Development and optimization of a metabolomic method for analysis of adherent cell cultures

Analytical Biochemistry

Volumn 404, Issue 1, 2010, Pages 30-39

  Danielsson, Anders P H ^a,b   Moritz, Thomas ^c   Mulder, Hindrik ^a   Spégel, Peter ^a  

^a LUND UNIVERSITY DIABETES CENTRE   (Sweden)

^b LUND INSTITUTE OF TECHNOLOGY   (Sweden)

^c SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Cell culture; Gas chromatography; Mass spectrometry; Metabolomics; Statistical design of experiments

Indexed keywords

BIOMOLECULES; CELLS; DESIGN OF EXPERIMENTS; GAS CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLITES; MULTIVARIANT ANALYSIS;

GAS CHROMATOGRAPHY/MASS SPECTROMETRY; INTERACTION EFFECT; LIMIT OF DETECTION; METABOLIC PATHWAYS; METABOLITE EXTRACTION; METABOLOMICS; MULTI VARIATE ANALYSIS; STATISTICAL DESIGN OF EXPERIMENTS;

CELL CULTURE;

ADHERENT CELL; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; CELL CULTURE; CELL DISRUPTION; CELL HETEROGENEITY; CLINICAL PROTOCOL; CONTROLLED STUDY; FLOW RATE; MASS FRAGMENTOGRAPHY; MATHEMATICAL MODEL; METABOLOME; METABOLOMICS; NONHUMAN; PRIORITY JOURNAL; PROCESS DESIGN; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; RAT; TEMPERATURE; VALIDATION PROCESS; ANIMAL; CELL ADHESION; DISCRIMINANT ANALYSIS; HIGH THROUGHPUT SCREENING; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES; TIME; TUMOR CELL LINE;

RATTUS;

ANIMALS; CELL ADHESION; CELL LINE, TUMOR; DISCRIMINANT ANALYSIS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HIGH-THROUGHPUT SCREENING ASSAYS; METABOLOME; METABOLOMICS; PRINCIPAL COMPONENT ANALYSIS; RATS; TEMPERATURE; TIME FACTORS;

EID: 77954086132     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2010.04.013     Document Type: Article

References (25)

1. Winder C.L., Dunn W.B., Schuler S., Broadhurst D., Jarvis R., Stephens G.M., Goodacre R. Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites. Anal. Chem. 2008, 80:2939-2948.
2. Canelas A.B., ten Pierick A., Ras C., Seifar R.M., van Dam J.C., van Gulik W.M., Heijnen J.J. Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics. Anal. Chem. 2009, 81:7379-7389.
3. Villas-Bôas S.G., Højer-Pedersen J., Åkesson M., Smedsgaard J., Nielsen J. Global metabolite analysis of yeast: Evaluation of sample preparation methods. Yeast 2005, 22:1155-1169.
4. Ewald J.C., Heux S., Zamboni N. High-throughput quantitative metabolomics: Workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal. Chem. 2009, 81:3623-3629.
5. Bolten C.J., Kiefer P., Letisse F., Portais J.-C., Wittmann C. Sampling for metabolome analysis of microorganisms. Anal. Chem. 2007, 79:3843-3849.
6. Teng Q., Huang W., Collette T.W., Ekman D.R., Tan C. A direct cell quenching method for cell-culture-based metabolomics. Metabolomics 2009, 5:199-208.
7. de Koning W., van Dam K. A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH. Anal. Biochem. 1992, 204:118-123.
8. Sellick C.A., Hansen R., Maqsood A.R., Dunn W.B., Stephens G.M., Goodacre R., Dickson A.J. Effective quenching processes for physiologically valid metabolite profiling of suspension cultured mammalian cells. Anal. Chem. 2008, 81:174-183.
9. Huie C.W. A review of modern sample-preparation techniques for the extraction and analysis of medicinal plants. Anal. Bioanal. Chem. 2002, 373:23-30.
10. Benthin B., Danz H., Hamburger M. Pressurized liquid extraction of medicinal plants. J. Chromatogr. A 1999, 837:211-219.
11. Gullberg J., Jonsson P., Nordström A., Sjöström M., Moritz T. 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. 2004, 331:283-295.
12. Parab G.S., Rao R., Lakshminarayanan S., Bing Y.V., Moochhala S.M., Swarup S. Data-driven optimization of metabolomics methods using rat liver samples. Anal. Chem. 2009, 81:1315-1323.
13. Jiye A., Trygg J., Gullberg J., Johansson A.I., Jonsson P., Antti H., Marklund S.L., Moritz T. Extraction and GC/MS analysis of the human blood plasma metabolome. Anal. Chem. 2005, 77:8086-8094.
14. Büscher J.M., Czernik D., Ewald J.C., Sauer U., Zamboni N. Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal. Chem. 2009, 81:2135-2143.
15. 1H NMR spectroscopy and chemometrics. Anal. Chem. 2009, 81:9755-9763.
16. Cozzolino D., Flood L., Bellon J., Gishen M., Lopes M.D.B. Combining near infrared spectroscopy and multivariate analysis as a tool to differentiate different strains of Saccharomyces cerevisiae: a metabolomic study. Yeast 2006, 23:1089-1096.
17. 13C metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. Anal. Chem. 2008, 80:9417-9425.
18. Araujo P.W., Brereton R.G. Experimental design: II. Optimization. Trends Anal. Chem. 1996, 15:63-70.
19. Araujo P.W., Brereton R.G. Experimental design: I. Screening. Trends Anal. Chem. 1996, 15:26-31.
20. Araujo P.W., Brereton R.G. Experimental design: III. Quantification. Trends Anal. Chem. 1996, 15:156-163.
21. P. Jonsson, A.I. Johansson, J. Gullberg, J. Trygg, J.A., B. Grung, S. Marklund, M. Sjostrom, H. Antti, T. Moritz, High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses, Anal. Chem. 77 (2005) 5635-5642.
22. Wold S. Cross-validatory estimation of the number of components in factor and principal components models. Technometrics 1978, 20:397-405.
23. Trygg J., Wold S. Orthogonal projections to latent structures (O-PLS). J. Chemometr. 2002, 16:119-128.
24. Pous-Torres S., Baeza-Baeza J.J., Torres-Lapasió J.R., García-Álvarez-Coque M.C. Peak capacity estimation in isocratic elution. J. Chromatogr. A 2008, 1205:78-89.
25. Kirkland J.J. Sampling and extra-column effects in high-performance liquid chromatography: influence of peak skew on plate count calculations. J. Chromatogr. Sci. 1977, 15:303-316.