Journal of Biomolecular NMR

, Volume 49, Issue 3–4, pp 307–323

Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra

  • Pascal Mercier
  • Michael J. Lewis
  • David Chang
  • David Baker
  • David S. Wishart
Article

Abstract

Nuclear magnetic resonance (NMR) and Mass Spectroscopy (MS) are the two most common spectroscopic analytical techniques employed in metabolomics. The large spectral datasets generated by NMR and MS are often analyzed using data reduction techniques like Principal Component Analysis (PCA). Although rapid, these methods are susceptible to solvent and matrix effects, high rates of false positives, lack of reproducibility and limited data transferability from one platform to the next. Given these limitations, a growing trend in both NMR and MS-based metabolomics is towards targeted profiling or “quantitative” metabolomics, wherein compounds are identified and quantified via spectral fitting prior to any statistical analysis. Despite the obvious advantages of this method, targeted profiling is hindered by the time required to perform manual or computer-assisted spectral fitting. In an effort to increase data analysis throughput for NMR-based metabolomics, we have developed an automatic method for identifying and quantifying metabolites in one-dimensional (1D) proton NMR spectra. This new algorithm is capable of using carefully constructed reference spectra and optimizing thousands of variables to reconstruct experimental NMR spectra of biofluids using rules and concepts derived from physical chemistry and NMR theory. The automated profiling program has been tested against spectra of synthetic mixtures as well as biological spectra of urine, serum and cerebral spinal fluid (CSF). Our results indicate that the algorithm can correctly identify compounds with high fidelity in each biofluid sample (except for urine). Furthermore, the metabolite concentrations exhibit a very high correlation with both simulated and manually-detected values.

Keywords

Metabolomics Nuclear magnetic resonance Targeted profiling Automated targeted spectral profiling 

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Pascal Mercier
    • 1
  • Michael J. Lewis
    • 1
  • David Chang
    • 1
    • 4
  • David Baker
    • 3
  • David S. Wishart
    • 2
  1. 1.Chenomx IncEdmontonCanada
  2. 2.Department of Computing Science and Biological SciencesUniversity of AlbertaEdmontonCanada
  3. 3.Pfizer IncGrotonUSA
  4. 4.Director of Products and ServicesEdmontonCanada

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