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Aggregation of proteins and in particular biopharmaceuticals results in a loss of time and money to industry. It is essential that any biopharmaceutical is monitored for purity and stability throughout the production process, as any loss in quality can reduce drug efficacy and result in undesirable immune responses such as anaphylaxis, or even death, upon administration to patients. A departure from normal protein structure can occur through changes in temperature, mechanical stress, freezing and/or thawing, and can ultimately lead to protein aggregation. Traditional, single element FTIR spectroscopy is currently implemented in the monitoring of pharmaceutical production, but FTIR spectroscopic imaging has the potential to monitor samples in a higher throughput capacity and could therefore potentially be used in tandem with lab-on-a-chip and microfluidic technologies to decrease time and financial costs to industry. Attenuated total reflection Fourier transform infra-red (ATR-FTIR) spectroscopic imaging is a label-free, non-destructive, and chemically specific technique that can be utilised for a wide range of biomedical applications. In this project FTIR spectroscopy, macro ATR-FTIR spectroscopic imaging, variable angle of incidence accessories, specifically designed PDMS devices, lysozyme, and isolated monoclonal antibodies (mAbs) have all been used to explore protein behaviour. Collectively, these enabled us to investigate the structure and distribution of aggregates close to the surface of the ATR internal reflection element (IRE) and observe how this distribution changes under stress conditions. The purpose of this research was to understand protein behaviour in static and flowing environments, under a range of stress conditions. This research also aims to demonstrate the suitability of FTIR spectroscopic imaging for biopharmaceutical process monitoring. ATR-FTIR spectroscopic imaging was therefore applied to study the effect of various stress conditions such as temperature, flow rate, and freeze thaw cycles on the aggregation and secondary structure of lysozyme and IgG mAbs. Hermetically sealed cells were manufactured which typically used PDMS to contain the samples under either static or flowing conditions. Results show interesting behaviours of proteins, particularly immunoglobulin G (IgG) monoclonal antibodies, under stress conditions, and the applicability of ATR-FTIR spectroscopy to successfully monitor these proteins in static and flowing set-ups. These developments pave the way for further provision of FTIR spectroscopic imaging as an analytical technique to monitor protein structures and biopharmaceutical processes. Optimisation of these techniques will ultimately lead to an increase in available research and development funds and a reduction in drug costs due to increased efficiency and a reduction in waste. These techniques could also result in a more streamlined production process which can lead to more rapid availability of drugs to market.