Summary of Study ST003172
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 PR001972. The data can be accessed directly via it's Project DOI: 10.21228/M8TJ0V 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 | ST003172 |
| Study Title | Untargeted Metabolomic Profile Of Chili Pepper (Capsicum Chinensed) Developmental Cycle |
| Study Summary | To explore the temporal dynamics of metabolites in chili peppers at various developmental stages, we employed a non-targeted metabolomics method based on liquid chromatography-mass spectrometry (LC-MS). The metabolome data collection began on the day of flowering (0 days post-anthesis), and continued for 7, 16, 30, 50, 55, and 60 DPA. This comprehensive dataset paved the way for future studies on metabolite changes and biological processes in chili peppers throughout their life cycle. |
| Institute | University of Alberta |
| Department | Department of Chemistry |
| Last Name | Yang |
| First Name | Bowen |
| Address | 11227 Saskatchewan Drive , Edmonton, Alberta, Canada T6G 2G2 |
| by8@ualberta.ca | |
| Phone | 8259758666 |
| Submit Date | 2024-04-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-04-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001972 |
| Project DOI: | doi: 10.21228/M8TJ0V |
| Project Title: | Untargeted Metabolomic Profile Of Chili Pepper (Capsicum Chinensed) Developmental Cycle |
| Project Summary: | To explore the temporal dynamics of metabolites in chili peppers at various developmental stages, we employed a non-targeted metabolomics method based on liquid chromatography-mass spectrometry (LC-MS). The metabolome data collection began on the day of flowering (0 days post-anthesis), and continued for 7, 16, 30, 50, 55, and 60 DPA. This comprehensive dataset paved the way for future studies on metabolite changes and biological processes in chili peppers throughout their life cycle. |
| Institute: | University of Alberta |
| Department: | Department of Chemistry |
| Last Name: | Yang |
| First Name: | Bowen |
| Address: | 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2 |
| Email: | by8@ualberta.ca |
| Phone: | 8259758666 |
Subject:
| Subject ID: | SU003291 |
| Subject Type: | Plant |
| Subject Species: | Chili Pepper (Capsicum Chinense) |
Factors:
Subject type: Plant; Subject species: Chili Pepper (Capsicum Chinense) (Factor headings shown in green)
| mb_sample_id | local_sample_id | day post-anthesis | POS/NEG | Sample source |
|---|---|---|---|---|
| SA343104 | 20230216-M-GL-LJ-NEG1-1 | 0 | NEG | Capsicum Chinense |
| SA343105 | 20230216-M-GL-LJ-NEG1-3 | 0 | NEG | Capsicum Chinense |
| SA343106 | 20230216-M-GL-LJ-NEG1-2 | 0 | NEG | Capsicum Chinense |
| SA343107 | 20230216-M-GL-LJ-POS1-2 | 0 | POS | Capsicum Chinense |
| SA343108 | 20230216-M-GL-LJ-POS1-3 | 0 | POS | Capsicum Chinense |
| SA343109 | 20230216-M-GL-LJ-POS1-1 | 0 | POS | Capsicum Chinense |
| SA343110 | 20230216-M-GL-LJ-NEG3-2 | 16 | NEG | Capsicum Chinense |
| SA343111 | 20230216-M-GL-LJ-NEG3-3 | 16 | NEG | Capsicum Chinense |
| SA343112 | 20230216-M-GL-LJ-NEG3-1 | 16 | NEG | Capsicum Chinense |
| SA343113 | 20230216-M-GL-LJ-POS3-3 | 16 | POS | Capsicum Chinense |
| SA343114 | 20230216-M-GL-LJ-POS3-2 | 16 | POS | Capsicum Chinense |
| SA343115 | 20230216-M-GL-LJ-POS3-1 | 16 | POS | Capsicum Chinense |
| SA343116 | 20230216-M-GL-LJ-NEG4-1 | 30 | NEG | Capsicum Chinense |
| SA343117 | 20230216-M-GL-LJ-NEG4-2 | 30 | NEG | Capsicum Chinense |
| SA343118 | 20230216-M-GL-LJ-NEG4-3 | 30 | NEG | Capsicum Chinense |
| SA343119 | 20230216-M-GL-LJ-POS4-2 | 30 | POS | Capsicum Chinense |
| SA343120 | 20230216-M-GL-LJ-POS4-3 | 30 | POS | Capsicum Chinense |
| SA343121 | 20230216-M-GL-LJ-POS4-1 | 30 | POS | Capsicum Chinense |
| SA343122 | 20230216-M-GL-LJ-NEG5-3 | 50 | NEG | Capsicum Chinense |
| SA343123 | 20230216-M-GL-LJ-NEG5-2 | 50 | NEG | Capsicum Chinense |
| SA343124 | 20230216-M-GL-LJ-NEG5-1 | 50 | NEG | Capsicum Chinense |
| SA343125 | 20230216-M-GL-LJ-POS5-1 | 50 | POS | Capsicum Chinense |
| SA343126 | 20230216-M-GL-LJ-POS5-3 | 50 | POS | Capsicum Chinense |
| SA343127 | 20230216-M-GL-LJ-POS5-2 | 50 | POS | Capsicum Chinense |
| SA343128 | 20230216-M-GL-LJ-NEG6-1 | 55 | NEG | Capsicum Chinense |
| SA343129 | 20230216-M-GL-LJ-NEG6-3 | 55 | NEG | Capsicum Chinense |
| SA343130 | 20230216-M-GL-LJ-NEG6-2 | 55 | NEG | Capsicum Chinense |
| SA343131 | 20230216-M-GL-LJ-POS6-3 | 55 | POS | Capsicum Chinense |
| SA343132 | 20230216-M-GL-LJ-POS6-1 | 55 | POS | Capsicum Chinense |
| SA343133 | 20230216-M-GL-LJ-POS6-2 | 55 | POS | Capsicum Chinense |
| SA343134 | 20230216-M-GL-LJ-NEG7-3 | 60 | NEG | Capsicum Chinense |
| SA343135 | 20230216-M-GL-LJ-NEG7-1 | 60 | NEG | Capsicum Chinense |
| SA343136 | 20230216-M-GL-LJ-NEG7-2 | 60 | NEG | Capsicum Chinense |
| SA343137 | 20230216-M-GL-LJ-POS7-2 | 60 | POS | Capsicum Chinense |
| SA343138 | 20230216-M-GL-LJ-POS7-3 | 60 | POS | Capsicum Chinense |
| SA343139 | 20230216-M-GL-LJ-POS7-1 | 60 | POS | Capsicum Chinense |
| SA343140 | 20230216-M-GL-LJ-NEG2-1 | 7 | NEG | Capsicum Chinense |
| SA343141 | 20230216-M-GL-LJ-NEG2-3 | 7 | NEG | Capsicum Chinense |
| SA343142 | 20230216-M-GL-LJ-NEG2-2 | 7 | NEG | Capsicum Chinense |
| SA343143 | 20230216-M-GL-LJ-POS2-1 | 7 | POS | Capsicum Chinense |
| SA343144 | 20230216-M-GL-LJ-POS2-3 | 7 | POS | Capsicum Chinense |
| SA343145 | 20230216-M-GL-LJ-POS2-2 | 7 | POS | Capsicum Chinense |
| SA343146 | 20230216-M-GL-LJ-NEGQC1 | QC | NEG | Capsicum Chinense |
| SA343147 | 20230216-M-GL-LJ-NEGQC2 | QC | NEG | Capsicum Chinense |
| SA343148 | 20230216-M-GL-LJ-NEGQC3 | QC | NEG | Capsicum Chinense |
| SA343149 | 20230216-M-GL-LJ-POSQC3 | QC | POS | Capsicum Chinense |
| SA343150 | 20230216-M-GL-LJ-POSQC2 | QC | POS | Capsicum Chinense |
| SA343151 | 20230216-M-GL-LJ-POSQC1 | QC | POS | Capsicum Chinense |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO003284 |
| Collection Summary: | Metabolic profiling data from chili peppers (Capsicum chinese L.) was collected. Pepper seedlings were grown in a greenhouse of Peking University Institute of Advanced Agricultural Sciences with a controlled environment of 25°C temperature, a light-dark cycle of 16 hours light and 8 hours dark, and 70% relative humidity. The fruits of peppers were sampled at seven distinct time points, starting from the day of flowering, i.e. 0 day post-anthesis (DPA) during which flowers were collected. Following this, fruits were harvested on days 7, 16, 30, 50, 55, and 60 DPA. The samples were ground and freeze-dried in liquid nitrogen, followed by extraction using 1.0 mL of 70% aqueous methanol for every 50 mg of the sample, and an ultrasonic process was employed for 30 minutes. The preparation of standards was conducted as follows: a mixed standard in the range of 20-50μg/mL was prepared using methanol of MS grade. For the amino acid standard solution, a 1mg/mL stock solution was prepared in water and subsequently diluted with 50% methanol to achieve a concentration of 50μg/mL. Three biological replicates were used metabolome analysis. |
| Sample Type: | Chili Pepper (Capsicum Chinense) |
Treatment:
| Treatment ID: | TR003300 |
| Treatment Summary: | Metabolic profiling data from chili peppers (Capsicum chinese L.) was collected. Pepper seedlings were grown in a greenhouse of Peking University Institute of Advanced Agricultural Sciences with a controlled environment of 25°C temperature, a light-dark cycle of 16 hours light and 8 hours dark, and 70% relative humidity. The fruits of peppers were sampled at seven distinct time points, starting from the day of flowering, i.e. 0 day post-anthesis (DPA) during which flowers were collected. Following this, fruits were harvested on days 7, 16, 30, 50, 55, and 60 DPA. The samples were ground and freeze-dried in liquid nitrogen, followed by extraction using 1.0 mL of 70% aqueous methanol for every 50 mg of the sample, and an ultrasonic process was employed for 30 minutes. The preparation of standards was conducted as follows: a mixed standard in the range of 20-50μg/mL was prepared using methanol of MS grade. For the amino acid standard solution, a 1mg/mL stock solution was prepared in water and subsequently diluted with 50% methanol to achieve a concentration of 50μg/mL. Three biological replicates were used metabolome analysis. |
Sample Preparation:
| Sampleprep ID: | SP003298 |
| Sampleprep Summary: | Metabolic profiling data from chili peppers (Capsicum chinese L.) was collected. Pepper seedlings were grown in a greenhouse of Peking University Institute of Advanced Agricultural Sciences with a controlled environment of 25°C temperature, a light-dark cycle of 16 hours light and 8 hours dark, and 70% relative humidity. The fruits of peppers were sampled at seven distinct time points, starting from the day of flowering, i.e. 0 day post-anthesis (DPA) during which flowers were collected. Following this, fruits were harvested on days 7, 16, 30, 50, 55, and 60 DPA. The samples were ground and freeze-dried in liquid nitrogen, followed by extraction using 1.0 mL of 70% aqueous methanol for every 50 mg of the sample, and an ultrasonic process was employed for 30 minutes. The preparation of standards was conducted as follows: a mixed standard in the range of 20-50μg/mL was prepared using methanol of MS grade. For the amino acid standard solution, a 1mg/mL stock solution was prepared in water and subsequently diluted with 50% methanol to achieve a concentration of 50μg/mL. Three biological replicates were used metabolome analysis. |
Combined analysis:
| Analysis ID | AN005206 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity H-Class |
| Column | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm, 1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Orbitrap Exploris™ 240 Mass Spectrometer |
| Ion Mode | UNSPECIFIED |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH003939 |
| Chromatography Summary: | Metabolic profiling data from chili peppers (Capsicum chinese L.) was collected. Pepper seedlings were grown in a greenhouse of Peking University Institute of Advanced Agricultural Sciences with a controlled environment of 25°C temperature, a light-dark cycle of 16 hours light and 8 hours dark, and 70% relative humidity. The fruits of peppers were sampled at seven distinct time points, starting from the day of flowering, i.e. 0 day post-anthesis (DPA) during which flowers were collected. Following this, fruits were harvested on days 7, 16, 30, 50, 55, and 60 DPA. The samples were ground and freeze-dried in liquid nitrogen, followed by extraction using 1.0 mL of 70% aqueous methanol for every 50 mg of the sample, and an ultrasonic process was employed for 30 minutes. The preparation of standards was conducted as follows: a mixed standard in the range of 20-50μg/mL was prepared using methanol of MS grade. For the amino acid standard solution, a 1mg/mL stock solution was prepared in water and subsequently diluted with 50% methanol to achieve a concentration of 50μg/mL. Three biological replicates were used metabolome analysis. The metabolome profiling was carried out using untargeted metabolomics based on liquid chromatography coupled with mass spectrometry (LC-MS). The samples were filtered through a 0.22 µm membrane and transferred into the lining tube of a sampling vial. Subsequent centrifugation was carried out at 12000 rcf and 4°C for 10 minutes. The processed samples were then analyzed using Thermo Scientific Orbitrap Exploris™ 240 (Thermo Fisher Scientific, USA). Chromatographic separation was achieved on a T3 C18 (1.7 µm, 2.1 mm × 150 mm column, USA) maintained at 40°C. The mobile phase consisted of A: 1% formic acid in water and B: 1% formic acid in acetonitrile, with a flow rate of 300 µL/min. A 3 µL sample was injected at an autosampler temperature of 10°C. The elution gradient was set as follows: 0-2.5 min, 3-10% B; 2.5-6 min, 10-44% B; 6-14 min, 44-80% B; 14-20 min, 80-95% B; 20-23 min, 95% B; 23-23.1 min, 95-3% B; 23.1-28 min, 3% B. MS was performed using both positive and negative ion scans, with a precursor ion scan mode. The auxiliary gas heater temperature was set at 350°C, and the ion transfer tube temperature was also maintained at 350°C. The sheath gas flow rate and auxiliary gas flow rate were set to 35 arb and 15 arb, respectively. The voltages were set to 3.5 KV for the positive spectrum and 3.2 KV for the negative spectrum. For MS1, the scan resolution was 60000, with a scan range of 80-1200. For MS2, the scan resolution was 15000, with a stepped collision energy of 20, 40, and 60 eV. Metabolite identification and quantification were performed using the Compound Discoverer software 3.3 (Thermo Fisher Scientific, USA). |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm, 1.8um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0-2.5 min，3-10% B；2.5-6 min，10-44% B；6-14 min，44-80% B；14-20 min，80-95% B；20-23 min，95% B；23-23.1 min，95-3% B；23.1-28 min，3% B |
| Flow Rate: | 300 μL/min |
| Solvent A: | 100% Water; 1% Formic Acid |
| Solvent B: | 100% Acetonitrile; 1% Formic Acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004939 |
| Analysis ID: | AN005206 |
| Instrument Name: | Orbitrap Exploris™ 240 Mass Spectrometer |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The metabolome profiling was carried out using untargeted metabolomics based on liquid chromatography coupled with mass spectrometry (LC-MS), with data collected in positive and negative modes respectively to improve coverage. The samples were filtered through a 0.22 µm membrane and transferred into the lining tube of a sampling vial. Subsequent centrifugation was carried out at 12000 rcf and 4°C for 10 minutes. The processed samples were then analyzed using Thermo Scientific Orbitrap Exploris™ 240 (Thermo Fisher Scientific, USA). Chromatographic separation was achieved on a T3 C18 (1.7 µm, 2.1 mm × 150 mm column, USA) maintained at 40°C. The mobile phase consisted of A: 1% formic acid in water and B: 1% formic acid in acetonitrile, with a flow rate of 300 µL/min. A 3 µL sample was injected at an autosampler temperature of 10°C. The elution gradient was set as follows: 0-2.5 min, 3-10% B; 2.5-6 min, 10-44% B; 6-14 min, 44-80% B; 14-20 min, 80-95% B; 20-23 min, 95% B; 23-23.1 min, 95-3% B; 23.1-28 min, 3% B. MS was performed using both positive and negative ion scans, with a precursor ion scan mode. The auxiliary gas heater temperature was set at 350°C, and the ion transfer tube temperature was also maintained at 350°C. The sheath gas flow rate and auxiliary gas flow rate were set to 35 arb and 15 arb, respectively. The voltages were set to 3.5 KV for the positive spectrum and 3.2 KV for the negative spectrum. For MS1, the scan resolution was 60000, with a scan range of 80-1200. For MS2, the scan resolution was 15000, with a stepped collision energy of 20, 40, and 60 eV. Metabolite identification and quantification were performed using the Compound Discoverer software 3.3 (Thermo Fisher Scientific, USA). |
| Ion Mode: | UNSPECIFIED |
