PXD005181-2

PXD005181 is an original dataset announced via ProteomeXchange.

Title	Specific mixing facilitates the comparative quantification of phosphorylation sites with significant dysregulations
Description	It is still a big challenge to accurately quantify the proteins or proteins PTM sites with extreme relative abundances in comparative protein samples, such as the significantly dysregulated ones. Herein, a novel quantification strategy, Mixing at Specific Ratio (MaSR) before isotope labeling, had been developed to improve the quantification accuracy and coverage of extreme proteins and protein phosphorylation sites. Briefly, the comparative protein samples were firstly mixed together at specific ratios of 9:1 and 1:9 (w/w), followed with mass differentiate light and heavy isotope labeling, respectively. The extreme proteins and protein phosphorylation sites, even if the newly expressed or disappeared ones, could be accurately quantified due to all of the proteins’ relative abundances had been adjusted to 2 orders of magnitude (1/9-9) by this strategy. The number of quantified phosphorylation sites with more than 20 folds changes was improved about 10 times in comparative quantification of pervanadate stimulated phosphoproteome of HeLa cells.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:10.737.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jing Liu
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-18 08:52:45	ID requested
1	2016-12-06 01:14:04	announced
⏵ 2	2023-11-14 08:49:11	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Technical

submitter keyword: LC-MSMS, mixing at specific ratio,comparative phosphoproteome quantification, stable isotope labeling, extreme relative abundance

Fangjun Wang
contact affiliation	Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS)
contact email	Wangfj@dicp.ac.cn
lab head
Jing Liu
contact affiliation	Dalian Medical University
contact email	liujing8166@163.com
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/2016/12/PXD005181

PRIDE project URI

• PRIDE
  1. PXD005181
     1. Label: PRIDE project
     2. Name: Specific mixing facilitates the comparative quantification of phosphorylation sites with significant dysregulations