#METABOLOMICS WORKBENCH araskind_20170619_105956 DATATRACK_ID:985 STUDY_ID:ST000690 ANALYSIS_ID:AN001066 PROJECT_ID:PR000489 VERSION 1 CREATED_ON June 30, 2017, 3:11 pm #PROJECT PR:PROJECT_TITLE Human oral keratinocytes growth and proliferation based on culture medium volume PR:PROJECT_TYPE MS analysis PR:PROJECT_SUMMARY Using different culture medium volume to affect cultured human oral PR:PROJECT_SUMMARY keratinocytes growth and proliferation rates PR:INSTITUTE University of Michigan PR:DEPARTMENT Oral & Maxillofacial Surgery PR:LABORATORY Feinberg Lab PR:LAST_NAME Feinberg PR:FIRST_NAME Stephen PR:ADDRESS Ann Arbor, MI PR:EMAIL sefein@umich.edu PR:PHONE 734-763-5963 #STUDY ST:STUDY_TITLE Human oral keratinocytes growth and proliferation based on culture medium volume ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY We seeded cells at density of 500k/T75 and cultured them at two different medium ST:STUDY_SUMMARY volume, one at 30ml, the other at 15ml. Culture medium is composed of 1x EDGS ST:STUDY_SUMMARY and 0.06mM calcium. We changed medium every day for 30ml culture, and every two ST:STUDY_SUMMARY days for 15ml culture. We collected spent medium when we changed medium. The ST:STUDY_SUMMARY collected spent medium was filtered through low protein binding 0.22um pore size ST:STUDY_SUMMARY filter and then stored at -80 degree C. For OA and SMT, spent medium was ST:STUDY_SUMMARY collected on the same day of D5 and D9 after cell seeding as marked on the ST:STUDY_SUMMARY tubes. For GK samples, 15ml and 30ml cultures were collected when cells reached ST:STUDY_SUMMARY at around 90% confluence, that is D5 for 15ml and D6 for 30 ml culture. The ST:STUDY_SUMMARY numbers 151, 152 were duplicated cell cultures in two T75s, same for 301 and ST:STUDY_SUMMARY 302. One major differences among GK, OA, and SMT is GK was from frozen cells; OA ST:STUDY_SUMMARY and SMT were fresh cells that were never frozen. Blank15 and Blank30 were ST:STUDY_SUMMARY complete medium without cells incubating in incubator for two days for Blank15 ST:STUDY_SUMMARY and one day for Blank30. Medium was collected in the same manner as others. 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 10 ST:TOTAL_SUBJECTS 5 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0003722 S00014307 Day:5 days | Line:GK | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003722 S00014308 Day:5 days | Line:GK | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003722 S00014309 Day:6 days | Line:GK | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003722 S00014310 Day:6 days | Line:GK | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014311 Day:5 days | Line:OA | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014312 Day:9 days | Line:OA | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014313 Day:5 days | Line:OA | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003723 S00014314 Day:9 days | Line:OA | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014315 Day:5 days | Line:SMT | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014316 Day:9 days | Line:SMT | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014317 Day:5 days | Line:SMT | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003724 S00014318 Day:9 days | Line:SMT | Volume:30ml SUBJECT_SAMPLE_FACTORS SU0003725 S00014319 Day:2 days | Line:Blank | Volume:15ml SUBJECT_SAMPLE_FACTORS SU0003725 S00014320 Day:2 days | Line:Blank | Volume:30ml SUBJECT_SAMPLE_FACTORS SU9999996 S00020128 Day:- | Line:- | Volume:- #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 S00014307 S00014308 S00014309 S00014310 S00014311 S00014312 S00014313 S00014314 S00014315 S00014316 S00014317 S00014318 S00014319 S00014320 Factors Day:5 days | Line:GK | Volume:15ml Day:5 days | Line:GK | Volume:15ml Day:6 days | Line:GK | Volume:30ml Day:6 days | Line:GK | Volume:30ml Day:5 days | Line:OA | Volume:15ml Day:9 days | Line:OA | Volume:15ml Day:5 days | Line:OA | Volume:30ml Day:9 days | Line:OA | Volume:30ml Day:5 days | Line:SMT | Volume:15ml Day:9 days | Line:SMT | Volume:15ml Day:5 days | Line:SMT | Volume:30ml Day:9 days | Line:SMT | Volume:30ml Day:2 days | Line:Blank | Volume:15ml Day:2 days | Line:Blank | Volume:30ml 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID 77305 75575 79774 84934 81861 69841 76087 78611 69204 3800 75201 77667 4-ACETAMIDOBUTANOATE 57874 57699 17467 117745 117621 5-OXOPROLINE 46100000 46000000 47100000 45800000 45300000 41200000 47600000 46900000 46800000 42100000 43700000 40200000 41800000 34400000 5?-DEOXY-5?-(METHYLTHIO)ADENOSINE 3809427 4341706 3568173 3248248 3695819 3040450 2232481 4765302 3446750 2721229 1993414 3397592 ADENINE 15100000 14600000 15600000 15300000 15000000 14000000 14900000 16100000 15200000 14100000 15100000 14700000 14500000 12600000 ADENOSINE 44956 42602 29531 38129 21285 64093 55965 45326 68760 83326 4393 AZELAIC ACID 45359 55600 55054 65355 54613 58953 55382 84953 72546 49382 84047 54719 54025 53251 CITRIC ACID 49272 41225 9028 38301 8690 16328 8808 26598 25613 4266 D-BIOTIN 24153 19258 22457 20233 15165 19254 25391 22625 19680 19644 17868 14399 11536 DIOCTYL PHTHALATE (M+H) 1332434 1262843 1337399 1366366 1365475 1376804 1390311 1390781 1401219 1391180 1390125 1377834 1388630 1392715 FOLIC ACID 174704 159957 173850 162066 164675 141710 150533 216066 170525 149612 146461 144416 118027 78999 GLUCOSE 179358 130455 1632096 1766557 1570026 43781 2527946 486786 1073829 50293 2559854 859372 3195929 2807964 GLUTAMATE 26744 11429 5167 GLUTAMINE 1376072 1069167 1781113 1795269 1598902 1224601 1457298 1799965 1536040 1372978 1286365 1738318 1381814 1436537 GUANINE 121186 131692 52269 42950 156156 45199 87953 39506 HYPOXANTHINE 1221376 1247592 577642 457446 990266 1843 333565 173493 507750 337080 ISOLEUCINE 15300000 15300000 16700000 16400000 16700000 14000000 16600000 17300000 16400000 14500000 17400000 15200000 16400000 14700000 KYNURENINE 66090 63612 57202 48274 21043 L-HISTIDINE 44880 170140 13321 11031 15375 10203 12403 12020 12472 171249 8313 190659 43632 164811 L-NORLEUCINE 18600000 18300000 22600000 22700000 21700000 16300000 23200000 20800000 21200000 17300000 22600000 20100000 22900000 19500000 METHIONINE 8185880 8120116 9089226 8929089 8994480 8025088 8892510 9151214 8989558 8097835 9126275 8695496 8425377 7348895 METHYL JASMONATE (M+H) 170692 154880 190862 155196 157597 140694 153100 146099 N-ACETYL-DL-METHIONINE 52356 53275 24840 22677 26948 73001 12201 32913 47412 55563 18079 27090 2108 2399 N-ACETYLPUTRESCINE 85027 81803 44390 60091 51118 208076 65340 138177 68747 152425 38794 73914 57843 42379 N-CYCLOHEXYLFORMAMIDE 51831 45686 55987 52795 50763 42230 55556 53716 57739 64509 57189 NICOTINAMIDE 220792 204407 288519 293696 300340 165552 311802 258494 263071 122486 311302 257604 335596 319256 PANTOTHENIC ACID 796305 764373 864191 808474 751555 679426 723121 938483 797821 701861 728653 679257 598777 415868 PROLINE 2293242 2305690 2203315 2120771 2107346 2615738 2058642 2352850 2152040 2545771 2078130 2214344 1997011 1867811 RIBOFLAVIN (VITAMIN B2) 116934 108023 119130 112848 182144 163092 156468 236041 188248 170471 155001 165595 82571 64931 THYMIDINE (M+H) 3478 10873 17432 73712 214023 2638 9651 153716 8857 320076 213682 THYMINE 129650 124554 125417 121011 70892 108079 33570 92941 112445 113451 64645 106320 TYROSINE 9173820 8781267 11300000 11200000 10700000 7905316 11400000 10200000 10600000 8123272 11600000 9889647 10700000 8704831 VALINE 1944462 1987013 2658980 2653286 2584431 1785836 2853585 2237450 2532872 1794688 2779215 2303454 3047076 2704155 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 0.937 535 4-ACETAMIDOBUTANOATE 145.0733 1.816 18189 5-OXOPROLINE 129.0427 1.171 7405 5?-DEOXY-5?-(METHYLTHIO)ADENOSINE 297.0898 4.47 439176 ADENINE 135.0544 0.866 190 ADENOSINE 267.0961 1.785 60961 AZELAIC ACID 188.1054 10.753 2266 CITRIC ACID 192.0262 0.882 311 D-BIOTIN 244.0892 6.262 171548 DIOCTYL PHTHALATE (M+H) 390.2774 23.079 8346 FOLIC ACID 441.1392 5.819 6037 GLUCOSE 180.0631 0.64 5793 GLUTAMATE 147.0542 0.853 33032 GLUTAMINE 146.0688 0.624 5961 GUANINE 151.0484 0.889 764 HYPOXANTHINE 136.0389 1.097 790 ISOLEUCINE 131.0946 1.487 6306 KYNURENINE 208.0836 2.18 161166 L-HISTIDINE 155.069 0.562 6274 L-NORLEUCINE 131.0947 1.589 21236 METHIONINE 149.0509 0.979 6137 METHYL JASMONATE (M+H) 224.1392 16.084 5281929 N-ACETYL-DL-METHIONINE 191.0606 4.077 448580 N-ACETYLPUTRESCINE 130.1098 0.767 122356 N-CYCLOHEXYLFORMAMIDE 127.0989 7.946 13017 NICOTINAMIDE 122.0483 1.128 936 PANTOTHENIC ACID 219.1104 3.283 6613 PROLINE 115.0633 0.69 145742 RIBOFLAVIN (VITAMIN B2) 376.1383 7.589 493570 THYMIDINE (M+H) 242.0908 2.739 5789 THYMINE 126.0435 1.701 1135 TYROSINE 181.0738 1.294 6057 VALINE 117.0791 0.875 6287 METABOLITES_END #END