Mass spectrometry in metabolomics

The determination of the genome and the transcriptome did not rely much on mass spectrometry, other techniques allowing the gene sequence to be reached more efficiently. For the proteome, at the contrary, mass spectrometry has a central role. No other technique can compete with its efficiency to determine protein sequence quickly on very low sample quantities. But knowledge of the genome, the transcriptome and the proteome does not reveal the phenotype of a living system, as it is difficult or impossible to establish a direct link between the protein and its enzymatic activity, and thus the produced metabolites. There is almost no way to predict the substrates and metabolites of unknown enzymes whose total sequence is known. And it often appears that even for known enzymes the known activities are only partial. To understand the cell, it is thus an essential task to link the expression of proteins to the produced metabolites. 

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. 

It is known that metabolomics is now widely used in the pharmaceutical industry, as the difference between the metablome of an organism without and with the influence of a drug is of paramount interest. This could give information not only on the drug metabolites, but 

As an example of the application of metabolomics, we will refer to the substrates of the enzyme fatty acyl amide hydrolase (FAAH) that regulates several brain lipids that have interesting pharmacological properties including effects on the control of pain. It is well known that some fatty acyl amides of ethanolamine are substrates of FAAH, such as the ethanolamide of arachidonic acid (anandamide), which is an endogenous ligand of cannabinoid receptors. 

Molecular Formula C24H48NO4S Calculated Exact Mass 446.3310 Observed Exact Mass 446.3310 

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Villas-Boas SG, et al. Mass spectrometry in metabolome analysis. Mass Spectrom Rev... 

Crews, B., Wikoff, W. R., Ratti, G. J., Woo, H. K., Kalisiak, E., Heideker, J., and Siuzdak, G. 2009. Variability analysis of human plasma and cerebral spinal fluid reveals statistical significance of changes in mass spectrometry-based metabolomics data. Anal. Chem. 81 8538-44. 

The versatility of mass spectrometry for metabolomic studies is based on the different sample introduction techniques, the various ionization methods, the ability to collect both MS and MS/MS spectra frequently, including accurate mass measurement, as well as performing SIM and SRM (Section 3.3.3.1). Acquisition of MS/MS spectra and their incorporation in the construction of searchable libraries, which include different fragmentation and structural information from the libraries of El... 

Mass spectrometry, just after a century of its existence continues to be one of the most important workhorses of chemistry. Over the years, it has become the single most important analytical tool in proteomics, metabolomics and several other disciplines. " Traditional materials science has been away from the influence of mass spectrometry as tools of solid state materials science such as X-ray diffraction, electron microscopy, electron spectroscopy and several others continue to be the principal means of analysis of solids. However, when dimension of matter reduces to the ultra-small regime, of the order of a nanometer, materials science requires mass spectrometry for detailed characterisation. This chapter explores this emerging influence of mass spectrometry in materials science taking noble metal clusters (M ) as examples. 

Mihaleva VV, Vorst O, Maliepaard C, Verhoeven HA, de Vos RCH, Hall RD, van Ham RCHJ. Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics. Metabolomics 2008 4 171-182. 

Tengstrand, E., Rosen, J., Hellenas, K. E., and Aberg, K. M. 2013. A concept study on non-targeted screening for chemical contaminants in food using liquid chromatography-mass spectrometry in combination with a metabolomics approach. Anal. Bioanal. Chem. 405 1237-1243. 

Hu, C.H. and Xu, G. 2013. Mass-spectrometry-based metabolomics analysis for foodomics Trends in Analytical Chemistry. 52 36-46. 

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. 

McDougall G, Martinussen I and Stewart D. 2008. Towards fruitful metabolomics high throughput analyses of polyphenol composition in berries using direct infusion mass spectrometry. J Chromatogr B 871(2) 362-369. 

The identification of changes in the metabolome can help characterize the biochemical functions of enzymes in the proteome [5, 24]. Not all metabolic changes, however, provide easy readouts. Therefore, more sophisticated analytical methods have been developed to detect and quantify changes in metabolome. The application of modem analytical tools, such as nuclear magnetic resonance (NMR) [19] and mass spectrometry (MS) [5, 24], are the primary tools of metabolomics researchers. In particular, MS has found increased usage as mass spectrometers have improved their sensitivity and mass resolution. 

We will briefly highlight some examples using NMR methods [14, 19] but the remainder of this chapter will focus on MS and liquid chromatography-mass spectrometry (LC-MS) metabolomics [5, 15, 18]. We should also point out that there are a number of examples of both NMR and MS methods being used in the discovery of medicinally important biomarkers [23, 31] however, this review will focus more on the use of metabolomics to characterize proteins. 

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. 

SpectConnect Massachusetts Institute of Technology Systematic identification of conserved metabolites in gas chromatography/mass spectrometry data for metabolomics (http //spectconnect.mit.edu/)... 

In what many consider to be a landmark publication on metabolomics, Fiehn et al. (2000) state it is crucial to perform unbiased (metabolite) analyses in order to define precisely the biochemical function of plant metabolism. The authors argue that for metabolomics/metabolite profiling to become a robust and sensitive method suited to automation, a mature technology such as gas chromatography-mass spectrometry (GC-MS) is required as an analytical technique. The authors go on to describe a simple sample preparation and analysis regime that allowed for the detection and quantification of more than 300 compounds from a single-leaf sample extract. 

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