#METABOLOMICS WORKBENCH araskind_20170802_132535 DATATRACK_ID:1181 STUDY_ID:ST000832 ANALYSIS_ID:AN001838 PROJECT_ID:PR000593 VERSION 1 CREATED_ON January 16, 2019, 8:47 am #PROJECT PR:PROJECT_TITLE Regulatory roles of glycolysis and its enzymes in photoreceptor survival PR:PROJECT_TYPE MS analysis PR:PROJECT_SUMMARY The goals specific to this proposal are to understand how the metabolic flux PR:PROJECT_SUMMARY through glycolysis and its associated pathways, such as oxidative PR:PROJECT_SUMMARY phosphorylation and pentose phosphate pathway, is regulated during periods of PR:PROJECT_SUMMARY photoreceptor stress. PR:INSTITUTE University of Michigan PR:DEPARTMENT Ophthamology and Visual Sciences PR:LABORATORY Besirli Lab PR:LAST_NAME Besirli PR:FIRST_NAME Cagri PR:ADDRESS Ann Arbor, MI PR:EMAIL cbesirli@umich.edu PR:PHONE 734-615-6099 #STUDY ST:STUDY_TITLE Rat Retinal Detachment Metabolomics Timecourse ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY Detachments were created in adult male Brown-Norway rats (300?400 g; Charles ST:STUDY_SUMMARY River Laboratories, Wilmington, MA). Briefly, rodents were anesthetized with a ST:STUDY_SUMMARY 50:50 mix of ketamine/xylazine, and pupils were dilated with topical ST:STUDY_SUMMARY phenylephrine (2.5%) and tropicamide (1%). A 20-gauge microvitreoretinal blade ST:STUDY_SUMMARY was used to create a sclerotomy 2 mm posterior to the limbus, carefully avoiding ST:STUDY_SUMMARY lens damage. A subretinal injector (Glaser, 32-gauge tip; BD Ophthalmic Systems, ST:STUDY_SUMMARY Franklin Lakes, NJ) was introduced through the sclerotomy into the vitreous ST:STUDY_SUMMARY cavity and then through a peripheral retinotomy into the subretinal space. ST:STUDY_SUMMARY Sodium hyaluronate (10 mg/mL, Healon O.D Abbott Medical Optics, Uppsala, ST:STUDY_SUMMARY Sweden) was slowly injected to detach the neurosensory retina from the ST:STUDY_SUMMARY underlying RPE. In all experiments, approximately one third to one half of the ST:STUDY_SUMMARY neurosensory retina was detached. Detachments were created in the left eye. The ST:STUDY_SUMMARY right eye served as the control, with all the steps of the procedure performed ST:STUDY_SUMMARY except for introduction of the subretinal injector and injection of the sodium ST:STUDY_SUMMARY hyaluronate. At varying intervals after creation of the detachment, the animals ST:STUDY_SUMMARY were euthanatized, and the eyes were enucleated.The retina was then dissected ST:STUDY_SUMMARY away from the retinal pigment epithelium taking just the detached portion in ST:STUDY_SUMMARY those eyes experimentally detached. All experiments were performed in accordance ST:STUDY_SUMMARY with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research ST:STUDY_SUMMARY and the guidelines established by the University Committee on Use and Care of ST:STUDY_SUMMARY Animals of the University of Michigan. 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 30 ST:TOTAL_SUBJECTS 21 #SUBJECT SU:SUBJECT_TYPE RAT SU:SUBJECT_SPECIES Rattus norvegicus SU:TAXONOMY_ID 10114 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0014158 S00021535 Attachment:Detached | Time:5 min Rat #=10.0 SUBJECT_SAMPLE_FACTORS SU0014158 S00021536 Attachment:Attached | Time:5 min Rat #=10.0 SUBJECT_SAMPLE_FACTORS SU0014159 S00021537 Attachment:Detached | Time:5 min Rat #=11.0 SUBJECT_SAMPLE_FACTORS SU0014159 S00021538 Attachment:Attached | Time:5 min Rat #=11.0 SUBJECT_SAMPLE_FACTORS SU0014160 S00021539 Attachment:Detached | Time:5 min Rat #=12.0 SUBJECT_SAMPLE_FACTORS SU0014160 S00021540 Attachment:Attached | Time:5 min Rat #=12.0 SUBJECT_SAMPLE_FACTORS SU0014161 S00021541 Attachment:Detached | Time:15 min Rat #=13.0 SUBJECT_SAMPLE_FACTORS SU0014161 S00021542 Attachment:Attached | Time:15 min Rat #=13.0 SUBJECT_SAMPLE_FACTORS SU0014162 S00021543 Attachment:Detached | Time:15 min Rat #=14.0 SUBJECT_SAMPLE_FACTORS SU0014162 S00021544 Attachment:Attached | Time:15 min Rat #=14.0 SUBJECT_SAMPLE_FACTORS SU0014163 S00021545 Attachment:Detached | Time:15 min Rat #=15.0 SUBJECT_SAMPLE_FACTORS SU0014163 S00021546 Attachment:Attached | Time:15 min Rat #=15.0 SUBJECT_SAMPLE_FACTORS SU0014164 S00021547 Attachment:Detached | Time:30 min Rat #=16.0 SUBJECT_SAMPLE_FACTORS SU0014164 S00021548 Attachment:Attached | Time:30 min Rat #=16.0 SUBJECT_SAMPLE_FACTORS SU0014165 S00021549 Attachment:Detached | Time:30 min Rat #=17.0 SUBJECT_SAMPLE_FACTORS SU0014165 S00021550 Attachment:Attached | Time:30 min Rat #=17.0 SUBJECT_SAMPLE_FACTORS SU0014166 S00021551 Attachment:Detached | Time:30 min Rat #=18.0 SUBJECT_SAMPLE_FACTORS SU0014166 S00021552 Attachment:Attached | Time:30 min Rat #=18.0 SUBJECT_SAMPLE_FACTORS SU0014167 S00021553 Attachment:Detached | Time:45 min Rat #=22.0 SUBJECT_SAMPLE_FACTORS SU0014167 S00021554 Attachment:Attached | Time:45 min Rat #=22.0 SUBJECT_SAMPLE_FACTORS SU0014168 S00021555 Attachment:Detached | Time:45 min Rat #=23.0 SUBJECT_SAMPLE_FACTORS SU0014168 S00021556 Attachment:Attached | Time:45 min Rat #=23.0 SUBJECT_SAMPLE_FACTORS SU0014169 S00021557 Attachment:Detached | Time:45 min Rat #=24.0 SUBJECT_SAMPLE_FACTORS SU0014169 S00021558 Attachment:Attached | Time:45 min Rat #=24.0 SUBJECT_SAMPLE_FACTORS SU0014170 S00021559 Attachment:Detached | Time:90 min Rat #=19.0 SUBJECT_SAMPLE_FACTORS SU0014170 S00021560 Attachment:Attached | Time:90 min Rat #=19.0 SUBJECT_SAMPLE_FACTORS SU0014171 S00021561 Attachment:Detached | Time:90 min Rat #=20.0 SUBJECT_SAMPLE_FACTORS SU0014171 S00021562 Attachment:Attached | Time:90 min Rat #=20.0 SUBJECT_SAMPLE_FACTORS SU0014172 S00021563 Attachment:Detached | Time:90 min Rat #=21.0 SUBJECT_SAMPLE_FACTORS SU0014172 S00021564 Attachment:Attached | Time:90 min Rat #=21.0 SUBJECT_SAMPLE_FACTORS SU0014173 S00021565 Attachment:Detached | Time:3 hr Rat #=7.0 SUBJECT_SAMPLE_FACTORS SU0014173 S00021566 Attachment:Attached | Time:3 hr Rat #=7.0 SUBJECT_SAMPLE_FACTORS SU0014174 S00021567 Attachment:Detached | Time:3 hr Rat #=8.0 SUBJECT_SAMPLE_FACTORS SU0014174 S00021568 Attachment:Attached | Time:3 hr Rat #=8.0 SUBJECT_SAMPLE_FACTORS SU0014175 S00021569 Attachment:Detached | Time:3 hr Rat #=9.0 SUBJECT_SAMPLE_FACTORS SU0014175 S00021570 Attachment:Attached | Time:3 hr Rat #=9.0 SUBJECT_SAMPLE_FACTORS SU0014176 S00021571 Attachment:Detached | Time:5 hr Rat #=1.0 SUBJECT_SAMPLE_FACTORS SU0014176 S00021572 Attachment:Attached | Time:5 hr Rat #=1.0 SUBJECT_SAMPLE_FACTORS SU0014177 S00021573 Attachment:Detached | Time:5 hr Rat #=2.0 SUBJECT_SAMPLE_FACTORS SU0014177 S00021574 Attachment:Attached | Time:5 hr Rat #=2.0 SUBJECT_SAMPLE_FACTORS SU0014178 S00021575 Attachment:Detached | Time:5 hr Rat #=3.0 SUBJECT_SAMPLE_FACTORS SU0014178 S00021576 Attachment:Attached | Time:5 hr Rat #=3.0 #COLLECTION CO:COLLECTION_SUMMARY - CO:SAMPLE_TYPE Retina #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME A011_Glycolysis-TCA-nucleotides.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE A011 - Glycolysis-TCA-nucleotides.pdf AN:ACQUISITION_PARAMETERS_FILE QTOF-002-HILIC-35min-1mm.m #MS MS:INSTRUMENT_NAME Agilent 6520B QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS none #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/ug protein MS_METABOLITE_DATA_START Samples S00021535 S00021536 S00021537 S00021538 S00021539 S00021540 S00021541 S00021542 S00021543 S00021544 S00021545 S00021546 S00021547 S00021548 S00021549 S00021550 S00021551 S00021552 S00021553 S00021554 S00021555 S00021556 S00021557 S00021558 S00021559 S00021560 S00021561 S00021562 S00021563 S00021564 S00021565 S00021566 S00021567 S00021568 S00021569 S00021570 S00021571 S00021572 S00021573 S00021574 S00021575 S00021576 Factors Attachment:Detached | Time:5 min Attachment:Attached | Time:5 min Attachment:Detached | Time:5 min Attachment:Attached | Time:5 min Attachment:Detached | Time:5 min Attachment:Attached | Time:5 min Attachment:Detached | Time:15 min Attachment:Attached | Time:15 min Attachment:Detached | Time:15 min Attachment:Attached | Time:15 min Attachment:Detached | Time:15 min Attachment:Attached | Time:15 min Attachment:Detached | Time:30 min Attachment:Attached | Time:30 min Attachment:Detached | Time:30 min Attachment:Attached | Time:30 min Attachment:Detached | Time:30 min Attachment:Attached | Time:30 min Attachment:Detached | Time:45 min Attachment:Attached | Time:45 min Attachment:Detached | Time:45 min Attachment:Attached | Time:45 min Attachment:Detached | Time:45 min Attachment:Attached | Time:45 min Attachment:Detached | Time:90 min Attachment:Attached | Time:90 min Attachment:Detached | Time:90 min Attachment:Attached | Time:90 min Attachment:Detached | Time:90 min Attachment:Attached | Time:90 min Attachment:Detached | Time:3 hr Attachment:Attached | Time:3 hr Attachment:Detached | Time:3 hr Attachment:Attached | Time:3 hr Attachment:Detached | Time:3 hr Attachment:Attached | Time:3 hr Attachment:Detached | Time:5 hr Attachment:Attached | Time:5 hr Attachment:Detached | Time:5 hr Attachment:Attached | Time:5 hr Attachment:Detached | Time:5 hr Attachment:Attached | Time:5 hr PHOSPHOENOLPYRUVATE 35.83059161 3.869789665 24.35641757 2.726737722 6.72259088 2.742470463 19.96237636 1.983423094 7.456342391 4.331712219 31.53939452 8.612261746 19.04800746 2.481207824 4.905154162 2.980459294 12.10753004 5.025339121 3.163054872 2.939886618 1.944186383 2.502283317 2.067880841 3.459683969 4.315063755 3.567313188 4.994534315 3.104328072 3.946631687 2.6088943 2.41142498 4.23341907 3.081285254 1.803307159 3.479981555 2.406413785 2.637715206 7.914866165 2.557941365 4.387849763 2.802780527 5.480978529 D-ERYTHROSE 4-PHOSPHATE 32.38287922 12.94604988 45.3998703 12.47340889 16.1703569 19.08948508 33.61414536 8.237662701 22.82094222 17.73491205 49.87304999 21.59119745 37.11039699 12.50761327 10.34940252 9.730505647 23.26285037 21.8979527 14.86335892 15.56200622 7.117523887 19.16662547 6.262737482 10.05400734 15.79037569 6.945867042 14.91133861 21.86931288 10.63525481 14.27527649 9.026810849 17.54775622 12.55719407 18.0795259 7.361402611 11.68770013 9.391392661 7.980404639 15.25983628 14.96094862 12.66256485 10.64195431 BETA-NAD+ 2.304525263 11.25260161 8.385666167 21.28003134 3.042841352 14.66231052 4.375789435 14.41040819 5.432504229 10.61221062 7.007030159 10.13061702 8.254368577 18.87972393 9.385788795 20.15918806 12.514206 8.906605599 7.999766779 16.75294079 9.163969832 19.70217426 5.833391874 16.26280775 7.471507124 19.1315424 8.283970078 11.42707785 8.568472888 10.45057917 7.918843718 12.15470376 11.82024374 19.39094694 9.964886177 16.99494226 7.648720954 18.01363416 16.61645074 21.00474168 7.781554803 21.75353248 COENZYME II .260944431 1.231165485 1.834919943 2.509784646 .624016162 1.470449379 .922078796 2.144282834 1.063655984 1.339068256 1.370158701 1.284594062 1.200731075 1.986424644 1.07156736 2.406435914 1.742751044 1.552625546 1.241025726 2.273433561 .919549716 2.059939922 .67994256 1.874725077 1.578677797 2.410171533 1.180009649 1.804635187 1.009531624 1.098962019 1.154607738 2.076143254 1.608342017 2.088216786 1.092752546 2.30495372 1.232593838 2.24393579 2.062989423 3.249228144 .980315458 3.899410343 D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE) 1.803163893 3.445507971 4.52829869 9.298671218 1.878906317 4.32406901 2.001906775 7.455967864 2.473613131 6.013717326 2.127969077 7.260125933 2.887253602 6.722096803 3.381412431 8.249719874 6.996154245 3.315494073 2.524126269 5.159158759 2.754866009 7.546927645 1.708894675 7.415902837 11.36320959 6.375230297 3.322145101 3.346593227 2.939237816 7.438650995 3.565643796 3.084817545 3.758999535 5.404080108 4.118080697 6.246199075 1.927832061 5.379220325 4.063482958 10.43847539 2.538249424 9.135650605 CITRIC ACID 133.3480392 356.5818086 347.8972717 450.4394721 96.65328076 502.5060637 210.5895354 184.6730602 211.69339 414.7794757 318.2672519 276.325533 286.8821587 530.4454732 196.6875442 615.8154641 272.5573675 347.123759 231.0135451 440.5920832 209.2639165 584.9868031 181.5609275 487.5836579 123.8309218 167.8582944 177.3400859 472.3873624 246.1689066 77.58982397 195.8680952 489.895044 504.0823015 611.9340034 242.3068001 657.2403072 221.3572514 477.3145552 550.3615133 643.2607252 260.7461874 551.5985295 NADH 1.820952836 16.23703769 5.108595997 29.63560873 26.92321437 4.13514974 10.02329761 3.033015021 12.62054654 5.370485402 8.748126709 9.296391776 34.0003389 7.126010507 28.05751668 7.19873346 6.467608214 5.949815933 19.82600331 6.826259884 29.06667884 2.534626697 21.25074365 38.0948223 27.0299796 26.82640037 8.198759638 7.545853636 9.50381209 5.941586938 13.46910151 10.75206831 35.29074038 9.113685128 28.93541436 3.876537488 23.58702295 26.8178159 23.81697855 3.085315158 25.00961402 FAD .294422627 .986579568 1.017202813 1.669576742 .345038933 1.284496032 .576099449 1.078345379 .580697482 1.030951388 .910005134 1.172068002 .773683632 1.467599489 .608335871 1.379964348 .963821697 1.002683823 .555166464 1.27125529 .525249914 1.700792497 .377887964 1.340385796 .775528249 1.301411446 .701751574 1.148765295 .509617828 .362739806 .665798471 1.253763648 1.040603033 1.468344037 .680766187 1.426622885 .548675345 1.447158867 1.49662764 1.830523983 .388928213 1.677588535 MALIC ACID 24.99225648 79.24034068 44.41224517 176.02225 35.5836854 86.32543978 29.31876412 189.0088895 27.13036501 85.70386323 38.54180989 106.6310282 28.47127539 91.64473789 31.42948616 100.7076562 87.16193167 44.72568288 22.14081919 95.05677419 18.91369579 92.94874624 11.8495056 80.85151751 142.1801977 211.286097 101.0100783 38.78407883 22.73585629 75.02072009 72.98917592 73.41336268 38.15941151 99.85469324 41.0384907 77.76276168 27.20282008 125.5579464 112.6731448 128.936685 29.32145477 136.82231 ADENOSINE TRIPHOSPHATE 57.62083015 17.67578846 30.94467678 41.24904264 20.31601206 36.94504162 13.30712119 27.64757096 22.93081816 32.86512799 14.49718427 166.4572787 22.44660474 72.03810239 19.43604362 44.60607577 31.90252149 32.6704024 11.87364761 38.25782408 37.19300905 38.76160706 16.27929212 40.114711 31.09414425 39.65466855 14.84801699 44.70584109 18.752013 19.27388231 19.89831392 25.11692834 40.29033625 43.02337796 18.93208407 37.81410859 20.47395641 32.07108261 20.06833536 66.02900782 25.7802191 48.23998095 ROBISON ESTER 12.8755999 26.85967983 26.89992214 53.446588 12.49020296 41.90217574 18.7799478 44.35219376 15.36332326 33.97958308 23.74605492 37.39569158 20.58402498 48.19072324 14.35282318 57.72800829 30.85563766 23.93377728 17.44412266 44.21460281 17.13930844 47.72897666 10.5836083 37.72637839 40.43470466 55.94770626 35.76970294 25.65315818 16.43668473 27.25599831 22.3973068 36.7497164 26.74757275 49.04317824 17.35178664 42.57797096 14.54070815 40.18503757 42.95833631 47.43527548 17.03135207 52.90909794 SUCROSE 1.737675312 24.52571513 4.31774318 72.76815232 1.321664741 17.78105203 2.250998906 104.3581207 2.150896861 11.16910159 2.412962263 11.66714173 3.524182788 26.83670636 2.385860427 59.61311384 6.784407366 4.412367049 1.693652608 12.2560599 1.782397733 16.20919158 1.393691494 13.50683613 41.36412421 165.1855702 8.853907529 3.068844296 2.654709446 30.12688418 9.687227154 8.854427105 3.958938972 26.41680776 5.157985175 19.06952803 2.855703897 19.58085058 39.64363976 12.18983229 3.642824732 32.33448819 ADENOSINE 5'-DIPHOSPHATE 1.203610328 4.998220754 1.842754043 10.36548086 .906519621 6.691142095 .789113296 21.4476097 1.514663963 4.767824383 .955307344 4.604708975 1.344568805 10.09310834 2.441072266 9.575186102 3.686234273 2.105768612 2.596588592 10.34017677 2.892951038 10.93068798 1.748258522 8.248731812 3.198273196 21.04406289 2.059753483 3.637306422 1.956574265 4.849731501 2.616872182 5.324320041 3.621183556 10.68944817 3.228954074 8.822610699 2.689731244 10.40821403 7.237586716 11.06540957 1.871153808 13.67641862 ADENOSINE 5'-MONOPHOSPHATE 1.095769335 2.784298169 1.697042594 7.025691798 .624458984 5.242505358 .735028176 13.92881955 1.063362853 3.115937186 1.377768554 5.136411563 .798627259 7.314105872 1.171886471 5.026801557 1.71467372 2.05936291 1.15100596 7.957657922 1.539042579 8.27461709 .797438358 4.405553209 1.231354664 35.62681758 .714586731 2.389566436 .866734765 3.320701811 1.468278799 3.94068933 1.616109194 11.86802999 1.922157767 6.244554939 1.188189754 7.638061625 3.720436416 6.724323974 .676051914 8.727734756 GLYCERATE 3-PHOSPHATE 216.587817 35.54513361 179.4024949 32.62017434 79.28874117 29.34800166 155.1758924 21.26680936 62.01491493 31.35063855 231.5758006 73.02114352 144.9115008 23.61745431 42.28944133 42.21482111 98.95436141 61.497309 36.98791713 37.51637166 18.24080005 19.38289787 17.92396403 22.88887226 45.09787359 37.24521546 46.23699868 31.83699955 35.60490426 17.43330663 26.83677044 36.28172732 35.29349149 27.88065443 20.85668806 24.90902265 26.50853547 58.91685984 29.12863934 21.12788976 27.30855602 19.04851922 RIBOSE PHOSPHATE 34.64109948 133.4211246 91.12566545 217.0238065 46.79207392 182.2347331 67.58383549 177.4974597 66.13809677 140.9968624 91.02060347 173.557314 87.13436158 182.4778831 75.7174329 181.0022119 160.3560942 104.1971764 79.96631567 193.1546368 76.79549619 195.5836167 52.32188806 150.5186791 109.7800087 144.6575753 88.50576313 112.9852142 67.55690299 30.19133776 110.4643364 180.7525191 116.5145101 211.612094 84.56803996 205.5251283 88.39691222 218.8616096 224.9861658 228.1322624 80.23978317 232.1981564 ACETOACETYL-COA 2.996703073 4.4294904 4.818520459 6.925343925 4.902307107 5.957743096 3.559182441 6.128876808 4.720140446 6.092439502 4.451097583 5.558543742 5.055031515 6.819920192 3.964265988 7.226888785 7.479711817 5.40565591 4.753705065 6.280454636 4.530615097 7.332054773 4.122724629 6.72119315 5.448665508 6.659630205 4.137862565 7.341346472 4.228879586 2.927462655 3.88678375 5.359461182 5.316413271 6.416802338 4.125842958 6.595232251 3.802308568 7.255979229 6.232508832 8.45645753 3.730535083 6.910856716 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 PHOSPHOENOLPYRUVATE 1005 D-ERYTHROSE 4-PHOSPHATE 122357 BETA-NAD+ 15938971 COENZYME II 15938972 D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE) 21125049 CITRIC ACID 311 NADH 439153 FAD 46906035 MALIC ACID 525 ADENOSINE TRIPHOSPHATE 5957 ROBISON ESTER 5958 SUCROSE 5988 ADENOSINE 5'-DIPHOSPHATE 6022 ADENOSINE 5'-MONOPHOSPHATE 6083 GLYCERATE 3-PHOSPHATE 724 RIBOSE PHOSPHATE 77982 ACETOACETYL-COA 92153 METABOLITES_END #END