Complex formulations that include excipients, ligands, surfactants, and preservatives provide a challenging environment to measure protein secondary structure and detect change. Traditional spectroscopic methodologies such as Fourier Transform Infrared, Circular Dichroism, and Nuclear Magnetic Resonance have limitations when these common environments are encountered due to interfering absorbances and concentration requirements. In this symposium, RedShiftBio will introduce the AQS3pro, an innovative technology designed for accurate measurement of protein secondary structure in complex formulation conditions. Powered by Microfluidic Modulation Spectroscopy (MMS), the AQS3pro utilizes infrared spectroscopy to provide high sensitivity measurements across a wide dynamic concentration range. In combination with the AQS3delta Data Analysis package, this novel technology facilitates a detailed look into the effect of the formulation environment on higher order structure. This presentation will include case studies examining the measured effects of complex formulation conditions, including ligand binding and purification methodologies, on protein structure and stability.