Abstract: Methods and systems for loading an ion trap are provided herein in which the total ion beam intensity and/or content of the ion beam are quickly interrogated so as to determine an optimum fill time for an ion trap. In various aspects, the methods and systems described herein are effective to prevent overfilling of the ion trap while decreasing the time associated with known techniques utilized to obtain a survey scan of the ion beam.

Abstract: Methods and systems for FTMS-based analysis having an improved duty cycle relative to conventional FTMS techniques are provided herein. In various aspects, the methods and systems described herein operate on a continuous ion beam, thereby eliminating the relatively long duration trapping and cooling steps associated with Penning traps or orbitraps of conventional FTMS systems, as well as provide increased resolving power by sequentially interrogating the continuous ion beam under different radially-confining field conditions.

Abstract: In one aspect, a method of performing Fourier Transform (FT) mass spectrometry is disclosed, which comprises passing a plurality of ions through an FT mass analyzer comprising a plurality of rods arranged in a multipole configuration, where the plurality of rods include an input port for receiving ions and an output port through which ions can exit the mass analyzer. The method can further include applying at least one RF voltage to at least one of the rods so as to generate an RF field for radial confinement of the ions as they pass through the mass analyzer, and applying a resonant burst of an AC signal to at least one of said rods so as to remove ions having selected m/z ratios, e.g., m/z ratios within a desired range, from the ions introduced into the FT mass analyzer.

Abstract: In one aspect, a method for performing mass spectrometry is disclosed, which comprises using a Fourier transform mass analyzer, which extends from an inlet port to an outlet port, to acquire a first mass spectrum of a first plurality of ions generated by ionizing a sample, where the first plurality of ions are radially confined within the mass analyzer under a first radial confinement condition. The method further includes using the Fourier transform mass analyzer to acquire a second mass spectrum of a second plurality of ions generated by ionizing the sample, where the second plurality of ions are radially confined within said mass analyzer using a second radial confinement condition, and comparing said first and second mass spectra to identify spurious mass signals.

Abstract: Methods and systems for FTMS-based analysis having an improved duty cycle relative to conventional FTMS techniques are provided herein. In various aspects, the methods and systems described herein operate on a continuous ion beam, thereby eliminating the relatively long duration trapping and cooling steps associated with Penning traps or orbitraps of conventional FTMS systems, as well as provide increased resolving power by sequentially interrogating the continuous ion beam under different radially-confining field conditions.

Abstract: Methods and systems for loading an ion trap are provided herein in which the total ion beam intensity and/or content of the ion beam are quickly interrogated so as to determine an optimum fill time for an ion trap. In various aspects, the methods and systems described herein are effective to prevent overfilling of the ion trap while decreasing the time associated with known techniques utilized to obtain a survey scan of the ion beam.

Abstract: Systems and methods described herein utilize a multipole ion guide that can receive ions from an ion source for transmission to downstream mass analyzers, while preventing unwanted/interfering/contaminating ions from being transmitted into the high-vacuum chambers of mass spectrometer systems. In various aspects, RF and/or DC signals can be provided to auxiliary electrodes interposed within a quadrupole rod set so as to control or manipulate the transmission of ions from the multipole ion guide.

Abstract: Systems and methods described herein utilize a multipole ion guide that can receive ions from an ion source for transmission to downstream mass analyzers, while preventing unwanted/interfering/contaminating ions from being transmitted into the high-vacuum chambers of mass spectrometer systems. In various aspects, RF and/or DC signals can be provided to auxiliary electrodes interposed within a quadrupole rod set so as to control or manipulate the transmission of ions from the multipole ion guide.

Abstract: A method for obtaining fragment ions having product ion spectrum with a mixture of high, medium and lower energy product ions. The method includes (a) providing a selected RF field to an ion optical element upstream of an ion containment field; (b) transmitting ions through the ion optical element and into the ion containment field such that the selected RF field determines, at least in part, a selected kinetic energy profile of the ions within the ion containment field, wherein the selected kinetic energy profile is selected to fragment the ions to concurrently provide a plurality of groups of product ions; and (c) detecting each group of product ions in the plurality of groups of product ions.

Abstract: A method for obtaining fragment ions having product ion spectrum with a mixture of high, medium and lower energy product ions. The method includes (a) providing a selected RF field to an ion optical element upstream of an ion containment field; (b) transmitting ions through the ion optical element and into the ion containment field such that the selected RF field determines, at least in part, a selected kinetic energy profile of the ions within the ion containment field, wherein the selected kinetic energy profile is selected to fragment the ions to concurrently provide a plurality of groups of product ions; and (c) detecting each group of product ions in the plurality of groups of product ions.

Abstract: A mass spectrometer system having an ion trap and a downstream mass spectrometer is provided. A plurality of groups of ions are provided to the ion trap and a first mass-to-charge ratio is selected. The downstream mass spectrometer is configured to filter out one of (i) ions having a first unselected mass-to-charge ratio different from the first mass-to-charge ratio, and (ii) mass signals for ions having the first unselected mass-to-charge ratio different from the first mass-to-charge ratio. A first group of ions is ejected of the first mass-to-charge ratio from the ion trap to the downstream mass spectrometer.

Abstract: A method of operating an ion trap spectrometer system having an ion trap is provided.

Abstract: A method and apparatus for trapping or guiding ions is provided. The ion trap or ion guide includes a first set of electrodes and a second set of electrodes, the first set of electrodes defining a first portion of an ion channel to trap or guide the introduced ions. In operation, periodic voltages are applied to electrodes in the first set of electrodes to generate a first oscillating electric potential that radially confines the ions in the ion channel, while periodic voltages are applied to electrodes in the second set of electrodes to generate a second oscillating electric potential that axially confines the ions in the ion channel.

Abstract: A mass spectrometer and a method of operating same is provided. The mass spectrometer has an elongated rod set. The rod set has an entrance end and an exit end. An RF drive voltage is applied to the rod set to radially confine a first group of ions and a second group of ions of opposite polarity in the rod set. An entrance auxiliary RF voltage is applied to the entrance end and an exit auxiliary RF voltage to the exit end relative to the RF drive voltage, to trap both the first group of ions and the second group of ions in the rod set.

Abstract: A method of analyzing a substance comprises ionizing the substance to form a string of ions. The ions are then subject to a first mass analysis step. In one embodiment, the ions are accelerated into a collision cell in known manner to form primary fragment ions. These primary fragment ions are then accelerated into a downstream mass analyzer, to promote secondary fragmentation. In another embodiment of the invention, ions are passed through the collision cell, without fragmentation, and then accelerated from the collision cell into a low pressure section, which may be a mass analyzer or a rod set for collecting and collimating ions. This is done under conditions that promote fragmentation. The operating conditions of the low pressure section can be such as to promote collection or retention of ions depending upon their mass, and more specifically to reject low mass ions.

Abstract: A method of analysing ions provides for separating ions with different charge states. Ions are first thermalized to have substantially the same energy, preferably in an ion trap. Then a barrier height is set to enable ions having a lower charge to escape, while retaining ions with higher charge states. Having effected separation of the ions either or both groups of ions can be subjected to various conventional mass analysis or other processing steps.

Abstract: A system and method are described for producing a modifiable fringing field in a multipole instrument, such as a mass spectrometer or an ion guide. The system includes a conductor arrangement having a first pole pair, a second pole pair and an end device for allowing ions to enter or exit the conductor arrangement. A first power supply provides a first voltage to the first pole pair, such that the application of the first voltage results in a fringing field near the end device. An end device power supply provides an end device voltage to the end device for modifying the fringing field to facilitate the entrance or exit of the ions.

Abstract: A system and method are described for producing a modifiable fringing field in a multipole instrument, such as a mass spectrometer or an ion guide. The system includes a conductor arrangement having a first pole pair, a second pole pair and an end device for allowing ions to enter or exit the conductor arrangement. A first power supply provides a first voltage to the first pole pair, such that the application of the first voltage results in a fringing field near the end device. An end device power supply provides an end device voltage to the end device for modifying the fringing field to facilitate the entrance or exit of the ions.

Abstract: A method of setting a fill time for a mass spectrometer including a linear ion is provided. The mass spectrometer is operated first in a transmission mode and ions are supplied to the mass spectrometer. Ions are detected as they pass through at least part of the mass spectrometer in a preset time period, to determine the ion current. From a desired maximum charge density for the ion trap and the ion current, a fill time for the ion trap is determined. The mass spectrometer is operated in a trapping mode to trap ions in the ion trap, and the ion trap is filled for the fill time, as just determined. This utilizes the ion trap to its maximum, while avoiding problems due to overfilling the trap, causing space charge effects.

Abstract: A method of analysing ions provides for separating ions with different charge states. Ions are first thermalized to have substantially the same energy, preferably in an ion trap. Then a barrier height is set to enable ions having a lower charge to escape, while retaining ions with higher charge states. Having effected separation of the ions either or both groups of ions can be subjected to various conventional mass analysis or other processing steps.