Improved resolution of human cerebrospinal fluid proteins on two-dimensional gels

Proteomics combines two-dimensional gel electro phoresis and peptide mass fingerprinting and can potentially identify a protein(s) unique to disease. Such proteins can be used either for diagnosis or may be relevant to the pathogenesis of disease. Because patients with multiple sclerosis (MS) have increased amounts of immunoglobulin (Ig) G in their cerebrospinal fluid (C SF) that is directed against an as yet unidentified protein, we are applying proteomics to MS C SF, studies that require optimal separation of proteins in human C SF. We found that recovery of proteins from C SF of MS patients was improved using ultrafiltration, rather than dialysis, for desalting. Resolution of these proteins was enhanced by aceto ne precipitatio n of desalted C SF before electrophoresis and by fractionation of C SF using C ibacron Blue sepharose affinity chromatography. Improved protein recovery and resolution will facilitate excision from gels for analysis by peptide mass fingerprinting.