Thioanisole is a commonly used scavenger in peptide synthesis to trap released nucleophiles during the global deprotection step of the peptide side chain. Thioanisole is recommended as a scavenger during the cleavage of many protecting groups such as benzyloxycarbonyl, Tosyl, Mts and Mtr. In addition, the properties of thioanisoles in avoiding undesired Met oxidation during the overall deprotection of peptide side chains have been widely used.

However, Thioanisole is not suitable for deprotection in the presence of high concentrations of strong acids due to the alkylation side reaction of Thioanisole on peptide residues containing sensitive amino acids such as Trp and Met.