GB2541004A

GB2541004A - Second ion source for lockmass calibration of matrix assisted laser desorption ionisation mass spectrometer

Info

Publication number: GB2541004A
Application number: GB1513846.4A
Authority: GB
Inventors: Robert Murray Paul; Mark Brown Jeffery
Original assignee: Micromass UK Ltd
Current assignee: Micromass UK Ltd
Priority date: 2015-08-05
Filing date: 2015-08-05
Publication date: 2017-02-08
Anticipated expiration: 2035-08-05
Also published as: GB2541004B; GB201513846D0

Abstract

A mass spectrometer or ion imaging apparatus comprising: a first ion source for acquiring an ion image of a target, whereby separate mass spectral data corresponding to different regions and/or different depths of the target are acquired; and a second ion source for generating calibrant, lockmass or reference ions. Also disclosed are methods of mass spectrometry and ion imaging using the above apparatuses. The second ion source is for generating calibrant, lockmass or reference ions. The second ion source may be arranged downstream of the first ion source, such that both the analyte and calibrant ions are detected simultaneously.

Description

SECOND ION SOURCE FOR LOCKMASS CALIBRATION OF MATRIX ASSISTED LASER DESORPTION IONISATION MASS SPECTROMETER

CROSS-REFERENCE TO RELATED APPLICATION

None.

FIELD OF THE INVENTION

The present invention relates generally to mass spectrometers and in particular to methods of calibrating mass spectrometers.

BACKGROUND

Mass spectrometers configured for Matrix Assisted Laser Desorption Ionisation ("MALDI") are known. MALDI is a soft ionisation technique for mass spectrometry in which analyte molecules are prepared on the surface of a target plate. The analyte molecules are supported in a solid polycrystalline matrix. A pulse of laser radiation, with a typical duration of a few nanoseconds, is directed onto the MALDI sample. The laser radiation is strongly absorbed by the matrix molecules.

The pulse of laser energy results in rapid heating of the region that is irradiated.

This heat causes a proportion of the matrix material to be vaporised and explosively ejected from the surface as a plume of gaseous material (desorption). Analyte ions embedded within the matrix that is desorbed are transferred to the gaseous phase along with the matrix.

Reactions between the matrix ions and the analyte molecules can result in the analyte molecules being ionised either through protonation/deprotonation or through the removal or addition of an ion. Upon dispersal of the initial MALDI plume, the remaining analyte ions are predominantly singly charged.

Although the absorption of the laser radiation occurs at all levels of laser fluence, there is a threshold energy density required in order to obtain desorption of material under illumination. MALDI imaging is a growing technique where the sample to be analysed may be a thin (typically 15 pm) section of tissue, with a layer of matrix deposited upon the surface of the sample. The sample is scanned in a raster manner, with the laser firing at specific locations or ranges of locations spaced along the raster pattern. Mass spectra are acquired at each location or range of locations and the relative abundance of ion masses are then displayed as an ion image of the tissue section.

Large matrix arrays can be generated to cover entire tissue sections (i.e. ion imaging) or smaller arrays can be used to study different areas within the tissue (e.g. depth profiling).

The aim of depth profiling is to obtain information on the variation of composition with depth below the initial surface of the sample. The information which is obtained is particularly useful for the analysis of layered structures such as those produced in the semiconductor industry.

Laser Desorption Ionisation relies upon the removal of ions from the surface of a sample and hence is, by its nature, a destructive technique. Laser Desorption Ionisation may be used for depth profiling applications. A depth profile of a sample may be obtained by recording sequentially spectra as the surface is gradually eroded away by the incident laser beam probe. A plot of the intensity of a given mass or mass to charge ratio signal as a function of time may be produced which is a direct reflection of the variation of its abundance or concentration with depth below the surface. MALDI tissue profiling and ion imaging techniques have become valuable tools for rapid, direct analysis of tissues to investigate spatial distributions of proteins.

However, the production of mass spectra relating to each of the different areas within a tissue sample requires discrete analyses which is time consuming and reduces instrument yield.

Matrix Assisted Laser Desorption Ionisation (“MALDI”) acquisitions are well known and it is known, for example, to pre-spot a reference or calibrant sample on a Matrix Assisted Laser Desorption Ionisation target plate which is mounted upon a moveable translation stage. During an imaging acquisition it is known to stop the imaging acquisition part way through and to move or translate the translation stage so that the pre-spotted reference or calibrant sample is then ionised by a laser. Ionisation of the reference or calibrant sample results in the generation of reference or calibrant ions which may then be used to calibrate the mass spectrometer or to check the calibration of the mass spectrometer. After the mass spectrometer has been calibrated (or recalibrated) the translation stage is then moved or translated so as to position the target plate back at the last location prior to the instrument being calibrated. The imaging acquisition of the analyte sample is then recommenced or resumed.

The conventional approach to calibrating a Matrix Assisted Laser Desorption Ionisation mass spectrometer suffers from the problem that it adds time to the experiment or acquisition as the translation stage needs to keep being moved backwards and forwards between acquiring the mass spectral data from the analyte sample and acquiring mass spectral data from the reference or calibrant sample.

Another problem with the known approach is that it increases the possibility that the translation stage may not return to exactly the same location as the last imaging acquisition and hence there may be a loss of fidelity in the resulting ion image.

It is therefore desired to provide an improved method of calibrating a Matrix Assisted Laser Desorption Ionisation mass spectrometer.

SUMMARY

According to an aspect there is provided a mass spectrometer comprising: a first ion source for acquiring, in use, an ion image of a target wherein separate mass spectral data corresponding to different regions and/or different depths of the target are acquired in use; and a second ion source for generating calibrant, lockmass or reference ions.

Various embodiments relate to the inclusion of a second ion source to produce lockmass calibrant ions parallel to or seeking to avoid Matrix Assisted Laser Desorption Ionisation (“MALDI”) ion optics.

According to various embodiments a Matrix Assisted Laser Desorption Ionisation acquisition may be paused and the acquisition may then switch to the second ion source (e.g. a glow discharge ion source) in order to allow calibrant ions to be acquired.

The various embodiments remove the requirement of needing to move a sample stage to the location of a pre-spotted reference sample and then having to return the sample stage to the last location and recommencing the imaging acquisition. The conventional approach introduces delay and re-registration problems.

The first ion source may comprise a Matrix Assisted Laser Desorption Ionisation (“MALDI”) ion source, a Desorption Electrospray Ionisation (“DESI”) ion source, a Laser Ablation Electrospray Ionisation (“LAESI”) ion source, an Atmospheric Solids Analysis Probe (“ASAP”) ion source, a Laser Desorption Ionization (“LDI”) ion source or a Dielectric Barrier Discharge ion source.

The second ion source may comprise a Glow Discharge (“GD”) ion source or a vacuum ionisation ion source.

The second ion source may be arranged with a vacuum chamber.

The mass spectrometer may further comprise a first differential pumping aperture and a vacuum chamber, wherein the first ion source generates analyte ions which pass in use through the first differential pumping aperture into the vacuum chamber.

The second ion source may be arranged downstream of the first differential pumping aperture so that the calibrant, lockmass or reference ions do not pass through the first differential pumping aperture.

The mass spectrometer may further comprise a device arranged to move the target relative to the first ion source so as to enable mass spectral data from different spatially separated regions of the target to be acquired.

The device may comprise a translation stage for translating or moving the target.

The first ion source may comprise a laser for ionising the target and generating analyte ions.

The mass spectrometer may further comprise a device for moving a laser beam emitted, in use, from the laser relative to the target so as to enable mass spectral data from different spatially separated regions of the target to be acquired.

The mass spectrometer may further comprise a first ion guiding device which may be arranged and adapted: (i) to receive and onwardly transmit analyte ions generated from the target by the first ion source; and/or (ii) to receive and onwardly transmit the calibrant, lockmass or reference ions.

The first ion guiding device may comprise an ion guide selected from the group consisting of: (i) a conjoined ion guide; (ii) a conjoined ion guide comprising a plurality of plate or ring electrodes; (iii) a conjoined ion guide comprising a plurality of rod electrodes; (iv) a plurality of plate or ring electrodes; (v) a plurality of rod electrodes; or (vi) a quadrupole rod set, a hexapole rod set, an octopole rod set or a multipole rod set.

The first ion guiding device may be arranged and adapted so that the analyte ions and the calibrant, lockmass or reference ions are transmitted through either: (i) substantially different ion paths through the first ion guiding device; or (ii) substantially similar ion paths through the first ion guiding device.

The first ion guiding device may comprise a first ion guide comprising a first plurality of electrodes, each electrode comprising at least one aperture through which ions are transmitted in use wherein a first ion guiding path may be formed along or within the first ion guide.

The first ion guiding device may comprise a first ion guide comprising a first plurality of electrodes, each electrode comprising a rod electrode wherein a first ion guiding path may be formed within an inscribed radius of the rod electrodes.

The analyte ions may be arranged to be transmitted along the first ion guiding path.

The first ion guiding device may further comprise a second ion guide comprising a second plurality of electrodes, each electrode comprising at least one aperture through which ions are transmitted in use wherein a second different ion guiding path may be formed along or within the second ion guide.

The first ion guiding device may comprise a second ion guide comprising a second plurality of electrodes, each electrode comprising a rod electrode wherein a second ion guiding path may be formed within an inscribed radius of the rod electrodes.

The second ion source may be arranged adjacent the first ion guide or adjacent the second ion guide.

The calibrant, lockmass or reference ions may be arranged to be transmitted along the second ion guiding path.

One or more pseudo-potential barriers may be formed, in use, at one or more points along the length of the first ion guiding device between the first ion guiding path and the second ion guiding path.

The first ion guiding device may comprise a second device arranged and adapted to transfer analyte ions from the first ion guiding path into the second ion guiding path by urging ions across the one or more pseudo-potential barriers.

The second ion source may be arranged adjacent the first ion guide.

The calibrant, lockmass or reference ions may be arranged to be transmitted along the first ion guiding path.

The first ion guiding device may be arranged and adapted to direct an ion beam away from an optic axis of an incident laser beam and/or along an optic axis of an incident laser beam.

The second ion source may be arranged adjacent to the entrance to the first ion guiding device and/or the first or second ion guide and/or may be inside or outside of the first ion guiding device and/or the first or second ion guide.

The mass spectrometer may further comprise one or more second ion guiding devices arranged upstream and/or downstream of the first ion guiding device.

The one or more second ion guiding devices may comprise one or more multipole rod set ion guides, one or more ion tunnel ion guides, one or more ion funnel ion guides, or one or more planar electrode ion guides.

The one or more second ion guiding devices may be arranged and adapted to receive the analyte ions generated from the target by the first ion source.

The one or more second ion guiding devices may be arranged and adapted to transmit the analyte ions onwards to the first ion guiding device.

The calibrant, lockmass or reference ions may not be transmitted, in use, through the one or more second ion guiding devices.

The one or more second ion guiding devices may be arranged in a first vacuum chamber.

The first ion guiding device may be also arranged in the first vacuum chamber.

The first ion guiding device may be arranged in a second vacuum chamber arranged downstream of the first vacuum chamber.

According to another aspect there is provided a method of mass spectrometry comprising: acquiring an ion image of a target using a first ion source wherein separate mass spectral data corresponding to different regions and/or different depths of the target are acquired; and generating calibrant, lockmass or reference ions using a second ion source.

According to another aspect there is provided ion imaging apparatus comprising: a first ion source for acquiring, in use, an ion image of a target wherein separate mass spectral data corresponding to different regions and/or different depths of the target are acquired in use; and a second ion source for generating calibrant, lockmass or reference ions.

According to another aspect there is provided a method of ion imaging comprising: acquiring an ion image of a target using a first ion source wherein separate mass spectral data corresponding to different regions and/or different depths of the target are acquired; and generating calibrant, lockmass or reference ions using a second ion source.

According to various embodiments: (a) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes have substantially circular, rectangular, square or elliptical apertures; and/or (b) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes have apertures which are substantially the same size or which have substantially the same area; and/or (c) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes have apertures which become progressively larger and/or smaller in size or in area in a direction along the axis or length of the first ion guide and/or the second ion guide; and/or (d) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes have apertures having internal diameters or dimensions selected from the group consisting of: (i) < 1.0 mm; (ii) < 2.0 mm; (iii) < 3.0 mm; (iv) < 4.0 mm; (v) < 5.0 mm; (vi) < 6.0 mm; (vii) < 7.0 mm; (viii) < 8.0 mm; (ix) < 9.0 mm; (x) < 10.0 mm; and (xi) > 10.0 mm; and/or (e) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes are spaced apart from one another by an axial distance selected from the group consisting of: (i) less than or equal to 5 mm; (ii) less than or equal to 4.5 mm; (iii) less than or equal to 4 mm; (iv) less than or equal to 3.5 mm; (v) less than or equal to 3 mm; (vi) less than or equal to 2.5 mm; (vii) less than or equal to 2 mm; (viii) less than or equal to 1.5 mm; (ix) less than or equal to 1 mm; (x) less than or equal to 0.8 mm; (xi) less than or equal to 0.6 mm; (xii) less than or equal to 0.4 mm; (xiii) less than or equal to 0.2 mm; (xiv) less than or equal to 0.1 mm; and (xv) less than or equal to 0.25 mm; and/or (f) at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes comprise apertures wherein the ratio of the internal diameter or dimension of the apertures to the centre-to-centre axial spacing between adjacent electrodes is selected from the group consisting of: (i) < 1.0; (ii) 1.0-1.2; (iii) 1.2-1.4; (iv) 1.4-1.6; (v) 1.6-1.8; (vi) 1.8-2.0; (vii) 2.0-2.2; (viii) 2.2-2.4: (ix) 2.4-2.6: (x) 2.6-2.8; (xi) 2.8-3.0; (xii) 3.0-3.2; (xiii) 3.2-3.4: (xiv) 3.4-3.6: (xv) 3.6-3.8: (xvi) 3.8-4.0; (xvii) 4.0-4.2; (xviii) 4.2-4.4: (xix) 4.4-4.6: (xx) 4.6-4.8: (xxi) 4.8-5.0; and (xxii) > 5.0; and/or (g) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes have a thickness or axial length selected from the group consisting of: (i) less than or equal to 5 mm; (ii) less than or equal to 4.5 mm; (iii) less than or equal to 4 mm; (iv) less than or equal to 3.5 mm; (v) less than or equal to 3 mm; (vi) less than or equal to 2.5 mm; (vii) less than or equal to 2 mm; (viii) less than or equal to 1.5 mm; (ix) less than or equal to 1 mm; (x) less than or equal to 0.8 mm; (xi) less than or equal to 0.6 mm; (xii) less than or equal to 0.4 mm; (xiii) less than or equal to 0.2 mm; (xiv) less than or equal to 0.1 mm; and (xv) less than or equal to 0.25 mm; and/or (h) the first plurality of electrodes have a first cross-sectional area or profile, wherein the first cross-sectional area or profile changes, increases, decreases or varies along at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide; and/or (i) the second plurality of electrodes have a second cross-sectional area or profile, wherein the second cross-sectional area or profile changes, increases, decreases or varies along at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the second ion guide.

According to various embodiments the first and/or second ion guiding device may comprise: a first ion guide comprising a first plurality of electrodes comprising one or more first rod sets wherein a first ion guiding path is formed along or within the first ion guide; a second ion guide comprising a first plurality of electrodes comprising one or more second rod sets wherein a second different ion guiding path is formed along or within the second ion guide; optionally a first device arranged and adapted to create one or more pseudopotential barriers at one or more points along the length of the ion guiding device between the first ion guiding path and the second ion guiding path; and optionally a second device arranged and adapted to transfer ions from the first ion guiding path into the second ion guiding path by urging ions across the one or more pseudo-potential barriers.

Optionally: (a) the first ion guide and/or the second ion guide comprise one or more axially segmented rod set ion guides; and/or (b) the first ion guide and/or the second ion guide comprise one or more segmented quadrupole, hexapole or octapole ion guides or an ion guide comprising four or more segmented rod sets; and/or (c) the first ion guide and/or the second ion guide comprise a plurality of electrodes having a cross-section selected from the group consisting of: (i) an approximately or substantially circular cross-section; (ii) an approximately or substantially hyperbolic surface; (iii) an arcuate or part-circular cross-section; (iv) an approximately or substantially rectangular cross-section; and (v) an approximately or substantially square cross-section; and/or (d) the first ion guide and/or the second ion guide comprise further comprise a plurality of ring electrodes arranged around the one or more first rod sets and/or the one or more second rod sets; and/or (e) the first ion guide and/or the second ion guide comprise 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30 or > 30 rod electrodes.

According to an embodiment the first and/or second ion guiding devices may comprise: a first ion guide comprising a first plurality of electrodes arranged in a plane in which ions travel in use and wherein a first ion guiding path is formed along or within the first ion guide; a second ion guide comprising a second plurality of electrodes arranged in a plane in which ions travel in use wherein a second different ion guiding path is formed along or within the second ion guide; optionally a device arranged and adapted to create a pseudo-potential barrier at one or more points along the length of the first and/or second ion guiding device between the first ion guiding path and the second ion guiding path; and optionally a device arranged and adapted to transfer ions from the first ion guiding path into the second ion guiding path by urging ions across the pseudo-potential barrier.

Optionally: (a) the first ion guide and/or the second ion guide may comprise a stack or array of planar, plate, mesh or curved electrodes, wherein the stack or array of planar, plate, mesh or curved electrodes comprises a plurality or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19 or 20 planar, plate, mesh or curved electrodes and wherein at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the planar, plate, mesh or curved electrodes are arranged generally in the plane in which ions travel in use; and/or (b) the first ion guide and/or the second ion guide are axially segmented so as to comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 axial segments, wherein at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes in an axial segment and/or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the second plurality of electrodes in an axial segment are maintained in use at the same DC voltage.

The first device may be arranged and adapted to create: (i) one or more radial or longitudinal pseudo-potential barriers at one or more points along the length of the first and/or second ion guiding device between the first ion guiding path and the second ion guiding path; and/or (ii) one or more non-axial pseudo-potential barriers at one or more points along the length of the first and/or second ion guiding device between the first ion guiding path and the second ion guiding path.

The second device may be arranged and adapted: (a) to transfer ions radially from the first ion guiding path into the second ion guiding path; and/or (b) to transfer ions with a non-zero radial component of velocity and an axial component of velocity from the first ion guiding path into the second ion guiding path; and/or (c) to transfer ions with a non-zero radial component of velocity and an axial component of velocity from the first ion guiding path into the second ion guiding path, wherein the ratio of the radial component of velocity to the axial component of velocity is selected from the group consisting of: (i) <0.1; (ii) 0.1-0.2; (iii) 0.2-0.3; (iv) 0.3-0.4; (v) 0.4-0.5; (vi) 0.5-0.6; (vii) 0.6-0.7; (viii) 0.7-0.8; (ix) 0.8-0.9; (x) 0.9-1.0; (xi) 1.0-1.1; (xii) 1.1-1.2; (xiii) 1.2-1.3; (xiv) 1.3-1.4; (xv) 1.4-1.5; (xvi) 1.5-1.6; (xvii) 1.6-1.7; (xviii) 1.7-1.8; (xix) 1.8-1.9; (xx) 1.9-2.0; (xxi) 2.0-3.0; (xxii) 3.0-4.0; (xxiii) 4.0-5.0; (xxiv) 5.0-6.0; (xxv) 6.0-7.0; (xxvi) 7.0-8.0; (xxvii) 8.0-9.0; (xxviii) 9.0-10.0; and (xxix) > 10.0; (d) to transfer ions from the first ion guiding path into the second ion guiding path by transferring ions across one or more radial pseudo-potential barriers arranged between the first ion guiding path and the second ion guiding path.

Optionally: (a) the first ion guide and the second ion guide are conjoined, merged, overlapped or open to one another for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (b) ions may be transferred radially between the first ion guide or the first ion guiding path and the second ion guide or the second ion guiding path over at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (c) one or more radial or longitudinal pseudo-potential barriers are formed, in use, which separate the first ion guide or the first ion guiding path from the second ion guide or the second ion guiding path along at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (d) a first pseudo-potential valley or field is formed within the first ion guide and a second pseudo-potential valley or field is formed within the second ion guide and wherein a pseudo-potential barrier separates the first pseudo-potential valley from the second pseudo-potential valley, wherein ions are confined radially within the first and/or second ion guiding device by either the first pseudo-potential valley or the second pseudo-potential valley and wherein at least some ions are urged or caused to transfer across the pseudopotential barrier; and/or (e) the degree of overlap or openness between the first ion guide and the second ion guide remains constant or varies, increases, decreases, increases in a stepped or linear manner or decreases in a stepped or linear manner along the length of the first and second ion guides.

Optionally: (a) one or more or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes are maintained in a mode of operation at a first potential or voltage selected from the group consisting of: (i) ± 0-10 V; (ii) ± 10-20 V; (iii) ± 20-30 V; (iv) ± 30-40 V; (v) ± 40-50 V; (vi) ± 50-60 V; (vii) ± 60-70 V; (viii) ± 70-80 V; (ix) ± 80-90 V; (x) ± 90-100 V; (xi) ± 100-150 V; (xii) ± 150-200 V; (xiii) ± 200-250 V; (xiv) ± 250-300 V; (xv) ± 300-350 V; (xvi) ± 350-400 V; (xvii) ± 400-450 V; (xviii) ± 450-500 V; (xix) ± 500-550 V; (xx) ± 550-600 V; (xxi) ± 600-650 V; (xxii) ± 650-700 V; (xxiii) ± 700-750 V; (xxiv) ± 750-800 V; (xxv) ± 800-850 V; (xxvi) ± 850-900 V; (xxvii) ± 900-950 V; (xxviii) ± 950-1000 V; and (xxix) > ± 1000 V; and/or (b) one or more or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the second plurality of electrodes are maintained in a mode of operation at a second potential or voltage selected from the group consisting of: (i) ± 0-10 V; (ii) ± 10-20 V; (iii) ± 20-30 V; (iv) ± 30-40 V; (v) ± 40-50 V; (vi) ± 50-60 V; (vii) ± 60-70 V; (viii) ± 70-80 V; (ix) ± 80-90 V; (x) ± 90-100 V; (xi) ± 100-150 V; (xii) ± 150-200 V; (xiii) ± 200-250 V; (xiv) ± 250-300 V; (xv) ± 300-350 V; (xvi) ± 350-400 V; (xvii) ± 400-450 V; (xviii) ± 450-500 V; (xix) ± 500-550 V; (xx) ± 550-600 V; (xxi) ± 600-650 V; (xxii) ± 650-700 V; (xxiii) ± 700-750 V; (xxiv) ± 750-800 V; (xxv) ± 800-850 V; (xxvi) ± 850-900 V; (xxvii) ± 900-950 V; (xxviii) ± 950-1000 V; and (xxix) > ± 1000 V; and/or (c) a potential difference is maintained in a mode of operation between one or more or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and one or more or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the second plurality of electrodes, wherein the potential difference is selected from the group consisting of: (i) ± 0-10 V; (ii) ± 10-20 V; (iii) ± 20-30 V; (iv) ± 30-40 V; (v) ± 40-50 V; (vi) ± 50-60 V; (vii) ± 60-70 V; (viii) ± 70-80 V; (ix) ± 80-90 V; (x) ± 90-100 V; (xi) ± 100-150 V; (xii) ± 150-200 V; (xiii) ± 200-250 V; (xiv) ± 250-300 V; (xv) ± 300-350 V; (xvi) ± 350-400 V; (xvii) ± 400-450 V; (xviii) ± 450-500 V; (xix) ± 500-550 V; (xx) ± 550-600 V; (xxi) ± 600-650 V; (xxii) ± 650-700 V; (xxiii) ± 700-750 V; (xxiv) ± 750-800 V; (xxv) ± 800-850 V; (xxvi) ± 850-900 V; (xxvii) ± 900-950 V; (xxviii) ± 950-1000 V; and (xxix) > ± 1000 V; and/or (d) the first plurality of electrodes or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes are maintained in use at substantially the same first DC voltage; and/or (e) the second plurality of electrodes or at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the second plurality of electrodes are maintained in use at substantially the same second DC voltage; and/or (f) at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes are maintained at substantially the same DC or DC bias voltage or are maintained at substantially different DC or DC bias voltages.

Optionally the first ion guide comprises a first central longitudinal axis and the second ion guide comprises a second central longitudinal axis and wherein: (i) the first central longitudinal axis is substantially parallel with the second central longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (ii) the first central longitudinal axis is not co-linear or co-axial with the second central longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (iii) the first central longitudinal axis is spaced at a constant distance or remains equidistant from the second central longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (iv) the first central longitudinal axis is a mirror image of the second central longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (v) the first central longitudinal axis substantially tracks, follows, mirrors or runs parallel to and/or alongside the second central longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (vi) the first central longitudinal axis converges towards or diverges away from the second central longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (vii) the first central longitudinal axis and the second central longitudinal form a X-shaped or Y-shaped coupler or splitter ion guiding path; and/or (viii) one or more crossover regions, sections or junctions are arranged between the first ion guide and the second ion guide wherein at least some ions may be transferred or are caused to be transferred from the first ion guide into the second ion guide and/or wherein at least some ions may be transferred from the second ion guide into the first ion guide.

According to various embodiments in use a first pseudo-potential valley may be formed within the first ion guide such that the first pseudo-potential valley has a first longitudinal axis and wherein in use a second pseudo-potential valley may be formed within the second ion guide such that the second pseudo-potential valley has a second longitudinal axis and wherein: (i) the first longitudinal axis is substantially parallel with the second longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (ii) the first longitudinal axis is not co-linear or co-axial with the second longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (iii) the first longitudinal axis is spaced at a constant distance or remains equidistant from the second longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (iv) the first longitudinal axis is a mirror image of the second longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (v) the first longitudinal axis substantially tracks, follows, mirrors or runs parallel to and/or alongside the second longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (vi) the first longitudinal axis converges towards or diverges away from the second longitudinal axis for at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide and/or the second ion guide; and/or (vii) the first longitudinal axis and the second longitudinal form a X-shaped or Y-shaped coupler or splitter ion guiding path; and/or (viii) one or more crossover regions, sections or junctions are arranged between the first ion guide and the second ion guide wherein at least some ions may be transferred or are caused to be transferred from the first ion guide into the second ion guide and/or wherein at least some ions may be transferred from the second ion guide into the first ion guide.

Optionally: (a) the first ion guide may comprise an ion guiding region having a first cross-sectional area and wherein the second ion guide comprises an ion guiding region having a second cross-sectional area, wherein the first and second cross-sectional areas are substantially the same or substantially different; and/or (b) the first ion guide may comprise an ion guiding region having a first cross-sectional area and wherein the second ion guide comprises an ion guiding region having a second cross-sectional area, wherein the ratio of the first cross-sectional area to the second cross-sectional area is selected from the group consisting of: (i) <0.1; (ii) 0.1-0.2; (iii) 0.2-0.3; (iv) 0.3-0.4; (v) 0.4-0.5; (vi) 0.5-0.6; (vii) 0.6-0.7; (viii) 0.7-0.8; (ix) 0.8-0.9; (x) 0.9-1.0; (xi) 1.0-1.1; (xii) 1.1-1.2; (xiii) 1.2-1.3; (xiv) 1.3-1.4; (xv) 1.4-1.5; (xvi) 1.5-1.6; (xvii) 1.6-1.7; (xviii) 1.7-1.8; (xix) 1.8-1.9; (xx) 1.9-2.0; (xxi) 2.0-2.5; (xxii) 2.5-3.0; (xxiii) 3.0-3.5; (xxiv) 3.5-4.0; (xxv) 4.0-4.5; (xxvi) 4.5-5.0; (xxvii) 5.0-6.0; (xxviii) 6.0-7.0; (xxix) 7.0-8.0; (xxx) 8.0-9.0; (xxxi) 9.0-10.0; and (xxxii) > 10.0; and/or (c) the first ion guide may comprise an ion guiding region having a first cross-sectional area or profile, and wherein the first cross-sectional area or profile changes, increases, decreases or varies along at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the first ion guide; and/or (d) the second ion guide may comprise an ion guiding region having a second cross-sectional area or profile, and wherein the second cross-sectional area or profile changes, increases, decreases or varies along at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the second ion guide; and/or (e) the first ion guide may comprise a plurality of axial sections and wherein the cross-sectional area or profile of first electrodes in an axial section is substantially the same or different and wherein the cross-sectional area or profile of first electrodes in further axial sections is substantially the same or different; and/or (f) the second ion guide may comprise a plurality of axial sections and wherein the cross-sectional area or profile of second electrodes in an axial section is substantially the same or different and wherein the cross-sectional area or profile of second electrodes in further axial sections is substantially the same or different; and/or (g) the first ion guide and/or the second ion guide may comprise a substantially constant or uniform cross-sectional area or profile.

Optionally, the first ion guide and/or the second ion guide comprise: (i) a first axial segment wherein the first ion guide and/or the second ion guide comprise a first cross-sectional area or profile; and/or (ii) a second different axial segment wherein the first ion guide and/or the second ion guide comprise a second cross-sectional area or profile; and/or (iii) a third different axial segment wherein the first ion guide and/or the second ion guide comprise a third cross-sectional area or profile; and/or (iv) a fourth different axial segment wherein the first ion guide and/or the second ion guide comprise a fourth cross-sectional area or profile; wherein the first, second, third and fourth cross-sectional area or profiles are substantially the same or different.

Optionally, the first and/or second ion guiding devices may be arranged and adapted so as to form: (i) a linear ion guide or ion guiding device; and/or (ii) an open-loop ion guide or ion guiding device; and/or (iii) a closed-loop ion guide or ion guiding device; and/or (iv) a helical, toroidal, part-toroidal, hemitoroidal, semitoroidal or spiral ion guide or ion guiding device; and/or (v) an ion guide or ion guiding device having a curved, labyrinthine, tortuous, serpentine, circular or convoluted ion guide or ion guiding path.

Optionally, the first ion guide and/or the second ion guide may comprise n axial segments or are segmented into n separate axial segments, wherein n is selected from the group consisting of: (i) 1-10; (ii) 11-20; (iii) 21-30; (iv) 31-40; (v) 41-50; (vi) 51-60; (vii) 61-70; (viii) 71-80; (ix) 81-90; (x) 91-100; and (xi) > 100; and wherein: (a) each axial segment comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or > 20 electrodes; and/or (b) the axial length of at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the axial segments is selected from the group consisting of: (i) < 1 mm; (ii) 1-2 mm; (iii) 2-3 mm; (iv) 3-4 mm; (v) 4-5 mm; (vi) 5-6 mm; (vii) 6-7 mm; (viii) 7-8 mm; (ix) 8-9 mm; (x) 9-10 mm; and (xi) > 10 mm; and/or (c) the axial spacing between at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the axial segments is selected from the group consisting of: (i) < 1 mm; (ii) 1-2 mm; (iii) 2-3 mm; (iv) 3-4 mm; (v) 4-5 mm; (vi) 5-6 mm; (vii) 6-7 mm; (viii) 7-8 mm; (ix) 8-9 mm; (x) 9-10 mm; and (xi) > 10 mm.

Optionally, the first ion guide and/or the second ion guide: (a) have a length selected from the group consisting of: (i) < 20 mm; (ii) 20-40 mm; (iii) 40-60 mm; (iv) 60-80 mm; (v) 80-100 mm; (vi) 100-120 mm; (vii) 120-140 mm; (viii) 140-160 mm; (ix) 160-180 mm; (x) 180-200 mm; and (xi) > 200 mm; and/or (b) comprise at least: (i) 10-20 electrodes; (ii) 20-30 electrodes; (iii) 30-40 electrodes; (iv) 40-50 electrodes; (v) 50-60 electrodes; (vi) 60-70 electrodes; (vii) 70-80 electrodes; (viii) 80-90 electrodes; (ix) 90-100 electrodes; (x) 100-110 electrodes; (xi) 110-120 electrodes; (xii) 120-130 electrodes; (xiii) 130-140 electrodes; (xiv) 140-150 electrodes; or (xv) >150 electrodes.

The first and/or second ion guiding device may comprise a first AC or RF voltage supply for applying a first AC or RF voltage to at least some of the first plurality of electrodes and/or the second plurality of electrodes, wherein either: (a) the first AC or RF voltage has an amplitude selected from the group consisting of: (i) < 50 V peak to peak; (ii) 50-100 V peak to peak; (iii) 100-150 V peak to peak; (iv) 150-200 V peak to peak; (v) 200-250 V peak to peak; (vi) 250-300 V peak to peak; (vii) 300-350 V peak to peak; (viii) 350-400 V peak to peak; (ix) 400-450 V peak to peak; (x) 450-500 V peak to peak; (xi) 500-550 V peak to peak; (xxii) 550-600 V peak to peak; (xxiii) 600-650 V peak to peak; (xxiv) 650-700 V peak to peak; (xxv) 700-750 V peak to peak; (xxvi) 750-800 V peak to peak; (xxvii) 800-850 V peak to peak; (xxviii) 850-900 V peak to peak; (xxix) 900-950 V peak to peak; (xxx) 950-1000 V peak to peak; and (xxxi) > 1000 V peak to peak; and/or (b) the first AC or RF voltage has a frequency selected from the group consisting of: (i) < 100 kHz; (ii) 100-200 kHz; (iii) 200-300 kHz; (iv) 300-400 kHz; (v) 400-500 kHz; (vi) 0. 5-1.0 MHz; (vii) 1.0-1.5 MHz; (viii) 1.5-2.0 MHz; (ix) 2.0-2.5 MHz; (x) 2.5-3.0 MHz; (xi) 3.0-3.5 MHz; (xii) 3.5-4.0 MHz; (xiii) 4.0-4.5 MHz; (xiv) 4.5-5.0 MHz; (xv) 5.0-5.5 MHz; (xvi) 5.5-6.0 MHz; (xvii) 6.0-6.5 MHz; (xviii) 6.5-7.0 MHz; (xix) 7.0-7.5 MHz; (xx) 7.5-8.0 MHz; (xxi) 8.0-8.5 MHz; (xxii) 8.5-9.0 MHz; (xxiii) 9.0-9.5 MHz; (xxiv) 9.5-10.0 MHz; and (xxv) > 10.0 MHz; and/or (c) the first AC or RF voltage supply is arranged to apply the first AC or RF voltage to at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the first plurality of electrodes and/or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or > 50 of the first plurality of electrodes; and/or (d) the first AC or RF voltage supply is arranged to apply the first AC or RF voltage to at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the second plurality of electrodes and/or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or > 50 of the second plurality of electrodes; and/or (e) the first AC or RF voltage supply is arranged to supply adjacent or neighbouring electrodes of the first plurality of electrodes with opposite phases of the first AC or RF voltage; and/or (f) the first AC or RF voltage supply is arranged to supply adjacent or neighbouring electrodes of the second plurality of electrodes with opposite phases of the first AC or RF voltage; and/or (g) the first AC or RF voltage generates one or more radial pseudo-potential wells which act to confine ions radially within the first ion guide and/or the second ion guide.

The first and/or second ion guiding device may further comprise a third device arranged and adapted to progressively increase, progressively decrease, progressively vary, scan, linearly increase, linearly decrease, increase in a stepped, progressive or other manner or decrease in a stepped, progressive or other manner the amplitude of the first AC or RF voltage by Χϊ Volts over a time period ti, wherein: (a) Xi is selected from the group consisting of: (i) < 50 V peak to peak; (ii) 50-100 V peak to peak; (iii) 100-150 V peak to peak; (iv) 150-200 V peak to peak; (v) 200-250 V peak to peak; (vi) 250-300 V peak to peak; (vii) 300-350 V peak to peak; (viii) 350-400 V peak to peak; (ix) 400-450 V peak to peak; (x) 450-500 V peak to peak; (xi) 500-550 V peak to peak; (xxii) 550-600 V peak to peak; (xxiii) 600-650 V peak to peak; (xxiv) 650-700 V peak to peak; (xxv) 700-750 V peak to peak; (xxvi) 750-800 V peak to peak; (xxvii) 800-850 V peak to peak; (xxviii) 850-900 V peak to peak; (xxix) 900-950 V peak to peak; (xxx) 950-1000 V peak to peak; and (xxxi) > 1000 V peak to peak; and/or (b) ti is selected from the group consisting of: (i) < 1 ms; (ii) 1-10 ms; (iii) 10-20 ms; (iv) 20-30 ms; (v) 30-40 ms; (vi) 40-50 ms; (vii) 50-60 ms; (viii) 60-70 ms; (ix) 70-80 ms; (x) 80-90 ms; (xi) 90-100 ms; (xii) 100-200 ms; (xiii) 200-300 ms; (xiv) 300-400 ms; (xv) 400-500 ms; (xvi) 500-600 ms; (xvii) 600-700 ms; (xviii) 700-800 ms; (xix) 800-900 ms; (xx) 900-1000 ms; (xxi) 1-2 s; (xxii) 2-3 s; (xxiii) 3-4 s; (xxiv) 4-5 s; and (xxv) > 5 s.

One or more first axial time averaged or pseudo-potential barriers, corrugations or wells may optionally be created, in use, along at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the axial length of the first ion guide.

The first and/or second ion guiding device may further comprises a second AC or RF voltage supply for applying a second AC or RF voltage to at least some of the first plurality of electrodes and/or the second plurality of electrodes, wherein either: (a) the second AC or RF voltage has an amplitude selected from the group consisting of: (i) < 50 V peak to peak; (ii) 50-100 V peak to peak; (iii) 100-150 V peak to peak; (iv) 150-200 V peak to peak; (v) 200-250 V peak to peak; (vi) 250-300 V peak to peak; (vii) 300-350 V peak to peak; (viii) 350-400 V peak to peak; (ix) 400-450 V peak to peak; (x) 450-500 V peak to peak; (xi) 500-550 V peak to peak; (xxii) 550-600 V peak to peak; (xxiii) 600-650 V peak to peak; (xxiv) 650-700 V peak to peak; (xxv) 700-750 V peak to peak; (xxvi) 750-800 V peak to peak; (xxvii) 800-850 V peak to peak; (xxviii) 850-900 V peak to peak; (xxix) 900-950 V peak to peak; (xxx) 950-1000 V peak to peak; and (xxxi) > 1000 V peak to peak; and/or (b) the second AC or RF voltage has a frequency selected from the group consisting of: (i) < 100 kHz; (ii) 100-200 kHz; (iii) 200-300 kHz; (iv) 300-400 kHz; (v) 400-500 kHz; (vi) 0.5-1.0 MHz; (vii) 1.0-1.5 MHz; (viii) 1.5-2.0 MHz; (ix) 2.0-2.5 MHz; (x) 2.5-3.0 MHz; (xi) 3.0-3.5 MHz; (xii) 3.5-4.0 MHz; (xiii) 4.0-4.5 MHz; (xiv) 4.5-5.0 MHz; (xv) 5.0-5.5 MHz; (xvi) 5.5-6.0 MHz; (xvii) 6.0-6.5 MHz; (xviii) 6.5-7.0 MHz; (xix) 7.0-7.5 MHz; (xx) 7.5- 8.0 MHz; (xxi) 8.0-8.5 MHz; (xxii) 8.5-9.0 MHz; (xxiii) 9.0-9.5 MHz; (xxiv) 9.5-10.0 MHz; and (xxv) > 10.0 MHz; and/or (c) the second AC or RF voltage supply is arranged to apply the second AC or RF voltage to at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the first plurality of electrodes and/or at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or > 50 of the first plurality of electrodes; and/or (d) the first AC or RF voltage supply is arranged to apply the second AC or RF voltage to at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the second plurality of electrodes and/or at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50 or > 50 of the second plurality of electrodes; and/or (e) the second AC or RF voltage supply is arranged to supply adjacent or neighbouring electrodes of the first plurality of electrodes with opposite phases of the second AC or RF voltage; and/or (f) the second AC or RF voltage supply is arranged to supply adjacent or neighbouring electrodes of the second plurality of electrodes with opposite phases of the second AC or RF voltage; and/or (g) the second AC or RF voltage generates one or more radial pseudo-potential wells which act to confine ions radially within the first ion guide and/or the second ion guide.

The first and/or second ion guiding device may further comprise a fourth device arranged and adapted to progressively increase, progressively decrease, progressively vary, scan, linearly increase, linearly decrease, increase in a stepped, progressive or other manner or decrease in a stepped, progressive or other manner the amplitude of the second AC or RF voltage by x2 Volts over a time period t2, wherein: (a) x2 is selected from the group consisting of: (i) < 50 V peak to peak; (ii) 50-100 V peak to peak; (iii) 100-150 V peak to peak; (iv) 150-200 V peak to peak; (v) 200-250 V peak to peak; (vi) 250-300 V peak to peak; (vii) 300-350 V peak to peak; (viii) 350-400 V peak to peak; (ix) 400-450 V peak to peak; (x) 450-500 V peak to peak; (xi) 500-550 V peak to peak; (xxii) 550-600 V peak to peak; (xxiii) 600-650 V peak to peak; (xxiv) 650-700 V peak to peak; (xxv) 700-750 V peak to peak; (xxvi) 750-800 V peak to peak; (xxvii) 800-850 V peak to peak; (xxviii) 850-900 V peak to peak; (xxix) 900-950 V peak to peak; (xxx) 950-1000 V peak to peak; and (xxxi) > 1000 V peak to peak; and/or (b) t2 is selected from the group consisting of: (i) < 1 ms; (ii) 1-10 ms; (iii) 10-20 ms; (iv) 20-30 ms; (v) 30-40 ms; (vi) 40-50 ms; (vii) 50-60 ms; (viii) 60-70 ms; (ix) 70-80 ms; (x) 80-90 ms; (xi) 90-100 ms; (xii) 100-200 ms; (xiii) 200-300 ms; (xiv) 300-400 ms; (xv) 400-500 ms; (xvi) 500-600 ms; (xvii) 600-700 ms; (xviii) 700-800 ms; (xix) 800-900 ms; (xx) 900-1000 ms; (xxi) 1-2 s; (xxii) 2-3 s; (xxiii) 3-4 s; (xxiv) 4-5 s; and (xxv) > 5 s.

Optionally, one or more second axial time averaged or pseudo-potential barriers, corrugations or wells are created, in use, along at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the axial length of the second ion guide.

Optionally, a non-zero axial and/or radial DC voltage gradient is maintained in use across or along one or more sections or portions of the first ion guide and/or the second ion guide.

Optionally, the first and/or second ion guiding device further comprise a device for driving or urging ions upstream and/or downstream along or around at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length or ion guiding path of the first ion guide and/or the second ion guide, wherein the device comprises: (i) a device for applying one more transient DC voltages or potentials or DC voltage or potential waveforms to at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the first plurality of electrodes and/or the second plurality of electrodes in order to urge at least some ions downstream and/or upstream along at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial length of the first ion guide and/or the second ion guide; and/or (ii) a device arranged and adapted to apply two or more phase-shifted AC or RF voltages to electrodes forming the first ion guide and/or the second ion guide in order to urge at least some ions downstream and/or upstream along at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial length of the first ion guide and/or the second ion guide; and/or (iii) a device arranged and adapted to apply one or more DC voltages to electrodes forming the first ion guide and/or the second ion guide in order create or form an axial and/or radial DC voltage gradient which has the effect of urging or driving at least some ions downstream and/or upstream along at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial length of the first ion guide and/or the second ion guide.

Optionally, the first and/or second ion guiding devices further comprise a fifth device arranged and adapted to progressively increase, progressively decrease, progressively vary, scan, linearly increase, linearly decrease, increase in a stepped, progressive or other manner or decrease in a stepped, progressive or other manner the amplitude, height or depth of the one or more transient DC voltages or potentials or DC voltage or potential waveforms by x3 Volts over a time period k; wherein x3 is selected from the group consisting of: (i) <0.1 V; (ii) 0.1-0.2 V; (iii) 0.2-0.3 V; (iv) 0.3-0.4 V; (v) 0.4-0.5 V; (vi) 0.5-0.6 V; (vii) 0.6-0.7 V; (viii) 0.7-0.8 V; (ix) 0.8-0.9 V; (x) 0.9-1.0 V; (xi) 1.0-1.5 V; (xii) 1.5-2.0 V; (xiii) 2.0-2.5 V; (xiv) 2.5-3.0 V; (xv) 3.0-3.5 V; (xvi) 3.5-4.0 V; (xvii) 4.0-4.5 V; (xviii) 4.5-5.0 V; (xix) 5.0-5.5 V; (xx) 5.5-6.0 V; (xxi) 6.0-6.5 V; (xxii) 6.5-7.0 V; (xxiii) 7.0-7.5 V; (xxiv) 7.5-8.0 V; (xxv) 8.0-8.5 V; (xxvi) 8.5-9.0 V; (xxvii) 9.0-9.5 V; (xxviii) 9.5-10.0 V; and (xxix) > 10.0 V; and/or wherein t3 is selected from the group consisting of: (i) < 1 ms; (ii) 1-10 ms; (iii) 10-20 ms; (iv) 20-30 ms; (v) 30-40 ms; (vi) 40-50 ms; (vii) 50-60 ms; (viii) 60-70 ms; (ix) 70-80 ms; (x) 80-90 ms; (xi) 90-100 ms; (xii) 100-200 ms; (xiii) 200-300 ms; (xiv) 300-400 ms; (xv) 400-500 ms; (xvi) 500-600 ms; (xvii) 600-700 ms; (xviii) 700-800 ms; (xix) 800-900 ms; (xx) 900-1000 ms; (xxi) 1-2 s; (xxii) 2-3 s; (xxiii) 3-4 s; (xxiv) 4-5 s; and (xxv) > 5 s.

Optionally, the first and/or second ion guiding devices further comprise a sixth device arranged and adapted to progressively increase, progressively decrease, progressively vary, scan, linearly increase, linearly decrease, increase in a stepped, progressive or other manner or decrease in a stepped, progressive or other manner the velocity or rate at which the one or more transient DC voltages or potentials or DC voltage or potential waveforms are applied to the electrodes by x4 m/s over a time period t4; wherein x4 is selected from the group consisting of: (i) < 1; (ii) 1-2; (iii) 2-3; (iv) 3-4; (v) 4-5; (vi) 5-6; (vii) 6-7; (viii) 7-8; (ix) 8-9; (x) 9-10; (xi) 10-11; (xii) 11-12; (xiii) 12-13; (xiv) 13-14; (xv) 14-15; (xvi) 15-16; (xvii) 16-17; (xviii) 17-18; (xix) 18-19; (xx) 19-20; (xxi) 20-30; (xxii) 30-40; (xxiii) 40-50; (xxiv) 50-60; (xxv) 60-70; (xxvi) 70-80; (xxvii) 80-90; (xxviii) 90-100; (xxix) 100-150; (xxx) 150-200; (xxxi) 200-250; (xxxii) 250-300; (xxxiii) 300-350; (xxxiv) 350-400; (xxxv) 400-450; (xxxvi) 450-500; and (xxxvii) > 500; and/or wherein t4 is selected from the group consisting of: (i) < 1 ms; (ii) 1-10 ms; (iii) 10-20 ms; (iv) 20-30 ms; (v) 30-40 ms; (vi) 40-50 ms; (vii) 50-60 ms; (viii) 60-70 ms; (ix) 70-80 ms; (x) 80-90 ms; (xi) 90-100 ms; (xii) 100-200 ms; (xiii) 200-300 ms; (xiv) 300-400 ms; (xv) 400-500 ms; (xvi) 500-600 ms; (xvii) 600-700 ms; (xviii) 700-800 ms; (xix) 800-900 ms; (xx) 900-1000 ms; (xxi) 1-2 s; (xxii) 2-3 s; (xxiii) 3-4 s; (xxiv) 4-5 s; and (xxv) > 5 s.

Optionally, the first and/or second ion guiding devices further comprise a device arranged to maintain a constant non-zero DC voltage gradient along at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length or ion guiding path of the first ion guide and/or the second ion guide.

Optionally, the second device is arranged and adapted to mass selectively or mass to charge ratio selectively transfer ions from the first ion guiding path or the first ion guide into the second ion guiding path or the second ion guide and/or from the second ion guiding path or the second ion guide into the first ion guiding path or the first ion guide.

Optionally, a parameter affecting the mass selective or mass to charge ratio selective transfer of ions from the first ion guiding path into the second ion guiding path and/or from the second ion guiding path into the first ion guiding path is progressively increased, progressively decreased, progressively varied, scanned, linearly increased, linearly decreased, increased in a stepped, progressive or other manner or decreased in a stepped, progressive or other manner.

The parameter may be selected from the group consisting of: (i) an axial and/or radial DC voltage gradient maintained, in use, across, along or between one or more sections or portions of the first ion guide and/or the second ion guide; and/or (ii) one or more AC or RF voltages applied to at least some or substantially all of the first plurality of electrodes and/or the second plurality of electrodes.

Optionally, the first ion guide and/or the second ion guide may be arranged and adapted to receive a beam or group of ions and to convert or partition the beam or group of ions such that at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 separate packets of ions are confined and/or isolated within the first ion guide and/or the second ion guide at any particular time, and wherein each packet of ions is separately confined and/or isolated in a separate axial potential well formed in the first ion guide and/or the second ion guide.

Optionally: (a) one or more portions of the first ion guide and/or the second ion guide comprise an ion mobility spectrometer or separator portion, section or stage wherein ions are caused to separate temporally according to their ion mobility in the ion mobility spectrometer or separator portion, section or stage; and/or (b) one or more portions of the first ion guide and/or the second ion guide comprise a Field Asymmetric Ion Mobility Spectrometer (“FAIMS”) portion, section or stage wherein ions are caused to separate temporally according to their rate of change of ion mobility with electric field strength in the Field Asymmetric Ion Mobility Spectrometer (“FAIMS”) portion, section or stage; and/or (c) in use a buffer gas is provided within one or more sections of the first ion guide and/or the second ion guide; and/or (d) in a mode of operation ions are arranged to be collisionally cooled without fragmenting upon interaction with gas molecules within a portion or region of the first ion guide and/or the second ion guide; and/or (e) in a mode of operation ions are arranged to be heated upon interaction with gas molecules within a portion or region of the first ion guide and/or the second ion guide; and/or (f) in a mode of operation ions are arranged to be fragmented upon interaction with gas molecules within a portion or region of the first ion guide and/or the second ion guide; and/or (g) in a mode of operation ions are arranged to unfold or at least partially unfold upon interaction with gas molecules within the first ion guide and/or the second ion guide; and/or (h) ions are trapped axially within a portion or region of the first ion guide and/or the second ion guide.

Optionally, the first ion guide and/or the second ion guide further comprise a collision, fragmentation or reaction device, wherein in a mode of operation ions are arranged to be fragmented within the first ion guide and/or the second ion guide by: (i) Collisional Induced Dissociation ("CID"); (ii) Surface Induced Dissociation ("SID"); (iii)

Electron Transfer Dissociation ("ETD"); (iv) Electron Capture Dissociation ("ECD"); (v) Electron Collision or Impact Dissociation; (vi) Photo Induced Dissociation ("PID"); (vii)

Laser Induced Dissociation; (viii) infrared radiation induced dissociation; (ix) ultraviolet radiation induced dissociation; (x) thermal or temperature dissociation; (xi) electric field induced dissociation; (xii) magnetic field induced dissociation; (xiii) enzyme digestion or enzyme degradation dissociation; (xiv) ion-ion reaction dissociation; (xv) ion-molecule reaction dissociation; (xvi) ion-atom reaction dissociation; (xvii) ion-metastable ion reaction dissociation; (xviii) ion-metastable molecule reaction dissociation; (xix) ion-metastable atom reaction dissociation; and (xx) Electron Ionisation Dissociation (“EID”).

Optionally, the first and/or second ion guiding devices further comprise: (i) a device for injecting ions into the first ion guide and/or the second ion guide; and/or (ii) a device for injecting ions into the first ion guide and/or the second ion guide comprising one, two, three or more than three discrete ion guiding channels or input ion guiding regions through which ions may be injected into the first ion guide and/or the second ion guide; and/or (iii) a device for injecting ions into the first ion guide and/or the second ion guide comprising a plurality of electrodes, each electrode comprising one, two, three or more than three apertures; and/or (iv) a device for injecting ions into the first ion guide and/or the second ion guide comprising one or more deflection electrodes, wherein in use one or more voltages are applied to the one or more deflection electrodes in order to direct ions from one or more ion guiding channels or input ion guiding regions into the first ion guide and/or the second ion guide.

Optionally, the first and/or second ion guiding devices further comprise: (i) a device for ejecting ions from the first and/or second ion guide; and/or (ii) a device for ejecting ions from the first and/or second ion guide, the device comprising one, two, three or more than three discrete ion guiding channels or exit ion guiding regions into which ions may be ejected from the first ion guide and/or the second ion guide; and/or (iii) a device for ejecting ions from the first and/or second ion guide, the device comprising a plurality of electrodes, each electrode comprising one, two, three or more than three apertures; and/or (iv) a device for ejecting ions from the first and/or second ion guide, the device comprising one or more deflection electrodes, wherein in use one or more voltages are applied to the one or more deflection electrodes in order to direct ions from the ion guide into one or more ion guiding channels or exit ion guiding regions.

Optionally, the first and/or second ion guiding devices further comprise: (a) a device for maintaining in a mode of operation at least a portion of the first ion guide and/or the second ion guide at a pressure selected from the group consisting of: (i) > 1.0 x 10'3 mbar; (ii) > 1.0x 10'2 mbar; (iii) > 1.0 x 10'1 mbar; (iv) > 1 mbar; (v) > 10 mbar; (vi) >100 mbar; (vii) > 5.0 x 10'3 mbar; (viii) > 5.0 x 10'2 mbar; (ix) 10'4-10'3 mbar; (x) 10'3-10'2 mbar; and (xi) 10'2-10'1 mbar; and/or (b) a device for maintaining in a mode of operation at least a length L of the first ion guide and/or a second ion guide at a pressure P wherein the product P x L is selected from the group consisting of: (i) > 1.0 x 10'3 mbar cm; (ii) > 1.0 x 10"2 mbar cm; (iii) > 1.0 x 10'1 mbar cm; (iv) > 1 mbar cm; (v) > 10 mbar cm; (vi) > 102 mbar cm; (vii) > 103 mbar cm; (viii) > 104 mbar cm; and (ix) > 105 mbar cm; and/or (c) a device for maintaining in a mode of operation the first ion guide and/or the second ion guide at a pressure selected from the group consisting of: (i) >100 mbar; (ii) > 10 mbar; (iii) > 1 mbar; (iv) >0.1 mbar; (v) > 10'2 mbar; (vi) > 10'3 mbar; (vii) > 10'4 mbar; (viii) > 10'5 mbar; (ix) > 10'6 mbar; (x) <100 mbar; (xi) <10 mbar; (xii) < 1 mbar; (xiii) <0.1 mbar; (xiv) < 10"2 mbar; (xv) < 10"3 mbar; (xvi) < 10"4 mbar; (xvii) < 10'5 mbar; (xviii) < 10'6 mbar; (xix) 10-100 mbar; (xx) 1-10 mbar; (xxi) 0.1-1 mbar; (xxii) 10"2 to 10'1 mbar; (xxiii) 10' 3 to 10"2 mbar; (xxiv) 10"4 to 10"3 mbar; and (xxv) 10"5 to 10"4 mbar.

The energy may be provided by a laser, for example from the group comprising: Nitrogen, Nd:YAG , C02, Er:YAG, UV and IR. The laser may comprise a pulse frequency, for example selected from the following ranges: 1-10 Hz, 10-100 Hz, 100-1000 Hz, 1000-10000 Hz, 10000-100000 Hz.

Alternatively, the energy may be provided by one or more of firing a laser at the back of the sample plate (as in laser spray), firing a ball bearing at the sample plate, heating a specific spot on the sample plate, a piezoelectric excitement of a spot on the sample plate.

The surface of the sample being analysed may further comprises a matrix, for example from the group comprising: 2,5-dihydroxy benzoic acid, 3,5-dimethoxy-4-hydroxycinnamic acid, 4-hydroxy-3-methoxycinnamic acid, a-cyano-4-hydroxycinnamic acid, Picolinic acid, 3-hydroxy picolinic acid.

The segregation means may contain a collision gas and/or ions segregated by the segregation means may be exposed to a source of heat, for example by providing a heated collision gas within the segregation means. Additionally or alternatively, the source of heat may comprise a radiant heat source.

According to an embodiment the mass spectrometer may further comprise: (a) an ion source selected from the group consisting of: (i) an Electrospray ionisation ("ESI") ion source; (ii) an Atmospheric Pressure Photo Ionisation ("APPI") ion source; (iii) an Atmospheric Pressure Chemical Ionisation ("APCI") ion source; (iv) a Matrix Assisted Laser Desorption Ionisation ("MALDI") ion source; (v) a Laser Desorption Ionisation ("LDI") ion source; (vi) an Atmospheric Pressure Ionisation ("API") ion source; (vii) a Desorption Ionisation on Silicon ("DIOS") ion source; (viii) an Electron Impact ("El") ion source; (ix) a Chemical Ionisation ("Cl") ion source; (x) a Field Ionisation ("FI") ion source; (xi) a Field Desorption ("FD") ion source; (xii) an Inductively Coupled Plasma ("ICP") ion source; (xiii) a Fast Atom Bombardment ("FAB") ion source; (xiv) a Liquid Secondary Ion Mass Spectrometry ("LSIMS") ion source; (xv) a Desorption Electrospray Ionisation ("DESI") ion source; (xvi) a Nickel-63 radioactive ion source; (xvii) an

Atmospheric Pressure Matrix Assisted Laser Desorption Ionisation ion source; (xviii) a Thermospray ion source; (xix) an Atmospheric Sampling Glow Discharge Ionisation (“ASGDI”) ion source; (xx) a Glow Discharge (“GD”) ion source; (xxi) an Impactor ion source; (xxii) a Direct Analysis in Real Time ("DART") ion source; (xxiii) a Laserspray Ionisation ("LSI") ion source; (xxiv) a Sonicspray Ionisation ("SSI") ion source; (xxv) a Matrix Assisted Inlet Ionisation ("MAN") ion source; (xxvi) a Solvent Assisted Inlet Ionisation ("SAN") ion source; (xxvii) a Desorption Electrospray Ionisation (“DESI”) ion source; and (xxviii) a Laser Ablation Electrospray Ionisation (“LAESI”) ion source; and/or (b) one or more continuous or pulsed ion sources; and/or (c) one or more ion guides; and/or (d) one or more ion mobility separation devices and/or one or more Field Asymmetric Ion Mobility Spectrometer devices; and/or (e) one or more ion traps or one or more ion trapping regions; and/or (f) one or more collision, fragmentation or reaction cells selected from the group consisting of: (i) a Collisional Induced Dissociation ("CID") fragmentation device; (ii) a Surface Induced Dissociation ("SID") fragmentation device; (iii) an Electron Transfer Dissociation ("ETD") fragmentation device; (iv) an Electron Capture Dissociation ("ECD") fragmentation device; (v) an Electron Collision or Impact Dissociation fragmentation device; (vi) a Photo Induced Dissociation ("PID") fragmentation device; (vii) a Laser Induced Dissociation fragmentation device; (viii) an infrared radiation induced dissociation device; (ix) an ultraviolet radiation induced dissociation device; (x) a nozzle-skimmer interface fragmentation device; (xi) an in-source fragmentation device; (xii) an in-source Collision Induced Dissociation fragmentation device; (xiii) a thermal or temperature source fragmentation device; (xiv) an electric field induced fragmentation device; (xv) a magnetic field induced fragmentation device; (xvi) an enzyme digestion or enzyme degradation fragmentation device; (xvii) an ion-ion reaction fragmentation device; (xviii) an ion-molecule reaction fragmentation device; (xix) an ion-atom reaction fragmentation device; (xx) an ion-metastable ion reaction fragmentation device; (xxi) an ion-metastable molecule reaction fragmentation device; (xxii) an ion-metastable atom reaction fragmentation device; (xxiii) an ion-ion reaction device for reacting ions to form adduct or product ions; (xxiv) an ion-molecule reaction device for reacting ions to form adduct or product ions; (xxv) an ion-atom reaction device for reacting ions to form adduct or product ions; (xxvi) an ion-metastable ion reaction device for reacting ions to form adduct or product ions; (xxvii) an ion-metastable molecule reaction device for reacting ions to form adduct or product ions; (xxviii) an ion-metastable atom reaction device for reacting ions to form adduct or product ions; and (xxix) an Electron Ionisation Dissociation (“EID”) fragmentation device; and/or (g) a mass analyser selected from the group consisting of: (i) a quadrupole mass analyser; (ii) a 2D or linear quadrupole mass analyser; (iii) a Paul or 3D quadrupole mass analyser; (iv) a Penning trap mass analyser; (v) an ion trap mass analyser; (vi) a magnetic sector mass analyser; (vii) Ion Cyclotron Resonance ("ICR") mass analyser; (viii) a Fourier Transform Ion Cyclotron Resonance ("FTICR") mass analyser; (ix) an electrostatic mass analyser arranged to generate an electrostatic field having a quadro-logarithmic potential distribution; (x) a Fourier Transform electrostatic mass analyser; (xi) a Fourier Transform mass analyser; (xii) a Time of Flight mass analyser; (xiii) an orthogonal acceleration Time of Flight mass analyser; and (xiv) a linear acceleration Time of Flight mass analyser; and/or (h) one or more energy analysers or electrostatic energy analysers; and/or (i) one or more ion detectors; and/or (j) one or more mass filters selected from the group consisting of: (i) a quadrupole mass filter; (ii) a 2D or linear quadrupole ion trap; (iii) a Paul or 3D quadrupole ion trap; (iv) a Penning ion trap; (v) an ion trap; (vi) a magnetic sector mass filter; (vii) a Time of Flight mass filter; and (viii) a Wien filter; and/or (k) a device or ion gate for pulsing ions; and/or (l) a device for converting a substantially continuous ion beam into a pulsed ion beam.

The mass spectrometer may further comprise either: (i) a C-trap and a mass analyser comprising an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with a quadro-logarithmic potential distribution, wherein in a first mode of operation ions are transmitted to the C-trap and are then injected into the mass analyser and wherein in a second mode of operation ions are transmitted to the C-trap and then to a collision cell or Electron Transfer Dissociation device wherein at least some ions are fragmented into fragment ions, and wherein the fragment ions are then transmitted to the C-trap before being injected into the mass analyser; and/or (ii) a stacked ring ion guide comprising a plurality of electrodes each having an aperture through which ions are transmitted in use and wherein the spacing of the electrodes increases along the length of the ion path, and wherein the apertures in the electrodes in an upstream section of the ion guide have a first diameter and wherein the apertures in the electrodes in a downstream section of the ion guide have a second diameter which is smaller than the first diameter, and wherein opposite phases of an AC or RF voltage are applied, in use, to successive electrodes.

According to an embodiment the mass spectrometer further comprises a device arranged and adapted to supply an AC or RF voltage to the electrodes. The AC or RF voltage optionally has an amplitude selected from the group consisting of: (i) about < 50 V peak to peak; (ii) about 50-100 V peak to peak; (iii) about 100-150 V peak to peak; (iv) about 150-200 V peak to peak; (v) about 200-250 V peak to peak; (vi) about 250-300 V peak to peak; (vii) about 300-350 V peak to peak; (viii) about 350-400 V peak to peak; (ix) about 400-450 V peak to peak; (x) about 450-500 V peak to peak; and (xi) > about 500 V peak to peak.

The AC or RF voltage may have a frequency selected from the group consisting of: (i) < about 100 kHz; (ii) about 100-200 kHz; (iii) about 200-300 kHz; (iv) about 300-400 kHz; (v) about 400-500 kHz; (vi) about 0.5-1.0 MHz; (vii) about 1.0-1.5 MHz; (viii) about 1.5-2.0 MHz; (ix) about 2.0-2.5 MHz; (x) about 2.5-3.0 MHz; (xi) about 3.0-3.5 MHz; (xii) about 3.5-4.0 MHz; (xiii) about 4.0-4.5 MHz; (xiv) about 4.5-5.0 MHz; (xv) about 5.0-5.5 MHz; (xvi) about 5.5-6.0 MHz; (xvii) about6.0-6.5 MHz; (xviii) about 6.5-7.0 MHz; (xix) about 7.0-7.5 MHz; (xx) about 7.5-8.0 MHz; (xxi) about 8.0-8.5 MHz; (xxii) about 8.5-9.0 MHz; (xxiii) about 9.0-9.5 MHz; (xxiv) about 9.5-10.0 MHz; and (xxv) > about 10.0 MHz.

The mass spectrometer may also comprise a chromatography or other separation device upstream of an ion source. According to an embodiment the chromatography separation device comprises a liquid chromatography or gas chromatography device. According to another embodiment the separation device may comprise: (i) a Capillary Electrophoresis (“CE”) separation device; (ii) a Capillary Electrochromatography (“CEC”) separation device; (iii) a substantially rigid ceramic-based multilayer microfluidic substrate (“ceramic tile”) separation device; or (iv) a supercritical fluid chromatography separation device.

The ion guide may be maintained at a pressure selected from the group consisting of: (i) < about 0.0001 mbar; (ii) about 0.0001-0.001 mbar; (iii) about 0.001-0.01 mbar; (iv) about 0.01-0.1 mbar; (v) about 0.1-1 mbar; (vi) about 1-10 mbar; (vii) about 10-100 mbar; (viii) about 100-1000 mbar; and (ix) > about 1000 mbar.

According to an embodiment analyte ions may be subjected to Electron Transfer Dissociation (“ETD”) fragmentation in an Electron Transfer Dissociation fragmentation device. Analyte ions may be caused to interact with ETD reagent ions within an ion guide or fragmentation device.

According to an embodiment in order to effect Electron Transfer Dissociation either: (a) analyte ions are fragmented or are induced to dissociate and form product or fragment ions upon interacting with reagent ions; and/or (b) electrons are transferred from one or more reagent anions or negatively charged ions to one or more multiply charged analyte cations or positively charged ions whereupon at least some of the multiply charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions; and/or (c) analyte ions are fragmented or are induced to dissociate and form product or fragment ions upon interacting with neutral reagent gas molecules or atoms or a nonionic reagent gas; and/or (d) electrons are transferred from one or more neutral, non-ionic or uncharged basic gases or vapours to one or more multiply charged analyte cations or positively charged ions whereupon at least some of the multiply charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions; and/or (e) electrons are transferred from one or more neutral, non-ionic or uncharged superbase reagent gases or vapours to one or more multiply charged analyte cations or positively charged ions whereupon at least some of the multiply charge analyte cations or positively charged ions are induced to dissociate and form product or fragment ions; and/or (f) electrons are transferred from one or more neutral, non-ionic or uncharged alkali metal gases or vapours to one or more multiply charged analyte cations or positively charged ions whereupon at least some of the multiply charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions; and/or (g) electrons are transferred from one or more neutral, non-ionic or uncharged gases, vapours or atoms to one or more multiply charged analyte cations or positively charged ions whereupon at least some of the multiply charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions, wherein the one or more neutral, non-ionic or uncharged gases, vapours or atoms are selected from the group consisting of: (i) sodium vapour or atoms; (ii) lithium vapour or atoms; (iii) potassium vapour or atoms; (iv) rubidium vapour or atoms; (v) caesium vapour or atoms; (vi) francium vapour or atoms; (vii) C6o vapour or atoms; and (viii) magnesium vapour or atoms.

The multiply charged analyte cations or positively charged ions may comprise peptides, polypeptides, proteins or biomolecules.

According to an embodiment in order to effect Electron Transfer Dissociation: (a) the reagent anions or negatively charged ions are derived from a polyaromatic hydrocarbon or a substituted polyaromatic hydrocarbon; and/or (b) the reagent anions or negatively charged ions are derived from the group consisting of: (i) anthracene; (ii) 9,10 diphenyl-anthracene; (iii) naphthalene; (iv) fluorine; (v) phenanthrene; (vi) pyrene; (vii) fluoranthene; (viii) chrysene; (ix) triphenylene; (x) perylene; (xi) acridine; (xii) 2,2' dipyridyl; (xiii) 2,2' biquinoline; (xiv) 9-anthracenecarbonitrile; (xv) dibenzothiophene; (xvi) 1,10'-phenanthroline; (xvii) 9' anthracenecarbonitrile; and (xviii) anthraquinone; and/or (c) the reagent ions or negatively charged ions comprise azobenzene anions or azobenzene radical anions.

According to an embodiment the process of Electron Transfer Dissociation fragmentation comprises interacting analyte ions with reagent ions, wherein the reagent ions comprise dicyanobenzene, 4-nitrotoluene or azulene. A chromatography detector may be provided wherein the chromatography detector comprises either: a destructive chromatography detector optionally selected from the group consisting of (i) a Flame Ionization Detector (FID); (ii) an aerosol-based detector or Nano Quantity Analyte Detector (NQAD); (iii) a Flame Photometric Detector (FPD); (iv) an Atomic-Emission Detector (AED); (v) a Nitrogen Phosphorus Detector (NPD); and (vi) an Evaporative Light Scattering Detector (ELSD); or a non-destructive chromatography detector optionally selected from the group consisting of: (i) a fixed or variable wavelength UV detector; (ii) a Thermal Conductivity Detector (TCD); (iii) a fluorescence detector; (iv) an Electron Capture Detector (ECD); (v) a conductivity monitor; (vi) a Photoionization Detector (PID); (vii) a Refractive Index Detector (RID); (viii) a radio flow detector; and (ix) a chiral detector.

The mass spectrometer may be operated in various modes of operation including a mass spectrometry ("MS") mode of operation, a tandem mass spectrometry ("MS/MS") mode of operation, a mode of operation in which parent or precursor ions are alternatively fragmented or reacted so as to produce fragment or product ions, and not fragmented or reacted or fragmented or reacted to a lesser degree, a Multiple Reaction Monitoring ("MRM") mode of operation, a Data Dependent Analysis ("DDA") mode of operation, a Data Independent Analysis ("DIA") mode of operation, a Quantification mode of operation or an Ion Mobility Spectrometry ("IMS") mode of operation.

BRIEF DESCRIPTION OF THE DRAWINGS

Various embodiments will now be described, by way of example only, and with reference to the accompanying drawing in which:

Fig. 1 shows a Matrix Assisted Laser Desorption Ionisation ion source according to an embodiment wherein a conjoined ion guide is used to direct analyte ions in a first mode of operation and wherein in a second mode of operation a secondary ion source is actuated in order to generate calibrant ions;

Fig. 2A shows a schematic of another embodiment wherein an ion guide comprising two RF rod sets is provided so as to generate a pseudo-potential well which guides ions around a laser optic axis of a MALDI ion source so as to avoid a mirror, Fig. 2B shows a first mode of operation wherein a laser beam is directed by the mirror onto the surface of a MALDI target plate at an angle which is substantially perpendicular to the surface of the MALDI target plate so that a MALDI acquisition is performed and Fig. 2C shows a second mode of operation wherein a second ion source is operated in order to produce a beam or pulse of calibrant or reference ions;

Fig. 3A illustrates another embodiment comprising a stacked plate geometry ion guide wherein the longitudinal direction of the ion guide runs substantially parallel with the plane of the sample target plate and which is shown being operated in a first mode of operation wherein a MALDI acquisition is performed, Fig. 3B shows a second mode of operation wherein a second ion source is operated in order to produce a beam or pulse of calibrant or reference ions and Fig. 3C shows a different view of the stacked plate geometry ion guide; and

Fig. 4A shows a further embodiment wherein a hexapole ion guide is arranged so as to run substantially parallel with the plane of a MALDI sample target plate and which is shown in a first mode of operation wherein a MALDI acquisition is performed, Fig. 4B shows a different view of the hexapole ion guide and Fig. 4C shows a second mode of operation wherein a second ion source is operated in order to produce a beam or pulse of calibrant or reference ions.

DETAILED DESCRIPTION

During a Matrix Assisted Laser Desorption Ionisation experiment it can be beneficial to acquire reference ions of known mass or mass to charge ratio in order to monitor any drift in, for example, the flight time of a Time of Flight mass analyser and hence be able to re-calibrate the mass analyser. This is of particular relevance when performing a Matrix Assisted Laser Desorption Ionisation imaging experiment which can take several hours to complete and during which extended time the Time of Flight mass analyser may be prone to flight time drift due to changing environmental parameters. A known method of Matrix Assisted Laser Desorption Ionisation calibration involves depositing a reference sample on a region of a MALDI target plate in an area away from the sample being analysed. At certain periods during the experiment the acquisition is paused and the sample plate is moved to a region where the reference sample is located. A portion of the sample plate where the reference sample is located is then sampled.

Once the reference sample has been sampled the sample plate is then translated back or returned to the last position where the experiment left off and the acquisition is then recommenced. This process adds time delay to the experiment as the translation stage has to keep moving backwards and forwards between the sample and the reference sample. The known approach can also introduce an increased possibility that the translation stage may not return back to exactly the same position prior to sampling the reference sample which will then result in a loss of fidelity of the resulting ion image.

According to various embodiments as shown in Fig. 1 a second ion source 2 is provided and may be arranged downstream of a primary ion source which may comprise a Matrix Assisted Laser Desorption Ionisation ion source 1 comprising a laser. The second ion source 2 is able to insert or inject a reference ion beam or pulse of ions which may then be onwardly transmitted to a mass analyser.

According to the particular embodiment shown and described with reference to Fig. 1 the reference ion beam or pulse of ions may be inserted or injected in the mass analyser via a conjoined ion guide 3. However, as will be detailed below other embodiments are also contemplated wherein other ion guiding arrangements may be used.

The mass spectrometer may be calibrated by stopping the laser firing (or otherwise switching OFF the primary ion source 1) and switching ON the second ion source 2 without needing to translate the MALDI sample plate 4 to sample a reference sample. Such an approach reduces the time taken to calibrate a mass analyser during a Matrix Assisted Laser Desorption Ionisation ion imaging experiment since the sample plate 4 does not need to be translated in order to sample calibrant from a reference location on the sample plate 4 (and then re-registered).

The second ion source 2 may comprise a glow discharge source or another vacuum ionisation ion source. The second ion source 2 may be arranged adjacent to the entrance to and/or inside or outside of the conjoined ion guide 3.

According to various embodiments the primary ion source 1 may be operated at atmospheric pressure and the second ion source 2 may be located in a vacuum chamber and operated at sub-atmospheric pressure.

It will be understood that the ions formed in a MALDI plume by the laser 1 must be transferred into an analyser. This requires locating electrodes in close proximity to the sample target. However, in high vacuum MALDI instruments, the requirement for electrostatic lenses also to be arranged along the ion optic axis to enable ion acceleration orthogonal to the sample plate 4 precludes the ability to locate laser optics along the same path. Consequently, conventional MALDI mass spectrometers have the laser incident at a non-zero angle of incidence relative to the perpendicular to the sample plate 4.

With intermediate pressure MALDI, wherein a hexapole ion guide may be used to transfer ions, the RF devices prevent the possibility of locating laser optics designed specifically to provide orthogonal illumination. Furthermore, the RF lenses limit the possibility of providing a final focus lens close to the MALDI sample plate. Similar constraints also apply to atmospheric pressure MALDI instrumentation.

Fig. 2A shows a schematic of another embodiment wherein two RF rod sets 5A,5B are provided. The two rod sets 5A,5B may comprise rods which have substantially similar or the same diameters but wherein each RF rod set 5A,5B comprises a different number of rods and hence wherein the two rod set arrangements have different inscribed radii.

With reference to Fig. 2B the two RF rod sets 5A,5B in combination may be used to generate a pseudo-potential well which acts to guide ions around a laser optic axis and in particular to guide analyte ions so as to avoid a mirror 6. The mirror 6 may be provided so as to direct a laser beam 1 onto a MALDI target plate 4 in a direction which is substantially perpendicular to the surface of the target plate 4.

As shown in Fig. 2A, RF and DC voltages may be applied to the conjoined ion guide rod sets as indicated. In particular, adjacent rods may be maintained at opposite phases of a RF voltage and the rods comprising the first rod set ion guide 5A may be maintained at a first DC voltage DC1 and the rods comprising the second rod set ion guide 5B may be maintained at a second different (e.g. lower) DC voltage DC2.

According to various embodiments the rods may be axially segmented and a continuous or an intermittent DC field may be applied along the ion guide to push ions along and/or through the device. After ions have passed through the second ion guide 5B the ions may be onwardly transmitted to an ion separation device which may be arranged to collect the ions from each pulse or group of pulses as required. The ion separation device may be arranged to maintain ions in packets so as to avoid merging of the consecutive packets.

Fig. 2B shows an embodiment wherein a laser pulse 1 is directed through a lens 12 and onto a target sample plate 4 using a dichroic mirror 6 to produce an ion beam 13 which is subsequently directed away from the laser optic axis. The sample plate 4 may be viewed by a camera 14 through the laser mirror 6.

The conjoined ion guide rod sets are shown being operated in a first mode of operation wherein a laser beam 1 is directed by the mirror 6 onto the surface of the MALDI target plate 4. The resulting analyte ions are then directed along a portion of the axial length of the first rod set 5A wherein the rods are maintained at a first DC voltage DC1.

The ions are then directed into the second rod set 5B wherein the rods are maintained at a second different DC voltage DC2. If the analyte ions comprise positively charged ions then the first DC voltage DC1 may be arranged to be greater than the second DC voltage DC2 so that ions are transferred generally radially from the first rod set ion guide 5A into the second rod set ion guide 5B.

Fig. 2C shows a second mode of operation wherein a second ion source 2 is operated in order to produce a beam or pulse of calibrant or reference ions. The primary ion source 1 may be switched OFF whilst the second ion source 2 is being operated. The second ion source 2 may comprise a glow discharge ion source or another vacuum ionisation ion source. The second ion source 2 may be arranged adjacent to the entrance to and/or inside or outside of the first rod set ion guide 5A or the second rod set ion guide 5B. A mass spectrometer is preferably provided for use in MALDI mass spectrometry using a combination of mirrors 6 to direct the laser pulse 1 from the laser head (not shown) to the sample target plate 4. An optical lens 6 focuses the laser radiation onto the laser target plate 4. An RF guide 5A is arranged to collect and guide the ions generated in the MALDI plume and may be configured in such a way as to direct the ions along a path 15 away from the optic axis of the incident laser pulse 1. The laser beam 1 may be directed orthogonal to the surface of the target sample plate 4.

The RF guide preferably comprises three separate regions: a first arrangement of rod electrodes having a relatively large inscribed diameter arranged such that the RF voltage applied to each adjacent rod is in anti-phase with its immediate neighbours; a second region comprising conjoined RF guides wherein both ion guides are arranged such that the RF voltage applied to adjacent rods is in anti-phase with its immediate neighbours and wherein a DC potential may be applied between the two ion guides so as optionally to drive ions across the radial pseudo-potential barrier which separates the two ion guiding regions; and a third region constructed using rod electrodes arranged such that the RF voltage applied to each adjacent rod is in anti-phase with its immediate neighbour and wherein the arrangement of rod electrodes has a relatively small inscribed diameter. A DC offset voltage may be maintained between the two conjoined ion guides. The ion guide provides a method of directing the ion beam away from the optic axis of the incident laser beam 1.

According to an embodiment the rods may be axially segmented and a DC potential difference or a DC pulsed square wave may be applied sequentially along the length of the ion guide to the axially segmented rods and may therefore provide a mechanism to propagate ions along the axial length of the ion guide.

According to an embodiment a pulsed DC square wave or other DC voltage may be arranged to collect and confine ions created from one or more pulses of the laser on an individual co-ordinate and transfer the ions into the mass spectrometer in one single packet keeping the ions segregated from the next packet.

The DC square wave may push sets of ions from the selected one or more pulses of the laser through the device and into the mass analysis section of the instrument. This may result in ions from each packet within the mass spectrometer being able to be identified as being from one individual spot upon the target plate or sample 4.

According to an embodiment two packets of ions may be produced from the same spot, each packet may contain ions produced from one or more pulses on the same coordinate upon the target 4. The two packets may both be transferred through an ion confinement device, and the first set of ions passed straight through a collision cell following the ion confinement device. The ions may be propelled through the collision cell with sufficiently low energy that there will be few, or no fragmentation of the ions within the packet. The second set of ions may also be passed through the ion confinement device and into the collision cell. However, in this instance, the ions may be passed through the collision cell with higher energy such that all, most, or a substantial number of the ions will be fragmented thereby resulting in the generation of daughter, fragment or product ions. Both these packets of ions may then pass through to the analyser for analysis to produce a mass spectrum. This may allow the parent and daughter ion mass spectra to be performed on ions from the same co-ordinate on the sample plate 4.

Once the two packets have been created in the ion confinement device, the sample plate may be moved on to the next co-ordinate where the laser 1 may again be pulsed to create a set of ions from the next co-ordinate. These ions may be similarly separated from the previous sets of ions, and similarly, two packets may be formed in the same way as for the previous co-ordinate.

The ion confinement device may comprise an RF ion confinement device.

Ions created from the first co-ordinate and ions created from the second co-ordinate may be segregated by transient DC voltages.

According to other embodiments ions created from the first co-ordinate and ions created from the second co-ordinate may be segregated by one or more permanent DC voltages.

Ions created from the first co-ordinate and ions created from the second co-ordinate may be segregated by one or more intermittent DC voltages.

The ions may be created by a pulsed energy source. Two or more pulses of energy may be applied to the first co-ordinate and the resulting ions may be segregated within one packet.

According to other embodiments the ions produced from each pulse of energy on the first co-ordinate may be segregated from each other.

The pulsed energy source may comprise a laser. The laser may be from the group comprising: Nitrogen, Nd:YAG , C02, Er:YAG, UV and IR.

The laser may have a pulse frequency selected from the following ranges: 1-10 Hz, 10-100 Hz, 100-1000 Hz, 1000-10000 Hz, 10000-100000 Hz.

Other embodiments are contemplated wherein the energy may be provided by firing a laser at the back of the sample plate 4, firing a ball bearing at the sample plate 4, heating a specific spot on the sample plate 4 or piezoelectric excitement of a spot on the sample plate 4.

The surface may also comprise a matrix to assist desorption and ionisation of the sample. The matrix may be from the group comprising: 2,5-dihydroxy benzoic acid, 3,5-dimethoxy-4-hydroxycinnamic acid, 4-hydroxy-3-methoxycinnamic acid, a-cyano-4-hydroxycinnamic acid, Picolinic acid, 3-hydroxy picolinic acid.

According to an embodiment the ion confinement device may contain a collision gas. The collision gas may be used to cool the ions produced by the laser pulse to enable the ions to be more easily handled throughout the mass spectrometer. According to other embodiments any fragmentation may be performed within the ion confinement device.

According to an embodiment the packets of ions segregated in the ion confinement device may be exposed to a source of heat in order to assist the desolvation of the ions. The source of heat may be a heated collision gas within the ion confinement device. The source of heat may alternatively comprise a radiant heat source. In a further embodiment a laser may be provided to assist desolvation of ions within the ion confinement device

The energy source may be provided on or along a first path and the ion confinement device surrounds at least a part of that first path.

Although various embodiments as described above show an energy source perpendicular to the sample surface other embodiments are contemplated wherein the energy source may be inclined at an angle to the sample surface.

According to various embodiments the energy source may be arranged so as to be perpendicular because this provides optimum ionisation from each laser pulse.

Furthermore, the energy source being perpendicular also provides optimum precision of the co-ordinate being exposed to energy from the energy source. Nonetheless, other embodiments are contemplated wherein the energy source is inclined at any angle to the sample surface provided that the energy source can provide energy to the sample. The angle between the energy source path and the sample surface may be in the range of 70°-90°, 50°-70°, 30°-50° and 10°-30°.

In one embodiment, a Field Asymmetric Ion Mobility Spectrometry (“FAIMS”) separation device may be provided downstream of the ion confinement device.

In one embodiment, an ion mobility separation (“IMS”) device may be provided downstream of the ion confinement device.

In one embodiment a mass filter may be provided downstream of the ion confinement device. The mass filter may comprise a quadrupole rod set.

The fragmentation of ions may be performed in a collision cell downstream of the ion confinement device.

Once ions have been collected from one co-ordinate, the surface may be moved relative to the energy source to enable the provision of energy to different co-ordinates.

The spectra produced from packets of ions from each co-ordinate may be correlated with the co-ordinates upon the sample surface from which the ions are produced.

With reference to Figs. 2B and 2C an aperture 16 may be provided between the sample plate 4 and the RF ion guide allowing differential pumping to create two different pressure regions. In particular, the second ion source 2 may be maintained at a lower pressure than the sample plate 4 (which may be maintained at atmospheric pressure).

Fig. 3A illustrates another embodiment wherein an ion guide comprising a stacked plate geometry ion guide is provided. The stacked plate geometry ion guide may run substantially parallel to the plane of the sample target plate 4. RF voltages of opposite polarity may be applied to sequential plates 7 of the stacked plate ion guide. According to various embodiments transient DC voltages or travelling DC pulses may be superimposed upon the RF voltage so as to urge ions axially along at least a portion of the axial length of the ion guide. DC voltages may also be applied to confining plates or electrodes 8,9 which may be arranged in a plane which is substantially parallel to the plane of the target plate 4. The confining plates or electrodes 8,9 may be arranged so as to confine ions radially within the ion guide. A transient, intermittent or continuous DC field may optionally be applied along at least a portion of the axial length of the ion guide in order to propel ions through or along the ion guide or along at least a portion of the axial length of the ion guide.

The sample plate 4 may be viewed by a camera 14 through a laser mirror 6. A first mode of operation is shown in Fig. 3A wherein a laser beam 1 is directed by the mirror 6 onto a target plate 4. The resulting analyte ions pass into the ion guide and are onwardly transmitted in a direction which may be substantially parallel to the plane of the target plate 4.

Fig. 3B shows a second mode of operation wherein a second ion source 2 is operated in order to produce a beam or pulse of calibrant or reference ions. The second ion source 2 may comprise a glow discharge ion source or another vacuum ionisation ion source. The second ion source 2 may be arranged at one end of the ion guide so that calibrant or reference ions follow a substantially similar path to that of analyte ions which are generated in the first mode of operation. The second ion source 2 may be arranged adjacent to the entrance to and/or inside or outside of the ion guide.

Fig. 3C shows a different view of the stacked plate geometry ion guide, laser beam 1 and second ion source 2.

Fig. 4A shows a further embodiment wherein a hexapole ion guide 10 is arranged so as to run substantially parallel to the plane of a sample target plate 4. A section or cutaway portion in the lower two rods of the hexapole ion guide 10 may be provided. An extraction electrode 11 may be provided adjacent the cut-away portion(s) and may be provided intermediate between the target plate 4 and the rods of the hexapole ion guide 10. The extraction electrode 11 may in use be provided with a DC voltage which acts to draw ions from the sample plate 4 into the RF confinement within the ion guiding region of the hexapole ion guide 10.

According to various embodiments a continuous or an intermittent DC field may be applied along at least a portion of the axial length of the ion guide 10 in order to push or urge ions through or along at least a portion of the axial length of the ion guide 10. An ion separation device may be provided downstream of the hexapole ion guide 10 and may be arranged to collect the ions from each pulse or group of pulses as required. The ion separation device may be arranged to maintain ions in packets so as to avoid merging of the consecutive packets.

Fig. 4B shows a different view of the hexapole ion guide 10, laser beam 1 and extraction electrode 11.

Fig. 4C shows a second mode of operation wherein a second ion source 2 is operated in order to produce a beam or pulse of calibrant or reference ions. The second ion source 2 may comprise a glow discharge ion source or another vacuum ionisation ion source. The second ion source 2 may be arranged adjacent to the entrance to and/or inside or outside of the hexapole ion guide 10.

Although the various embodiments shown and described above in relation to Figs. 1-4 relate to a primary or first ion source 1 which comprises a Matrix Assisted Laser Desorption Ionisation (“MALDI”) ion source (either vacuum or atmospheric) other embodiments are equally contemplated wherein the primary or first ion source 1 may comprise a Desorption Electrospray Ionisation (“DESI”) ion source, a Laser Ablation Electrospray Ionisation (“LAESI”) ion source, an Atmospheric Solids Analysis Probe (“ASAP”) ion source, a Laser Desorption Ionization (“LDI”) ion source, a Dielectric Barrier Discharge ion source or another off-line (i.e. spatially separated rather than temporally separated) ion source.

According to various embodiments the conjoined ion guides 3,5A,5B as shown and described above with reference to Figs. 1-2 may be modified (or replaced) so as to comprise either a stacked ring ion guide, a parallel quadrupole, hexapole, octopole or multipole RF device or one or more electrostatic devices. Similarly, the stacked plate ion guide shown and described with reference to Figs. 3A-3C and the hexapole ion guide 10 shown and described with reference to Figs. 4A-4C may be modified (or replaced) so as to comprise either a stacked ring ion guide, a parallel quadrupole, hexapole, octopole or multipole RF device or one or more electrostatic devices.

Although the present invention has been described with reference to preferred embodiments, it will be understood by those skilled in the art that various changes in form and detail may be made without departing from the scope of the invention as set forth in the accompanying claims.

Claims

1. A mass spectrometer comprising: a first ion source for acquiring, in use, an ion image of a target wherein separate mass spectral data corresponding to different regions and/or different depths of said target are acquired in use; and a second ion source for generating calibrant, lockmass or reference ions.

2. A mass spectrometer as claimed in claim 1, wherein said first ion source comprises a Matrix Assisted Laser Desorption Ionisation (“MALDI”) ion source, a Desorption Electrospray Ionisation (“DESI”) ion source, a Laser Ablation Electrospray Ionisation (“LAESI”) ion source, an Atmospheric Solids Analysis Probe (“ASAP”) ion source, a Laser Desorption Ionization (“LDI”) ion source or a Dielectric Barrier Discharge ion source.

3. A mass spectrometer as claimed in claim 1 or 2, wherein said second ion source comprises a Glow Discharge (“GD”) ion source or a vacuum ionisation ion source.

4. A mass spectrometer as claimed in claim 1, 2 or 3, wherein said second ion source is arranged with a vacuum chamber.

5. A mass spectrometer as claimed in any preceding claim, further comprising a first differential pumping aperture and a vacuum chamber, wherein said first ion source generates analyte ions which pass in use through said first differential pumping aperture into said vacuum chamber.

6. A mass spectrometer as claimed in claim 5, wherein said second ion source is arranged downstream of said first differential pumping aperture so that said calibrant, lockmass or reference ions do not pass through said first differential pumping aperture.

7. A mass spectrometer as claimed in any preceding claim, further comprising a device arranged to move said target relative to said first ion source so as to enable mass spectral data from different spatially separated regions of said target to be acquired.

8. A mass spectrometer as claimed in claim 7, wherein said device comprises a translation stage for translating or moving said target.

9. A mass spectrometer as claimed in any preceding claim, wherein said first ion source comprises a laser for ionising said target and generating analyte ions.

10. A mass spectrometer as claimed in claim 9, further comprising a device for moving a laser beam emitted, in use, from said laser relative to said target so as to enable mass spectral data from different spatially separated regions of said target to be acquired.

11. A mass spectrometer as claimed in any preceding claim, further comprising a first ion guiding device which is arranged and adapted: (i) to receive and onwardly transmit analyte ions generated from said target by said first ion source; and/or (ii) to receive and onwardly transmit said calibrant, lockmass or reference ions.

12. A mass spectrometer as claimed in claim 11, wherein said first ion guiding device comprises an ion guide selected from the group consisting of: (i) a conjoined ion guide; (ii) a conjoined ion guide comprising a plurality of plate or ring electrodes; (iii) a conjoined ion guide comprising a plurality of rod electrodes; (iv) a plurality of plate or ring electrodes; (v) a plurality of rod electrodes; or (vi) a quadrupole rod set, a hexapole rod set, an octopole rod set or a multipole rod set.

13. A mass spectrometer as claimed in claim 11 or 12, wherein said first ion guiding device is arranged and adapted so that said analyte ions and said calibrant, lockmass or reference ions are transmitted through either: (i) substantially different ion paths through said first ion guiding device; or (ii) substantially similar ion paths through said first ion guiding device.

14. A mass spectrometer as claimed in any of claims 11, 12 or 13, wherein said first ion guiding device comprises a first ion guide comprising a first plurality of electrodes, each electrode comprising at least one aperture through which ions are transmitted in use wherein a first ion guiding path is formed along or within said first ion guide.

15. A mass spectrometer as claimed in any of claims 11, 12 or 13, wherein said first ion guiding device comprises a first ion guide comprising a first plurality of electrodes, each electrode comprising a rod electrode wherein a first ion guiding path is formed within an inscribed radius of said rod electrodes.

16. A mass spectrometer as claimed in claim 14 or 15, wherein said analyte ions are arranged to be transmitted along said first ion guiding path.

17. A mass spectrometer as claimed in claim 14, 15 or 16, wherein said first ion guiding device further comprises a second ion guide comprising a second plurality of electrodes, each electrode comprising at least one aperture through which ions are transmitted in use wherein a second different ion guiding path is formed along or within said second ion guide.

18. A mass spectrometer as claimed in claim 14, 15 or 16, wherein said first ion guiding device comprises a second ion guide comprising a second plurality of electrodes, each electrode comprising a rod electrode wherein a second ion guiding path is formed within an inscribed radius of said rod electrodes.

19. A mass spectrometer as claimed in any of claims 14-18, wherein said second ion source is arranged adjacent said first ion guide or adjacent said second ion guide.

20. A mass spectrometer as claimed in claim 17, 18 or 19, wherein said calibrant, lockmass or reference ions are arranged to be transmitted along said second ion guiding path.

21. A mass spectrometer as claimed in any of claims 17-20, wherein one or more pseudo-potential barriers are formed, in use, at one or more points along the length of said first ion guiding device between said first ion guiding path and said second ion guiding path.

22. A mass spectrometer as claimed in claim 21, wherein said first ion guiding device comprises a second device arranged and adapted to transfer said analyte ions from said first ion guiding path into said second ion guiding path by urging ions across said one or more pseudo-potential barriers.

23. A mass spectrometer as claimed in any of claims 11, 12 or 13, wherein said first ion guiding device comprises a first ion guide comprising a first plurality of electrodes, each electrode comprising a rod electrode wherein a first ion guiding path is formed within an inscribed radius of said rod electrodes.

24. A mass spectrometer as claimed in any of claims 11, 12 or 13, wherein said first ion guiding device comprises a first ion guide comprising a first plurality of electrodes, each electrode comprising at least one aperture through which ions are transmitted in use wherein a first ion guiding path is formed along or within said first ion guide.

25. A mass spectrometer as claimed in claim 23 or 24, wherein said analyte ions are arranged to be transmitted along said first ion guiding path.

26. A mass spectrometer as claimed in claim 23, 24 or 25, wherein said second ion source is arranged adjacent said first ion guide.

27. A mass spectrometer as claimed in any of claims 23-26, wherein said calibrant, lockmass or reference ions are arranged to be transmitted along said first ion guiding path.

28. A mass spectrometer as claimed in any of claims 11-27, wherein said first ion guiding device is arranged and adapted to direct an ion beam away from an optic axis of an incident laser beam and/or along an optic axis of an incident laser beam.

29. A mass spectrometer as claimed in any of claims 11-28, wherein said second ion source is arranged adjacent to the entrance to said first ion guiding device and/or said first or second ion guide; and/or wherein said second ion source is inside or outside of said first ion guiding device and/or said first or second ion guide.

30. A mass spectrometer as claimed in any preceding claim, further comprising one or more second ion guiding devices arranged upstream and/or downstream of said first ion guiding device.

31. A mass spectrometer as claimed in claim 30, wherein said one or more second ion guiding devices comprise one or more multipole rod set ion guides, one or more ion tunnel ion guides, one or more ion funnel ion guides, or one or more planar electrode ion guides.

32. A mass spectrometer as claimed in claim 31, wherein said one or more second ion guiding devices are arranged and adapted to receive said analyte ions generated from said target by said first ion source.

33. A mass spectrometer as claimed in claim 31 or 32, wherein said one or more second ion guiding devices are arranged and adapted to transmit said analyte ions onwards to said first ion guiding device.

34. A mass spectrometer as claimed in claim 32 or 33, wherein said calibrant, lockmass or reference ions are not transmitted, in use, through said one or more second ion guiding devices.

35. A mass spectrometer as claimed in any of claims 30-34, wherein said one or more second ion guiding devices are arranged in a first vacuum chamber.

36. A mass spectrometer as claimed in claim 35, wherein said first ion guiding device is also arranged in said first vacuum chamber.

37. A mass spectrometer as claimed in claim 35, wherein said first ion guiding device is arranged in a second vacuum chamber arranged downstream of said first vacuum chamber.

38. A method of mass spectrometry comprising: acquiring an ion image of a target using a first ion source wherein separate mass spectral data corresponding to different regions and/or different depths of said target are acquired; and generating calibrant, lockmass or reference ions using a second ion source.

39. Ion imaging apparatus comprising: a first ion source for acquiring, in use, an ion image of a target wherein separate mass spectral data corresponding to different regions and/or different depths of said target are acquired in use; and a second ion source for generating calibrant, lockmass or reference ions.

40. A method of ion imaging comprising: acquiring an ion image of a target using a first ion source wherein separate mass spectral data corresponding to different regions and/or different depths of said target are acquired; and generating calibrant, lockmass or reference ions using a second ion source.