Glycosylation is the most common posttranslational modification of proteins. It is a complex process involving many functional proteins and resulting'in a great diversity of structures. The retention of glucose residues on N-linked oligosaccharides following ER a-glucosidase inhibition by imino sugars such as N-butyl deoxynojirimycin, increases the protein misfolding and the amount of glycoprotein destined for degradation via the endoplasmic reticulum associated degradation (ERAD) pathway. Intracellular peptide N-glycosidases (PNGases) act generating free oligosaccharides (FOS) and the protein is targeted for digestion. Free oligosaccharides were extracted from cells treated with NB-DNJ and subjected to ion-exchange chromatography before fluorescence labelling with 2-AA (anthranilic acid) and lectin-affinity chromatography. Separation of labelled FOS by NP-HPLC provided a rapid and sensitive method for the detection of all FOS species resulting from the degradation of glycoprotein exported from the ER. A. robust, cellular-based assay for ER a-glucosidase activity in the presence of inhibitor was developed that provided meaningful kinetics for a-glucosidase-mediated hydrolysis ofN-linked oligosaccharides as proteins are folded in the ER. Furthermore, the origin of FOS generation was studied, to determine the relative amount of FOS produced as a result of ERAD (protein derived) relative to the amount produced by a possible hydrolytic activity of oligosaccharyltransferase (lipid linked derived). A dual localisation of PNGase activity and non-proteasomal and proteasomal ERAD were demonstrated. Analysis of FOS in endomannosidase negative/non-utilised cells revealed the extent of ER/Golgi recycling of glycoproteins and the role of this enzyme in qua~ity control pathways in cells. Oral administration of NB-DNJ results in the production of glucosylated free oligosaccharide in vivo. Further to cellular based assays these glucosylated free oligosaccharides were detected in murine and human samples. The observed differences in the free oligosaccharides produced in different tissues can be explained according to hypothesises generated from culture cell studies. The effects observed with NB-DNJ, a therapeutic with considerable potential for treating lysosomal storage disorders and reducing viral infectious processes, was dose and time dependent so enabling the pharmokinetics of NB-DNJ to be observed. These studies also elucidated a transrenal method of clearance of glucosylated FOS and demonstrate that glucosylated FOS are excellent non-invasive in vivo biomarkers for a-glucosidase inhibition and protein misfolding in the ER.