The flax, Linum usitatissimum L., is particularly suitable for studying the transduction and long-term signal storage of environmental signals. To investigate the underlying molecular mechanisms, we have focused on the initial changes in the proteome since these offer the possibility of reflecting the plant's history of exposure to stress. In principle, this 'proteome signature' might be revealed by two-dimensional electrophoresis (2-DE). We have therefore determined the potential of 2-DE to study the kinetics of changes to the proteome of flax induced by a 1 min cold shock. Protein identification is difficult with flax because of the lack of knowledge of gene sequences. Nevertheless, 2-DE analysis can be informative providing the significance of changes can be evaluated. We have developed a stringent threshold method to determine the significance of changes in gels obtained with proteins extracted from hypocotyls at different times after cold shock. This allowed us to reliably detect and characterize the kinetics of a set of seven spots that responded to cold shock and that constitute candidates for a proteome signature of long-term signal storage.