The Factor Xa Cleavage Capture Kit is designed for highly specific cleavage of fusion proteins followed by convenient affinity-based capture and removal of Factor Xa. After cleavage of the target protein, Factor Xa is removed with greater than 99% efficiency from the reaction by affinity capture on Xarrest™ Agarose. Following capture of Factor Xa, the agarose is removed by spin-filtration. No buffer changes are necessary because the same buffer conditions are used for both cleavage and capture. The kit includes a Cleavage Control Protein for conducting control digests in parallel with experimental samples, or to test cleavage under customized buffer conditions. The 49 kDa Xa Cleavage Control Protein is cleaved into two proteolytic fragments of 32 kDa and 17 kDa, which are easily visualized by standard SDS-PAGE followed by Coomassie blue staining. The Xa Cleavage Control Protein also features an amino terminal S•Tag™ sequence enabling sensitive detection of the 17 kDa proteolytic product with Western Blot reagents.