PXD022914 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-12-04 03:03:48 | ID requested | |
⏵ 1 | 2021-09-07 04:24:40 | announced | |
Publication List
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] |
Keyword List
submitter keyword: Label–free proteomics, Panax ginseng, Ginsenosides |
Cytochromes p450, UDP–glycosyltransferase, MEP pathway, MVA pathway, TCA/acetone, Methanol/chloroform |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022914
- Label: PRIDE project
- Name: Optimization of Protein Isolation and Label–free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng