#METABOLOMICS WORKBENCH amitch_20160831_104813 DATATRACK_ID:716 STUDY_ID:ST000474 ANALYSIS_ID:AN000738 PROJECT_ID:PR000362 VERSION 1 CREATED_ON September 13, 2016, 2:11 pm #PROJECT PR:PROJECT_TITLE Metabolomic testing of a putative MDH inhibitor PR:PROJECT_SUMMARY Testing for metabolomic changes after treatment of leukemia cells with a PR:PROJECT_SUMMARY putative MDH inhibitor PR:INSTITUTE Case Western Reserve University PR:DEPARTMENT Pathology PR:LABORATORY Foundation and Institutional funds PR:LAST_NAME Wald PR:FIRST_NAME David PR:ADDRESS 2103 Cornell Rd WRB3-530 Cleveland, OH 44106 PR:EMAIL dnw@case.edu PR:PHONE NA #STUDY ST:STUDY_TITLE Metabolomic testing of a putative MDH inhibitor (targeted) ST:STUDY_TYPE drug treatment (single dose and timepoint) ST:STUDY_SUMMARY HL-60 cells will be treated for 15hr with a putative MDH inhibitor or vehicle ST:STUDY_SUMMARY (n=5 per group) ST:INSTITUTE University of Florida ST:DEPARTMENT SECIM ST:LABORATORY Case Western University ST:LAST_NAME Wald ST:FIRST_NAME David ST:ADDRESS 2103 Cornell Rd WRB3-530 Cleveland, OH 44106 ST:EMAIL dnw@case.edu ST:PHONE 2163685668 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 20 ST:STUDY_COMMENTS Total subjects: 10 for global testing and 10 for targeted testing #SUBJECT SU:SUBJECT_TYPE Human leukemia cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:CELL_STRAIN_DETAILS HL-60 SU:SUBJECT_COMMENTS immortalized SU:CELL_COUNTS 10 million per sample #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS untreat ut1 Treatment:- SUBJECT_SAMPLE_FACTORS untreat ut2 Treatment:- SUBJECT_SAMPLE_FACTORS untreat ut3 Treatment:- SUBJECT_SAMPLE_FACTORS untreat ut4 Treatment:- SUBJECT_SAMPLE_FACTORS untreat ut5 Treatment:- SUBJECT_SAMPLE_FACTORS treat tx1 Treatment:MDH inhib SUBJECT_SAMPLE_FACTORS treat tx2 Treatment:MDH inhib SUBJECT_SAMPLE_FACTORS treat tx3 Treatment:MDH inhib SUBJECT_SAMPLE_FACTORS treat tx4 Treatment:MDH inhib SUBJECT_SAMPLE_FACTORS treat tx5 Treatment:MDH inhib #COLLECTION CO:COLLECTION_SUMMARY Cells were centrifuged to remove growth media/drug and either flash frozen or CO:COLLECTION_SUMMARY washed 1x in PBS. The cells were washed for the targeted assay but not for the CO:COLLECTION_SUMMARY global assay. CO:SAMPLE_TYPE cell CO:STORAGE_CONDITIONS flash frozen CO:TISSUE_CELL_QUANTITY_TAKEN 10 million per sample #TREATMENT TR:TREATMENT_SUMMARY Cells were treated for 15hr with 1 micromolar of drug or vehicle TR:CELL_GROWTH_CONTAINER flasks TR:CELL_GROWTH_RATE ~24hr per division TR:CELL_MEDIA RPMI with 10% FBS TR:CELL_ENVIR_COND 5% CO2 incubator TR:CELL_MEDIA_LASTCHANGED 15 hr #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Amino Acid|Global SP:SAMPLEPREP_PROTOCOL_FILENAME SB_OA_Assay.pdf;Appendix C_Protein_DNA_quant.pdf SP:SAMPLE_SPIKING Appendix A - Internal Standard Prep GLCMS.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Amino acids CH:CHROMATOGRAPHY_TYPE Reversed phase MS:INSTRUMENT_NAME Thermo Quantiva QQQ CH:COLUMN_NAME Waters Acquity BEH C18 (100 x 2mm, 1.7um) CH:METHODS_FILENAME SB_OA_Assay.pdf #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Thermo Quantiva QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Total nmoles (with relative protein adjustment) MS_METABOLITE_DATA_START Samples ut1 ut2 ut3 ut4 ut5 tx1 tx2 tx3 tx4 tx5 Factors Treatment:- Treatment:- Treatment:- Treatment:- Treatment:- Treatment:MDH inhib Treatment:MDH inhib Treatment:MDH inhib Treatment:MDH inhib Treatment:MDH inhib Lactate 41.94 46.29 36.76 40.93 39.02 21.16 16.53 15.44 18.54 14.91 Pyruvate 0.55 0.75 0.60 0.43 0.37 0.12 0.25 0.16 0.33 0.19 _3_HBA Succinate 1.18 1.32 0.79 1.06 1.10 0.37 0.21 0.17 0.21 0.18 Fumarate 0.33 0.29 0.36 0.47 0.49 0.21 0.22 0.17 0.20 0.18 Malate 4.91 4.77 3.88 4.70 4.71 2.15 2.02 1.66 1.97 1.70 a-KG 1.37 1.53 1.67 1.80 1.62 0.60 0.47 0.34 0.33 0.46 Citrate 3.41 1.85 3.41 3.42 3.42 1.66 1.75 1.43 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name retention index quantified m/z PubChem ID KEGG ID Lactate 3.98 196.1 107689 Pyruvate 6.68 299.1 1060 _3_HBA 4.21 210.1 441 Succinate 5.44 329.1 1110 Fumarate 5.59 327.1 444972 Malate 5.28 345.1 525 a-KG 6.59 462.2 164533 Citrate 5.95 508.25 311 METABOLITES_END #END