Characterization and interpretation of disease-associated alterations of protein glycosylation are the central aims of the emerging glycoproteomics projects, which are expected to lead to more sensitive and specific diagnosis and improve therapeutic outcomes for various diseases. Here we report a new approach to identify carbohydrate-targeting serum biomarkers, termed isotopic glycosidase elution and labeling on lectin-column chromatography (IGEL). This technology is based on glycan structure-specific enrichment of glycopeptides by lectin-column chromatography and site-directed tagging of N-glycosylation sites by (18)O during the elution with N-glycosidase. The combination of IGEL with 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) stable isotope labeling enabled us not only to identify N-glycosylation sites effectively but also to compare glycan structures on each glycosylation site quantitatively in a single LC/MS/MS analysis. We applied this method to eight sera from lung cancer patients and controls, and finally identified 107 glycopeptides in their sera, including A2GL_Asn151, A2GL_Asn290, CD14_Asn132, CO8A_Asn417, C163A_Asn64, TIMP1_Asn30, and TSP1_Asn1049 which showed the significant change of the affinity to Concanavalin A (ConA) lectin between the lung cancer samples and the controls (p < 0.05 and more than twofold change). These screening results were further confirmed by the conventional lectin-column chromatography and immunoblot analysis using additional serum samples. Our novel methodology, which should be valuable for diverse biomarker discoveries, can provide high-throughput and quantitative profiling of glycan structure alterations.