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.

The invention generally relates to ion traps and methods of use thereof. In certain embodiments, the invention provides a system that includes a mass spectrometer including an ion trap, and a central processing unit (CPU). The CPU has storage that is coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply a constant radio frequency (RF) signal to the ion trap, and apply a first alternating current (AC) signal to the ion trap the frequency of which varies as a function of time.

A mass spectrometry method comprises: receiving a stream of ions at an inlet end of an ion transport device; accumulating a first portion of the ion stream at a first electrical potential well at a first position within the ion transport device between the inlet and outlet ends; creating a generally descending potential profile within the ion transport apparatus between a second position and the outlet end and, simultaneously, creating a second potential well at a third position within the ion transport apparatus, the second position disposed between the first position and the inlet end, the third position disposed between the second position and the inlet end; and transporting the accumulated first portion of the ion stream from the first position to the outlet end under the impetus of the generally descending potential profile and, simultaneously, accumulating a second portion of the ion stream at the second potential well.

The invention generally relates to mass spectrometry via frequency tagging.

The invention generally relates to ion traps and methods of use thereof. In certain embodiments, the invention provides a system that includes a mass spectrometer including an ion trap, and a central processing unit (CPU). The CPU has storage that is coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply a constant radio frequency (RF) signal to the ion trap, and apply a first alternating current (AC) signal to the ion trap the frequency of which varies as a function of time.

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.

The invention generally relates to two-dimensional mass spectrometry using ion micropacket detection. In certain aspects, the invention provides systems including a mass spectrometer having an ion trap and one or more detectors. The system includes a central processing unit (CPU), and storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to: apply one or more scan functions to the ion trap that excite a precursor ion and eject a product ion from the ion trap; and determine a secular frequency of the product ion by detecting micropackets of the product ion as the micropackets are ejected from the ion trap.

Control of an amplitude of a signal applied to rods of a quadrupole is described. In one aspect, a mass spectrometer includes a quadrupole mass analyzer and a resonant circuit to generate a radio frequency (RF) signal applied to rods of the quadrupole mass analyzer. An amplitude control circuit can be inductively coupled with inductors of the resonant circuit to selectively discharge energy from the resonant circuit and, therefore, adjust the amplitude of the signal in particular situations.

The invention generally relates to logical operations in mass spectrometry. The system comprising a mass spectrometer comprising one or more ion traps; and a central processing unit (CPU), and storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply one or more scan functions to the one or more ion traps, the scan functions being combine together.

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.