PXD011063

PXD011063 is an original dataset announced via ProteomeXchange.

Title	Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries
Description	We report a LC-MS/MS O-glycoproteomics strategy using Data Independent Acquisition (DIA) mode that holds the potential for enabling direct analysis of O-glycoproteins with characterization of sites and structures of O-glycans on a proteome-wide scale with quantification of stoichiometries. To explore the use of a DIA strategy for O-glycoproteomics, we built a spectral library of O-glycopeptides with the most common core1 O-glycan structures. This Glyco-DIA library consists of sublibraries obtained from cell lines and human serum, and it currently covers 2,076 O-glycoproteins (11,452 unique glycopeptide sequences) and the five most common core1 O-glycan structures. Applying the Glyco-DIA library to human serum without enrichment for glycopeptides enabled us to identify and quantify nearly 293 distinct glycopeptide sequences bearing up to 5 different core1 O-glycans from 159 glycoproteins in a singleshot analysis. The DIA method is expandable and widely applicable to different glycoproteomes, and it may represent the first direct and comprehensive approach to glycoproteomics.
HostingRepository	PRIDE
AnnounceDate	2019-11-27
AnnouncementXML	Submission_2019-11-27_00:30:19.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sergey Vakhrushev
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-11 08:50:41	ID requested
1	2019-08-06 02:45:22	announced
2	2019-08-08 03:21:15	announced	Updated publication reference for PubMed record(s): 31384044.
⏵ 3	2019-11-27 00:30:21	announced	2019-11-27: Updated project metadata.

Ye Z, Mao Y, Clausen H, Vakhrushev SY, Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries. Nat Methods, 16(9):902-910(2019) [pubmed]

curator keyword: Technical

submitter keyword: Glycoproteomics, Data Independent Acquisition, mass spectrometry, O-glycosylation, human serum

Sergey Vakhrushev
contact affiliation	Copenhagen Center for Glycomics, University of Copenhagen
contact email	seva@sund.ku.dk
lab head
Sergey Vakhrushev
contact affiliation	Department of Cellular and Molecular Medicine
contact email	seva@sund.ku.dk
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/2019/11/PXD011063

PRIDE project URI

• PRIDE
  1. PXD011063
     1. Label: PRIDE project
     2. Name: Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries