#METABOLOMICS WORKBENCH efahy_20230425_000035 DATATRACK_ID:3930 STUDY_ID:ST002614 ANALYSIS_ID:AN004286 PROJECT_ID:PR001020 VERSION 1 CREATED_ON April 25, 2023, 7:56 am #PROJECT PR:PROJECT_TITLE Molecular Transducer of Physical Activity Consortium PR:PROJECT_SUMMARY MoTrPAC is a national research consortium designed to discover and perform PR:PROJECT_SUMMARY preliminary characterization of the range of molecular transducers (the PR:PROJECT_SUMMARY "molecular map") that underlie the effects of physical activity in humans. The PR:PROJECT_SUMMARY program's goal is to study the molecular changes that occur during and after PR:PROJECT_SUMMARY exercise and ultimately to advance the understanding of how physical activity PR:PROJECT_SUMMARY improves and preserves health. Preclinical and clinical studies will examine the PR:PROJECT_SUMMARY systemic effects of endurance and resistance exercise across a range of ages and PR:PROJECT_SUMMARY fitness levels by molecular probing of multiple tissues before and after acute PR:PROJECT_SUMMARY and chronic exercise. This program is the largest targeted NIH investment of PR:PROJECT_SUMMARY funds into the mechanisms of how physical activity improves health and prevents PR:PROJECT_SUMMARY disease. The MoTrPAC program is supported by the NIH Common Fund and is managed PR:PROJECT_SUMMARY by a trans-agency working group representing multiple NIH institutes and PR:PROJECT_SUMMARY centers, led by the NIH Office of Strategic Coordination, National Institute of PR:PROJECT_SUMMARY Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes PR:PROJECT_SUMMARY and Digestive and Kidney Diseases, National Institute on Aging, and National PR:PROJECT_SUMMARY Institute of Biomedical Imaging and Bioengineering. MoTrPAC Steering Committee: PR:PROJECT_SUMMARY Wendy Kohrt, Chair, Russ Tracy, Co-Chair; NIH Program Manager, Concepcion PR:PROJECT_SUMMARY Nierras. Euan Ashley and Matthew Wheeler are the PIs for the Motrpac PR:PROJECT_SUMMARY Bioinformatics / Data Coordination Center. PR:INSTITUTE MoTrPAC PR:LAST_NAME Ashley PR:FIRST_NAME Euan A. PR:ADDRESS 300 Pasteur Dr Rm A265. MC 5319. Stanford CA 94305. USA PR:EMAIL euan@stanford.edu PR:PHONE (650) 498-4900 #STUDY ST:STUDY_TITLE MoTrPAC: Endurance exercise training study in young adult rats, Rat Liver Powder ST:STUDY_TITLE - Targeted Keto Acids ST:STUDY_SUMMARY The goal of the endurance exercise training study in young adult rats (internal ST:STUDY_SUMMARY code: PASS1B-06) was to perform exercise training studies in adult (6 month) ST:STUDY_SUMMARY F344 rats, and from these rats collect as many tissues as feasible in order to ST:STUDY_SUMMARY provide high quality samples for detailed analysis by chemical analysis sites. ST:STUDY_SUMMARY Tissues were collected from 10-12 rats sedentary control rats concurrent with ST:STUDY_SUMMARY the collection of the 8-week training groups. The 8-week training group and ST:STUDY_SUMMARY controls were from the same cohort and same age at euthanasia (either 8). For ST:STUDY_SUMMARY the older age group, an additional set of controls (n=5-6) were collected with ST:STUDY_SUMMARY the 1-2 week training group. Rats were either sedentary or underwent an exercise ST:STUDY_SUMMARY training program. Rats were exercised on the rodent treadmill 5 days per week ST:STUDY_SUMMARY using a progressive training protocol designed to exercise the rats at ST:STUDY_SUMMARY approximately 70% of VO2max as outlined in the Table on the next page. Training ST:STUDY_SUMMARY was performed no earlier than 10:00 am and no later than 5:00 pm over 5 ST:STUDY_SUMMARY consecutive days per week. Training was initiated with the treadmill set at 70% ST:STUDY_SUMMARY of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of ST:STUDY_SUMMARY exercise was increased by one minute each day until day 31 of training (start of ST:STUDY_SUMMARY week 7), when a duration of 50 min was reached. Speed and grade of each training ST:STUDY_SUMMARY session increased in larger increments due to treadmill parameters. The highest ST:STUDY_SUMMARY intensity and duration of training began on day 31. This intensity was ST:STUDY_SUMMARY maintained for the final 10 days of the protocol to ensure steady state had been ST:STUDY_SUMMARY achieved. If any rats were unable to perform at least 4 days of training per ST:STUDY_SUMMARY week they were removed from the study and euthanized. It is important to note ST:STUDY_SUMMARY that the starting treadmill speed varied depending on the sex and age of the ST:STUDY_SUMMARY rat. The initial and maximum speeds were based on VO2max measurements obtained ST:STUDY_SUMMARY during the pre-training testing of the compliant rats. Rats assigned to the ST:STUDY_SUMMARY control group followed a schedule similar to the training group. They were ST:STUDY_SUMMARY placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The ST:STUDY_SUMMARY treadmill was set at 0 m/min at an incline that corresponded to the incline ST:STUDY_SUMMARY being used by the training group. ST:INSTITUTE Duke University ST:DEPARTMENT Duke Molecular Physiology Institute ST:LABORATORY Metabolomics Core Laboratory ST:LAST_NAME Newgard ST:FIRST_NAME Christopher ST:ADDRESS 300 N Duke St, Durham, NC 27701 ST:EMAIL chris.newgard@duke.edu ST:PHONE (919) 668-6059 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Rattus norvegicus SU:TAXONOMY_ID 10116 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 80010816802_1 Group:QC-ExternalStandard | Timepoint:0 hour | Sex:- raw_file=Motorpac_PASS1B_Liver_081020_a023.zip SUBJECT_SAMPLE_FACTORS - 80011826802_1 Group:QC-ExternalStandard | Timepoint:0 hour | Sex:- raw_file=Motorpac_PASS1B_Liver_081020_a024.zip SUBJECT_SAMPLE_FACTORS 07AF7369-F082-4CA7-99D5-D973F4A162C9 90252016811 Group:Control | Timepoint:8 weeks of training or control time | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a025.zip SUBJECT_SAMPLE_FACTORS 4E974304-21EB-42E8-A729-A7FB6B406E64 90439016811 Group:Training | Timepoint:2 weeks of training | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a026.zip SUBJECT_SAMPLE_FACTORS B73AB139-7210-4498-9CCF-E1DBE6EBA71C 90559016811 Group:Training | Timepoint:1 week of training or control time | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a027.zip SUBJECT_SAMPLE_FACTORS E4271AF1-899A-4A65-9D8D-BF18CEE3F1CF 90292016811 Group:Training | Timepoint:4 weeks of training | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a028.zip SUBJECT_SAMPLE_FACTORS DC8B35E8-4AA8-4829-8569-F223D069620C 90578016811 Group:Training | Timepoint:2 weeks of training | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a029.zip SUBJECT_SAMPLE_FACTORS B137E81D-A9DE-4E3A-8E2B-AD6C22920B7E 90576016811 Group:Training | Timepoint:2 weeks of training | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a030.zip SUBJECT_SAMPLE_FACTORS CFE06932-9314-4BCC-B2D9-73883D5FCDFB 90223016811 Group:Training | Timepoint:8 weeks of training or control time | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a031.zip SUBJECT_SAMPLE_FACTORS 9F3E1040-D409-421E-B635-2572DC20ED89 90283016811 Group:Training | Timepoint:4 weeks of training | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a032.zip SUBJECT_SAMPLE_FACTORS 1628FB23-6F66-47D4-8D82-63C87726F0FD 90245016811 Group:Control | Timepoint:8 weeks of training or control time | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a033.zip SUBJECT_SAMPLE_FACTORS 89D6F615-D17C-4EB9-88EB-A602940FF179 90416016811 Group:Training | Timepoint:4 weeks of training | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a034.zip SUBJECT_SAMPLE_FACTORS 3719CB62-B551-49BE-94A0-E51DFE13D30D 90225016811 Group:Training | Timepoint:8 weeks of training or control time | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a035.zip SUBJECT_SAMPLE_FACTORS 2B969165-1A52-43AA-8FD9-39AFA62F094F 90267016811 Group:Training | Timepoint:8 weeks of training or control time | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a036.zip SUBJECT_SAMPLE_FACTORS FDA87A8D-3634-4C42-9A1A-0EA03B58BB01 90449016811 Group:Training | Timepoint:2 weeks of training | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a037.zip SUBJECT_SAMPLE_FACTORS 1F9BD644-303F-43E7-94BE-FF6654306F5E 90585016811 Group:Training | Timepoint:2 weeks of training | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a038.zip SUBJECT_SAMPLE_FACTORS EA5C8932-9325-4DA5-96BB-50CD49CEDD10 90560016811 Group:Training | Timepoint:1 week of training or control time | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a039.zip SUBJECT_SAMPLE_FACTORS 0DBFEB04-1B58-43CF-BAFD-9AA9915B67F6 90426016811 Group:Training | Timepoint:1 week of training or control time | Sex:Male raw_file=Motorpac_PASS1B_Liver_081020_a040.zip SUBJECT_SAMPLE_FACTORS A77AC89A-1D9E-4516-9DA4-2BE99C8126EF 90266016811 Group:Control | Timepoint:8 weeks of training or control time | Sex:Female raw_file=Motorpac_PASS1B_Liver_081020_a041.zip SUBJECT_SAMPLE_FACTORS - 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80010816802_4 Group:QC-ExternalStandard | Timepoint:0 hour | Sex:- raw_file=Motorpac_PASS1B_Liver_081020_a079.zip SUBJECT_SAMPLE_FACTORS - 80011826802_4 Group:QC-ExternalStandard | Timepoint:0 hour | Sex:- raw_file=Motorpac_PASS1B_Liver_081020_a080.zip #COLLECTION CO:SAMPLE_TYPE Liver #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 10 µl of plasma or 300 µl of tissue homogenate prepared at 100 mg/ml in 3M SP:SAMPLEPREP_SUMMARY perchloric acid containing isotopically labeled internal standards KIC-d3, SP:SAMPLEPREP_SUMMARY KIV-5C13, (Cambridge Isotope Laboratories), and KMV-d8 (Toronto Research SP:SAMPLEPREP_SUMMARY Chemicals) are precipitated with 150 µl of 3M PCA. 200 µl of 25 M SP:SAMPLEPREP_SUMMARY o-phenylenediamine (OPD) in 3M HCl is added to the supernatants and the samples SP:SAMPLEPREP_SUMMARY are incubated at 80oC for 20 minutes. Keto acids are extracted with ethyl SP:SAMPLEPREP_SUMMARY acetate. The extracts are dried under nitrogen and reconstituted in 200 mM SP:SAMPLEPREP_SUMMARY ammonium acetate. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The analytical column is used at 30°C. 10 µl of the sample are injected onto the CH:CHROMATOGRAPHY_SUMMARY column and eluted at a flow rate of 0.4 ml/min. The gradient begins with 45% CH:CHROMATOGRAPHY_SUMMARY eluent A (5 mM ammonium acetate in water) and is then programmed as follows: 0 CH:CHROMATOGRAPHY_SUMMARY to 2 min – gradient to 55% eluent B (methanol); 2 to 2.5 min - gradient to 95% CH:CHROMATOGRAPHY_SUMMARY eluent B; 2.5 to 3.2 min - hold at 95% eluent B, return to 45% A, and CH:CHROMATOGRAPHY_SUMMARY re-equilibrate the column at initial conditions for 1 minute. CH:CHROMATOGRAPHY_TYPE RP CH:INSTRUMENT_NAME Waters Acquity UPLC CH:COLUMN_NAME Waters Acquity UPLC BEH C18 (50 x 2.1 mm,1.7 um) CH:SOLVENT_A 100% water; 5 mM ammonium acetate CH:SOLVENT_B 100% methanol CH:FLOW_GRADIENT 45% A and 55% B for 2 minutes, followed by a linear gradient to 95% B from 2 to CH:FLOW_GRADIENT 2.5 minutes, held at 95% B for 0.7 minutes, returned to 45% A, and finally the CH:FLOW_GRADIENT column was re-equilibrated at initial conditions for 1 minute. The total run CH:FLOW_GRADIENT time was 4.7 minutes. CH:FLOW_RATE 0.4 ml/min CH:COLUMN_TEMPERATURE 30C #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_DETAILS: Ion ratios of keto acids to respective internal standards are computed from AN:ANALYSIS_DETAILS: extracted ion chromatograms using a software package TargetLynx (Waters, AN:ANALYSIS_DETAILS: Milford, MA). The ratios are converted to concentrations using calibrators AN:ANALYSIS_DETAILS: constructed from authentic keto acids (Sigma, MO, USA) and Dialyzed Fetal Bovine AN:ANALYSIS_DETAILS: Serum (Sigma, MO, USA). The values are expressed in µM units for plasma samples AN:ANALYSIS_DETAILS: or pmol/mg for tissue samples. #MS MS:INSTRUMENT_TYPE Triple quadrupole MS:INSTRUMENT_NAME Waters Xevo TQ-S MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Mass transitions of m/z 203 -> 161 (ketoleucine or KIC), 206 -> 161 (KIC-d3), MS:MS_COMMENTS 189 -> 174 (ketoisovalerate or KIV), 194 -> 178 (KIV-5C13), 203 -> 174 MS:MS_COMMENTS (3-methyl-2-oxovalerate or KMV), and 211 -> 177 (KMV-d8) are monitored in a MS:MS_COMMENTS positive ion electrospray ionization mode. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/mg of tissue MS_METABOLITE_DATA_START Samples 90217016811 90218016811 90222016811 90223016811 90225016811 90227016811 90229016811 90232016811 90237016811 90239016811 90245016811 90248016811 90251016811 90252016811 90254016811 90258016811 90259016811 90265016811 90266016811 90267016811 90280016811 90281016811 90283016811 90289016811 90292016811 90406016811 90410016811 90412016811 90416016811 90420016811 90421016811 90422016811 90423016811 90426016811 90430016811 90439016811 90441016811 90444016811 90449016811 90450016811 90559016811 90560016811 90564016811 90567016811 90571016811 90576016811 90578016811 90581016811 90585016811 90587016811 80010816802_1 80010816802_2 80010816802_3 80010816802_4 80011826802_1 80011826802_2 80011826802_3 80011826802_4 ketoisovalerate 0.257058922 0.241453044 0.220836858 0.264204771 0.260618157 0.197373284 0.245505097 0.316224363 0.29489633 0.327696052 0.382727305 0.347353982 0.257113679 0.235429723 0.179987789 0.378155057 0.396307157 0.22792795 0.574706979 0.493392143 0.270310228 0.342316296 0.228201737 0.368983181 0.377388452 0.204546512 0.177441567 0.438497784 0.277319184 0.308695212 0.123751872 0.151842452 0.179768759 0.269351973 0.208023611 0.211062651 0.224943668 0.245450339 0.298921004 0.207257007 0.211281681 0.276525201 0.219276271 0.312966294 0.139987461 0.254156776 0.340399784 0.265108269 0.220480935 0.159371603 0.206517781 0.243013632 0.246244322 0.216976457 0.235238072 0.215470627 0.214731401 0.193211717 ketoleucine 0.24175987 0.275469059 0.259279528 0.368007814 0.192763735 0.208278703 0.238947604 0.383532282 0.148328032 0.232163963 0.187110701 0.324892735 0.323315586 0.144470667 0.207423622 0.573645267 0.242804969 0.131530443 0.282309706 0.261920778 0.236382362 0.118799238 0.196763614 0.224373226 0.343286475 0.151786359 0.192146177 0.252077847 0.145173733 0.241246822 0.153249497 0.149430136 0.118115174 0.139226171 0.198739801 0.195604504 0.133183599 0.198853812 0.141468383 0.170389119 0.152869461 0.210026869 0.105307962 0.156099767 0.117089077 0.14460368 0.119882341 0.128889193 0.125715893 0.126304948 0.192545215 0.186502643 0.186559649 0.180270054 0.142266458 0.136907951 0.131967484 0.134342709 3-methyl-2-oxovalerate 0.408785212 0.37969264 0.490717767 0.541164394 0.273999378 0.253935076 0.456918262 0.577463628 0.285341226 0.489813611 0.285607155 0.446201345 0.446680016 0.28874511 0.282522385 0.588499658 0.307014395 0.228645281 0.468512742 0.418225672 0.418651158 0.252392691 0.325602793 0.411444497 0.259546167 0.277921822 0.258615417 0.324273151 0.289383339 0.281245928 0.38586218 0.378070476 0.310790579 0.304700817 0.367194003 0.432665587 0.330868177 0.4051154 0.39727051 0.387989608 0.234256371 0.324087001 0.252738398 0.335495332 0.209604804 0.229815366 0.286537904 0.304461482 0.245638109 0.278081379 0.631127989 0.642243798 0.65030143 0.623203321 0.303557325 0.296776149 0.291058688 0.296882521 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name formula mz neutral_mass refmet_name rt 3-methyl-2-oxovalerate C6H10O3 0 130.063 3-Methyl-2-oxovaleric acid 0 ketoleucine C6H10O3 0 130.063 Ketoleucine 0 ketoisovalerate C5H8O3 0 116.0473 Ketoisovaleric acid 0 METABOLITES_END #END