Phenylthiohydantoin-isoleucine is primarily used in the field of protein sequencing and amino acid analysis. It serves as a derivative in the Edman degradation process, a method for determining the amino acid sequence in peptides and proteins. By converting isoleucine into this stable compound, researchers can accurately identify and analyze the amino acid's position within a protein chain. This application is crucial in biochemistry and molecular biology for understanding protein structure and function, aiding in the study of diseases, drug development, and genetic research. Additionally, it is utilized in quality control processes for synthetic peptides to ensure accurate sequence confirmation.