Phenylthiohydantoin-methionine is primarily used in protein sequencing and peptide analysis. It plays a crucial role in the Edman degradation process, where it helps in the stepwise identification of amino acids in a peptide chain. This compound is particularly valuable in biochemical research for determining the sequence of proteins, aiding in the study of protein structure and function. Its application is essential in fields like molecular biology, proteomics, and pharmaceutical development, where understanding protein sequences is critical for drug design and disease research.