Systems and methods for automatic gain control in mass spectrometers are disclosed. An exemplary system may include a mass spectrometer, comprising a lens configured to receive a supply of ions, and a mass analyzer. The mass analyzer may include an ion trap for trapping the supplied ions. The mass analyzer may also include an ion detector for detecting ions that exit the ion trap. The lens may focus the ions non-uniformly based on mass of the ions to compensate for space charge effects reflected in a measurement output of the mass spectrometer. An exemplary method may include focusing an ion beam into a mass analyzer. The method may also include obtaining a mass spectrum and identifying a space charge characteristic based on the mass spectrum. The method may further include defocusing the lens based on the identified space charge characteristic, wherein defocusing the lens is configured to divert lighter ions away from the entrance aperture. The method may include obtaining a mass spectrum of a defocused ion beam generated from the sample.