Chinese hamster ovary (CHO) cells are one of the most commonly used cell lines in the production of biopharmaceuticals. The reduction of culture temperature during the exponential phase of a culture is a strategy that is commonly employed in the bioprocessing industry to increase process yield. Lower culture temperature results in a marked reduction in cell growth, increased specific productivity and prolonged cell viability. In order to understand the mechanisms involved at the post-transcriptional level in the cellular response to temperature-shift a phosphoproteomic analysis of SEAP secreting CHO cells was conducted. Using a liquid-chromatography mass spectrometry-based label-free approach in conjunction with Gallium, Iron and Titanium phosphopeptide enrichment strategies 1,307 unique phosphopeptides (1,480 phosphosites) were identified. Gene Ontology analysis revealed enrichment of pathways involved in protein synthesis and cell cycle progression. 92 phosphopeptides were determined as being significantly differentially-expressed 36hrs post temperature-shift, including translation initiation factors EIF5B, EIF4G3, Transcription activator BRG1 and the tumour suppressor protein, Protein NDRG1. Such proteins are potentially involved in controlling growth and recombinant protein production in CHO cells. While the effects of temperature-shift can result in an increase in overall product yield, it can also have implications for the extracellular-milieu from which the product must be purified. The second aspect of this thesis identifies changes in the host cell protein (HCP) profile of an IgG-producing and non-producing cell line over time in culture under both temperature-shifted and non-temperature-shifted conditions. This includes the identification of proteases (Cathepsin B, Cathepsin D, MMP9) and glycosidases (beta-galactosidase and α-N-acetylgalactosaminidase), that could negatively impact product quality. In addition, proteins that could enhance cell growth such as vascular endothelial growth factor isoforms A and C and Hepatomaderived growth factor were also identified. It was also found that the cell line and culture conditions used both impacted on the HCP profile generated.