{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001615","ANALYSIS_ID":"AN002650","VERSION":"1","CREATED_ON":"December 3, 2020, 11:07 am"},

"PROJECT":{"PROJECT_TITLE":"Unique metabolomic profile of skeletal muscle in chronic limb threatening ischemia","PROJECT_TYPE":"NMR","PROJECT_SUMMARY":"This project is focused on a cross-sectional analysis of non-PAD controls and CLTI patients undergoing either a vascular intervention or undergoing limb amputation was performed and involved a detailed assessment of the limb muscle metabolome using HR-MAS and solution state NMR spectroscopy. It was hypothesized that patients undergoing limb amputation would present with altered muscle metabolite features compared with non-PAD controls.","INSTITUTE":"University of Florida","DEPARTMENT":"Applied Physiology and Kinesiology","LABORATORY":"Rm 42 and Rm 43","LAST_NAME":"Ryan","FIRST_NAME":"Terence","ADDRESS":"University of Florida, Applied Physiology and Kinesiology, 1864 stadium RD, Gainesville, FL 32611","EMAIL":"ryant@ufl.edu","PHONE":"352-294-1700","FUNDING_SOURCE":"National Institutes of Health and the National Heart, Lung, and Blood, Institute numbers R01-HL149704 (to T.E.R.) and R01-HL148597 (to S.T.S.); as well as the American Heart Association grant number 18CDA34110044 (to T.E.R.). A portion of this work was supported by pilot funds (awarded to T.E.R.) from The University of Florida Claude D. Pepper Older Americans Independence Center P30AG028740. (if applicable)","PROJECT_COMMENTS":"PAD metabolomic study via NMR. A detailed assessment of the limb muscle metabolome using semi-solid and solution state NMR spectroscopy.","PUBLICATIONS":"Journal of Clinical Medicine","CONTRIBUTORS":"Ram B. Khattri, Kyoungrae Kim, Trace Thome, Zachary R. Salyers, Kerri A. O’Malley, Scott A. Berceli, Salvatore T. Scali, Terence E. Ryan*"},

"STUDY":{"STUDY_TITLE":"Unique metabolomic profile of skeletal muscle in chronic limb threatening ischemia (organic phase samples)","STUDY_TYPE":"NMR","STUDY_SUMMARY":"This project is focused on a cross-sectional analysis of non-PAD controls and CLTI patients undergoing either a vascular intervention or undergoing limb amputation was performed and involved a detailed assessment of the limb muscle metabolome using HR-MAS and solution state NMR spectroscopy. It was hypothesized that patients undergoing limb amputation would present with altered muscle metaolite features compared with non-PAD controls.","INSTITUTE":"University of Florida","DEPARTMENT":"Applied Physiology and Kinesiology","LABORATORY":"Rm 42 and Rm 43","LAST_NAME":"Ryan","FIRST_NAME":"Terence","ADDRESS":"University of Florida, Applied Physiology and Kinesiology, 1864 stadium RD, Gainesville, FL 32611","EMAIL":"ryant@ufl.edu","PHONE":"352-294-1700","NUM_GROUPS":"3","TOTAL_SUBJECTS":"30","NUM_MALES":"25","NUM_FEMALES":"5","STUDY_COMMENTS":"PAD metabolomic study via NMR. A detailed assessment of the limb muscle metabolome using semi-solid and solution state NMR spectroscopy","PUBLICATIONS":"Journal of Clinical Medicine"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"55-82 years","GENDER":"Male and female","HUMAN_RACE":"unknown","HUMAN_ETHNICITY":"unknown","HUMAN_MEDICATIONS":"Asprin, ACE inhibitor, statins, cilostazol","HUMAN_SMOKING_STATUS":"Controls = 4, CLTI Pre-surgery = 7, and CLTI Amputation = 9"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation1a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation1a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation2a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation2a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation3a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation3a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation4a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation4a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation5a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation5a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation6a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation6a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation7a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation7a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation8a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation8a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation9a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation9a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Amputation10a",
"Factors":{"Group":"CLTI_Amputation"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Amputation10a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Pre_surgery1a",
"Factors":{"Group":"CLTI_Pre_surgery"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Pre_surgery1a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Pre_surgery2a",
"Factors":{"Group":"CLTI_Pre_surgery"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Pre_surgery2a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Pre_surgery5a",
"Factors":{"Group":"CLTI_Pre_surgery"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Pre_surgery5a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Pre_surgery6a",
"Factors":{"Group":"CLTI_Pre_surgery"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Pre_surgery6a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Pre_surgery7a",
"Factors":{"Group":"CLTI_Pre_surgery"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Pre_surgery7a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CLTI_Pre_surgery9a",
"Factors":{"Group":"CLTI_Pre_surgery"},
"Additional sample data":{"RAW_FILE_NAME":"CLTI_Pre_surgery9a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control2a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control2a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control3a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control3a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control4a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control4a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control5a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control5a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control6a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control6a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control7a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control7a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control8a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control8a.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Control10a",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Control10a.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Gastrocnemius muscle specimens were obtained from ten older adult non-PAD controls (Control), ten patients with critical limb ischemia (CLI) undergoing surgical intervention (CLTI Pre-surgery), and ten CLI patients undergoing limb amputation (CLTI Amputation). Five pre-surgery patients underwent bypass interventions and five underwent endovascular procedures. Muscle specimens were collected within the confines of the operating rooms (CLI patients) or via percutaneous muscle biopsy using sterile procedures. A portion of the muscle was quickly trimmed of fat/connective tissue and snap frozen in liquid nitrogen for metabolomics analysis.","SAMPLE_TYPE":"Muscle","COLLECTION_METHOD":"Muscle specimens were collected within the confines of the operating rooms (CLI patients) or via percutaneous muscle biopsy using sterile procedures. A portion of the muscle was quickly trimmed of fat/connective tissue and snap frozen in liquid nitrogen for metabolomics analysis.","STORAGE_CONDITIONS":"-80℃","STORAGE_VIALS":"cryovials"},

"TREATMENT":{"TREATMENT_SUMMARY":"This was a prospective cohort study that examined the metabolomic profile of skeletal muscle from CLTI patients undergoing surgerical intervention or amputation, as well as a cohort of non-PAD controls. CLTI patients exhibited severe symptomology (Rutherford Classification 3-6), with high incidence of common PAD risk factors including hypertension, hyperlipidemia, coronary artery disease, and diabetes.Ten patients with critical limb ischemia (CLI) undergoing surgical intervention (CLTI Pre-surgery), and ten CLI patients undergoing limb amputation (CLTI Amputation). Five pre-surgery patients underwent bypass interventions and five underwent endovascular procedures. Muscle specimens were collected within the confines of the operating rooms (CLI patients) or via percutaneous muscle biopsy using sterile procedures.","HUMAN_FASTING":"non-fasted","HUMAN_ENDP_CLINICAL_SIGNS":"N/A"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction. Both polar and non-polar metabolites were extracted from the gastrocnemius muscle specimens using FOLCH extraction. In brief, wet weigh of the frozen tissues were determined and immediately homogenized in 1 mL of ice-cold methanol using a PowerLyzer 24 Homogenizer (QIAGEN Group, Hilden, Germany). All enzymatic activities are halted once the sample was homogenized in the methanol. Homogenization was followed by centrifugation (13.2K r.p.m., 4 oC, 30 minutes) and supernatant was transferred into a new glass vial consisting a mixture of 3 mL of ice-cold chloroform and methanol (2:1 v/v) ratio. The cold mixture was vortexed for several minutes and left in an ice bath 15 minutes to allow for phase separation. Next, 1 mL of ice-cold 0.9% saline was added to the mixture followed by vigorous mixing. The mixture was again left in the ice bath for 45 minutes for phase separation. The upper methanol/water layer was transferred to a new falcon tube. To the lower chloroform layer, 1 mL of ice-cold 0.9% saline was added and all steps were followed as mentioned above. Following a 45-minute incubation, upper methanol/water layer was again transferred to the previous falcon tube and dried using a Labconco freeze drier (Labconco Corporation, MO, USA). The chloroform layer was dried under a stream of nitrogen gas. The dried samples (both aqueous and organic phases) were stored at -80 oC until resuspension for NMR experiments. Lyophilized organic phase sample were re-suspended in 80 µL of CDCl3 along with 10 mM of pyrazine. All samples were loaded in 1.7 mm NMR tube to acquire spectra.","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"Deuterated chloroform (80 microliter) with 10 mM pyrazine was used to re-suspend organic phase samples.","SAMPLE_SPIKING":"10 mM of pyrazine for organic phase samples."},

"ANALYSIS":{"DATA_FORMAT":"fid, 1r"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance Neo 600 MHz/54mm console","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"10mM pyrazine","SPECTROMETER_FREQUENCY":"600.2328273 MHz","NMR_PROBE":"1.7 mm TXI CryoProbe","NMR_SOLVENT":"Deuterated chloroform","NMR_TUBE_SIZE":"1.7 mm O.D.","SHIMMING_METHOD":"Topshim","PULSE_SEQUENCE":"noesypr1d","WATER_SUPPRESSION":"none","PULSE_WIDTH":"90-degree","RECEIVER_GAIN":"101","CHEMICAL_SHIFT_REF_CPD":"CDCl3 at 7.26 ppm and pyrazine at 8.61 ppm","TEMPERATURE":"25 o C","NUMBER_OF_SCANS":"128 scans","DUMMY_SCANS":"8","ACQUISITION_TIME":"4 s","RELAXATION_DELAY":"1 s","SPECTRAL_WIDTH":"7142.9 Hz","NUM_DATA_POINTS_ACQUIRED":"28571","REAL_DATA_POINTS":"65536","LINE_BROADENING":"0.22 Hz","ZERO_FILLING":"65,536 points","APODIZATION":"Exponential","BASELINE_CORRECTION_METHOD":"Spline","CHEMICAL_SHIFT_REF_STD":"7.26ppm for CDCl3"},

"NMR_METABOLITE_DATA":{
"Units":"A.U.",

"Data":[{"Metabolite":"C18-CH3 chol+V26C1C1:W25","CLTI_Amputation1a":"2.714041568","CLTI_Amputation2a":"2.505950482","CLTI_Amputation3a":"3.319406373","CLTI_Amputation4a":"3.188474262","CLTI_Amputation5a":"2.704978038","CLTI_Amputation6a":"3.074472658","CLTI_Amputation7a":"2.797740242","CLTI_Amputation8a":"3.710180502","CLTI_Amputation9a":"1.607834751","CLTI_Amputation10a":"3.06792606","CLTI_Pre_surgery1a":"2.244804577","CLTI_Pre_surgery2a":"2.363162949","CLTI_Pre_surgery5a":"2.543305963","CLTI_Pre_surgery6a":"3.185292817","CLTI_Pre_surgery7a":"3.437542525","CLTI_Pre_surgery9a":"2.353380253","Control2a":"2.238660449","Control3a":"1.708933109","Control4a":"1.918673926","Control5a":"1.899426647","Control6a":"2.096208669","Control7a":"2.740330267","Control8a":"1.507798502","Control10a":"2.420962339"},{"Metabolite":"CH3-protons","CLTI_Amputation1a":"368.8836615","CLTI_Amputation2a":"374.2847304","CLTI_Amputation3a":"343.5151808","CLTI_Amputation4a":"349.9381038","CLTI_Amputation5a":"141.7790904","CLTI_Amputation6a":"531.5804148","CLTI_Amputation7a":"399.7925022","CLTI_Amputation8a":"228.7786528","CLTI_Amputation9a":"92.31654578","CLTI_Amputation10a":"646.0032584","CLTI_Pre_surgery1a":"737.500607","CLTI_Pre_surgery2a":"620.9208463","CLTI_Pre_surgery5a":"244.5379919","CLTI_Pre_surgery6a":"181.221034","CLTI_Pre_surgery7a":"380.5336032","CLTI_Pre_surgery9a":"282.4544822","Control2a":"300.8408581","Control3a":"76.95000272","Control4a":"170.7987152","Control5a":"142.2055761","Control6a":"135.3437887","Control7a":"152.4311938","Control8a":"282.3657315","Control10a":"123.61555"},{"Metabolite":"C19-CH3 Chol","CLTI_Amputation1a":"10.14325014","CLTI_Amputation2a":"10.01120228","CLTI_Amputation3a":"10.56855559","CLTI_Amputation4a":"9.280217434","CLTI_Amputation5a":"3.840617024","CLTI_Amputation6a":"13.30996851","CLTI_Amputation7a":"9.378840179","CLTI_Amputation8a":"8.112021443","CLTI_Amputation9a":"2.202381707","CLTI_Amputation10a":"17.93696818","CLTI_Pre_surgery1a":"17.83191403","CLTI_Pre_surgery2a":"13.89713123","CLTI_Pre_surgery5a":"3.846828281","CLTI_Pre_surgery6a":"4.172201081","CLTI_Pre_surgery7a":"7.430344221","CLTI_Pre_surgery9a":"6.581953649","Control2a":"9.013446641","Control3a":"2.177849695","Control4a":"2.668400507","Control5a":"2.464515706","Control6a":"2.832968864","Control7a":"3.761590142","Control8a":"7.100257967","Control10a":"3.496630225"},{"Metabolite":"CH2n chol","CLTI_Amputation1a":"294.3170626","CLTI_Amputation2a":"322.0096512","CLTI_Amputation3a":"272.252103","CLTI_Amputation4a":"352.9859101","CLTI_Amputation5a":"218.6316986","CLTI_Amputation6a":"428.0540119","CLTI_Amputation7a":"426.7218723","CLTI_Amputation8a":"230.1589942","CLTI_Amputation9a":"166.3593249","CLTI_Amputation10a":"483.0326103","CLTI_Pre_surgery1a":"589.3042625","CLTI_Pre_surgery2a":"461.8404083","CLTI_Pre_surgery5a":"438.1115566","CLTI_Pre_surgery6a":"355.5962827","CLTI_Pre_surgery7a":"526.8400508","CLTI_Pre_surgery9a":"292.556382","Control2a":"248.475611","Control3a":"141.1412704","Control4a":"296.8791359","Control5a":"263.0163829","Control6a":"239.8529979","Control7a":"287.3815193","Control8a":"269.7529788","Control10a":"220.7052698"},{"Metabolite":"CH2n aliphatic 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}