The production of biological drugs for the treatment of serious diseases is a complex process utilizing a mammalian cell expression system combined with a complex set of purifications steps to produce drugs of high quality and at optimized yields. In order to maximize both quality and yield, the cell culture process must be developed ensuring maximal cell growth and productivity characteristics, as well as scalability and robustness in a manufacturing setting. The purification method must also be optimized for high yield of product, while maintaining or enhancing the product quality profile of the drug and removing cell culture related impurities to acceptably low levels. Limitations of the biopharmaceutical process can have great impact on the cost of drug production, as well as on the safety and efficacy of the drug. Understanding the biology of the cells used to produce biopharmaceuticals can enable the development of better processes. This thesis describes the characterization of biopharmaceutical processes using proteomics technology.