We are quantifying the dilysyl-malondialdehyde crosslink by mass spectrometry. We are currently reacting MDA with lysine but because of the relative reactivities of the alpha and epsilon amines, most of our internal standard is crosslinked at the alpha amine position. Although the mass is the same, it elutes slightly later on HPLC and not all the fragments are identical between the alpha (standard) and epsilon (sample) crosslinks. 

Would someone have an idea on how we could protect the alpha amines prior to the reaction with MDA in a way that could then be later deprotected without hydrolyzing the diamide crosslink?

Thanks