Cross-platform analysis of longitudinal data in metabolomics

Molecular BioSystems

Volumn 7, Issue 12, 2011, Pages 3214-3222

  Nevedomskaya, Ekaterina ^a   Mayboroda, Oleg A ^a   Deelder, André M ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; FEMALE; HUMAN; LONGITUDINAL STUDY; MALE; MASS SPECTROMETRY; METABOLOME; METABOLOMICS; METHODOLOGY; MIDDLE AGED; NUCLEAR MAGNETIC RESONANCE IMAGING; NUTRITIONAL STATUS; PRINCIPAL COMPONENT ANALYSIS; URINALYSIS;

ADULT; FEMALE; HUMANS; LONGITUDINAL STUDIES; MAGNETIC RESONANCE IMAGING; MALE; MASS SPECTROMETRY; METABOLOME; METABOLOMICS; MIDDLE AGED; NUTRITIONAL STATUS; PRINCIPAL COMPONENT ANALYSIS; URINALYSIS;

EID: 80755125363     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c1mb05280b     Document Type: Article

References (44)

1. J. C. Lindon E. Holmes M. E. Bollard E. G. Stanley J. K. Nicholson Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis Biomarkers 2004 9 1 1 31 (Pubitemid 38660013)
2. J. K. Nicholson J. Connelly J. C. Lindon E. Holmes Metabonomics: a platform for studying drug toxicity and gene function Nat. Rev. Drug Discovery 2002 1 2 153 161 (Pubitemid 41646523)
3. B. R. Underwood D. Broadhurst W. B. Dunn D. I. Ellis A. W. Michell C. Vacher D. E. Mosedale D. B. Kell R. A. Barker D. J. Grainger D. C. Rubinsztein Huntington disease patients and transgenic mice have similar pro-catabolic serum metabolite profiles Brain 2006 129 Pt 4 877 886
4. M. Bogdanov W. R. Matson L. Wang T. Matson R. Saunders-Pullman S. S. Bressman B. M. Flint Metabolomic profiling to develop blood biomarkers for Parkinson's disease Brain 2008 131 Pt 2 389 396 (Pubitemid 351197614)
5. I. L. Simone F. Federico M. Trojano C. Tortorella M. Liguori P. Giannini E. Picciola G. Natile P. Livrea High resolution proton MR spectroscopy of cerebrospinal fluid in MS patients. Comparison with biochemical changes in demyelinating plaques J. Neurol. Sci. 1996 144 1-2 182 190 (Pubitemid 27019176)
6. C. M. Slupsky H. Steed T. H. Wells K. Dabbs A. Schepansky V. Capstick W. Faught M. B. Sawyer Urine metabolite analysis offers potential early diagnosis of ovarian and breast cancers Clin. Cancer Res. 2010 16 23 5835 5841
7. S. Nishiumi M. Shinohara A. Ikeda T. Yoshie N. Hatano S. Kakuyama S. Mizuno T. Sanuki H. Kutsumi E. Fukusaki T. Azuma T. Takenawa M. Yoshida Serum metabolomics as a novel diagnostic approach for pancreatic cancer Metabolomics 2010 6 4 518 528
8. H. Wang V. K. Tso C. M. Slupsky R. N. Fedorak Metabolomics and detection of colorectal cancer in humans: a systematic review Future Oncol. 2010 6 9 1395 1406
9. I. Barba G. de Leon E. Martin A. Cuevas S. Aguade J. Candell-Riera J. A. Barrabes D. Garcia-Dorado Nuclear magnetic resonance-based metabolomics predicts exercise-induced ischemia in patients with suspected coronary artery disease Magn. Reson. Med. 2008 60 1 27 32 (Pubitemid 351956606)
10. E. Holmes R. L. Loo J. Stamler M. Bictash I. K. Yap Q. Chan T. Ebbels M. de Iorio I. J. Brown K. A. Veselkov M. L. Daviglus H. Kesteloot H. Ueshima L. Zhao J. K. Nicholson P. Elliott Human metabolic phenotype diversity and its association with diet and blood pressure Nature 2008 453 7193 396 400 (Pubitemid 351693125)
11. C. M. Slupsky K. N. Rankin J. Wagner H. Fu D. Chang A. M. Weljie E. J. Saude B. Lix D. J. Adamko S. Shah R. Greiner B. D. Sykes T. J. Marrie Investigations of the effects of gender, diurnal variation, and age in human urinary metabolomic profiles Anal. Chem. 2007 79 18 6995 7004 (Pubitemid 47438678)
12. M. K. Friswell H. Gika I. J. Stratford G. Theodoridis B. Telfer I. D. Wilson A. J. Mcbain Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice PLoS One 2010 5 1
13. F. P. Martin N. Sprenger I. Montoliu S. Rezzi S. Kochhar J. K. Nicholson Dietary modulation of gut functional ecology studied by fecal metabonomics J. Proteome Res. 2010 9 10 5284 5295
14. A. N. Phipps J. Stewart B. Wright I. D. Wilson Effect of diet on the urinary excretion of hippuric acid and other dietary-derived aromatics in rat. A complex interaction between diet, gut microflora and substrate specificity Xenobiotica 1998 28 5 527 537 (Pubitemid 28238263)
15. S. Rezzi F. P. Martin C. Alonso M. Guilarte M. Vicario L. Ramos C. Martinez B. Lobo E. Saperas J. R. Malagelada J. Santos S. Kochhar Metabotyping of Biofluids Reveals Stress-Based Differences in Gut Permeability in Healthy Individuals J. Proteome Res. 2009 8 10 4799 4809
16. H. C. Keun T. M. D. Ebbels M. E. Bollard O. Beckonert H. Antti E. Holmes J. C. Lindon J. K. Nicholson Geometric trajectory analysis of metabolic responses to toxicity can define treatment specific profiles Chem. Res. Toxicol. 2004 17 5 579 587 (Pubitemid 38669514)
17. E. J. van Velzen J. A. Westerhuis J. P. van Duynhoven F. A. van Dorsten C. H. Grun D. M. Jacobs G. S. Duchateau D. J. Vis A. K. Smilde Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites J. Proteome Res. 2009 8 7 3317 3330
18. M. Wallace Y. Z. H. Y. Hashim M. Wingfield M. Culliton F. McAuliffe M. J. Gibney L. Brennan Effects of menstrual cycle phase on metabolomic profiles in premenopausal women Hum. Reprod. 2010 25 4 949 956
19. A. K. Smilde J. A. Westerhuis H. C. J. Hoefsloot S. Bijlsma C. M. Rubingh D. J. Vis R. H. Jellema H. Pijl F. Roelfsema J. van der Greef Dynamic metabolomic data analysis: a tutorial review Metabolomics 2010 6 1 3 17
20. J. A. Westerhuis E. J. J. van Velzen H. C. J. Hoefsloot A. K. Smilde Multivariate paired data analysis: multilevel PLSDA versus OPLSDA Metabolomics 2010 6 1 119 128
21. J. J. Jansen H. C. J. Hoefsloot J. van der Greef M. E. Timmerman A. K. Smilde Multilevel component analysis of time-resolved metabolic fingerprinting data Anal. Chim. Acta 2005 530 2 173 183 (Pubitemid 40215740)
22. M. Assfalg I. Bertini D. Colangiuli C. Luchinat H. Schafer B. Schutz M. Spraul Evidence of different metabolic phenotypes in humans Proc. Natl. Acad. Sci. U. S. A. 2008 105 5 1420 1424 (Pubitemid 351346527)
23. M. Turk A. Pentland Eigenfaces for Recognition J. Cognit. Neurosci. 1991 3 1 71 86
24. J. van der Greef P. Stroobant R. van der Heijden The role of analytical sciences in medical systems biology Curr. Opin. Chem. Biol. 2004 8 5 559 565 (Pubitemid 39278355)
25. J. van der Greef A. Smilde Symbiosis of chemometrics and metabolomics: past, present, and future J. Chemom. 2005 19 5-7 376 386
26. A. K. Smilde M. J. van der Werf S. Bijlsma B. J. C. van der Werff-van-der Vat R. H. Jellema Fusion of mass spectrometry-based metabolomics data Anal. Chem. 2005 77 20 6729 6736 (Pubitemid 41504459)
27. A. V. Diez-Roux Multilevel analysis in public health research Annu. Rev. Public Health 2000 21 171 192 (Pubitemid 30480321)
28. A. D. Weston L. Hood Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine J. Proteome Res. 2004 3 2 179 196 (Pubitemid 38500984)
29. L. K. Schnackenberg J. Kaput R. D. Beger Metabolomics: a tool for personalizing medicine? Pers. Med. 2008 5 5 495 504
30. R. Elliott C. Pico Y. Dommels I. Wybranska J. Hesketh J. Keijer Nutrigenomic approaches for benefit-risk analysis of foods and food components: defining markers of health Br. J. Nutr. 2007 98 6 1095 1100 (Pubitemid 350193775)
31. E. Holmes H. Antti Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological NMR spectra Analyst 2002 127 12 1549 1557 (Pubitemid 36020854)
32. J. van der Greef T. Hankemeier R. N. McBurney Metabolomics-based systems biology and personalized medicine: moving towards n = 1 clinical trials? Pharmacogenomics 2006 7 7 1087 1094 (Pubitemid 44644787)
33. P. Bernini I. Bertini C. Luchinat S. Nepi E. Saccenti H. Schafer B. Schutz M. Spraul L. Tenori Individual Human Phenotypes in Metabolic Space and Time J. Proteome Res. 2009 8 9 4264 4271
34. J. C. Lindon J. K. Nicholson Analytical technologies for metabonomics and metabolomics, and multi-omic information recovery TrAC, Trends Anal. Chem. 2008 27 3 194 204 (Pubitemid 351436617)
35. J. M. Johnson T. W. Yu F. H. Strobel D. P. Jones A practical approach to detect unique metabolic patterns for personalized medicine Analyst 2010 135 11 2864 2870
36. J. C. Lindon J. K. Nicholson Spectroscopic and Statistical Techniques for Information Recovery in Metabonomics and Metabolomics Annu. Rev. Anal. Chem. 2008 1 45 69
37. D. G. Robertson Metabonomics in toxicology: a review Toxicol. Sci. 2005 85 2 809 822 (Pubitemid 40846857)
38. W. B. Dunn D. I. Broadhurst H. J. Atherton R. Goodacre J. L. Griffin Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy Chem. Soc. Rev. 2011 40 1 387 426
39. E. J. Want I. D. Wilson H. Gika G. Theodoridis R. S. Plumb J. Shockcor E. Holmes J. K. Nicholson Global metabolic profiling procedures for urine using UPLC-MS Nat. Protocols 2010 5 6 1005 1018
40. 1H-NMR thermometer suitable for cryoprobes Magn. Reson. Chem. 2007 45 2 175 178
41. A. Kumar R. R. Ernst K. Wuthrich A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules Biochem. Biophys. Res. Commun. 1980 95 1 1 6
42. 1H NMR metabonomics Anal. Chem. 2006 78 13 4281 4290
43. C. A. Smith E. J. Want G. O'Maille R. Abagyan G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal. Chem. 2006 78 3 779 787 (Pubitemid 43228585)
44. H. Wold, Estimation of principal components and related models by iterative least squares, in Multivariate Analysis, ed., P. R. Krishnaiah, Academic Press, New York, 1966, pp. 391-420