I wish to know how to use DIPEA or N,N-Diisopropylethylamine or Hünig's base for deprotonation of primary amine groups in polyethylenimine. Is it added based on molar ratio or weight ratio?
DIPEA is a good base used for deprotonation of carboxylic acid in peptides/amino acids to give you the intermediate carboxylate. It is added based on molar ratio.
First, DIPEA will be able to deprotonate your PEI if it is an ammonium salt. I don't think the DIPEA is basic enough to deprotonate a primary amine.
Then, I am happy with John George Hardy about the conjugaison in water of a protein. Have a look on couplig reagent compatible with water. Have you the possibility to transform some of your amine into isothiocyanate ?