Subcellular metabolomics: the choice of method depends on the aim of the study

Plant metabolism is compartmentalized at the level of organs, cells, subcellular compartments and molecular assemblies. The rapid progress of in-depth metabolite profiling and kinetic flux analysis has elucidated the environmentally dependent dynamics of metabolism. However, for a full understanding of metabolism and compartmentation, including modelling and simulation (e.g. of photosynthesis), metabolome analysis must consider subcellular localization. Here, the advantages and drawbacks of methods developed to analyze this are assessed. It is argued that the selection of method depends on the aim of a particular study, and results (using different methods) should ideally be compared: no single method is best.