For protein isolation we dissect out the areas that we are interested in (example hippocampus, cerebellum, cortex etc) at the time of killing. These areas are then snap frozen in liquid nitrogen and stored at -80 until we want to isolate the protein. If we are not interested in specific areas we just bisect the brain and then freeze in liquid nitrogen.
We don't have any major issues with this protocol. Of course it is best to compare fresh brain and stored brain for your protein of interest as all protocols do not serve for all conditions.
Good luck.