I know that if you treat the cells with PI-PLC, the GPI-linked proteins will be cleaved off from the cell surface. Please look at PI-PLC protocol. They describe how to collect GPI-linked cell surface protein. 

Deo, thank you for your answer. So you would suggest treated cells with PI-PLC and running western blot of supernatant, rather than performing a lysis for total protein extraction?

I think add PI-PLC in lysis  buffer and follow the regular procedure. I think it should work. Here is another protocol described in this paper

Intracellular Retention of Glycosylphosphatidyl Inositol-Linked Proteins in Caveolin-Deficient Cells by Sotgia  et al.

Thank you Deo. Much appreciated