Proteomics, a new branch of science related to genomics, involves complex analysis of proteins of cells, tissues or biological fluids. Proteomics is today based on two-dimensional electrophoresis, the crucial technology in making protein maps. It consists of a special procedure for preparation of a sample, isoelectric focusation, sodium dodecyl sulfate polyacrylamide gel electrophoresis and gel visualization. Two-dimensional separations of complex protein mixtures in gels are compared, evaluated by image analysis and protein maps are constructed. Individual proteins on the maps can be characterized by various methods, most frequently by mass spectrometry, and identified in databases using the information on their structure. Proteomic methods find useful applications in comparing complex protein composition in biology, especially in microbiology and medicine, where they can contribute to revealing new relations between concentrations of proteins and their physiological functions.