Summary of Study ST002966
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 PR001845. The data can be accessed directly via it's Project DOI: 10.21228/M87B0H 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 | ST002966 |
| Study Title | Metabolomics reveal the pathway of benzylisoquinoline alkaloids in Corydalis yanhusuo bulbs |
| Study Type | spatial and temporal distribution |
| Study Summary | In general, bulbs of Corydalis yanhusuo can be divided into "mother-bulb (MB)" and "son-bulb (SB)" according to different parts. The mother bulbs are formed by the degeneration and re-expansion of their original stem and are used as medicinal material in production. Son bulbs emerge from axillary buds on horizontally elongated rhizomes, of which the larger bulb can also be used as medicine, while the smaller bulb is reserved as a seed stem for "seed". In this study, materials of C. yanhusuo bulbs were cultivated in the field, which was proposed and identified by Professor Da-xia Chen. Widely targeted metabolome sequencing of C. yanhusuo bulbs was performed by UPLC-ESI MS/MS system, and its metabolites were successfully identified and annotated in self-built database (the MetWare database). A total of 702 metabolites were identified in all samples, including 216 alkaloids, 120 lipids, 67 amino acids and their derivatives, 59 organic acids, 63 phenolic acids, 19 terpenoids, 28 flavonoids, 4 lignin and coumarins, 43 nucleotides and their derivatives, 1 tannin, 3 quinones and 79 other substances. The numbers of up-accumulated and down-accumulated metabolites in MB-A vs MB-C and SB-A vs SB-C were 135 and 148, 90 and 210, respectively. There were 184 kinds of DAMs between SB-A and MB-A (including 144 down-accumulated and 40 up-accumulated compounds in the MB-A samples) and 127 kinds of DAMs between SB-C and MB-C (including 57 down-accumulated and 40 up-accumulated compounds in the MB-C samples) . |
| Institute | Chongqing Academy of Chinese Materia Medica, Chongqing, China |
| Laboratory | Department of Traditional Chinese Medicine |
| Last Name | Zhao |
| First Name | Xiao |
| Address | Nanshan stree, Chongqing, Nanan District, 400065, China |
| 321427953@qq.com | |
| Phone | 02389029062 |
| Submit Date | 2023-11-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | APCIESI |
| Release Date | 2023-11-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001845 |
| Project DOI: | doi: 10.21228/M87B0H |
| Project Title: | Widely targeted metabolomics of Corydalis yanhusuo bulbs |
| Project Type: | MS quantitative analysis |
| Project Summary: | Distribution and accumulation patterns of benzylisoquinoline alkaloids in bulbs of different developmental stages and sub organ parts of Corydalis yanhusuo |
| Institute: | Chongqing Academy of Chinese Materia Medica, Chongqing, China |
| Laboratory: | Department of Traditional Chinese Medicine |
| Last Name: | Zhao |
| First Name: | Xiao |
| Address: | Nanshan stree, Chongqing, Nanan District, 400065, China |
| Email: | 321427953@qq.com |
| Phone: | 02389029062 |
Subject:
| Subject ID: | SU003079 |
| Subject Type: | Plant |
| Subject Species: | Corydalis yanhusuo |
Factors:
Subject type: Plant; Subject species: Corydalis yanhusuo (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA322956 | MB-A1 | mother-bulb expansion period |
| SA322957 | MB-A3 | mother-bulb expansion period |
| SA322958 | MB-A2 | mother-bulb expansion period |
| SA322959 | MB-C2 | mother-bulb maturity period |
| SA322960 | MB-C3 | mother-bulb maturity period |
| SA322961 | MB-C1 | mother-bulb maturity period |
| SA322962 | SB-A1 | son-bulb expansion period |
| SA322963 | SB-A3 | son-bulb expansion period |
| SA322964 | SB-A2 | son-bulb expansion period |
| SA322965 | SB-C3 | son-bulb maturity period |
| SA322966 | SB-C1 | son-bulb maturity period |
| SA322967 | SB-C2 | son-bulb maturity period |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003072 |
| Collection Summary: | In this study, materials of C. yanhusuo bulbs were cultivated in the field, which was proposed and identified by Professor Da-xia Chen. On April 6th (expansion period) and April 26th (maturity period), samples of the "mother bulb" and "son bulb" of C. yanhusuo were collected. After washing, the samples were immediately placed into liquid nitrogen for quick freezing and then transferred to an ultralow temperature refrigerator for storage |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR003088 |
| Treatment Summary: | Different suborgan parts and development periods of C. yanhusuo bulb. MB-A: mother-bulb expansion period, SB-A: son-bulb expansion period, MB-C: mother-bulb maturity period, SB-C: son-bulb maturity period. |
Sample Preparation:
| Sampleprep ID: | SP003085 |
| Sampleprep Summary: | After vacuum freeze-drying, the biological sample was crushed at 30 Hz for 1.5 minutes using a mixer (MM 400, Retsch) with zirconia beads. One hundred milligrams of lyophilized powder was accurately weighed, dissolved in 1.2 ml of 70% methanol solution, rotated every 30 minutes for 30 seconds, repeated 6 times, and placed in a refrigerator at 4 °C for 12 h. Finally, after centrifuging the solution at 12 000 rpm for 10 minutes, the extract was filtered (SCAA-104, 0.22 μm pore size; ANPEL, Shanghai, China, http://www.anpel.com.cn/) to perform UPLC‒MS/MS analysis. |
Combined analysis:
| Analysis ID | AN004873 | AN004874 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | SHIMADZU Nexera X2 | SHIMADZU Nexera X2 |
| Column | Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um) | Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um) |
| MS Type | ESI | APCI |
| MS instrument type | QTRAP | QTRAP |
| MS instrument name | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH003677 |
| Instrument Name: | SHIMADZU Nexera X2 |
| Column Name: | Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40°C |
| Flow Gradient: | 95% A, 5% B. Within 9 min, a linear gradient to 5% A, 95% B was programmed, and a composition of 5% A, 95% B was kept for 1 min. Subsequently, a composition of 95% A, 5.0% B was adjusted within 1.1 min and kept for 2.9 min |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | pure water with 0.1% formic acid |
| Solvent B: | acetonitrile with 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004617 |
| Analysis ID: | AN004873 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | LIT and triple quadrupole (QQQ) scans were acquired on a triple quadrupole-linear ion trap mass spectrometer (Q TRAP), AB4500 Q TRAP UPLC/MS/MS System, equipped with an ESI Turbo Ion-Spray interface, operating in positive and negative ion mode and controlled by Analyst 1.6.3 software (AB Sciex). The ESI source operation parameters were as follows: ion source, turbo spray; source temperature 550°C; ion spray voltage (IS) 5500 V (positive ion mode)/-4500 V (negative ion mode); ion source gas I (GSI), gas II(GSII), curtain gas (CUR) were set at 50, 60, and 25.0 psi, respectively; the collision-activated dissociation(CAD) was high. Instrument tuning and mass calibration were performed with 10 and 100 μmol/L polypropylene glycol solutions in QQQ and LIT modes, respectively. QQQ scans were acquired as MRM experiments with collision gas (nitrogen) set to medium. DP and CE for individual MRM transitions was done with further DP and CE optimization. A specific set of MRM transitions were monitored for each period according to the metabolites eluted within this period. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004618 |
| Analysis ID: | AN004874 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | APCI |
| MS Comments: | LIT and triple quadrupole (QQQ) scans were acquired on a triple quadrupole-linear ion trap mass spectrometer (Q TRAP), AB4500 Q TRAP UPLC/MS/MS System, equipped with an ESI Turbo Ion-Spray interface, operating in positive and negative ion mode and controlled by Analyst 1.6.3 software (AB Sciex). The ESI source operation parameters were as follows: ion source, turbo spray; source temperature 550°C; ion spray voltage (IS) 5500 V (positive ion mode)/-4500 V (negative ion mode); ion source gas I (GSI), gas II(GSII), curtain gas (CUR) were set at 50, 60, and 25.0 psi, respectively; the collision-activated dissociation(CAD) was high. Instrument tuning and mass calibration were performed with 10 and 100 μmol/L polypropylene glycol solutions in QQQ and LIT modes, respectively. QQQ scans were acquired as MRM experiments with collision gas (nitrogen) set to medium. DP and CE for individual MRM transitions was done with further DP and CE optimization. A specific set of MRM transitions were monitored for each period according to the metabolites eluted within this period. |
| Ion Mode: | NEGATIVE |
