Chinese hamster ovary (CHO) cells are the most commonly used host cell line for the production of human therapeutic proteins. Improvements in CHO cell yields to date have largely been attributed to bioprocess and media formulation improvements. Genetic engineering of CHO cell lines with desirable phenotypes has recently become an area of interest amongst researchers; however, for this to be possible we must gain an improved understanding of the systems biology of CHO cells and the intracellular pathways which drive desirable production phenotypes. This thesis explores the use of advanced proteomic and molecular biology techniques to characterise desirable phenotypes related to growth and specific productivity (Qp) in industrially relevant Chinese hamster ovary (CHO) cell lines. Panels of clonally derived industrially relevant CHO cell lines (CDCLs) were characterised using LC-MS/MS and miRNA profiling. MiR-200a was identified as a miRNA which is highly expressed in high Qp CDCLs and when overexpressed in CHO cells results in increased titre and Qp. Results suggested that miR-200a plays an important role in post-transcriptional regulation of the UPR. Phosphoproteome analysis of high and low Qp CHO CDCLs allowed us to investigate phosphorylation events associated with high/low Qp phenotypes. Phosphoproteins and total proteins associated with amino acid sensing were highlighted as important in high Qp CDCLs. Intracellular pathways associated with high/low transcript copy numbers (TCN) in CHO cells were also investigated. IRE1 mediated UPR was found to be highly expressed in high TCN CDCLs and this is suggested to result in maximised folding capacity in these cells. Growth related phenotypes were also characterised in CHO CDCLs and proteins/pathways associated with fast growth rate and extended viable cell density phenotypes were identified. The proteomic and molecular data presented in this thesis provides a deeper understanding into the intracellular pathways which influence desirable phenotypes in CHO cells.