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.

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Study IDST000116
Study TitleComparative metabolomics analysis of the key metabolic nodes in propionic acid synthesis in Propionibacterium acidipropionici
Study Typestrains comparison
Study SummaryThe parental P. acidipropionici and its genome-shuffled mutant were compared via metabolomics to find the key metabolic nodes influencing PA production.
Institute
Jiangnan University
DepartmentKey Laboratory of Carbohydrate Chemistry and Biotechnology
Last NameGuan
First NameNingzi
Address1800 Lihu Ave, Binhu, Wuxi, Jiangsu, China
Emailcaimo-zi@163.com
Submit Date2014-11-14
Raw Data AvailableNo
Analysis Type DetailLC-MS
Release Date2015-02-03
Release Version1
Ningzi Guan Ningzi Guan
https://dx.doi.org/10.21228/M8W300
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:Propionibacterium acidipropionici
Taxonomy ID:GCMCC1.2230/WSH1105
Genotype Strain:wild type mutant
Species Group:Microorganism

Factors:

Subject type: Bacterial cells; Subject species: Propionibacterium acidipropionici (Factor headings shown in green)

mb_sample_id local_sample_id Growth phase
SA006140Late exponential phase-P2Late exponential phase
SA006141Late exponential phase-S1Late exponential phase
SA006142Late exponential phase-S2Late exponential phase
SA006143Late exponential phase-S3Late exponential phase
SA006144Late exponential phase-P1 Late exponential phase
SA006145Late exponential phase-P3Late exponential phase
SA006146Middle exponential phase-P3Middle exponential phase
SA006147Middle exponential phase-S3Middle exponential phase
SA006148Middle exponential phase-S1 Middle exponential phase
SA006149Middle exponential phase-P2Middle exponential phase
SA006150Middle exponential phase-P1 Middle exponential phase
SA006151Middle exponential phase-S2Middle exponential phase
SA006152Stationary phase-S2Stationary phase
SA006153Stationary phase-S3Stationary phase
SA006154Stationary phase-S1Stationary phase
SA006155Stationary phase-P2Stationary phase
SA006156Stationary phase-P1Stationary phase
SA006157Stationary phase-P3Stationary 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 POSITIVE/NEGATIVE
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:1 mM ammonium formate
Solvent B:80% methanol (v/v) containing 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:POSITIVE/NEGATIVE
Collision Energy:0.4
Collision Gas:N2
Dry Gas Flow:1.5 L/min
Dry Gas Temp:350°C
Mass Accuracy:5ppm
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