Glycans and glycoconjugates exert myriad important biological functions, extending and diversifying the functionality of protein molecules. Extensive studies have focused on the protein and gene realms; however, due to the lack of means for external amplification and the inherent heterogeneity of glycans and glycoconjugates, their researches have not adequately informed the understanding of critical biological and pathological processes. Researchers in glycoscience have strived to bridge this gap and redefine our understanding of carbohydrate functions. Glycosaminoglycans (GAGs) represent the most highly charged and poly-disperse animal glycans. GAGs exist on the surfaces of most mammalian cells and in the extracellular matrices. They play critical roles in anticoagulation, angiogenesis, inflammation, metastasis, cell proliferation and differentiation. Heparin and heparan sulfate (HS) are the most highly sulfated and structurally diverse GAGs, regulating a variety of cell functions by interacting directly with many growth factors and their receptors. Examples include fibroblast growth factor, bone morphogenetic protein and Wnt. These interactions rely on the unique structural properties of HS/heparin molecules. Extracellular enzymes (Sulfs and heparanase) also alter the fine structure of HS molecules. In order to investigate to the correlation between structure and function for mature HS/heparin chains, we employed mass spectrometry (MS) coupled with liquid chromatography (LC) as a sensitive and robust platform for composition profiling and detailed structural characterization. We developed a novel HPLC-chip based LC-MS platform to enable HS oligosaccharide profiling. In this thesis work, the chip LC-MS platform was improved for effective and informative tandem MS for HS oligosaccharides. We also advanced electron-based ion dissociation methods for more detailed and reliable sequence determination of HS oligosaccharides. These newly developed methods enable the investigation of the HS/heparin structural changes induced by HS extracellular remodeling enzymes, human Sulfs and heparanase. Application of the methods revealed the recognition preferences of these remodeling enzymes at the oligosaccharide level and led to the discovery of a novel peeling reaction induced by the 3-O-sulfation at the reducing end of HS saccharides.