1H NMR-based metabolomics methods for chemical genomics experiments

Methods in Molecular Biology

Volumn 1056, Issue , 2014, Pages 225-239

  Orr, Daniel J ^a   Barding Jr , Gregory A ^a   Tolley, Christiana E ^a   Hicks, Glenn R ^a   Raikhel, Natasha V ^a   Larive, Cynthia K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chemical genomics; Metabolic profiling; Metabolomics; NMR spectroscopy; Normalization; Sample preparation; Sortin1; Tissue extraction

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; GENOMICS; METABOLOMICS; NONHUMAN; PLANT GENOME; PLANT METABOLISM; PLANT TISSUE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SEEDLING; UNIVARIATE ANALYSIS; ANALYTIC METHOD; INTERMETHOD COMPARISON; METABOLITE; MULTIVARIATE ANALYSIS; ARABIDOPSIS; DRUG EFFECT; GENETICS; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRINCIPAL COMPONENT ANALYSIS; PROTEIN TRANSPORT; STATISTICAL ANALYSIS;

TISSUE EXTRACT; ARABIDOPSIS PROTEIN; INDENE DERIVATIVE; PYRIDINE DERIVATIVE; SORTIN1 COMPOUND;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DATA INTERPRETATION, STATISTICAL; GENOME, PLANT; GENOMICS; INDENES; MAGNETIC RESONANCE SPECTROSCOPY; METABOLOMICS; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN TRANSPORT; PYRIDINES; SEEDLING;

EID: 84892853974     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-592-7_21     Document Type: Article

References (37)

1. Nicholson JK, Lindon JC, Holmes E (1999) 'Metabonomics': Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29:1181-1189
2. Fiehn O (2002) Metabolomics-The link between genotypes and phenotypes. Plant Mol Biol 48: 155-171
3. Robertson DG (2005) Metabonomics in toxicology: A review. Toxicol Sci 85:809-822
4. Robertson DG, Watkins PB, Reily MD (2011) Metabolomics in toxicology: Preclinical and clinical applications. Toxicol Sci 120: S146-S170
5. Zouhar J, Hicks GR, Raikhel NV (2004) Sorting inhibitors (Sortins): Chemical compounds to study vacuolar sorting in Arabidopsis. Proc Natl Acad Sci U S A 101:9497-9501
6. Fiehn O (2008) Extending the breadth of metabolite profi ling by gas chromatography coupled to mass spectrometry. Trends Analyt Chem 27:261-269
7. Koek MM, Jellema RH, van der Greef J, Tas AC, Hankemeier T (2011) Quantitative metabolomics based on gas chromatography mass spectrometry: Status and perspectives. Metabolomics 7:307-328
8. Lei Z, Huhman DV, Sumner LW (2011) Mass spectrometry strategies in metabolomics. J Biol Chem 286:25435-25442
9. Scalbert A, Brennan L, Fiehn O, Hankemeier T, Kristal BS, van Ommen B, Pujos-Guillot E, Verheij E, Wishart D, Wopereis S (2009) Massspectrometry-based metabolomics: Limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics 5:435-458
10. Keun HC, Ebbels TMD, Antti H, Bollard ME, Beckonert O, Schlotterbeck G, Senn H, Niederhauser U, Holmes E, Lindon JC, Nicholson JK (2002) Analytical reproducibility in H-1 NMR-based metabonomic urinalysis. Chem Res Toxicol 15:1380-1386
11. Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, Fan TWM, Fiehn O, Goodacre R, Griffi n JL, Hankemeier T, Hardy N, Harnly J, Higashi R, Kopka J, Lane AN, Lindon JC, Marriott P, Nicholls AW, Reily MD, Thaden JJ, Viant MR (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3:211-221
12. Sanderfoot AA, Pilgrim M, Adam L, Raikhel NV (2001) Disruption of individual members of Arabidopsis syntaxin gene families indicates each has essential functions. Plant Cell 13:659-666
13. Lukowitz W, Mayer U, Jurgens G (1996) Cytokinesis in the Arabidopsis embryo involves the syntaxin-related KNOLLE gene product. Cell 84:61-71
14. Rojo E, Gillmor CS, Kovaleva V, Somerville CR, Raikhel NV (2001) VACUOLELESS1 is an essential gene required for vacuole formation and morphogenesis in Arabidopsis. Dev Cell 1:303-310
15. Rosado A, Hicks GR, Norambuena L, Rogachev I, Meir S, Pourcel L, Zouhar J, Brown MQ, Boirsdore MP, Puckrin RS, Cutler SR, Rojo E, Aharoni A, Raikhel NV (2011) Sortin1-hypersensitive mutants link vacuolartrafficking defects and fl avonoid metabolism in Arabidopsis vegetative tissues. Chem Biol 18:187-197
16. Lee DY, Fiehn O (2008) High quality metabolomic data for Chlamydomonas reinhardtii . Plant Methods 4:13
17. Kaiser KA, Barding GA, Larive CK (2009) A comparison of metabolite extraction strategies for H-1-NMR-based metabolic profi ling using mature leaf tissue from the model plant Arabidopsis thaliana . Magn Reson Chem 47: S147-S156
18. Sekiyama Y, Chikayama E, Kikuchi J (2011) Evaluation of a semipolar solvent system as a step toward heteronuclear multidimensional NMR-based metabolomics for C-13-labelled bacteria, plants, and animals. Anal Chem 83: 719-726
19. Davis RA, Charlton AJ, Godward J, Jones SA, Harrison M, Wilson JC (2007) Adaptive binning: An improved binning method for metabolomics data using the undecimated wavelet transform. Chemometr Intell Lab Syst 85: 144-154
20. Holmes E, Foxall PJD, Nicholson JK, Neild GH, Brown SM, Beddell CR, Sweatman BC, Rahr E, Lindon JC, Spraul M, Neidig P (1994) Automatic data reduction and pattern recognition methods for analysis of H-1 nuclear magnetic resonance spectra of human urine from normal and pathological states. Anal Biochem 220:284-296
21. Craig A, Cloareo O, Holmes E, Nicholson JK, Lindon JC (2006) Scaling and normalization effects in NMR spectroscopic metabonomic data sets. Anal Chem 78:2262-2267
22. De Meyer T, Sinnaeve D, Van Gasse B, Tsiporkova E, Rietzschel ER, De Buyzere ML, Gillebert TC, Bekaert S, Martins JC, Van Criekinge W (2008) NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm. Anal Chem 80:3783-3790
23. Dieterle F, Ross A, Schlotterbeck G, Senn H (2006) Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in H-1 NMR metabonomics. Anal Chem 78: 4281-4290
24. Anderson PE, Mahle DA, Doom TE, Reo NV, DelRaso NJ, Raymer ML (2011) Dynamic adaptive binning: An improved quantifi cation technique for NMR spectroscopic data. Metabolomics 7:179-190
25. Broadhurst DI, Kell DB (2006) Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics 2:171-196
26. Kaiser KA, Merrywell CE, Fang F, Larive CK (2008) In: Holzgrabe U, Wawer I, Diehl B (eds) NMR spectroscopy in pharmaceutical analysis. Elsevier, Oxford, pp 233-267
27. Barding GA Jr, Salditos R, Larive CK (2012) Quantitative NMR for bioanalysis and metabolomics. Anal. Bioanal. Chem. 404:1165-1179
28. Fiehn O, Kopka J, Trethewey R, Willmitzer L (2000) Identifi cation of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadruple mass spectrometry. Anal Chem 72:3573-3580
29. Glasoe PK, Long FA (1960) Use of glass electrodes to measure acidities in deuterium oxide. J Phys Chem 64:188-190
30. Larive CK, Jayawickrama D, Orfi L (1997) Quantitative analysis of peptides with NMR spectroscopy. Appl Spectrosc 51:1531-1536
31. Smallcombe SH, Patt SL, Keifer PA (1995) WET solvent suppression and its applications to LC NMR and high-resolution NMR spectroscopy. J Magn Reson A 117:295-303
32. Liu ML, Mao XA, Ye CH, Huang H, Nicholson JK, Lindon JC (1998) Improved WATERGATE pulse sequences for solvent suppression in NMR spectroscopy. J Magn Reson 132: 125-129
33. Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL (2008) Metabolite identifi cation via the Madison Metabolomics Consortium Database. Nat Biotechnol 26:162-164
34. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I (2009) HMDB: A knowledgebase for the human metabolome. Nucleic Acids Res 37:D603-D610
35. Braunschweiler L, Ernst RR (1983) Coherence transfer by isotropic mixing: Application to proton correlation spectroscopy. J Magn Reson 53:521-528
36. Bodenhausen G, Ruben DJ (1980) Natural abundance N-15 NMR by enhanced heteronuclear spectroscopy. Chem Phys Lett 69: 185-189
37. Cobas C, Seoane F, Dominguez S, Sykora S, Davies A (2011) A new approach to improving automated analysis of proton NMR spectra through Global Spectral Deconvolution 8GSD. Spectrosc Eur 23:26-30