Studies on the use of trifluoromethanesulfonic acid as a deprotection reagent in Boc chemistry solid phase peptide synthesis (SPPS) are presented. Under suitable conditions, trifluoromethanesulfonic acid performs comparably to anhydrous hydrogen fluoride for this purpose. Obviation of hydrogen fluoride in Boc chemistry SPPS enables the straightforward synthesis of peptide-(alpha)-thioesters for use in native chemical ligation, and may stimulate renewed interest in Boc chemistry SPPS for cases where the Fmoc strategy proves unsatisfactory.