In peptide analysis, trifluoroacetic acid (TFA) is a common mobile phase modifier for better peak shape under HPLC-UV condition.However when mass spectrometry is involved, TFA is no longer the ideal choice due to its ion suppression effect.Formic acid is therefore employed to buffer the pH and control the silanol activity on the HPLC stationary phases.It certainly reduces the ion suppression effect, but under the formic acid condition, some of the peptide peaks are not as symmetrical or efficient as with the traditional UV-based methods with TFA.This phenomenon may involve charge-charge interactions between the peptide analytes as well as between the peptide and silica surface.Such interactions may be mitigated by pH and/or mobile phase additives that may function as counterions in an ion-exchange process.This study presents the chromatographic behavior of reversed-phase peptide separations as a function of pH and counterion concentration.