Summary of study ST000256

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000208. The data can be accessed directly via it's Project DOI: 10.21228/M8HC70 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000256
Study TitleSignal Intensities Derived from Different NMR Probes and Parameters Contribute to Variations in Quantification of Metabolites
Study TypeSingle timepoint; healthy controls
Study SummaryHealthy volunteers
Institute
University of Michigan
DepartmentClinical Pharmacy
LaboratoryThe NMR Metabolomics Laboratory (Stringer)
Last NameStringer
First NameKathleen
AddressUniversity Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
EmailNMRmetabolomics@umich.edu
Submit Date2015-09-18
Num GroupsN/A
Total Subjects19
Study CommentsData were also generated by the University of Alberta (UA)
Raw Data AvailableYes
Raw Data File Type(s)fid, propcar, text
Analysis Type DetailNMR
Release Date2015-09-18
Release Version1
Kathleen Stringer Kathleen Stringer
https://dx.doi.org/10.21228/M8HC70
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000208
Project DOI:doi: 10.21228/M8HC70
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 (University of Michigan);Alberta Respiratory Centre(University of Alberta);Department of Chemistry(University of Alberta)
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:NMRmetabolomics@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 Toronto’s NMR 3 mm probe and spectrometer were provided by Canada Foundation for Innovation grant #19119.

Subject:

Subject ID:SU000276
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

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Gender Race
SA011664Urine13F AA
SA011665Urine8F AA
SA011666Urine9F C
SA011667Urine16F C
SA011668Urine20F C
SA011669Urine7F C
SA011670Urine10F C
SA011671Urine6F C
SA011672Urine2F C
SA011673Urine17M C
SA011674Urine19M C
SA011675Urine3M C
SA011676Urine18M C
SA011677Urine14M C
SA011678Urine5M C
SA011679Urine1M C
SA011680Urine12M C
SA011681Urine4M C
SA011682Urine15M C
Showing results 1 to 19 of 19

Collection:

Collection ID:CO000268
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 ID:TR000288
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000282
Sampleprep Protocol Filename:SOP_for_urine_sample_processing
Processing Method:Centrifugation
Processing Storage Conditions:4C
Extraction Method:N/A
Extract Concentration Dilution:N/A
Extract Enrichment:N/A
Extract Cleanup:N/A
Extract Storage:N/A
Sample Resuspension:N/A

Chromatography:

Chromatography ID:CH000286

Analysis:

Analysis ID:AN000404
Laboratory Name:University of Michigan Biochemical NMR Core Laboratory
Analysis Type:NMR
Software Version:VNMRJ 3.2
Operator Name:Michael Finkel
Chromatography ID:CH000286
Num Factors:3
Num Metabolites:59
  
Analysis ID:AN000405
Laboratory Name:University of Alberta National High Field Nuclear Magnetic Resonance Centre
Analysis Type:NMR
Software Version:VNMRJ 2.2c
Operator Name:Ryan McKay
Chromatography ID:CH000286
Num Factors:3
Num Metabolites:59

NMR:

NMR ID:NM000056
Analysis ID:AN000404
Instrument Name:Agilent 500/54 VNMRS
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Shimming Method:Healthy urine quantified metabolite data
Receiver Gain:10% (~0.5mM)
Offset Frequency:500 MHz
Presaturation Power Level:ONE-Probe
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 ID:NM000057
Analysis ID:AN000405
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
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