Extracellular matrix plays a pivotal role in biofilm biology. Despite importance of matrix proteins as potential targets for development of antibacterial therapeutics little is known about matrix proteomes. While P. aeruginosa is one of the most important pathogens with emerging antibiotic resistance only few studies are devoted to matrix proteomes and there are no studies describing matrix proteome for any clinical isolates. As matrix responsible for some extracellular functions, it is expected that protein composition should be different in comparison with embedded in biofilm cells and this difference reflects possible active processes in matrix. Here we report the first matrix proteome for clinical isolate of P. aeruginosa in comparison with embedded cells. We have identified the largest number of proteins in matrix among all published studies. Ten proteins were unique for matrix and not present inside cells, but most of these proteins do not have well described function with respect to extracellular component of biofilm. Functional classification of enriched in matrix proteins resulted in several bioprocess groups of proteins. Top three groups were: oxidation-reduction processes, nucleoside metabolism and fatty acid synthesis. Finally, we discuss obtained data in prism of possible directions for antibiofilm therapeutic development.