Previous studies have shown that the ion response of a compound can be suppressed by the presence of a large amount of a coeluting substance in a gas chromatographic-mass spectrometric (GC-MS) system. In the present study, the change in the ion current of a constant amount of diazepam-d5 in the presence of a 100-fold amount of diazepam was used to monitor this condition in the Hewlett Packard mass selective detector (MSD). It was observed that a reduced recovery of ions occurred when the potentials of the MSD source elements were established by the autotune algorithm. Increasing the ion focus or the entrance lens potentials or both increased the recovery of the ion current of diazepam-d5 in the presence of large amounts of diazepam. The data suggested that the decreased recovery of ion current observed when the autotune source parameters were used was due to insufficient energy on the focusing lenses to extract a constant fraction of the ions from the source when a high concentration of molecules was present.