How do you estimate the isoelectric point of a peptide?

Question

It seems relative easy for a free amino acid, but if I had a peptide arg-cys-tyr how do i determine which pka values (i.e. ionizable groups) to use? Are the terminal ends of this peptide included in the overall PI calculation as well?

Answer 1

You subject the tripeptide arg-cys-tyr to electrophoresis at various pH's. The pH at which the tripeptide does not migrate is the isoelectric point.