PXD054874

PXD054874 is an original dataset announced via ProteomeXchange.

Title	Improving quantitative glycoproteomics by systematic evaluation of different glycopeptide enrichment, quantification, and mass spectrometry strategies
Description	In this study, we conducted a systematic investigation into a glycoproteomic workflow. Firstly, Label-free and TMT labeling strategies were utilized for intact N-glycopeptide quantification. A total of 2,924 unique intact N-glycopeptides can be quantified after being labeled using TMT approach. Compared to label-free method, TMT labeling for its high precision with the CV averaging 8% and multiplex analysis capabilities. Subsequently, we compared the capacity of ZIC-HILIC and MAX enrichment methods, revealing that the ZIC- HILIC method demonstrated superior performance in enriching intact N-glycopeptides, which can identify 3,004 GPSMs from a single injection of patient-derived xenograft (PDX) sample. Furthermore, we systematically evaluated different higher-energy collisional dissociation (HCD) collision energies, determining that the stepped collision energy HCD (sceHCD) settings of 25, 35, and 45 was the optimal for both the identification and quantification of intact N-glycopeptides.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_00:27:24.160.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhenyu Sun
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Exploris 480; Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-14 02:50:38	ID requested
⏵ 1	2025-05-07 00:27:24	announced

10.1021/acs.analchem.4c04466;

Sun Z, Lih TM, Woo J, Jiao L, Hu Y, Wang Y, Liu H, Zhang H, Improving Glycoproteomic Analysis Workflow by Systematic Evaluation of Glycopeptide Enrichment, Quantification, Mass Spectrometry Approach, and Data Analysis Strategies. Anal Chem, 96(52):20481-20490(2024) [pubmed]

submitter keyword: glycoproteomics, intact glycopeptide, identification, quantification

Hui Zhang
contact affiliation	Johns Hopkins School of Medicine
contact email	huizhang@jhu.edu
lab head
Zhenyu Sun
contact affiliation	Johns Hopkins University School of Medicine
contact email	zsun51@jh.edu
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/PXD054874

PRIDE project URI

• PRIDE
  1. PXD054874
     1. Label: PRIDE project
     2. Name: Improving quantitative glycoproteomics by systematic evaluation of different glycopeptide enrichment, quantification, and mass spectrometry strategies