Summary of Study ST002232

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 PR001422. The data can be accessed directly via it's Project DOI: 10.21228/M8X411 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	ST002232
Study Title	Steady-state metabolomics Saccharomyces cerevisiae mitochondrial fatty acid synthesis (mtFAS) mutants and CTP1 overexpression
Study Type	Steady-state targeted and untargeted metabolomics
Study Summary	The goal of this work was to analyze metabolic changes in yeast with the mct1 gene knock-out or CTP1 overexpression conditions using liquid chromatography-mass spectrometry (LC-MS).
Institute	University of Utah
Department	Biochemistry
Laboratory	Rutter
Last Name	Berg
First Name	Jordan
Address	15 N Medical Drive East RM 5520, Salt Lake City, UT 84112-5650 USA
Email	jordan.berg@biochem.utah.edu
Phone	+1 (801) 581 3340
Submit Date	2022-07-10
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2022-08-08
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP002324
Sampleprep Summary:	The conditions for liquid chromatography are described in previous studies [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. Briefly, a hydrophilic interaction liquid chromatography method (HILIC) with an Xbridge amide column (100 × 2.1 mm, 3.5 μm) (Waters) was employed on a Dionex (Ultimate 3000 UHPLC) for compound separation and detection at room temperature. The mobile phase A was 20 mM ammonium acetate and 15 mM ammonium hydroxide in water with 3% acetonitrile, pH 9.0, and the mobile phase B was acetonitrile. The linear gradient was as follows: 0 min, 85% B; 1.5 min, 85% B, 5.5 min, 35% B; 10 min, 35% B, 10.5 min, 35% B, 14.5 min, 35% B, 15 min, 85% B, and 20 min, 85% B. The flow rate was 0.15 ml/min from 0 to 10 min and 15 to 20 min, and 0.3 ml/min from 10.5 to 14.5 min. All solvents were LC-MS grade and purchased from Thermo Fisher Scientific. Mass spectrometry was performed as described in previous studies [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. Briefly, the Q Exactive MS (Thermo Scientific) is equipped with a heated electrospray ionization probe (HESI), and the relevant parameters are as listed: evaporation temperature, 120°C; sheath gas, 30; auxiliary gas, 10; sweep gas, 3; spray voltage, 3.6 kV for positive mode and 2.5 kV for negative mode. Capillary temperature was set at 320°C, and S-lens was 55. A full scan range from 60 to 900 (m/z) was used. The resolution was set at 70,000. The maximum injection time was 200 ms. Automated gain control (AGC) was targeted at 3,000,000 ions. Data were collected, metabolites were identified, and their peak area was recorded using El-MAVEN software [Agrawal et al., Methods Mol. Biol., 2019; Clasquin et al., Curr. Protoc. Bioinformatics, 2012; Melamud et al., Anal. Chem., 2010]. These data were transferred to an Excel spreadsheet (Microsoft, Redmond WA). Metabolite identity was established using a combination of an in-house metabolite library developed using pure purchased standards, the NIST (https://www.nist.gov) and Fiehn libraries [Kind et al, Anal. Chem., 2009]. P-values were derived using a homoscedastic, two-tailed Student's T-test and adjusted using the Benjamini-Hochberg correction procedure.

Sampleprep ID:

SP002324

Sampleprep Summary:

The conditions for liquid chromatography are described in previous studies [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. Briefly, a hydrophilic interaction liquid chromatography method (HILIC) with an Xbridge amide column (100 × 2.1 mm, 3.5 μm) (Waters) was employed on a Dionex (Ultimate 3000 UHPLC) for compound separation and detection at room temperature. The mobile phase A was 20 mM ammonium acetate and 15 mM ammonium hydroxide in water with 3% acetonitrile, pH 9.0, and the mobile phase B was acetonitrile. The linear gradient was as follows: 0 min, 85% B; 1.5 min, 85% B, 5.5 min, 35% B; 10 min, 35% B, 10.5 min, 35% B, 14.5 min, 35% B, 15 min, 85% B, and 20 min, 85% B. The flow rate was 0.15 ml/min from 0 to 10 min and 15 to 20 min, and 0.3 ml/min from 10.5 to 14.5 min. All solvents were LC-MS grade and purchased from Thermo Fisher Scientific. Mass spectrometry was performed as described in previous studies [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. Briefly, the Q Exactive MS (Thermo Scientific) is equipped with a heated electrospray ionization probe (HESI), and the relevant parameters are as listed: evaporation temperature, 120°C; sheath gas, 30; auxiliary gas, 10; sweep gas, 3; spray voltage, 3.6 kV for positive mode and 2.5 kV for negative mode. Capillary temperature was set at 320°C, and S-lens was 55. A full scan range from 60 to 900 (m/z) was used. The resolution was set at 70,000. The maximum injection time was 200 ms. Automated gain control (AGC) was targeted at 3,000,000 ions. Data were collected, metabolites were identified, and their peak area was recorded using El-MAVEN software [Agrawal et al., Methods Mol. Biol., 2019; Clasquin et al., Curr. Protoc. Bioinformatics, 2012; Melamud et al., Anal. Chem., 2010]. These data were transferred to an Excel spreadsheet (Microsoft, Redmond WA). Metabolite identity was established using a combination of an in-house metabolite library developed using pure purchased standards, the NIST (https://www.nist.gov) and Fiehn libraries [Kind et al, Anal. Chem., 2009]. P-values were derived using a homoscedastic, two-tailed Student's T-test and adjusted using the Benjamini-Hochberg correction procedure.