Characterization of a side reaction using stepwise detection in peptide synthesis with Fmoc chemistry

Abstract

Publisher Summary Solid phase peptide synthesis almost always employs either Boc or Fmoc chemistry; Boc chemistry requires acidic conditions for deblocking, and the potential side reactions have been extensively studied; however, in Fmoc chemistry repetitive basic conditions are required for deblocking, and only a few of the base-catalyzed side reactions have been characterized. This chapter describes a method used to demonstrate that a side reaction well known in Boc chemistry, but thought not to occur under the conditions of Fmoc. Stepwise analysis is an efficient and direct method to monitor the progress of side reactions in Fmoc chemistry. The analysis involves stepwise micro-scale TFA cleavage in conjunction with HPLC and MS. Micro-scale TFA cleavage can be conveniently carried out on a small amount of sample. MS analysis of peptide ladders provides a rapid method for monitoring and identification of side reactions in peptide synthesis.