#METABOLOMICS WORKBENCH ychsiao_UNC_20230731_065656 DATATRACK_ID:4193 STUDY_ID:ST002802 ANALYSIS_ID:AN004558 PROJECT_ID:PR001749 VERSION 1 CREATED_ON July 31, 2023, 7:52 am #PROJECT PR:PROJECT_TITLE Nontargeted Serum Metabolomic Profiling of FXR-null and Wild-type Mice PR:PROJECT_SUMMARY This study analyzed the serum metabolome of 10 FXR-knockout and 10 wild-type PR:PROJECT_SUMMARY mice by RPLC-HRMS. PR:INSTITUTE University of North Carolina at Chapel Hill PR:DEPARTMENT Department of Environmental Sciences and Engineering PR:LABORATORY Kun Lu PR:LAST_NAME Hsiao PR:FIRST_NAME Yun-Chung PR:ADDRESS 135 Dauer Dr. MHRC1104 PR:EMAIL ychsiao@live.unc.edu PR:PHONE 9842159592 PR:FUNDING_SOURCE The research was supported by the UNC Superfund Research program (P42ES031007), PR:FUNDING_SOURCE University of North Carolina Center for Environmental Health and Susceptibility PR:FUNDING_SOURCE grant (P30ES010126). #STUDY ST:STUDY_TITLE Nontargeted Serum Metabolomic Profiling of FXR-null and Wild-type Mice ST:STUDY_SUMMARY This study analyzed the serum metabolome of 10 FXR-knockout and 10 wild-type ST:STUDY_SUMMARY mice by RPLC-HRMS. ST:INSTITUTE University of North Carolina at Chapel Hill ST:DEPARTMENT Department of Environmental Sciences and Engineering ST:LABORATORY Kun Lu ST:LAST_NAME Hsiao ST:FIRST_NAME Yun-Chung ST:ADDRESS 135 Dauer Dr. MHRC1104 ST:EMAIL ychsiao@live.unc.edu ST:PHONE 9842159592 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 20 ST:NUM_MALES 20 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:AGE_OR_AGE_RANGE 6 months SU:WEIGHT_OR_WEIGHT_RANGE 27-43 SU:GENDER Male SU:ANIMAL_ANIMAL_SUPPLIER The Jackson Laboratory #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 - G31-Con-31A1A Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO4_Sample_G31-Con-31A1A_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A1B Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO8_Sample_G31-Con-31A1B_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A2A Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO15_Sample_G31-Con-31A2A_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A2B Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO19_Sample_G31-Con-31A2B_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A3A Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO26_Sample_G31-Con-31A3A_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A3B Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO30_Sample_G31-Con-31A3B_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A4A Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO37_Sample_G31-Con-31A4A_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A4B Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO41_Sample_G31-Con-31A4B_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A5A Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO48_Sample_G31-Con-31A5A_10uL.raw SUBJECT_SAMPLE_FACTORS - G31-Con-31A5B Genotype:Wild-type RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO52_Sample_G31-Con-31A5B_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A1A Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO6_Sample_G32-Con-32A1A_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A1B Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO10_Sample_G32-Con-32A1B_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A2A Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO17_Sample_G32-Con-32A2A_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A2B Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO21_Sample_G32-Con-32A2B_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A5A Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO28_Sample_G32-Con-32A5A_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A5B Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO32_Sample_G32-Con-32A5B_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A6A Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO39_Sample_G32-Con-32A6A_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A6B Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO43_Sample_G32-Con-32A6B_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A8A Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO50_Sample_G32-Con-32A8A_10uL.raw SUBJECT_SAMPLE_FACTORS - G32-Con-32A8B Genotype:FXR-knockout RAW_FILE_NAME=T3_400uL_pos_20230711_serum_IO54_Sample_G32-Con-32A8B_10uL.raw #COLLECTION CO:COLLECTION_SUMMARY Serum samples from each mouse were collected from heart blood immediately after CO:COLLECTION_SUMMARY carbon dioxide euthanasia. CO:SAMPLE_TYPE Blood (serum) #TREATMENT TR:TREATMENT_SUMMARY No treatment. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Serum samples from each mouse were thawed and 20 μL was consumed to extract SP:SAMPLEPREP_SUMMARY metabolites for each mice. Metabolite extraction was facilitated by adding 180 SP:SAMPLEPREP_SUMMARY μL methanol containing stable isotope-labeled chemicals ([D5]-glutamine, SP:SAMPLEPREP_SUMMARY [D2]-𝛾-aminobutyric acid, [D3]-tryptophan, [D2]-indole-3-propionic acid, SP:SAMPLEPREP_SUMMARY [D2]-indole-3-acetic acid, [D13]-acetylcholine in 500 nM; [D4]-serotonin in 250 SP:SAMPLEPREP_SUMMARY nM; and [D4]-kynurenic acid in 50 nM), and incubated under -20°C for 1 hr, SP:SAMPLEPREP_SUMMARY followed by centrifugation under 15,000 ×g, 4°C for 10 minutes to collect the SP:SAMPLEPREP_SUMMARY supernatant (150 μL). The supernatant was dried by SpeedVac® and reconstituted SP:SAMPLEPREP_SUMMARY with 100 μL 2% acetonitrile in water. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The serum analytes were injected (10 μL) into a Waters Acquity UPLC HSS T3 CH:CHROMATOGRAPHY_SUMMARY (reverse phase C18, 100 Å, 1.8 μm, 2.1 mm × 100 mm) analytical column CH:CHROMATOGRAPHY_SUMMARY controlled at 40 °C, with the mobile phase composed of water (A) and CH:CHROMATOGRAPHY_SUMMARY acetonitrile (B) both added with 0.1% formic acid at a flow rate of 0.4 mL/min. CH:CHROMATOGRAPHY_SUMMARY The 15-min-gradient for chromatographic separation was set as the following: 2% CH:CHROMATOGRAPHY_SUMMARY B from 0-1 min; 2%-15% B from 1-3 min; 15%-50% B from 3-6 min; 50%-98% B from CH:CHROMATOGRAPHY_SUMMARY 6-7.5 min; 98% B held from 7.5-11.5 min; 98%-2% B from 11.5-11.6 min; and 2% B CH:CHROMATOGRAPHY_SUMMARY held from 11.6-15 min for a final re-equilibration. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) CH:SOLVENT_A 100% water; 0.1% formic acid CH:SOLVENT_B 100% acetonitrile; 0.1% formic acid CH:FLOW_GRADIENT 2% B from 0-1 min; 2%-15% B from 1-3 min; 15%-50% B from 3-6 min; 50%-98% B from CH:FLOW_GRADIENT 6-7.5 min; 98% B held from 7.5-11.5 min; 98%-2% B from 11.5-11.6 min; and 2% B CH:FLOW_GRADIENT held from 11.6-15 min for a final re-equilibration. CH:FLOW_RATE 0.4 mL/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 The mass spectrometry was set to scan under the positive mode with the sheath MS:MS_COMMENTS gas, auxiliary gas, and sweep gas set to flow rates of 50, 13, and 3 psi, MS:MS_COMMENTS respectively. With the spray voltage set to 3.5 kV, the capillary and auxiliary MS:MS_COMMENTS gas heating temperature were respectively controlled to 263°C and 425°C to MS:MS_COMMENTS fully scan across m/z 70 to 1,000. The resolution was set to 70,000 FWHM (m/z MS:MS_COMMENTS 200). The automatic gain control (AGC) and the maximal injection time (MIT) was MS:MS_COMMENTS set to 2×105 and 50 msec, respectively. Routine mass calibrations were MS:MS_COMMENTS conducted before and after the sample analysis. The samples were MS:MS_COMMENTS blocked-randomized for the injection order. Quality control samples for the MS:MS_COMMENTS serum analytes were prepared by pooling the aliquots of each sample. Method MS:MS_COMMENTS blank samples were prepared for the serum samples by surrogating the biospecimen MS:MS_COMMENTS with water and following the same experimental procedures. If MS/MS spectrums MS:MS_COMMENTS were to be collected, the parallel reaction monitoring (PRM) mode was used, with MS:MS_COMMENTS the isolation width, AGC, and MIT set to 1.2, 3×105 and 100 msec, respectively, MS:MS_COMMENTS at the resolution of 17,500 FWHM (m/z 200). MS:MS_RESULTS_FILE ST002802_AN004558_Results.txt UNITS:m/z Has m/z:Yes Has RT:Yes RT units:Minutes #END