One of the limitations in protein analysis by microchip capillary electrophoresis (MCE) is the adsorption of the analytes onto the walls of the separation channel because of the electrostatic or hydrophobic interactions of proteins with the channel. Capillary coatings are required to prevent protein adsorption phenomena onto the capillary wall and to increase the repeatability of the separations. In addition of that, capillary coatings should thus ensure high separation efficiency and good repeatability. In this work, thiol-ene based microchips were used for analysis of PolyK-SIINFEKL peptide. MCE-LIF(laser-induced fluorescence) method was developed in this work for future studying of binding ratios between oncolytic adenovirus and MHC-I epitope peptide (PolyK-SIINFEKL peptide). Since the peptides used in research have been fluorescently labeled with fluorescein isothiocyanate (FITC-peptides) optimization of the MCE-LIF method involved measurements of the fluorescein to adjust settings such as a detection slit size, injection time and photomultiplier tube settings. Validation characteristics such as detection limit, quantitation limit and linearity were demonstrated only on fluorescein samples due to the protein adsorption onto the microchannels (SIINFEKL peptide -non interactive with virus and PolyK-SIINFEKL peptide-interactive with virus). Successful microchannel coatings should have been done prior to method validation by FITC-peptides. Conventional PEGylation on allyl-rich thiol-ene microchannels was a viable approach to reduce both the surface charge and hydrophobicity of the native surfaces, as expected, but was not enough to eliminate nonspecific adsorption of the peptide on allyl-rich thiol-ene surfaces. Using the peptide non fluorescent analogue as the dynamic coating on thiol-rich thiol-ene microchannels showed more promising results. The dynamic peptide coating facilitated MCE analysis of the fluorescent polyK-SIINFEKL peptide on thiol-rich thiol-ene surfaces.