Summary of Study ST000887
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 PR000616. The data can be accessed directly via it's Project DOI: 10.21228/M89X34 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 | ST000887 |
| Study Title | Evaluation of Quenching and Extraction Procedures for Performing Metabolomics in Acidithiobacillus ferrooxidans |
| Study Summary | To perform a Metabolomic Analysis of At. ferrooxidans during its early exponential growth phase as well as its late exponential growth phase. |
| Institute | Laurentian University |
| Last Name | Doran |
| First Name | Marney |
| Address | Laurentian University |
| mdoran@laurentian.ca | |
| Phone | 8196740310 |
| Submit Date | 2017-10-26 |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-11-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000616 |
| Project DOI: | doi: 10.21228/M89X34 |
| Project Title: | Evaluation of Quenching and Extraction Procedures for Performing Metabolomics in Acidithiobacillus ferrooxidans |
| Project Type: | Metabolomic Analysis of At.ferrooxidans at Two Different Growth Phases |
| Project Summary: | To perform a Metabolomic Analysis of At. ferrooxidans during its early exponential growth phase as well as its late exponential growth phase. |
| Institute: | Laurentian University |
| Department: | Biochemistry/Chemistry |
| Laboratory: | Merritt Lab |
| Last Name: | Merritt |
| First Name: | Thomas |
| Address: | Laurentian University, Sudbury, Ontario, Canada P3E 2C6 |
| Email: | tmerritt@laurentian.ca |
| Phone: | (705)675-1151 ext 2189 |
| Funding Source: | Natural Science and Engineering Research Council(NSERC), Canada Research Chair(CRC) |
Subject:
| Subject ID: | SU001169 |
| Subject Type: | Bacteria |
| Subject Species: | Acidithiobacillus ferrooxidans ATCC 23270 |
| Taxonomy ID: | 243159 |
| Genotype Strain: | ATCC 23270 |
| Cell Biosource Or Supplier: | American Type Culture Collection |
| Cell Strain Details: | ATCC 23270 |
Factors:
Subject type: Bacteria; Subject species: Acidithiobacillus ferrooxidans ATCC 23270 (Factor headings shown in green)
| mb_sample_id | local_sample_id | Optic Density(OD) |
|---|---|---|
| SA076763 | 1-Early Exponential Phase | 0.65 |
| SA076764 | 6-Early Exponential Phase | 0.65 |
| SA076765 | 5-Early Exponential Phase | 0.65 |
| SA076766 | 2-Early Exponential Phase | 0.65 |
| SA076767 | 3-Early Exponential Phase | 0.65 |
| SA076768 | 4-Early Exponential Phase | 0.65 |
| SA076769 | 12-Late Exponential Phase | 0.85 |
| SA076770 | 11-Late Exponential Phase | 0.85 |
| SA076771 | 7-Late Exponential Phase | 0.85 |
| SA076772 | 8-Late Exponential Phase | 0.85 |
| SA076773 | 9-Late Exponential Phase | 0.85 |
| SA076774 | 10-Late Exponential Phase | 0.85 |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO001163 |
| Collection Summary: | Replicate cultures of Acidithiobacillus ferrooxidans (American Type Culture Collection strain 23270) were grown in 1 L of Tuovinen and Kelly (1973) liquid medium ([FeSO4·7H2O] = 33.4 g/L; 0.3 % (w/v) (NH4)2SO4; MgSO4·7H2O; K2HPO4, pH 2.5). Cells were incubated on a gyratory shaker at 180 rpm and 30 °C. Cells harvested for the metabolomic comparison of two points in the growth curve were in late exponential growth phase (OD425 = 0.85) or in early exponential growth phase (OD425 = 0.65). The cells were harvested via centrifugation at 14,000 x g for 5 min at 4 °C then transferred into a 1.5 mL centrifuge tube. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR001183 |
| Treatment Summary: | After the cells were concentrated into a 1.5ml centrifuge tube, the cellular metabolism was quenched using 40ul of 60% MeOH and 40% H2O (v/v) with 0.85% (w/v) of Ammonium Formate, adjusted to pH 2.5 and cooled to -20 °C. The quenched cells were centrifuged for 5 minutes at 2,319 x g at 4 °C. The cells were then placed on dry ice, the cell supernatant was removed and an isopropanol:methanol:water (IMW) (3:3:2) extraction solution that was cooled to -20 °C was added. These solutions were then vigorously vortexed and then centrifuged at 15,682 x g for 10 min. The extraction liquid was then collected and placed at -80 °C until further analysis. |
Sample Preparation:
| Sampleprep ID: | SP001176 |
| Sampleprep Summary: | Immediately prior to analysis the extraction solution was evaporated to dryness and reconstituted in 80:20 Acetonitrile:Water. The samples were normalized based on Gcdw. |
Combined analysis:
| Analysis ID | AN001821 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker MicrOTOF II |
| Ion Mode | POSITIVE |
| Units | m/z-retention time features |
Chromatography:
| Chromatography ID: | CH001290 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Flow Gradient: | (t= 0-1 minute) 3% A, 97% B; (t= 24 minute) 40% A, 60% B; (t= 28 minute) 40% A, 60% B (t= 33 minutes) 3% A, 97% B; (t= 34minutes) 3% A, 97% B. HPLC flow rate 0.4 mL/min. |
| Flow Rate: | 0.4ml/min |
| Solvent A: | 100% water; 20 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001684 |
| Analysis ID: | AN001821 |
| Instrument Name: | Bruker MicrOTOF II |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | None |
| Ion Mode: | POSITIVE |
