The first use of epitope tagging was described by Munro and Pelham in 1984. The FLAG-tag was the second example of a fully functional, improved epitope tag, published in the scientific literature. and was the only epitope tag to be patented. It has since become one of the most commonly used protein tags in laboratories worldwide. Unlike some other tags (e.g. myc, HA), where a monoclonal antibody was first isolated against an existing protein, then the epitope was characterized and used as a tag, the FLAG epitope was an idealized, artificial design, to which monoclonal antibodies were raised. The FLAG-tag's sequence was optimized for compatibility with proteins it is attached to, in that FLAG-tag is more hydrophilic than other common epitope tags and therefore less likely to reduce the activity of proteins to which FLAG-tag is appended. In addition, N-terminal FLAG tags can be removed readily from proteins once they have been isolated, by treatment with the specific protease, enterokinase (enteropeptidase).
The third report of epitope tagging, (HA-tag), appeared about one year after the Flag system had been first shipped.