Taraxacum koksaghyz is currently one of the most investigated plants as a potential source of natural rubber. This poly(cis-1,4-isoprene) polymer and further valuable secondary metabolites are produced in laticifer cells, which exist as a network of elongated tubules throughout the plant and have a milky cytoplasm known as latex. However, a detailed analysis of the overall laticifer system and a deeper knowledge about the interaction with the surrounding tissues has not been performed. Therefore, we used a bacterial ribonuclease for the development of transgenic dandelion plants with omitted latex production. Comprehensive histological, biochemical and proteomic analyses served to characterize these plants. Thereby, we were able to generate a molecular map based on the protein expression pattern of laticifers and whole Taraxacum koksaghyz roots at different stages of plant development. This enables us to understand the interplay and tissue specificity of different biosynthesis routes and narrow down biological functions of latex.