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
| Study ID | ST000256 |
| 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 |
| NMRmetabolomics@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) |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2015-09-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 Torontos 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 |
|---|---|---|---|
| SA011664 | Urine13 | F | AA |
| SA011665 | Urine8 | F | AA |
| SA011666 | Urine9 | F | C |
| SA011667 | Urine16 | F | C |
| SA011668 | Urine20 | F | C |
| SA011669 | Urine7 | F | C |
| SA011670 | Urine10 | F | C |
| SA011671 | Urine6 | F | C |
| SA011672 | Urine2 | F | C |
| SA011673 | Urine17 | M | C |
| SA011674 | Urine19 | M | C |
| SA011675 | Urine3 | M | C |
| SA011676 | Urine18 | M | C |
| SA011677 | Urine14 | M | C |
| SA011678 | Urine5 | M | C |
| SA011679 | Urine1 | M | C |
| SA011680 | Urine12 | M | C |
| SA011681 | Urine4 | M | C |
| SA011682 | Urine15 | M | C |
| Showing results 1 to 19 of 19 |
Collection:
| Collection ID: | CO000268 |
| Collection Summary: | - |
| 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 Summary: | - |
| 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 |
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 |
