New proteomic initiatives to study multiple sclerosis

Abstract

Neurological diseases, including MS, often provoke changes in the functioning of the endothelial and epithelial brain barriers and give rise to disease associated alterations of the CSF proteome. Therefore, CSF analysis is believed to represent a valuable approach to identify disease-related proteins. The goal of this chapter is the construction of a protein database of CSF from MS patients, using gel-based and gel-free identification approaches. In a first setup, twodimensional gel electrophoresis was applied on individual CSF samples of five MS patients and high-performance liquid chromatography (HPLC) coupled to electrospray ionization tandem mass spectrometry (ESI-MS/MS) resulted in the identification of 65 different proteins. Eighteen of these proteins have not been described previously on 20 gels of CSF and their potential relation to MS is discussed. In a second setup, unseparated protein mixtures from ultrafiltered CSF of MS and non-MS patients were digested with trypsin and analyzed by offline strong cation exchange chromatography (SCX) coupled to on-line reversed phase LC-ESI-MS/MS. Alternatively, the trypsin-treated sub-proteomes were analyzed directly by LC-ESI-MS/MS and gas-phase fractionation in the mass spectrometer. Taken together, both gel-free proteomic approaches in combination with a three-step evaluation process including the search engines Sequest and Mascot, and the validation software Scaffold, resulted in the identification of 148 proteins. Sixty proteins were identified in CSF for the first time by mass spectrometry. In addition, the capacity of the gel-free approach to identify disease-related molecules is discussed. Finally, three identified proteins, cystatin A, annexin A5 and psoriasin were validated with respect to their expression in CSF and/or brain slices of MS and control patients.