#METABOLOMICS WORKBENCH araskind_20170619_105249 DATATRACK_ID:983 STUDY_ID:ST000701 ANALYSIS_ID:AN001089 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 NEGATIVE #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 2-AMINO-4-METHYLPENTANOIC ACID (LEUCINE) 1391276 1110259 837851 2-OXOBUTANOATE 226672 71474 102198 3-HYDROXY-3-METHYL-GLUTARIC ACID 829412 954839 797239 4-ACETAMIDOBUTANOATE 124544 159546 138647 4-PYRIDOXIC ACID 26483 40237 26589 5-HYDROXYTRYPTOPHAN 32782 41014 36101 5-OXOPROLINE 27500000 34500000 54000000 5-OXOPROLINE - 1.1521429 20000000 34500000 54000000 ACONITIC ACID 28501 104982 262566 ALLANTOIN 75200 71515 76195 ASPARTATE 63662 61443 56896 AZELAIC ACID 32334 52621 36208 CITRAMALIC ACID 47960 39806 44563 CITRIC ACID 524972 1306839 7118927 CITRIC ACID - 1.1011429 559374 455608 871055 CORTISONE (M+HCOO) 63597 CORTISONE - 13.411 51006 CYTIDINE 17189 13120 26270 ELAIDIC ACID 17782 20668 50740 FOLIC ACID 926503 1142792 966264 FRUCTOSE - 0.6068571 546130 443684 369243 GLUCONIC ACID 201518 GLUTAMINE 918666 475939 359480 GLUTAMINE - 0.6102857 49346 26265 20926 GLYCERALDEHYDE (-H2O) 159196 148200 81228 GLYCERALDEHYDE - 0.6068571 159196 148200 81228 GLYCERALDEHYDE - 0.6637143 1039625 1047592 928093 GLYCERALDEHYDE - 0.6767143 470857 512118 477674 GLYCERIC ACID (-H2O) 114799 333369 457552 GLYCERIC ACID - 0.76766676 88225 57612 GLYCERIC ACID - 0.8618571 407632 368875 477665 HIPPURIC ACID 672120 936991 803579 HISTAMINE 76525 HYPOXANTHINE 146870 86263 54700 ISOLEUCINE 1224888 937092 688107 ITACONIC ACID 92442 297457 593387 L-HISTIDINE 195399 180819 166181 LYSINE 53278 54962 53018 MALATE 127838 304156 474014 METHIONINE 170298 101591 N-ACETYL-DL-GLUTAMIC ACID 18082 46452 115553 N-ACETYL-L-ALANINE 96091 113711 N-ACETYL-L-ASPARTIC ACID 49818 N-ACETYLGALACTOSAMINE (M+Cl) 133275 175652 163685 N-ACETYLGLYCINE - 0.90571433 156100 257522 212767 N-ALPHA-ACETYL-L-ASPARAGINE (2M-H) 17381 25367 35782 O-ACETYLSERINE 117007 31150 47996 PANTOTHENIC ACID 5982250 7181470 6310808 PANTOTHENIC ACID - 3.2937143 5246095 6211673 5527089 PHENYLACETIC ACID (M+HCOO) 85256 157939 230113 PYRUVIC ACID 378018 1112285 791446 PYRUVIC ACID - 0.9791428 107903 94345 70739 RAFFINOSE (M+Cl) 35752 38104 32557 RIBOFLAVIN (VITAMIN B2) 124121 117989 111264 RIBOFLAVIN (VITAMIN B2) - 7.6341434 63024 47115 46087 STACHYOSE (M+Cl) 23159 25419 21131 STEARIC ACID 42556 35026 31656 SUCCINATE 1247004 1328165 1171721 SUCCINATE - 1.3074285 35533 58240 59230 THYMIDINE 103803 115856 186444 TRYPTOPHAN 1828182 2036208 1615432 TYROSINE 3449796 2909711 2322563 URIC ACID 903416 1134205 810483 URIDINE (M-H) 2327152 1957182 2887925 URIDINE - 1.3322858 2267209 1907790 2815527 URIDINE - 1.3334286 1822020 1539944 2259699 URSODIOL-2 WATER 11612 13384 46552 VALINE 195656 155312 126117 XANTHOSINE 23074 40688 50920 XANTHOSINE - 2.3645713 27643 35918 30595 XYLOSE 121661 201999 253347 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 2-AMINO-4-METHYLPENTANOIC ACID (LEUCINE) 131.0948 1.58 6106 2-OXOBUTANOATE 102.0318 0.903 58 3-HYDROXY-3-METHYL-GLUTARIC ACID 162.0529 1.623 1662 4-ACETAMIDOBUTANOATE 145.0735 1.819 18189 4-PYRIDOXIC ACID 183.053 1.879 6723 5-HYDROXYTRYPTOPHAN 220.0842 1.784 439280 5-OXOPROLINE 129.0426 1.145 7405 5-OXOPROLINE - 1.1521429 129.0425 1.152 7405 ACONITIC ACID 174.0162 1.116 444212 ALLANTOIN 158.0432 0.658 439714 ASPARTATE 276.0591 0.658 5960 AZELAIC ACID 188.1047 10.775 2266 CITRAMALIC ACID 148.0368 1.394 441696 CITRIC ACID 192.027 0.997 311 CITRIC ACID - 1.1011429 192.0269 1.101 311 CORTISONE (M+HCOO) 406.1991 13.416 222786 CORTISONE - 13.411 396.17 13.411 222786 CYTIDINE 243.0846 0.836 6175 ELAIDIC ACID 282.2556 22.911 637517 FOLIC ACID 441.1398 5.829 6037 FRUCTOSE - 0.6068571 180.0628 0.607 5984 GLUCONIC ACID 196.0569 0.673 10690 GLUTAMINE 146.0689 0.611 5961 GLUTAMINE - 0.6102857 128.0583 0.61 5961 GLYCERALDEHYDE (-H2O) 72.0214 0.607 79014 GLYCERALDEHYDE - 0.6068571 72.0216 0.607 79014 GLYCERALDEHYDE - 0.6637143 90.0316 0.664 79014 GLYCERALDEHYDE - 0.6767143 136.0368 0.677 79014 GLYCERIC ACID (-H2O) 88.0153 0.772 439194 GLYCERIC ACID - 0.76766676 106.0268 0.768 439194 GLYCERIC ACID - 0.8618571 134.0216 0.862 439194 HIPPURIC ACID 179.0582 4.823 464 HISTAMINE 147.0554 0.621 774 HYPOXANTHINE 136.0382 1.088 790 ISOLEUCINE 131.0944 1.479 6306 ITACONIC ACID 130.0269 0.992 811 L-HISTIDINE 155.0693 0.61 6274 LYSINE 146.104 0.588 5962 MALATE 134.0207 0.778 222656 METHIONINE 149.0504 0.982 6137 N-ACETYL-DL-GLUTAMIC ACID 189.0637 1.292 185 N-ACETYL-L-ALANINE 131.0567 1.483 88064 N-ACETYL-L-ASPARTIC ACID 175.0478 0.962 65065 N-ACETYLGALACTOSAMINE (M+Cl) 257.0673 0.702 35717 N-ACETYLGLYCINE - 0.90571433 244.0694 0.906 1097 N-ALPHA-ACETYL-L-ASPARAGINE (2M-H) 348.0813 0.725 99715 O-ACETYLSERINE 147.0524 0.848 99478 PANTOTHENIC ACID 219.1108 3.294 6613 PANTOTHENIC ACID - 3.2937143 219.1112 3.294 6613 PHENYLACETIC ACID (M+HCOO) 182.0578 3.813 999 PYRUVIC ACID 88.0161 0.867 1060 PYRUVIC ACID - 0.9791428 134.0218 0.979 1060 RAFFINOSE (M+Cl) 540.1436 0.749 439242 RIBOFLAVIN (VITAMIN B2) 376.1374 7.61 493570 RIBOFLAVIN (VITAMIN B2) - 7.6341434 412.1144 7.634 493570 STACHYOSE (M+Cl) 702.1971 0.804 439531 STEARIC ACID 284.2717 23.169 5281 SUCCINATE 118.0269 1.292 1110 SUCCINATE - 1.3074285 100.0164 1.307 1110 THYMIDINE 242.0899 2.746 5789 TRYPTOPHAN 204.0901 3.602 6305 TYROSINE 181.0739 1.296 6057 URIC ACID 168.0283 0.998 1175 URIDINE (M-H) 244.07 1.332 6029 URIDINE - 1.3322858 244.0704 1.332 6029 URIDINE - 1.3334286 280.0466 1.333 6029 URSODIOL-2 WATER 392.292 21.704 31401 VALINE 117.0789 0.872 6287 XANTHOSINE 284.0758 2.271 64959 XANTHOSINE - 2.3645713 284.0756 2.365 64959 XYLOSE 150.0522 0.702 135191 METABOLITES_END #END