It is now understood that a cohesive series of quality control checkpoints ensures the accuracy of gene expression in eukaryotic cells. Although initiated in the nucleus to monitor the integrity of inherited genetic information, the quality control program encompasses post-translational events that facilitate the structural maturation of encoded proteins or target them for degradation if unable to adopt native structure. Given the fact that many genetic mutations actually manifest themselves at the level of aberrant protein structure, a current challenge in the post-genomics era is to elucidate how post-translational checkpoints can modify the severity of numerous loss-of-function and gain-of-toxic-function diseases, possibly influencing an individual's susceptibility toward the development of the associated pathologies. The purpose of this chapter is to describe the experimental methodology by which alpha1-antitrypsin has been used as a molecular reagent to define the mechanisms by which the processing and recognition of asparagine-linked oligosaccharides can orchestrate the fate of newly synthesized glycoproteins in the early secretory pathway. The conceptual framework, and associated techniques, can serve as a roadmap for the investigation of other mutated glycoproteins, many of which can contribute to disease.