New modes of data partitioning based on PARS peak alignment for improved multivariate biomarker/biopattern detection in 1H-NMR spectroscopic metabolic profiling of urine

Metabolomics

Volumn 2, Issue 1, 2006, Pages 1-19

  Torgrip, Ralf J O ^a,b   Lindberg, J ^b   Linder, M ^b   Karlberg, B ^a   Jacobsson, S P ^a,b   Kolmert, J ^b   Gustafsson, I ^b   Schuppe Koistinen, I ^b  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b ASTRAZENECA R AND D   (Sweden)

Author keywords

1H NMR; Biofluid; Hepatic steatosis; Metabolic profiling; Multivariate; Peak alignment; Urine

Indexed keywords

EID: 33744941560     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-005-0013-z     Document Type: Article

References (25)

1. Andersson P.M., Sjöström M., Lundstedt T. (1998). Preprocessing peptide sequences for multivariate sequence-property analysis. Chemom. Intell. Lab. Syst. 42:41-50
2. 1H-NMR Spectroscopy of Urine and Pattern Recognition. Anal. Biochem. 195:194-202
3. Bro, R. (1997). PARAFAC. Tutorial and applications. Chemom. Intell. Lab. Syst. 149-171
4. Brown T.R. and Stoyanova R. (1996) NMR spectral quantitation by principal-component analysis. II. Determination of frequency and phase shifts. J. Magn. Reson. B. 112: 32-43
5. Cloarec O., Dumas M.E., Trygg J., Craig A., Barton R.H., Lindon J.C., Nicholson J.K. and 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
6. Connor S., Wu W., Sweatman B., Manini J., Haselden J., Crowther D. and Waterfield C. (2004) Effects of feeding and body weight loss on the 1H-NMR based urine metabolic profiles of male Wistar Han rats: implications for biomarker discovery. Biomarkers 9: 156-179
7. Dyrby M., Baunsgaard D., Bro R. and Engelsen S.B. (2005) Multiway chemometric analysis of the metabolic response to toxins monitored by NMR. Chemom. Intell. Lab. Syst. 76:79-89
8. Ebbels, T., David, M., Holmes, E., Lindon, J.C. and Nicholson, J.K. (2002). Methods for spectral analysis and their applications: Spectral replacement., Patent: WO 2002052293, A1 20020704
9. Farber E. (1967) Ethionine fatty liver. Adv. Lipid Res. 5: 119-183
10. Forshed, J., Torgrip, R.J.O., Åberg K.M., Karlberg B., Lindberg J. and Jacobsson S.P. (2005) A comparison of methods for alignment of NMR peaks in the context of cluster analysis. J. Pharm. Biomed. Anal. 38:824-832
11. Glaser G. and Mager J. (1974). Biochemical studies on the mechanism of action of liver poisons. III Depletion of glutathione and ethionine poisoning. Biochem. Biophys. Acta 237-244
12. Golub G.H. and van Loan C.F. (1989) Matrix Computations, 2 edn. The Johns Hopkins University Press, London
13. Harshman, R.A. (1970). Foundations of the PARAFAC procedure: Model and conditions for an "exploratory" multi mode factor analysis. UCLA Working Papers in phonetics 1-84
14. Holmes E., Nicholson J.K., Nicholls A.W., Lindon J.C., Connor S.C., Polley S. and Connelly J. (1998) The identification of novel biomarkers of renal toxicity using automatic data reduction techniques and PCA of proton NMR spectra of urine. Chemom. Intell. Lab. Syst. 44:245-255
15. Hotelling, H. (1933). Analysis of a complex of statistical variables into principal components. J. Educ. Psychol. 417-520
16. Jackson J.E. (1991) A users guide to principal components. Wiley, New York
17. Karstang T.V. and Manne R. (1992) Optimized scaling. A novel approach to linear calibration with closed data sets. Chemom. Intell. Lab. Syst. 14: 165-173
18. Keun H.C., Ebbels T.M.D., Henrik A., Bollard M.E., Beckonert O., Holmes E., Lindon J.C. and Nicholson J.K. (2003) Improved analysis of multivariate data by variable stability scaling: Application to NMR-based metabolic profiling. Anal. Chim. Acta 490: 265-276
19. Matlab (2002). The MathWorks, Inc. 3 Apple Hill Drive, Natick, MA, 01760-2098, USA. Ver. 6.5.0.180913a (R13)
20. Pearson, K. (1901). On lines and planes of closest fit to systems of points in space. Philos. Mag. 559-572
21. Siuda R., Balcerowska G. and Aberdam D. (1998) Spurious principal components in the set of spectra subjected to disturbances: I. Presentation of the problem. Chemom. Intell. Lab. Syst. 40:193-201
22. Spraul M., Neidig P., Klauck U., Kessler P., Holmes E., Nicholson J.K., Sweatman B.C., Salman S.R., Farrant R.D., Rahr E., Beddel C.R. and Lindon J.C. (1994) Automatic reduction of NMR spectroscopic data for statistical and pattern recognition classification of samples. J. Pharm. Biomed. Anal. 12: 1215-1225
23. Torgrip R.J.O., Åberg M., Karlberg B. and Jacobsson S. (2003) Peak Alignment using reduced set mapping. J. Chemom. 17: 573-582
24. Wold, S., Johansson, E. and Cocchi, M. (1993). in Kubiny, H. (Ed), 3D-QSAR in drug design: Theory, methods and applications. ESCOM Science, Ledien
25. Åberg M., Torgrip R.J.O. and Jacobsson S.P. (2005) Extensions to peak alignment using reduced set mapping and classification of LC-UV data from peptide mapping. J. Chemom. 19: 1-9