Summary of Study ST000116
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 PR000105. The data can be accessed directly via it's Project DOI: 10.21228/M8W300 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000116 |
| Study Title | Comparative metabolomics analysis of the key metabolic nodes in propionic acid synthesis in Propionibacterium acidipropionici |
| Study Type | strains comparison |
| Study Summary | The parental P. acidipropionici and its genome-shuffled mutant were compared via metabolomics to find the key metabolic nodes influencing PA production. |
| Institute | Jiangnan University |
| Department | Key Laboratory of Carbohydrate Chemistry and Biotechnology |
| Last Name | Guan |
| First Name | Ningzi |
| Address | 1800 Lihu Ave, Binhu, Wuxi, Jiangsu, China |
| caimo-zi@163.com | |
| Submit Date | 2014-11-14 |
| Raw Data Available | No |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-02-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000105 |
| Project DOI: | doi: 10.21228/M8W300 |
| Project Title: | Comparative metabolomics analysis of the key metabolic nodes in propionic acid synthesis in Propionibacterium acidipropionici |
| Project Type: | MS analysis |
| Institute: | Jiangnan University |
| Department: | Key Laboratory of Carbohydrate Chemistry and Biotechnology |
| Last Name: | Guan |
| First Name: | Ningzi |
| Address: | 1800 Lihu Ave, Binhu, Wuxi, Jiangsu, China |
| Email: | caimo-zi@163.com |
Subject:
| Subject ID: | SU000135 |
| Subject Type: | Bacterial cells |
| Subject Species: | Acidipropionibacterium acidipropionici |
| Taxonomy ID: | 1748 |
| Genotype Strain: | GCMCC1.2230/WSH1105 |
| Species Group: | Microorganism |
Factors:
Subject type: Bacterial cells; Subject species: Acidipropionibacterium acidipropionici (Factor headings shown in green)
| mb_sample_id | local_sample_id | Growth phase |
|---|---|---|
| SA006140 | Late exponential phase-P2 | Late exponential phase |
| SA006141 | Late exponential phase-S1 | Late exponential phase |
| SA006142 | Late exponential phase-S2 | Late exponential phase |
| SA006143 | Late exponential phase-S3 | Late exponential phase |
| SA006144 | Late exponential phase-P1 | Late exponential phase |
| SA006145 | Late exponential phase-P3 | Late exponential phase |
| SA006146 | Middle exponential phase-P3 | Middle exponential phase |
| SA006147 | Middle exponential phase-S3 | Middle exponential phase |
| SA006148 | Middle exponential phase-S1 | Middle exponential phase |
| SA006149 | Middle exponential phase-P2 | Middle exponential phase |
| SA006150 | Middle exponential phase-P1 | Middle exponential phase |
| SA006151 | Middle exponential phase-S2 | Middle exponential phase |
| SA006152 | Stationary phase-S2 | Stationary phase |
| SA006153 | Stationary phase-S3 | Stationary phase |
| SA006154 | Stationary phase-S1 | Stationary phase |
| SA006155 | Stationary phase-P2 | Stationary phase |
| SA006156 | Stationary phase-P1 | Stationary phase |
| SA006157 | Stationary phase-P3 | Stationary phase |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO000119 |
| Collection Summary: | The cells were quenched by immediately adding a threefold volume of pre-chilled 60% (v/v) methanol solution containing 70 mM 4-(2-hydroxyethyl)-1-piperazine ethanesulphonic acid, and pelleted in a centrifuge (4,000 × g, ?4°C, 10 min) |
| Collection Protocol Filename: | Protocol_Methods-G.docx |
| Sample Type: | cell |
| Collection Time: | Samples were collected at the middle exponential phase, late exponential phase, and the end of fermentation |
| Storage Conditions: | -80°C |
| Collection Vials: | 50mL centrifuge tube |
| Storage Vials: | 50mL centrifuge tube |
| Collection Tube Temp: | pre-chilled at -80°C |
| Additives: | pre-chilled 60% (v/v) methanol solution containing 70 mM 4-(2-hydroxyethyl)-1-piperazine ethanesulphonic acid |
Treatment:
| Treatment ID: | TR000137 |
| Cell Storage: | -80°C |
| Cell Growth Container: | 250 mL anaerobic jars |
| Cell Inoc Proc: | inoculated at 1% |
| Cell Media: | 10 g/L yeast extract, 5 g/L tryptic soy broth, 1.5 g/L KH2PO4, 2.5 g/L K2HPO4 |
| Cell Envir Cond: | incubated at 32°C, anaerobic |
Sample Preparation:
| Sampleprep ID: | SP000132 |
| Sampleprep Summary: | After quenching at 40°C, the cells were pelleted in a centrifuge (4,000 × g, ?4°C, 10 min). The pellets were washed with methanol solution and resuspended in 1 mL 35% perchloric acid to extract the metabolites from the cells. The mixture was frozen in liquid nitrogen and thawed three times. The supernatant was neutralized by adding K2CO3 solution with an initial concentration of 5 M, and an extract containing all metabolites was collected via centrifugation at 10,000 × g for 5 min at 4°C |
| Processing Method: | Homogenization and solvent removal |
| Processing Storage Conditions: | on ice |
| Extraction Method: | 35% perchloric acid and 5 M K2CO3 |
| Extract Storage: | -80°C |
| Cell Type: | wildtype cells, genome shffled cells |
Combined analysis:
| Analysis ID | AN000197 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | LCMS-IT-TOF |
| Column | Shim-Pack VP-ODS 150 L 2.0 |
| MS Type | ESI |
| MS instrument type | IT-TOF |
| MS instrument name | Shimadzu LCMS-IT-TOF |
| Ion Mode | UNSPECIFIED |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH000130 |
| Chromatography Summary: | LC-MS |
| Instrument Name: | LCMS-IT-TOF |
| Column Name: | Shim-Pack VP-ODS 150 L 2.0 |
| Column Pressure: | 18 MPa |
| Column Temperature: | 40C |
| Flow Gradient: | 2% to 60% B for 15 min, 60% to 76% B for 15 min, and 76% to 2% B for 5 min (A:1 mM ammonium formate; B: 80% methanol (v/v) containing 1 mM ammonium formate) |
| Flow Rate: | 0.2 mL/min |
| Retention Time: | 35 min |
| Sample Injection: | 10 ?L |
| Solvent A: | 100% water; 1 mM ammonium formate |
| Solvent B: | 80% methanol/20% water; 1 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000160 |
| Analysis ID: | AN000197 |
| Instrument Name: | Shimadzu LCMS-IT-TOF |
| Instrument Type: | IT-TOF |
| MS Type: | ESI |
| Ion Mode: | UNSPECIFIED |
| Collision Energy: | 0.4 |
| Collision Gas: | N2 |
| Dry Gas Flow: | 1.5 L/min |
| Dry Gas Temp: | 350°C |
| Mass Accuracy: | 5ppm |
| Acquisition Parameters File: | Protocol_Methods-G.docx |
