The article presents a relatively new area of studies – proteomics – which investigates the composition, structure and function of proteins and the interactions among proteins occurring in cells. Then the most important analytical techniques of proteomics are described: two-dimensional electrophoresis, matrix-assisted laser-desorption ionization time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry techniques. In order to introduce issues related to proteomics, the examples of proteome microorganisms including specific pathogens (Staphylococcus aureus, Vibrio cholerae, Bacillus subtilis, Mycobacterium avium, Borrelia spp., Aspergillus flavus) are presented. Based on the results of the proteome, in this review the following applications of proteomic have been documented: species identification, the metabolism studies of microorganism and host-pathogen interactions and even the possibility of differentiating the enzymatic potential of the microorganisms utilizing lignocellulosic biomass. The potential of proteomic analysis was discussed in the summary of the article.

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