PXD016428-1

PXD016428 is an original dataset announced via ProteomeXchange.

Title	Glyco-CPLL: an integrated method for in-depth and comprehensive N-glycoproteome profiling of human plasma
Description	N-glycoproteins are involved in various biological processes. Certain distinctive glycoforms on specific glycoproteins enhance the specificity and/or sensitivity of cancer diagnosis. Therefore, the characterization of plasma N-glycoproteome is essential for new biomarker discovery. Absence of suitable analytical methods for in-depth and large-scale analyses of low-abundance plasma glycoproteins make it challenging to investigate the role of glycosylation. In this study, we developed an integrated method termed Glyco-CPLL, which integrates combinatorial peptide ligand libraries, high-pH reversed-phase pre-fractionation, hydrophilic interaction chromatography, trypsin and PNGase F digestion, shotgun proteomics, and various analysis software (MaxQuant and pGlyco2.0) for the low-abundance plasma glycoproteomic profiling. Then, we utilized the method to perform a comparative study and to explore papillary thyroid carcinoma-related proteins and glycosylations with reference to healthy controls. Finally, a large and comprehensive human plasma N-glycoproteomic database was established, containing 786 proteins, 369 N-glycoproteins, 862 glycosites, 171 glycan compositions, and 1644 unique intact N-glycopeptides. Additionally, several low-abundance plasma glycoproteins were identified, including SVEP1 (~0.54 ng/mL), F8 (~0.83 ng/mL), ADAMTS13 (~1.2 ng/mL). These results suggest that this method will be useful for analyzing plasma intact glycopeptides in future studies. Besides, the Glyco-CPLL method has a great potential to be translated to clinical applications.
HostingRepository	PRIDE
AnnounceDate	2020-01-09
AnnouncementXML	Submission_2020-01-09_02:04:23.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	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-25 02:11:57	ID requested
⏵ 1	2020-01-09 02:04:25	announced
2	2024-10-22 05:00:05	announced	2024-10-22: Updated project metadata.

Zhang Y, Mao Y, Zhao W, Su T, Zhong Y, Fu L, Zhu J, Cheng J, Yang H, Glyco-CPLL: An Integrated Method for In-Depth and Comprehensive N-Glycoproteome Profiling of Human Plasma. J Proteome Res, 19(2):655-666(2020) [pubmed]

submitter keyword: Mass Spectrometry

Papillary Thyroid Carcinoma

N-glycoproteomics

Combinatorial Peptide Ligands Library

Yong Zhang
contact affiliation	Sichuan University,West China Hospital
contact email	nankai1989@foxmail.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. PXD016428
     1. Label: PRIDE project
     2. Name: Glyco-CPLL: an integrated method for in-depth and comprehensive N-glycoproteome profiling of human plasma