Although the process of reconstruction is identical for prokaryotic and eukaryotic metabolic networks, the authors emphasize that in eukaryotic systems, e.g., metabolism of higher plants, it is more challenging due to the size of genomes and cellular compartmentation . Additional complexity arises from network gaps and mass-balance errors resulting from incomplete genome annotation and reaction stoichiometry errors which severely affect the Inhibitors,research,lifescience,medical predictive power of network models . Beyond that, model
simulations provide only information about a steady state, i.e., a snapshot, of the system, which is pre-defined by the experimental design. Recently, in several studies genome-scale metabolic modeling in Arabidopsis
thaliana was applied to address questions like ATP demand for growth Inhibitors,research,lifescience,medical and maintenance , the metabolic activity of key enzymes responsible for the supply of redox equivalents in plastids during the photorespiratory cycle  or to predict the design of genetic manipulations that are expected to increase vitamin E content in metabolically engineered Inhibitors,research,lifescience,medical seed strains . With respect to such comprehensive metabolic network simulations, quantitative measurement of metabolism is necessary to validate the output of such simulations, which can be accomplished applying bioanalytical Selleck GSK2656157 methods in metabolomics science . Mass spectrometry is one of the crucial technologies in this field, Inhibitors,research,lifescience,medical and an overview of different techniques in context with their characteristic features has recently been presented . A recent development is the use of two-dimensional gas chromatography coupled with fast acquisition rate time-of-flight mass spectrometry (GC x GC-TOF-MS). Inhibitors,research,lifescience,medical The coupling of two gas chromatography columns with different characteristics, for
example a hydrophobic and a polar column, increases the separation efficiency of a complex metabolomics sample. A complete strategy to perform a convenient data extraction and alignment using two-dimensional gas chromatography coupled with mass spectrometry (GC x GC-MS) technology is already available . Another important extension of current metabolomics Cell press platforms for metabolomics is the integration of gas chromatography coupled to mass spectrometry (GC-MS) with liquid chromatography coupled to mass spectrometry (LC-MS) . This approach enables the analysis of components of the primary metabolism by GC-MS, for example carbohydrates and amino acids, and higher molecular masses by LC-MS, e.g., secondary metabolites [53,54]. Beyond the development of techniques and new platforms, the improvement of databases, experimental standards and data compatibility among different laboratories is crucial for efficient metabolomics science .