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Practical Aspects of NMR-Based Metabolomics

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Part of the Handbook of Experimental Pharmacology book series (HEP,volume 277)

Abstract

While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for >40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5–10 years.

Keywords

  • Applications
  • Experimental methods
  • NMR spectroscopy
  • Targeted metabolomics
  • Untargeted metabolomics

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Acknowledgments

The authors wish to thank Genome Alberta (a division of Genome Canada), The Canadian Institutes of Health Research (CIHR), Western Economic Diversification (WED), and Alberta Innovates Health Solutions (AIHS) for financial support.

Glossary

Baseline correction:

A spectral processing technique that yields a more pleasant looking NMR spectrum where signal-free regions appear as completely flat lines with zero intensity

BEST:

Band-Selective Excitation Transient

Chemometrics:

A branch of information science that uses mathematical and statistical methods to identify patterns and extract information from large data sets collected on analytical instruments, such as UV, IR, and NMR spectrometers

CPMG:

Carr-Purcell-Meiboom-Gill

CPMG experiment:

A pulse that can filter out the signals arising from large molecules, such as proteins or lipoproteins, from the spectrum (without the need for ultrafiltration or solvent extraction)

COSY:

COrrelated SpectroscopY

DSS:

4,4-dimethyl-4-silapentane-1-sulfonic acid, a chemical shift reference compound

ERETIC:

Electronic REference To access In vivo Concentrations, an electronic reference signal

HSQC:

Heteronuclear Single Quantum Coherence Spectroscopy

IEM:

Inborn error of metabolism. They are rare genetic disorders characterized by significant changes (several-fold increase or absence) in the concentration of specific metabolites that result from disturbances in normal metabolism

INADEQUATE:

Incredible Natural Abundance DoublE QUAntum Transfer Experiment

IUPAC:

The International Union of Pure and Applied Chemistry

IUBMB:

The International Union of Biochemistry and Molecular Biology

Metabolomics:

A branch of analytical chemistry that comprehensively characterizes the molecules in various biofluids and tissues

Metabolites:

The chemical constituents of the metabolome

Metabolome:

The complete collection of all chemicals or metabolites found within cells, biofluids, organs, or organisms

Metnoesy experiment:

A simple 1D NOESY pulse sequence that provides solvent suppression before the experiment and during the mixing time without the use of gradients

NOESY:

Nuclear Overhauser Effect Spectroscopy

Phasing:

An NMR spectral adjustment process that is designed to maximize the absorptive character of NMR peaks over all regions of an NMR spectrum

Relaxation delay:

The sum of the acquisition time and acquisition delay prior to the next scan

SABRE-SHEATH:

Signal Amplification by Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei

SOFAST:

Band-Selective Optimized Flip Angle Short Transient

STOCSY:

Statistical total correlation spectroscopy

T1:

Longitudinal relaxation time

T2:

Transverse relaxation time

Targeted metabolomics:

A metabolomics technique that uses spectral deconvolution software to identify and quantify fluid-specific or targeted metabolites in individual spectra

TSP:

Trimethylsilylpropanoic acid, a chemical shift reference compound

Untargeted metabolomics:

A metabolomics technique that uses spectral alignment, spectral binning, and multivariate statistical analysis to identify spectral features of interest

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Correspondence to David S. Wishart .

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Wishart, D.S., Rout, M., Lee, B.L., Berjanskii, M., LeVatte, M., Lipfert, M. (2022). Practical Aspects of NMR-Based Metabolomics. In: Ghini, V., Stringer, K.A., Luchinat, C. (eds) Metabolomics and Its Impact on Health and Diseases. Handbook of Experimental Pharmacology, vol 277. Springer, Cham. https://doi.org/10.1007/164_2022_613

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