The review briefly presents principles and stages of execution of such highly effective methods of protein separation as capillary, 2D gel-electrophoresis, liquid chromatography, the possibility of their successful combination with tandem mass-spectrometry and application in various fields of proteomics. The main problems of proteomic analysis as well as ways of solving by using mass-spectrometry are examined. 2 main approaches during protein identification are described in the review, characteristics and possibilities of various top-down and bottom-up proteomic analytical programs are provided.