{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000256","ANALYSIS_ID":"AN000405","VERSION":"1","CREATED_ON":"01-03-2020"},

"PROJECT":{"PROJECT_TITLE":"Signal Intensities Derived from Different NMR Probes and Parameters Contribute to Variations in Quantification of Metabolites","PROJECT_TYPE":"Cross-center Quantitative NMR Urine Metabolomics Study","PROJECT_SUMMARY":"We discovered that serious issues could arise that may complicate interpretation of metabolomic data when identical samples are analyzed at more than one NMR facility, or using slightly different NMR parameters on the same instrument. This is important because cross-center validation metabolomics studies are essential for the reliable application ofmetabolomics to clinical biomarker discovery. To test the reproducibility of quantified metabolite data at multiple sites, technical replicates of urine samples were assayed by 1D-1H-NMR at the University of Alberta and the University of Michigan. Urine samples were obtained from healthy controls under a standard operating procedure for collection and processing. Subsequent analysis using standard statistical techniques revealed that quantitative data across sites can be achieved, but also that previously unrecognized NMR parameter differences can dramatically and widely perturb results. We
present here a confirmed validation of NMR analysis at two sites, and report the range and magnitude that common NMR parameters involved in solvent suppression can have on quantitated metabolomics data. Specifically, saturation power levels greatly influenced peak height intensities in a frequency-dependent manner for a number of metabolites, which markedly impacted the quantification of metabolites. We also investigated other NMR parameters to determine their effects on further quantitative accuracy and precision. Collectively, these findings highlight the importance of and need for consistent use of NMR parameter settings within and across centers in order to generate reliable, reproducible quantified NMR metabolomics data. This study was published: PLoS One. 2014 Jan 21;9(1):e85732. doi: 10.1371/journal.pone.0085732. eCollection 2014.","INSTITUTE":"University of Alberta","DEPARTMENT":"Clinical Pharmacy and Bioinformatics and Computational medicine (UMich); and the Pulmonary Research Group and the Department of Chemistry (UAlberta)","LABORATORY":"NMR Metabolomics Laboratory, University of Michigan","LAST_NAME":"Stringer","FIRST_NAME":"Kathleen","ADDRESS":"College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109","EMAIL":"stringek@umich.edu","FUNDING_SOURCE":"This work was supported by a grant from the Department of Computational Medicine and Bioinformatics, Department of Medicine, University of Michigan; the University of Michigan Claude D. Pepper Older Americans Independence Center (NIA Grant AGA024824); and the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1TR000433-06. The University of Torontos NMR 3 mm probe and spectrometer were provided by Canada Foundation for Innovation grant #19119.","DOI":"http://dx.doi.org/10.21228/M8HC70"}, "STUDY":{"STUDY_TITLE":"Signal Intensities Derived from Different NMR Probes and Parameters Contribute to Variations in Quantification of Metabolites","STUDY_TYPE":"Single timepoint; healthy controls","STUDY_SUMMARY":"Healthy volunteers","INSTITUTE":"University of Michigan","DEPARTMENT":"Clinical Pharmacy","LABORATORY":"The NMR Metabolomics Laboratory (Stringer)","LAST_NAME":"Stringer","FIRST_NAME":"Kathleen","ADDRESS":"University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105","EMAIL":"stringek@umich.edu","SUBMIT_DATE":"2015-09-18","NUM_GROUPS":"N/A","TOTAL_SUBJECTS":"19","STUDY_COMMENTS":"Data were also generated by the University of Alberta (UA)"}, "SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"Mean (+SD): 54+8 years","WEIGHT_OR_WEIGHT_RANGE":"Mean (+SD): 76+11 kg; BMI < 30","GENDER":"males and females (see study design)","HUMAN_RACE":"Caucasian (C) and African American (AA)","HUMAN_MEDICATIONS":"None","HUMAN_PRESCRIPTION_OTC":"None","HUMAN_SMOKING_STATUS":"Non-smokers","HUMAN_ALCOHOL_DRUG_USE":"None","HUMAN_INCLUSION_CRITERIA":"Healthy, non-smoking, medication free adults","SPECIES_GROUP":"Human"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"CCMB13", "Sample ID":"Urine13", "Factors":{"Gender":"F","Race":"AA"} }, { "Subject ID":"CCMB08", "Sample ID":"Urine8", "Factors":{"Gender":"F","Race":"AA"} }, { "Subject ID":"CCMB10", "Sample ID":"Urine10", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB16", "Sample ID":"Urine16", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB02", "Sample ID":"Urine2", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB20", "Sample ID":"Urine20", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB06", "Sample ID":"Urine6", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB07", "Sample ID":"Urine7", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB09", "Sample ID":"Urine9", "Factors":{"Gender":"F","Race":"C"} }, { "Subject ID":"CCMB01", "Sample ID":"Urine1", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB12", "Sample ID":"Urine12", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB14", "Sample ID":"Urine14", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB15", "Sample ID":"Urine15", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB17", "Sample ID":"Urine17", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB18", "Sample ID":"Urine18", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB19", "Sample ID":"Urine19", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB03", "Sample ID":"Urine3", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB04", "Sample ID":"Urine4", "Factors":{"Gender":"M","Race":"C"} }, { "Subject ID":"CCMB05", "Sample ID":"Urine5", "Factors":{"Gender":"M","Race":"C"} } ], "COLLECTION":{"COLLECTION_PROTOCOL_ID":"Clean catch urine collection","COLLECTION_PROTOCOL_FILENAME":"SOP_for_urine_sample_collection","SAMPLE_TYPE":"Urine","COLLECTION_METHOD":"clean catch into NaN3 coated collection cups","COLLECTION_LOCATION":"Michigan Clinical Research Unit","COLLECTION_FREQUENCY":"1","COLLECTION_TIME":"Fasting, between 0830-0930","VOLUMEORAMOUNT_COLLECTED":"30-50ml","STORAGE_CONDITIONS":"Initial 4C then -80C following processing","COLLECTION_VIALS":"Urine collection cup","COLLECTION_TUBE_TEMP":"RT","ADDITIVES":"NaN3"}, "TREATMENT":{"TREATMENT_SUMMARY":"No treatment"}, "SAMPLEPREP":{"SAMPLEPREP_PROTOCOL_FILENAME":"SOP_for_urine_sample_processing","PROCESSING_METHOD":"Centrifugation","PROCESSING_STORAGE_CONDITIONS":"4C","EXTRACTION_METHOD":"N/A","EXTRACT_ENRICHMENT":"N/A","EXTRACT_CLEANUP":"N/A","EXTRACT_STORAGE":"N/A","SAMPLE_RESUSPENSION":"N/A"}, "CHROMATOGRAPHY":[], "ANALYSIS":{"LABORATORY_NAME":"University of Alberta National High Field Nuclear Magnetic Resonance Centre","ANALYSIS_TYPE":"NMR","SOFTWARE_VERSION":"VNMRJ 2.2c","OPERATOR_NAME":"Ryan McKay","ANALYSIS_DISPLAY":"1H NMR 600 MHz","NUM_FACTORS":"3","NUM_METABOLITES":"59"}, "NM":{"INSTRUMENT_NAME":"Oxford 600","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D 1H","SHIMMING_METHOD":"Healthy urine quantified metabolite data","RECEIVER_GAIN":"10% (~0.5mM)","OFFSET_FREQUENCY":"600 MHz","PRESATURATION_POWER_LEVEL":"HX probe with Z-axis gradient coils","CHEMICAL_SHIFT_REF_CPD":"D2O","TEMPERATURE":"5mm","NUMBER_OF_SCANS":"Auto shim (gradient shimming), and manual when necessary.","DUMMY_SCANS":"1D-NOESY","ACQUISITION_TIME":"saturation at 80 Hz induced field strength","RELAXATION_DELAY":"5.5ms","REAL_DATA_POINTS":"around -178Hz","ZERO_FILLING":"DSS-d6","APODIZATION":"25C"}, "NMR_METABOLITE_DATA":{ "Units":"", 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