Abstract: The studies for risk assessment of transgenic crops require amounts of transgenic protein, but it is extremely difficult to prepare the required amount of purified protein from transgenic plants. Nevertheless, ample protein of high purity may be produced by over-expressing the protein in microbes. Using microbial proteins in a study for risk assessment can solve this problem, but the microbial proteins must be equivalent with transgenic plant proteins. In this article, we describe a typical set of methods used to compare the equivalence for micro-protein with transgenic protein, which for the purposes of providing reference for the risk assessment using micro-proteins instead of trans-proteins.