Ion storage biases in the ion funnel trap of a Hybrid ion mobility spectrometer/time of flight mass spectrometer

A detailed experimental characterization on the ion storage biases in an ion funnel trap, related to ion structure, charge state and RF voltage applied to the ion funnel trap, is reported by using both cytochrome C and ubiquitin samples. It was first observed experimentally that an unavoidable ion overflow would occur when the incoming ions exceeded the capacity of ion funnel trap. The conformers with extended structures would lose preferentially in the ion overflow process. Accordingly, a significant structural bias in the ion mobility spectrometry/time of flight mass spectrometry (IMS-TOF MS) spectrum was created, as the peak intensities for conformers with compact structures and extended structures would continuously increase and decrease, respectively, when the ion overflow time of the ion funnel trap was increased. Furthermore, the experimental results also showed that the effect of this ion structural bias was more significant when the RF voltage applied to the ion funnel trap was increased. In addition, an ion charge state bias in the ion funnel trap was also observed. The effect of the ion structural bias depends significantly on the specific charge state of the ions. For a given analyte, its lower charge state ions show a greater sensitivity to the ion structural bias than the higher charge state ones under the same ion funnel trap operating conditions. Therefore, it is extremely important to set a reasonable operation condition for the ion funnel trap to avoid ion storage biases in IMS-TOF MS.