Glycosylation on neuronal cell surface plays an important role in neuro-biological functions including synaptic plasticity and memory formation. Despite its biological importances, molecular-level investigation into brain glycome has remained in relative uncertainty due to the lack of effective analytical methods. In this study, a highly sensitive MS-compatible method for glycan/glycolipid extraction from brain tissue was combined with structure-specific nano-LC/MS and MS/MS to build up brain glycome library including N- and O-glycans and gangliosides. Briefly, N-glycans were enzymatically released by PNGaseF, while O-glycans were concentrated by beta-elimination method. Gangliosides were extracted based on modified Folch method. Purified and enriched glycans and gangliosides by SPE were identified and quantified by positive ion mode of nano-LC PGC Chip/Q-TOF MS and negative ion mode of nano-LC C18 Chip/Q-TOF, respectively. The biosynthetic library of mouse brain glycome was constructed using about one hundred glycans and 70 gangliosides with brain-specific glycans characterized by tandem MS using diagnostic fragment ions. The constructed library of mouse brain glycome was applied for monitoring glycome alteration in various neurobiological environments including different developmental stages and KO conditions (Maneal, Galnt13, St8sia3) with high speed and accuracy. This approach could be useful as the informative data for glycome study related the specific neurodiseases.