There have been significant improvements in characterizing glycoproteins and glycans in the recent years. This dissertation focuses on further expanding the tools for glycan and glycoprotein characterizations and investigating the biological roles of glycans on immune cells and antibodies. Chapter I introduces glycans with focus on their biosynthesis, structures, and biological functions especially in the context of immunity and immunoglobulins. Additionally, the analytical tools for studying glycans and glycoproteins are presented. Chapter II uses analytical methods to unravel changes in glycosylation of immune cell membrane and their secreted antibodies (IgG1) with glycoenzyme inhibitors, and monosaccharide supplementations. Furthermore, the interactions of IgG1 glycans with Fc receptors was explored through molecular modeling. Effects of glycan changes on cell transcriptome and viability were also assessed by 3′ Tag-RNA-Seq and cell proliferation assay. This is the first study that explores changes in glycosylation of cell membrane and secreted proteins in parallel and evaluates changes in transcriptome as the result of induced glycan changes with glycoenzyme inhibitors. Chapter III probes deeper into the context of glycosylation changes and their effects on immunity and diseases by identifying antibody glycan biomarkers in a rare autoimmune disease (n=10, pemphigus vulgaris). Additionally, the enrichment of glycan markers on auto-reactive antibodies is demonstrated by capturing the disease specific autoantibodies on Desmoglein-3 (Dsg3) target protein using ELISA, and glycoproteome profiling of the captured antibodies using LC-MS/MS. Chapter IV presents a novel approach for absolute quantitation of proteins, which addresses the issues often encountered in determining protein abundances, namely the lack of protein standards and heterogeneity of PTMs in proteins. This method combines qualitative analysis (protein identification) and quantification (absolute concentration measurements) of proteins into a single analysis. The method was applied to a set of bovine milk protein samples (n = 60) in duplicates, yielding the absolute concentrations of over 600 proteins in bovine milk.