Continual growth in the biopharmaceutical industry in recombinant protein production has resulted in an ever increasing demand for optimised production processes, particularly in the area of upstream mammalian cell culture bioprocessing. The inefficient energy demands of mammalian cells in culture persists as a limiting factor for optimisation of cell culture processes. The Process Analytical Technology (PAT) framework initiative, put forward by the FDA in 2001, outlines measures for the strict monitoring and control of critical process parameters (CPP-s) affecting cell growth, productivity and product quality. The identification of CPP-s affecting protein quality (namely glycosylation and/or aggregation) has never been more important in seeking recombinant protein drug approval. A project was designed aimed at addressing the issue of CPP identification in high density CHO cell cultures producing the recombinant protein IgG1. Initial studies identified the importance of L-glutamine for cell growth and productivity, but also for increased complexity of the glycoform on the IgG1 protein. This was identified by comparing cultures containing 4 mM L-Glutamine to cultures containing 0 and 4 mM L-glutamate. Interestingly this study also identified that the impact of the by-product ammonia on recombinant protein quality may be over-estimated by investigating such effects through the incorporation of high initial ammonia concentrations (~15 mM). In addressing the title of the project, encapsulation as a mode of cultivation for suspension adapted mammalian cells was also investigated, with significantly increased yields in cell (3.7-fold) and product titres being achieved for batch encapsulated cultures in comparison to suspension cultures. Research to date has failed to identify if encapsulation may have implications on protein quality. Initial studies identified that the quality of the protein harvested at the end of the stationary growth period in both batch and suspension cultures was relatively similar. In order to further increase the maximum cell yields and product titres obtained in an encapsulated culture, a control-fed perfusion strategy was designed and applied to the encapsulated cells. Further increased cell yields, 10-fold higher than that which was achieved in a suspension batch cultures were noted. The volumetric titre of recombinant protein in the control-fed perfusion cultures was determined to be ~2.65- fold higher than that achieved in the batch encapsulated cultures. The rIgG1 had a higher degree of complexity at the end of the extended growth period in the control-fed perfusion culture in comparison to batch encapsulated cultures. The importance of monitoring cell viability and optimising the rate of perfusion was noted by the occurrence of a decrease in glycan complexity, associated with the accumulation of dead cells and glycosidase release.