Several kinases are activated during the defence response following microbial elicitation. While studying the regulation of these kinases in greater detail, it has become clear that the means by which phosphorylation events transmit specific information to the cell is highly complex. To gain a better understanding of the molecular events leading to a response, it will be increasingly important to identify not only the protein targets of phosphorylation but also the specific sites of phosphorylation. New developments in peptide-based phosphoproteome analysis appear to hold the promise of achieving these goals at the whole-cell level.