Abstract
Nuclear magnetic resonance (NMR) is one of the main tools applied in the field of metabolomics. Extracting all the valuable information from large datasets of \(^1\)H-NMR spectra is a huge challenge for high throughput metabolomics analysis. The tools that currently exist to improve signal assignment and metabolite quantification do not have the versatility of allowing the quantification of unknown signals or choosing different quantification approaches in the same analysis. Moreover, graphical features and informative outputs are needed in order to be aware of the reliability of the final results in a field where position shifting, baseline masking and signal overlap may produce errors between samples. Here we present a software package called Dolphin 1D, which aim is to improve targeted metabolite analysis in large datasets of \(^1\)H-NMR by combining user interactivity with automatic algorithms. Its performance has been tested on a multi-matrix set composed by total serum, urine, liver aqueous extracts and brain aqueous extracts of rat. Our strategy pretends to offer a useful solution for every kind of matrix, avoiding black-box processes and subjectivities user-user in automatic signal quantification.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Nicholson, J.K., Lindon, J.C., Holmes, E.: ‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica Fate Foreign Compd. Biol. Syst. 29(11), 1181–1189 (1999)
Chen, H.W., Pan, Z.Z., Talaty, N., Raftery, D., Cooks, R.G.: Combining desorption electrospray ionization mass spectrometry and nuclear magnetic resonance for differential metabolomics without sample preparation. Rapid Commun. Mass Spectrom. 20, 1577–1584 (2006)
Beckonert, O., Keun, H.C., Ebbels, T.M.D., Bundy, J.G., Holmes, E., Lindon, J.C., Nicholson, J.K.: Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat. Protoc. 2, 2692–2703 (2007)
Alves, A.C., Rantalainen, M., Holmes, E., Nicholson, J.K., Ebbels, T.M.D.: Analytic properties of statistical total correlation spectroscopy based information recovery in H-1 NMR metabolic data sets. Anal. Chem. 81, 2075–2084 (2009)
Anderson, P.E., Reo, N.V., DelRaso, N.J., Doom, T.E., Raymer, M.L.: Gaussian binning: a new kernel-based method for processing NMR spectroscopic data for metabolomics. Metabolomics 4, 261–272 (2008)
Jacob, D., Deborde, C., Moing, A.: An efficient spectra processing method for metabolite identification from H-1-NMR metabolomics data. Anal. Bioanal. Chem. 405, 5049–5061 (2013)
Eads, C.D., Furnish, C.M., Noda, I., Juhlin, K.D., Cooper, D.A., Morrall, S.W.: Molecular factor analysis applied to collections of NMR spectra. Anal. Chem. 76, 1982–1990 (2004)
Ochs, M.F., Stoyanova, R.S., Arias-Mendoza, F., Brown, T.R.: A new method for spectral decomposition using a bilinear Bayesian approach. J. Magn. Reson. 137, 161–176 (1999)
Stoyanova, R., Nicholson, J.K., Lindon, J.C., Brown, T.R.: Sample classification based on Bayesian spectral decomposition of metabonomic NMR data sets. Anal. Chem. 76, 3666–3674 (2004)
Hao, J., Astle, W., De Iorio, M., Ebbels, T.M.D.: BATMAN - an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model. Bioinformatics 28, 2088–2090 (2012)
Hao, J., Liebeke, M., Astle, W., De Iorio, M., Bundy, J.G., Ebbels, T.M.D.: Bayesian deconvolution and quantification of metabolites in complex 1d NMR spectra using BATMAN. Nat. Protoc. 9, 1416–1427 (2014)
Laatikainen, R., Niemitz, M., Malaisse, W.J., Biesemans, M., Willem, R.: A computational strategy for the deconvolution of NMR spectra with multiplet structures and constraints: Analysis of overlapping C-13-H-2 multiplets of C-13 enriched metabolites from cell suspensions incubated in deuterated media. Magn. Reson. Med. 36, 359–365 (1996)
Soininen, P., Haarala, J., Vepsalainen, J., Niemitz, M., Laatikainen, R.: Strategies for organic impurity quantification by H-1 NMR spectroscopy: constrained total-line-shape fitting. Anal. Chimica Acta 542, 178–185 (2005)
Vinaixa, M., Rodriguez, M.A., Rull, A., Beltran, R., Blade, C., Brezmes, J., Canellas, N., Joven, J., Correig, X.: Metabolomic assessment of the effect of dietary cholesterol in the progressive development of fatty liver disease. J. Proteome Res. 9, 2527–2538 (2010)
Domange, C., Canlet, C., Traore, A., Bielicki, G., Keller, C., Paris, A., Priymenko, N.: Orthologous metabonomic qualification of a rodent model combined with magnetic resonance imaging for an integrated evaluation of the toxicity of hypochoeris radicata. Chem. Res. Toxicol. 21, 2082–2096 (2008)
Cohen, S.M., Ohnishi, T., Clark, N.M., He, J., Arnold, L.L.: Investigations of rodent urinary bladder carcinogens: collection, processing, and evaluation of urine and bladders. Toxicol. Pathol. 35, 337–347 (2007)
Wishart, D.S., Jewison, T., Guo, A.C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E., Bouatra, S., Sinelnikov, I., Arndt, D., Xia, J., Liu, P., Yallou, F., Bjorndahl, T., Perez-Pineiro, R., Eisner, R., Allen, F., Neveu, V., Greiner, R., Scalbert, A.: HMDB 3.0-the human metabolome database in 2013. Nucleic Acids Res. 41, D801–D807 (2013)
Ludwig, C., Easton, J.M., Lodi, A., Tiziani, S., Manzoor, S.E., Southam, A.D., Byrne, J.J., Bishop, L.M., He, S., Arvanitis, T.N., Guenther, U.L., Viant, M.R.: Birmingham metabolite library: a publicly accessible database of 1-D H-1 and 2-D H-1 J-resolved NMR spectra of authentic metabolite standards (BML-NMR). Metabolomics 8, 8–18 (2012)
Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C.F., Tolmie, D.E., Wenger, R.K., Yao, H., Markley, J.L.: BioMagResBank. Nucleic Acids Res. 36, D402–D408 (2008)
Gomez, J., Brezmes, J., Mallol, R., Rodriguez, M.A., Vinaixa, M., Salek, R.M., Correig, X., Canellas, N.: Dolphin: a tool for automatic targeted metabolite profiling using 1d and 2d H-1-NMR data. Anal. Bioanal. Chem. 406, 7967–7976
Serkova, N., Fuller, T.F., Klawitter, J., Freise, C.E., Niemann, C.U.: H-1-NMR-based metabolic signatures of mild and severe ischemia/reperfusion injury in rat kidney transplants. Kidney International 67(3), 1142–1151 WOS:000227013500037 (2005)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Gómez, J., Vinaixa, M., Rodríguez, M.A., Salek, R.M., Correig, X., Cañellas, N. (2015). Dolphin 1D: Improving Automation of Targeted Metabolomics in Multi-matrix Datasets of \(^1\)H-NMR Spectra. In: Overbeek, R., Rocha, M., Fdez-Riverola, F., De Paz, J. (eds) 9th International Conference on Practical Applications of Computational Biology and Bioinformatics. Advances in Intelligent Systems and Computing, vol 375. Springer, Cham. https://doi.org/10.1007/978-3-319-19776-0_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-19776-0_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19775-3
Online ISBN: 978-3-319-19776-0
eBook Packages: EngineeringEngineering (R0)