#METABOLOMICS WORKBENCH efahy_20160120_191932 DATATRACK_ID:482 STUDY_ID:ST000336 ANALYSIS_ID:AN004437 PROJECT_ID:PR000268 VERSION 1 CREATED_ON June 14, 2023, 9:54 am #PROJECT PR:PROJECT_TITLE Urine metabolomics to track disease progression in DMD PR:PROJECT_SUMMARY Duchenne Muscular Dystrophy (DMD) is an X-linked recessive form of muscular PR:PROJECT_SUMMARY dystrophy that affects males via a mutation in the gene for the muscle protein, PR:PROJECT_SUMMARY dystrophin. Progression of the disease results in severe muscle loss, ultimately PR:PROJECT_SUMMARY leading to paralysis and death. Steroid therapy has been a commonly employed PR:PROJECT_SUMMARY method for reducing the severity of symptoms. This study aims to quantify the PR:PROJECT_SUMMARY urine levels of amino acids and organic acids in patients with DMD both with and PR:PROJECT_SUMMARY without steroid treatment. Track the progression of DMD in patients who have PR:PROJECT_SUMMARY provided multiple urine samples. PR:INSTITUTE University of Florida PR:DEPARTMENT Physiology and Functional Genomics PR:LAST_NAME Walter PR:FIRST_NAME Glenn PR:ADDRESS - PR:EMAIL glennw@ufl.edu PR:PHONE - #STUDY ST:STUDY_TITLE Targeted LC/MS of urine from boys with DMD and controls ST:STUDY_TYPE Natural History ST:STUDY_SUMMARY Quantify the urine levels of amino acids and organic acids in patients with DMD ST:STUDY_SUMMARY both with and without steroid treatment. Track the progression of DMD in ST:STUDY_SUMMARY patients who have provided multiple urine samples. ST:INSTITUTE University of Florida ST:DEPARTMENT SECIM ST:LABORATORY Sanford Burnham ST:LAST_NAME Lee ST:FIRST_NAME Brittany ST:ADDRESS - ST:EMAIL balm22@ufl.edu ST:PHONE - ST:SUBMIT_DATE 2015-05-07 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 58 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:AGE_OR_AGE_RANGE 5-14 SU:GENDER Males #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS SU001 SA001 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU002 SA002 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU003 SA003 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU004 SA004 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU005 SA005 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU006 SA006 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU007 SA007 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU008 SA008 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU009 SA009 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU010 SA010 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU011 SA011 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU012 SA012 Diagnosis:Controls | steroid_status:- SUBJECT_SAMPLE_FACTORS SU013 SA013 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU014 SA014 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU015 SA015 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU016 SA016 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU017 SA017 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU018 SA018 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU019 SA019 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU020 SA020 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU021 SA021 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU022 SA022 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU023 SA023 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU024 SA024 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU025 SA025 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU026 SA026 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU027 SA027 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU028 SA028 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU029 SA029 Diagnosis:DMD | steroid_status:- SUBJECT_SAMPLE_FACTORS SU030 SA030 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU031 SA031 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU032 SA032 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU033 SA033 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU034 SA034 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU035 SA035 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU036 SA036 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU037 SA037 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU038 SA038 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU039 SA039 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU040 SA040 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU041 SA041 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU042 SA042 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU043 SA043 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU044 SA044 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU045 SA045 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU046 SA046 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU047 SA047 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU048 SA048 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU049 SA049 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU050 SA050 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU051 SA051 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU052 SA052 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU053 SA053 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU054 SA054 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU055 SA055 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU056 SA056 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU057 SA057 Diagnosis:DMD | steroid_status:1 SUBJECT_SAMPLE_FACTORS SU058 SA058 Diagnosis:DMD | steroid_status:1 #COLLECTION CO:COLLECTION_SUMMARY Subjects are consented and given a bag containing a urine collection cup, CO:COLLECTION_SUMMARY antiseptic wipes and directions of how to give a clean catch urine sample. They CO:COLLECTION_SUMMARY are then lead to a restroom where they collect their own urine sample using a CO:COLLECTION_SUMMARY clean catch method (direction provided). Urine samples are then placed on ice CO:COLLECTION_SUMMARY and brought to the UF CTSI Biorepository. There, samples are transferred into CO:COLLECTION_SUMMARY 500uL aliquots and stored at -80C. Samples will remain there until samples will CO:COLLECTION_SUMMARY be removed and ran on the NMR for this study. CO:SAMPLE_TYPE Urine #TREATMENT TR:TREATMENT_SUMMARY No treatment, samples are from a Natural History Clinical Trial. Samples are TR:TREATMENT_SUMMARY either boys with DMD or control boys all within the ages 5-14. Unaffected, TR:TREATMENT_SUMMARY control boys are moderately active (less than 3 low to moderate exercise bouts TR:TREATMENT_SUMMARY per week) #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME SB_AA_Assay.pdf, SB_OA_Assay.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Organic Acids assay CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Dionex UltiMate 3000 HPLC CH:COLUMN_NAME Acquity UPLC BEH C18 2.1 x 100 mm, 1.7 µm column, Waters Corp CH:SOLVENT_A - CH:SOLVENT_B - CH:FLOW_GRADIENT - CH:FLOW_RATE - CH:COLUMN_TEMPERATURE - CH:METHODS_FILENAME SB_OA_Assay.pdf #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Quantiva QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS OA assay- HESI #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS umol/mg Creatinine MS_METABOLITE_DATA_START Samples SA001 SA002 SA003 SA004 SA005 SA006 SA007 SA008 SA009 SA010 SA011 SA012 SA013 SA014 SA015 SA016 SA017 SA018 SA019 SA020 SA021 SA022 SA023 SA024 SA025 SA026 SA027 SA028 SA029 SA030 SA031 SA032 SA033 SA034 SA035 SA036 SA037 SA038 SA039 SA040 SA041 SA042 SA043 SA044 SA045 SA046 SA047 SA048 SA049 SA050 SA051 SA052 SA053 SA054 SA055 SA056 SA057 SA058 Factors Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:Controls | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:- Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Diagnosis:DMD | steroid_status:1 Lactate 8.34 5.55 6.94 12.7 18.39 6.8 9.31 15.53 7.18 13.72 19.03 36.26 26.77 34.12 16.88 6.85 75.07 208.57 49.62 18.34 23.32 46.71 18.01 24.23 20.93 23.46 39.3 5.03 15.24 27.03 38.32 50.64 94.27 17.63 23.24 12.99 19.81 14.75 74.53 19.83 70.81 31.38 25.52 26.15 121.54 24.56 98.27 13.82 90.02 12.67 21.76 9.82 18.84 42.26 23.45 Pyruvate 3.37 2.99 5.9 4.02 5.45 3.54 3.55 5.88 3.64 4.04 5.39 7.27 12.72 12.29 9.27 5.42 1.95 16.79 40.39 12.22 4.63 9.32 15.74 9.77 11.3 8.33 7.93 13.47 2.43 15.31 12.43 22 16.59 15.85 2.07 8.17 5.95 7.07 5.98 15.22 10.39 9.02 11.4 12.12 8.96 21.37 11.09 9.84 6.26 7.23 7.92 7.13 7.8 7.72 13.45 8.36 _3_HBA 7.29 7.57 10.46 13.06 14.52 10.29 7.4 11.98 10.64 8.79 11.28 19.21 29.27 17.98 14.17 16.01 8.06 14.77 41.92 32.64 34.82 16.04 23.27 9.65 15.27 14.5 11.2 27.15 6.24 17.36 23.21 30.52 22.62 37.13 24.59 8.22 5.4 12.19 17.97 34.82 18.32 28.25 17.06 55.65 32.6 21.24 14.5 31.59 13.35 63.78 17.24 5.52 8.78 12.83 16.88 11.49 Succinate 3.03 1.76 2.01 18.83 3.77 4.25 6.94 3.37 3.67 8.35 1.63 1.92 9.57 5.16 5.26 16.7 3.1 6.66 13.57 6.74 4.66 4.52 2.82 6.17 14.85 4.37 3.23 14.54 1.93 1.98 9.29 10.02 9.35 2.45 46.47 9.2 1.06 3.85 3.77 14.1 5.04 52.98 3.59 5.77 2.66 2.33 8.2 17.14 2.9 3.11 5.84 1.15 1.77 1.63 7.15 3.46 Fumarate 0.22 0.23 0.39 1.43 0.28 0.31 0.42 0.53 0.9 0.63 0.51 0.95 3.24 1.73 3.61 0.8 0.23 1.37 5.47 1.48 0.69 0.82 1.68 1 1.29 0.47 0.6 1.72 0.16 0.64 0.74 4.36 9.64 1.39 0.58 0.71 0.35 0.54 0.69 4.12 1.27 2.49 0.79 1.25 0.9 0.37 0.88 1.51 0.55 3.51 0.6 0.42 0.5 0.23 0.71 0.61 Malate 0.66 0.92 0.95 3.8 1.17 1.33 1 1.81 1.82 2.36 1.29 3.62 8.65 4.2 7.93 2.37 0.67 3.56 13.84 5.75 2.04 2.87 5.19 2.02 3.7 1.79 4.96 5.1 0.55 1.62 1.82 12.84 16.82 5 2.63 1.95 1 1.85 2.06 10.82 2.51 6.96 2.27 2.28 2.54 1.75 2.09 3.63 1.86 9.18 2.28 1.05 1.09 0.93 2.58 1.31 a-KG 6.95 10.98 16.41 2.64 11.48 4.02 14.65 22.83 28.06 23.77 13.73 21.28 151.68 62.79 65.54 40.57 8.17 32.01 114.31 43.2 24.38 38.62 40 38.7 56.86 38.88 26.64 78.41 7.77 24.82 17 238.29 92.35 28.31 22.63 47.59 10.89 24.42 30.07 95.58 28.28 14.31 41.47 39.94 23.23 18.69 28.23 17.7 27.96 17.38 34.9 8.97 24.44 16.55 52.95 15.86 Citrate 400.44 350.49 256.04 638.98 457.95 155.51 378.47 376.3 365.7 424.89 266.5 218.68 1436.03 428.25 563.71 403.11 154.9 385.18 923.81 1336 593.32 604.95 682.81 906.13 1178.6 491.02 219.82 818.72 38.38 193.24 248.15 507.45 106.7 902.9 237.78 50.29 409.43 559.9 581.1 722.02 598.15 247.27 839.62 251 98.01 369.78 255.13 165.94 220.23 262.93 169.76 116.26 206.75 505.31 151.12 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Retention Index Moverz Quant PubChem CID Lactate 3.98 196.1, 91.062 107689 Pyruvate 6.68 299.1, 91.186 1060 _3_HBA 4.21 210.1, 91.153 441 Succinate 5.44 329.1, 206.233 1110 Fumarate 5.59 327.1, 91.192 444972 Malate 5.28 345.1, 91.18 525 a-KG 6.59 462.2, 91.2 164533 Citrate 5.95 508.25, 385 311 METABOLITES_END #END