The peak intensities observed in the molecular ion regions of fast-atom bombardment/liquid secondary ion mass spectra contain contributions from the parent ion species, its one- and two-electron reduction/oxidation products, and chemical background signal due to beaminduced damage. There are several solution and instrumental parameters that can affect the distribution of peak intensities in the molecular ion region. In this study, the analyte concentration and primary beam density and energy were varied systematically to investigate their effects on the measured peak intensities. A computer algorithm, Simbroc (Simulated Background and Reduction/Oxidation Calculations), was designed to deconvolute the observed intensities into their individual components so that the true effects of experimental parameters on redox extent and background levels could be evaluated. The algorithm is based on a comprehensive seven-variable mathematical model for experimental data simulation. The results obtained using the algorithm after its validation indicate that the primary beam energy does not significantly affect redox extent or background levels. Changes in analyte concentration and primary beam density tend to play a more important role in the generation of redox products and beam-induced damage. The background level generally increases as the analyte concentration is lowered for the peptide systems used in this study. An increase in the primary beam density often leads to higher background levels, although the effect is less detectable for samples that have a low (less than 3%) background signal. The apparent two-electron reduction is generally lower at the higher concentrations; however, the "true" reduction occurring for pentaphenylalanine does not show a significant concentration effect.