A mass spectrometry method comprises: storing a first packet of ions within an ion storage apparatus; transferring the first ion packet into an electrostatic trap mass analyzer through a set of electrostatic lenses, wherein, during the transfer, either the lenses are operated in a first mode of operation or an injection voltage of a first pre-determined magnitude is applied to an electrode of the mass analyzer; mass analyzing the first ion packet using the mass analyzer; storing a second packet of ions within the ion storage apparatus; transferring the second ion packet into the mass analyzer through the set of lenses, wherein, during the transfer, either the lenses are operated in a second mode of operation or an injection voltage of a second pre-determined magnitude is applied to the electrode of the mass analyzer; and mass analyzing the second packet of ions using the electrostatic trap mass analyzer.

A method of processing ions in a mass spectrometer comprises introducing one or more precursor ions into a collision cell to fragment at least a portion of said ions, where the collision cell is configured to confine ions having m/z ratios above a selected threshold (i.e., high m/z ions). The ions are released from the collision cell and introduced into a downstream analyzer ion trap to radially confine high m/z ions. The collision cell and the analyzer ion trap are configured to confine ions having m/z ratios below said selected threshold (i.e., low m/z ions). Ions are introduced into the collision cell and undergo fragmentation. The fragment ions are released from the collision cell and introduced into the analyzer ion trap, thus loading the analyzer ion trap with both high m/z and low m/z ions. The ions are released from the analyzer ion trap and detected by a detector.

A mass spectrometry method comprises: storing a first packet of ions within an ion storage apparatus; transferring the first ion packet into an electrostatic trap mass analyzer through a set of electrostatic lenses, wherein, during the transfer, either the lenses are operated in a first mode of operation or an injection voltage of a first pre-determined magnitude is applied to an electrode of the mass analyzer; mass analyzing the first ion packet using the mass analyzer; storing a second packet of ions within the ion storage apparatus; transferring the second ion packet into the mass analyzer through the set of lenses, wherein, during the transfer, either the lenses are operated in a second mode of operation or an injection voltage of a second pre-determined magnitude is applied to the electrode of the mass analyzer; and mass analyzing the second packet of ions using the electrostatic trap mass analyzer.

The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.

A mass spectrometer is disclosed comprising an ion optics device housing having one or more external electrical connectors (1719) provided thereon. An ion optics device (301) is arranged inside the ion optics device housing, the ion optics device (301) comprising one or more electrodes for manipulating ions, the one or more electrodes being electrically connected to the one or more external electrical connectors (1719) provided on the ion optics device housing. A voltage supply housing (1717) is provided having one or more external electrical connectors provided thereon. One or more voltage supplies are arranged inside the voltage supply housing (1717), the one or more voltage supplies being in electrical communication with the one or more external electrical connectors provided on the voltage supply housing. The one or more external electrical connectors provided on the voltage supply housing are directly physically and electrically connected to the one or more external electrical connectors (1719) provided on the ion optics device housing.

Trapping ions in an ion trapping assembly is described. In one aspect, this is implemented by introducing ions into the ion trapping assembly, applying a first RF trapping amplitude to the ion trapping assembly so as to trap introduced ions which have m/z ratios within a first range of m/z ratios, and cooling the trapped ions. In some aspects, also performed is reducing the RF trapping amplitude from the first RF trapping amplitude to a second, lower, RF trapping amplitude so as to reduce the low mass cut-off of the ion trapping assembly and trapping, at the second, lower RF trapping amplitude, introduced ions having m/z ratios within a second range of m/z ratios. A lower mass limit of the second range of m/z ratios is below the low mass cut-off of the ion trapping assembly when the first RF trapping amplitude is applied.

The present invention relates to the technical field of mass spectra. Disclosed are a novel ion storage system and method based on a quadrupole-ion trap tandem mass spectrometry. The system sequentially comprises a heating capillary, a tube lens, a skimmer, a first ion guide, a second ion guide, a quadrupole mass analyzer, an ion trap mass analyzer, and a detector; a first lens is provided between the first ion guide and the second ion guide; a second lens and a third lens are provided between the second ion guide and the quadrupole mass analyzer, wherein operation modes of the first ion guide and the second ion guide comprise an ion transmission mode and an ion storage mode. Compared with conventional time sequence control methods, more ions are stored during the same time according to the present invention, thereby improving the sensitivity of the instrument.

The invention generally relates to systems and methods for separating ions at about or above atmospheric pressure. In certain embodiments, the invention provides systems that include an ionization source that generates ions and an ion trap. The ion trap is maintained at about or above atmospheric pressure and includes a plurality of electrodes and at least one inlet configured to receive a gas flow and at least one outlet. The system is configured such that a combination of a gas flow and one or more electric fields produced by the electrodes separates the ions based on mass-to-charge ratio and sends the separated ions through the at least one outlet of the ion trap.

An ion trap apparatus is provided. The ion trap apparatus comprises two or more radio frequency (RF) rails formed with substantially parallel longitudinal axes and with substantially coplanar upper surfaces; and two or more sequences of trapping and/or transport (TT) electrodes with each sequence formed to extend substantially parallel to the substantially parallel longitudinal axes of the RF rails. The two or more RF rails and the two or more sequences of TT electrodes define an ion trap. The two or more sequences of TT electrodes are arranged into a number of zones. Each zone comprises wide matched groups of TT electrodes and at least one narrow matched group of TT electrodes. A wide TT electrode is longer and/or wider in a direction substantially parallel to the substantially parallel longitudinal axes of the RF rails than a narrow TT electrode.

A mass spectrometer comprises: a first ion optical device in a relatively low gas pressure region; a second ion optical device in a relatively high gas pressure region, the first and second ion optical devices receiving respective RF voltages from respective RF power supplies for generating respective RF fields that confine ions in respective trapping regions of the ion optical devices; and a gas conductance restriction, restricting gas flow from the relatively high gas pressure region to the relatively low gas pressure region, the gas conductance restriction having an aperture to allow ions to pass from the second to the first ion optical device. The first and second RF power supplies are independent to allow the RF voltages for generating the first RF field to have a different amplitude from the RF voltages for generating the second RF field.