Abstract: In one aspect, a method of operating a mass spectrometer having an ion source, at least one ion optic positioned downstream of the ion source and at least one ion mass filter positioned downstream of the ion optic is disclosed, which includes transitioning an operational mode of the mass spectrometer from an active mass collection mode to a park mass mode, and configuring the ion optic to function as a bandpass ion filter for substantially inhibiting passage of ions generated by the ion source during the park mass mode to the downstream ion mass filter.

Abstract: A mass spectrometer comprises a first mass filter for receiving a plurality of ions and having a transmission bandwidth configured to allow transmission of ions having m/z ratios within a desired range, and a second mass filter that is disposed downstream of the first mass filter for selecting ions having a target m/z value within a transmission window thereof for mass analysis. The transmission bandwidth of the first mass filter encompasses at least two m/z ratios of interest such that one of said m/z ratios corresponds to said target m/z value within the transmission window of said second mass filter.

Abstract: In one aspect, a method of modulating transmission of ions in a mass spectrometer is disclosed, which comprises generating an ion beam comprising a plurality of ions, directing the ion beam to an ion optic positioned in the path of the ion beam, wherein the ion optic includes at least one opening through which the ions can pass, and applying one or more voltage pulses at a selected duty cycle to said ion optic so as to obtain a desired attenuation of brightness of the ion beam passing through the ion optic, where a pulse width of said voltage pulses at said selected duty cycle is determined by identifying a pulse width on a calibration normalized ion intensity versus pulse width relation for said ions that corresponds to said desired attenuation on an ideal normalized ion intensity versus pulse width relation for said ions.

Abstract: Apparatus and methods for controlling contamination of components contained within the high-vacuum chambers of mass spectrometer systems are provided. The apparatus and methods employ a beam of neutral gas injected in a contra-flow configuration to incoming particle stream from the ionization chamber. The contra-flow can be in the directly opposite counter-flow direction (e.g., 180 degrees) or at a cross-flow angle to the incoming ion stream (e.g., flowing at an angle between about 10 degrees and 170 degrees). The contra-flow disrupts the axial gas flow and diverts neutral molecules and other undesirable contaminants before they reach the high vacuum stages (e.g., beyond the IQ0 orifice) of the spectrometer. By reducing the transmission of contaminants into the sensitive components housed deep within the mass spectrometer, the present invention can increase throughput, improve robustness, and/or decrease the downtime typically required to vent/disassemble/clean the fouled components.

Abstract: Methods and apparatus are disclosed for reducing ion reflections between multipole segments in a mass spectrometer by matching the effective potential between the two segments. Mass spectrometers having at least two multipole segments separated from each other along a longitudinal axis of the mass spectrometer such that a boundary region exists through which ions are drawn from an upstream segment to a downstream segment, and wherein each multipole segment further includes a set of spaced-apart rod-shaped electrodes disposed around the longitudinal axis and having a field radius defined by an inscribed circle between the innermost portions of each electrode. Effective potential matching can be achieved by either supplying RF signals of different amplitudes to each segment and/or by modifying the field strength of the segments. In one embodiment, the multipole segments are configured such that the upstream multipole segment has a smaller field radius than the downstream segment.

Abstract: In one aspect, a method of modulating transmission of ions in a mass spectrometer is disclosed, which comprises generating an ion beam comprising a plurality of ions, directing the ion beam to an ion optic positioned in the path of the ion beam, wherein the ion optic includes at least one opening through which the ions can pass, and applying one or more voltage pulses at a selected duty cycle to said ion optic so as to obtain a desired attenuation of brightness of the ion beam passing through the ion optic, where a pulse width of said voltage pulses at said selected duty cycle is determined by identifying a pulse width on a calibration normalized ion intensity versus pulse width relation for said ions that corresponds to said desired attenuation on an ideal normalized ion intensity versus pulse width relation for said ions.

Abstract: Methods and apparatus are disclosed for reducing ion reflections between multipole segments in a mass spectrometer by matching the effective potential between the two segments. Mass spectrometers having at least two multipole segments separated from each other along a longitudinal axis of the mass spectrometer such that a boundary region exists through which ions are drawn from an upstream segment to a downstream segment, and wherein each multipole segment further includes a set of spaced-apart rod-shaped electrodes disposed around the longitudinal axis and having a field radius defined by an inscribed circle between the innermost portions of each electrode. Effective potential matching can be achieved by either supplying RF signals of different amplitudes to each segment and/or by modifying the field strength of the segments. In one embodiment, the multipole segments are configured such that the upstream multipole segment has a smaller field radius than the downstream segment.

Abstract: Apparatus and methods for controlling contamination of components contained within the high-vacuum chambers of mass spectrometer systems are provided. The apparatus and methods employ a beam of neutral gas injected in a contra-flow configuration to incoming particle stream from the ionization chamber. The contra-flow can be in the directly opposite counter-flow direction (e.g., 180 degrees) or at a cross-flow angle to the incoming ion stream (e.g., flowing at an angle between about 10 degrees and 170 degrees). The contra-flow disrupts the axial gas flow and diverts neutral molecules and other undesirable contaminants before they reach the high vacuum stages (e.g., beyond the IQ0 orifice) of the spectrometer. By reducing the transmission of contaminants into the sensitive components housed deep within the mass spectrometer, the present invention can increase throughput, improve robustness, and/or decrease the downtime typically required to vent/disassemble/clean the fouled components.

Abstract: A mass spectrometer system can include a mass analyzer operable to mass transmit streams of ions to a detector in a mass dependent fashion for measurement of ion flux intensity. An ion attenuator can be located in the extraction region between the mass analyzer and detector, downstream of the mass analyzer, and can be operable to provide selective attenuation of the ion beam by attenuating ion flux intensity also in mass dependent fashion. Higher concentration ions can be selected and attenuated, while other lower concentration ions can be left unattenuated. Different ions can be attenuated to different degrees. Locating the ion attenuator downstream of the mass analyzer so that the ion beam is already mass differentiated when attenuated can avoid mass discriminatory effects associated with ion beam attenuators. Selective attenuation of only certain ions but not others can extend the dynamic range of the detector without necessarily sacrificing detector sensitivity.

Abstract: Methods for fragmenting ions in an ion trap are described.

Abstract: Methods for fragmenting ions retained in an ion trap are described. In various embodiments, a non-steady-state pressure of a neutral collision gas of less than about 5×10?4 Torr and an excitation amplitude of less than about 500 mV (peak to ground) is used to fragment ions with greater than about 80% fragmentation efficiency. In various embodiments, duration of ion excitation is greater than about 25 ms.

Abstract: Methods for cooling ions retained in an ion trap are described. In various embodiments, a cooling gas is delivered into a linear ion trap causing a non-steady state pressure elevation in at least a portion of the trap above about 8×10?5 Torr for a duration less than the ion-retention time. In various embodiments, the duration of pressure elevation can be based upon a period of time required for an ion to lose a desired amount of its kinetic energy.

Abstract: Methods for cooling ions retained in an ion trap are described. In various embodiments, a cooling gas is delivered into a linear ion trap causing a non-steady state pressure elevation in at least a portion of the trap above about 8×10?5 Torr for a duration less than the ion-retention time. In various embodiments, the duration of pressure elevation can be based upon a period of time required for an ion to lose a desired amount of its kinetic energy.

Abstract: A method of processing multiple precursor ions in a tandem mass spectrometer includes generating a plurality of precursor ions with an ion source. At least some of the plurality of precursor ions is trapped in an ion trap. At least two precursor ions of interest are isolated from the plurality of precursor ions with a filtered noise field. Precursor ions of interest are sequentially ejected toward a collision cell. The sequentially ejected precursor ions of interest are fragmented in a collision cell. The mass-to-charge ratio spectra of the fragmented ions are then determined with a mass spectrometer.

Abstract: Methods for fragmenting ions in an ion trap are described.

Abstract: Methods for fragmenting ions retained in an ion trap are described. In various embodiments, a non-steady-state pressure of a neutral collision gas of less than about 5×10?4 Torr and an excitation amplitude of less than about 500 mV (peak to ground) is used to fragment ions with greater than about 80% fragmentation efficiency. In various embodiments, duration of ion excitation is greater than about 25 ms.

Abstract: In a mass spectrometer, ions from an ion source pass through an inlet aperture into a vacuum chamber for transmitting prior to mass analysis by the mass analyzer. The configuration of the inlet aperture forms a sonic orifice or sonic nozzle and with a predetermined vacuum chamber pressure, a supersonic free jet expansion is created in the vacuum chamber that entrains the ions within the barrel shock and Mach disc. Once formed, at least one ion guide with a predetermined cross-section to essentially radially confine the supersonic free jet expansion can focus the ions for transmission through the vacuum chamber. This effectively improves the ion transmission between the ion source and the mass analyzer.

Abstract: In a mass spectrometer, ions from an ion source pass through an inlet aperture into a vacuum chamber for transmitting prior to mass analysis by the mass analyzer. The configuration of the inlet aperture forms a sonic orifice or sonic nozzle and with a predetermined vacuum chamber pressure, a supersonic free jet expansion is created in the vacuum chamber that entrains the ions within the barrel shock and Mach disc. Once formed, an ion guide with a predetermined cross-section to essentially radially confine the supersonic free jet expansion can focus the ions for transmission through the vacuum chamber. This effectively improves the ion transmission between the ion source and the mass analyzer.

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.

Abstract: In the field of mass spectrometry, a method and apparatus for fragmenting ions with a relatively high degree of resolution and efficiency. The technique includes trapping the ions in a linear ion trap, in which the background or neutral gas pressure is preferably on the order of 10-5 Torr. The trapped ions are resonantly excited for a relatively extended period of time, e.g., exceeding 50 ms, at relatively low excitation levels, e.g., less than 1 Volt (0-pk). The technique allows selective dissociation of ions with a high discrimination. High fragmentation efficiency may be achieved by superimposing a higher order multipole field onto the quadrupolar RF field used to trap the ions. The multipole field, preferably an octopole field, dampens the radial oscillatory motion of resonantly excited ions at the periphery of the trap. This reduces the probability that ions will eject radially from the trap thus increasing the probability of collision induced dissociation.