Most protein labeling protocols recommend to separate the free labels by extensive dialysis or by size exclusion chromatography. Does anyone know if it is possible to do the same by using Ni affinity chromatography? If so, is it reliable?
We have done this before but be careful of the amount of DTT you add to quench the maleimide before adding it to the column and be sure to extensively wash before eluting your labeled protein
The protein has presumably already been purified, so there is no need to include a low concentration of imidazole in the binding buffer to prevent non-specific protein binding.
I have applied this approach in the last week and it indeed worked very well. The only detail is that I used a buffer with 20 mM of imidazole as wash buffer because it was what I had in hands at the time.