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 mass spectrometer includes a radio frequency ion trap; and a controller. The controller is configured to cause an ion population to be injected into the radio frequency ion trap; supply a first isolation waveform to the radio frequency ion trap for a first duration, and supply a second isolation waveform to the radio frequency ion trap for a second duration. The first isolation waveform has at least a first wide notch at a first mass-to-charge ratio, and the second isolation waveform has at least a first narrow notch at the first mass-to-charge ratio. The first and second isolation waveforms are effective to isolate one or more precursor ions from the ion population.

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.

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.

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.

Systems and methods are provided for multiplexed precursor ion selection using a filtered noise field (FNF). Two or more different precursor ions are selected using a processor. The processor calculates an FNF waveform. The calculated FNF waveform is applied to a continuous beam of ions using the processor. The processors sends information to a mass spectrometer, which includes an ion source that provides the continuous beam of ions and a first quadrupole that receives the continuous beam of ions, so that the first quadrupole applies the calculated FNF waveform to the continuous beam of ions. The first quadrupole applies the calculated FNF waveform to the continuous beam of ions by applying the calculated FNF waveform between pairs of rods or between pairs of auxiliary electrodes placed between rods.

This disclosure describes a method of adjusting the amplitude of broadband waveforms for isolation, especially during injection to a multipole trapping device. Isolation during injection to a trapping device is known to be an effective way of accumulating a desired population of ions while rejecting unwanted species. The waveform amplitude required to eject unwanted species varies as a function of isolation time, but using automated gain control, the time required to accumulate a given population of ions may vary over several orders of magnitude. Thus, when the injection times are very long, precursor ions of interest are resonated for a long time and may be inadvertently ejected from the trap, using conventional methods. By setting the waveform amplitude lower for longer accumulation times, good isolation efficiency can be maintained for the precursor, while still rejecting unwanted ions.

This disclosure describes a method of adjusting the amplitude of broadband waveforms for isolation, especially during injection to a multipole trapping device. Isolation during injection to a trapping device is known to be an effective way of accumulating a desired population of ions while rejecting unwanted species. The waveform amplitude required to eject unwanted species varies as a function of isolation time, but using automated gain control, the time required to accumulate a given population of ions may vary over several orders of magnitude. Thus, when the injection times are very long, precursor ions of interest are resonated for a long time and may be inadvertently ejected from the trap, using conventional methods. By setting the waveform amplitude lower for longer accumulation times, good isolation efficiency can be maintained for the precursor, while still rejecting unwanted ions.

A collision or reaction device for a mass spectrometer is disclosed comprising a first device arranged and adapted to cause first ions to collide or react with charged particles and/or neutral particles or otherwise dissociate so as to form second ions. A second device is arranged and adapted to apply a broadband excitation with one or more frequency notches to the first device so as to cause the second ions and/or ions derived from the second ions to be substantially ejected from the collision or reaction region. The collision or reaction device further comprises a device arranged and adapted to determine the time when the second ions and/or ions derived from the second ions are substantially ejected from the first device.