Methyl benzimidate hydrochloride is primarily used in the field of biochemistry and molecular biology as a reagent for modifying proteins and peptides. It is particularly valuable for introducing ester groups into molecules, which can be useful in cross-linking studies or for labeling proteins. This compound is often employed in the synthesis of affinity chromatography matrices, where it helps in the immobilization of ligands onto solid supports. Additionally, it plays a role in the preparation of immunogens and in the study of protein-protein interactions, making it a versatile tool in research and diagnostic applications. Its ability to react with amino groups under mild conditions makes it a preferred choice for various bioconjugation strategies.