Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA160384

Local Sample ID:	15cm_3
Subject ID:	SU001790
Subject Type:	Plant
Subject Species:	Panax notoginseng
Taxonomy ID:	44586
Gender:	Not applicable

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Subject:

Subject ID:	SU001790
Subject Type:	Plant
Subject Species:	Panax notoginseng
Taxonomy ID:	44586
Gender:	Not applicable

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
15cm_3	SA160384	FL018806	15cm	Treatment

Collection:

Collection ID:	CO001783
Collection Summary:	Fresh fibrous root of Panax notoginseng were washed with sterile water and then flash-frozen in liquid N2
Sample Type:	Fibrous root

Treatment:

Treatment ID:	TR001803
Treatment Summary:	The experimental design for P. notoginseng cultivation is as follows: Each plastic basin (65×40×18 cm) contains about 40 kg natural soil, which was collected from a pine forest in Xundian Country, Yunnan, China (103.29°E, 25.51°N; altitude of 1960 m), then sieved to remove the residue of plant. The soil had the following characteristics: pH 5.17, electrical conductivity 458 μS cm-1, available potassium (K) 6.90 mg kg-1, available phosphate (P) 5.18 mg kg-1, alkali-hydrolyzable nitrogen (N) 172.38 mg kg-1 and organic matter 47830 mg kg-1. 4, 12, 15, 28, 45 healthy one-year old seedlings were planted in January 3, 2016 at a plant spacing of 30 cm, 20 cm, 15 cm, 10 cm and 8 cm, respectively. There were four repeats for each treatment, and a total of 20 plastic basins were placed in a completely randomized block design in greenhouse. The fresh fibrous root of P. notoginseng was collected in November 30, 2016.

Treatment ID:

TR001803

Treatment Summary:

The experimental design for P. notoginseng cultivation is as follows: Each plastic basin (65×40×18 cm) contains about 40 kg natural soil, which was collected from a pine forest in Xundian Country, Yunnan, China (103.29°E, 25.51°N; altitude of 1960 m), then sieved to remove the residue of plant. The soil had the following characteristics: pH 5.17, electrical conductivity 458 μS cm-1, available potassium (K) 6.90 mg kg-1, available phosphate (P) 5.18 mg kg-1, alkali-hydrolyzable nitrogen (N) 172.38 mg kg-1 and organic matter 47830 mg kg-1. 4, 12, 15, 28, 45 healthy one-year old seedlings were planted in January 3, 2016 at a plant spacing of 30 cm, 20 cm, 15 cm, 10 cm and 8 cm, respectively. There were four repeats for each treatment, and a total of 20 plastic basins were placed in a completely randomized block design in greenhouse. The fresh fibrous root of P. notoginseng was collected in November 30, 2016.

Sample Preparation:

Sampleprep ID:	SP001796
Sampleprep Summary:	Approximately 60 mg of frozen powder fibrous roots and 1 mL of methanol (CH3OH) containing 0.5 mg of ribitol were added into a prechilled 2 mL lock-cap centrifuge tube, then vortexed for 10 s. A 300 μL extraction aliquot (H2O:methanol:chloroform=1:2.5:1, v:v:v) was added and ultrasonically extracted for 30 min at 37°C. Then, the sample was centrifuged (1600 g, 3 min) to separate the polar and nonpolar phases. Then the upper polar phase was transferred to a fresh centrifuge tube and added 200 μL sterile water, and then vortexed and centrifuged (1600 g, 4°C for 3 min). A 250 μL aliquot of the upper phase was transferred to a fresh centrifuge tube, dried for 3-4 h at room temperature using a SpeedVac (Christ, Germany). Adding 80 μL of methoxyamine hydrochloride solution (20 mg mL-1 dissolved in pyridine) to each sample and incubating for 90 min at 30°C to protect carbonyl moieties. And then, 40 μL N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) was added and incubating at 37°C for 30 min to trimethylsilylate the acidic protons. After this step, the sample was centrifuged (1600 g, 4°C for 3 min), then the supernatant was stored at 4°C for further analysis.

Sampleprep ID:

SP001796

Sampleprep Summary:

Approximately 60 mg of frozen powder fibrous roots and 1 mL of methanol (CH3OH) containing 0.5 mg of ribitol were added into a prechilled 2 mL lock-cap centrifuge tube, then vortexed for 10 s. A 300 μL extraction aliquot (H2O:methanol:chloroform=1:2.5:1, v:v:v) was added and ultrasonically extracted for 30 min at 37°C. Then, the sample was centrifuged (1600 g, 3 min) to separate the polar and nonpolar phases. Then the upper polar phase was transferred to a fresh centrifuge tube and added 200 μL sterile water, and then vortexed and centrifuged (1600 g, 4°C for 3 min). A 250 μL aliquot of the upper phase was transferred to a fresh centrifuge tube, dried for 3-4 h at room temperature using a SpeedVac (Christ, Germany). Adding 80 μL of methoxyamine hydrochloride solution (20 mg mL-1 dissolved in pyridine) to each sample and incubating for 90 min at 30°C to protect carbonyl moieties. And then, 40 μL N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) was added and incubating at 37°C for 30 min to trimethylsilylate the acidic protons. After this step, the sample was centrifuged (1600 g, 4°C for 3 min), then the supernatant was stored at 4°C for further analysis.

Combined analysis:

Analysis ID	AN002788
Analysis type	MS
Chromatography type	GC
Chromatography system	Shimadzu GCMS-QP2010 ultra
Column	Agilent HP5-MS (30m x 0.25mm, 0.25 um)
MS Type	EI
MS instrument type	GC-TOF
MS instrument name	Shimadzu QP2010 Ultra
Ion Mode	UNSPECIFIED
Units	Peak area

Chromatography:

Chromatography ID:	CH002063
Instrument Name:	Shimadzu GCMS-QP2010 ultra
Column Name:	Agilent HP5-MS (30m x 0.25mm, 0.25 um)
Chromatography Type:	GC

MS:

MS ID:	MS002584
Analysis ID:	AN002788
Instrument Name:	Shimadzu QP2010 Ultra
Instrument Type:	GC-TOF
MS Type:	EI
MS Comments:	Mass spectra were obtained in electron impact (EI) ionization mode at 70 eV by monitoring the full-scan range (m/z 45-600);the raw peak obtained by data baseline filtering and calibration, peak alignment, deconvolution analysis and peak identification using MS-DIAL with the Fiehn library. The peak areas of metabolites in raw MS-Dial output (Supplementary Table S2) were normalization by sum, transformation by log and scaling by Pareto method on Metaboanalyst 4.0 (http://www.metaboanalyst.ca/MetaboAnalyst/)
Ion Mode:	UNSPECIFIED