Proteomics can be defined as functional analysis of the full set of proteins by high-throughput technologies in a given system. The workflow of proteomics is a multi-step process comprising sample preparation, separation, quantification and identification of proteins. Due to the high complexity of different protein species and the wide dynamic range of protein amount within a cell system it is necessary to apply appropriate analysis methods. One approach is to separate proteins first by two-dimensional gel electrophoresis (2-DE) according to charge and molecular weight. Proteins are then fragmented and analyzed using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Identification of proteins can be achieved by comparing the mass/charge-ratios of these peptides to respective databases. Proteome analysis with respect to the identification of disease-associated patterns of molecules in different tissues is in the early stages, because standardisation of these techniques often remains to be established. However, proteome analyses is a promising tool to obtain holistic insights into the physiological status of a cell or cellular system. Compared to RNA-based studies some advantages are obvious: (1) post-translational modifications, e. g. phosphorylation, contributing to the activity status can be detected at the protein level only, (2) RNA-levels do not necessarily coincide with protein levels for a particular gene, (3) feedback-mechanisms within regulatory pathways can control protein activity without measurable changes in mRNA content.