In order for neuroproteomics to function correctly, proteins must be separated in terms of the proteome from which they came.  For example, one set might be under normal conditions, while another might be under diseased conditions.  Proteins are commonly separated using two-dimensional polyacrylamide gel electrophoresis (2D PAGE).  For this technique, proteins are run across an immobile gel with a pH gradient until they stop at the point where their net charge is neutral.  After separating by charge in one direction, sodium dodecyl sulfate is run in the other direction to separate the proteins by size.  A two-dimensional map is created using this technique that can be used to match additional proteins later.
	One can usually match the function of a protein by identifying in an 2D PAGE in simple proteomics because many intracellular somatic pathways are known.  In neuroproteomics, however, many proteins combine to give an end result that may be neurological disease or breakdown.  It is necessary then to study each protein individually and find a correlation between the different proteins to determine the cause of a neurological disease.  New techniques are being developed that can identify proteins once they are separated out using 2D PAGE.