Tandem Affinity Purification - Disadvantages

Disadvantages

However, there is also the possibility that a tag added to a protein might obscure binding of the new protein to its interacting partners. In addition, the tag may also affect protein expression levels. On the other hand, the tag may also not be sufficiently exposed to the affinity beads, hence skewing the results.

There may also be a possibility of a cleavage of the proteins by the TEV protease, although this is unlikely to be frequent given the high specificity of the TEV protease.