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.

A method of operating a collision cell (10) in a mass spectrometer is disclosed. The collision cell comprises an entrance aperture (116), an exit aperture (117) and electrodes (113, 114) for producing electric fields. The method comprises feeding ions in a forward axial direction (LD) through the entrance aperture into the collision cell, producing a first electric field to trap ions, and subsequently producing a second electric field to accelerate trapped ions in the forward axial direction. The method further comprises producing a gas flow (G1) which is, at least at the entrance aperture (116) of the collision cell, contrary to the forward axial direction (LD), so as to reduce the kinetic energy of ions in dependence on their collisional cross sections. A collision cell arranged for carrying out the method is also disclosed, as well as a mass spectrometer comprising such a collision cell.

In one aspect, a method of processing ions in a mass spectrometer is disclosed, which comprises trapping a plurality of ions having different mass-to-charge (m/z) ratios in a collision cell, releasing said ions from the collision cell in a descending order in m/z ratio, and receiving the ions in a mass analyzer having a plurality of rods to at least one of which an RF voltage is applied, where the RF voltage is varied from a first value to a lower second value as the released ions are received by the mass analyzer.

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.

In one aspect, a method of processing ions in a mass spectrometer is disclosed, which comprises trapping a plurality of ions having different mass-to-charge (m/z) ratios in a collision cell, releasing said ions from the collision cell in a descending order in m/z ratio, and receiving the ions in a mass analyzer having a plurality of rods to at least one of which an RF voltage is applied, where the RF voltage is varied from a first value to a lower second value as the released ions are received by the mass analyzer.

At least one molecule is ionized and a mass spectrometer mass analyzes an m/z range, producing an m/z mass spectrum. A range of N sequential charge states is received. A copy of the m/z mass spectrum is created for each of the N charge states, producing N m/z spectra. Each spectrum of the N spectra is converted to a neutral mass mass spectrum using a different charge state of the N charge states, producing N neutral mass mass spectra. The N neutral mass mass spectra are aligned by neutral mass. When two or more spectra of the N neutral mass mass spectra corresponding to two or more different and sequential charge states include a neutral mass peak above a predetermined intensity threshold at a neutral mass value within a predetermined neutral mass tolerance, the neutral mass value is identified as a neutral mass of the at least one molecule.

A method of analyzing a sample, the method includes separating precursor ions from the sample into narrow mass range groups based on mass-to-charge ratio; fragmenting the ions from each group to create groups of fragment ions; and mass analyzing fragment ions from each group of fragment ions using a long transient time mass analyzer, wherein the separation and fragmentation are decoupled from the mass analyzing and the cycle time of the high transient mass analyzer is greater than about five times longer than the cycle time of a narrow mass range scan time, and wherein the separation and fragmentation has a high duty cycle and the mass analyzing has a high duty cycle.

In one aspect, a method of processing ions in a mass spectrometer is disclosed, which comprises trapping a plurality of ions having different mass-to-charge (m/z) ratios in a collision cell, releasing said ions from the collision cell in a descending order in m/z ratio, and receiving the ions in a mass analyzer having a plurality of rods to at least one of which an RF voltage is applied, where the RF voltage is varied from a first value to a lower second value as the released ions are received by the mass analyzer.

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 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.