The broad scope of the available raw neuronal proteins to map requires that initial studies be focused on small areas of the neurons.  When taking samples, there are a few places that interest neurologists most.  The most important place to start for neurologists is the plasma membrane.  This is where most of the communication between neurons takes place.  The proteins being mapped here include ion channels, neurotransmitter receptors, and molecule transporters.  Along the plasma membrane, the proteins involved in creating cholesterol-rich lipid rafts are being studied because they have been shown to be crucial for glutamate uptake during the initial stages of neuron formation.  As mentioned before, vesicle proteins are also being studied closely because they are involved in disease.
	Collecting samples to study, however, requires special consideration to ensure that the reproducibility of the samples is not compromised.  When taking a global sample of one area of the brain for example, proteins that are ubiquitous and relatively unimportant show up very clear in the SDS PAGE.  Other unexplored, more specific proteins barely show up and are therefore ignored.  It is usually necessary to divide up the plasma membrane proteome, for example, into subproteomes characterized by specific function.  This allows these more specific classes of peptides to show up more clearly.  In a way, dividing into subproteomes is simply applying a magnifying lens to a specific section of a global proteome’s SDS PAGE map.  This method seems to be most effective when applied to each cellular organelle separately.  Mitochondrial proteins, for example, which are more effective at transporting electrons across its membrane, can be specifically targeted effectively in order to match their electron-transporting ability to their amino acid sequence.