Evaluation of metabolite extraction strategies from tissue samples using NMR metabolomics

Bligh E.G., Dyer W.J. (1959) A rapid method for total lipid extraction and purification. Can. J. Biochem. Physiol. 37:911–917

Bouchereau A., Guenot P., Larher F. (2000) Analysis of amines in plant materials. J. Chromatogr. B Biomed. Sci. Appl. 29:49–67

Bundy J.G., Spurgeon D.J., Svendsen C., Hankard P.K., Weeks J.M., Osborn D., Lindon J.C., Nicholson J.K. (2004) Environmental metabonomics: applying combination biomarker analysis in earthworms at a metal contaminated site. Ecotoxicology 13:797–806

Castrillo J.I., Hayes A., Mohammed S., Gaskell S.J., Oliver S.G. (2003) An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62:929–937

Choi Y.H., Tapias E.C., Kim H.K., Lefeber A.W., Erkelens C., Verhoeven J.T., Brzin J., Zel J., Verpoorte R. (2004) Metabolic discrimination of Catharanthus roseus leaves infected by phytoplasma using 1H NMR spectroscopy and multivariate data analysis. Plant Physiol. 135:2398–2410

Cloarec O., Dumas M.E., Trygg J., Craig A., Barton R.H., Lindon J.C., Nicholson J.K., Holmes E. (2005) Evaluation of the orthogonal projection on latent structure model limitations caused by chemical shift variability and improved visualization of biomarker changes in 1H NMR spectroscopic metabonomic studies. Anal. Chem. 77:517–526

Coen M., Lenz E.M., Nicholson J.K., Wilson I.D., Pognan F., Lindon J.C. (2003) An Integrated Metabonomic Investigation of Acetaminophen Toxicity in the Mouse Using NMR Spectroscopy. Chem. Res. Toxicol. 16:295–303

Defernez M., Colquhoun I.J. (2003) Factors affecting the robustness of metabolite fingerprinting using 1H NMR spectra. Phytochemistry 62:1009–1017

Fan T. (1996) Metabolite profiling by one and two dimensional NMR analysis of complex mixtures. Prog. Nucl. Magn. Reson. 28:161–219

Garrod S., Humpher E., Connor S.C., Connelly J.C., Spraul M., Nicholson J.K., Holmes E. (2001) High-resolution 1H NMR and magic angle spinning NMR spectroscopic investigation of the biochemical effects of 2-bromoethanamine in intact renal and hepatic tissue. Magn. Reson. Med. 45:781–790

Gullberg J., Jonsson P., Nordstrom A., Sjostrom M., Moritz T. (2004) Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal. Biochem. 331:283–295

Heijne W.H., Lamers R.J., van Bladeren P.J., Groten J.P., van Nesselrooij J.H., van Ommen B. (2005) Profiles of metabolites and gene expression in rats with chemically induced hepatic necrosis. Toxicol. Pathol. 33:425–433

Holmes E., Nicholls A.W., Lindon J.C., Connor S.C., Connelly J.C., Haselden J.N., Damment S.J., Spraul M., Neidig P., Nicholson J.K. (2000) Chemometric models for toxicity classification based on NMR spectra of biofluids. Chem. Res. Toxicol. 13:471–478

Kim H.K., Choi Y.H., Luijendijk T.J., Rocha R.A., Verpoorte R. (2004) Comparison of extraction methods for secologanin and the quantitative analysis of secologanin from Symphoricarpos albus using 1H NMR. Phytochem. Anal. 15:257–261

Le Belle J.E., Harris N.G., Williams S.R., Bhakoo K.K. (2002) A comparison of cell and tissue extraction techniques using high-resolution 1H-NMR spectroscopy. NMR Biomed. 15:37–44

Pears M.R., Cooper J.D., Mitchison H.M., Mortishire-Smith R.J., Pearce D.A., Griffin J.L. (2005) High resolution 1H NMR-based metabolomics indicates a neurotransmitter cycling deficit in cerebral tissue from a mouse model of Batten disease. J. Biol. Chem. 280:42508–42514

Purohit P.V., Rocke D.M., Viant M.R., Woodruff D.L. (2004) Discrimination models using variance-stabilizing transformation of metabolomic NMR data. OMICS 8:118–130

Rosenblum E.S., Viant M.R., Braid B.M., Moore J.D., Friedman C.S., Tjeerdema R.S. (2005) Characterizing the metabolic actions of natural stresses in the California red abalone Haliotis rufescens using 1H NMR metabolomics. Metabolomics 1:199–209

Stentiford G.D., Viant M.R., Ward D.G., Johnson P.J., Martin A., Wenbin W., Cooper H.J., Lyons B.P., Feist S.W. (2005) Liver tumors in wild flatfish: a histopathological proteomic and metabolomic study. OMICS 9:281–299

Viant M.R. (2003) Improved methods for the acquisition and interpretation of NMR metabolomic data. Biochem. Biophys. Res. Commun. 24:943–948

Viant M.R., Rosenblum E.S., Tjeerdema R.S. (2003a) NMR-based metabolomics: a powerful approach for characterizing the effects of environmental stressors on organism health. Environ. Sci. Technol. 37:4982–4989

Viant M.R., Werner I., Rosenblum E.S., Gantner A.S., Tjeerdema R.S., Johnson M.L. (2003b) Correlation between heat-shock protein induction and reduced metabolic condition in juvenile steelhead trout (Oncorhynchus mykiss) chronically exposed to elevated temperature. Fish Physiol. Biochem. 29:159–171

Viant M.R., Lyeth B.G., Miller M.G., Berman R.F. (2005a) An NMR metabolomic investigation of early metabolic disturbances following traumatic brain injury in a mammalian model. NMR Biomed. 18:507–516

Viant M.R., Bundy J.G., Pincetich C.A., de Ropp J.S., Tjeerdema R.S. (2005b) NMR-derived developmental metabolic trajectories: an approach for visualizing the toxic actions of trichloroethylene during embryogenesis. Metabolomics 1:149–158

Want E.J., O’Maille G., Smith C.A., Brandon T.R., Uritboonthai W., Qin C., Trauger S.A., Siuzdak G. (2006) Solvent-dependent metabolite distribution clustering and protein extraction for serum profiling with mass spectrometry. Anal. Chem. 78:743–752

Warne M.A., Lenz E.M., Osborn D., Weeks J.M., Nicholson J.K. (2001) Comparative biochemistry and short-term starvation effects on the earthworms Eisenia veneta and Lumbricus terrestris studied by 1H NMR spectroscopy and pattern recognition. Soil Biol. Biochem. 33:1171–1180