PXD016865

PXD016865 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-20 02:25:57	ID requested
⏵ 1	2020-05-10 22:29:45	announced

Dataset with its publication pending

ProteomeXchange project tag: China Human Proteome Project (CNHPP), Human Proteome Project

submitter keyword: Human, Stomach, LC-MSMS, HCD, Stepped NCEs

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

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

• PRIDE
  1. PXD016865
     1. Label: PRIDE project
     2. Name: Human stomach LC-MSMS China Human Proteome Project