A dissociation device fragments a precursor ion, producing at least two different product ions with overlapping m/z values in the dissociation device. The dissociation device applies an AC voltage and a DC voltage creating a pseudopotential that traps ions below a threshold m/z including the at least two product ions. The dissociation device receives a charge reducing reagent that causes the trapped at least two product ions to be charge reduced until their m/z values increase above the threshold m/z set by the AC voltage. The increase in the m/z values of the at least two product ions decreases their overlap. The at least two product ions with increased m/z values are transmitted to another device for subsequent mass analysis by applying the DC voltage to the dissociation device relative to a DC voltage applied to the other device.

A method includes obtaining a first mass spectrum; selecting a first peak of the first mass spectrum; isolating precursor ions in an isolation window including the first peak; fragmenting and analyzing the isolated ions to obtain a second mass spectrum; performing a real-time search of the second mass spectrum for both the target precursor and near isobaric precursors ions that are co-isolated with the target precursor in an isolation window; adding the precursor ions that produced an identification during the real-time search to the exclusion list; selecting a second peak present in the first mass spectrum and not on the exclusion list; and fragmenting and analyzing ions of the second peak to obtain a third mass spectrum.

A sampling period of an A/D converter is set in accordance with an ion pulse ejection operation of a collision cell of an accumulation type. Start timing of the sampling period is changed in accordance with a selected m/z of a second mass analysis unit. In addition, end timing of the sampling period may be changed in accordance with the selected m/z of the second mass analysis unit. In place of the sampling period, a data cut-out period may be changed.

In one aspect, a method of processing ions in a mass spectrometer is disclosed, which comprises trapping a plurality of ions having different mass-to-charge (m/z) ratios in a collision cell, releasing said ions from the collision cell in a descending order in m/z ratio, and receiving the ions in a mass analyzer having a plurality of rods to at least one of which an RF voltage is applied, where the RF voltage is varied from a first value to a lower second value as the released ions are received by the mass analyzer.

A space-time buffer includes a plurality of discrete trapping regions and a controller. The plurality of discrete trapping regions is configured to trap ions as individual trapping regions or as combinations of trapping regions. The controller is configured to combine at least a portion of the plurality of trapping regions into a larger trap region; fill the larger trap region with a plurality of ions; split the larger trap region into individual trapping regions each containing a portion of the plurality of ions; and eject ions from the trapping regions.

In one aspect, a mass analyzer is disclosed, which comprises a quadrupole having an input end for receiving ions and an output end through which ions can exit the quadrupole, said quadrupole having a plurality of rods to at least some of which an RF voltage can be applied for generating a quadrupolar field for causing radial confinement of the ions as they propagate through the quadrupole and further generating fringing fields in proximity of said output end. The mass analyzer further includes at least a voltage source for applying a voltage pulse to at least one of said rods so as to excite radial oscillations of at least a portion of the ions passing through the quadrupole at secular frequencies thereof, where the radially-excited ions interact with the fringing fields as they exit the quadrupole such that their radial oscillations are converted into axial oscillations.

In one aspect, a method of processing ions in a mass spectrometer is disclosed, which comprises trapping a plurality of ions having different mass-to-charge (m/z) ratios in a collision cell, releasing said ions from the collision cell in a descending order in m/z ratio, and receiving the ions in a mass analyzer having a plurality of rods to at least one of which an RF voltage is applied, where the RF voltage is varied from a first value to a lower second value as the released ions are received by the mass analyzer.

A method of separating ions is disclosed comprising: providing an ion separation device comprising a plurality of electrodes; providing a gas flow (5) so as to urge ions in a first direction along the device; applying voltages to said electrodes so that a plurality of travelling potentials (4) urge the ions in a second opposite direction; and varying at least one operational parameter of the travelling potentials (4) as a function of position along the device such that ions of different mobility or mass to charge ratio become trapped at different locations along the device.

A method is disclosed comprising: trapping ions in an ion trap (40); applying a first force on the ions within the ion trap in a first direction, said force having a magnitude that is dependent upon the value of a physicochemical property of the ions; applying a second force on these ions in the opposite direction so that the ions separate according to the physicochemical property value as a result of the first and second forces; and then pulsing or driving ions out of one or more regions of the ion trap.

A method for operating scientific analytical equipment such as mass spectrometers for the purpose of improving the performance and/or service life. Such method may include: providing an ion stream comprising ions having a range of masses, separating the ions of the ion stream on the basis of mass, and controlling the timing and/or order of impact of the separated ions on an electron emissive surface of the ion detector so as to modify one or more parameters of the ion detector.