Compared to HILIC-HPLC, significant improvements in efficiency, selectivity and analysis speed offered by UPLC profiling of fluorescently labeled serum N-glycans on a sub-2 μm HILIC phase enabled the identification of stomach adenocarcinoma associated alterations. Differential glycosylation present on four highly abundant proteins, IgG, haptoglobin, transferrin and α1-acid glycoprotein, isolated from pathologically staged cancer serum using either affinity purification or 2-DE, were screened for targeted stomach cancer progression markers. The developed CE based method also enabled rapid and high efficiency separations of complex carbohydrate pools. Mere differences in linkage type or anomericity of isomeric oligosaccharides revealed differential migration, thus reflecting the separation principle based on discrepancies in hydrodynamic radii and associated molecular conformations. High precision induced by internal standards and GU normalization permits comparative studies of biomedical interest by CE. In a proof of concept study, sophisticated N-glycan features, such as core or antennary fucosylation, altered in inflammatory and malignant lung diseases, were successfully accentuated by CE-LIF. The standardized CE method not only revealed its potential for large scale studies, but also paves the way for a database enabling direct deduction of carbohydrate structural information from experimental CE data, similar to the HILIC-HPLC sources. Both UPLC and CE-LIF revealed excellent but different selectivity for IgG N-glycans. Exhaustive glycan elucidation using an elaborate combination of weak anion exchange enrichment and exoglycosidase array digestion with subsequent profiling exceeded 48 hours. Combination of the data individually generated using each technique demonstrated that complete structural annotation was possible within a total analysis time of 20 minutes due to the advantageous orthogonality of the separation mechanisms. Parallel use of both analytical techniques offers a powerful platform for rapid, comprehensive and confident analysis of IgG N-glycans present on therapeutic antibodies or on antibodies of biomedical significance. The orthogonal selectivity of UPLC and CE decisively contributed to characterizing mono- and bis-mannose-6-phosphate bearing oligosaccharides present on recombinant β-glucuronidase used for lysosomal storage disorder treatment. Exoglycosidase digestion and anion exchange fractionation were not definitive for identifying M6P decorated glycans. Mixed oxide affinity purification and alkaline phosphatase digestion, however, identified the glycan carriers of the M6P tag and glycoproteomic analysis revealed their respective site of attachment.