I don't know of any resin/linker that can provide that functionality. But you can use a linker designed for sensitive or orthogonal cleavage chemistry, to preserve your side chain blockers. Then modify the blocked peptide before deblocking in full strength cleavage cocktail.

Good luck!

Cap with Isocyanate ?

Thank you John and Philippe for your valuable insights. I think the simplest approach involves reductive amination of the appropriate primary amine to FIA AM resin, to generate a resin-bound secondary amine. Acylation of this group with the C-terminal residue of the peptide, chain extension, and TFA cleavage, results in the peptide N-alkylamide. For peptide N-methyl- and N-ethylamide, FIA-AM resins are available with Novabiochem, pre-derivatized with methylamine and ethylamine: Methyl indole AM resin and Ethyl indole AM resins respectively.

Way to go