Sodium 2-(acetylthio)ethanesulfonate is primarily used in the field of biochemistry and molecular biology as a reagent for protein modification and analysis. It is often employed in the study of protein structure and function, particularly in the modification of cysteine residues within proteins. This chemical facilitates the introduction of specific functional groups, enabling researchers to probe protein interactions, folding, and dynamics.

Additionally, it finds application in the development of biosensors and diagnostic tools, where it aids in the immobilization or labeling of biomolecules for detection purposes. Its role in creating stable thioether linkages makes it valuable in designing targeted drug delivery systems and therapeutic agents, enhancing their specificity and efficacy. In industrial settings, it may also be utilized in the synthesis of specialty chemicals and polymers, contributing to the production of advanced materials with tailored properties.