N-Carbobenzoxy-L-isoleucine is primarily used in peptide synthesis as a protecting group for the amino acid isoleucine. It helps in preventing unwanted reactions at the amino group during the formation of peptide bonds. This compound is particularly valuable in solid-phase peptide synthesis, where selective deprotection is required to build complex peptides step-by-step. Additionally, it finds application in the preparation of modified peptides and bioactive compounds, contributing to research in drug development and biochemical studies. Its stability under various reaction conditions makes it a reliable choice in organic and medicinal chemistry.