The model of microinjection of mRNAs to Xenopus oocites is a powerful tool on this field. You can review papers written by Gerardo Gamba.

Hi Ricky, you have to be more specific about what you want to do.

You can do ultracentrifugation of cell lysates to enrich for cell membrane and nuclear membrane fractions like Subash suggested.

You can also do cell surface biotinylation to specifically label cell surface proteins and isolate them using immobilized avidin. You can treat cells with digitonin to release intracellular proteins without solubilizing the whole cell.

Then you can do a gentle cell lysis method that does not solubilize the nucleus, pass the lysate through immobilized avidin to get rid of cell surface proteins, do ultracentrifugation and biotinylate proteins in the nuclear fraction. Re-centrifuge the nuclear fraction to get rid of soluble proteins in the nuclear fraction and then solubilize and analyze by western and probe with labeled avidin.   

Yes Ricky, you have to explain what kind protein do you want to isolate? you can use ultra centrifuge to separate the organelle cells? Is there any ultra centrifuge in your university? if not, you can use this equipment in my laboratory of Brawijaya University. 

regard

Thanks for your answer Mr. Subash Chandra Malik, Mr. Gabriel López-Velázquez, Mr. Steingrimur Stefansson,

@Mrs Fatchiyah Fatchiyah , i am still writing the draft not yet become proposal..thanks for your kindness..