Protein differences among different disease phenotypes

If you have a protein in a child and an adult that are the same, biologically, and yet produce different disease spectra, you suspect that either the proteins are different (post-translational changes, folding, epitopes, etc) or somehow their binding with ligands/receptors are altered in some fashion. How should one go about finding out the fastest way about possible differences in the proteins OR their interactions with their receptors/ligands?

JA