What kinds of impurities turn up in synthesized peptides?

Most impurities come from the synthesis itself. The common ones: - Deletion and truncated sequences, when a coupling step fails to finish (des-Xaa, or chains capped early). These are the most frequent impurities in Fmoc solid-phase synthesis. - Epimers, from racemization during coupling. - Aspartimide and the deamidation/isoaspartyl products it leads to, near Asp/Asn sites. - Oxidation at methionine and cysteine, plus disulfide scrambling in cysteine peptides. - Adducts from incomplete deprotection or cleavage scavengers. Separate from the chain: counterions and solvent. Per work indexed in PubMed, peptides cleaved with trifluoroacetic acid usually arrive as TFA salts with residual water, which is why net peptide content runs below 100%. Third-party HPLC and mass-spec testing (services like Janoshik or Finnrick) is what shows which of these a given vial holds. These are research-use compounds, not approved for human use.