RCDC kit from Biorad is generally used to quantify the protein when it is having any detergent or reducing agent or both. Since detergents and reducing agents interfere in protein assay this kit has been developed to overcome that problem (Reducing Agent Compatible and Detergent Compatible : RCDC). Now its your discretion to use this kit before or after the clean up? And I would also like to know that What do you mean by Cleanup? Does it mean removal of unwanted ingredients after extraction ? Good luck... 

Just came across this paper:

http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.1999.00579.x/full

They performed BioRad Dc Protein Assay without clean-up. Please take a look :)

Btw, have you compared the protein quantity before and after the clean-up?

http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.1999.00579.x/full

Hi

From my expertise i can tell that the sensitivity of the Kit is 10 fold less sensitive than BCA. But It tolerates many additives as detergents  DC or high urea

Just  compare results  before and after clean-up

Thanks for the suggestions everyone. Deepti, the reason for clean-up is largely to remove phenolic compounds seeing that we are dealing with a plant extract. severe vertical streaking on the 2D analysis was initially observed (possible contaminants such as phenolic compounds) and to a lesser extent horizontal streaking. However, there is a loss of protein after that clean up.   

Adrian, Polyphenols are known to form precipitates with protein specially the bulky ones and therefore you would be experiencing loss of protein during the clean up process. How do you do the clean up is done, is very essential in this case.