Summary of Study ST003307

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002057. The data can be accessed directly via it's Project DOI: 10.21228/M8QN7M This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003307
Study TitleUntargeted metabolomics of rhizosphere soil from 4-years Panax ginseng that was treated with endo-borneol under field condition
Study SummaryTo study the rhizosphere soil matabolism of 4-years Panax ginseng that were leaf-sprayed with endo-borneol at different concentrations (0, 0.1 mg/L, and 100 mg/L) under field condition, liquid chromarography tandem mass spectrometry was used for examination. Each treatment is set with 6 replicates for assessing nontargeted metabolomics. The LC-MS/MS analysis was performed using a Thermo UHPLC-Q Exactive HF-X system equipped with an ACQUITY HSS T3 column. As a result, a total of 296 and 569 metabolites were identified in negative ion mode and positive mode, respectively.
Institute
Yunnan University
DepartmentSchool of Agriculture
LaboratoryKey Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China
Last NameXing-Yu
First NameJi
AddressRoad Fengyuan, District Panlong, Kunming, Yunnan, China
Emailxingyu.ji@hotmail.com
Phone＋86-13354989110
Submit Date2024-06-03
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-07-15
Release Version1
Ji Xing-Yu Ji Xing-Yu
https://dx.doi.org/10.21228/M8QN7M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002057
Project DOI:doi: 10.21228/M8QN7M
Project Title:Use of untargeted metabolomics for assessing soil from Panax ginseng that were leaf-sprayed with endo-borneol
Project Summary:To study the rhizosphere soil matabolism of 4-years Panax ginseng that wereleaf-sprayed with endo-borneol at different concentrations (0, 0.1 mg/L, and 100 mg/L) under field condition, liquid chromarography tandem mass spectrometry was used for examination. Each treatment is set with 6 replicates for assessing nontargeted metabolomics. The LC-MS/MS analysis was performed using a Thermo UHPLC-Q Exactive HF-X system equipped with an ACQUITY HSS T3 column. As a result, a total of 296 and 569 metabolites were identified in negative ion mode and positive mode, respectively.
Institute:Yunnan University
Department:School of Agriculture
Laboratory:State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
Last Name:Ji
First Name:Xing-Yu
Address:Yuhua Road, Chenggong, Kunming, Yunnan Province, 650100, China
Email:xingyu.ji@hotmail.com
Phone:＋86-13354989110
Funding Source:Natural Science Foundation of China
Project Comments:U23A20202
Publications:still under review
Contributors:Xing-Yu Ji, Shusheng Zhu

Subject:

Subject ID:SU003428
Subject Type:Soil sample

Factors:

Subject type: Soil sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id endo-borneol concentration Sample source
SA358657T3_6_pos0.1 mg/L soil
SA358658CK_5_neg0.1 mg/L soil
SA358659CK_6_neg0.1 mg/L soil
SA358660T3_1_neg0.1 mg/L soil
SA358661T3_2_neg0.1 mg/L soil
SA358662T3_3_neg0.1 mg/L soil
SA358663T3_4_neg0.1 mg/L soil
SA358664T3_5_pos0.1 mg/L soil
SA358665T3_4_pos0.1 mg/L soil
SA358666T3_3_pos0.1 mg/L soil
SA358667T3_2_pos0.1 mg/L soil
SA358668T3_1_pos0.1 mg/L soil
SA358669CK_6_pos0.1 mg/L soil
SA358670CK_5_pos0.1 mg/L soil
SA358671T3_5_neg0.1 mg/L soil
SA358672T3_6_neg0.1 mg/L soil
SA358673CK_2_neg0 soil
SA358674CK_4_neg0 soil
SA358675CK_3_neg0 soil
SA358676CK_1_pos0 soil
SA358677CK_2_pos0 soil
SA358678CK_4_pos0 soil
SA358679CK_3_pos0 soil
SA358680CK_1_neg0 soil
SA358681T7_6_pos100 mg/L soil
SA358682T7_6_neg100 mg/L soil
SA358683T7_5_neg100 mg/L soil
SA358684T7_4_neg100 mg/L soil
SA358685T7_3_neg100 mg/L soil
SA358686T7_2_neg100 mg/L soil
SA358687T7_1_neg100 mg/L soil
SA358688T7_1_pos100 mg/L soil
SA358689T7_2_pos100 mg/L soil
SA358690T7_3_pos100 mg/L soil
SA358691T7_4_pos100 mg/L soil
SA358692T7_5_pos100 mg/L soil
SA358693QC3_posQC soil
SA358694QC2_posQC soil
SA358695QC1_negQC soil
SA358696QC2_negQC soil
SA358697QC3_negQC soil
SA358698QC1_posQC soil
Showing results 1 to 42 of 42

Collection:

Collection ID:CO003421
Collection Summary:Rhizosphere soil samples were collected from Panax ginseng that were leaf sprayed with endo-borneol at 0, 0.1, 100 mg/L. The samples were snap-frozen using liquid nitrogen and stored in -80°C for metabolism analysis.
Sample Type:Soil
Collection Method:Gently brushed from the roots of Panax ginseng
Collection Location:Laobiangou, County Benxi, Liaoning, China
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003437
Treatment Summary:Panax ginseng were leaf sprayed with endo-borneol at 0, 0.1, 100 mg/L from July to August, 2021. Six replicates were set for each group as six plots.Then the rhizosphere soil of Panax ginseng from each treatment was collected.

Sample Preparation:

Sampleprep ID:SP003435
Sampleprep Summary:50 mg solid sample was added to a 2 mL centrifuge tube and a 6 mm diameter grinding bead was added. 400 μL of extraction solution (methanol: water = 4:1 (v:v)) containing 0.02 mg/mL of internal standard (L-2-chlorophenylalanine) was used for metabolite extraction. Samples were ground by the Wonbio-96c (Shanghai wanbo biotechnology co., ltd) frozen tissue grinder for 6 min (-10°C, 50 Hz), followed by low-temperature ultrasonic extraction for 30 min (5°C, 40 kHz). The samples were left at -20°C for 30 min, centrifuged for 15 min (4°C, 13000 g), and the supernatant was transferred to the injection vial for LC-MS/MS analysis.

Combined analysis:

Analysis ID AN005418 AN005419
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Horizon Thermo Vanquish Horizon
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH004108
Instrument Name:Thermo Vanquish Horizon
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40℃
Flow Gradient:0-3 min: 0-20% B, 3-9 min: 20-60% B, 9-11 min: 60-100% B, maintain for 2.5 min, 13.5-13.6 min: 100% to 0% B, maintain for 2.4 min
Flow Rate:0.40 mL/min
Solvent A:95% water/5% acetonitrile; 0.1% formic acid
Solvent B:47.5% acetonitrile/47.5% isopropanol/5% water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005144
Analysis ID:AN005418
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Full MS resolution was 60000, and MS/MS resolution was 7500. Data acquisition was performed with the Data Dependent Acquisition (DDA) mode. The detection was carried out over a mass range of 70-1050 m/z.
Ion Mode:POSITIVE
  
MS ID:MS005145
Analysis ID:AN005419
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Full MS resolution was 60000, and MS/MS resolution was 7500. Data acquisition was performed with the Data Dependent Acquisition (DDA) mode. The detection was carried out over a mass range of 70-1050 m/z.
Ion Mode:NEGATIVE
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