Metabolomics chemical analysis

One last interesting point should be drawn to the combination of transcriptomics, proteomics, and metabolomics. Proteomics and metabolomics are both based on similar chemical analysis techniques LC-MS. It might be possible that in the future new work based on the combination of both or all three will be published. Virtually, high-resolution instruments such as the latest... 

Given the sensitive, label-free, and multiplexed analysis that MS can provide and the automated, low-volume fluidic operations enabled by microfluidics, the combination of microfluidics with ESI-MS is expected to see increased use for chemical and biochemical analyses in the years to come. In particular, the ability of microfluidics to process minute volumes and perform sample handling operations in a high-throughput, automated fashion can extend MS-based proteomics and metabolomics studies to samples that are too small for current processes, including in-depth chemical analysis of single cells. 

Sumner LW, et al. Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics 2007 3 211-221. 

A. W.,ReiIy,M.D.,Thaden, J.J.,Viant,M.R. (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics, 3, 211-221. 

Sumner L, Amberg A, Barrett D, et al. (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3 211-221 Van Loo J, Cummings J, Delzenne N, et al. (1999) Functional food properties of non-digestible oligosaccharides a consensus report from the ENDO project (DGXIIAIRII-CT94-1095). Br J Nutr 81 121-132... 

Before we describe the chemistry of the compartments involved, note that like prokaryotes, a number of oxidative enzymes are found in the cytoplasm but they do not release damaging chemicals (see Section 6.10). We also observed that such kinds of kinetic compartments are not enclosed by physical limitations such as membranes. We have also mentioned that increased size itself makes for kinetic compartments if diffusion is restricted. In this section, we see many additional advantages of eukaryotes from those given in Section 7.4. How deceptive it can be to use just the DNA, the all-embracing proteome, metabolome or metallome in discussing evolution without the recognition of the thermodynamic importance of compartments and their concentrations These data could be useful both here and in simpler studies of single-compartment bacteria even in the analysis of species but not much information is available. 

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 combined genomics and chemical approaches to plant terpenoid research are not restricted to the few plant species for which more or less complete genome sequences are now available. The discovery of many of the genes and enzymes for the formation of terpenoids such as menthol and related monoter-penes in peppermint Mentha x piperita) (15), artemisinin in Artemisia annua (16), Taxol in the yew tree (Taxus) (17), or conifer diterpene resin acids in species of spmce (Picea ) and pine (Pinus) (18) have been possible on the foundation of highly specialized efforts of EST and full-length cDNA sequencing combined with characterization of recombinant enzymes and analysis of the terpenoid metabolome of the target plant species. 

The challenge of proteiomic and metabolomic analysis lies in the complexity (e.g., PTMs of proteins and the array of different chemical classes of metabolites), and the large range of concentrations, of the components present in the sample and in the need for high-throughput and reproducible methodologies for their identification and quantification. A detailed discussion of protein and peptide analysis by MS may be found elsewhere in this volume (see Chapter 9.12). 

---