Are NP40 and DTT required for SUMO Protease activity? Will they interfere with downstream applications?
Yes, they are both required, although it might be possible to substitute the NP40 with another detergent via dialysis if you have concern about interference with mass spectrometry. DTT is an absolute requirement.
What enzyme should I choose if I do not want any extra amino acids left on my protein of interest after cleavage?
SUMO protease, also known as Ulp, is a recombinant fragment of ULP1 (Ubl-specific protease 1) from Saccharomyces cerevisiae. It is highly specific for the SUMO protein fusion, recognizing the tertiary structure of SUMO rather than an amino acid sequence. The SUMO protease itself has a His tag for easy removal from the protein mix after cleavage.