Increasing Isolation Efficiency Using a Segmented Quadrupole Mass Filter Operated with Rectangular Waveforms

The performance of a segmented quadrupole mass filter operated with rectangular waveforms and capacitively coupled rectangular waveforms applied to the prefilters was examined on a home-built quadrupole-Orbitrap platform. For peak widths of 50 m/z, 100% isolation efficiency was achieved, which fell to approximately 20% for 5 m/z peak width for a rectangular waveform of 150 V0–p. Due to a small exit aperture following the mass filter, peak structure was observed in both experimental peak shapes and those simulated using SIMION. A larger radius quadrupole was examined and achieved similar performance. While the segmented quadrupole does remove the defocusing effects of the fringing fields, the ion beam is only slightly refocused due to the low RF voltage which limits achievable gains in isolation efficiency.


Derivation of the Number of RF Cycles in a Digital Mass Filter
The ion's transit time through the quadrupole can be calculated from the ion's axial kinetic energy, where  is the number of charges on the ion,  is the charge of an electron,  is the axial accelerating potential,  is the mass of the ion, and  is the ion velocity.
By substituting the length of the quadrupole () and transit time () for velocity, the transit time is calculated: Dividing the transit time by the period of the RF waveform gives the transit time in RF cycles ( "# ).To determine the period, the RF drive frequency is calculated from Mathieu where  "# is the 0 to peak amplitude of the RF,  $ is the quadrupole field radius, and Ω is the angular frequency (Ω = 2).After solving for For a digital mass filter operated in the first stability  ≈ 0.59.Unlike a sinusoidal quadrupole where drive frequency is constant, the number of RF cycles is independent of   ⁄ in the digital mass filter.

Figure S1 .
Figure S1.(a) Original ion funnel design with the heated capillary coaxial with the ion funnel axis.(b) Modified ion funnel design with the heated capillary offset by 0.375x the radius of the first funnel electrode to eliminate the line-of-sight into further vacuum regions.

Figure S2 .
Figure S2.Stopping curves for various voltage differences between MP1 DC and the Q2 entrance lens DC.The ion kinetic energy varied from 4.25 eV for 0 V, 5.25 eV for 1 V, to 19.7 eV for 20 V.All other inter-optic voltage differences were kept constant.

Figure S3 .
Figure S3.The parameter μ, the increment of exponential growth of the ion oscillation over one RF cycle, in the x and y direction for (a) sinusoidal and (b) digital operation.The maximum for the sinusoidal quadrupole is plotted as a horizontal line.

Figure S5 .
Figure S5.Example SIMION calculated ion trajectories in both the xz and zy plane for the (a) 4 mm r0 mass filter and the (b) 5.25 mm r0 mass filter.The decrease in the number of RF cycles that the ions experience in the 5.25 mm r0 mass filter can be seen as the drive frequency is reduced.

Figure S6 .
Figure S6.Orbitrap intensity for the m/z 1421.97 tune mix ion as a function of q1 RF voltage with a (a) 4 mm r0 and a (b) 5.25 mm r0.The RF voltage of the octopole ion guide between q1 and Q2 was maintained at a constant RF voltage of 450 Vp-p.The intensities between the two plots are not comparable as they are from different nanoelectrospray tips with different full scan intensities.

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