Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA242932

Local Sample ID:	OilPalm_Drought_Control_R3_POS
Subject ID:	SU002519
Subject Type:	Plant
Subject Species:	Elaeis guineensis Jacq.
Taxonomy ID:	NCBI:txid51953

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Subject:

Subject ID:	SU002519
Subject Type:	Plant
Subject Species:	Elaeis guineensis Jacq.
Taxonomy ID:	NCBI:txid51953

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
OilPalm_Drought_Control_R3_POS	SA242932	FL030407	Control	Group

Collection:

Collection ID:	CO002512
Collection Summary:	The oil palm plants used in this study are clones of the ones used in the Bittencourt et al. (2022) study. All plants—from both studies—came from the same embryogenic calluses. The young oil palm plants used in both studies were clones regenerated out of embryogenic calluses obtained from the leaves of an adult plant—genotype AM33, a Deli x Ghana from ASD Costa Rica; and were subjected to treatments when they were in the growth stage known as “bifid” saplings. Before starting the experiments, plants were standardized according to their developmental stage, size, and the number of leaves. The experiment consisted of two water availability levels (field capacity—control and water deprivation—stressed), with four replicates in a completely randomized design. For the metabolomics analysis, we collected the apical leaves from control and stressed plants 14 days after imposing the treatments (DAT).
Sample Type:	Plant

Treatment:

Treatment ID:	TR002531
Treatment Summary:	The experiment consisted of treatments—control and drought-stressed plants—with four plants kept in a substrate in the field capacity (control), and four plants submitted to drought stress. The young oil palm plants were subjected to treatments when they were in the growth stage known as “bifid” saplings. Drought stress consisted of total suppression of irrigation for 14 consecutive days. At the end of this period, the substrate water potential, as measured by the water potential meter Decagon mod. WP4C (Decagon Devices, Pullman, WA, USA), was 0.19 ± 0.03 MPa (control) and − 13.61 ± 1.79 MPa (drought stress), while the relative water content of leaves was 90.50 ± 0.95% (control) and 49.18 ± 9.76% (stressed plants). Before the onset of drought stress, oil palm leaves had the highest gas exchange rates, as measured by an infrared gas analyzer Li-Cor model 6400XT (Li-Cor, Lincoln, NE, USA). Under drought, leaf gas exchange rates in drought-stressed plants dropped to negligible values (data not shown).

Treatment ID:

TR002531

Treatment Summary:

The experiment consisted of treatments—control and drought-stressed plants—with four plants kept in a substrate in the field capacity (control), and four plants submitted to drought stress. The young oil palm plants were subjected to treatments when they were in the growth stage known as “bifid” saplings. Drought stress consisted of total suppression of irrigation for 14 consecutive days. At the end of this period, the substrate water potential, as measured by the water potential meter Decagon mod. WP4C (Decagon Devices, Pullman, WA, USA), was 0.19 ± 0.03 MPa (control) and − 13.61 ± 1.79 MPa (drought stress), while the relative water content of leaves was 90.50 ± 0.95% (control) and 49.18 ± 9.76% (stressed plants). Before the onset of drought stress, oil palm leaves had the highest gas exchange rates, as measured by an infrared gas analyzer Li-Cor model 6400XT (Li-Cor, Lincoln, NE, USA). Under drought, leaf gas exchange rates in drought-stressed plants dropped to negligible values (data not shown).

Sample Preparation:

Sampleprep ID:	SP002525
Sampleprep Summary:	Leaf samples with approximately 50 mg were collected for the metabolomics analysis; four replicates per plant. After harvesting, samples were immediately frozen in liquid nitrogen and stored at − 80 °C until metabolites extraction and analysis. Each sample was ground in a ball mill (Biospec Products, USA) before solvent extraction. Metabolites were extracted using an adapted protocol from The Max Planck Institute, called All-in-One, which provides a polar fraction for secondary metabolite analysis, a nonpolar fraction for lipidomics, and a protein pellet for proteomics; all obtained from the same plant sample. Each ground sample was added to a microtube and mixed with 1 mL of a methanol and methyl-tert-butyl-ether (1:3) solution at − 20°C. After homogenization, they were incubated at 4 °C for 10 min. Each microtube was ultrasonicated in an ice bath for another 10 min. Then, 500 μL of a methanol and water (1:3) solution was added to the microtube before centrifugation (12,000 rpm at 4 °C for 5 min). Three phases were separate: an upper non-polar (green), a lower polar (brown), and a remaining protein pellet. Samples were transferred to fresh microtubes and vacuum-dried in a speed vac (Centrivap, Labconco, Kansas City, MO, USA) overnight at room temperature (~ 22 °C).

Sampleprep ID:

SP002525

Sampleprep Summary:

Leaf samples with approximately 50 mg were collected for the metabolomics analysis; four replicates per plant. After harvesting, samples were immediately frozen in liquid nitrogen and stored at − 80 °C until metabolites extraction and analysis. Each sample was ground in a ball mill (Biospec Products, USA) before solvent extraction. Metabolites were extracted using an adapted protocol from The Max Planck Institute, called All-in-One, which provides a polar fraction for secondary metabolite analysis, a nonpolar fraction for lipidomics, and a protein pellet for proteomics; all obtained from the same plant sample. Each ground sample was added to a microtube and mixed with 1 mL of a methanol and methyl-tert-butyl-ether (1:3) solution at − 20°C. After homogenization, they were incubated at 4 °C for 10 min. Each microtube was ultrasonicated in an ice bath for another 10 min. Then, 500 μL of a methanol and water (1:3) solution was added to the microtube before centrifugation (12,000 rpm at 4 °C for 5 min). Three phases were separate: an upper non-polar (green), a lower polar (brown), and a remaining protein pellet. Samples were transferred to fresh microtubes and vacuum-dried in a speed vac (Centrivap, Labconco, Kansas City, MO, USA) overnight at room temperature (~ 22 °C).

Combined analysis:

Analysis ID	AN003955	AN003956
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Shimadzu Nexera X2	Shimadzu Nexera X2
Column	Waters Acquity BEH C18 (150 x 2mm, 1.7um)	Waters Acquity BEH C18 (150 x 2mm, 1.7um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Bruker maXis Impact qTOF	Bruker maXis Impact qTOF
Ion Mode	POSITIVE	NEGATIVE
Units	Peak intensity	Peak intensity

Chromatography:

Chromatography ID:	CH002927
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Acquity BEH C18 (150 x 2mm, 1.7um)
Column Temperature:	-
Flow Gradient:	-
Flow Rate:	-
Solvent A:	-
Solvent B:	-
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003690
Analysis ID:	AN003955
Instrument Name:	Bruker maXis Impact qTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	High-resolution mass spectrometry (HRMS) was performed in a MaXis 4G Q-TOF MS system (Bruker Daltonics, Germany) using an electrospray source in the positive and negative ion modes (ESI(+)–MS and ESI(−)–MS). The MS instrument settings used were: endplate offset, 500 V; capillary voltage, 3800 V; nebulizer pressure, 4 bar; dry gas flow, 9 L/min, dry temperature, 200 °C; and column temperature, 40 °C. The acquisition spectra rate was 3.00 Hz, monitoring a mass range from 70 to 1200 m/z. Sodium formate solution (10 mM NaOH solution in 50/50 v/v isopropanol/water containing 0.2% formic acid) was directly injected through a 6-port valve at the beginning of each chromatographic run to external calibration. UHPLC–MS data was acquired by the HyStar Application version 3.2 (Bruker Daltonics, Germany), and data processing was done using Data Analysis 4.2 (Bruker Daltonics, Germany).
Ion Mode:	POSITIVE

MS ID:	MS003691
Analysis ID:	AN003956
Instrument Name:	Bruker maXis Impact qTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	High-resolution mass spectrometry (HRMS) was performed in a MaXis 4G Q-TOF MS system (Bruker Daltonics, Germany) using an electrospray source in the positive and negative ion modes (ESI(+)–MS and ESI(−)–MS). The MS instrument settings used were: endplate offset, 500 V; capillary voltage, 3800 V; nebulizer pressure, 4 bar; dry gas flow, 9 L/min, dry temperature, 200 °C; and column temperature, 40 °C. The acquisition spectra rate was 3.00 Hz, monitoring a mass range from 70 to 1200 m/z. Sodium formate solution (10 mM NaOH solution in 50/50 v/v isopropanol/water containing 0.2% formic acid) was directly injected through a 6-port valve at the beginning of each chromatographic run to external calibration. UHPLC–MS data was acquired by the HyStar Application version 3.2 (Bruker Daltonics, Germany), and data processing was done using Data Analysis 4.2 (Bruker Daltonics, Germany).
Ion Mode:	NEGATIVE