Abstract: Collision induced dissociation of precursor ions in an ion trap is performed by determining a predicted fragmentation-optimized excitation voltage amplitude based on an indicator of damping gas pressure, such as a damping gas flow rate, and optionally other parameters including precursor ion m/z and an indicator of the Mathieu parameter q. The excitation voltage may then be applied to electrodes of the ion trap in steps of increasing amplitude, wherein at least one of the amplitudes corresponds to the predicted optimum value. Application of the excitation voltage in this manner produces favorable fragmentation efficiencies over a range of operating parameters and for ions of differing chemical properties.

Abstract: The invention provides a two-dimensional ion trap, comprising a plurality of elongate electrodes positioned between first and second end electrodes, the plurality of electrodes and first and second end electrodes defining a trapping volume. A controller in electrical communication with the plurality of elongate electrodes and the first and second end electrodes is configured to progressively vary a periodic voltage applied to at least one of the plurality of elongate electrodes to cause ions to be radially ejected from the ion trap in order of their mass to charge ratios. Concurrently, the controller is configured to progressively vary a DC offset of least one of the first and second end electrodes with respect to the plurality of elongate electrodes.

Abstract: A method for determining a time of elution of a peptide of interest from a liquid chromatography column includes a step of obtaining chromatographic data for each of a plurality of candidate fragment ions of the peptide of interest. A time along a common chromatographic time is scale determined corresponding to maximum overlay of the ion signals measured for each of the plurality of candidate fragment ions. Finally, the determined time is assigned as the time of elution of the peptide of interest from the liquid chromatography column. In particular, the chromatographic data is acquired during selective reaction monitoring of an eluate from the liquid chromatography column containing the peptide of interest. The chromatographic data includes ion signals measured along the common chromatographic time scale for each of the plurality of candidate fragment ions.

Abstract: This invention relates to a method of trapping ions and to an ion trapping assembly. In particular, the present invention has application in gas-assisted trapping of ions in an ion trap prior to a mass analysis of the ions in a mass spectrometer. The invention provides a method of trapping ions in a target ion trap of an ion trapping assembly that comprises a series of volumes arranged such that ions can traverse from one volume to the next, the volumes including the target ion trap, whereby ions are allowed to pass repeatedly through the volumes such that they also pass into and out from the target ion trap without being trapped. Potentials may be used to reflect the ions from respective ends of the ion trapping assembly. Optionally, a potential well and/or gas-assisted cooling may be used to cause the ions to settle in the target ion trap.

Abstract: A method of operating a gas-filled collision cell in a mass spectrometer is provided. The collision cell has a longitudinal axis. Ions are caused to enter the collision cell. A trapping field is generated within the collision cell so as to trap the ions within a trapping volume of the collision cell, the trapping volume being defined by the trapping field and extending along the longitudinal axis. Trapped ions are processed in the collision cell and a DC potential gradient is provided, using an electrode arrangement, resulting in a non-zero electric field at all points along the axial length of the trapping volume so as to cause processed ions to exit the collision cell. The electric field along the axial length of the trapping volume has a standard deviation that is no greater than its mean value.

Abstract: This invention relates to a mass spectrometer including a reaction cell and to a method of using such a mass spectrometer. In particular, although not exclusively, this invention relates to a tandem mass spectrometer and to tandem mass spectrometry. The invention provides a method of mass spectrometry using a mass spectrometer having a longitudinal axis, comprising guiding ions to travel along the longitudinal axis of the mass spectrometer in a forwards direction to pass through an intermediate ion store and then to enter a reaction cell, to process the ions within the reaction cell, to eject the processed ions to travel back along the longitudinal axis to enter the intermediate ion store once more, and to eject one or more pulses of the processed ions in an off-axis direction to a mass analyser.

Abstract: A method for calibrating an ion trap mass spectrometer is disclosed. The method includes establishing an optimal phase and amplitude-m/z relationship by acquiring peak quality data at varying values of amplitude and phase. The resonant ejection voltage applied to the electrodes of the ion trap may then be controlled during analytical scans in accordance with the established relationship between m/z and resonant ejection voltage amplitude.

Abstract: An electrostatic trap such as an orbitrap is disclosed, with an electrode structure. An electrostatic trapping field of the form U?(r, ?, z) is generated to trap ions within the trap so that they undergo isochronous oscillations. The trapping field U?(r, ?, z) is the result of a perturbation W to an ideal field U(r, ?, z) which, for example, is hyperlogarithmic in the case of an orbitrap. The perturbation W may be introduced in various ways, such as by distorting the geometry of the trap so that it no longer follows an equipotential of the ideal field U(r, ?, z), or by adding a distortion field (either electric or magnetic). The magnitude of the perturbation is such that at least some of the trapped ions have an absolute phase spread of more than zero but less than 2 ? radians over an ion detection period Tm.

Abstract: A dual ion trap mass analyzer includes adjacently positioned first and second two-dimensional ion traps respectively maintained at relatively high and low pressures. Functions favoring high pressure (cooling and fragmentation) may be performed in the first trap, and functions favoring low pressure (isolation and analytical scanning) may be performed in the second trap. Ions may be transferred between the first and second trap through a plate lens having a small aperture that presents a pumping restriction and allows different pressures to be maintained in the two traps. The differential-pressure environment of the dual ion trap mass analyzer facilitates the use of high-resolution analytical scan modes without sacrificing ion capture and fragmentation efficiencies.

Abstract: A technique is disclosed for conducting collision induced dissociation (CID) in a quadrupole ion trap (QIT) having higher order field components. In order to compensate for the shift in the frequency of motion with amplitude of the excited ions arising from the influence of higher-order field components, the amplitude of the RF voltages applied to the QIT is monotonically varied during the excitation period to prolong the condition of resonance, resulting in higher average kinetic energies of the excited ions. Thus, higher fragmentation efficiencies may be obtained, or a targeted level of fragmentation may be achieved in less time relative to conventional CID.

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: The invention provides a magnetic lens for generating a magnetic imaging field to focus charged particles emitted from a sample, the lens comprising a central pole piece and an outer pole piece disposed about the central pole piece, wherein the lens comprises a magnetic moveable element for movement relative to at least one of the pole pieces, whereby a focal length of the lens is variable by said movement of the magnetic moveable element, thereby enabling a zoom facility for changing the magnification of an image. The movement of the moveable element preferably changes the magnetic circuit between the pole pieces. Also provided is a method of focusing charged particles emitted from a sample and a charged particle energy analyzer, such as an imaging photoelectron spectroscopy system.

Abstract: This invention relates to mass spectrometers comprising a reaction cell and where mass spectra are collected both from unreacted ions and also from reaction product ions. In particular, although not exclusively, this invention finds use in tandem mass spectrometry where mass spectra are collected from precursor and fragment ions. The present invention provides an arrangement where ions may be sent to a reaction cell for fragmentation or other processing before onward transport to a mass analyser. Alternatively, ions may be passed directly to a mass analyser along a bypass path.

Abstract: A method of transporting gas and entrained ions between higher and lower pressure regions of a mass spectrometer comprises providing an ion transfer conduit 60 between the higher and lower pressure regions. The ion transfer conduit 60 includes an electrode assembly 300 which defines an ion transfer channel. The electrode assembly 300 has a first set of ring electrodes 305 of a first width D1, and a second set of ring electrodes of a second width D2 (?D1) and interleaved with the first ring electrodes 305. A DC voltage of magnitude V1 and a first polarity is supplied to the first ring electrodes 205 and a DC voltage of magnitude V2 which may be less than or equal to the magnitude of V1 but with an opposed polarity is applied to the second ring electrodes 310. The pressure of the ion transfer conduit 60 is controlled so as to maintain viscous flow of gas and ions within the ion transfer channel.

Abstract: An ion transfer arrangement for transporting ions between higher and lower pressure regions of the mass spectrometer comprises an ion transfer conduit 60. The conduit 60 has an inlet opening towards a relatively high pressure chamber 40 and an outlet 70 opening towards a relatively low pressure chamber. The conduit 60 also has at least one side wall surrounding an ion transfer channel 115. The side wall includes a plurality of apertures 140 formed in the longitudinal direction of the side wall so as to permit a flow of gas from within the ion transfer channel 115 to a lower pressure region outside of the side wall of the conduit 60.

Abstract: A method for determining a low cylinder pressure condition of a gas chromatograph includes providing gas from the cylinder to an inlet of the gas chromatograph. In particular, the gas is provided at a predetermined inlet pressure that is higher than an inlet pressure that is required for a predetermined gas chromatographic analysis routine. The inlet pressure of the gas being supplied to the inlet is increased, in order to attempt to achieve a predetermined check value. It is then determined if the inlet pressure actually increases to at least the predetermined check value. If it is determined that the inlet pressure of the gas does not increase to at least the predetermined check value, then an indication of a low cylinder pressure condition is provided.

Abstract: A front-end reagent ion source for a mass spectrometer is disclosed. Reagent vapor is supplied to a reagent ionization volume located within a chamber of the mass spectrometer and maintained at a low vacuum pressure. Reagent ions are formed by interaction of the reagent vapor molecules with an electrical discharge (e.g., a glow discharge) within the ionization volume, and pass into the chamber of the mass spectrometer. At least one ion optical element located along the analyte ion path transports the reagent ions to successive chambers of the mass spectrometer. The reagent ions may be combined with the analyte ions to perform ion-ion studies such as electron transfer dissociation (ETD).

Abstract: A mass spectrometer and method of mass spectrometry wherein charged particles in a beam undergo multiple changes of direction. A detection arrangement detects a first portion of the charged particle beam, and provides a first output based upon the intensity of the detected first portion of the charged particle beam. The detection arrangement detects a second portion of the charged particle beam that has travelled a greater path length through the mass spectrometer than the first portion of the charged particle beam, and provides a second output based upon the detected second portion of the charged particle beam. A controller adjusts the parameters of the charged particle beam and/or the detection arrangement, based upon the first output of the detection arrangement, so as to adjust the second output of the detection arrangement.

Abstract: The present invention provides a radio frequency (RF) power supply in a mass spectrometer. The power supply provides an RF signal to electrodes of a storage device to create a trapping field. The RF field is usually collapsed prior to ion ejection. In an illustrative embodiment the RF power supply includes a RF signal supply; a coil arranged to receive the signal provided by the RF signal supply and to provide an output RF signal for supply to electrodes of an ion storage device; and a shunt including a switch operative to switch between a first open position and a second closed position in which the shunt shorts the coil output.

Abstract: An ion trap comprises substantially elongate electrodes 10, 20 some of which are curved along their axis of elongation and which define a trapping volume between them. The sectional area of this trapping volume towards the extremities of the trap in the direction of elongation is different to the sectional area away from its extremities (eg towards the middle of the trap). In a preferred embodiment, the trap has a plurality of elongate electrodes, wherein opposed electrodes have different radii of curvature so that the trap splays towards its extremities. Thereby, a wider mass range of ions can be trapped and ejected, a higher space charge capacity (for a given trap length) is provided, and sharper ion beam focussing on ejection is possible.