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: Rapid and efficient fragmentation of ions in an ion trap for MS/MS analysis is achieved by a pulsed fragmentation technique. Ions of interest are placed at an elevated value of Q and subjected to a relatively high amplitude, short-duration resonance excitation pulse to cause the ions to undergo collision-induced fragmentation. The Q value of the ions of interest is then reduced before significant numbers of ion fragments are expelled from the ion trap, thereby decreasing the low-mass cutoff and allowing retention and subsequent measurement of lower-mass ion fragments.

Abstract: A mass spectrometer 10 comprises an ion source 12 which generates nebulized ions which enter an ion cooler 20 via an ion source block 16. Ions within a window of m/z of interest are extracted via a quadrupole mass filter 24 and passed to a linear trap 30. Ions are trapped in a potential well in the linear trap 30 and are bunched at the bottom of the potential well adjacent an exit segment 50. Ions are gated out of the linear trap 30 into an electrostatic ion trap 130 and are detected by a secondary electron multiplier 10. By bunching the ions in the linear trap 30 prior to ejection, and by focussing the ions in time of flight (TOF) upon the entrance of the electrostatic trap 130, the ions arrive at the electrostatic trap 130 as a convolution of short, energetic packets of similar m/z. Such packets are particularly suited to an electrostatic trap because the FWHM of each packet's TOF distribution is less than the period of oscillation of those ions in the electrostatic trap.

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: An aperture design for a linear ion trap is provided in which the aperture is optimized to minimize possible axial field inhomogeneities whilst preserving the structural integrity of the quadrupole rods. In general, the invention provides a linear ion trap for trapping and subsequently ejecting ions. The linear ion trap comprises a plurality of rods which define an interior trapping volume which has an axis extending longitudinally. One or more of the rods includes an aperture which extends both radially through the rod and longitudinally along the rod. The aperture being configured such that the ions can pass from the interior trapping volume through the aperture to a region outside the interior trapping volume. At least one recess is disposed adjacent the aperture, extending longitudinally along the rod and facing the interior trapping volume, the recess not extending radially through the rod.

Abstract: A mass spectrometer 10 comprises an ion source 12 which generates nebulized ions which enter an ion cooler 20 via an ion source block 16. Ions within a window of m/z of interest are extracted via a quadrupole mass filter 24 and passed to a linear trap 30. Ions are trapped in a potential well in the linear trap 30 and are bunched at the bottom of the potential well adjacent an exit segment 50. Ions are gated out of the linear trap 30 into an electrostatic ion trap 130 and are detected by a secondary electron multiplier 10. By bunching the ions in the linear trap 30 prior to ejection, and by focussing the ions in time of flight (TOF) upon the entrance of the electrostatic trap 130, the ions arrive at the electrostatic trap 130 as a convolution of short, energetic packets of similar m/z. Such packets are particularly suited to an electrostatic trap because the FWHM of each packet's TOF distribution is less than the period of oscillation of those ions in the electrostatic trap.

Abstract: Rapid and efficient fragmentation of ions in an ion trap for MS/MS analysis is achieved by a pulsed fragmentation technique. Ions of interest are placed at an elevated value of Q and subjected to a relatively high amplitude, short-duration resonance excitation pulse to cause the ions to undergo collision-induced fragmentation. The Q value of the ions of interest is then rapidly reduced, thereby decreasing the low-mass cutoff and allowing retention and subsequent analysis of low-mass ion fragments.

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). Thus the mass-to-charge ratio isolation window is controlled and has an improved resolution without increasing the number of frequency components.

Abstract: A detector assembly has a current measuring device with a saturation threshold level, and a gain variation means. A signal is generated in response to the particles detected, a first data point corresponding to a peak of interest is acquired from the signal. If the first data point is near, at or above the saturation threshold level of the current measuring device, the gain of the gain variation means is adjusted such that the peak of interest in the signal is reduced in intensity.

Abstract: A mass spectrometer 10 comprises an ion source 12 which generates nebulized ions which enter an ion cooler 20 via an ion source block 16. Ions within a window of m/z of interest are extracted via a quadrupole mass filter 24 and passed to a linear trap 30. Ions are trapped in a potential well in the linear trap 30 and are bunched at the bottom of the potential well adjacent an exit segment 50. Ions are gated out of the linear trap 30 into an electrostatic ion trap 130 and are detected by a secondary electron multiplier 10. By bunching the ions in the linear trap 30 prior to ejection, and by focussing the ions in time of flight (TOF) upon the entrance of the electrostatic trap 130, the ions arrive at the electrostatic trap 130 as a convolution of short, energetic packets of similar m/z. Such packets are particularly suited to an electrostatic trap because the FWHM of each packet's TOF distribution is less than the period of oscillation of those ions in the electrostatic trap.

Abstract: A three section linear or two-dimensional (2D) quadrupole ion trap as a high performance mass spectrometer is described. Mass analysis is performed by ejecting ions radically out slots formed in at least two of the rods using the mass selective instability mode of operation. The slot geometry is optimized to enable ions of different mass ranges to be scanned out of differently dimensioned slots. Multiple detectors arranged to receive ejected ions in multiple directions provide the ability to simultaneously or sequentially scan or perform mass analysis of ions of different natures.