PXD016865 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Human stomach LC-MSMS China Human Proteome Project |
Description | With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptide characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30±10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of independent NCE setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR≤1%, site-specific IDs with site-determining fragment ions and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767->6,746), 57% (599->942), and 97% (1771->3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method. |
HostingRepository | PRIDE |
AnnounceDate | 2020-05-11 |
AnnouncementXML | Submission_2020-05-10_22:29:44.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Yue Wang |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | complex glycosylation; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-12-20 02:25:57 | ID requested | |
⏵ 1 | 2020-05-10 22:29:45 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
ProteomeXchange project tag: China Human Proteome Project (CNHPP), Human Proteome Project |
submitter keyword: Human, Stomach, LC-MSMS, HCD, Stepped NCEs |
Contact List
Zhixin Tian |
contact affiliation | professor |
contact email | zhixintian@tongji.edu.cn |
lab head | |
Yue Wang |
contact affiliation | Tongji University |
contact email | 1710074@tongji.edu.cn |
dataset submitter | |
Full Dataset Link List
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/2020/05/PXD016865 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD016865
- Label: PRIDE project
- Name: Human stomach LC-MSMS China Human Proteome Project