Recent advances in the proteomic technology in search of biomarker or biomarker signature that accurately identifies the clinical syndrome would allow for improved diagnosis and disease monitoring. Diagnosing Multiple Sclerosis(MS) and other demyelinating diseases such as neuromyelitis optica (NMO) is not always easy clinically and the pathogenesis of the two demyelinating diseases remains mystery. Here we adopted CLINPROT system, a magnetic bead-based purification followed by MALDI-TOF MS to profile human cerebrospinal fluids proteins and peptides. CSF samples from patients with definite MS (remission and relapse), NMO (remission and relapse) and primary progressive multiple sclerosis (PPMS) were analyzed. We used a reagent set of chemically coated magnetic beads, reversed phase ClinProtTM and a- cyano-4-hydroxycinnamic acid as the matrix solution. The eluted samples were then dropped onto a MALDI sample plate (AnchorchipTM), and spectra were obtained by an Autoflex II and a subsequent tandem MS analysis was performed by Ultraflex (Bruker Daltonics). The criteria for peak detection were: signal-to-noise ratio >5, 2-Da peak-width filter. The pretreated data were graphed as spectra and evaluated by statistical analysis using the ClinProToolsTM software (Bruker Daltonics).Reproducible profiles were obtained as clear signals and approximately fifty peaks were detected from each of CSF samples. A differential distribution of samples from MS and NMO both in remission was noticeable, while samples from PPMS were not separated effectively using the same platform. One of the key variables contributing to the classification of the samples with an m/z of 3,511 was defined as c-terminal fragment (182-212) of neuroendocrine peptide 7B2 by the tandem MS analysis. The application of CLINPROT system for CSF samples holds the potential to advance our understanding of the biochemical basis of MS and NMO.
