Question: if we can separate proteins by gel electrophoris so why we use sds electrophoresis for protein separation?

Answer

The porosity of agarose gel is higher than that of the sds. Because proteins are much smaller in the size of molecules compared to the nucleic acids, a small porosity (sds) is chosen for proteins while the large porosity would be better for DNA and RNA.

Explanation

SDS is n anionic compound which denatures proteins and also causes unfolding of polypeptide into a linear orientation. SDS also provides an even distribution of negative charge which aids also in providing direction of seperation of proteins.