#METABOLOMICS WORKBENCH j_berg_20220710_145254 DATATRACK_ID:3333 STUDY_ID:ST002232 ANALYSIS_ID:AN003642 PROJECT_ID:PR001422 VERSION 1 CREATED_ON July 21, 2022, 12:17 pm #PROJECT PR:PROJECT_TITLE Steady-state metabolomics Saccharomyces cerevisiae mitochondrial fatty acid PR:PROJECT_TITLE synthesis (mtFAS) mutants and CTP1 overexpression PR:PROJECT_TYPE Steady-state targeted and untargeted metabolomics PR:PROJECT_SUMMARY The goal of this work was to analyze metabolic changes in yeast with the mct1 PR:PROJECT_SUMMARY gene knock-out or CTP1 overexpression conditions using liquid PR:PROJECT_SUMMARY chromatography-mass spectrometry (LC-MS). PR:INSTITUTE University of Utah PR:DEPARTMENT Biochemistry PR:LABORATORY Rutter PR:LAST_NAME Berg PR:FIRST_NAME Jordan PR:ADDRESS 15 N Medical Drive East RM 5520, Salt Lake City, UT 84112-5650 USA PR:EMAIL jordan.berg@biochem.utah.edu PR:PHONE +1 (801) 581 3340 PR:FUNDING_SOURCE R35GM131854 PR:PUBLICATIONS https://doi.org/10.1101/2020.06.25.171850 PR:CONTRIBUTORS Yeyun Ouyang, Ahmad Cluntun, Jordan Berg #STUDY ST:STUDY_TITLE Steady-state metabolomics Saccharomyces cerevisiae mitochondrial fatty acid ST:STUDY_TITLE synthesis (mtFAS) mutants and CTP1 overexpression ST:STUDY_TYPE Steady-state targeted and untargeted metabolomics ST:STUDY_SUMMARY The goal of this work was to analyze metabolic changes in yeast with the mct1 ST:STUDY_SUMMARY gene knock-out or CTP1 overexpression conditions using liquid ST:STUDY_SUMMARY chromatography-mass spectrometry (LC-MS). ST:INSTITUTE University of Utah ST:DEPARTMENT Biochemistry ST:LABORATORY Rutter ST:LAST_NAME Berg ST:FIRST_NAME Jordan ST:ADDRESS 15 N Medical Drive East RM 5520, Salt Lake City, UT 84112-5650 USA ST:EMAIL jordan.berg@biochem.utah.edu ST:PHONE +1 (801) 581 3340 #SUBJECT SU:SUBJECT_TYPE Yeast SU:SUBJECT_SPECIES Saccharomyces cerevisiae SU:TAXONOMY_ID 4932 SU:GENOTYPE_STRAIN BY4743 (MATa/ extalpha, his3/his3, leu2/leu2, ura3/ura3, met15/MET15, SU:GENOTYPE_STRAIN lys2/LYS2) #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - WT_EV1_SD Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=WT_EV1_SD.mzXML SUBJECT_SAMPLE_FACTORS - WT_EV1_SR Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=WT_EV1_SR.mzXML SUBJECT_SAMPLE_FACTORS - WT_EV2_SD Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=WT_EV2_SD.mzXML SUBJECT_SAMPLE_FACTORS - WT_EV2_SR Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=WT_EV2_SR.mzXML SUBJECT_SAMPLE_FACTORS - WT_EV3_SD Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=WT_EV3_SD.mzXML SUBJECT_SAMPLE_FACTORS - WT_EV3_SR Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=WT_EV3_SR.mzXML SUBJECT_SAMPLE_FACTORS - WT_A1_SD Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=WT_A1_SD.mzXML SUBJECT_SAMPLE_FACTORS - WT_A1_SR Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=WT_A1_SR.mzXML SUBJECT_SAMPLE_FACTORS - WT_A2_SD Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=WT_A2_SD.mzXML SUBJECT_SAMPLE_FACTORS - WT_A2_SR Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=WT_A2_SR.mzXML SUBJECT_SAMPLE_FACTORS - WT_A3_SD Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=WT_A3_SD.mzXML SUBJECT_SAMPLE_FACTORS - WT_A3_SR Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=WT_A3_SR.mzXML SUBJECT_SAMPLE_FACTORS - MCT_EV1_SD Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=MCT_EV1_SD.mzXML SUBJECT_SAMPLE_FACTORS - MCT_EV2_SD Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=MCT_EV2_SD.mzXML SUBJECT_SAMPLE_FACTORS - MCT_EV3_SD Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=MCT_EV3_SD.mzXML SUBJECT_SAMPLE_FACTORS - MCT_EV1_SR Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=MCT_EV1_SR.mzXML SUBJECT_SAMPLE_FACTORS - MCT_EV2_SR Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=MCT_EV2_SR.mzXML SUBJECT_SAMPLE_FACTORS - MCT_EV3_SR Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=MCT_EV3_SR.mzXML SUBJECT_SAMPLE_FACTORS - MCT_A1_SD Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=MCT_A1_SD.mzXML SUBJECT_SAMPLE_FACTORS - MCT_A1_SR Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 RAW_FILE_NAME=MCT_A1_SR.mzXML SUBJECT_SAMPLE_FACTORS - MCT_A2_SD Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=MCT_A2_SD.mzXML SUBJECT_SAMPLE_FACTORS - MCT_A2_SR Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 RAW_FILE_NAME=MCT_A2_SR.mzXML SUBJECT_SAMPLE_FACTORS - MCT_A3_SD Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=MCT_A3_SD.mzXML SUBJECT_SAMPLE_FACTORS - MCT_A3_SR Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 RAW_FILE_NAME=MCT_A3_SR.mzXML #COLLECTION CO:COLLECTION_SUMMARY Metabolomics data were generated by growing the appropriate yeast strains in CO:COLLECTION_SUMMARY synthetic complete media supplemented with 2% glucose until they reached CO:COLLECTION_SUMMARY saturation (n=3). Cells were then transferred to S-minimal media containing 2% CO:COLLECTION_SUMMARY raffinose and leucine and harvested after approximately 8 hours (n=3) at CO:COLLECTION_SUMMARY OD600=0.6-0.8. The procedures for metabolite extraction were performed as CO:COLLECTION_SUMMARY previously described in [Bricker et al., Science, 2012]. Yeast cultures were CO:COLLECTION_SUMMARY pelleted, snap-frozen and kept at −80°C. 5ml of 75% boiled ethanol was added CO:COLLECTION_SUMMARY to every frozen pellet. Pellets were vortexed and incubated at 90°C for 5 CO:COLLECTION_SUMMARY minutes. All samples were then centrifuged at 5,000 Relative Centrifugal Force CO:COLLECTION_SUMMARY (RCF) for 10 minutes. Supernatants were transferred to fresh tubes, evaporated CO:COLLECTION_SUMMARY overnight in a Speed Vacuum, and then stored at −80°C until they were run on CO:COLLECTION_SUMMARY the mass spectrometer. CO:SAMPLE_TYPE Yeast cells #TREATMENT TR:TREATMENT_SUMMARY N/A #SAMPLEPREP SP:SAMPLEPREP_SUMMARY The conditions for liquid chromatography are described in previous studies SP:SAMPLEPREP_SUMMARY [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. Briefly, a SP:SAMPLEPREP_SUMMARY hydrophilic interaction liquid chromatography method (HILIC) with an Xbridge SP:SAMPLEPREP_SUMMARY amide column (100 × 2.1 mm, 3.5 μm) (Waters) was employed on a Dionex SP:SAMPLEPREP_SUMMARY (Ultimate 3000 UHPLC) for compound separation and detection at room temperature. SP:SAMPLEPREP_SUMMARY The mobile phase A was 20 mM ammonium acetate and 15 mM ammonium hydroxide in SP:SAMPLEPREP_SUMMARY water with 3% acetonitrile, pH 9.0, and the mobile phase B was acetonitrile. The SP:SAMPLEPREP_SUMMARY linear gradient was as follows: 0 min, 85% B; 1.5 min, 85% B, 5.5 min, 35% B; 10 SP:SAMPLEPREP_SUMMARY min, 35% B, 10.5 min, 35% B, 14.5 min, 35% B, 15 min, 85% B, and 20 min, 85% B. SP:SAMPLEPREP_SUMMARY The flow rate was 0.15 ml/min from 0 to 10 min and 15 to 20 min, and 0.3 ml/min SP:SAMPLEPREP_SUMMARY from 10.5 to 14.5 min. All solvents were LC-MS grade and purchased from Thermo SP:SAMPLEPREP_SUMMARY Fisher Scientific. Mass spectrometry was performed as described in previous SP:SAMPLEPREP_SUMMARY studies [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. SP:SAMPLEPREP_SUMMARY Briefly, the Q Exactive MS (Thermo Scientific) is equipped with a heated SP:SAMPLEPREP_SUMMARY electrospray ionization probe (HESI), and the relevant parameters are as listed: SP:SAMPLEPREP_SUMMARY evaporation temperature, 120°C; sheath gas, 30; auxiliary gas, 10; sweep gas, SP:SAMPLEPREP_SUMMARY 3; spray voltage, 3.6 kV for positive mode and 2.5 kV for negative mode. SP:SAMPLEPREP_SUMMARY Capillary temperature was set at 320°C, and S-lens was 55. A full scan range SP:SAMPLEPREP_SUMMARY from 60 to 900 (m/z) was used. The resolution was set at 70,000. The maximum SP:SAMPLEPREP_SUMMARY injection time was 200 ms. Automated gain control (AGC) was targeted at SP:SAMPLEPREP_SUMMARY 3,000,000 ions. Data were collected, metabolites were identified, and their peak SP:SAMPLEPREP_SUMMARY area was recorded using El-MAVEN software [Agrawal et al., Methods Mol. Biol., SP:SAMPLEPREP_SUMMARY 2019; Clasquin et al., Curr. Protoc. Bioinformatics, 2012; Melamud et al., Anal. SP:SAMPLEPREP_SUMMARY Chem., 2010]. These data were transferred to an Excel spreadsheet (Microsoft, SP:SAMPLEPREP_SUMMARY Redmond WA). Metabolite identity was established using a combination of an SP:SAMPLEPREP_SUMMARY in-house metabolite library developed using pure purchased standards, the NIST SP:SAMPLEPREP_SUMMARY (https://www.nist.gov) and Fiehn libraries [Kind et al, Anal. Chem., 2009]. SP:SAMPLEPREP_SUMMARY P-values were derived using a homoscedastic, two-tailed Student's T-test and SP:SAMPLEPREP_SUMMARY adjusted using the Benjamini-Hochberg correction procedure. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The conditions for liquid chromatography are described in previous studies CH:CHROMATOGRAPHY_SUMMARY [Cluntun et al., Cancer Metab., 2015; Lukey et al., Cell Rep., 2019]. Briefly, a CH:CHROMATOGRAPHY_SUMMARY hydrophilic interaction liquid chromatography method (HILIC) with an Xbridge CH:CHROMATOGRAPHY_SUMMARY amide column (100 × 2.1 mm, 3.5 μm) (Waters) was employed on a Dionex CH:CHROMATOGRAPHY_SUMMARY (Ultimate 3000 UHPLC) for compound separation and detection at room temperature. CH:CHROMATOGRAPHY_SUMMARY The mobile phase A was 20 mM ammonium acetate and 15 mM ammonium hydroxide in CH:CHROMATOGRAPHY_SUMMARY water with 3% acetonitrile, pH 9.0, and the mobile phase B was acetonitrile. The CH:CHROMATOGRAPHY_SUMMARY linear gradient was as follows: 0 min, 85% B; 1.5 min, 85% B, 5.5 min, 35% B; 10 CH:CHROMATOGRAPHY_SUMMARY min, 35% B, 10.5 min, 35% B, 14.5 min, 35% B, 15 min, 85% B, and 20 min, 85% B. CH:CHROMATOGRAPHY_SUMMARY The flow rate was 0.15 ml/min from 0 to 10 min and 15 to 20 min, and 0.3 ml/min CH:CHROMATOGRAPHY_SUMMARY from 10.5 to 14.5 min. All solvents were LC-MS grade and purchased from Thermo CH:CHROMATOGRAPHY_SUMMARY Fisher Scientific. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME Waters XBridge Amide (100 x 4.6mm, 3.5um) CH: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, CH:FLOW_GRADIENT 14.5 min, 35% B, 15 min, 85% B, and 20 min, 85% B CH: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 CH:FLOW_RATE min CH:SOLVENT_A 20 mM ammonium acetate and 15 mM ammonium hydroxide in water with 3% CH:SOLVENT_A acetonitrile, pH 9.0 CH:SOLVENT_B acetonitrile #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Q Exactive MS:INSTRUMENT_TYPE LC-Q Exactive MS:MS_TYPE Other MS:ION_MODE UNSPECIFIED MS:MS_COMMENTS Data were collected, metabolites were identified, and their peak area was MS:MS_COMMENTS recorded using El-MAVEN software [Agrawal et al., Methods Mol. Biol., 2019; MS:MS_COMMENTS Clasquin et al., Curr. Protoc. Bioinformatics, 2012; Melamud et al., Anal. MS:MS_COMMENTS Chem., 2010]. These data were transferred to an Excel spreadsheet (Microsoft, MS:MS_COMMENTS Redmond WA). Metabolite identity was established using a combination of an MS:MS_COMMENTS in-house metabolite library developed using pure purchased standards, the NIST MS:MS_COMMENTS (https://www.nist.gov) and Fiehn libraries [Kind et al, Anal. Chem., 2009]. MS:MS_COMMENTS P-values were derived using a homoscedastic, two-tailed Student's T-test and MS:MS_COMMENTS adjusted using the Benjamini-Hochberg correction procedure. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS peak height MS_METABOLITE_DATA_START Samples MCT_A1_SD MCT_A2_SD MCT_A3_SD MCT_A1_SR MCT_A2_SR MCT_A3_SR MCT_EV1_SD MCT_EV2_SD MCT_EV3_SD MCT_EV1_SR MCT_EV2_SR MCT_EV3_SR WT_A1_SD WT_A2_SD WT_A3_SD WT_A1_SR WT_A2_SR WT_A3_SR WT_EV1_SD WT_EV2_SD WT_EV3_SD WT_EV1_SR WT_EV2_SR WT_EV3_SR Factors Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:mct1 deletion | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:CTP1-overexpression vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% glucose | Experimental Factor 2 - Replicate:replicate 3 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 1 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 2 Strain:BY4743 | Genotype:wild type | Experimental Factor 1 - Vector:empty vector | Experimental Factor 2 - Media:S-complete + 2% raffinose | Experimental Factor 2 - Replicate:replicate 3 Citric acid 230000000 160000000 360000000 230000000 200000000 220000000 200000000 280000000 200000000 180000000 170000000 110000000 130000000 260000000 170000000 90000000 81000000 85000000 56000000 120000000 160000000 63000000 60000000 52000000 Glucose 7500000 9200000 13000000 170000000 160000000 160000000 8400000 13000000 7000000 230000000 180000000 120000000 3200000 12000000 8700000 150000000 170000000 170000000 4200000 11000000 14000000 170000000 17000000 150000000 Pyruvic acid 9700000 13000000 12000000 5000000 4700000 3800000 7800000 12000000 9800000 5000000 5500000 5300000 6400000 11000000 10000000 4200000 6400000 6100000 10000000 16000000 13000000 5700000 6300000 4500000 Aspartic acid 680000000 930000000 1100000000 820000000 850000000 940000000 950000000 1100000000 950000000 890000000 990000000 670000000 470000000 720000000 1100000000 740000000 890000000 430000000 500000000 840000000 980000000 690000000 720000000 530000000 ATP 10000000 9000000 13000000 3300000 5900000 6500000 10000000 12000000 21000000 860000 2400000 1500000 9100000 8700000 7600000 2900000 3900000 3400000 8300000 10000000 13000000 1900000 4400000 4500000 Oxoglutaric acid 12000000 11000000 20000000 3600000 690000 1000000 15000000 21000000 24000000 3700000 2000000 3000000 16000000 24000000 14000000 3800000 2700000 1500000 9600000 13000000 11000000 3000000 1800000 1600000 Glutamine 67000000 92000000 84000000 78000000 73000000 39000000 110000000 110000000 110000000 81000000 85000000 73000000 73000000 62000000 77000000 80000000 80000000 46000000 86000000 100000000 69000000 93000000 79000000 79000000 Glutamic acid 630000000 880000000 930000000 850000000 770000000 590000000 1000000000 1100000000 950000000 950000000 990000000 700000000 790000000 1200000000 1300000000 1400000000 1400000000 830000000 1000000000 1500000000 1300000000 1600000000 1400000000 1200000000 Oxidized glutathione 60000000 45000000 89000000 19000000 27000000 22000000 95000000 100000000 110000000 21000000 35000000 19000000 83000000 80000000 79000000 21000000 30000000 19000000 59000000 130000000 140000000 29000000 33000000 39000000 Sucrose 6000000 6600000 11000000 130000000 120000000 120000000 1100000 980000 910000 180000000 140000000 84000000 650000 2300000 2700000 110000000 120000000 120000000 980000 980000 960000 140000000 130000000 100000000 Mannose 7500000 9200000 13000000 170000000 160000000 160000000 8400000 13000000 7000000 230000000 180000000 120000000 3200000 12000000 8700000 150000000 170000000 170000000 4200000 11000000 14000000 170000000 170000000 150000000 D-Malic acid 14000000 8800000 9300000 49000000 34000000 48000000 24000000 17000000 14000000 64000000 45000000 29000000 4600000 9800000 15000000 24000000 20000000 15000000 7900000 6500000 6500000 20000000 24000000 12000000 Lysine 500000000 1900000000 1100000000 840000000 890000000 970000000 980000000 1200000000 890000000 960000000 1100000000 1200000000 990000000 1100000000 1100000000 920000000 990000000 1000000000 920000000 1300000000 1400000000 880000000 1000000000 1000000000 Leucine 1900000000 1200000000 2700000000 2700000000 810000000 2700000000 2300000000 2700000000 820000000 1000000000 2700000000 2500000000 2100000000 1000000000 1600000000 2800000000 2800000000 1600000000 1500000000 1500000000 1700000000 2500000000 1100000000 1300000000 Lactose 6000000 6600000 11000000 130000000 120000000 120000000 1100000 980000 910000 180000000 140000000 84000000 650000 2300000 2700000 110000000 120000000 120000000 980000 980000 960000 140000000 130000000 100000000 "Fructose 1,6-bisphosphate" 150000000 170000000 200000000 160000000 130000000 140000000 250000000 260000000 330000000 110000000 120000000 67000000 240000000 230000000 250000000 90000000 120000000 140000000 130000000 280000000 320000000 140000000 160000000 130000000 Fructose 7500000 9200000 13000000 170000000 160000000 160000000 8400000 13000000 7000000 230000000 180000000 120000000 3200000 12000000 8700000 150000000 170000000 170000000 4200000 11000000 14000000 170000000 170000000 150000000 Fructose 6-phosphate 78750000 89600000 106500000 165000000 145000000 150000000 129200000 136500000 168500000 170000000 150000000 93500000 121600000 121000000 129350000 120000000 145000000 155000000 67100000 145500000 167000000 155000000 165000000 140000000 Coenzyme A 240000 260000 260000 59000 98000 34000 250000 350000 470000 73000 97000 62000 270000 330000 160000 270000 120000 70000 400000 530000 180000 200000 230000 120000 Asparagine 31000000 36000000 36000000 30000000 26000000 27000000 35000000 36000000 33000000 26000000 28000000 24000000 33000000 37000000 32000000 32000000 31000000 30000000 26000000 31000000 31000000 27000000 29000000 32000000 Arginine 160000000 170000000 270000000 210000000 220000000 230000000 240000000 300000000 290000000 240000000 250000000 280000000 250000000 280000000 260000000 260000000 270000000 270000000 230000000 330000000 350000000 260000000 290000000 270000000 Alanine 110000000 130000000 150000000 150000000 140000000 160000000 170000000 190000000 170000000 160000000 180000000 150000000 110000000 130000000 160000000 130000000 150000000 61000000 93000000 170000000 190000000 130000000 130000000 98000000 Acetoacetic acid 96000000 92000000 120000000 4300000 1200000 4700000 130000000 140000000 130000000 3900000 3400000 4800000 110000000 170000000 130000000 5100000 4100000 2400000 85000000 87000000 100000000 4000000 2500000 1000000 Valine 215000000 140000000 330000000 135000000 66650000 139650000 420000000 470000000 172000000 56550000 168000000 205000000 270000000 335000000 315000000 128950000 128350000 56800000 195000000 250000000 255000000 108100000 81850000 107600000 Fumaric acid 33500000 36500000 51500000 57500000 62000000 71000000 54000000 58000000 54500000 58000000 73000000 70500000 27000000 43500000 44500000 43500000 48500000 29000000 21000000 42000000 43150000 33000000 35000000 25900000 Succinic acid 20000000 28000000 44500000 70000000 45500000 121500000 60500000 70500000 46000000 101500000 165000000 195000000 30500000 45000000 35000000 31500000 48000000 23000000 56000000 32500000 43500000 91000000 31500000 34500000 Adenosine 690000 1800000 1100000 1800000 3300000 3000000 970000 1300000 1000000 8100000 8100000 13000000 800000 1400000 2100000 3200000 5400000 5200000 990000 1700000 2400000 8000000 6900000 6300000 Inosine 83000000 29000000 110000000 120000000 36000000 100000000 54000000 31000000 10000000 25000000 47000000 41000000 36000000 23000000 51000000 34000000 46000000 11000000 40000000 14000000 40000000 22000000 5200000 18000000 Adenine 800000000 790000000 730000000 730000000 740000000 640000000 490000000 96000000 69000000 440000000 390000000 760000000 410000000 740000000 700000000 540000000 630000000 490000000 300000000 430000000 450000000 270000000 420000000 530000000 Uracil 67000000 79000000 100000000 160000000 52000000 73000000 89000000 86000000 43000000 50000000 140000000 89000000 56000000 57000000 110000000 120000000 150000000 46000000 56000000 78000000 70000000 67000000 66000000 52000000 Hypoxanthine 270000000 280000000 310000000 370000000 280000000 360000000 250000000 300000000 280000000 350000000 300000000 370000000 170000000 380000000 320000000 340000000 340000000 380000000 320000000 390000000 540000000 390000000 350000000 370000000 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Formula Exact mass Super class Main class Sub class Citric acid C6H8O7 192.027 Organic acids TCA acids TCA acids Glucose C6H12O6 180.0634 Carbohydrates Monosaccharides Hexoses Pyruvic acid C3H4O3 88.016 Organic acids Short-chain acids Short-chain acids Aspartic acid C4H7NO4 133.0375 Organic acids Amino acids and peptides Amino acids ATP C10H16N5O13P3 506.9958 Nucleic acids Purines Purine rNTP Oxoglutaric acid C5H6O5 146.0215 Organic acids TCA acids TCA acids Glutamine C5H10N2O3 146.0691 Organic acids Amino acids and peptides Amino acids Glutamic acid C5H9NO4 147.0532 Organic acids Amino acids and peptides Amino acids Oxidized glutathione C20H32N6O12S2 612.152 Organic acids Amino acids and peptides Peptides Sucrose C12H22O11 342.1162 Carbohydrates Disaccharides Disaccharides Mannose C6H12O6 180.0634 Carbohydrates Monosaccharides Hexoses D-Malic acid C4H6O5 134.0215 Organic acids Hydroxy acids Beta hydroxy acids Lysine C6H14N2O2 146.1055 Organic acids Amino acids and peptides Amino acids Leucine C6H13NO2 131.0946 Organic acids Amino acids and peptides Amino acids Lactose C12H22O11 342.1162 Carbohydrates Disaccharides Disaccharides "Fructose 1,6-bisphosphate" C6H14O12P2 339.9961 Carbohydrates Monosaccharides Monosaccharide phosphates Fructose C6H12O6 180.0634 Carbohydrates Monosaccharides Hexoses Fructose 6-phosphate C6H13O9P 260.0297 Carbohydrates Monosaccharides Monosaccharide phosphates Coenzyme A C21H36N7O16P3S 767.1152 Nucleic acids Purines Coenzyme A Asparagine C4H8N2O3 132.0535 Organic acids Amino acids and peptides Amino acids Arginine C6H14N4O2 174.1117 Organic acids Amino acids and peptides Amino acids Alanine C3H7NO2 89.0477 Organic acids Amino acids and peptides Amino acids Acetoacetic acid C4H6O3 102.0317 Fatty Acyls Fatty acids Oxo FA Valine C5H11NO2 117.079 Organic acids Amino acids and peptides Amino acids Fumaric acid C4H4O4 116.011 Organic acids TCA acids TCA acids Succinic acid C4H6O4 118.0266 Organic acids TCA acids TCA acids Adenosine C10H13N5O4 267.0968 Nucleic acids Purines Purine ribonucleosides Inosine C10H12N4O5 268.0808 Nucleic acids Purines Purine ribonucleosides Adenine C5H5N5 135.0545 Nucleic acids Purines 6-aminopurines Uracil C4H4N2O2 112.0273 Nucleic acids Pyrimidines Pyrimidines Hypoxanthine C5H4N4O 136.0385 Nucleic acids Purines Hypoxanthines METABOLITES_END #END