Phenyl isothiocyanate is widely used in biochemistry for the sequencing of amino acids in proteins. It reacts with the N-terminal amino acid of a peptide or protein under alkaline conditions, forming a phenylthiocarbamoyl derivative. This derivative can then be cleaved under acidic conditions, allowing for the identification of the amino acid. This process is a key step in the Edman degradation method, which is a cornerstone technique for protein analysis.

In addition to protein sequencing, phenyl isothiocyanate is utilized in the synthesis of various organic compounds, including pharmaceuticals and agrochemicals. It serves as a reagent in the preparation of thioureas, which are important intermediates in the production of drugs and pesticides. Its ability to introduce the isothiocyanate functional group makes it valuable in the development of compounds with potential therapeutic and agricultural applications.

Furthermore, phenyl isothiocyanate is employed in the field of analytical chemistry as a derivatizing agent for the detection and quantification of amines and amino acids in complex mixtures. This enhances the sensitivity and specificity of analytical methods such as high-performance liquid chromatography (HPLC) and mass spectrometry (MS), enabling precise measurement of these compounds in biological and environmental samples.