#METABOLOMICS WORKBENCH araskind_20170619_105249 DATATRACK_ID:983 STUDY_ID:ST000701 ANALYSIS_ID:AN001090 PROJECT_ID:PR000148 VERSION 1 CREATED_ON July 1, 2017, 5:17 pm #PROJECT PR:PROJECT_TITLE Differences in metabolism in mouse embryonic fibroblasts (control vs PR:PROJECT_TITLE SCF-beta-TrCP knockout) PR:PROJECT_TYPE MS analysis PR:PROJECT_SUMMARY Metabolic phenotypes of a clock mutant mouse PR:INSTITUTE Florida State University PR:DEPARTMENT Biomedical Sciences PR:LABORATORY Lee Lab PR:LAST_NAME Lee PR:FIRST_NAME Choogon PR:ADDRESS Tallahassee, FL PR:EMAIL choogon.lee@med.fsu.edu PR:PHONE 850-645-1478 #STUDY ST:STUDY_TITLE Differences in metabolism in mouse embryonic fibroblasts (control vs ST:STUDY_TITLE SCF-beta-TrCP knockout) ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY Mouse embryonic fibroblasts were grown in DMED supplemented with 10%FBS. The ST:STUDY_SUMMARY same number of cells were plated in eight 6cm dishes. When the cells were ~70% ST:STUDY_SUMMARY confluent, four dishes received ethanol (carrier) and the other four received ST:STUDY_SUMMARY tamoxifen (1uM final) to induce knockout. The cells and media were harvested 4 ST:STUDY_SUMMARY days later. The media harvested from control and knockout dishes will be ST:STUDY_SUMMARY compared with the starting medium. The cells were washed with cold PBS twice ST:STUDY_SUMMARY while they are attached to the dishes. The whole dish with cells attached were ST:STUDY_SUMMARY immediately frozen in dry ice and wrapped with aluminum foil and stored at -80C. ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research Core Facilities ST:LABORATORY Metabolomics core ST:LAST_NAME Kachman ST:FIRST_NAME Maureen ST:ADDRESS 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 ST:EMAIL mkachman@med.umich.edu ST:PHONE (734) 232-8175 ST:NUM_GROUPS 6 ST:TOTAL_SUBJECTS 3 #SUBJECT SU:SUBJECT_TYPE Mouse SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0003080 S00013515 GENOTYPE:Control | Sample type:Fresh media SUBJECT_SAMPLE_FACTORS SU0003080 S00013516 GENOTYPE:Control | Sample type:Spent media SUBJECT_SAMPLE_FACTORS SU0003080 S00013517 GENOTYPE:Knockout | Sample type:Spent media SUBJECT_SAMPLE_FACTORS SU0003081 S00013518 GENOTYPE:Control | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013519 GENOTYPE:Control | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013520 GENOTYPE:Control | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013521 GENOTYPE:Control | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013522 GENOTYPE:Knockout | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013523 GENOTYPE:Knockout | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013524 GENOTYPE:Knockout | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU0003081 S00013525 GENOTYPE:Knockout | Sample type:Fibroblasts SUBJECT_SAMPLE_FACTORS SU9999996 S00020124 GENOTYPE:Pooled | Sample type:Spent media SUBJECT_SAMPLE_FACTORS SU9999996 S00020125 GENOTYPE:Pooled | Sample type:Fibroblasts #COLLECTION CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME A003 - Untargeted Metabolomics.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Waters Acquity HSS T3 (50 x 2.1mm, 1.8um) #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE A003 - Untargeted Metabolomics.pdf #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS peak area MS_METABOLITE_DATA_START Samples S00013515 S00013516 S00013517 Factors GENOTYPE:Control | Sample type:Fresh media GENOTYPE:Control | Sample type:Spent media GENOTYPE:Knockout | Sample type:Spent media 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID 58658 52049 52163 3-METHOXYTYROSINE 13073 15381 14093 4-ACETAMIDOBUTANOATE 1292969 1438383 1306899 4-METHYL-2-OXOPENTANOATE (2M+H) 227123 250501 208554 4-PYRIDOXIC ACID 133113 83132 70167 5-AMINOPENTANOIC ACID 570976 429626 544772 5-HYDROXYINDOLEACETIC ACID 19449 85865 67923 5-METHYLCYTOSINE 24401 27164 22435 5-OXOPROLINE 3753116 6093461 3804960 5-OXOPROLINE + 1.1064999 2681669 5-OXOPROLINE + 1.193 11900000 5-OXOPROLINE + 1.1945 5283789 5-OXOPROLINE + 1.1962668 12400000 12900000 15100000 ASPARAGINE (2M+H) 2029136 2376962 2650601 AZELAIC ACID (M+Na) 43412 74490 44188 CORTISONE (M+Na) 140616 CREATINE 674062 481632 313995 CYTIDINE (2M+Na) 53127 42986 156404 CYTIDINE + 0.84499997 412473 280032 546008 CYTIDINE + 0.9324 76858 42288 43171 D-PSICOSE 2755468 1278285 1840878 D-SORBITOL (M+Na) 132592 69741 42485 DEOXYCYTIDINE 150126 1962401 1193994 DEOXYCYTIDINE + 0.94733334 11075 124792 13672 DEOXYCYTIDINE + 0.95839995 75910 165527 64117 DIOCTYL PHTHALATE (2M+Na) 1138629 1135136 776612 DIOCTYL PHTHALATE + 23.077934 3636466 3568208 3122059 DIOCTYL PHTHALATE + 23.0814 97355 106202 85518 DL-3-AMINO-ISOBUTANOIC ACID 143576 139800 121796 DL-PIPECOLIC ACID 158973 162616 200518 DL-PIPECOLIC ACID + 0.94628567 110051 81947 FOLIC ACID 525396 871411 707790 GLUCOSE (2M+Na) 94869 75089 42274 GLUCOSE + 0.677 42532 GUANINE 269546 54844 95038 HIPPURIC ACID 936565 1571289 1407964 HYPOXANTHINE 2139079 514190 639273 ISOLEUCINE 26400000 35500000 33000000 KYNURENINE 147386 184577 170278 L-CARNITINE 383986 425476 407477 L-CARNITINE + 0.7405333 126058 125774 125815 METHIONINE 5956127 5679696 5914247 METHYL JASMONATE (M+Na) 132906 146048 108937 N-ACETYLGALACTOSAMINE (M+Na) 61162 60978 43570 N-CYCLOHEXYLFORMAMIDE 80340 61669 99044 NICOTINAMIDE 1697552 1728335 O-ACETYLCARNITINE 2817505 2411103 2214838 PANTOTHENIC ACID (-H2O) 135135 138033 138715 PANTOTHENIC ACID + 3.2942002 11800000 13400000 12200000 PANTOTHENIC ACID + 3.2942002 :5 11100000 12600000 11300000 PIMELIC ACID (2M+H) 23341 44586 28994 PROLINE 197948 628201 907495 RIBOFLAVIN (VITAMIN B2) 41637 48534 48901 RIBOFLAVIN (VITAMIN B2) + 7.631134 287349 327246 324484 SALICYLAMIDE 137087 166886 136794 SORBITOL (M+Na) 187016 177957 151110 THYMIDINE (M+Na) 63693 71851 130474 TRYPTOPHAN 12200000 13100000 11300000 TYROSINE 16800000 17000000 16200000 TYROSINE + 1.2937 2397810 2541424 URIDINE (M+Na) 154156 122927 299115 URIDINE + 1.3391539 7639 6419 14618 UROCANIC ACID 28805 79993 72968 VALINE 3807534 3497801 3589374 XANTHOSINE 33426 61999 86564 XANTHOSINE + 2.3653998 32496 48704 43886 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID 101.0479 0.989 535 3-METHOXYTYROSINE 211.0838 1.996 9307 4-ACETAMIDOBUTANOATE 145.0737 1.822 18189 4-METHYL-2-OXOPENTANOATE (2M+H) 260.1234 4.868 70 4-PYRIDOXIC ACID 183.0535 1.88 6723 5-AMINOPENTANOIC ACID 117.0789 0.725 138 5-HYDROXYINDOLEACETIC ACID 191.0587 4.259 1826 5-METHYLCYTOSINE 272.1012 0.766 65040 5-OXOPROLINE 129.0427 1.111 7405 5-OXOPROLINE + 1.1064999 258.0836 1.106 7405 5-OXOPROLINE + 1.193 129.0421 1.193 7405 5-OXOPROLINE + 1.1945 151.0246 1.195 7405 5-OXOPROLINE + 1.1962668 129.0428 1.196 7405 ASPARAGINE (2M+H) 264.1043 0.667 6267 AZELAIC ACID (M+Na) 210.0873 10.785 2266 CORTISONE (M+Na) 382.1758 13.415 222786 CREATINE 131.0698 0.694 586 CYTIDINE (2M+Na) 508.1533 0.833 6175 CYTIDINE + 0.84499997 243.0864 0.845 6175 CYTIDINE + 0.9324 225.0759 0.932 6175 D-PSICOSE 202.0451 0.698 90008 D-SORBITOL (M+Na) 204.0588 0.864 5780 DEOXYCYTIDINE 227.0911 0.944 13711 DEOXYCYTIDINE + 0.94733334 476.1628 0.947 13711 DEOXYCYTIDINE + 0.95839995 249.0723 0.958 13711 DIOCTYL PHTHALATE (2M+Na) 802.5365 23.078 8346 DIOCTYL PHTHALATE + 23.077934 412.2591 23.078 8346 DIOCTYL PHTHALATE + 23.0814 390.2775 23.081 8346 DL-3-AMINO-ISOBUTANOIC ACID 85.0529 1.821 64956 DL-PIPECOLIC ACID 129.0799 0.954 849 DL-PIPECOLIC ACID + 0.94628567 129.0791 0.946 849 FOLIC ACID 441.1389 5.83 6037 GLUCOSE (2M+Na) 382.1089 0.696 5793 GLUCOSE + 0.677 382.1094 0.677 5793 GUANINE 151.0493 0.905 764 HIPPURIC ACID 179.0583 4.818 464 HYPOXANTHINE 136.0384 1.087 790 ISOLEUCINE 131.0944 1.575 6306 KYNURENINE 208.0844 2.197 161166 L-CARNITINE 161.1047 0.715 10917 L-CARNITINE + 0.7405333 143.0935 0.741 10917 METHIONINE 149.0508 0.984 6137 METHYL JASMONATE (M+Na) 246.1224 16.1 5281929 N-ACETYLGALACTOSAMINE (M+Na) 243.0724 0.711 35717 N-CYCLOHEXYLFORMAMIDE 127.0985 7.965 13017 NICOTINAMIDE 122.0484 1.133 936 O-ACETYLCARNITINE 203.1157 0.917 18230 PANTOTHENIC ACID (-H2O) 201.0999 3.296 6613 PANTOTHENIC ACID + 3.2942002 219.1106 3.294 6613 PANTOTHENIC ACID + 3.2942002 :5 219.1112 3.294 6613 PIMELIC ACID (2M+H) 322.0801 5.83 385 PROLINE 115.0633 0.697 145742 RIBOFLAVIN (VITAMIN B2) 376.1381 7.612 493570 RIBOFLAVIN (VITAMIN B2) + 7.631134 398.1203 7.631 493570 SALICYLAMIDE 137.0477 5.381 5147 SORBITOL (M+Na) 204.0595 0.723 5780 THYMIDINE (M+Na) 264.073 2.751 5789 TRYPTOPHAN 204.0897 3.605 6305 TYROSINE 181.0736 1.295 6057 TYROSINE + 1.2937 203.0557 1.294 6057 URIDINE (M+Na) 266.0516 1.338 6029 URIDINE + 1.3391539 282.0245 1.339 6029 UROCANIC ACID 138.0428 0.923 736715 VALINE 117.079 0.877 6287 XANTHOSINE 284.0757 2.271 64959 XANTHOSINE + 2.3653998 284.0756 2.365 64959 METABOLITES_END #END