RATIONALE: The influence of hydrophobicity originating from an amino acid phenylalanine (Phe) residue on the ion yields of peptides has been empirically evaluated using positive-and negative-ion electrospray ionization (ESI) mass spectrometry. The enhancement effect of hydrophobicity was compared with that of the presence of basic and acidic residues of peptides. METHODS: In order to empirically understand the ion yields in soft ionization methods, we have divided the total ionization process into ionization efficiency of analyte molecules and the rate of desorption or vaporization of molecules. The ion yields of protonated and deprotonated molecules of peptides were evaluated. RESULTS: The presence of a Phe residue resulted in an increase in the ion yields of both the analyte ions [M + nH] n+ and [M-nH] n-. The relationship between the ion yields and hydrophobicities of peptides was evaluated using the partition coefficient measured by thin-layer chromatography (PACTLC). A peptide containing a Phe residue at its C-terminus gave a higher ion yield than when it was at the N-terminus. CONCLUSIONS: The ion yields of peptides increased with increasing hydrophobicity both in positive-and negative-ion ESI. The enhancement effect of hydrophobicity on the ion yields was higher than that of basicity and acidity of the peptides in ESI
