I am now synthesizing a cyclic peptide (32 amino acide residues) contain a disulfide bond formed by SH of two Cys. My workmates have synthesized the peptide before. The problem they came across was that each batch they did showed poor reproducibility. RP-HPLC analysis of the linear precursor showed a small peak ahead or behind the main peak. Since I have synthesized many peptides, almost RP-HPLC of every peptide I synthesized showed this similar phenomenon. This great affected the yield of the product.
Does the phenomenon I described above normal or not? What can i do or what protocol can i take to avoid the formation of the small peak ahead or behind the main peak?