The ion trap comprises a multipole electrode assembly, a first confining electrode, and a second confining electrode. The multipole electrode assembly is configured to confine ions of the first polarity to an ion channel extending in an axial direction of the multipole electrode assembly. The first confining electrode is provided adjacent to the multipole electrode assembly and extends in the axial direction of the multipole electrode assembly. The second confining electrode is provided adjacent to the multipole electrode assembly and extends in the axial direction of the multipole electrode assembly aligned with the first confining electrode. The first and second confining electrodes are spaced apart in the axial direction in order to define an ion confining region of the ion channel between the first and second confining electrodes. The first and second confining electrodes are configured to receive a DC potential of the first polarity to further confine ions within the ion channel in the ion confining region.

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.

Ions are injected into an orbital electrostatic trap. An ejection potential is applied to an ion storage device, to cause ions stored in the ion storage device to be ejected towards the orbital electrostatic trap. Synchronous injection potentials are applied to a central electrode of the orbital electrostatic trap and a deflector electrode associated with the orbital electrostatic trap, to cause the ions ejected from the ion storage device to be captured by the electrostatic trap such that they orbit the central electrode. Application of the ejection potential and application of the synchronous injection potentials are each started at respective different times, the difference in times being selected based on desired values of mass-to-charge ratios of ions to be captured by the orbital electrostatic trap.

A mass spectrometer ion reaction device, useful for performing ion-ion reactions (eg. ETD, PTR) is described. The device includes a plurality of non-linear rods, that form a pair of quadrupole rod sets. The device includes an axial passageway, that allows injections of ions of both polarities into the device, and a three dimensional trapping region. Anions and cations that are injected into the device are spatially separated into different trapping regions by a DC dipole electric field generated by a DC voltage source. The device also includes a plurality of lenses to confine, transmit or receive ions in/from the device.

A device and associated method are disclosed for interfacing an ion trap to a pulsed mass analyzer (such as a time-of-flight analyzer) in a mass spectrometer. The device includes a plurality of separate confinement cells and structures for directing ions into a selected one of the confinement cells. Ions are ejected from the ion trap in a series of temporally successive ion packets. Each ion packet (which may consist of ions of like mass-to-charge ratio), is received by the ion interface device, fragmented to form product ions, and then stored and cooled in the selected confinement cell. Storage and cooling of the ion packet occurs concurrently with the receipt and storage of at least one later-ejected ion packet. After a predetermined cooling period, the ion packet is released to the mass analyzer for acquisition of a mass spectrum.

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 method of injecting ions into an electrostatic trap, comprising: generating ions in an ion source; transporting the ions from the ion source to an ion store downstream of the ion source; releasing the ions from the ion store to an ion guide downstream of the ion store; and accelerating the ions from the ion guide as a pulse into an orbital electrostatic trap for mass analysis, wherein the average velocity of the ions as the ions exit from the ion guide is substantially higher than the average velocity of the ions as they exit from the ion store, wherein there is a delay between releasing the ions from the ion store and accelerating the ions from the ion guide. Also an apparatus suitable for the method.

A mass spectrometry method comprises: introducing a first packet of ions into an electrostatic trap mass analyzer through a set of electrostatic lenses, wherein, during the introducing of the first packet, 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; introducing a second packet of ions into the mass analyzer through the set of lenses, wherein, during the introducing of the second packet, 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.

Ions provided from an ion source are separated ions into a plurality of different ion groups according to at least one ion property. At least some of the different ion groups are stored in an ion storage array, which comprises a plurality of independently operable storage cells, each storage cell being arranged to receive and store a different ion group. A controller is programmed to cause selective switching of each of the storage cells between an ion receiving mode and an ion storage mode, and between the ion storage mode and an ion release mode. In particular, the switching of each storage cell is controllable independently of the switching of any of the other storage cells. Upon release from a respective storage cell of the array, ions are provided to one or more mass analyzers for subsequent analysis.

A tuning system may acquire, from a mass spectrometer during a batch of one or more analytical runs performed with the mass spectrometer, tune data associated with an operating characteristic of the mass spectrometer. The tuning system may determine, based on the tune data, a value of an operating parameter configured to adjust the operating characteristic of the mass spectrometer and set the operating parameter to the determined value.