Abstract: Systems and methods are provided to perform sequential windowed acquisition of mass spectrometry data. A mass range and a mass window width parameter are received for a sample. A plurality of ions from the sample that are within the mass range are collected in an ion trap of a mass spectrometer. Two or more mass adjacent or overlapping windows are calculated to span the mass range using the mass window width parameter. Ions within each mass window are ejected from the ion trap. A mass spectrum is then detected from the ejected ions of the each mass window with a mass analyzer of the mass spectrometer, producing a collection of mass spectra for the mass range. The two or more mass windows can all have the same width, can all have different widths, or can have at least two mass windows with different widths.

Abstract: 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.

Abstract: Systems and methods are provided for selecting and fragmenting a first precursor ion in an MS3 experiment. One or more first excitation parameters are calculated that define a first dipole excitation using a processor. The first dipole excitation is used to select a first precursor ion and fragment the first precursor ion to produce a second precursor ion. The first dipole excitation is applied to the continuous beam of ions by sending a first set of data including the first excitation parameters to a mass spectrometer. The first set of data is sent so that a first quadrupole applies the first dipole excitation to a continuous beam of ions. The mass spectrometer includes an ion source that provides the continuous beam of ions and the first quadrupole that receives the continuous beam of ions and is adapted to apply dipole excitation to the continuous beam of ions.

Abstract: An electron multiplier is positioned relative to at least one dynode to direct a beam of secondary particles from the at least one dynode to a collector area of the electron multiplier and not to a channel area of the electron multiplier for a range of electron multiplier voltages applied by one or more voltage sources to the electron multiplier and for a dynode voltage applied by the one or more voltage sources to the at least one dynode. The electron multiplier includes an aperture with an entrance cone and walls of the entrance cone comprise the collector area and an apex of the entrance cone comprises the channel area. An electron multiplier voltage of the range of electron multiplier voltages is applied to the electron multiplier and the dynode voltage is applied to the at least one dynode using the one or more voltage sources.

Abstract: A method and apparatus for clearing ions from a multipole ion transmission device which includes introducing a DC or RF clear out pulse to one or more of the rods of the multipole device. The DC pulse is selected so as to supply sufficient kinetic energy to the ions to overcome a pseudo-potential trapping well generated by the RF potentials of the ion transmission device. For an RF pulse, the auxiliary RF signal uses frequencies that correspond to the ejected ion's frequencies of motion. In select embodiments, the multipole device can be a quadrupole or the apparatus can be part of a tandem mass spectrometer.

Abstract: Systems and methods are provided to perform dead time correction. An observed ion count rate is obtained using a non-paralyzable detection system of a mass spectrometer. The detection system includes an ion detector, a comparator/discriminator, a mono-stable circuit and a counter. The non-paralyzable detection system exhibits dead time extension at high count rates. The extension of the dead time occurs because the mono-stable circuit requires a rising edge to trigger and can only be triggered again after the output pulse from the comparator/discriminator has gone low. This allows a second comparator/discriminator pulse arriving just before the end of the dead time started by a first comparator/discriminator pulse to extend the dead time to the trailing edge of the second comparator/discriminator pulse. A true ion count rate is calculated by performing dead time correction of the observed ion count rate.

Abstract: An electron multiplier is positioned relative to at least one dynode to direct a beam of secondary particles from the at least one dynode to a collector area of the electron multiplier and not to a channel area of the electron multiplier for a range of electron multiplier voltages applied by one or more voltage sources to the electron multiplier and for a dynode voltage applied by the one or more voltage sources to the at least one dynode. The electron multiplier includes an aperture with an entrance cone and walls of the entrance cone comprise the collector area and an apex of the entrance cone comprises the channel area. An electron multiplier voltage of the range of electron multiplier voltages is applied to the electron multiplier and the dynode voltage is applied to the at least one dynode using the one or more voltage sources.

Abstract: 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 auxinary electrodes placed between rods.

Abstract: Systems and methods are provided for selecting and fragmenting a first precursor ion in an MS3 experiment. One or more first excitation parameters are calculated that define a first dipole excitation using a processor. The first dipole excitation is used to select a first precursor ion and fragment the first precursor ion to produce a second precursor ion. The first dipole excitation is applied to the continuous beam of ions by sending a first set of data including the first excitation parameters to a mass spectrometer. The first set of data is sent so that a first quadrupole applies the first dipole excitation to a continuous beam of ions. The mass spectrometer includes an ion source that provides the continuous beam of ions and the first quadrupole that receives the continuous beam of ions and is adapted to apply dipole excitation to the continuous beam of ions.

Abstract: Systems, devices, circuits, and methods are provided for an improved mass spectrometry detection system that comprises an ion source and a detector that operate at opposite polarities. In some embodiments, the system can comprise a positive and negative multiplier, each of which can be configured to provide voltage to each of the ion source and the detector. In some embodiments, the system can comprise switches that allow the change between positive and negative polarities for the ion source or detector to occur quickly. A variety of embodiments of systems, devices, circuits, and methods in conjunction with the disclosures are provided.

Abstract: Systems, devices, and methods are provided for an improved mass spectrometry detection system for pulse counting applications. The detector can comprise an electron multiplier and circuitry, such as a transimpedance amplifier, that allows for the gain of the detector to be decreased, which in turn leads to a pulse counting detector with a high dynamic range. In some embodiments, the detector can operate at count rates of up to about 20 million counts per second without reaching saturation. Further, the lifetime of the detector can be extended. A variety of embodiments of systems, devices, and methods in conjunction with the disclosures are provided.

Abstract: Systems and methods are provided to perform dead time correction. An observed ion count rate is obtained using a non-paralyzable detection system of a mass spectrometer. The detection system includes an ion detector, a comparator/discriminator, a mono-stable circuit and a counter. The non-paralyzable detection system exhibits dead time extension at high count rates. The extension of the dead time occurs because the mono-stable circuit requires a rising edge to trigger and can only be triggered again after the output pulse from the comparator/discriminator has gone low. This allows a second comparator/discriminator pulse arriving just before the end of the dead time started by a first comparator/discriminator pulse to extend the dead time to the trailing edge of the second comparator/discriminator pulse. A true ion count rate is calculated by performing dead time correction of the observed ion count rate.

Abstract: Systems and methods are provided to perform sequential windowed acquisition of mass spectrometry data. A mass range and a mass window width parameter are received for a sample. A plurality of ions from the sample that are within the mass range are collected in an ion trap of a mass spectrometer. Two or more mass adjacent or overlapping windows are calculated to span the mass range using the mass window width parameter. Ions within each mass window are ejected from the ion trap. A mass spectrum is then detected from the ejected ions of the each mass window with a mass analyzer of the mass spectrometer, producing a collection of mass spectra for the mass range. The two or more mass windows can all have the same width, can all have different widths, or can have at least two mass windows with different widths.

Abstract: Systems, devices, circuits, and methods are provided for an improved mass spectrometry detection system that comprises an ion source and a detector that operate at opposite polarities. In some embodiments, the system can comprise a positive and negative multiplier, each of which can be configured to provide voltage to each of the ion source and the detector. In some embodiments, the system can comprise switches that allow the change between positive and negative polarities for the ion source or detector to occur quickly. A variety of embodiments of systems, devices, circuits, and methods in conjunction with the disclosures are provided.

Abstract: The invention provides a multipole ion trap. The trap has a longitudinal axis. An oscillating on-axis potential is set up along the longitudinal axis, providing a potential well in which ions are trapped. In some embodiments, rods forming the poles are symmetrically and equidistantly positioned about the longitudinal axis and RF signal with different magnitudes are applied to the poles. In other embodiments, the rods are not positioned symmetrically about the longitudinal axis and the RF signals applied to the poles may have the same or different magnitudes. Poles used in the invention may include two or more rods. An ion trap according to the invention may include more than two poles, and in some embodiments, a third or additional pole may be added to provide the oscillating on-axis potential. The ion trap may be used mass selectively scan ions, fragment ions and to trap and separate differently charged ions, among other uses.