Metabolomics analysis

Castrillo, J. L. Hayes, A. Mohammed, S. Gaskell, S. J. Oliver, S. G. An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 2003, 62, 929-937. 

O. Fiehn, Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks. Comp. Fund. Genom. 2, 155 168 (2001). 

S. G. Villas Boas, U. Roessner, M. Hansen, J. Smedsgaard, and J. Nielsen, Metabolome Analysis An Introduction, John Wiley Sons, Hoboken, NJ, 2007. 

Metabolomics analysis with the devTOX platform was performed in collaboration with Stemina Biomarker Discovery, Inc. 

Prior to metabolomic analysis, sample treatment is typically needed, as CSF contains approximately 0.3 mg/mL protein (114) that may hinder metabolite analysis. Consequently, CSF sample treatment is essentially directed to protein removal by means of organic solvent addition (84,88) or by ultrafiltration (85,89,90). The final metabolic extract composition will depend in a great extent on the sample treatment (115), and it will be selected mostly regarding the metabolomic approach and the analytical technique that will be afterward applied. 

Targeted analysis refers to metabolome analysis that targets one, or a few metabolites, and typically uses an internal standard for quantitation. The most common method is isotope dilution mass spectrometry (IDMS) [34], which relies on the use of stable isotope internal standards to enable the absolute quantitation of metabolites. This method has proven highly effective and has been successfully used in numerous studies. 

A solution to this hurdle was first given by genomics, when several genome-wide techniques such as transcriptome and metabolome analysis started to be routinely applied on microbial systems. These techniques, besides requiring significant expertise in data analysis [217], allow the extraction of a vast quantity of information. Unfortunately, the sole presence of this wealth of data is not sufficient to understand the cell behavior from a holistic perspective. To address this issue,... 

In comparison with NMR, mass spectrometry is more sensitive and, thus, can be used for compounds of lower concentration. While it is easily possible to measure picomoles of compounds, detection limits at the attomole levels can be reached. Mass spectrometry also has the ability to identify compounds through elucidation of their chemical structure by MS/MS and determination of their exact masses. This is true at least for compounds below 500 Da, the limit at which very high-resolution mass spectrometry can unambiguously determine the elemental composition. In 2005, this could only be done by FTICR. Orbitrap appears to be a good alternative, with a more limited mass range but a better signal-to-noise ratio. Furthermore, mass spectrometry allows relative concentration determinations to be made between samples with a dynamic range of about 10000. Absolute quantification is also possible but needs reference compounds to be used. It should be mentioned that if mass spectrometry is an important technique for metabolome analysis, another key tool is specific software to manipulate, summarize and analyse the complex multivariant data obtained. 

The increasing accessibility of bench-top LC-MS systems to researchers of all disciplines, combined with the tandem and high-resolution mass spectrometry capabilities of such instruments, will only increase the number of applications to which LC-MS can be directed. The examples documented in this chapter illustrate some of the diversity and power of the techniques, including analytical applications for known analytes in various matrices, metabolomic analysis, the tentative structural identification of novel compounds, and the screening of extracts for minor, and perhaps novel, components of the alkaloidal profile of plants. 

Metabolomic Analysis of Plasma Samples from Patients with Amyotrophic Lateral Sclerosis Using NMR... 

Terabe, S., Markuszewski, M.J., Inoue, N., Otsuka, K., Nishioka, T. Capillary electrophoretic techniques toward the metabolome analysis. Pure Appl. Chem. 73, 1563-1572 (2001)... 

Markuszewski, M.J., Szczykowska, M., Siluk, D., Kaliszan, R. Human red blood cells targeted metabolome analysis of glycolysis cycle metabolites by capillary electrophoresis using an indirect photometric detection method. J. Pharm. Biomed. Anal. 39, 636-642 (2005)... 

Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H., Tomita, M., Nishioka, T. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J. Proteome Res. 2, 488 94 (2003)... 

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