PARAFASCA: ASCA combined with PARAFAC for the analysis of metabolic fingerprinting data

Journal of Chemometrics

Volumn 22, Issue 2, 2008, Pages 114-121

  Jansen, Jeroen J ^b   Bro, Rasmus ^c   Hoefsloot, Huub C J ^a   Van Den Berg, Frans W J ^c   Westerhuis, Johan A ^a   Smilde, Age K ^a,d  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d TNO   (Netherlands)

Author keywords

ASCA; Experimental design; Metabolomics; Multiway analysis; PARAFAC

Indexed keywords

DESIGN OF EXPERIMENTS; HYDRAZINE; METABOLISM; MULTIVARIANT ANALYSIS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STATISTICS;

ANOVA-SIMULTANEOUS COMPONENT ANALYSE; COMPONENT ANALYSIS; FINGERPRINTING DATA; GENOMICS; METABOLIC FINGERPRINTING; METABOLOMICS; MULTIVARIATE DATA; MULTIWAY ANALYSIS; PARALLEL FACTOR ANALYSIS; PRINCIPAL-COMPONENT ANALYSIS;

PRINCIPAL COMPONENT ANALYSIS;

EID: 53649107769     PISSN: 08869383     EISSN: 1099128X     Source Type: Journal    
DOI: 10.1002/cem.1105     Document Type: Article

References (23)

1. Calabrese EJ, Baldwin LA. Defining hormesis. Hum. Exp. Toxicol. 2002; 21: 91-97.
2. Dunn WB, Bailey NJ, Johnson HE. Measuring the metabolome: current analytical technologies. Analyst 2005; 130; 606-625.
3. Fraser PD, Enfissi EMA, Goodfellow M, Eguchi T, Bramley PM. Metabolite profiling of plant carotenoids using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Plant J. 2007; 49: 552-564.
4. Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 2000; 23: 131-142.
5. von Roepenack-Lahaye E, Degenkolb T, Zerjeski M, Franz M, Roth U, Wessjohann L, Schmidt J, Scheel D, Clemens S. Profiling of arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol. 2004; 134: 548-559.
6. Benavente F, van der Heijden R, Tjaden UR, van der Greef J, Hankemeier T. Metabolite profiling of human urine by CE-ESI-MS using separation electrolytes at low pH. Electrophoresis 2006; 27: 4570-4584.
7. Lamers R-JAN, DeGroot J, Spies-Faber EJ, Jellema RH, Kraus VB, Verzijl N, TeKoppele JM, Spijksma GK, Vogels JTWE, van der Greef J, van esselrooij JHJ. Identification of disease- and nutrient-related metabolic fingerprints in osteoarthritic guinea pigs. J. Nutr. 2003; 133: 1776-1780.
8. Chang WT, Thissen U, Ehlert KA, Koek KM, Jellema RM, Hankemeier T, van der Greef J, Wang M. Effects of growth conditions and processing on Rehmannia glutinosa using fingerprint strategy. Planta Med. 2006; 72: 458-467.
9. Wael E-D. Pattern recognition approaches in biomedical and clinical magnetic resonance spectroscopy: a review. NMR Biomed. 1997; 10: 99-124.
10. Fiehn O. Metabolomics-the link between genotypes and phenotypes. Plant Mol. Biol. 2002; 48: 155-171.
11. Jolliffe IT. Principal Component Analysis. Springer-Verlag: New York, 2002.
12. Jackson JE. A User's Guide to Principal Components. Wiley-Interscience: New York, 1991.
13. Jansen JJ, Hoefsloot HCJ, van der Greef J, Timmerman ME, Smilde AK. Multilevel component analysis of time-resolved metabolomics data. Anal. Chim. Acta 2005; 530: 173-183.
14. Jansen JJ, Hoefsloot HCJ, van der Greef J, Timmerman ME, Westerhuis JA, Smilde AK. ASCA: analysis of multivariate data obtained from an experimental design. J. Chemometr. 2005; 19: 469-481.
15. Smilde AK, Jansen JJ, Hoefsloot HCJ, Lamers R, van der Greef J, Timmerman ME. ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data. Bioinformatics 2005; 21: 3043-3048.
16. Smilde AK, Bro R, Geladi P. Multi-way Analysis: Applications in the Chemical Sciences (1st edition). John Wiley & Sons: New York, 2004.
17. Harshman RA. Foundations for the PARAFAC procedure: model and conditions for an 'explanatory' multi-mode factor analysis. UCLA Work. Pap, Phon. 1970; 16: 1-84.
18. Bro R. PARAFAC: a tutorial. Chemometr. Intell. Lab. 1997; 38: 149-171.
19. Carroll JD, Chang JJ. Analysis of individual differences in multidimensional scaling via an N-way generalization of "Eckart-Young" decomposition. Psychometrika 1970; 35: 283-319.
20. Sinha AE, Hope JL, Prazen BJ, Nilsson EJ, Jack RM, Synovec RE. Algorithm for locating analytes of interest based on mass spectral similarity in GC × GC-TOF-MS data: analysis of metabolites in human infant urine. J. Chromatogr. A 2004; 1058: 209-215.
21. Idborg H, Edlund PO, Jacobsson SP. Multivariate approaches for efficient detection of potential metabolites from liquid chromatography/mass spectrometry data. Rapid Commun. Mass Spectrom. 2004; 18: 944-954.
22. Dyrby M, Baunsgaard D, Bro R, Engelsen SB. Multiway chemometric analysis of the metabolic response to toxins monitored by NMR. Chemometr. Intell. Lab. 2005; 76: 79.
23. Andersson CA, Bro R. The N-way toolbox for MATLAB. Chemometr. Intell. Lab. 2000; 52: 1-14.