Quantitative metabolic network profiling of Escherichia coli: An overview of analytical methods for measurement of intracellular metabolites

Understanding the mechanism of metabolic network response to extracellular changes has become one of the primary objectives of systems biology. Quantitative metabolic network profiling of model organisms such as E. coli is the principal approach. Well-designed analytical protocols for the determination of intracellular metabolites may provide a crucial premise to quantitative profiling of cellular metabolism. This article reviews and evaluates the existing methods for determining intracellular metabolites of E. coli in terms of sample preparation and mass spectrometry (MS) analysis. Critical issues including the variation of metabolic status and interference of external pools during cell sampling, sample loss during quenching procedures, degradation of metabolites and efficiency of extraction, and matrix effects in separation and quantification are discussed. Moreover, suggestions are provided to solve the analytical problems based on the results from the recent studies in order to establish a precise and reliable analytical platform for the intracellular metabolites.