SUMMARY

In-process monitoring and control of biomanufacturing workflows remains a significant challenge in the development, production, and application of cell-based therapies. The fundamental biochemical processes and mechanisms of action of such advanced therapies are still largely unknown, including the critical quality attributes that correlate to therapeutic function, performance, and potency and the critical process parameters that impact quality throughout manufacturing. This dissertation demonstrates a new integrated microfluidic platform for rapid, at-line intracellular analysis of a small number of cells via electrospray ionization mass spectrometry. By increasing the speed of label-free metabolic measurements from a minimal number of cells, spectral markers and metabolic pathways correlated with internal cell processes are detected at early time points and tracked throughout the culture process while reducing the analytical time and resources required by conventional methods of cell assessment. To further enhance detection of metabolites from the complex intracellular environment, a novel liquid-liquid extraction scheme that enables continuous-flow sample conditioning of complex solutions was demonstrated. This cost-effective sample conditioning scheme can be easily implemented in existing mass spectrometry workflows and is particularly suited for rapid, in-line sample preparation of biochemically diverse, low volume samples. By providing rapid, in situ analysis of cell state, the integrated platform represents a crucial step toward enabling untargeted discovery of biomarkers and real-time, in-process monitoring of internal cell dynamics within bioprocessing systems. These capabilities represent a critical milestone toward fully automated quality monitoring with integrated feedback control in cell-based therapy manufacturing, two unmet challenges that must be overcome if the transformative potential of cell therapies is to be fully realized.