PXD022914-1

PXD022914 is an original dataset announced via ProteomeXchange.

Title	Optimization of Protein Isolation and Label–free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng
Description	Korean ginseng is one of the most valuable medicinal plants worldwide. Yet, our understanding of ginseng proteomics is largely limited due to difficulties in extraction and resolution of ginseng proteins because of the presence of natural contaminants such as polysaccharides, phenols, and glycosides. Here, we compared four different protein extraction methods, namely, TCA/acetone, TCA/acetone–MeOH/chloroform, Phenol–TCA/acetone, and Phenol–MeOH/chloroform methods. Consequently, the TCA/acetone–MeOH/chloroform method displayed the highest extraction efficiency, thus it was used for the comparative proteome profiling of leaf, root, shoot, and fruit by a label–free quantitative proteomics approach. This approach led to the identification of 2,604 significantly modulated proteins among four tissues. We could pinpoint differential pathways and proteins associated with ginsenoside biosynthesis including the methylerythritol 4–phosphate (MEP) pathway, the mevalonate (MVA) pathway, UDP–glycosyltransferases (UGTs), and oxidoreductases (CYP450s). The current study reports an efficient and reproducible method for the isolation of proteins from a wide range of ginseng tissues and provides a detailed organ–based proteome map and a more comprehensive view of enzymatic alterations in ginsenoside biosynthesis.
HostingRepository	PRIDE
AnnounceDate	2021-09-07
AnnouncementXML	Submission_2021-09-07_04:24:39.080.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sun Tae Kim
SpeciesList	scientific name: Panax ginseng; NCBI TaxID: 4054;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-04 03:03:48	ID requested
⏵ 1	2021-09-07 04:24:40	announced

Van Nguyen T, Kim SW, Min CW, Gupta R, Lee GH, Jang JW, Rathi D, Shin HW, Jung JY, Jo IH, Hong WJ, Jung KH, Kim S, Kim YJ, Kim ST, Optimization of Protein Isolation and Label-Free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng. Plants (Basel), 10(7):(2021) [pubmed]

submitter keyword: Label–free proteomics, Panax ginseng, Ginsenosides

Cytochromes p450, UDP–glycosyltransferase, MEP pathway, MVA pathway, TCA/acetone, Methanol/chloroform

Sun Tae Kim
contact affiliation	Department of Plant Bioscience, Life and Industry Convergence Research Institute,Pusan National University, Miryang 50463, Republic of Korea
contact email	stkim5505@gmail.com
lab head
Sun Tae Kim
contact affiliation	Pusan National University
contact email	stkim5505@gmail.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/2021/09/PXD022914

PRIDE project URI

• PRIDE
  1. PXD022914
     1. Label: PRIDE project
     2. Name: Optimization of Protein Isolation and Label–free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng