The importance of anatomy and physiology in plant metabolomics

Plant metabolomics offers some unique opportunities in the assignment of biochemical pathways. The genetics of model plants is well-characterized which enables functional genomic approaches, qualitative trait loci identification and genetic engineering. Metabolomics has successfully supported the identification of gene function. As a specialized system, a number of key features of plants create challenges in sample preparation and interpretation of metabolomic data. Significantly, most plant tissues are composed of multiple cell types which are difficult to isolate, often resulting in limited numbers per cell type. This hinders spatial resolution of the analysis of metabolites. Secondly, cells are surrounded by a dynamic cell wall which is in constant turnover, interfering with the metabolome. Thirdly, green plant cells are capable of fixing carbon through photosynthesis producing metabolite-captured energy. This also implies a strong light-dependency in plant metabolism. Finally, plants are characterized by a diversity of secondary metabolites produced in response to environmental stimuli.