PXD030622

PXD030622 is an original dataset announced via ProteomeXchange.

Title	Comprehensive human plasma N-glycoproteome profiling based on EThcD-sceHCD-MS/MS
Description	N-glycoproteins are involved in various biological processes. More than one-third of plasma tumor protein biomarkers approved by the Food and Drug Administration (FDA) are glycoproteins which would enhance the specificity and/or sensitivity of cancer diagnosis. Therefore, the characterization of plasma N-glycoproteome is essential. In previous studies, we developed an integrated method based on combinatorial peptide ligands library (CPLL) and stepped collision energy/higher-energy collisional dissociation (sceHCD) for in-depth and comprehensive N‑glycoproteome profiling of human plasma. Recently, we presented a new mass spectrometry fragmentation method (EThcD-sceHCD) which outperformed sceHCD in the accuracy of identification. Herein, we integrated CPLL into EThcD-sceHCD, and compared the performance of EThcD-sceHCD with those previous approaches (EThcD and sceHCD) in pooled prostatic cancer (PCa) patients’ plasma intact N-glycopeptide analysis. We found that EThcD-sceHCD outperformed other methods in both the depth and accuracy of intact N-glycopeptides identification, and sceHCD and EThcD-sceHCD have good complementarity. Combining sceHCD and EThcD-sceHCD can cover almost all glycoproteins and intact N-glycopeptides. Our study holds great potential for human plasma biomarker discovery.
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-11_23:36:34.807.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	2021-12-23 00:41:46	ID requested
⏵ 1	2022-08-11 23:36:35	announced

Mao Y, Su T, Lin T, Yang H, Zhao Y, Zhang Y, Dai X, Comprehensive Plasma N-Glycoproteome Profiling Based on EThcD-sceHCD-MS/MS. Front Chem, 10():920009(2022) [pubmed]

submitter keyword: Mass Spectrometry

Human plasma

N-glycoproteomics

Combinatorial Peptide Ligands Library

EThcD-sceHCD

Yong Zhang
contact affiliation	West China Hospital, Sichuan University
contact email	nankai1989@foxmail.com
lab head
Yong Zhang
contact affiliation	Sichuan University
contact email	nankai1989@foxmail.com
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/2022/08/PXD030622

PRIDE project URI

• PRIDE
  1. PXD030622
     1. Label: PRIDE project
     2. Name: Comprehensive human plasma N-glycoproteome profiling based on EThcD-sceHCD-MS/MS