What are the disadvantages of tagging fluorescent proteins (FPs) to label target proteins?

There are also several limitations of tagging fluorescent proteins to label target proteins. One disadvantage is the unknown effect on the target protein. When one adds protein tags (particularly large ones) it may alter the structure and function of the target protein. More specifically, it may cause a reduced or complete loss of function. For example, the addition of His-tag has been found to reduce the activity of several enzymes significantly. Another disadvantage is the potential for protein instability after the tag is removed. This may cause instability to the target protein, and the solution would be to co-express the protein by binding it with antibody fragments or chaperons (e.g. disulfide isomerase) to make it more suitable. Another disadvantage is that non-native sequences may interfere with the function of drugs and trigger an immune response upon administration. Lastly, there are additional steps to take when removing protein tags. The process of removing the tags may take extended periods of time and is complex. It often includes the addition of a protease and cleavage site between the tag and protein.