Abstract: 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.

Abstract: A method for determining a compensation factor parameter, c, for controlling an amount of ions ionised that are injected from an ion storage unit into mass analyser, where c is an adjustment factor that is applied to optimized injection times that are based on an optimized visible charge of a reference sample, the method comprising: detecting at least one mass spectrum for at least one amount of injected ions; determining from the at least one detected mass spectrum, a slope, s(sample), of a linear correlation of a relative m/z shift with visible total charge Qv of detected mass spectra; determining the compensation factor c as c=s(reference)/s(sample) where s(reference) is the slope of a linear correlation between reference-sample relative m/z shift values and reference-sample visible charge values determined from a plurality of mass spectra detected from a plurality of respective pre-selected amounts of a clean reference sample.

Abstract: A mass spectrometer includes a controller operable to: transfer first ions of a first charge into an ion trap; apply an RF pseudopotential that radially confines the first ions in an elongate ion channel of the trap; generate a first potential well that confines the first ions within a first volume; after a specified pre-cooling time, transfer second ions of a second, opposite charge into the trap; apply one or more additional DC potentials that generate a second potential well that confines the second ions within a second volume, the first potential well being within the second potential well; cause, after cooling the second ions, the first ions and the second ions to interact and generate product ions; and generate at least one third potential well that confines the product ions, that is adjacent to the second potential well and that has a same polarity as the first potential well.

Abstract: 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.

Abstract: A vacuum pump system for evacuating at least five volumes comprising a turbomolecular pump and a forevacuum pump arranged to pump an output of the turbomolecular pump arrangement to atmosphere. The turbomolecular pump has at least five pumping stages separated by rotor blades. Not more than three pumping stages have pumping speeds in excess of ? of the highest pumping speed when under vacuum and/or a pumping port cross section in excess of ? of the highest pumping port cross section, and at least two pumping stages have pumping speeds less than ¼ of the highest pumping speed when under vacuum and/or a pumping port cross section of less than ¼ of the biggest pumping port cross section. The ratio of pressures between the pumping stage with the highest pressure and the pumping stage with the lowest pressure is at least 100000:1 when under vacuum.

Abstract: An interface for receiving ions in a carrier gas from an atmospheric pressure ion source at a spectrometer that is configured to analyse the received ions at a lower pressure includes an interface vacuum chamber having a downstream aperture; a support assembly defining an axial bore arranged to allow a removable capillary tube to extend therethrough; ions being received from the atmospheric pressure ion source through the capillary tube and directed towards the downstream aperture; and a jet disruptor, positioned downstream from the axial bore and configured to disrupt gas flow between the axial bore and the downstream aperture only when the capillary tube is not fully inserted through the axial bore.

Abstract: A mass spectrometry method comprises: providing a multiplexed sample comprising a mixture of biomolecule-containing samples respectively tagged with mass tags; acquiring MS2 spectra by data-dependent acquisition (DDA) of the multiplexed sample or another mass tagged mixture of the samples during chromatographic elution; acquiring MS2 spectra by data-independent acquisition (DIA) during the elution; forming a spectral library from the DDA MS2 spectra comprising a plurality of the MS2 spectra and the biomolecule retention times; matching fragment-ion peaks in the DIA MS2 spectra to fragment-ion peaks in the MS2 library spectra to find matched biomolecules; determining a total abundance for each matched biomolecule from the DIA MS2 spectra at each of a plurality of retention times; determining abundances of respective reporter ions from the DIA MS2 spectra at the plurality of retention times; and deconvoluting relative abundances of the biomolecules in each respectively tagged biomolecule-containing sample based

Abstract: 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.

Abstract: An ion optical arrangement (1) for use in a mass spectrometer comprises electrodes (11) defining an ion optical path, a housing (18) for accommodating the electrodes, a voltage source for providing voltages to the electrodes to produce electric fields, and a valve for allowing gas to enter and/or leave the housing. The valve comprises an electrostatic mechanism and/or a pneumatic mechanism. The electrostatic mechanism may comprise a flexible foil (30, 31) configured for covering at least one opening (16) in the ion optical arrangement when a first voltage is applied and being spaced apart from the at least one opening when a second voltage is applied. The pneumatic mechanism may comprise a Bourdon tube.

Abstract: A time-of-flight (ToF) mass spectrometer, comprising: a pulsed ion injector for forming an ion beam that travels along an ion path; a detector for detecting ions in the ion beam that arrive at the detector at times according to their m/z values; an ion focusing arrangement located between the ion injector and the detector for focusing the ion beam in at least one direction orthogonal to the ion path; and a variable voltage supply for supplying the ion focusing arrangement with at least one variable voltage that is dependent on a charge state and/or an amount of ions of at least one species of ions in the ion beam. A corresponding method of mass spectrometry is provided. The charge state and/or an amount of ions may be acquired from a pre-scan, or predicted. Tuning of the spectrometer based on a charge state and/or an amount of ions of at least one species of ions in the ion beam may be performed on the fly.

Abstract: The present invention provides an electrode arrangement 10, 10? for an ion trap, ion filter, an ion guide, a reaction cell or an ion analyser. The electrode arrangement 10, 10? comprises an RF electrode 12a, 12b, 12a?, 12b? mechanically coupled to a dielectric material 11. The RF electrode 12a, 12b, 12a?, 12b? is mechanically coupled to the dielectric material 11 by a plurality of separators 13 that are spaced apart and configured to define a gap between the RF electrode 12a, 12b, 12a?, 12b? and the dielectric material 11. Each of the plurality of separators 13 comprises a projecting portion 13b and the dielectric material 11 comprises corresponding receiving portions 11a such that on coupling of the RF electrode 12a, 12b, 12a?, 12b? to the dielectric material 11, the projecting portion 13b of each separator 13 is received within the corresponding receiving portion 11a of the dielectric material 11.

Abstract: An ion optical arrangement (1) for use in a mass spectrometer comprises electrodes (11, 12, 14) comprising a multipole arrangement defining an ion optical axis, and a voltage source for providing voltages to the electrodes to produce electric fields. The ion optical arrangement is configured for producing a radio frequency electric focusing field for focusing ions on the ion optical axis. The radio frequency electric focusing field has a varying frequency so as to reduce any mass dependence of ion trajectories through the ion optical arrangement. The ion optical arrangement may further be configured for producing a static electric field in response to a DC bias voltage applied to the multipole arrangement. A superimposed varying electric field may be produced by superimposing an AC voltage upon the DC bias voltage.

Abstract: An ion guide may comprise a set of plate electrodes, each plate electrode having a plurality of apertures formed therethrough. The set of plate electrodes are spatially arranged such that a relative positioning of each plurality of apertures of a respective plate electrode of the set of plate electrodes and respective adjacent plate electrodes of the set of plate electrodes defines a continuous ion flight path through the respective plurality of apertures of each plate electrode of the set of plate electrodes. The continuous ion flight path has a helical-based and/or spiral-based shape.

Abstract: A component of an ion optical device is manufactured. The component comprises aligned first and second electrode sets. A first material is machined to provide a part-machined first electrode set that comprises the first electrode set attached to a frame part of the first material. A second material is machined to provide a part-machined second electrode set that comprises the second electrode set attached to a frame part of the second material. The component of the ion optical device is assembled by aligning the part-machined first and second electrode sets. Subsequent to aligning the part-machined first and second electrode sets, the part-machined first electrode set is further machined to separate the first electrode set from the frame part of the first material and the part-machined second electrode set is further machined to separate the second electrode set from the frame part of the second material.

Abstract: A plasma source chamber (10) for use in a spectrometer comprises an inner housing (11) for accommodating a plasma source (31) and an outer housing (12) accommodating the inner housing. The outer housing (12) comprises at least one outer air inlet opening (21) in a first wall and at least one outer air outlet opening (22) in a second wall. Walls of the inner housing and walls of the outer housing define a spacing (25) so as to allow a first air flow (1) from the at least one outer air inlet opening (21) to the at least one outer air outlet opening (22) through the spacing (25) between the inner housing and the outer housing. The inner housing (11) comprises at least one inner air inlet opening (23) in a first wall and at least one inner air outlet opening (24) in a second wall to allow a second air flow (2) from the at least one inner air inlet opening to the at least one inner air outlet opening through the inner housing.

Abstract: There is provided a method of identifying spurious peaks in a mass spectrum produced from a time-varying transient signal detected in a mass spectrometer. The method comprises the steps of generating, using a regularized inversion algorithm having one or more adjustable parameters, a first mass spectrum from the time-varying transient signal, according to a first set of values of said one or more adjustable parameters. Generating, using the regularized inversion algorithm, one or more perturbed mass spectra from the transient signal, according to one or more respective perturbed versions of the first set of values. Identifying one or more spurious peaks in the first mass spectrum by comparing the first mass spectrum with at least one of the perturbed mass spectra. There are also provided corresponding systems and computer readable media.

Abstract: There is disclosed a method for eliminating an added crosstalk signal from a measured data signal, which is generated by an image current. There is further disclosed a signal processing unit for carrying out the method. There is still further disclosed a mass spectrometer and a mass analyser comprising the signal processing unit for carrying out the method. There is yet still further disclosed a Fourier transform mass spectrometer configured to eliminate the added crosstalk signal from a measured data signal.

Abstract: A diagnostic testing method for a detector of a spectrometer. The spectrometer comprises a source of line spectra configured to emit at least one branched pair of spectral lines from an excited species. The method comprises performing a plurality of detector diagnostic measurements and diagnosing a detector operating condition. Each detector diagnostic measurement comprises measuring an intensity of a first spectral line emitted by an excited species of the source of line spectra using the detector, and measuring an intensity of a second spectral line emitted by the excited species of the source of line spectra using the detector. The first and second spectral lines emitted by the excited species of the source of line spectra form a branched pair of spectral lines, and the spectrometer is controlled to vary the intensity of the first and second spectral lines incident on the detector for the plurality of detector diagnostic measurements.

Abstract: A method of mass spectrometry for analyzing a sample within a mass range of interest includes the steps: ionizing the sample to produce a plurality of precursor ions; performing an MS1 scan of the precursor ions comprising mass analyzing the precursor ions across the mass range of interest, to obtain an MS1 mass spectrum of the precursor ions; determining ion intensity values within the MS1 mass spectrum; selecting precursor mass segments within the mass range of interest, and for each precursor mass segment: fragmenting the precursor ions within that precursor mass segment; and performing an MS2 scan of the fragmented ions by: controlling an amount of fragmented ions for that precursor mass segment, based on an intensity value for that precursor mass segment derived from the MS1 spectrum; and mass analyzing the amount of fragmented ions.

Abstract: A mass spectrometry method comprising steps of generating an ion beam from an ion source; directing the ion beam into a collision cell; introducing into the collision cell through a gas inlet on the collision cell a charge-neutral analyte gas or reaction gas; ionizing the analyte gas or reaction gas in the collision cell by means of collisions between the analyte gas or reaction gas and the ion beam; transmitting ions from the ionized analyte gas or reaction gas from the collision cell into a mass analyzer; and mass analyzing the transmitted ions of the ionized analyte or reaction gas. The methods can be applied in isotope ratio mass spectrometry to determine the isotope abundance or isotope ratio of a reaction gas used in mass shift reactions between the gas and sample ions, to determine a corrected isotope abundance or ratio of the sample ions.