{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000336","ANALYSIS_ID":"AN004437","VERSION":"1","CREATED_ON":"June 14, 2023, 9:54 am"},

"PROJECT":{"PROJECT_TITLE":"Urine metabolomics to track disease progression in DMD","PROJECT_SUMMARY":"Duchenne Muscular Dystrophy (DMD) is an X-linked recessive form of muscular dystrophy that affects males via a mutation in the gene for the muscle protein, dystrophin. Progression of the disease results in severe muscle loss, ultimately leading to paralysis and death. Steroid therapy has been a commonly employed method for reducing the severity of symptoms. This study aims to quantify the urine levels of amino acids and organic acids in patients with DMD both with and without steroid treatment. Track the progression of DMD in patients who have provided multiple urine samples.","INSTITUTE":"University of Florida","DEPARTMENT":"Physiology and Functional Genomics","LAST_NAME":"Walter","FIRST_NAME":"Glenn","ADDRESS":"-","EMAIL":"glennw@ufl.edu","PHONE":"-"},

"STUDY":{"STUDY_TITLE":"Targeted LC/MS of urine from boys with DMD and controls","STUDY_TYPE":"Natural History","STUDY_SUMMARY":"Quantify the urine levels of amino acids and organic acids in patients with DMD both with and without steroid treatment. Track the progression of DMD in patients who have provided multiple urine samples.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LABORATORY":"Sanford Burnham","LAST_NAME":"Lee","FIRST_NAME":"Brittany","ADDRESS":"-","EMAIL":"balm22@ufl.edu","PHONE":"-","SUBMIT_DATE":"2015-05-07","NUM_GROUPS":"2","TOTAL_SUBJECTS":"58"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"5-14","GENDER":"Males"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"SU001",
"Sample ID":"SA001",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU002",
"Sample ID":"SA002",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU003",
"Sample ID":"SA003",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU004",
"Sample ID":"SA004",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU005",
"Sample ID":"SA005",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU006",
"Sample ID":"SA006",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU007",
"Sample ID":"SA007",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU008",
"Sample ID":"SA008",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU009",
"Sample ID":"SA009",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU010",
"Sample ID":"SA010",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU011",
"Sample ID":"SA011",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU012",
"Sample ID":"SA012",
"Factors":{"Diagnosis":"Controls","steroid_status":"-"}
},
{
"Subject ID":"SU013",
"Sample ID":"SA013",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU014",
"Sample ID":"SA014",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU015",
"Sample ID":"SA015",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU016",
"Sample ID":"SA016",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU017",
"Sample ID":"SA017",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU018",
"Sample ID":"SA018",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU019",
"Sample ID":"SA019",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU020",
"Sample ID":"SA020",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU021",
"Sample ID":"SA021",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU022",
"Sample ID":"SA022",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU023",
"Sample ID":"SA023",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU024",
"Sample ID":"SA024",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU025",
"Sample ID":"SA025",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU026",
"Sample ID":"SA026",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU027",
"Sample ID":"SA027",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU028",
"Sample ID":"SA028",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU029",
"Sample ID":"SA029",
"Factors":{"Diagnosis":"DMD","steroid_status":"-"}
},
{
"Subject ID":"SU030",
"Sample ID":"SA030",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU031",
"Sample ID":"SA031",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU032",
"Sample ID":"SA032",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU033",
"Sample ID":"SA033",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU034",
"Sample ID":"SA034",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU035",
"Sample ID":"SA035",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU036",
"Sample ID":"SA036",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU037",
"Sample ID":"SA037",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU038",
"Sample ID":"SA038",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU039",
"Sample ID":"SA039",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU040",
"Sample ID":"SA040",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU041",
"Sample ID":"SA041",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU042",
"Sample ID":"SA042",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU043",
"Sample ID":"SA043",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU044",
"Sample ID":"SA044",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU045",
"Sample ID":"SA045",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU046",
"Sample ID":"SA046",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU047",
"Sample ID":"SA047",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU048",
"Sample ID":"SA048",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU049",
"Sample ID":"SA049",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU050",
"Sample ID":"SA050",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU051",
"Sample ID":"SA051",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU052",
"Sample ID":"SA052",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU053",
"Sample ID":"SA053",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU054",
"Sample ID":"SA054",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU055",
"Sample ID":"SA055",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU056",
"Sample ID":"SA056",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU057",
"Sample ID":"SA057",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
},
{
"Subject ID":"SU058",
"Sample ID":"SA058",
"Factors":{"Diagnosis":"DMD","steroid_status":"1"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Subjects are consented and given a bag containing a urine collection cup, antiseptic wipes and directions of how to give a clean catch urine sample. They are then lead to a restroom where they collect their own urine sample using a clean catch method (direction provided). Urine samples are then placed on ice and brought to the UF CTSI Biorepository. There, samples are transferred into 500uL aliquots and stored at -80C. Samples will remain there until samples will be removed and ran on the NMR for this study.","SAMPLE_TYPE":"Urine"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment, samples are from a Natural History Clinical Trial. Samples are either boys with DMD or control boys all within the ages 5-14. Unaffected, control boys are moderately active (less than 3 low to moderate exercise bouts per week)"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","SAMPLEPREP_PROTOCOL_FILENAME":"SB_AA_Assay.pdf, SB_OA_Assay.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Organic Acids assay","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Dionex UltiMate 3000 HPLC","COLUMN_NAME":"Acquity UPLC BEH C18 2.1 x 100 mm, 1.7 µm column, Waters Corp","SOLVENT_A":"-","SOLVENT_B":"-","FLOW_GRADIENT":"-","FLOW_RATE":"-","COLUMN_TEMPERATURE":"-","METHODS_FILENAME":"SB_OA_Assay.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Quantiva QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"OA assay- HESI"},

"MS_METABOLITE_DATA":{
"Units":"umol/mg Creatinine",

"Data":[{"Metabolite":"Lactate","SA001":"8.34","SA002":"5.55","SA003":"6.94","SA004":"12.7","SA005":"18.39","SA006":"6.8","SA007":"9.31","SA008":"15.53","SA009":"7.18","SA010":"13.72","SA011":"19.03","SA012":"","SA013":"36.26","SA014":"26.77","SA015":"34.12","SA016":"16.88","SA017":"6.85","SA018":"","SA019":"75.07","SA020":"208.57","SA021":"49.62","SA022":"18.34","SA023":"23.32","SA024":"46.71","SA025":"18.01","SA026":"24.23","SA027":"20.93","SA028":"23.46","SA029":"39.3","SA030":"5.03","SA031":"15.24","SA032":"27.03","SA033":"38.32","SA034":"50.64","SA035":"94.27","SA036":"17.63","SA037":"23.24","SA038":"12.99","SA039":"19.81","SA040":"14.75","SA041":"74.53","SA042":"19.83","SA043":"70.81","SA044":"31.38","SA045":"25.52","SA046":"26.15","SA047":"121.54","SA048":"24.56","SA049":"98.27","SA050":"13.82","SA051":"90.02","SA052":"12.67","SA053":"21.76","SA054":"","SA055":"9.82","SA056":"18.84","SA057":"42.26","SA058":"23.45"},{"Metabolite":"Pyruvate","SA001":"3.37","SA002":"2.99","SA003":"5.9","SA004":"4.02","SA005":"5.45","SA006":"3.54","SA007":"3.55","SA008":"5.88","SA009":"3.64","SA010":"4.04","SA011":"5.39","SA012":"7.27","SA013":"12.72","SA014":"12.29","SA015":"9.27","SA016":"5.42","SA017":"1.95","SA018":"","SA019":"16.79","SA020":"40.39","SA021":"12.22","SA022":"4.63","SA023":"9.32","SA024":"15.74","SA025":"9.77","SA026":"11.3","SA027":"8.33","SA028":"7.93","SA029":"13.47","SA030":"2.43","SA031":"15.31","SA032":"12.43","SA033":"22","SA034":"16.59","SA035":"15.85","SA036":"2.07","SA037":"8.17","SA038":"5.95","SA039":"7.07","SA040":"5.98","SA041":"15.22","SA042":"10.39","SA043":"9.02","SA044":"11.4","SA045":"12.12","SA046":"8.96","SA047":"21.37","SA048":"11.09","SA049":"9.84","SA050":"6.26","SA051":"7.23","SA052":"7.92","SA053":"7.13","SA054":"","SA055":"7.8","SA056":"7.72","SA057":"13.45","SA058":"8.36"},{"Metabolite":"_3_HBA","SA001":"7.29","SA002":"7.57","SA003":"10.46","SA004":"13.06","SA005":"14.52","SA006":"10.29","SA007":"7.4","SA008":"11.98","SA009":"10.64","SA010":"8.79","SA011":"11.28","SA012":"19.21","SA013":"29.27","SA014":"17.98","SA015":"14.17","SA016":"16.01","SA017":"8.06","SA018":"","SA019":"14.77","SA020":"41.92","SA021":"32.64","SA022":"34.82","SA023":"16.04","SA024":"23.27","SA025":"9.65","SA026":"15.27","SA027":"14.5","SA028":"11.2","SA029":"27.15","SA030":"6.24","SA031":"17.36","SA032":"23.21","SA033":"30.52","SA034":"22.62","SA035":"37.13","SA036":"24.59","SA037":"8.22","SA038":"5.4","SA039":"12.19","SA040":"17.97","SA041":"34.82","SA042":"18.32","SA043":"28.25","SA044":"17.06","SA045":"55.65","SA046":"32.6","SA047":"21.24","SA048":"14.5","SA049":"31.59","SA050":"13.35","SA051":"63.78","SA052":"17.24","SA053":"5.52","SA054":"","SA055":"8.78","SA056":"12.83","SA057":"16.88","SA058":"11.49"},{"Metabolite":"Succinate","SA001":"3.03","SA002":"1.76","SA003":"2.01","SA004":"18.83","SA005":"3.77","SA006":"4.25","SA007":"6.94","SA008":"3.37","SA009":"3.67","SA010":"8.35","SA011":"1.63","SA012":"1.92","SA013":"9.57","SA014":"5.16","SA015":"5.26","SA016":"16.7","SA017":"3.1","SA018":"","SA019":"6.66","SA020":"13.57","SA021":"6.74","SA022":"4.66","SA023":"4.52","SA024":"2.82","SA025":"6.17","SA026":"14.85","SA027":"4.37","SA028":"3.23","SA029":"14.54","SA030":"1.93","SA031":"1.98","SA032":"9.29","SA033":"10.02","SA034":"9.35","SA035":"2.45","SA036":"46.47","SA037":"9.2","SA038":"1.06","SA039":"3.85","SA040":"3.77","SA041":"14.1","SA042":"5.04","SA043":"52.98","SA044":"3.59","SA045":"5.77","SA046":"2.66","SA047":"2.33","SA048":"8.2","SA049":"17.14","SA050":"2.9","SA051":"3.11","SA052":"5.84","SA053":"1.15","SA054":"","SA055":"1.77","SA056":"1.63","SA057":"7.15","SA058":"3.46"},{"Metabolite":"Fumarate","SA001":"0.22","SA002":"0.23","SA003":"0.39","SA004":"1.43","SA005":"0.28","SA006":"0.31","SA007":"0.42","SA008":"0.53","SA009":"0.9","SA010":"0.63","SA011":"0.51","SA012":"0.95","SA013":"3.24","SA014":"1.73","SA015":"3.61","SA016":"0.8","SA017":"0.23","SA018":"","SA019":"1.37","SA020":"5.47","SA021":"1.48","SA022":"0.69","SA023":"0.82","SA024":"1.68","SA025":"1","SA026":"1.29","SA027":"0.47","SA028":"0.6","SA029":"1.72","SA030":"0.16","SA031":"0.64","SA032":"0.74","SA033":"4.36","SA034":"9.64","SA035":"1.39","SA036":"0.58","SA037":"0.71","SA038":"0.35","SA039":"0.54","SA040":"0.69","SA041":"4.12","SA042":"1.27","SA043":"2.49","SA044":"0.79","SA045":"1.25","SA046":"0.9","SA047":"0.37","SA048":"0.88","SA049":"1.51","SA050":"0.55","SA051":"3.51","SA052":"0.6","SA053":"0.42","SA054":"","SA055":"0.5","SA056":"0.23","SA057":"0.71","SA058":"0.61"},{"Metabolite":"Malate","SA001":"0.66","SA002":"0.92","SA003":"0.95","SA004":"3.8","SA005":"1.17","SA006":"1.33","SA007":"1","SA008":"1.81","SA009":"1.82","SA010":"2.36","SA011":"1.29","SA012":"3.62","SA013":"8.65","SA014":"4.2","SA015":"7.93","SA016":"2.37","SA017":"0.67","SA018":"","SA019":"3.56","SA020":"13.84","SA021":"5.75","SA022":"2.04","SA023":"2.87","SA024":"5.19","SA025":"2.02","SA026":"3.7","SA027":"1.79","SA028":"4.96","SA029":"5.1","SA030":"0.55","SA031":"1.62","SA032":"1.82","SA033":"12.84","SA034":"16.82","SA035":"5","SA036":"2.63","SA037":"1.95","SA038":"1","SA039":"1.85","SA040":"2.06","SA041":"10.82","SA042":"2.51","SA043":"6.96","SA044":"2.27","SA045":"2.28","SA046":"2.54","SA047":"1.75","SA048":"2.09","SA049":"3.63","SA050":"1.86","SA051":"9.18","SA052":"2.28","SA053":"1.05","SA054":"","SA055":"1.09","SA056":"0.93","SA057":"2.58","SA058":"1.31"},{"Metabolite":"a-KG","SA001":"6.95","SA002":"10.98","SA003":"16.41","SA004":"2.64","SA005":"11.48","SA006":"4.02","SA007":"14.65","SA008":"22.83","SA009":"28.06","SA010":"23.77","SA011":"13.73","SA012":"21.28","SA013":"151.68","SA014":"62.79","SA015":"65.54","SA016":"40.57","SA017":"8.17","SA018":"","SA019":"32.01","SA020":"114.31","SA021":"43.2","SA022":"24.38","SA023":"38.62","SA024":"40","SA025":"38.7","SA026":"56.86","SA027":"38.88","SA028":"26.64","SA029":"78.41","SA030":"7.77","SA031":"24.82","SA032":"17","SA033":"238.29","SA034":"92.35","SA035":"28.31","SA036":"22.63","SA037":"47.59","SA038":"10.89","SA039":"24.42","SA040":"30.07","SA041":"95.58","SA042":"28.28","SA043":"14.31","SA044":"41.47","SA045":"39.94","SA046":"23.23","SA047":"18.69","SA048":"28.23","SA049":"17.7","SA050":"27.96","SA051":"17.38","SA052":"34.9","SA053":"8.97","SA054":"","SA055":"24.44","SA056":"16.55","SA057":"52.95","SA058":"15.86"},{"Metabolite":"Citrate","SA001":"400.44","SA002":"350.49","SA003":"256.04","SA004":"638.98","SA005":"457.95","SA006":"155.51","SA007":"378.47","SA008":"376.3","SA009":"365.7","SA010":"424.89","SA011":"266.5","SA012":"218.68","SA013":"1436.03","SA014":"428.25","SA015":"563.71","SA016":"403.11","SA017":"154.9","SA018":"","SA019":"385.18","SA020":"923.81","SA021":"1336","SA022":"593.32","SA023":"604.95","SA024":"682.81","SA025":"906.13","SA026":"1178.6","SA027":"491.02","SA028":"219.82","SA029":"818.72","SA030":"38.38","SA031":"193.24","SA032":"248.15","SA033":"","SA034":"507.45","SA035":"106.7","SA036":"902.9","SA037":"237.78","SA038":"50.29","SA039":"409.43","SA040":"559.9","SA041":"581.1","SA042":"722.02","SA043":"598.15","SA044":"247.27","SA045":"839.62","SA046":"251","SA047":"98.01","SA048":"369.78","SA049":"255.13","SA050":"165.94","SA051":"220.23","SA052":"262.93","SA053":"169.76","SA054":"","SA055":"116.26","SA056":"206.75","SA057":"505.31","SA058":"151.12"}],

"Metabolites":[{"Metabolite":"Lactate","Retention Index":"3.98","Moverz Quant":"196.1, 91.062","PubChem CID":"107689"},{"Metabolite":"Pyruvate","Retention Index":"6.68","Moverz Quant":"299.1, 91.186","PubChem CID":"1060"},{"Metabolite":"_3_HBA","Retention Index":"4.21","Moverz Quant":"210.1, 91.153","PubChem CID":"441"},{"Metabolite":"Succinate","Retention Index":"5.44","Moverz Quant":"329.1, 206.233","PubChem CID":"1110"},{"Metabolite":"Fumarate","Retention Index":"5.59","Moverz Quant":"327.1, 91.192","PubChem CID":"444972"},{"Metabolite":"Malate","Retention Index":"5.28","Moverz Quant":"345.1, 91.18","PubChem CID":"525"},{"Metabolite":"a-KG","Retention Index":"6.59","Moverz Quant":"462.2, 91.2","PubChem CID":"164533"},{"Metabolite":"Citrate","Retention Index":"5.95","Moverz Quant":"508.25, 385","PubChem CID":"311"}]
}

}