From Discovery to Delivery: A Rapid and Targeted Proteomics Workflow for Monitoring Chinese Hamster Ovary Biomanufacturing

Chinese hamster ovary (CHO) cells are the industrial workhorse for manufacturing biopharmaceuticals, including monoclonal antibodies. CHO cell line development requires a more data-driven approach for the accelerated identification of hyper-productive cell lines. Traditional methods, which rely on time-consuming hierarchical screening, often fail to elucidate the underlying cellular mechanisms driving optimal bioreactor performance. Big data analytics, coupled with advancements in ‘omics’ technologies, are revolutionizing the study of industrial cell lines. However, translating this knowledge into practical methods widely utilized in industrial biomanufacturing remains a significant challenge. This study leverages discovery proteomics to characterize dynamic changes within the CHO cell proteome during a 14 day fed-batch bioreactor cultivation. Utilizing a global untargeted proteomics workflow, we identify 3358 proteins, using a ZenoTOF 7600 and a Cyclic IMS QToF. By mapping relative abundances to key cellular processes, eight protein targets were selected as potential biomarkers. To bridge the gap between discovery and industrial applications, we translated these findings into a rapid 15 minute targeted triple quadrupole (MRM) assay. This approach demonstrates the potential of repurposing discovery proteomics for targeted biomarker identification in biotherapeutic production. By monitoring these biomarkers we can potentially streamline the screening of biomanufacturing cell lines and culture conditions, ultimately accelerating biotherapeutic development.