PXD031032 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Re-analysis of glycoproteomics data with Glyco-Decipher |
Description | Reanalysis of submissions PXD005411, PXD005413, PXD005412, PXD005553, PXD005555, PXD005565 and PXD019937 using Glyco-Decipher. 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_22:50:47.014.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Zheng Fang |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-01-17 08:52:39 | ID requested | |
⏵ 1 | 2022-03-03 22:50:47 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Glycoproteomics |
Glycopeptide |
Reanalysis |
Glycosylation |
N-Glycosylation |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD031032
- Label: PRIDE project
- Name: Re-analysis of glycoproteomics data with Glyco-Decipher