A protein’s function is highly informed by its structure. Understanding the structural nuances of proteins could greatly inform studies into their function. Limited proteolysis-Mass spectrometry (LiP-MS) is a novel method for observing the structure of proteins. LiP-MS determines protein structures through treating complex protein samples (such as blood) with a broad specificity protease for a small amount of time to cleave accessible regions of the peptide backbone. Then the protein sample is fully digested with sequence-specific proteases to make fragments suitable for MS analysis. This treatment allows LiP-MS to determine global protein structural changes such as those mediated by changes when exposed to environmental stimulus. Next, LiP-MS allows for a targeted analysis of protein structure in complex solutions. However, there are limitations of LiP-MS. The visualization of proteins is only as informative as the variety and breadth of LiP-MS ratios generated. As of now the range of LiP-MS ratios does not provide a clear enough picture for medical use. For our study, we aim to optimize the LiP-MS protocol to better its accuracy in quantifying the presence of misfolded proteins found in cerebrospinal fluid of individuals with Alzheimer’s disease. With this optimization of the LiP-MS protocol, we hope to investigate proteins associated with Alzheimer's disease in their misfolded state to create a screening assay for earlier diagnosis and prognosis of Alzheimer’s disease and other neurodegenerative diseases. Prior to our study, LiP-MS was unable to provide detailed information on the structural changes that occurred. We altered a variety of experimental LiP-MS variables and compared them to current, standard LiP-MS protocols. We found that though some aspects could change, the current experimental variables are effective at generating LiP-MS ratios. Further work is needed to improve LiP-MS to potentially allow for screening against diseases that involve protein misfolding, such as Alzheimer’s disease.