Understanding Peptide Salt Forms: Acetate vs TFA

During peptide synthesis, the final cleavage and purification steps leave the peptide associated with counterions — negatively charged molecules that balance the positive charges on basic amino acid residues (Lys, Arg, His, and the N-terminus). The counterion becomes part of the lyophilized powder you receive. The most common counterion from synthesis is trifluoroacetate (TFA), because trifluoroacetic acid is used in the cleavage step of Fmoc solid-phase synthesis. Acetate salt is obtained by performing an additional counterion exchange step after synthesis.

TFA salt is the default form from standard Fmoc SPPS because TFA is used to cleave the peptide from the resin. TFA counterions are heavier than acetate, meaning a 5 mg vial of TFA-salt peptide contains slightly less actual peptide by weight (the rest being TFA counterions). For a typical peptide with 3 basic residues, TFA content can be 15-25% of total weight. TFA is generally considered non-toxic at the levels present in research peptides. However, TFA can interfere with certain cell-based assays, particularly at higher concentrations, and can affect mass spectrometry analysis.

Acetate salt is produced by exchanging TFA counterions for acetate counterions, typically through multiple rounds of dissolution in dilute acetic acid followed by lyophilization. Acetate is lighter than TFA, so acetate-salt peptide contains more actual peptide per milligram of powder. Acetate salt is preferred for cell culture applications, in vivo studies, and situations where TFA interference is a concern. It is also the preferred form for peptides used in clinical or GLP studies.

Yes. Because the counterion contributes to the total weight, the same mass of TFA-salt and acetate-salt peptide contains different amounts of actual peptide. For precise quantitative research, this must be accounted for. Most suppliers report the peptide content or net peptide weight on the COA to help researchers calculate accurate concentrations.