The aim of this Master Thesis is the optimization and verification of conditions of separation of proteins from biological materials. For the separation a developed technique called micropreparative isoelectric focusing is being used. The theoretical part describes analytical methods of biological materials with a focus on proteins which were used for the optimization of the developing system in general. This part of the Master Thesis also presents this method itself. Furthermore, basic characteristics of other techniques used to control the efficiency of the micropreparative isoelectric focusing are introduced. The experimental part depicts the individual steps of optimization of the micropreparative isoelectric focusing. The ideal separation procedure was firstly found out on the individual standard proteins, secondly on their mixture and lastly the optimised procedure was applied to a real biological sample. The efficiency of the micropreparative isoelectric focusing was verified by SDS-PAGE and MALDI-TOF mass spectrometry.