Overview of NMR Spectroscopy-Based Metabolomics: Opportunities and Challenges

  • G. A. Nagana Gowda
  • Daniel RafteryEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2037)


The fast-growing field of metabolomics is impacting numerous areas of basic and life sciences. In metabolomics, analytical methods play a pivotal role, and nuclear magnetic resonance (NMR) and mass spectrometry (MS) have proven to be the most suitable and powerful methods. Although NMR exhibits lower sensitivity and resolution compared to MS, NMR’s numerous important characteristics far outweigh its limitations. Some of its characteristics include excellent reproducibility and quantitative accuracy, the capability to analyze intact biospecimens, an unparalleled ability to identify unknown metabolites, the ability to trace in-cell and in-organelle metabolism in real time, and the capacity to trace metabolic pathways atom by atom using 2H, 13C, or 15N isotopes. Each of these characteristics has been exploited extensively in numerous studies. In parallel, the field has witnessed significant progress in instrumentation, methods development, databases, and automation that are focused on higher throughput and alleviating the limitations of NMR, in particular, resolution and sensitivity. Despite the advances, however, the high complexity of biological mixtures combined with the limitations in sensitivity and resolution continues to pose major challenges. These challenges need to be dealt with effectively to better realize the potential of metabolomics, in general. As a result, multifaceted efforts continue to focus on addressing the challenges as well as reaping the benefits of NMR-based metabolomics. This chapter highlights the current status with emphasis on the opportunities and challenges in NMR-based metabolomics.

Key words

NMR Metabolomics Biomarkers Pathways Historical perspective 


  1. 1.
    Antic T, DeMay RM (2014) The fascinating history of urine examination. J Am Soc Cytopathol 3:103e107CrossRefGoogle Scholar
  2. 2.
    Bhishagratna KKL (1911) An English translation of “The Sushruta Samhita”, vol II. The Bharat Mihir Press, CalcuttaGoogle Scholar
  3. 3.
    Jacob R (2015) Sickening sweet. Distillations 1(4):12–15Google Scholar
  4. 4.
    Das S (2001) Susruta, the pioneer urologist of antiquity. J Urol 165(5):1405–1408PubMedCrossRefGoogle Scholar
  5. 5.
    Karamanou M, Protogerou A, Tsoucalas G, Androutsos G, Poulakou-Rebelakou E (2016) Milestones in the history of diabetes mellitus: the main contributors. World J Diabetes 7(1):1–7PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Williams RJ et al (1951) Individual metabolic patterns and human disease: an exploratory study utilizing predominantly paper chromatographic methods. Biochemical Institute Studies IV, University of Texas Publication No. 5109, University of Texas, Austin, 204 ppGoogle Scholar
  7. 7.
    Gates SC, Sweeley CC (1978) Quantitative metabolic profiling based on gas chromatography. Clin Chem 24(10):1663–1673PubMedGoogle Scholar
  8. 8.
    Nagana Gowda GA, Djukovic D (2014) Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol Biol 1198:3–12CrossRefGoogle Scholar
  9. 9.
    Pauling L, Robinson AB, Teranishi R, Cary P (1971) Quantitative analysis of urine vapor and breath by gas-liquid partition chromatography. Proc Natl Acad Sci U S A 68(10):2374–2376PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Bloch F, Hansen WW, Packard M (1946) Nuclear induction. Phys Rev 69:127CrossRefGoogle Scholar
  11. 11.
    Purcell EM, Torrey HC, Pound RV (1946) Resonance absorption by nuclear magnetic moments in a solid. Phys Rev 69:37–38CrossRefGoogle Scholar
  12. 12.
    Becker ED (1993) A brief history of nuclear magnetic resonance. Anal Chem 65(6):295A–302APubMedCrossRefGoogle Scholar
  13. 13.
    Hoult DI, Busby SJ, Gadian DG, Radda GK, Richards RE, Seeley PJ (1974) Observation of tissue metabolites using 31P nuclear magnetic resonance. Nature 252(5481):285–287PubMedCrossRefGoogle Scholar
  14. 14.
    Navon G, Ogawa S, Shulman RG, Yamane T (1977) High-resolution 31P nuclear magnetic resonance studies of metabolism in aerobic Escherichia coli cells. Proc Natl Acad Sci U S A 74(3):888–891PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Navon G, Ogawa S, Shulman RG, Yamane T (1977) 31P nuclear magnetic resonance studies of Ehrlich ascites tumor cells. Proc Natl Acad Sci U S A 74(1):87–91PubMedPubMedCentralCrossRefGoogle Scholar
  16. 16.
    Burt CT, Glonek T, Barany M (1976) Analysis of phosphate metabolites, the intracellular pH, and the state of adenosine triphosphate in intact muscle by phosphorus nuclear magnetic resonance. J Biol Chem 251:2584–2591PubMedGoogle Scholar
  17. 17.
    Henderson TO, Costello AJR, Omachi A (1974) Phosphate metabolism in intact human erythrocytes: determination by phosphorus-31 nuclear magnetic resonance spectroscopy. Proc Natl Acad Sci U S A 71:2487–2490PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Moon RB, Richards JH (1973) Determination of intracellular pH by 31P magnetic resonance. J Biol Chem 248:7276–7278PubMedPubMedCentralGoogle Scholar
  19. 19.
    Salhany JM, Yamane T, Shulman RG, Ogawa S (1975) High resolution 31P nuclear magnetic resonance studies of intact yeast cells. Proc Natl Acad Sci U S A 72:4966–4970PubMedPubMedCentralCrossRefGoogle Scholar
  20. 20.
    Nicholson JK, Wilson ID (1989) High resolution proton magnetic resonance spectroscopy of biological fluids. Prog Nucl Magn Reson Spectrosc 21(4–5):449–501CrossRefGoogle Scholar
  21. 21.
    Nagana Gowda GA, Gowda YN, Raftery D (2015) Expanding the limits of human blood metabolite quantitation using NMR spectroscopy. Anal Chem 87(1):706–715PubMedCrossRefGoogle Scholar
  22. 22.
    Nagana Gowda GA, Abell L, Lee CF, Tian R (2016) Raftery D (2016) simultaneous analysis of major coenzymes of cellular redox reactions and energy using ex vivo (1)H NMR spectroscopy. Anal Chem 88(9):4817–4824PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Nagana Gowda GA, Abell L, Lee CF, Tian R (2019) Extending the scope of 1H NMR spectroscopy for the analysis of cellular coenzyme A and acetyl coenzyme A. Anal Chem 91(3):2464–2471PubMedCrossRefGoogle Scholar
  24. 24.
    Nagana Gowda GA, Raftery D (2017) Recent advances in NMR-based metabolomics. Anal Chem 89(1):490–510PubMedCrossRefGoogle Scholar
  25. 25.
    Leenders J, Frédérich M, de Tullio P (2015) Nuclear magnetic resonance: a key metabolomics platform in the drug discovery process. Drug Discov Today Technol 13:39–46PubMedCrossRefGoogle Scholar
  26. 26.
    Johanningsmeier SD, Harris GK, Klevorn CM (2016) Metabolomic technologies for improving the quality of food: practice and promise. Annu Rev Food Sci Technol 7:413–438PubMedCrossRefGoogle Scholar
  27. 27.
    Sumner LW, Lei Z, Nikolau BJ, Saito K (2015) Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Nat Prod Rep 32:212–229PubMedCrossRefGoogle Scholar
  28. 28.
    Mahrous EA, Farag MA (2015) Two dimensional NMR spectroscopic approaches for exploring plant metabolome: a review. J Adv Res 6(1):3–15PubMedCrossRefGoogle Scholar
  29. 29.
    Lloyd SG, Zeng H, Wang P, Chatham JC (2004) Lactate isotopomer analysis by 1H NMR spectroscopy: consideration of long-range nuclear spin-spin interactions. Magn Reson Med 51:1279–1282PubMedCrossRefGoogle Scholar
  30. 30.
    Lane AN, Fan TWM (2007) Quantification and identification of isotopomer distributions of metabolites in crude cell extracts using 1H TOCSY. Metabolomics 3:79–86CrossRefGoogle Scholar
  31. 31.
    Lane AN, Fan TW, Bousamra M 2nd, Higashi RM, Yan J, Miller DM (2011) Stable isotope-resolved metabolomics (SIRM) in cancer research with clinical application to nonsmall cell lung cancer. OMICS 15(3):173–182PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Mashimo T, Pichumani K, Vemireddy V, Hatanpaa KJ, Singh DK, Sirasanagandla S et al (2014) Acetate is a bioenergetic substrate for human glioblastoma and brain metastases. Cell 159(7):1603–1614PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Wen H, An YJ, Xu WJ, Kang KW, Park S (2015) Real-time monitoring of cancer cell metabolism and effects of an anticancer agent using 2D in-cell NMR spectroscopy. Angew Chem Int Ed Engl 54(18):5374–5377PubMedCrossRefGoogle Scholar
  34. 34.
    Xu WJ, Wen H, Kim HS, Ko YJ, Dong SM, Park IS, Yook JI, Park S (2018) Observation of acetyl phosphate formation in mammalian mitochondria using real-time in-organelle NMR metabolomics. Proc Natl Acad Sci U S A 115(16):4152–4157PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Kc R, Henry ID, Park GH, Aghdasi A, Raftery D (2010) New solenoidal microcoil NMR probe using zero-susceptibility wire. Concepts Magn Reson Part B Magn Reson Eng 37B(1):13–19PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Grimes JH, O’Connell TM (2011) The application of micro-coil NMR probe technology to metabolomics of urine and serum. J Biomol NMR 49:297–305PubMedCrossRefGoogle Scholar
  37. 37.
    Bird SS, Sheldon DP, Gathungu RM, Vouros P, Kautz R, Matson WR et al (2012) Structural characterization of plasma metabolites detected via LC-electrochemical coulometric array using LC-UV fractionation, MS, and NMR. Anal Chem 84:9889–9898PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Cloarec O, Campbell A, Tseng LH, Braumann U, Spraul M, Scarfe G et al (2007) Virtual chromatographic resolution enhancement in cryoflow LC-NMR experiments via statistical total correlation spectroscopy. Anal Chem 79:3304–3311PubMedCrossRefGoogle Scholar
  39. 39.
    Lenz EM, Wilson ID (2007) Analytical strategies in metabonomics. J Proteome Res 6:443–458PubMedCrossRefGoogle Scholar
  40. 40.
    Djukovic D, Liu S, Henry I, Tobias B, Raftery D (2006) Signal enhancement in HPLC/microcoil NMR using automated column trapping. Anal Chem 78:7154–7160PubMedPubMedCentralCrossRefGoogle Scholar
  41. 41.
    Djukovic D, Appiah-Amponsah E, Shanaiah N, Nagana Gowda GA, Henry I, Everly M et al (2008) Ibuprofen metabolite profiling using a combination of SPE/column-trapping and HPLC-micro-coil NMR. J Pharm Biomed Anal 47:328–334PubMedCrossRefGoogle Scholar
  42. 42.
    Garcia E, Andrews C, Hua J, Kim HL, Sukumaran DK, Szyperski T et al (2011) Diagnosis of early stage ovarian cancer by 1H NMR metabonomics of serum explored by use of a microflow NMR probe. J Proteome Res 10:1765–1771PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Hyberts SG, Heffron GJ, Tarragona NG, Solanky K, Edmonds KA, Luithardt H et al (2007) Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction. J Am Chem Soc 129(16):5108–5116PubMedPubMedCentralCrossRefGoogle Scholar
  44. 44.
    Hyberts SG, Arthanari H, Wagner G (2012) Applications of non-uniform sampling and processing. Top Curr Chem 316:125–148PubMedPubMedCentralCrossRefGoogle Scholar
  45. 45.
    Rai RK, Sinha N (2012) Fast and accurate quantitative metabolic profiling of body fluids by nonlinear sampling of 1H–13C two-dimensional nuclear magnetic resonance spectroscopy. Anal Chem 84(22):10005–10011PubMedCrossRefGoogle Scholar
  46. 46.
    Motta A, Paris D, Melck D (2010) Monitoring real-time metabolism of living cells by fast two-dimensional NMR spectroscopy. Anal Chem 82(6):2405–2411PubMedCrossRefGoogle Scholar
  47. 47.
    Bruschweiler R, Zhang F (2004) Covariance nuclear magnetic resonance spectroscopy. J Chem Phys 120:5253–5260PubMedCrossRefGoogle Scholar
  48. 48.
    Frydman L, Scherf T, Lupulescu A (2002) The acquisition of multidimensional NMR spectra within a single scan. Proc Natl Acad Sci U S A 99:15858–15862PubMedPubMedCentralCrossRefGoogle Scholar
  49. 49.
    Giraudeau P, Remaud GS, Akoka S (2009) Evaluation of ultrafast 2D NMR for quantitative analysis. Anal Chem 81(1):479–484PubMedCrossRefGoogle Scholar
  50. 50.
    Bhattacharya P, Chekmenev EY, Perman WH, Harris KC, Lin AP, Norton VA et al (2007) Towards hyperpolarized (13)C-succinate imaging of brain cancer. J Magn Reson 186:150–155PubMedPubMedCentralCrossRefGoogle Scholar
  51. 51.
    Shchepin RV, Coffey AM, Waddell KW, Chekmenev EY (2012) PASADENA hyperpolarized 13C phospholactate. J Am Chem Soc 134(9):3957–3960PubMedPubMedCentralCrossRefGoogle Scholar
  52. 52.
    Ardenkjaer-Larsen JH, Fridlund B, Gram A, Hansson G, Hansson L, Lerche MH et al (2003) Increase in signal-to-noise ratio of > 10,000 times in liquid-state NMR. Proc Natl Acad Sci U S A 100(18):10158–10163PubMedPubMedCentralCrossRefGoogle Scholar
  53. 53.
    Girard DA (1989) A fast ‘Monte-Carlo cross-validation’ procedure for large least squares problems with noisy data. Numer Math 56(1):1–23CrossRefGoogle Scholar
  54. 54.
    Chen C, Deng L, Wei S, Nagana Gowda GA, Gu H, Chiorean EG et al (2015) Exploring metabolic profile differences between colorectal polyp patients and controls using seemingly unrelated regression. J Proteome Res 14(6):2492–2499PubMedPubMedCentralCrossRefGoogle Scholar
  55. 55.
    Chen C, Nagana Gowda GA, Zhu J, Deng L, Gu H, Chiorean EG et al (2017) Altered metabolite levels and correlations in patients with colorectal cancer and polyps detected using seemingly unrelated regression analysis. Metabolomics 13:125. Scholar
  56. 56.
    Maciejewski MW, Schuyler AD, Gryk MR, Moraru II, Romero PR, Ulrich EL et al (2017) NMRbox: a resource for biomolecular NMR computation. Biophys J 112(8):1529–1534PubMedPubMedCentralCrossRefGoogle Scholar
  57. 57.
    Nagana Gowda GA, Raftery D (2015) Can NMR solve some significant challenges in metabolomics? J Magn Reson 260:144–160PubMedCrossRefGoogle Scholar
  58. 58.
    Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C et al (2016) Metabolomics workbench: an international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res 44(D1):D463–D470PubMedCrossRefGoogle Scholar
  59. 59.
    Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P et al (2016) MetaboLights: an open-access database repository for metabolomics data. Curr Protoc Bioinformatics 53:14.13.1–14.13.18Google Scholar

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

Authors and Affiliations

  1. 1.Northwest Metabolomics Research CenterUniversity of WashingtonSeattleUSA
  2. 2.Department of Anesthesiology and Pain MedicineUniversity of WashingtonSeattleUSA
  3. 3.Mitochondria and Metabolism CenterUniversity of WashingtonSeattleUSA
  4. 4.Fred Hutchinson Cancer Research CenterSeattleUSA

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