#METABOLOMICS WORKBENCH kenanazam_20160912_110837_mwtab.txt DATATRACK_ID:735 STUDY_ID:ST000475 ANALYSIS_ID:AN000739 PROJECT_ID:PR000362 VERSION 1 CREATED_ON September 13, 2016, 2:12 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 (global) 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 Global CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Scientific-Dionex Ultimate 3000 CH:COLUMN_NAME ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) CH:METHODS_FILENAME Consolidated_Cellular_Metabolomics_SOP.pdf #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS peak area MS_METABOLITE_DATA_START Samples tx3 ut4 ut3 ut5 ut2 tx2 tx1 ut1 tx5 tx4 Factors Treatment:MDH inhib Treatment:- Treatment:- Treatment:- Treatment:- Treatment:MDH inhib Treatment:MDH inhib Treatment:- Treatment:MDH inhib Treatment:MDH inhib 1-AMINOCYCLOPROPANE-1-CARBOXYLATE 7800000.0000 19000000.0000 17800000.0000 16500000.0000 18700000.0000 9050000.0000 13400000.0000 18900000.0000 6600000.0000 8780000.0000 3-UREIDOPROPIONATE 344000.0000 623000.0000 1250000.0000 801000.0000 865000.0000 213000.0000 430000.0000 985000.0000 219000.0000 341000.0000 4-AMINOBUTANOATE (GABA) 2850000.0000 2380000.0000 2510000.0000 2260000.0000 2380000.0000 4070000.0000 4340000.0000 2470000.0000 3660000.0000 2670000.0000 4-HYDROXYPROLINE 16600000.0000 46100000.0000 44800000.0000 40500000.0000 46300000.0000 18500000.0000 23900000.0000 44000000.0000 17300000.0000 15700000.0000 ADENINE 3950000.0000 10800000.0000 10500000.0000 7690000.0000 9420000.0000 5290000.0000 6100000.0000 10500000.0000 4900000.0000 6470000.0000 ALANINE/SARCOSINE 7370000.0000 21300000.0000 19200000.0000 17800000.0000 21200000.0000 7600000.0000 11600000.0000 21700000.0000 7700000.0000 7200000.0000 ALDO/KETO-HEXOSE 27200000.0000 38700000.0000 44600000.0000 44300000.0000 44600000.0000 35300000.0000 36800000.0000 41100000.0000 34000000.0000 27100000.0000 ALDOPENTOSE 2700000.0000 5870000.0000 5310000.0000 5770000.0000 5430000.0000 2430000.0000 4020000.0000 5380000.0000 2510000.0000 2390000.0000 BETAINE 15600000.0000 111000000.0000 104000000.0000 105000000.0000 112000000.0000 11000000.0000 11300000.0000 106000000.0000 16200000.0000 10600000.0000 Butyrylcarnitine 647000.0000 7120000.0000 6030000.0000 5240000.0000 7280000.0000 520000.0000 1510000.0000 7560000.0000 476000.0000 490000.0000 Choline 70600000.0000 182000000.0000 173000000.0000 158000000.0000 170000000.0000 68800000.0000 115000000.0000 189000000.0000 62600000.0000 62900000.0000 CMP 3770000.0000 4810000.0000 4320000.0000 4550000.0000 5500000.0000 3150000.0000 4070000.0000 4910000.0000 3250000.0000 3330000.0000 CREATINE 46400000.0000 384000000.0000 317000000.0000 284000000.0000 368000000.0000 39600000.0000 83700000.0000 356000000.0000 36300000.0000 38300000.0000 Creatine-D3 57100000.0000 51700000.0000 53000000.0000 55200000.0000 51300000.0000 58500000.0000 70800000.0000 54600000.0000 56200000.0000 52800000.0000 CREATININE 1950000.0000 5150000.0000 5570000.0000 4820000.0000 5360000.0000 1960000.0000 2940000.0000 5690000.0000 2870000.0000 1700000.0000 CYS-GLY 2580000.0000 2180000.0000 1670000.0000 1870000.0000 1950000.0000 1930000.0000 3940000.0000 2260000.0000 2190000.0000 1900000.0000 CYTOSINE 1290000.0000 1510000.0000 1500000.0000 1380000.0000 1620000.0000 1220000.0000 1290000.0000 1620000.0000 1100000.0000 1280000.0000 Dibutyl phthalate 33400000.0000 35100000.0000 31900000.0000 34200000.0000 34300000.0000 33800000.0000 33100000.0000 33200000.0000 33200000.0000 32400000.0000 DIETHANOLAMINE 790000.0000 296000.0000 162000.0000 1210000.0000 275000.0000 794000.0000 3590000.0000 672000.0000 764000.0000 1040000.0000 DIHYDROXYACETONE PHOSPHATE 3500000.0000 3510000.0000 3900000.0000 4580000.0000 3670000.0000 3480000.0000 4370000.0000 2700000.0000 3190000.0000 3190000.0000 Diphenylamine 585000.0000 747000.0000 680000.0000 832000.0000 858000.0000 506000.0000 647000.0000 839000.0000 593000.0000 576000.0000 Dipropylene glycol 8360000.0000 8230000.0000 8120000.0000 10100000.0000 8140000.0000 9530000.0000 8080000.0000 13100000.0000 7610000.0000 9010000.0000 Erucamide 2960000.0000 50300000.0000 881000.0000 3080000.0000 359000000.0000 15300000.0000 9360000.0000 1020000.0000 40300000.0000 25300000.0000 GLUCOSAMINE/MANNOSAMINE 4870000.0000 9010000.0000 9240000.0000 8380000.0000 11100000.0000 6080000.0000 6960000.0000 8530000.0000 6240000.0000 4510000.0000 Glycerophosphocholine 22000000.0000 35100000.0000 38300000.0000 27500000.0000 42600000.0000 28200000.0000 54000000.0000 38600000.0000 30000000.0000 22100000.0000 Glycyl-L-leucine 434000.0000 1310000.0000 918000.0000 1100000.0000 1150000.0000 294000.0000 531000.0000 1290000.0000 359000.0000 291000.0000 GUANINE 970000.0000 2900000.0000 2830000.0000 2540000.0000 3000000.0000 1580000.0000 1590000.0000 3120000.0000 778000.0000 699000.0000 GUANOSINE 2970000.0000 13900000.0000 10800000.0000 11700000.0000 13600000.0000 2380000.0000 5080000.0000 13100000.0000 2530000.0000 2430000.0000 HEXOSE-6-PHOSPHATE 2310000.0000 5810000.0000 5980000.0000 5830000.0000 6820000.0000 2930000.0000 4190000.0000 6030000.0000 2960000.0000 2000000.0000 HEXOSE-DISACCHARIDE 610000.0000 1160000.0000 1990000.0000 1600000.0000 1160000.0000 1020000.0000 1200000.0000 1310000.0000 995000.0000 656000.0000 INOSINE 4400000.0000 27600000.0000 19800000.0000 20400000.0000 25400000.0000 3590000.0000 8080000.0000 23500000.0000 3390000.0000 3480000.0000 Isocytosine 646000.0000 2160000.0000 1920000.0000 1950000.0000 2260000.0000 320000.0000 932000.0000 2180000.0000 603000.0000 396000.0000 L-CARNITINE 9490000.0000 42000000.0000 37600000.0000 45700000.0000 33300000.0000 9470000.0000 15000000.0000 35700000.0000 7960000.0000 8470000.0000 L-CYSTEINE 29700000.0000 36400000.0000 34300000.0000 31800000.0000 36300000.0000 26600000.0000 45200000.0000 37700000.0000 26700000.0000 24500000.0000 Leu Pro 403000.0000 2100000.0000 1240000.0000 1730000.0000 1900000.0000 217000.0000 664000.0000 2030000.0000 346000.0000 258000.0000 LEUCINE 104000000.0000 457000000.0000 427000000.0000 394000000.0000 466000000.0000 111000000.0000 170000000.0000 425000000.0000 112000000.0000 89700000.0000 L-GLUTAMIC ACID 130000000.0000 414000000.0000 367000000.0000 316000000.0000 405000000.0000 121000000.0000 199000000.0000 385000000.0000 116000000.0000 118000000.0000 L-GLUTAMINE 97800000.0000 268000000.0000 261000000.0000 239000000.0000 276000000.0000 113000000.0000 133000000.0000 253000000.0000 109000000.0000 91500000.0000 L-Isoleucine 66400000.0000 198000000.0000 198000000.0000 176000000.0000 207000000.0000 76300000.0000 108000000.0000 187000000.0000 75200000.0000 58200000.0000 LL-2,6-DIAMINOHEPTANEDIOATE 383000.0000 1460000.0000 1100000.0000 1200000.0000 1160000.0000 261000.0000 488000.0000 1390000.0000 275000.0000 177000.0000 L-Leucine 13C6 97900000.0000 92300000.0000 98500000.0000 97500000.0000 91100000.0000 99700000.0000 122000000.0000 98600000.0000 94200000.0000 93100000.0000 L-Leucine-D10 117000000.0000 110000000.0000 117000000.0000 116000000.0000 110000000.0000 120000000.0000 145000000.0000 117000000.0000 112000000.0000 108000000.0000 L-METHIONINE 14800000.0000 41000000.0000 37800000.0000 35700000.0000 40900000.0000 15400000.0000 23400000.0000 38900000.0000 15700000.0000 13000000.0000 L-Phenylalanine 13C6 50800000.0000 49000000.0000 50200000.0000 52000000.0000 49300000.0000 51500000.0000 63000000.0000 51400000.0000 48600000.0000 46500000.0000 L-PROLINE 46400000.0000 225000000.0000 200000000.0000 191000000.0000 210000000.0000 46100000.0000 70000000.0000 225000000.0000 44700000.0000 40400000.0000 L-Tryptophan 13C11 190000000.0000 193000000.0000 199000000.0000 202000000.0000 198000000.0000 185000000.0000 231000000.0000 198000000.0000 175000000.0000 175000000.0000 L-Tyrosine 13C6 24600000.0000 23500000.0000 24400000.0000 25200000.0000 23600000.0000 25000000.0000 31100000.0000 24600000.0000 24200000.0000 22900000.0000 L-VALINE/5-AMINOPENTANOATE/L-NORVALINE 36400000.0000 96600000.0000 94800000.0000 87300000.0000 97100000.0000 38500000.0000 54900000.0000 96600000.0000 39200000.0000 32800000.0000 LysoPC (18:2) 913000.0000 1490000.0000 1900000.0000 2150000.0000 1750000.0000 2670000.0000 517000.0000 3380000.0000 10900000.0000 6730000.0000 LysoPE (18:0) 53900.0000 2880000.0000 3000000.0000 1770000.0000 3980000.0000 177000.0000 22000.0000 7410000.0000 1950000.0000 1040000.0000 LysoPE (18:1) 415000.0000 562000.0000 752000.0000 635000.0000 688000.0000 1110000.0000 391000.0000 1470000.0000 8640000.0000 4490000.0000 LysoPE (20:4) 970000.0000 960000.0000 1350000.0000 1320000.0000 1280000.0000 2090000.0000 861000.0000 2630000.0000 1680000.0000 6360000.0000 METHYL BETA-D-GALACTOSIDE 2340000.0000 4450000.0000 3900000.0000 4360000.0000 4110000.0000 2040000.0000 3050000.0000 3950000.0000 2310000.0000 2150000.0000 Monobutyl phthalate 1820000.0000 1890000.0000 1780000.0000 1860000.0000 1830000.0000 1770000.0000 1880000.0000 2010000.0000 1720000.0000 1770000.0000 N-ACETYL-HEXOSAMINE 1280000.0000 3950000.0000 3860000.0000 3790000.0000 4100000.0000 1270000.0000 1940000.0000 4520000.0000 1300000.0000 1230000.0000 N-ACETYLNEURAMINATE 3030000.0000 6190000.0000 4720000.0000 5790000.0000 5920000.0000 2500000.0000 3930000.0000 5390000.0000 2900000.0000 2660000.0000 N-ACETYLPUTRESCINE 811000.0000 1240000.0000 1100000.0000 802000.0000 1290000.0000 716000.0000 1110000.0000 897000.0000 636000.0000 689000.0000 N-BOC-L-Aspartic Acid 19400000.0000 17400000.0000 18500000.0000 18800000.0000 17600000.0000 19700000.0000 24000000.0000 18500000.0000 18700000.0000 18200000.0000 Orthophosphate 33800000.0000 53100000.0000 55900000.0000 52300000.0000 55400000.0000 34700000.0000 44600000.0000 54800000.0000 33200000.0000 31500000.0000 Pantothenic Acid 397000.0000 2850000.0000 2200000.0000 2280000.0000 2770000.0000 358000.0000 751000.0000 2640000.0000 387000.0000 329000.0000 PEG n5 4580000.0000 8350000.0000 52700000.0000 16800000.0000 4860000.0000 5760000.0000 7420000.0000 6700000.0000 6890000.0000 3850000.0000 PHENETHYLAMINE 3870000.0000 4470000.0000 4210000.0000 4130000.0000 3770000.0000 3230000.0000 3790000.0000 6430000.0000 3310000.0000 3550000.0000 PHOSPHOCHOLINE 121000000.0000 632000000.0000 547000000.0000 529000000.0000 628000000.0000 107000000.0000 206000000.0000 645000000.0000 110000000.0000 103000000.0000 Pyroglutamic Acid 19400000.0000 48600000.0000 52600000.0000 45100000.0000 50900000.0000 21500000.0000 28200000.0000 45900000.0000 21200000.0000 17400000.0000 THREONINE/HOMOSERINE 15000000.0000 36000000.0000 33100000.0000 31300000.0000 35900000.0000 16000000.0000 22900000.0000 36300000.0000 15800000.0000 14300000.0000 TRANS-CINNAMATE 766000.0000 804000.0000 693000.0000 1030000.0000 811000.0000 922000.0000 686000.0000 922000.0000 773000.0000 841000.0000 Triethyl phosphate 6370000.0000 5820000.0000 5500000.0000 4010000.0000 4020000.0000 5500000.0000 6540000.0000 11300000.0000 5360000.0000 7020000.0000 Trigonelline 812000.0000 3790000.0000 3780000.0000 3430000.0000 3520000.0000 792000.0000 1640000.0000 3720000.0000 764000.0000 674000.0000 Tryptophan 7730000.0000 20900000.0000 20600000.0000 18100000.0000 21700000.0000 8610000.0000 12700000.0000 20600000.0000 8580000.0000 6990000.0000 Tryptophan-2,3,3-D3 273000000.0000 282000000.0000 282000000.0000 297000000.0000 293000000.0000 268000000.0000 338000000.0000 288000000.0000 258000000.0000 248000000.0000 Tryptophan-2,3,3-D3-NH3 91300000.0000 93700000.0000 95200000.0000 97500000.0000 95100000.0000 88300000.0000 111000000.0000 95000000.0000 84700000.0000 84200000.0000 Tryptophan-NH3 2920000.0000 7760000.0000 7830000.0000 6600000.0000 8080000.0000 3150000.0000 4610000.0000 7610000.0000 3150000.0000 2540000.0000 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name retention index quantified m/z PubChem ID KEGG ID 1-AMINOCYCLOPROPANE-1-CARBOXYLATE 0.74 102.0550 535 3-UREIDOPROPIONATE 1.14 133.0599 111 4-AMINOBUTANOATE (GABA) 0.76 104.0708 119 4-HYDROXYPROLINE 0.73 132.0658 5810 ADENINE 1.44 136.0619 190 ALANINE/SARCOSINE 0.71 90.0550 ALDO/KETO-HEXOSE 0.71 203.0527 ALDOPENTOSE 0.77 173.0418 BETAINE 0.75 118.0861 247 Butyrylcarnitine 7.40 232.1542 213144 Choline 0.81 104.1072 305 CMP 0.98 324.0590 6131 CREATINE 0.87 132.0766 586 Creatine-D3 0.86 135.0954 CREATININE 0.88 114.0663 588 CYS-GLY 0.89 179.0484 439498 CYTOSINE 0.97 112.0504 597 Dibutyl phthalate 14.67 279.1582 3026 DIETHANOLAMINE 0.71 106.0862 8113 DIHYDROXYACETONE PHOSPHATE 0.71 171.0055 668 Diphenylamine 13.68 170.0962 11487 Dipropylene glycol 6.32 157.0838 6510 Erucamide 16.85 338.3418 5365371 GLUCOSAMINE/MANNOSAMINE 0.71 180.0864 Glycerophosphocholine 0.74 258.1095 71920 Glycyl-L-leucine 6.66 189.1234 92843 GUANINE 1.67 152.0564 764 GUANOSINE 6.08 284.0981 6802 HEXOSE-6-PHOSPHATE 0.72 261.0369 HEXOSE-DISACCHARIDE 0.78 365.1056 INOSINE 5.86 269.0871 6021 Isocytosine 1.42 112.0505 66950 L-CARNITINE 0.89 162.1127 10917 L-CYSTEINE 0.75 122.0271 5862 Leu Pro 7.26 229.1541 LEUCINE 2.31 132.1018 857 L-GLUTAMIC ACID 0.74 148.0606 33032 L-GLUTAMINE 0.71 147.0763 5961 L-Isoleucine 2.02 132.1018 6306 LL-2,6-DIAMINOHEPTANEDIOATE 0.89 191.1025 439283 L-Leucine 13C6 2.31 138.1221 L-Leucine-D10 2.27 142.1647 16213587 L-METHIONINE 1.31 150.0583 6137 L-Phenylalanine 13C6 5.96 172.1062 L-PROLINE 0.83 116.0706 145742 L-Tryptophan 13C11 7.61 216.1345 L-Tyrosine 13C6 3.09 188.1013 L-VALINE/5-AMINOPENTANOATE/L-NORVALINE 1.06 118.0861 LysoPC (18:2) 13.17 520.3387 LysoPE (18:0) 14.61 482.3259 LysoPE (18:1) 13.53 480.3077 9547071 LysoPE (20:4) 12.89 502.2913 METHYL BETA-D-GALACTOSIDE 1.00 217.0687 94214 Monobutyl phthalate 12.40 223.0960 8575 N-ACETYL-HEXOSAMINE 0.82 244.0792 N-ACETYLNEURAMINATE 0.79 310.1122 439197 N-ACETYLPUTRESCINE 1.04 131.1179 122356 N-BOC-L-Aspartic Acid 8.49 134.0448 99718 Orthophosphate 0.71 98.9845 1061 Pantothenic Acid 6.53 220.1174 6613 PEG n5 7.03 261.1309 62551 PHENETHYLAMINE 6.85 122.0964 1001 PHOSPHOCHOLINE 0.72 184.0735 1014 Pyroglutamic Acid 1.67 130.0500 7405 THREONINE/HOMOSERINE 0.72 120.0654 TRANS-CINNAMATE 9.76 149.0596 444539 Triethyl phosphate 9.30 183.0780 6535 Trigonelline 0.83 138.0543 5570 Tryptophan 7.61 205.0976 6305 Tryptophan-2,3,3-D3 7.61 208.1157 Tryptophan-2,3,3-D3-NH3 7.61 191.0892 Tryptophan-NH3 7.61 188.0707 METABOLITES_END #END