Protein size...if the mutation in a protein is making it three amino acids less in size...

Depending on the position and/or net charge difference that it results in you can use proteolytic cleavage or isoelectric focussing, as basic methods to answer these questions.

As the difference is of only three amino acids i dont think there will be much difference in size and net charge...

Mass Spectrometry?

MS is suituable for even crude, low concentration protein solution, but suggest to perform in silico trypsin digestion of your proteins to make sure you obtain the peptides differ in MW.

http://web.expasy.org/peptide_cutter/