Proteome studies of human cerebrospinal fluid and brain tissue using a preparative two-dimensional electophoresis approach prior to mass spectrometry

A preparative proteomic approach, involving liquid phase isoelectric focusi ng (IEF) in combination with one-dimensional electrophoresis and electroelu tion followed by mass spectrometry and database searches, was found to be a n important tool for identifying low-abundant proteins (mug/L) in human cer ebrospinal fluid (CSF) and membrane proteins in human frontal cortex. Sever al neuron-related proteins, such as amyloid precursor-like protein, chromog ranins A and B, glial fibrillary acid protein, p-trace, transthyretin, ubiq uitin, and cystatin C, were identified in CSF. Several types of proteins we re also characterized from a detergent-solubilized human frontal cortex hom ogenate including membrane proteins such as synaptophysin, syntaxin and Na/K+ ATPase. One-third of the identified proteins have not previously been i dentified in human CSF or human frontal cortex using proteomic techniques. The absence of these proteins in two-dimensional electrophoresis maps might be due to insufficient amounts or low solubility. The advantages of using preparative liquid phase electrophoretic separations for identifying protei ns from complex biological mixtures are speed of analysis, high loadability in the IEF separation, nondiscrimination of membrane proteins or low abund ance proteins, yielding sufficient amounts for characterzation by mass spec trometry. The use of this strategy in proteome studies of CSF/brain tissue is expected to offer new perspectives in studies of the pathology of neurod egenerative diseases, and reveal new potential markers for brain disorders.