What is a counterion?

In chemical terms, a counterion is an ion of opposite charge to another ion in a solution or an electrochemical system. In peptide synthesis, counterions such as TFA are used for solubility and HPLC separation. Most peptides except those that do not have basic amino acids such as Arg, Lys, His or those with blocked N-termini exist in the form of their salts. Synthetic peptides that are purified by HPLC are usually obtained as TFA salts. Their basic amino acid residues and N-termini are protonated and have trifluoroacetate (CF3COO -) counterions. Specifically, peptides lacking basic amino acids, such as Arg, His and Lys or containing blocked N-termini, require TFA for protonation and hence, are obtained as TFA salts. GenScript provides a guaranteed TFA removal service.
In some cases TFA couterions may be harmful to biological assays (see Top 5 reasons peptide assays fail). GenScript can replace TFA counterions with acetate or HCl, upon requesting our TFA removal service.