The goal of proteomic research is the identification of all protein species in all cells and tissues of certain organisms and lately these research projects include identification of protein functions. In early stages of proteome research it was considered that genome and proteome are in a direct relation. However, the discovery of PTM of proteins has shown us that the central dogma of molecular biology may not be so correct after all. PTM can have different effects on their target proteins and such may include changes in regulation of their enzymatic activity, their localization in cell compartments or membranes, inclusion in metabolic or biochemical pathways, or they can serve as markers for targeting proteins bound to degradation. Technological breakthroughs have allowed us to gain better understanding in PTM, especially by development of MS methods. Further development of research options with application of bioinformatics analysis would allow us to gain better knowledge of PTM, their components and localization. The final goal would be achieved when it would be simple to determine which proteins would undergo PTM, foresee the site of the modification and finally, to determine their function.