Abstract: 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 and supply an isolation waveform to the radio frequency ion trap. The isolation waveform has at least one notch at a target mass-to-charge ratio and a frequency profile determined to eject unwanted ions at a plurality of frequencies in a substantially similar amount of time.

Abstract: A method is described for identifying the occurrence and location of charging of ion optic devices arranged along the ion path of a mass spectrometer. The method includes repeatedly performing a sequence of introducing a beam of discharge ions to a location on the ion path, and subsequently measuring the intensities of opposite-polarity sample ions delivered to a mass analyzer, with the discharge ions being delivered to a location further downstream in the ion path at each successive sequence.

Abstract: An apparatus for a mass spectrometer comprises: a set of four rod electrodes defining an ion occupation volume therebetween having entrance and exit ends, at least one of the rod electrodes having a slot passing therethrough; first and second ion optics disposed adjacent to the entrance and exit ends, respectively; a voltage supply system; and at least one supplemental electrode disposed at least partially within the at least one slot, wherein the voltage supply system is configured so as to supply a radio-frequency (RF) voltage, a direct-current (DC) filtering voltage and an oscillatory dipole resonant ejection voltage across members of the set of rod electrodes and so at to supply a secondary ion-trapping RF voltage and a secondary DC filtering voltage to the at least one supplemental electrode and to supply DC voltages across the rod electrodes and each of the first and second ion optics.

Abstract: An apparatus for a mass spectrometer comprises: a set of four rod electrodes defining an ion occupation volume therebetween having entrance and exit ends, at least one of the rod electrodes having a slot passing therethrough; first and second ion optics disposed adjacent to the entrance and exit ends, respectively; a voltage supply system; and at least one supplemental electrode disposed at least partially within the at least one slot, wherein the voltage supply system is configured so as to supply a radio-frequency (RF) voltage, a direct-current (DC) filtering voltage and an oscillatory dipole resonant ejection voltage across members of the set of rod electrodes and so at to supply a secondary ion-trapping RF voltage and a secondary DC filtering voltage to the at least one supplemental electrode and to supply DC voltages across the rod electrodes and each of the first and second ion optics.

Abstract: A method is described for identifying the occurrence and location of charging of ion optic devices arranged along the ion path of a mass spectrometer. The method includes repeatedly performing a sequence of introducing a beam of discharge ions to a location on the ion path, and subsequently measuring the intensities of opposite-polarity sample ions delivered to a mass analyzer, with the discharge ions being delivered to a location further downstream in the ion path at each successive sequence.

Abstract: Methods for operating a mass spectrometer having at least one component having mass-dependent transmission, comprising: injecting a first sample of ions having a first mass range into an ion accumulator for a first injection time under first operating conditions suitable for optimizing transmission of ions of the first range; acquiring a full-scan mass spectrum of the first sample of ions; selecting ion species having a second mass range different than the first range; calculating a second injection time, the second injection time suitable for injecting a population of the selected ion species into the ion accumulator under second operating conditions suitable for optimizing transmission of ions of the second range; injecting a second sample of ions having the selected ion species into the ion accumulator for the second injection time under the second operating conditions; and acquiring a mass spectrum of ions derived from the selected ion species.

Abstract: A two-dimensional radial-ejection ion trap is constructed from four apertured electrodes having inwardly facing hyperbolic surfaces, with each electrode being spaced from the centerline by a distance r that is greater than the hyperbolic radius r0 defined by the hyperbolic surfaces. This geometry produces a balanced symmetrical trapping field that has a negligible octopole field component and a relatively large dodecapole or icosapolar field component. In one specific implementation, the ion trap is selectably operable as a quadrupole mass filter by applying a filtering DC voltage to the electrodes.

Abstract: A method of calibrating an ion trap having electrodes to which main RF trapping and resonant ejection voltages are applied comprises: identifying, for each of a plurality of ion types having different respective mass-to-charge ratios, an optimum resonant ejection voltage amplitude at which a mass peak quality is optimized when the ion trap mass analyzer is operated at a selected scan rate; determining a best-fit function of the form Vreseject=mc(a+bm), where Vreseject and m represent resonant ejection voltage amplitude and mass-to-charge ratio and a, b and c are constants; identifying, for each of a plurality of ion types, a respective RF voltage amplitude at which ions of each respective type are ejected from the ion trap using a resonant ejection voltage calculated according to the best-fit function; and determining a second best-fit function relating the identified trapping voltage amplitudes to mass-to-charge; ratio.

Abstract: The invention provides a two-dimensional ion trap, comprising a plurality of elongate electrodes positioned between first and second end electrodes, the plurality of electrodes and first and second end electrodes defining a trapping volume. A controller in electrical communication with the plurality of elongate electrodes and the first and second end electrodes is configured to progressively vary a periodic voltage applied to at least one of the plurality of elongate electrodes to cause ions to be radially ejected from the ion trap in order of their mass to charge ratios. Concurrently, the controller is configured to progressively vary a DC offset of least one of the first and second end electrodes with respect to the plurality of elongate electrodes.

Abstract: A method of calibrating ion collision energy used in a mass spectrometer, comprises: (a) obtaining fragment ion yield data for each of a plurality of precursor ion populations having respective mass-to-charge ratios at each of a plurality of settings of a fragmentation-energy-related variable; (b) locating, for each mass-to-charge ratio, reference values of the fragmentation-energy-related variable, each reference value corresponding to a respective reference feature of the ion yield data at the mass-to-charge ratio; (c) determining, from the plurality of locating steps, the variation, with mass-to-charge-ratio, of each of the reference values of the fragmentation-energy-related variable; (d) associating each of the reference values of the fragmentation-energy related variable with respective reference values of a dimensionless useable-fragmentation-energy variable; and (e) storing parameters describing the variation of each of the reference values of the fragmentation-energy-related variable with mass-to-cha

Abstract: A method for calibrating an ion trap mass spectrometer is disclosed. The method includes establishing an optimal phase and amplitude-m/z relationship by acquiring peak quality data at varying values of amplitude and phase. The resonant ejection voltage applied to the electrodes of the ion trap may then be controlled during analytical scans in accordance with the established relationship between m/z and resonant ejection voltage amplitude.

Abstract: A dual ion trap mass analyzer includes adjacently positioned first and second two-dimensional ion traps respectively maintained at relatively high and low pressures. Functions favoring high pressure (cooling and fragmentation) may be performed in the first trap, and functions favoring low pressure (isolation and analytical scanning) may be performed in the second trap. Ions may be transferred between the first and second trap through a plate lens having a small aperture that presents a pumping restriction and allows different pressures to be maintained in the two traps. The differential-pressure environment of the dual ion trap mass analyzer facilitates the use of high-resolution analytical scan modes without sacrificing ion capture and fragmentation efficiencies.

Abstract: A technique is disclosed for conducting collision induced dissociation (CID) in a quadrupole ion trap (QIT) having higher order field components. In order to compensate for the shift in the frequency of motion with amplitude of the excited ions arising from the influence of higher-order field components, the amplitude of the RF voltages applied to the QIT is monotonically varied during the excitation period to prolong the condition of resonance, resulting in higher average kinetic energies of the excited ions. Thus, higher fragmentation efficiencies may be obtained, or a targeted level of fragmentation may be achieved in less time relative to conventional CID.

Abstract: Methods and apparatus for data-dependent mass spectrometric MS/MS or MSn analysis are disclosed. The methods may include determination of the charge state of an ion species of interest, followed by automated selection of a dissociation type (e.g., CAD, ETD, or ETD followed by a non-dissociative charge reduction or collisional activation) based at least partially on the determined charge state. The ion species of interest is then dissociated in accordance with the selected dissociation type, and an MS/MS or MSn spectrum of the resultant product ions may be acquired.

Abstract: A method of calibrating ion collision energy used in a mass spectrometer, comprises: (a) obtaining fragment ion yield data for each of a plurality of precursor ion populations having respective mass-to-charge ratios at each of a plurality of settings of a fragmentation-energy-related variable; (b) locating, for each mass-to-charge ratio, reference values of the fragmentation-energy-related variable, each reference value corresponding to a respective reference feature of the ion yield data at the mass-to-charge ratio; (c) determining, from the plurality of locating steps, the variation, with mass-to-charge-ratio, of each of the reference values of the fragmentation-energy-related variable; (d) associating each of the reference values of the fragmentation-energy related variable with respective reference values of a dimensionless useable-fragmentation-energy variable; and (e) storing parameters describing the variation of each of the reference values of the fragmentation-energy-related variable with mass-to-cha

Abstract: A two-dimensional radial-ejection ion trap is constructed from four apertured electrodes having inwardly facing hyperbolic surfaces, with each electrode being spaced from the centerline by a distance r that is greater than the hyperbolic radius r0 defined by the hyperbolic surfaces. This geometry produces a balanced symmetrical trapping field that has a negligible octopole field component and a relatively large dodecapole or icosapolar field component. In one specific implementation, the ion trap is selectably operable as a quadrupole mass filter by applying a filtering DC voltage to the electrodes.

Abstract: An automatic gain control (AGC) technique and apparatus is introduced herein for any temporally non-uniform ion beam, such as, for example, an ion beam produced by a MALDI ion source so as to minimize space charge effects. The disclosed configurations and techniques can be achieved by using an ion optical gating element and applying a desired signal waveform (e.g., a square wave) having a predetermined duty cycle. The applied voltage amplitude of such a signal can be configured to switch between a voltage which fully transmits the ions, and a voltage which does not transmit any ions. The frequency is chosen to result in a period which is significantly lower than the smallest non-uniformity period. Techniques of the present invention can also be extended to methods of AGC which can use a single ion injection event from the ion source to avoid variations in ion numbers from an unstable ion source.

Abstract: A two-dimensional radial-ejection ion trap is constructed from four apertured electrodes having inwardly facing hyberbolic surfaces, with each electrode being spaced from the centerline by a distance r that is greater than the hyperbolic radius r0 defined by the hyperbolic surfaces. This geometry produces a balanced symmetrical trapping field that has a negligible octopole field component and a relatively large dodecapole or icosapolar field component. In one specific implementation, the ion trap is selectably operable as a quadrupole mass filter by applying a filtering DC voltage to the electrodes.

Abstract: Ions in a predefined narrow mass to charge ratio range are isolated in an ion trap by adjusting the field and using ejection frequency waveform(s). The ejection waveforms have frequency components in a first and a second dimension, and, are applied across electrodes aligned along a first and a second dimension. Thus the mass-to-charge ratio isolation window is controlled and has an improved resolution without increasing the number of frequency components.

Abstract: A method for calibrating an ion trap mass spectrometer is disclosed. The method includes establishing an optimal phase and amplitude-m/z relationship by acquiring peak quality data at varying values of amplitude and phase. The resonant ejection voltage applied to the electrodes of the ion trap may then be controlled during analytical scans in accordance with the established relationship between m/z and resonant ejection voltage amplitude.