Iodoacetic acid is primarily used in biochemical research as an alkylating agent to modify proteins and enzymes. It is particularly effective in inhibiting enzymes by reacting with cysteine residues, which are crucial for the enzyme's activity. This property makes it valuable in studying enzyme mechanisms and identifying active sites.

In addition to its role in enzyme inhibition, iodoacetic acid is utilized in peptide synthesis to protect thiol groups during chemical reactions. This ensures that specific functional groups remain intact while other parts of the molecule undergo modification.

Furthermore, iodoacetic acid is employed in the preparation of derivatives for analytical purposes, such as in the derivatization of compounds for gas chromatography or mass spectrometry. Its ability to introduce iodine atoms into molecules aids in detection and analysis.

In some cases, it is also used in organic synthesis to introduce acetic acid groups into target molecules, facilitating the creation of complex chemical structures.