The relative effectiveness of trifluoroacetic acid (TFA), pentafluoropropanoic acid (PFPA), heptafluorobutyric acid (HFBA) and undecafluorocaproic acid (UFCA) as hydrophobic counter-ions in the reversedphase high performance liquid chromatography (RP-HPLC) of peptides was assessed. Four solvent systems were compared each containing 0.01M of a perfluorocarboxylic acid throughout. Twelve standard peptides and proteins were loaded onto the RP-HPLC column which was eluted with a linear gradient of 20-58.4% aqueous acetonitrile over 90 minutes. The retention times of the peptide standards were different in each solvent system. In progressing from TFA to PFPA, HFBA and UFCA all the peptides showed greater retention times. However, the effect was most marked with peptides having the greatest number of basic groups. By exploiting this behaviour a different type of chromatography can be introduced into the RP-HPLC purification of peptides. For instance, column fractions obtained from the use of the TFA solvent system can be re-chromatographed in a solvent system containing HFBA. It is possible by this procedure to purify naturally occurring peptides on the basis of their overall positive charges. At 0.01M each acid solution is sufficiently U.V. transparent to permit monitoring of column effluents at 210 nm. TFA, PFPA, HFBA and UFCA solvent systems are also completely volatile and this property facilitates the bioassay, radioimmunoassay and amino acid analysis of column fractions.
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