The complexity of nature is tremendous, particularly at the epigenetic level. Proteomic studies must therefore complement genomic discoveries to better understand biological processes. Because of the very large number of modified proteins and their great variability in physico-chemical properties, no single method can be used to analyze all of them. Mass spectrometry has demonstrated its superior ability to rapidly identify and partially characterize numerous proteins in low abundance and has become a central element in most proteomic projects. Studies of protein function are necessary to understand biological pathways and this is being tackled using several approaches such as two hybrid systems, phage technology or affinity methods. Finally, mathematical and bioinformatic developments will be essential to study nature's complex systems.