Aberrant glycosylation is a well-known event in autoimmune diseases and cancers. Indeed, several glycans are widely recognized as the powerful biomarker for screening disease states. Bechet disease (BD) is a type of inflammatory disorder include painful mouth sores, genital sores, and arthritis. Although many diagnostic criteria of BD have been proposed, it is still challenging to establish reliable diagnosis method. Here, we created glycan isomeric-based novel approach for inflammation disease monitoring. Unlike the conventional glycomic approach with global mass spectrometric profiling of serum released glycan, we have developed new platform to quantify isomer-specific glycan using PGC/MRM-MS. Especially, we have targeted sialylated glycans which are known to highly present in immunoglobulin proteins closely related with inflammation diseases. Serum N-glycans released from BD patients (n=47) and heathy control (n=47), respectively were selectively fractionated by PGC-SPE prior to MS analysis. Targeted acidic glycans were chromatographically separated to obtain isomer-specific information and relatively quantified by PGC-MRM MS. Total eleven N-glycan isomers were monitored for the diagnosis of BD. We found that BD patients contained significant quantity of mono/di-sialylated bi-antennary N-glycans consisting of Hex5 HexNAc4 NeuAc1-2 compared with healthy control group. Expression level in patient cohort were 5 to 10-folds higher than those in control group showing complete separation. Four bi-antennary acid glycan isomers showed high diagnostic efficacy providing AUC of ROC curve over 0.98. Interestingly, these marker glycans exhibits unique correlations with biological characteristics of cohorts. Specially, two isomers of Hex5 HexNAc4 NeuAc1 and two isomers of Hex5 HexNAc4 NeuAc2 could completely distinguish male and female groups in healthy control cohort. Glycan expression level in female groups were 6 to 10 times higher than that of male groups resulting in 1.0 AUC in ROC curve. Our novel approach that targeting isomer-specific glycan will provide significant insight into the glycobiological aspects of the BD process.