounceDate	2021-11-25
AnnouncementXML	Submission_2021-11-25_07:35:19.709.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yong Zhang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-07 21:39:36	ID requested
⏵ 1	2021-11-25 07:35:20	announced

Dataset with its publication pending

submitter keyword: Chronic kidney disease, Immunoglobulin G, Glycosylation, LC-MS/MS

Yong Zhang
contact affiliation	West China Hospital, Sichuan University
contact email	nankai1989@fooxmail.com
lab head
Yong Zhang
contact affiliation	Sichuan University
contact email	nankai1989@foxmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027174
     1. Label: PRIDE project
     2. Name: Systems analysis of plasma IgG intact N-glycopeptides from pa-tients with chronic kidney diseases via combined electron-transfer/higher-energy collisional dissociation and stepped colli-sion energy/higher-energy collisional dissociation mass spectrom-etry within half an hour