Depends whether you are interested in a specific localization of the protein in the brain, or need to verify a general level.
General I would suggest either using microdialysis, implanted stereotaxicallly or a micro-PET-scan using a tracer to target your desired protein.
If you have access to PET-tracers autoradiography might be a good method too.
Depending on how stable your protein is, you can also try to homogenate the tissue and make HPLC-analysis of it. Remember that some proteins and transmitters will degrade, oxidate and so on, so you need to work fast, and freeze fast.
If you have no access to these tech. you can slice, stain with IHC and then count positive cells using non-biases stereology to see difference between animals,