Process and systems for peptide synthesis

The invention provides methods of synthesizing peptides, involving the steps of providing a composition including a peptide fragment, wherein the peptide fragment has at least one amino acid residue and includes a base-sensitive, N-terminal protecting group; removing the base-sensitive, N-terminal protecting group from the peptide fragment using a deprotection reagent that includes a base, whereby an N-terminal functionality on the peptide fragment is deprotected; removing the base from the composition to provide a residual base content of more than 100 ppm; causing a reactive peptide fragment having a reactive C-terminus and a base-sensitive N-terminal protecting group to react with the deprotected N-terminal functionality of the peptide fragment under conditions such that the reactive peptide fragment is added to the peptide fragment; and optionally repeating the deprotection and coupling steps until a desired peptide is obtained. Also provided are methods of synthesizing peptides, wherein base is removed from the composition to a point where the composition would provide a positive chloranil test. Also provided are methods of synthesizing peptides, wherein coupling is performed in basic reaction mixtures.