The present disclosure is directed to an ion funnel and associated systems, where the ion funnel includes a plurality of electrodes each define an opening having an associated inner dimension and receive a RF voltage. The associated inner dimensions progressively reduce in size from approximately a first inner dimension to approximately a second inner dimension. The electrodes define a slope parameter with respect to adjacent electrodes, which is less than 0.04 for at least a majority of the electrodes. Additional systems and methods are provided for transferring ions from an ion funnel to an ion mobility device having a pressure greater than that of the ion funnel, for selectively transferring ions from the ion funnel to the ion mobility device, and for stripping ions of certain molecules adducted thereto during transfer.

An apparatus for analysing ions, including a first mass analyser configured to eject groups of ions in a predetermined sequence during different time windows; an ion transport device having a plurality of electrodes arranged around a transport channel; control means configured to control voltages applied to the electrodes to generate a transport potential in a transport channel, the transport potential having a plurality of potential wells configured to move along the transport channel such that each group of ions received by the ion transport device is respectively transported along the transport channel by one or more selected potential; fragmentation means configured to fragment precursor ions in each group of ions so as to produce product ions; and a second mass analyser configured to produce a respective mass spectrum using each group of ions after the group of ions has been fragmented and transported.

An apparatus for analysing ions, including a first mass analyser configured to eject groups of ions in a predetermined sequence during different time windows; an ion transport device having a plurality of electrodes arranged around a transport channel; control means configured to control voltages applied to the electrodes to generate a transport potential in a transport channel, the transport potential having a plurality of potential wells configured to move along the transport channel such that each group of ions received by the ion transport device is respectively transported along the transport channel by one or more selected potential; fragmentation means configured to fragment precursor ions in each group of ions so as to produce product ions; and a second mass analyser configured to produce a respective mass spectrum using each group of ions after the group of ions has been fragmented and transported.

A method of reducing fragmentation of ions generated from a sample during transport of the ions through an ion transport apparatus that comprises an ion funnel portion, comprises: applying a selected DC potential difference between an outlet end of the ion transport apparatus and an exit ion lens that is disposed adjacent to the outlet end, wherein a sign of the selected DC potential difference is chosen so as to accelerate the ions from the outlet end of the ion transport apparatus towards and through the exit ion lens.

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 charge filter instrument includes a field-free drift region, a plurality of charge detection cylinders in the drift region through which ions drifting axially therethrough pass, a plurality of charge sensitive amplifiers each coupled to at least one charge detection cylinder and configured to produce a charge detection signal corresponding to a charge of one or more of ions passing therethrough, a single inlet, single outlet charge deflector or a single inlet, multiple outlet charge steering device coupled to the outlet end of the drift region, means for determining charge magnitudes or charge states of ions drifting axially through the drift region based on the charge detection signals, and means for controlling the charge deflector or the charge steering device to pass through the single outlet or through a specified one of the multiple outlets only ions having a specified charge magnitude or charge state.

In one aspect, a method of calibrating a Fourier Transform (FT) multipole mass spectrometer is disclosed, which comprises measuring a plurality of secular frequencies of a calibrant ion in a multipole FT mass analyzer for a plurality of RF voltages (V.sub.RF) applied to at least one rod of the multipole mass analyzer adjusted q analyzer, calculating Mathieu β and q parameters for each of 5 the measured secular frequencies, and determining RF voltage amplitude (V.sub.RF) for each calculated q parameter. For each calculated q parameter, an offset RF voltage amplitude (ΔV.sub.RF) corresponding to a deviation of the applied V.sub.RF and the calculated V.sub.RF is determined so as to generate a ΔV.sub.RFv.s. q calibration curve.

The present invention is concerned with a device for charged particle transportation and manipulation. Embodiments provide a capability of combining positively and negatively charged particles in a single transported packet. Embodiments contain an aggregate of electrodes arranged to form a channel for transportation of charged particles, as well as a source of power supply that provides supply voltage to be applied to the electrodes, the voltage to ensure creation, inside the said channel, of a non-uniform high-frequency electric field, the pseudopotential of which field has one or more local extrema along the length of the channel used for charged particle transportation, at least, within a certain interval of time, whereas, at least one of the said extrema of the pseudopotential is transposed with time, at least within a certain interval of time, at least within a part of the length of the channel used for charged particle transportation.

The present invention is concerned with a device for charged particle transportation and manipulation. Embodiments provide a capability of combining positively and negatively charged particles in a single transported packet. Embodiments contain an aggregate of electrodes arranged to form a channel for transportation of charged particles, as well as a source of power supply that provides supply voltage to be applied to the electrodes, the voltage to ensure creation, inside the said channel, of a non-uniform high-frequency electric field, the pseudopotential of which field has one or more local extrema along the length of the channel used for charged particle transportation, at least, within a certain interval of time, whereas, at least one of the said extrema of the pseudopotential is transposed with time, at least within a certain interval of time, at least within a part of the length of the channel used for charged particle transportation.

A hybrid mass spectrometer comprising: an ion source for generating ions from a sample, a first mass spectral system comprising a nanoelectromechanical mass spectral (NEMS-MS) system, a second mass spectral system including at least one mass analyzer adapted to separate the charged particles according to their mass-to-charge ratios, and an integration zone coupling the first and second mass spectral systems, the integration zone including at least one directional device for controllably routing the ions to a selected one or both of the first and second mass spectral systems for analysis thereby. The second system can be an orbital electrostatic trap system. The ion beam can be electrically directed to one or the other system by ion optics. A chip with resonators can be used with cooling. Uses include analysis of large mass complexes found in biological systems, native single molecule analysis, and size and shape analysis.