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PXD016865

PXD016865 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHuman stomach LC-MSMS China Human Proteome Project
DescriptionWith 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.
HostingRepositoryPRIDE
AnnounceDate2020-05-11
AnnouncementXMLSubmission_2020-05-10_22:29:44.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterYue Wang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListcomplex glycosylation; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-12-20 02:25:57ID requested
12020-05-10 22:29:45announced
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 affiliationprofessor
contact emailzhixintian@tongji.edu.cn
lab head
Yue Wang
contact affiliationTongji University
contact email1710074@tongji.edu.cn
dataset submitter
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Dataset FTP location
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PRIDE project URI
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