#METABOLOMICS WORKBENCH dionpatr95_20250225_104901 DATATRACK_ID:5675 STUDY_ID:ST003854 ANALYSIS_ID:AN006332 PROJECT_ID:PR002411 VERSION 1 CREATED_ON February 25, 2025, 11:32 am #PROJECT PR:PROJECT_TITLE Laboratory evolutions lead to reproducible mutations in PDR3 conferring PR:PROJECT_TITLE resistance to MCHM PR:PROJECT_TYPE LCMS untargeted analysis PR:PROJECT_SUMMARY Investigation of the effects of MCHM treatment on the metabolome using PR:PROJECT_SUMMARY Saccharomyces cerevisiae YJM789 wildtype and PDR3 deletion strains. PR:INSTITUTE West Virginia University PR:DEPARTMENT Biology PR:LABORATORY Gallagher Lab PR:LAST_NAME Patriarcheas PR:FIRST_NAME Dionysios PR:ADDRESS PO Box 6057, Morgantown, West Virginia, 26506, USA PR:EMAIL dp00034@mix.wvu.edu PR:PHONE 3046851480 PR:FUNDING_SOURCE - PR:PROJECT_COMMENTS - PR:PUBLICATIONS Laboratory evolutions lead to reproducible mutations in PDR3 conferring PR:PUBLICATIONS resistance to MCHM #STUDY ST:STUDY_TITLE Laboratory evolutions lead to reproducible mutations in PDR3 conferring ST:STUDY_TITLE resistance to MCHM ST:STUDY_TYPE LCMS untargeted analysis ST:STUDY_SUMMARY Investigation of the effects of MCHM on the metabolome using Saccharomyces ST:STUDY_SUMMARY cerevisiae YJM789 wildtype and PDR3 deletion strains. ST:INSTITUTE West Virginia University ST:DEPARTMENT Biology ST:LABORATORY Gallagher Lab ST:LAST_NAME Patriarcheas ST:FIRST_NAME Dionysios ST:ADDRESS PO Box 6057, Morgantown, West Virginia, 26506, USA ST:EMAIL dp00034@mix.wvu.edu ST:PHONE 3046851480 #SUBJECT SU:SUBJECT_TYPE Yeast SU:SUBJECT_SPECIES Saccharomyces cerevisiae SU:TAXONOMY_ID 4932 SU:GENOTYPE_STRAIN YJM789 #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 PDR3_Control1.mzML PDR3_Control1 Sample:PDR3Control | Strain:PDR3_KO | Sample source:Culture Condition=YPD_media; SampleID=9; RAW_FILE_NAME(RawFileName)=PDR3_Control1.raw SUBJECT_SAMPLE_FACTORS PDR3_Control2.mzML PDR3_Control2 Sample:PDR3Control | Strain:PDR3_KO | Sample source:Culture Condition=YPD_media; SampleID=10; RAW_FILE_NAME(RawFileName)=PDR3_Control2.raw SUBJECT_SAMPLE_FACTORS PDR3_Control3.mzML PDR3_Control3 Sample:PDR3Control | Strain:PDR3_KO | Sample source:Culture Condition=YPD_media; SampleID=11; RAW_FILE_NAME(RawFileName)=PDR3_Control3.raw SUBJECT_SAMPLE_FACTORS PDR3_Control4.mzML PDR3_Control4 Sample:PDR3Control | Strain:PDR3_KO | Sample source:Culture Condition=YPD_media; SampleID=12; RAW_FILE_NAME(RawFileName)=PDR3_Control4.raw SUBJECT_SAMPLE_FACTORS PDR3_MCHM1.mzML PDR3_MCHM1 Sample:PDR3MCHM | Strain:PDR3_KO | Sample source:Culture Condition=MCHM; SampleID=13; RAW_FILE_NAME(RawFileName)=PDR3_MCHM1.raw SUBJECT_SAMPLE_FACTORS PDR3_MCHM2.mzML PDR3_MCHM2 Sample:PDR3MCHM | Strain:PDR3_KO | Sample source:Culture Condition=MCHM; SampleID=14; RAW_FILE_NAME(RawFileName)=PDR3_MCHM2.raw SUBJECT_SAMPLE_FACTORS PDR3_MCHM3.mzML PDR3_MCHM3 Sample:PDR3MCHM | Strain:PDR3_KO | Sample source:Culture Condition=MCHM; SampleID=15; RAW_FILE_NAME(RawFileName)=PDR3_MCHM3.raw SUBJECT_SAMPLE_FACTORS PDR3_MCHM4.mzML PDR3_MCHM4 Sample:PDR3MCHM | Strain:PDR3_KO | Sample source:Culture Condition=MCHM; SampleID=16; RAW_FILE_NAME(RawFileName)=PDR3_MCHM4.raw SUBJECT_SAMPLE_FACTORS YJM789_Control1.mzML YJM789_Control1 Sample:YJM789Control | Strain:Wildtype | Sample source:Culture Condition=YPD_media; SampleID=1; RAW_FILE_NAME(RawFileName)=YJM789_Control1.raw SUBJECT_SAMPLE_FACTORS YJM789_Control2.mzML YJM789_Control2 Sample:YJM789Control | Strain:Wildtype | Sample source:Culture Condition=YPD_media; SampleID=2; RAW_FILE_NAME(RawFileName)=YJM789_Control2.raw SUBJECT_SAMPLE_FACTORS YJM789_Control3.mzML YJM789_Control3 Sample:YJM789Control | Strain:Wildtype | Sample source:Culture Condition=YPD_media; SampleID=3; RAW_FILE_NAME(RawFileName)=YJM789_Control3.raw SUBJECT_SAMPLE_FACTORS YJM789_Control4.mzML YJM789_Control4 Sample:YJM789Control | Strain:Wildtype | Sample source:Culture Condition=YPD_media; SampleID=4; RAW_FILE_NAME(RawFileName)=YJM789_Control4.raw SUBJECT_SAMPLE_FACTORS YJM789_MCHM1.mzML YJM789_MCHM1 Sample:YJM789MCHM | Strain:Wildtype | Sample source:Culture Condition=MCHM; SampleID=5; RAW_FILE_NAME(RawFileName)=YJM789_MCHM1.raw SUBJECT_SAMPLE_FACTORS YJM789_MCHM2.mzML YJM789_MCHM2 Sample:YJM789MCHM | Strain:Wildtype | Sample source:Culture Condition=MCHM; SampleID=6; RAW_FILE_NAME(RawFileName)=YJM789_MCHM2.raw SUBJECT_SAMPLE_FACTORS YJM789_MCHM3.mzML YJM789_MCHM3 Sample:YJM789MCHM | Strain:Wildtype | Sample source:Culture Condition=MCHM; SampleID=7; RAW_FILE_NAME(RawFileName)=YJM789_MCHM3.raw SUBJECT_SAMPLE_FACTORS YJM789_MCHM4.mzML YJM789_MCHM4 Sample:YJM789MCHM | Strain:Wildtype | Sample source:Culture Condition=MCHM; SampleID=8; RAW_FILE_NAME(RawFileName)=YJM789_MCHM4.raw #COLLECTION CO:COLLECTION_SUMMARY Metabolites were extracted via a cold methanol acetonitrile extraction from 2 OD CO:COLLECTION_SUMMARY unites of mid-logarithmic phase cells. CO:SAMPLE_TYPE Culture Media #TREATMENT TR:TREATMENT_SUMMARY Untreated cells were harvested in mid logarithmic phase. Treated cells were TR:TREATMENT_SUMMARY exposed to 650 ppm of MCHM for 30 minutes. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Liquid cell cultures were grown to mid-logarithmic phase and were subsequently SP:SAMPLEPREP_SUMMARY exposed to 30 mins of MCHM treatment at 650 ppm. Cells were quenched in cold SP:SAMPLEPREP_SUMMARY methanol and metabolites were extracted with a methanol-acetonitrile extraction SP:SAMPLEPREP_SUMMARY protocol as described in Crutchfield et al 2010 SP:SAMPLEPREP_SUMMARY (https://www.sciencedirect.com/science/article/pii/S0076687910700161). #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC BEH Amide (50 x 2.1mm,1.7um) CH:SOLVENT_A HPLC Water CH:SOLVENT_B Acetonitrile with 0.1% Formic acid CH:FLOW_GRADIENT The gradient started at 95% acetonitrile with 0.1% formic acid for 3 minutes at CH:FLOW_GRADIENT a flow rate of 1.2 mL/min, remained at 45% acetonitrile until minute 3.5, and CH:FLOW_GRADIENT then returned to 95% acetonitrile at minute 3.6 until minute 5. CH:FLOW_RATE 1.2ml/min CH:COLUMN_TEMPERATURE 40 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Resolution: 70,000, 1e6 AGC target and a scan range of 50-750 m/z. MS:MS_RESULTS_FILE ST003854_AN006332_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Seconds #END