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

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001422
Project DOI:	doi: 10.21228/M8X411
Project Title:	Steady-state metabolomics Saccharomyces cerevisiae mitochondrial fatty acid synthesis (mtFAS) mutants and CTP1 overexpression
Project Type:	Steady-state targeted and untargeted metabolomics
Project 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
Funding Source:	R35GM131854
Publications:	https://doi.org/10.1101/2020.06.25.171850
Contributors:	Yeyun Ouyang, Ahmad Cluntun, Jordan Berg

Subject:

Subject ID:	SU002318
Subject Type:	Yeast
Subject Species:	Saccharomyces cerevisiae
Taxonomy ID:	4932
Genotype Strain:	BY4743 (MATa/\textalpha, his3/his3, leu2/leu2, ura3/ura3, met15/MET15, lys2/LYS2)

Factors:

Subject type: Yeast; Subject species: Saccharomyces cerevisiae (Factor headings shown in green)

mb_sample_id	local_sample_id	Strain	Genotype	Experimental Factor 1 - Vector	Experimental Factor 2 - Media	Experimental Factor 2 - Replicate
SA212639	MCT_A1_SD	BY4743	mct1 deletion	CTP1-overexpression vector	S-complete + 2% glucose	replicate 1
SA212640	MCT_A2_SD	BY4743	mct1 deletion	CTP1-overexpression vector	S-complete + 2% glucose	replicate 2
SA212641	MCT_A3_SD	BY4743	mct1 deletion	CTP1-overexpression vector	S-complete + 2% glucose	replicate 3
SA212642	MCT_A1_SR	BY4743	mct1 deletion	CTP1-overexpression vector	S-complete + 2% raffinose	replicate 1
SA212643	MCT_A2_SR	BY4743	mct1 deletion	CTP1-overexpression vector	S-complete + 2% raffinose	replicate 2
SA212644	MCT_A3_SR	BY4743	mct1 deletion	CTP1-overexpression vector	S-complete + 2% raffinose	replicate 3
SA212645	MCT_EV1_SD	BY4743	mct1 deletion	empty vector	S-complete + 2% glucose	replicate 1
SA212646	MCT_EV2_SD	BY4743	mct1 deletion	empty vector	S-complete + 2% glucose	replicate 2
SA212647	MCT_EV3_SD	BY4743	mct1 deletion	empty vector	S-complete + 2% glucose	replicate 3
SA212648	MCT_EV1_SR	BY4743	mct1 deletion	empty vector	S-complete + 2% raffinose	replicate 1
SA212649	MCT_EV2_SR	BY4743	mct1 deletion	empty vector	S-complete + 2% raffinose	replicate 2
SA212650	MCT_EV3_SR	BY4743	mct1 deletion	empty vector	S-complete + 2% raffinose	replicate 3
SA212651	WT_A1_SD	BY4743	wild type	CTP1-overexpression vector	S-complete + 2% glucose	replicate 1
SA212652	WT_A2_SD	BY4743	wild type	CTP1-overexpression vector	S-complete + 2% glucose	replicate 2
SA212653	WT_A3_SD	BY4743	wild type	CTP1-overexpression vector	S-complete + 2% glucose	replicate 3
SA212654	WT_A1_SR	BY4743	wild type	CTP1-overexpression vector	S-complete + 2% raffinose	replicate 1
SA212655	WT_A2_SR	BY4743	wild type	CTP1-overexpression vector	S-complete + 2% raffinose	replicate 2
SA212656	WT_A3_SR	BY4743	wild type	CTP1-overexpression vector	S-complete + 2% raffinose	replicate 3
SA212657	WT_EV1_SD	BY4743	wild type	empty vector	S-complete + 2% glucose	replicate 1
SA212658	WT_EV2_SD	BY4743	wild type	empty vector	S-complete + 2% glucose	replicate 2
SA212659	WT_EV3_SD	BY4743	wild type	empty vector	S-complete + 2% glucose	replicate 3
SA212660	WT_EV1_SR	BY4743	wild type	empty vector	S-complete + 2% raffinose	replicate 1
SA212661	WT_EV2_SR	BY4743	wild type	empty vector	S-complete + 2% raffinose	replicate 2
SA212662	WT_EV3_SR	BY4743	wild type	empty vector	S-complete + 2% raffinose	replicate 3

Showing results 1 to 24 of 24

Showing results 1 to 24 of 24

Collection:

Collection ID:	CO002311
Collection Summary:	Metabolomics data were generated by growing the appropriate yeast strains in synthetic complete media supplemented with 2% glucose until they reached saturation (n=3). Cells were then transferred to S-minimal media containing 2% raffinose and leucine and harvested after approximately 8 hours (n=3) at OD600=0.6-0.8. The procedures for metabolite extraction were performed as previously described in [Bricker et al., Science, 2012]. Yeast cultures were pelleted, snap-frozen and kept at −80°C. 5ml of 75% boiled ethanol was added to every frozen pellet. Pellets were vortexed and incubated at 90°C for 5 minutes. All samples were then centrifuged at 5,000 Relative Centrifugal Force (RCF) for 10 minutes. Supernatants were transferred to fresh tubes, evaporated overnight in a Speed Vacuum, and then stored at −80°C until they were run on the mass spectrometer.
Sample Type:	Yeast cells

Treatment:

Treatment ID:	TR002330
Treatment Summary:	N/A

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.

Combined analysis:

Analysis ID	AN003642
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Dionex Ultimate 3000
Column	Waters XBridge Amide (100 x 4.6mm,3.5um)
MS Type	ESI
MS instrument type	LC-Q Exactive
MS instrument name	Thermo Q-Exactive
Ion Mode	UNSPECIFIED
Units	peak height

Chromatography:

Chromatography ID:	CH002696
Chromatography 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.
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters XBridge Amide (100 x 4.6mm,3.5um)
Flow Gradient:	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
Flow Rate:	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
Solvent A:	100% water; 20 mM ammonium acetate; 15 mM ammonium hydroxide; 3% acetonitrile, pH 9.0
Solvent B:	100% acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS003393
Analysis ID:	AN003642
Instrument Name:	Thermo Q-Exactive
Instrument Type:	LC-Q Exactive
MS Type:	ESI
MS Comments:	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.
Ion Mode:	UNSPECIFIED