Proteins provide innumerable cellular functions and benefits for all kingdoms in the domains of life. Advancements in the high throughput collection and analysis of proteins have led to ever-deeper understanding of biological pathways, evolution, and coding biases. There has been a renaissance of the study of proteins using new approaches that are largely possible because of the amount of data now available for analysis. The research in this dissertation investigates some of the new techniques available in this field, to find the limitations of these techniques as well as improve upon them.