Metabolome profiling

Maharjan, R. P. Ferenci,T. Global metabolite analysis the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal. Biochem. 2003,313, 154-154. 

As in the other -omics, analyses may be directed at a specific metabolite, at all metabolites in a given system in a shot-gun approach, or at accessible groups of molecules in profiling experiments. In that also the technology varies. In addition, the chemistry of different metabolites is very heterogeneous since it involves hydrophobic lipids, hydrophilic carbohydrates, ionic inorganic species, and other secondary natural products and already the choice of solvent in metabolite extraction dictates which types of molecules will be present (Fig. 10.8). Therefore, total metabolome profiling is not possible, because no analytical method will be able to accommodate all the different molecule classes at once. 

The authors also combined metabolomics results with results obtained from AFP determinations. The model was created using linear discriminant analysis. Principal component analysis was also carried out. Thanks to the created model, it was possible to detect metabolites of potential diagnostic value. Moreover, analysis of metabolomic profiles decreased the number of patients that were incorrectly classified with the use of AFP marker [21]. 

Wu, H., Xue, R., Dong, L., Liu, T., Deng, C., Zeng, H., Shen, X. Metabolomic profiling of human urine in hepatocellular carcinoma patients using gas chromatography/mass spectrometry. Anal. Chim. Acta 648, 98-104 (2009)... 

Wilmes A et al (2013) Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress. J Proteomics 79 180-194... 

Nordstrom et al. [121] also compared the differences between UPLC and HPLC for metabolomic profiling. This time a Waters Acquity system was coupled to Micromass Q-Tof-Micro mass spectrometer and data were acquired in the m/z 100-1000 range with an acquisition of 2 spectra per second. About 20% more components were detected using UPLC versus HPLC and the length of the chromatographic separation was one of the most crucial parameters affecting the number of detected features. These examples demonstrate the importance of appropriate mass analyzers when utilizing UPLC. For more on UPLC see Chapter 8. 

Ritchie, S., Comprehensive metabolomic profiling of serum and cerebrospinal fluid Understanding disease, human variability, and toxicity, in Surrogate Tissue Analysis, 1st edition, Burczynski, M.E., and Rockett, J.C., Eds., CRC Press LLC, Boca Raton, FL, 2006, p. 165. 

Boemsen, K.O., Gatzek, S., andlmbert, G., Controlled protein precipitation in combination with chip-based nanospray infusion mass spectrometry. An approach for metabolomics profiling of plasma, Anal. Chem., 77(22), 7255, 2005. 

Some of the functions of the S. coelicolor CYPs are in secondary metabolism operons, for example, CYP158A2 located downstream of a Type III polyketide synthase and CYP105N1 located downstream of a nonribosomal peptide synthase. These are currently subject to functional studies using the tools of gene disruption and metabolite/metabolome profiling, although not all the secondary metabolite genes identified... 

The analytical system of choice is expected to provide simultaneous access to the metabolites of interest and globally relevant cofactors. In addition, it is desirable to have a platform that can be flexibly extended for purposes of untargeted metabolome profiling. From this perspective, two conceptually different systems hold prime attention high-pressure liquid chromatography and capillary electrophoresis. 

Narrow therapeutic index combined with the inter-individual variations in drug pharmacokinetics, response, and toxicity adds uncertainty to the clinical trials and use of novel anticancer agents. Pharmacogenetic and metabolomic profiling of the patients promise to at least partly address these concerns, thus helping in the individualization of medication for patients and improved... 

Kamleh A, et al. Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography A method with wide applicability to analysis of biomolecules. Rapid Commun Mass Spectrom 2008 22 1912-1918. 

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