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Automated Tools for the Analysis of 1D-NMR and 2D-NMR Spectra

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NMR-Based Metabolomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2037))

Abstract

Nuclear magnetic resonance (NMR) spectroscopy is becoming increasingly automated. Most modern NMR spectrometers are now equipped with auto-tune/auto-match probes along with automated locking and shimming systems. Likewise, more and more instruments, especially for NMR-based metabolomics applications, are equipped with automated sample changers. All this instrumental automation allows NMR data to be collected at a rate of >100 samples/day. However, a continuing bottleneck in NMR-based metabolomics has been the time required to manually analyze and annotate the collected NMR spectra. In many cases, manual spectral annotation and analysis can take one or more hours per spectrum. Fortunately, over the past few years, several software tools have been developed that largely automate the spectral deconvolution or spectral annotation process. Using these tools requires that the samples must be prepared and the NMR spectra must be acquired in a very specific manner. In this chapter, we will describe the step-by-step preparation of biofluid samples along with the required protocols for acquiring optimal spectra for automated NMR metabolomics analysis. We will also discuss the use of three common tools (Chenomx NMR Suite, Bayesil, and COLMARm) for (semi-) automated profiling, and annotation of 1D- and 2D-NMR spectra of biofluids.

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References

  1. Nicholson JK, Wilson ID (2003) Opinion: understanding ’global’ systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2(8):668–676

    Article  CAS  Google Scholar 

  2. Wishart DS (2008) Quantitative metabolomics using NMR. Trac Trend Anal Chem 27(3):228–237

    Article  CAS  Google Scholar 

  3. Alonso A, Marsal S, Julia A (2015) Analytical methods in untargeted metabolomics: state of the art in 2015. Front Bioeng Biotechnol 3:23. https://doi.org/10.3389/fbioe.2015.00023

    Article  PubMed  PubMed Central  Google Scholar 

  4. Mercier P, Lewis MJ, Chang D, Baker D, Wishart DS (2011) Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra. J Biomol NMR 49(3–4):307–323

    Article  CAS  Google Scholar 

  5. Monakhova YB, Schutz B, Schafer H, Spraul M, Kuballa T, Hahn H, Lachenmeier DW (2014) Validation studies for multicomponent quantitative NMR analysis: the example of apple fruit juice. Accred Qual Assur 19(1):17–29

    Article  CAS  Google Scholar 

  6. Spraul M, Link M, Schaefer H, Fang F, Schuetz B (2015) Wine analysis to check quality and authenticity by fully-automated 1H-NMR. Bio Web Conf 5:02022. https://doi.org/10.1051/bioconf/20150502022

    Article  Google Scholar 

  7. Hao J, Liebeke M, Astle W, De Iorio M, Bundy JG, Ebbels TM (2014) Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN. Nat Protoc 9(6):1416–1427

    Article  CAS  Google Scholar 

  8. Ravanbakhsh S, Liu P, Bjorndahl TC, Mandal R, Grant JR, Wilson M, Eisner R, Sinelnikov I, Hu X, Luchinat C, Greiner R, Wishart DS (2015) Accurate, fully-automated NMR spectral profiling for metabolomics. PLoS One 10(5):e0124219. https://doi.org/10.1371/journal.pone.0124219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Rohnisch HE, Eriksson J, Mullner E, Agback P, Sandstrom C, Moazzami AA (2018) AQuA: an automated quantification algorithm for high-throughput NMR-based metabolomics and its application in human plasma. Anal Chem 90(3):2095–2102

    Article  Google Scholar 

  10. Tardivel PJC, Canlet C, Lefort G, Tremblay-Franco M, Debrauwer L, Concordet D et al (2017) ASICS: an automatic method for identification and quantification of metabolites in complex 1D H-1 NMR spectra. Metabolomics 13(10):ARTN 109. https://doi.org/10.1007/s11306-017-1244-5

    Article  CAS  Google Scholar 

  11. Canueto D, Gomez J, Salek RM, Correig X, Canellas N (2018) rDolphin: a GUI R package for proficient automatic profiling of 1D H-1-NMR spectra of study datasets. Metabolomics 14(3):ARTN 24. https://doi.org/10.1007/s11306-018-1319-y

    Article  CAS  Google Scholar 

  12. Lewis IA, Schommer SC, Markley JL (2009) rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magn Reson Chem 47:S123–S126

    Article  CAS  Google Scholar 

  13. Bingol K, Li DW, Bruschweiler-Li L, Cabrera OA, Megraw T, Zhang FL et al (2015) Unified and isomer-specific NMR metabolomics database for the accurate analysis of C-13-H-1 HSQC spectra. ACS Chem Biol 10(2):452–459

    Article  CAS  Google Scholar 

  14. Bingol K, Bruschweiler-Li L, Li DW, Bruschweiler R (2014) Customized metabolomics database for the analysis of NMR H-1-H-1 TOCSY and C-13-H-1 HSQC-TOCSY spectra of complex mixtures. Anal Chem 86(11):5494–5501

    Article  CAS  Google Scholar 

  15. Zheng C, Zhang SC, Ragg S, Raftery D, Vitek O (2011) Identification and quantification of metabolites in H-1 NMR spectra by Bayesian model selection. Bioinformatics 27(12):1637–1644

    Article  CAS  Google Scholar 

  16. Bingol K, Li DW, Zhang B, Bruschweiler R (2016) Comprehensive metabolite identification strategy using multiple two-dimensional NMR spectra of a complex mixture implemented in the COLMARm web server. Anal Chem 88(24):12411–12418

    Article  CAS  Google Scholar 

  17. Teng Q, Huang WL, Collette TW, Ekman DR, Tan C (2009) A direct cell quenching method for cell-culture based metabolomics. Metabolomics 5(2):199–208

    Article  CAS  Google Scholar 

  18. Sellick CA, Hansen R, Maqsood AR, Dunn WB, Stephens GM, Goodacre R et al (2009) Effective quenching processes for physiologically valid metabolite profiling of suspension cultured mammalian cells. Anal Chem 81(1):174–183

    Article  CAS  Google Scholar 

  19. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) Nmrpipe–a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6(3):277–293

    Article  CAS  Google Scholar 

  20. Helmus JJ, Jaroniec CP (2013) Nmrglue: an open source python package for the analysis of multidimensional NMR data. J Biomol NMR 55(4):355–367

    Article  CAS  Google Scholar 

  21. Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S et al (2011) The human serum metabolome. PLoS One 6(2):ARTN e16957. https://doi.org/10.1371/journal.pone.0016957

    Article  CAS  Google Scholar 

  22. Wishart DS, Lewis MJ, Morrissey JA, Flegel MD, Jeroncic K, Xiong YP et al (2008) The human cerebrospinal fluid metabolome. J Chromatogr B 871(2):164–173

    Article  CAS  Google Scholar 

  23. Dame ZT, Aziat F, Mandal R, Krishnamurthy R, Bouatra S, Borzouie S et al (2015) The human saliva metabolome. Metabolomics 11(6):1864–1883

    Article  CAS  Google Scholar 

  24. Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31(8):1325–1327

    Article  Google Scholar 

  25. Chong J, Soufan O, Li C, Caraus I, Li SZ, Bourque G et al (2018) MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Res 46(W1):W486–W494

    Article  CAS  Google Scholar 

  26. Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vazquez-Fresno R et al (2018) HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res 46(D1):D608–D617. https://doi.org/10.1093/nar/gkx1089

    Article  CAS  Google Scholar 

  27. Goldansaz SA, Guo AC, Sajed T, Steele MA, Plastow GS, Wishart DS (2017) Livestock metabolomics and the livestock metabolome: a systematic review. PLoS One 12(5):ARTN e0177675. https://doi.org/10.1371/journal.pone.0177675

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

    Matthias Lipfert, Manoj Kumar Rout, Mark Berjanskii & David S. Wishart

  2. Department of Computing Science, University of Alberta, Edmonton, AB, Canada

    David S. Wishart

Authors
  1. Matthias Lipfert
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  2. Manoj Kumar Rout
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  3. Mark Berjanskii
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  4. David S. Wishart
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Corresponding author

Correspondence to David S. Wishart .

Editor information

Editors and Affiliations

  1. Northwest Metabolomics Research Center, Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA

    G. A. Nagana Gowda

  2. Northwest Metabolomics Research Center, Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Fred Hutch Cancer Research Center, Seattle, WA, USA

    Daniel Raftery

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Lipfert, M., Rout, M.K., Berjanskii, M., Wishart, D.S. (2019). Automated Tools for the Analysis of 1D-NMR and 2D-NMR Spectra. In: Gowda, G., Raftery, D. (eds) NMR-Based Metabolomics. Methods in Molecular Biology, vol 2037. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9690-2_24

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  • DOI: https://doi.org/10.1007/978-1-4939-9690-2_24

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9689-6

  • Online ISBN: 978-1-4939-9690-2

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