Devices and methods of generating resonance excitation for an ion manipulation apparatus are provided. The ion manipulation apparatus can be operated as an ion filtration apparatus used with particle mass spectrometry system. The devices and methods can be capable of generating a resonance excitation to effect an ion filtration in a multipole apparatus. The resonance excitation is generated by mixing a radio frequency signal with a plurality of alternative current voltage signals having different frequencies. The resonance excitation can be added to at least one electrode of the multipole apparatus. The generation of mixed alternative current voltage signal is performed in a time domain, therefore no time-consuming inverse Fourier transform procedure is needed, which significantly improves an analysis speed and a throughput of the particle mass spectrometry system.

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.

In various aspects, methods and systems disclosed herein are capable of operating a Fourier Transform Mass Spectrometry (FTMS) quadrupole mass analyzer in two operational modes: transmitting mode and trapping mode. In the trapping mode, ions are first trapped and cooled within the FTMS quadrupole mass analyzer prior to being subjected to an excitation pulse and ejected from the FTMS quadrupole mass analyzer for detection. However, in transmitting mode, the FTMS quadrupole mass analyzer may provide more rapid analysis because the excitation pulse is applied to the ions of an ion beam that is being continuously transmitted through the FTMS quadrupole mass analyzer.

A mass spectrometer includes a controller operable to: transfer first ions of a first charge into an ion trap; apply an RF pseudopotential that radially confines the first ions in an elongate ion channel of the trap; generate a first potential well that confines the first ions within a first volume; after a specified pre-cooling time, transfer second ions of a second, opposite charge into the trap; apply one or more additional DC potentials that generate a second potential well that confines the second ions within a second volume, the first potential well being within the second potential well; cause, after cooling the second ions, the first ions and the second ions to interact and generate product ions; and generate at least one third potential well that confines the product ions, that is adjacent to the second potential well and that has a same polarity as the first potential well.

The disclosure features mass spectrometry systems and methods that include an ion source, an ion trap, a detector subsystem featuring first and second detector elements, and a controller electrically connected to the ion source, the ion trap, and the detector subsystem and configured so that during operation of the system, the controller: applies an electrical signal to the ion source to generate positively and negatively charged particles from sample particles in the system; applies an electrical signal to the ion trap to eject a plurality of particles from the ion trap through a common aperture of the ion trap, and determines information about the sample particles based on first and second electrical signals generated by the ejected particles.

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.

A method for multiple transition monitoring of at least one analyte in a sample using a quadrupole mass analyzer is provided and comprises at least one voltage application step, wherein a direct current (DC) voltage and a radio frequency (AC) voltage are applied between two pairs of electrodes of at least one mass filter of the analyzer, wherein the AC voltage has an amplitude V.sub.AC and the DC voltage has an applicable voltage V.sub.DC, wherein a supplementary AC voltage is superimposed on top of the AC and the DC voltage, wherein an amplitude ΔV.sub.DC of the supplementary AC voltage is

[00001]$\le \frac{V_{\mathrm{DC},\max }}{2^{b+1}},$

wherein V.sub.DC,max is a maximum voltage output of the DC voltage and b is a bit size of at least one electronics board of the mass filter of the analyzer; and wherein at least one transition of the analyte is determined with at least one detector of the analyzer.

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 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.

Control of an amplitude of a signal applied to a component of a mass spectrometer is described. In one aspect, a mass spectrometer includes a component and a resonant circuit to generate a radio frequency (RF) signal applied to the component. 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.