A computer-enhanced comparative study of brain region polypeptides and proteins by two-dimensional gel electrophoresis

A reproducible and quantitative strategy for identifying tissue-specific proteins of the central nervous system is described. The methods include a simple extraction procedure, two-dimensional polyacrylamide gel electrophoresis (2-DGE), silver staining, and computerized analysis. Acetic acid protein extractions of brain regions from three groups of male Sprague—Dawley rats were compared by computer analysis using 2-DGE with GELCODE silver staining. Protein spot mapping and characterizations of molecular weight and pI were compiled for the pineal gland, retina, hypothalamus and cerebral cortex. Regionally specific protein spots were identified using the Visage System (BioImage) for data acquisition and a new set of algorithms (University of Arizona) for assigning isoelectric point (pI) and molecular weight determinations, spot matching and selection of unique spots. Seventeen newly identified acidic proteins are unique to the pineal gland. Some others are also common to the retina but not in other regions examined. Further study of these and other regionally specific proteins are of particular interest under conditions which alter biological or disease mechanisms.