The goal of this work is to further the development, apply, and evaluate the application of three proteomics methods for protein target discovery and the analysis of disease states. The three methods under investigation in this work include the Pulse Proteolysis (PP), Thermal Proteomics Profiling (TPP) and Stability of Protein from Rates of Oxidation (SPROX) techniques that have been recently reported in the literature. These three techniques will be applied to selected protein target discovery study and disease state study. Through the course of these studies the strength and limitation will be investigated and novel workflows will be explored to potentially overcome the limitations that are exposed. Currently under investigation is a novel pulse-proteolysis in which quantitative proteomics read-outs involving isotope labelling strategies have been combined with a protein precipitation step to make the pulse proteolysis technique amenable to solution phase, bottom-up shotgun proteomics methods.