FAQ: I have a very low concentration of protein and would prefer not to denature as a separate step with buffer exchange before digestion. What denaturants can he use in the Trypsin reaction itself?

Trypsin cannot tolerate SDS but will tolerate low levels (>0.01%) of most non-ionic detergents. Also heating your protein to 95 C for 1 minute (if your protein remains soluble when heated) or putting it into urea or guanidinium, no more than 0.25 M for either, or you'll denature the Trypsin itself, should work.