Control of chemical mass shifts in the quadrupole ion trap through selection of resonance ejection working point and rf scan direction

Compound-dependent chemical mass shifts are observed and their origin is elucidated in a modified Finnigan GCQ quadrupole ion trap mass spectrometer. The dependence of chemical mass shifts on ion trap geometry, specifically the center to end-cap spacing, z0, and the size of the apertures in the end caps, is demonstrated. The effects of the working point (qeject value) used for resonance ejection and the direction of the rf mass analysis scan are also studied, and the results are found to be in agreement with a previously proposed model for the chemical mass shift mechanism. It is shown that chemical mass shifts are present when resonance ejection is used, unless the qeject is chosen to correspond to a nonlinear resonance point, where the shifts are removed. The shifts are also removed by performing the mass analysis scan in the reverse direction, i.e., from high mass to low mass.