PXD023980

PXD023980 is an original dataset announced via ProteomeXchange.

Title	GproDIA enables intact glycopeptide characterization using data‐independent acquisition glycoproteomics with comprehensive statistical control
Description	Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomic studies, but is still in the early stage of development in the field of glycoproteomics. We propose GlycoSWATH, a pipeline for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptide using wide isolation windows. We further adapt a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GlycoSWATH outperforms the state-of-the-art DDA method for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.
HostingRepository	iProX
AnnounceDate	2021-06-22
AnnouncementXML	Submission_2021-09-08_20:59:47.357.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yi Yang
SpeciesList	scientific name: Schizosaccharomyces pombe; NCBI TaxID: 4896; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	N-glycosylated residue; acetylated residue; oxidation
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-03 20:47:45	ID requested
⏵ 1	2021-09-08 20:59:47	announced

Dataset with its publication pending

submitter keyword: glycoproteomics,intact glycopeptide,data-independent acquisition

Liang Qiao
contact affiliation	Fudan University
contact email	liang_qiao@fudan.edu.cn
lab head
Yi Yang
contact affiliation	Fudan University
contact email	13307110210@fudan.edu.cn
dataset submitter

iProX dataset URI