Your best bet is to resynthesize the peptide without the methylation.

Adam is right, you should re-synthesize the peptide... modifications of the N-term is usually irrevocable without harming the rest of the AA in the sequence. Did you actually mean the N-term modification? Why do you methylate the amide bonds?

Marcus its not the N-term modification. Its one of the amide bond in the peptide which we methylate, so instead of -CO-NH- in the peptide we have -CO-N(CH3)- at that peptide bond.

There are various utility of N-methylated peptide. You can go through some of the paper published from Horst Kessler's group in Department of Chem from Technical University of Munich.

Hope you understood.

Thanks by the way. :-)

Thanks Adam. Resynthesis of the peptide is the best option, I agree.

But I want to do this kind of reaction for some other reason.