PXD031025

PXD031025 is an original dataset announced via ProteomeXchange.

Title	Human serum glycoproteome - Glyco-Decipher
Description	Identification results of peptide-spectrum matches supporting Glyco-Decipher manuscript (Glyco-Decipher: Glycan database-independent peptide matching enables discovery of new glycans and in-depth characterization of site-specific N-glycosylation). Recently, several elegant bioinformatics tools have been developed to identify glycopeptides from tandem mass spectra for site-specific glycoproteomics studies. These glycan database-dependent tools have substantially improved glycoproteomics analysis but fail to identify glycopeptides with unexpected glycans. We present a platform called Glyco-Decipher to interpret the glycoproteomics data of N-linked glycopeptides. It adopts a glycan database-independent peptide matching scheme that allows the unbiased profiling of glycans and the discovery of new glycans linked with modifications. Reanalysis of several large-scale datasets showed that Glyco-Decipher outperformed the open search method in glycan blind searching and the popular glycan database-dependent software tools in glycopeptide identification. Our glycan database-independent search also revealed that modified glycans are responsible for a large fraction of unassigned glycopeptide spectra in shotgun glycoproteomics.
HostingRepository	PRIDE
AnnounceDate	2022-03-04
AnnouncementXML	Submission_2022-03-03_22:40:12.554.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zheng Fang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-17 01:03:06	ID requested
⏵ 1	2022-03-03 22:40:12	announced

Dataset with its publication pending

submitter keyword: Glycoproteomics

Glycopeptide

Glycosylation

N-Glycosylation

Mingliang Ye
contact affiliation	CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
contact email	mingliang@dicp.ac.cn
lab head
Zheng Fang
contact affiliation	Dalian Institute of Chemical Physics, Chinese Academy of Sciences
contact email	zhengfang@dicp.ac.cn
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/2022/03/PXD031025

PRIDE project URI

• PRIDE
  1. PXD031025
     1. Label: PRIDE project
     2. Name: Human serum glycoproteome - Glyco-Decipher