The mammalian immune system has evolved the ability use glycan binding proteins to regulate immune cell responses, and to use glycans in generating an immune response to pathogens. Receptors that recognize glycans help immune cells to distinguish between self and non-self and help identify and generate immune responses against pathogens that carry ‘non-self’ glycans. For pathogens that decorate themselves with ‘self-like’ glycans to shield immune attack, such as HIV, the immune system can use glycans as part of the immune epitope or avoid the glycan shield to develop pathogen specific immune responses. While current tools to study the roles of glycans in immuno-biology are limiting, only mass spectrometry has the sensitivity needed to systematically extract information about the glycome proteo-glycome in biological samples. In our own work, we have turned to the power of mass spectrometry-based glycan profiling and glyco-proteomics whenever possible. Examples include identification the glycoprotein ligands of the B cell inhibitory protein CD22 using in situ glycan-protein crosslinking, analysis of the impact of glycosyltransferase inhibitors on the cellular glycome, and analysis of site-specific glycosylation of HIV envelope glycoprotein, the target for all known broadly neutralizing antibodies of HIV. As will be seen from these examples, the existing tools for studying the glycome are powerful, yet they lag far behind those available for studying the genome and proteome. In the foreseeable future, mass spectrometry-based methods will undoubtably provide the basis for transformative technologies needed to elucidate the mammalian glycome and its roles in biology (Supported by NIH research grants: AI113867; AI100663; AI050143).