New approaches for the treatment of multiple sclerosis involve the design and synthesis of peptide or nonpeptide analogues of myelin sheath, which could alter the immune response of patients. For this purpose, the cyclo(75-82) myelin basic protein (MBP)(74-85) analogue was conjugated to mannan (a polymannose) via (Lys-Gly)(5) linker. Monitoring of synthesis of the (Lys-Gly)(5)-containing cyclic analogue of MBP, mannan oxidation, and the conjugation reaction of this analogue to oxidized mannan was performed with capillary electrophoresis (CE) in operating buffers of different pH values. The (Lys-Gly)(5)cyclo(75-82)MBP(74-85) was efficiently synthesized by solid-phase synthesis and purified to a high degree, as confirmed by CE analysis in a low-pH (3.0) phosphate buffer and normal polarity. Oxidation of mannan was monitored using a high-pH (9.3) borate buffer, and the generation of heterogeneous products and even UV-absorbing peaks was shown by CE. CE analysis in a pH 5.1 phosphate buffer offers high resolution of oxidized mannan and the conjugation product and can be used for screening of the reaction products. Mannan-peptide conjugates of varying degrees of substitution and unreacted mannan were observed. The developed CE analysis presents distinct advantages over sodium dodecyl sulfate-polyacrylamide gel electrophoresis such as high versatility, high separation efficiency, short analysis time, low cost, and low solvent consumption.