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. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST003307
Study Title	Untargeted metabolomics of rhizosphere soil from 4-years Panax ginseng that was treated with endo-borneol under field condition
Study Summary	To 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
Department	School of Agriculture
Laboratory	Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China
Last Name	Xing-Yu
First Name	Ji
Address	Road Fengyuan, District Panlong, Kunming, Yunnan, China
Email	xingyu.ji@hotmail.com
Phone	＋86-13354989110
Submit Date	2024-06-03
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2024-07-15
Release Version	1

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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
SA358673	CK_2_neg	0
SA358674	CK_4_neg	0
SA358675	CK_3_neg	0
SA358676	CK_1_pos	0
SA358677	CK_2_pos	0
SA358678	CK_4_pos	0
SA358679	CK_3_pos	0
SA358680	CK_1_neg	0
SA358657	T3_6_pos	0.1 mg/L
SA358658	CK_5_neg	0.1 mg/L
SA358659	CK_6_neg	0.1 mg/L
SA358660	T3_1_neg	0.1 mg/L
SA358661	T3_2_neg	0.1 mg/L
SA358662	T3_3_neg	0.1 mg/L
SA358663	T3_4_neg	0.1 mg/L
SA358664	T3_5_pos	0.1 mg/L
SA358665	T3_4_pos	0.1 mg/L
SA358666	T3_3_pos	0.1 mg/L
SA358667	T3_2_pos	0.1 mg/L
SA358668	T3_1_pos	0.1 mg/L
SA358669	CK_6_pos	0.1 mg/L
SA358670	CK_5_pos	0.1 mg/L
SA358671	T3_5_neg	0.1 mg/L
SA358672	T3_6_neg	0.1 mg/L
SA358681	T7_6_pos	100 mg/L
SA358682	T7_6_neg	100 mg/L
SA358683	T7_5_neg	100 mg/L
SA358684	T7_4_neg	100 mg/L
SA358685	T7_3_neg	100 mg/L
SA358686	T7_2_neg	100 mg/L
SA358687	T7_1_neg	100 mg/L
SA358688	T7_1_pos	100 mg/L
SA358689	T7_2_pos	100 mg/L
SA358690	T7_3_pos	100 mg/L
SA358691	T7_4_pos	100 mg/L
SA358692	T7_5_pos	100 mg/L
SA358693	QC3_pos	QC
SA358694	QC2_pos	QC
SA358695	QC1_neg	QC
SA358696	QC2_neg	QC
SA358697	QC3_neg	QC
SA358698	QC1_pos	QC

Showing results 1 to 42 of 42

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.

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
Chromatography ID	CH004108	CH004108
MS ID	MS005144	MS005145
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