The most effective way to conduct trace analyses of complex samples is to couple a high-resolution separation method to a sensitive, information-rich detector. The latest generation quadrupole ion trap uses an automatic gain control (AGC) scan function and an axial modulation voltage to achieve maximum sensitivity. With these capabilities, an ion trap gas chromatography-mass spectrometry system can separate, quantitate, and identify low picogram quantities of trace analytes present in a complex sample. The AGC scan function uses a target value (AGC-TV) during analysis to maximize signal intensity by varying ionization time. Filament emission current (FEC) is also a major affector of ion trap signal intensity when electron ionization (EI) is used. Maximum sensitivity was achieved when AGC-TV and FEC were optimized. Additionally, useful information about selected types of compounds were also obtained from analyses conducted with non-optimum AGC-TV and FEC settings. In these specific cases, the effects seen when non-optimal AGC-TV or FEC settings were used could be explained in terms of the inherent ion chemistries of the compounds.