Ethyl acetimidate hydrochloride is primarily used in biochemical research as a reagent for modifying proteins and peptides. It is particularly valuable in the study of protein structure and function, where it aids in the selective modification of lysine residues. This chemical is also employed in the synthesis of various organic compounds, including pharmaceuticals and agrochemicals, due to its ability to act as a versatile intermediate. Additionally, it finds application in the preparation of imidate esters, which are useful in further chemical transformations. Its role in crosslinking biomolecules makes it a key tool in understanding molecular interactions and developing advanced materials.