Tools for Enhanced NMR-Based Metabolomics Analysis

  • John L. MarkleyEmail author
  • Hesam Dashti
  • Jonathan R. Wedell
  • William M. Westler
  • Hamid R. Eghbalnia
Part of the Methods in Molecular Biology book series (MIMB, volume 2037)


Metabolomics is the study of profiles of small molecules in biological fluids, cells, or organs. These profiles can be thought of as the “fingerprints” left behind from chemical processes occurring in biological systems. Because of its potential for groundbreaking applications in disease diagnostics, biomarker discovery, and systems biology, metabolomics has emerged as a rapidly growing area of research. Metabolomics investigations often, but not always, involve the identification and quantification of endogenous and exogenous metabolites in biological samples. Software tools and databases play a crucial role in advancing the rigor, robustness, reproducibility, and validation of these studies. Specifically, the establishment of a robust library of spectral signatures with unique compound descriptors and atom identities plays a key role in profiling studies based on data from nuclear magnetic resonance (NMR) spectroscopy. Here, we discuss developments leading to a rigorous basis for unique identification of compounds, reproducible numbering of atoms, the compact representation of NMR spectra of metabolites and small molecules, tools for improved compound identification, quantification and visualization, and approaches toward the goal of rigorous analysis of metabolomics data.

Key words

NMR Metabolomics Identification Quantification Numbering of atoms 



This work received funding from the National Institutes of Health (NIH). Grants from the NIH National Institute of General Medical Science provided support to the National Magnetic Resonance Facility at Madison (P41 GM103399) and the Biological Magnetic Resonance Data Bank (R01 GM109046) and partial support for HRE, HD, and JRW (P41 GM111135 to the National Center for Biomolecular NMR Data Processing and Analysis). H.D. currently is supported by National Heart, Lung, and Blood Institute grant T32 HL007575.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • John L. Markley
    • 1
    Email author
  • Hesam Dashti
    • 2
  • Jonathan R. Wedell
    • 1
  • William M. Westler
    • 1
  • Hamid R. Eghbalnia
    • 1
  1. 1.Department of BiochemistryUniversity of Wisconsin MadisonMadisonUSA
  2. 2.Department of Medicine, Brigham and Women’s HospitalHarvard Medical SchoolBostonUSA

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