The proteome is by definition the complete set of proteins of a cell at any defined moment. This definition includes in its widest sense all possible modifications of cellular proteins at any given time (Kahn, 1995; Wilkins et al., 1996). Due to the lack of technical means to display and analyse the whole proteome at once, the term ‘proteomics’ which describes the analytical approach to investigate the proteome of a given system refers to a general concept rather than to any particular experiment. Among the experimental approaches currently used in proteomics, the mapping of the proteins of particular subcellular structures proves to be an increasingly successful concept which is applied to explore more and more defined subcellular structures that can be isolated and sufficiently purified (Dreger, 2003). Most of the recent subcellular proteomics studies have been performed at this mapping level. The results of such experiments are mainly qualitative, and at best semi-quantitative.