Nearly all processes running in cells of living organisms are accomplished by the effect of proteins. Their synthesis is regulated by the respective genome. Many genome research projects have elucidated the structure of an enormous number of genes in different organisms. Using the well-known Genetic Code it is possible to construct amino acid sequences from the determined gene sequences. This knowledge per se, however, does not lead to the status of the proteins as which they are existing in vivo. The reason for that lies in posttranslational events like glycosylation, further processing and other modifications which are presently unforeseeable. It is thus in reality impossible to predict the actual and complete endowment of the cells of an organism with proteins, i e. their proteome, from their genome because some of the relevant important information cannot be delivered by genome research.

The most important properties by which cellular proteomes of an organism can differ at diverse environmental conditions or at different points in time are:

• presence or absence of individual proteins within the entirety of typically about 10 000   proteins per cell;
• different quantity of individual proteins over a broad range of concentrations due to   the variation in copy number from about 102 to about 106 per cell;
• posttranslational modifications of proteins like e. g. phosphorylation or   dephosphorylation or splicing processes for protein maturation;
• topological distribution patterns in different cell compartments;
• networks of interactions with other proteins.

With the rapidly developing repertoire of proteomic methods it is possible to address the investigation of these factors and situations. Actual proteome analysis is based to a great extent on high resolution 2D gel electrophoresis in combination with highly sensitive mass spectrometric methods. A great potential is attributed to newly developed high through put procedures based on chromatographic separation techniques which are linked with quantification by mass spectroscopy. Automation to a large extent is a prerequisite for an effective proteome analysis and at the same time the availability of more and more sophisticated bioinformatics tools plays an essential role.

The composition of proteomes can provide important information about the status of the corresponding cells or tissues and can therefore reveal dependences on endogenous influences, i. e. originating from the cell’s program itself or exogenous ones, i. e. coming from the environment. Consequently, proteomics has its main applications in the following fields:

• searching of proteins which appear or disappear in correlation with disease (e .g   cancer or neurodegenerative disease):
  candidates of interest can later be analysed for their potential as diagnostic marker or   if they are useful as targets for the development of therapeutic drugs.
• elucidation of biological action mechanisms:
  as an example, the identification of proteins in signalling chains being relevant for basic   research or disease onset may be mentioned;
• detection of drug side effects:
  preferably sensitive cell lines are used and the effect of the candidate substance on   the cellular proteome is analysed.

Proteome analysis has clearly the potential of developing into a powerful platform technology which can be used for the elucidation of physiological and pathological processes on the level of single proteins, the most important group of biological molecules for building and maintaining a living organism. In the actual post genome era proteomics is expected to provide crucial contributions for the whole Life Science field.