Liquid-liquid phase separation is a form of polymer chemistry, recently found to be particularly relevant to cell biology, that involves the de-mixing of enclosed molecules into a dense and depleted phase. This results in the formation of various membrane-less organelles, such as P bodies and stress granules. Despite the ever-growing library of proteins having the ability to phase separate in vitro and in vivo, the underlying molecular mechanisms that result in the formation of these membrane-less organelles is not well defined. The biophysical experimentation used to study liquid-liquid phase separation has been very limiting, in part due to the highly dynamic nature of the resulting membrane-less organelles. This dissertation describes the technological development of utilizing hydrogen-deuterium exchange mass spectrometry (HXMS) to uncover local changes in protein structure upon liquid-liquid phase separation. I first investigated the structure and dynamics of TAR DNA-binding protein of 43 kDa (TDP-43). As the initial protein within this study, I devised a series of prerequisites necessary to make this and future studies tractable. I devised a purification scheme that culminates in the high-purity, high-yield production of recombinant protein suitable for mass spectrometry. To date, I have identified conditions that yield a set of partially overlapping peptide probes with which to measure H/DX rates under diverse experimental conditions. I then investigated the structure and dynamics of the chromosomal passenger complex (CPC). I have identified four main regions within the CPC complex that displays differential deuterium exchange when compared to the depleted phase, all of which are enriched in charged amino acids. By combining information from HXMS, crystal packing of the non-catalytic subunits of the CPC, and various mutational studies, I demonstrate that CPC phase separation is reliant upon specific electrostatic interactions between different CPC heterotrimers. Taken together, I demonstrate that HXMS can be used to uncover local changes in protein structure upon liquid-liquid phase separation. This approach has the potential to pave the way for future biophysical studies and be expanded to any protein that is involved in phase separation.