Well-designed experiments make proteomic studies on stressed plants meaningful

Analysis of the impact of abiotic stresses on plants is technically demanding. The cultivation of plants, application of treatments, choice of tissues and preparation of biological samples for proteomic analysis is as important as the subse’uent identification of proteins. With appropriate precautions, proteomics will greatly improve our understanding of the mechanisms of abiotic stress tolerance. Hence, this chapter summarises some of the major design faults that can compromise the interpretation of ‘stress experiments’. The examples of salt, drought, thermal stress and waterlogging are taken as representative of commonly encountered stresses, with recommendations for ways to avoid artefacts in design. The importance of interactions between these stresses is then discussed, pointing out the relevance of carefully constructed time courses and attendant physiological measurements to define the degree of stress. Tissue selection is also emphasised, recognising that stresses have differential impacts on different organs. Finally, the significance of choice of plant species is discussed, with recognition of the value of model species and the importance of expanding the range of taxa used if the full range of stress acclimation responses is to be identified through proteomics.