Summary of Study ST003918

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 PR002451. The data can be accessed directly via it's Project DOI: 10.21228/M8TG05 This work is supported by NIH grant, U2C- DK119886.

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

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.

Study ID	ST003918
Study Title	Metabolomic Insights into the Impact of Germination Conditions on Nutritional Quality of Cowpea (Vigna unguiculata) Seeds
Study Type	GC Metabolomics of germination
Study Summary	Cowpea (Vigna unguiculata) is a robust and adaptable pulse crop that grows in arid and tropical regions. It serves as a vital source of nutrition, providing proteins, carbohydrates, fibers, minerals, and vitamins. This pioneer study used integrated metabolomics to investigate the effects of germination conditions (i.e. temperature [25 °C to 35 °C], light exposure [0–12 h], and water content [80%–140%]) on the metabolic content in cowpea seeds. These data can be valuable for optimizing germination conditions to enhance the nutritional quality of pulses and provide a deeper understanding of the impact of germination on seed metabolism, benefiting the food industry and consumers.
Institute	INRAE
Department	IJPB/Institut Jean-Pierre BOURGIN
Laboratory	Physiology of germination
Last Name	RAJJOU
First Name	Loïc
Address	Route de st-Cyr, Versailles, Ile-de-France, 78026, France
Email	loic.rajjou@inrae.fr
Phone	+33 (0) 1 30 83 38 91
Submit Date	2025-01-13
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2025-06-09
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002451
Project DOI:	doi: 10.21228/M8TG05
Project Title:	Metabolomic changes in Vigna unguiculata imbibed seeds produced under combined stresses (heat stress, light stress and humidity)
Project Type:	Research
Project Summary:	Vigna unguiculata seeds germination and GC-MS based metabolomic analysis - phenotype of the cowpea genotype under the different stress applied - effect of heat stress - effect of light stress - effect of humidity percentage - the results of the metabolites profiling of the genotype under stress condition - specify which type of metabolites are affected or not affected by the stress condition
Institute:	INRAE
Department:	IJPB/Institut Jean-Pierre Bourgin
Laboratory:	Physiology of germination
Last Name:	RAJJOU
First Name:	Loïc
Address:	Route de st-Cyr, Versailles, Ile-de-France, 78026, France
Email:	loic.rajjou@inrae.fr
Phone:	+33 (0) 1 30 83 38 91

Subject:

Subject ID:	SU004053
Subject Type:	Plant
Subject Species:	Vigna unguiculata
Taxonomy ID:	3917

Factors:

Subject type: Plant; Subject species: Vigna unguiculata (Factor headings shown in green)

mb_sample_id	local_sample_id	Culture_Condition_Light	Culture_Condition_Temperature	Culture_Condition_Humidity	Culture_Condition_Imbibition	Sample source
SA443832	temp_25°C-G-light_0H-H_140-R1	0 H	25°C	140	Control	Seed
SA443833	temp_25°C-G-light_0H-H_140-R2	0 H	25°C	140	Control	Seed
SA443834	temp_25°C-G-light_0H-H_140-R3	0 H	25°C	140	Control	Seed
SA443835	temp_25°C-G-light_0H-H_80-R1	0 H	25°C	80	Control	Seed
SA443836	temp_25°C-G-light_0H-H_80-R2	0 H	25°C	80	Control	Seed
SA443837	temp_25°C-G-light_0H-H_80-R3	0 H	25°C	80	Control	Seed
SA443838	temp_35°C-G-light_0H-H_140-R1	0 H	35°C	140	Control	Seed
SA443839	temp_35°C-G-light_0H-H_140-R3	0 H	35°C	140	Control	Seed
SA443840	temp_35°C-G-light_0H-H_140-R2	0 H	35°C	140	Control	Seed
SA443841	temp_35°C-G-light_0H-H_80-R3	0 H	35°C	80	Control	Seed
SA443842	temp_35°C-G-light_0H-H_80-R2	0 H	35°C	80	Control	Seed
SA443843	temp_35°C-G-light_0H-H_80-R1	0 H	35°C	80	Control	Seed
SA443844	temp_25°C-G-light_12H-H_140-R1	12 H	25°C	140	Control	Seed
SA443845	temp_25°C-G-light_12H-H_140-R2	12 H	25°C	140	Control	Seed
SA443846	temp_25°C-G-light_12H-H_140-R3	12 H	25°C	140	Control	Seed
SA443847	temp_25°C-G-light_12H-H_80-R1	12 H	25°C	80	Control	Seed
SA443848	temp_25°C-G-light_12H-H_80-R3	12 H	25°C	80	Control	Seed
SA443849	temp_25°C-G-light_12H-H_80-R2	12 H	25°C	80	Control	Seed
SA443850	temp_35°C-G-light_12H-H_140-R3	12 H	35°C	140	Control	Seed
SA443851	temp_35°C-G-light_12H-H_140-R2	12 H	35°C	140	Control	Seed
SA443852	temp_35°C-G-light_12H-H_140-R1	12 H	35°C	140	Control	Seed
SA443853	temp_35°C-G-light_12H-H_80-R1	12 H	35°C	80	Control	Seed
SA443854	temp_35°C-G-light_12H-H_80-R2	12 H	35°C	80	Control	Seed
SA443855	temp_35°C-G-light_12H-H_80-R3	12 H	35°C	80	Control	Seed
SA443856	temp_30°C-G-light_6H-H_110-R3	6 H	30°C	110	Control	Seed
SA443857	temp_30°C-G-light_6H-H_110-R2	6 H	30°C	110	Control	Seed
SA443858	temp_30°C-G-light_6H-H_110-R1	6 H	30°C	110	Control	Seed
SA443859	temp_25°C-C-R2	Control	25°C	Control	Control	Seed
SA443860	temp_25°C-C-R3	Control	25°C	Control	Control	Seed
SA443861	temp_25°C-C-R1	Control	25°C	Control	Control	Seed
SA443862	temp_30°C-I5H-R1	Control	30°C	Control	5 H	Seed
SA443863	temp_30°C-I5H-R2	Control	30°C	Control	5 H	Seed
SA443864	temp_30°C-I5H-R3	Control	30°C	Control	5 H	Seed

Showing results 1 to 33 of 33

Showing results 1 to 33 of 33

Collection:

Collection ID:	CO004046
Collection Summary:	Cowpea seeds (80 g) were soaked in 320 mL of water (1:4 w/v ratio, pH 6.0) at 30 °C for 5 hours to complete the water uptake phase and initiate germination. After soaking, the seeds were drained and transferred to a controlled environment for germination. A factorial experimental design was applied, testing three variables—temperature (25 and 35 °C), light regime (dark vs. 12 h light/12 h dark), and water content (80% and 140% of seed dry weight)—each at two levels. In addition, a medium condition was included as a reference, with seeds incubated at 30 °C under a 6 h light/18 h dark cycle and at 110% of seed dry weight. Germination was conducted in a BINDER-KMF 240 chamber maintained at 95% relative humidity. To ensure precise control of moisture levels, water was manually sprayed 18 hours after the start of germination: 60 mL for the 110% condition and 120 mL for the 140% condition (dry basis). Water content was monitored hourly by measuring seed weight. Illumination was provided by a white LED light source. After 24 hours, seeds were categorized as non-germinated (no radicle emergence), germinated (radicle < 5 mm), or sprouted (radicle > 5 mm). Only germinated seeds were retained for subsequent -omics analyses. These seeds were collected and immediately stored at –40 °C. All samples were freeze-dried and finely ground using a QIAGEN TissueLyser II ball mill. The resulting flour was freeze-dried once more and stored at –20 °C until analysis.
Sample Type:	Seeds
Storage Conditions:	-20℃

Treatment:

Treatment ID:	TR004062
Treatment Summary:	Cowpea seeds (80 g) were soaked in 320 mL of water (1:4 w/v ratio, pH 6.0) at 30 °C for 5 hours to complete the water uptake phase and initiate germination. After soaking, the seeds were drained and transferred to a controlled environment for germination. A factorial experimental design was applied, testing three variables—temperature (25 and 35 °C), light regime (dark vs. 12 h light/12 h dark), and water content (80% and 140% of seed dry weight)—each at two levels. In addition, a medium condition was included as a reference, with seeds incubated at 30 °C under a 6 h light/18 h dark cycle and at 110% of seed dry weight. Germination was conducted in a BINDER-KMF 240 chamber maintained at 95% relative humidity. To ensure precise control of moisture levels, water was manually sprayed 18 hours after the start of germination: 60 mL for the 110% condition and 120 mL for the 140% condition (dry basis). Water content was monitored hourly by measuring seed weight. Illumination was provided by a white LED light source. After 24 hours, seeds were categorized as non-germinated (no radicle emergence), germinated (radicle < 5 mm), or sprouted (radicle > 5 mm). Only germinated seeds were retained for subsequent -omics analyses. These seeds were collected and immediately stored at –40 °C. All samples were freeze-dried and finely ground using a QIAGEN TissueLyser II ball mill. The resulting flour was freeze-dried once more and stored at –20 °C until analysis.

Treatment ID:

TR004062

Treatment Summary:

Cowpea seeds (80 g) were soaked in 320 mL of water (1:4 w/v ratio, pH 6.0) at 30 °C for 5 hours to complete the water uptake phase and initiate germination. After soaking, the seeds were drained and transferred to a controlled environment for germination. A factorial experimental design was applied, testing three variables—temperature (25 and 35 °C), light regime (dark vs. 12 h light/12 h dark), and water content (80% and 140% of seed dry weight)—each at two levels. In addition, a medium condition was included as a reference, with seeds incubated at 30 °C under a 6 h light/18 h dark cycle and at 110% of seed dry weight. Germination was conducted in a BINDER-KMF 240 chamber maintained at 95% relative humidity. To ensure precise control of moisture levels, water was manually sprayed 18 hours after the start of germination: 60 mL for the 110% condition and 120 mL for the 140% condition (dry basis). Water content was monitored hourly by measuring seed weight. Illumination was provided by a white LED light source. After 24 hours, seeds were categorized as non-germinated (no radicle emergence), germinated (radicle < 5 mm), or sprouted (radicle > 5 mm). Only germinated seeds were retained for subsequent -omics analyses. These seeds were collected and immediately stored at –40 °C. All samples were freeze-dried and finely ground using a QIAGEN TissueLyser II ball mill. The resulting flour was freeze-dried once more and stored at –20 °C until analysis.

Sample Preparation:

Sampleprep ID:	SP004059
Sampleprep Summary:	Metabolite samples were prepared from three biological replicates of 20 mg each of dry, soaked, or germinated cowpea flour. Each sample was placed in 2 mL Safe-Lock Eppendorf tubes (Eppendorf AG, Hamburg, Germany). The frozen, ground samples were resuspended in 1 mL of water/acetonitrile/isopropanol (2:3:3, v/v/v) at -20 °C, supplemented with ribitol at a final concentration of 4 µg/mL, and extracted at 4 °C with shaking at 1400 rpm for 10 minutes using an Eppendorf Thermomixer. The samples were then centrifuged at 20,000×g for 5 minutes to remove insoluble material. Twenty-five microliters of the resulting extract were collected, dried for 150 minutes using a SpeedVac (Savant SPD131DDA, Thermo Fisher Scientific, Waltham, MA, USA), and stored at -80 °C. Prior to further analysis, the samples were thawed at room temperature for 15 minutes and then dried again for 1 hour in the SpeedVac. Subsequently, 10 µL of 20 mg/mL methoxyamine in pyridine was added to each sample, as well as to blanks, and amino acid and sugar standards. The reaction was conducted at 28 °C for 90 minutes with continuous shaking in the Eppendorf Thermomixer. After this, 90 µL of N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) were added, and the reaction continued for 30 minutes at 37 °C. After cooling, 50 µL of each sample were transferred to Agilent vials for injection. Two hours after the derivatization process, 1 µL of each sample was injected in splitless mode into an Agilent 7890A gas chromatograph coupled to an Agilent 5975C mass spectrometer. The chromatographic separation was performed using an Rxi-5SilMS column from Restek (30 m with a 10 m Integra-Guard pre-column). Before each series of analyses, the GC liner (Restek #20994) was replaced, and 10 cm of the column was trimmed. The oven temperature program began at 70 °C (held for 7 minutes), followed by a ramp of 10 °C/min to 325 °C, where it was held for 4 minutes (total run time: 36.5 minutes). Helium was used as the carrier gas with a constant flow rate of 1.52 mL/min. The following GC-MS temperatures were used: injector at 250 °C, transfer line at 290 °C, ion source at 250 °C, and quadrupole at 150 °C. Samples and blanks were analyzed in randomized order. Amino acid standards were injected at the beginning and end of the analysis to monitor derivatization stability. Additionally, an alkane mix (C10, C12, C15, C19, C22, C28, C32, and C36) was injected midway through the run queue for external retention index (RI) calibration. Data were acquired at a rate of five scans per second. Raw Agilent data files were converted to NetCDF format and analyzed using AMDIS (http://chemdata.nist.gov/massspc/amdis/). Metabolite identification was carried out using an in-house retention index/mass spectral library. Peak areas were quantified using QuanLynx software (Waters Corporation, Milford, MA, USA) after conversion of the NetCDF files into MassLynx (Waters) format.

Sampleprep ID:

SP004059

Sampleprep Summary:

Metabolite samples were prepared from three biological replicates of 20 mg each of dry, soaked, or germinated cowpea flour. Each sample was placed in 2 mL Safe-Lock Eppendorf tubes (Eppendorf AG, Hamburg, Germany). The frozen, ground samples were resuspended in 1 mL of water/acetonitrile/isopropanol (2:3:3, v/v/v) at -20 °C, supplemented with ribitol at a final concentration of 4 µg/mL, and extracted at 4 °C with shaking at 1400 rpm for 10 minutes using an Eppendorf Thermomixer. The samples were then centrifuged at 20,000×g for 5 minutes to remove insoluble material. Twenty-five microliters of the resulting extract were collected, dried for 150 minutes using a SpeedVac (Savant SPD131DDA, Thermo Fisher Scientific, Waltham, MA, USA), and stored at -80 °C. Prior to further analysis, the samples were thawed at room temperature for 15 minutes and then dried again for 1 hour in the SpeedVac. Subsequently, 10 µL of 20 mg/mL methoxyamine in pyridine was added to each sample, as well as to blanks, and amino acid and sugar standards. The reaction was conducted at 28 °C for 90 minutes with continuous shaking in the Eppendorf Thermomixer. After this, 90 µL of N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) were added, and the reaction continued for 30 minutes at 37 °C. After cooling, 50 µL of each sample were transferred to Agilent vials for injection. Two hours after the derivatization process, 1 µL of each sample was injected in splitless mode into an Agilent 7890A gas chromatograph coupled to an Agilent 5975C mass spectrometer. The chromatographic separation was performed using an Rxi-5SilMS column from Restek (30 m with a 10 m Integra-Guard pre-column). Before each series of analyses, the GC liner (Restek #20994) was replaced, and 10 cm of the column was trimmed. The oven temperature program began at 70 °C (held for 7 minutes), followed by a ramp of 10 °C/min to 325 °C, where it was held for 4 minutes (total run time: 36.5 minutes). Helium was used as the carrier gas with a constant flow rate of 1.52 mL/min. The following GC-MS temperatures were used: injector at 250 °C, transfer line at 290 °C, ion source at 250 °C, and quadrupole at 150 °C. Samples and blanks were analyzed in randomized order. Amino acid standards were injected at the beginning and end of the analysis to monitor derivatization stability. Additionally, an alkane mix (C10, C12, C15, C19, C22, C28, C32, and C36) was injected midway through the run queue for external retention index (RI) calibration. Data were acquired at a rate of five scans per second. Raw Agilent data files were converted to NetCDF format and analyzed using AMDIS (http://chemdata.nist.gov/massspc/amdis/). Metabolite identification was carried out using an in-house retention index/mass spectral library. Peak areas were quantified using QuanLynx software (Waters Corporation, Milford, MA, USA) after conversion of the NetCDF files into MassLynx (Waters) format.

Combined analysis:

Analysis ID	AN006434
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890A
Column	Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
MS Type	EI
MS instrument type	Single quadrupole
MS instrument name	Agilent 5975C
Ion Mode	POSITIVE
Units	µg/mg Dry Weight

Chromatography:

Chromatography ID:	CH004882
Chromatography Summary:	The instrument was an Agilent 7890A gas chromatograph coupled to an Agilent 5975C mass spectrometer.The column was an Rxi-5SilMS from Restek (30 m with 10 m integra-guard column). Before each series of analysis, the liner (Restek # 20994) was replaced and 10 cm of the column was trimmed. Oven temperature program was as follow: initial temperature was 70°C for 7 minutes, temperature ramp increase by 10°C/minutes to 325°C and the final hold was 325°C for 4 minutes which brings the total run lenght to 36.5 minutes. Helium constant flow was set at 1.52 mL/min. The temperature settings were the following: - Injector: 250°C - Transfer line: 290°C - Ion source: 250°C - Quadrupole: 150°C. 5 scans per second were acquired.
Instrument Name:	Agilent 7890A
Column Name:	Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
Column Temperature:	Oven temperature ramp was 70 °C for 7 min then 10 °C/min to 325 °C with final hold at 325°C for 4 minutes (total run length 36.5 minutes)
Flow Gradient:	NA
Flow Rate:	1.52mL/min
Solvent A:	NA
Solvent B:	NA
Chromatography Type:	GC

MS:

MS ID:	MS006135
Analysis ID:	AN006434
Instrument Name:	Agilent 5975C
Instrument Type:	Single quadrupole
MS Type:	EI
MS Comments:	Temperatures were the following: injector: 250°C, transfer line: 290°C, ion source: 250 °C and quadrupole 150 °C. Samples and blanks were randomized during analysis. Amino acid standards were injected at the beginning and end of the sequence to monitor derivatization stability. Additionally, an alkane mix (C10, C12, C15, C19, C22, C28, C32 and C36) was injected in the middle of the sequence for external retention index calibration. A data acquisition rate of five scans per seconds was employed. Raw Agilent data files were converted into NetCDF format and anlyzed using AMDIS (http://chemdata.nist.gov/massspc/amdis/). Metabolite identificationwas performed using a home retention indices/mass spectra library. Peak areas were then determined using QuanLynx software (Waters Corporation, Milford, MA, USA) after converting the NetCDF files into MassLynx format.
Ion Mode:	POSITIVE