Proteomics, the parallel separation, identification and quantification of all proteins produced by a tissue or cell culture, together with the analysis of protein properties like posttranslational modifications and interactions, provides more detailed information about the biological system under study than the determination of the static genome or expression profiling based on mRNA. To benefit fully from the power of proteomics, some of the inherent problems have to be solved. Most methods of protein separation fail to recover all proteins. Protein abundance spans several orders of magnitude and there is no amplification method, analogous to the polymerase chain reaction method for amplifying genes. In order to overcome these problems, proteomic technologies have to be very sensitive as well as to cover a broad dynamic range. Advantages and disadvantages of different established and emerging methods used for protein separation and identification are discussed and the evolving chip-based approaches are evaluated. Results of proteomic experiments consist of far more than a mere sequence of nucleic-acid bases or amino acids. The essential information of a proteomic approach is difficult to extract, standardise and integrate into databases. This, however, is necessary to allow laboratory and organism independent use of experimental data. Discussion on related databases and data integration are presented.