Lipooligosaccharide (LOS) is the major component of the external membrane of Campylobacter jejuni. LOS contains a hydrophobic moiety, lipid A, and a hydrophilic moiety, oligosaccharide. Due to the unique mimicry of human ganglioside structures and potential involvement in the induction of the autoimmune polyneuropathies, Guillain-Barre and Miller Fisher syndromes, the structural characterization of C. jejuni LOS has received much attention. We have been using capillary zone electrophoresis-mass spectrometry to analyze O-deacylated LOS from C. jejuni. In an attempt to optimize the separation conditions, the effect of methanol on the separation of LOS was investigated. It was found that methanol resulted in stronger adsorption of LOS onto the wall of fused-silica capillary. In this paper, we applied this adsorption to perform electrophoresis-assisted open-tubular liquid chromatography electrospray mass spectrometry for the analysis of O-deacylated LOS mixtures from C. jejuni. The analytical potential of the proposed strategy for the analysis of O-deacylated LOS glycoforms from five bacterial colonies is demonstrated. Online tandem mass spectrometry is shown to provide a powerful tool for characterization of variations in the hexosamine backbone, phosphorylation of the lipid A, and sialic acid sequence information.