Transporting of ions through stages in mass spectrometers is commonly performed using several interfacing apparatus. In some cases, gating mechanisms can be utilized to control the flow of ions between the various stages. A skimmer cone consisting of a large cone shaped disc that contains a small hole or aperture at the centre is used to select ions that may be radially separated. Generally ions from the central portion of an ion beam are selected for transmission with the remaining ions being removed. The pulsing of the skimmer voltage can be utilized to introduce an artificial duty cycle to cause modulation of an ion beam which can reduce the total ion current in exceptionally bright beams. Such pulsing consists of switching the voltage of the skimmer between two voltages, one in which ions can pass through the skimmer and one in which the ions cannot. The phenomenon of skimmer pulsing is mass dependent and has also exhibited surprisingly non-linear behavior in some cases.
In particular, the linearity of an ion signal seen when pulsing a single gating lens over a wide duty cycle range is not very good at lower duty cycles. This affects fill time linearity on the quardupole trapping instruments and ITC (Total ion current) linearity on Time-of-Flight mass spectrometer instruments.
It has been discovered that this deviation from linearity is caused by ion mobility effects. The gating effect caused by the presence of devices such as a skimmer lens generates an axial electric field that penetrates upstream and causes a mobility dependent depletion of ions when regions of higher pressure exist. This phenomenon is more easily seen when the axial gas velocity is low and ion mobility effects are at their greatest, such as when the orifice diameter of the gating lens is small.
The normal situation is conceptually represented in FIG. 1. When the stopping potential is applied to the gating lens (labeled IQ0), a zone is created (zone of perturbation) on both sides of the lens where ions therein have their trajectories spoiled such that they are deflected away from a stable trajectory and are either ejected or contact one of the rods and will therefore not pass on to the next section of the analyzer. In particular, the field created on the high pressure side (left side) causes the ions with high mobility to deviate from an acceptable to an unacceptable trajectory preferentially relative to low mobility ions.
This results in the presence of non-linear behavior when the modulation frequency is varied. This manifests itself as a non-linear relationship between intensity counts and the time period in which the stopping potential is applied. With all other things being equal, a linear relationship between intensity and modulation frequency would be expected. This non-linear behavior is observed when the IQ0 lens ID is small. In this case the axial velocity of the ions due to the gas flow will be lower and the effect of the electric field will have a proportionally larger effect on the combined forces (gas flow+electrodynamics) on the ion motion.