WO2019229455A1

WO2019229455A1 - Bench-top time of flight mass spectrometer

Info

Publication number: WO2019229455A1
Application number: PCT/GB2019/051496
Authority: WO
Inventors: Jason Lee Wildgoose; Peter Carney; Ruth WAMSLEY; William Johnson; Paul MCIVER; David Wallis; James Harrison
Original assignee: Micromass Uk Limited
Priority date: 2018-05-31
Filing date: 2019-05-31
Publication date: 2019-12-05
Also published as: GB201907724D0; GB201808942D0; GB202211823D0; GB2574328A; GB2606328A; GB2606328B

Abstract

A mass spectrometer comprising: an ion guide (301) comprising a first portion (1811) configured to guide ions along a first axial path, a second portion (1812) configured to guide ions along a second different axial path, and a transition portion (1813) configured to urge ions from the first axial path onto the second axial path; a downstream electrode (1713) arranged downstream of the ion guide (301); and a voltage supply arranged and configured to apply a potential difference between the ion guide (301) and the downstream electrode (1713) so as to accelerate ions to collide with gas and fragment.

Description

BENCH-TOP TIME OF FLIGHT MASS SPECTROMETER

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority from and the benefit of United Kingdom patent application No. 1808942.5 filed on 31 May 2018. The entire content of this application is incorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates generally to mass spectrometry and in particular to a small footprint or bench-top Time of Flight (“TOF”) mass spectrometer which has particular application in the biopharmaceutical industry.

BACKGROUND

Conventional mass spectrometers which may be used, for example, in the biopharmaceutical industry tend to be relatively complex and have a relatively large footprint.

Scientists in the biopharmaceutical industry need to collect high resolution accurate mass data for their samples in order to provide more comprehensive information than can be obtained using LCUV analysis. Conventionally, this is typically achieved either by running relatively complex mass spectrometry equipment or by outsourcing the analysis to a specialist service.

It is desired to provide a reduced footprint Time of Flight (“TOF”) mass

spectrometer which may have particular application in the biopharmaceutical industry.

SUMMARY

From a first aspect the present invention provides a mass spectrometer comprising: an ion guide comprising a first portion configured to guide ions along a first axial path, a second portion configured to guide ions along a second different axial path, and a transition portion configured to urge ions from the first axial path onto the second axial path; a downstream electrode arranged downstream of the ion guide; and a voltage supply arranged and configured to apply a potential difference between the ion guide and the downstream electrode, in a fragmentation mode, so as to accelerate ions

therebetween; wherein the spectrometer is configured to maintain the gas pressure between the ion guide and downstream electrode such that when the voltage supply causes the ions to be accelerated, in the fragmentation mode, the ions collide with gas and fragment to form fragment ions. The ion guide may be the first ion guide described herein.

The form of the ion guide enables high gas loads to be handled, thereby enabling relatively high gas pressures to be used, which in turn enables efficient Collisionally Induced Dissociation (CID) to be performed. The form of the ion guide is therefore synergistic with the fragmentation technique described herein. Although the form of the ion guide is known, it has previously been used for focussing a relatively diffuse ion cloud into the mass spectrometer (by using an ion guide having a radially larger first portion than the second portion). It has not been recognised that such an ion guide can handle higher gas loads and so is synergistic with the fragmentation technique described herein. In contrast, in the known techniques the operational conditions are selected such that the ions are collisionally cooled by the background gas such that they are better able to be focussed, i.e. the average energy of the ions is reduced. This is contrary to the techniques described herein, which deliberately increase the energy of the ions by accelerating them through the gas so as to cause them to fragment.

The spectrometer may be configured to operate the voltage supply in: (i) a high- fragmentation mode, in which a relatively high potential difference is applied between the ion guide and the downstream electrode such that ions collide with the gas and fragment to form said fragment ions; and (ii) a low-fragmentation mode, in which a lower or no potential difference is applied between the ion guide and the downstream electrode.

The ions may be fragmented at a lower rate in the low-fragmentation mode, or substantially not fragmented.

The spectrometer may be configured to switch between the high-fragmentation mode and low-fragmentation mode in a single experimental run.

The spectrometer may be configured to mass analyse fragment ions in the high- fragmentation mode, mass analyse precursor ions in low-fragmentation mode, and correlate the fragment ions analysed in the high-fragmentation mode with their respective precursor ions analysed in the low-fragmentation mode.

The method may correlate the fragment ions analysed in the high-fragmentation mode with their respective precursor ions analysed in the low-fragmentation mode by: (i) matching the ion signal intensity profiles of fragment ions (as a function of time) with ion signal intensity profiles of precursor ions (as a function of time); and/or (ii) matching the fragment ions to their precursor ions based on the times at which the fragment and precursor ions are detected (e.g. based on the detected elution times of the ions in the experiment(s)).

The voltage supply may be configured to apply a pulsed voltage to an electrode of the ion guide and/or said downstream electrode so as to switch from the low- fragmentation mode to the high-fragmentation mode.

The ion guide may comprise a plurality of axially spaced electrodes and one or more voltage supply configured to apply a plurality of different DC potentials to different respective ones of the axially spaced electrodes so as to generate a DC gradient for urging ions through and out of the ion guide. Said one or more voltage supply may be configured to increase the DC potential of an electrode at the downstream end of the ion guide when switching from the low-frag entation mode to the high-fragmentation mode and also to increase at least some of the DC potentials in said plurality of different DC potentials so as to maintain a potential gradient along the ion guide that urges ions along and out of the ion guide.

Each of the DC potentials in said plurality of different DC potentials that are increased may be increased by the same amount, or a proportional amount, to the increase to the potential of the electrode at the downstream end of the ion guide.

This ensures that the potential gradient(s) for urging ions through and out of the ion guide are maintained even when the spectrometer is in the high-fragmentation mode.

Conversely, when the spectrometer switches from the high-fragmentation mode to the low-fragmentation mode, the electric potential applied to electrode at the downstream end of the ion guide may be decreased so that the ions are not accelerated so as to fragment. The potentials applied to the other upstream electrodes of the ion guide may also be decreased, e.g. by the same or a proportional amount.

The spectrometer may be configured to control the voltage supplies so as to maintain substantially the same voltage gradient along the ion guide in both the high and low fragmentation modes.

The first portion and transition portion of the ion guide may each comprise a plurality of axially spaced electrodes arranged about said first axial path and through which ions are transmitted in use, and the spectrometer may be configured to apply different DC voltages to different respective ones of these electrodes so as to maintain a first voltage gradient along the first portion and transition portion for driving ions through the ion guide. The transition portion and second portion of the ion guide may each comprise a plurality of axially spaced electrodes arranged about said second axial path and through which ions are transmitted in use, and wherein the spectrometer is configured to apply different DC voltages to different respective ones of these electrodes so as to maintain a second voltage gradient along the transition portion and second portion for driving ions through the ion guide. At any given axial location along the transition region of the ion guide, the potential of the first gradient may be higher than the potential of the second gradient.

This aspect is considered to be new in its own right. Embodiments of the invention are therefore contemplated wherein the ion guide is not operated in a fragmentation mode but, for example, the first and second voltage gradients are applied.

The first and second voltage gradients may maintain the above relationship with each other in the high and/or low fragmentation modes.

An AC or RF voltage supply may be connected to said electrodes for applying an AC or RF voltage to the electrodes for radially confining ions within the ion guide to said axis. The spectrometer may be configured to operate the voltage supply in: (i) a low- attenuation mode, in which a relatively high peak-to-peak amplitude AC or RF voltage is applied to the electrodes for providing relatively strong radial confinement of the ions; and (ii) a high-attenuation mode, in which a lower peak-to-peak amplitude AC or RF voltage is applied to the electrodes for providing weaker radial confinement of the ions. Either attenuation mode may be used with either fragmentation mode.

The above-described ability of the spectrometer to handle high gas loads also enables a relatively large ion sampling orifice to be provided, enabling a relatively high proportion of the ions from an ion source to enter for subsequent analysis. The ion transmission rate and sensitivity may consequently be relatively high. Although a large ion sampling orifice would conventionally provide high chemical noise and be seen as undesirable, the ion guide of the embodiments of the present invention enables a high gas pressure and hence improved fragmentation, whilst also providing a good signal-to-noise ratio. The high signal-to-noise ratio is provided as the ion guide of the embodiments is able to separate neutral species and/or large cluster species from the analyte ions. More specifically, the ions are transferred from the first axial path of the ion guide to the second axial path of the ion guide, whereas the neutral species and/or large cluster species may continue along the first axial path. The ion guide therefore enables the ions to be onwardly transmitted and for the neutral species and/or large cluster species not to be.

For example, the neutral species and/or large cluster species may be pumped away by a vacuum pump.

The spectrometer may comprise a first vacuum chamber, a second vacuum chamber adjacent the first vacuum chamber, and a differential pumping aperture separating the first and second vacuum chambers; wherein the ion guide is located in the first vacuum chamber and the downstream electrode is an electrode in which the differential pumping aperture is formed.

The embodiments of the invention enable fragmentation in the first vacuum chamber. In contrast, conventional instruments provide a fragmentation cell in the lower pressure regions downstream of the first vacuum chamber, which then requires a dedicated gas supply to the fragmentation cell in order to provide the required gas pressure for CID fragmentation. Furthermore, as the ion guide of the embodiments of the present invention enables a high gas pressure in the first vacuum chamber, the gas pressure may be significantly higher than the traditional dedicated fragmentation cells mentioned above. Therefore, the embodiments provide for more efficient fragmentation of molecular ions than traditional fragmentation cells.

The spectrometer may be configured to maintain the first vacuum chamber at a gas pressure selected from: ³ 0.01 mBar; ³ 0.05 mBar; ³ 0.1 mBar; ³ 0.2 mBar; ³ 0.3 mBar; ³ 0.4 mBar; ³ 0.5 mBar; ³ 0.6 mBar; ³ 0.7 mBar; ³ 0.8 mBar; ³ 0.9 mBar; ³ 1 mBar; ³ 1.2 mBar; ³ 1.4 mBar; ³ 1.6 mBar; ³ 1.8 mBar; or ³ 2 mBar. The preferred range may be 1-5 mBar.

The first vacuum chamber may have an ion sampling orifice, or other ion inlet aperture, at an upstream end thereof which separates the first vacuum chamber from an atmospheric pressure region in which the ion source may be located. Alternatively, the ion inlet aperture may separate the first vacuum chamber from a higher pressure region at a pressure other than atmospheric pressure and in which the ion source may not be located. The ion sampling orifice, or other ion inlet aperture, may have a diameter of: ³ 0.5 mm; ³ 0.55 mm; ³ 0.6 mm; ³ 0.65 mm; ³ 0.7 mm; ³ 0.75 mm; ³ 0.8 mm; ³ 0.85 mm; ³ 0.9 mm; ³ 0.95 mm; or ³ 1 mm.

The ion guide enables a high gas load in the first vacuum chamber and so a relatively large inlet aperture may be able to be used, enabling an increased ion transmission through the inlet aperture and into the first vacuum chamber.

A central axis of the first axial path of the ion guide may pass through said inlet aperture and/or a central axis of the first axial path of the ion guide may be coaxial with a central axis said inlet aperture.

A central axis of the second axial path of the ion guide may pass through said differential pumping aperture and/or a central axis of the second axial path of the first ion guide may be coaxial with a central axis of said differential pumping aperture.

The first portion of the ion guide may have a larger radial cross-section than the second portion of the ion guide.

The ion guide may be configured such that the first axial path of the first ion guide is substantially parallel to and displaced from the second axial path of the ion guide.

The first and/or second portion of the ion guide may comprise a plurality of electrodes, wherein the plurality of electrodes are axially spaced electrodes and each electrode is an electrode having an aperture through which ions are transmitted in use. However, it is contemplated that other electrodes may be used, such as multipole or plate electrodes.

The transition portion of the ion guide may comprise: at least one first electrode, each of which only partially surrounds the first axial path and has a radial opening in its side that is directed towards the second axial path; at least one second electrode, each of which only partially surrounds the second axial path and has a radial opening in its side that is directed towards the first axial path; and electrodes for providing a potential difference so as to urge ions in the direction from the first axial path to the second axial path.

The spectrometer may comprise one or more RF voltage supply for supplying RF voltages to the electrodes of the first and/or second portions of the ion guide, and/or to the transition portion of the ion guide, for radially confining ions within these portions.

Different phases of an RF voltage may be applied to axially adjacent electrodes in each portion, e.g. opposite phases.

Although the ions have been described as being fragmented by being accelerated between the ion guide and the downstream electrode so as to collide with gas, it is contemplated that additionally, or alternatively, the ions may be fragmented within the ion guide. Accordingly, an aspect of the present invention provides a mass spectrometer comprising: an ion guide comprising a first portion configured to guide ions along a first axial path, a second portion configured to guide ions along a second different axial path, and a transition portion configured to urge ions from the first axial path onto the second axial path; and a voltage supply arranged and configured to apply a potential difference to urge ions along the ion guide, in a fragmentation mode, so as to accelerate the ions; wherein the spectrometer is configured to maintain the gas pressure in the ion guide such that when the voltage supply causes the ions to be accelerated, in the fragmentation mode, the ions collide with gas and fragment to form fragment ions. This aspect may comprise the features described above in relation to the first aspect, except that the ions are accelerated to fragment within the ion guide.

The first aspect of the present invention also provides a method of mass spectrometry comprising:

providing a mass spectrometer as described above;

guiding ions through the first portion of the ion guide along the first axial path, urging ions from the first axial path onto the second axial path, and guiding ions through the second portion of the ion guide to the downstream electrode;

applying said potential difference between the ion guide and the downstream electrode, in the fragmentation mode, so as to accelerate ions therebetween; and

maintaining the gas pressure between the ion guide and the downstream electrode such that the ions accelerated by the potential difference, in the fragmentation mode, are caused to collide with gas and fragment to form fragment ions.

From a second aspect the present invention provides a mass spectrometer comprising:

an ion guide having a plurality of electrodes arranged to guide ions along a longitudinal axis; and

an AC or RF voltage supply connected to said electrodes for applying an AC or RF voltage to the electrodes for radially confining ions within the ion guide to said axis;

wherein the spectrometer is configured to operate the voltage supply in: (i) a low- attenuation mode, in which a relatively high peak-to-peak amplitude AC or RF voltage is applied to the electrodes for providing relatively strong radial confinement of the ions; and (ii) a high-attenuation mode, in which a lower peak-to-peak amplitude AC or RF voltage is applied to the electrodes for providing weaker radial confinement of the ions.

Accordingly, in the high attenuation mode, the ion guide attenuates the ion beam passing therethrough by a relatively high amount, and in the low attenuation mode the ion guide attenuates the ion beam passing therethrough by lower amount (e.g. substantially no attenuation). In the high attenuation mode the ions will be radially confined less well than in the low attenuation mode and hence ions may be lost to the electrodes of the ion guide (or to a vacuum chamber in which the ion guide is housed) at a higher rate.

Substantially all species of ions passing through the ion guide may be attenuated substantially proportionally in the high attenuation mode, relative to the low-attenuation mode.

The attenuation technique described herein may therefore provide a relatively high signal-to-noise ratio at the ion detector of the spectrometer, as compared to other attenuation techniques.

The spectrometer may comprise an ion detector downstream of the ion guide, and may be configured to switch from the low attenuation mode to the high attenuation mode when the detector detects an ion signal above a threshold intensity or threshold ion impact rate; and/or to switch from the high attenuation mode to the low attenuation mode when the detector detects an ion signal below a threshold intensity or threshold ion impact rate.

The spectrometer may comprise a time of flight mass analyser arranged downstream of the ion guide for receiving ions transmitted by the ion guide, or ions derived therefrom.

It has been recognised that it may be desirable to attenuate the ions being transmitted to the time of flight mass analyser, e.g. in order to prevent detector saturation if the ion source is particularly intense. For example, if the analyte is provided to the ion source in a particularly dirty solvent then contaminant ions may be generated in relatively high abundancy and may obscure the analyte ion signal. This has not been problematic in previous instruments, such as those having quadrupole mass analysers, as the quadrupole mass filter therein filters out ions other than those in a narrow range of mass to charge ratios that are desired to be transmitted.

Although two attenuation modes have been described, it is contemplated that three or more attenuation modes may be provided by varying the peak-to-peak amplitude of the AC or RF voltage applied to the electrodes of the ion guide between three or more respective values.

The AC or RF voltages applied to the electrodes of the ion guide may not be varied in peak-to-peak amplitude other than between the attenuation mode, e.g. the peak- to-peak amplitude may not be scanned during the experimental run other than to switch between the attenuation modes.

The ion guide may have any of the features of the ion guide described herein above, or the first ion guide described elsewhere herein. For example, the ion guide may have the following features.

The ion guide may comprise a first portion configured to guide ions along a first axial path, a second portion configured to guide ions along a second different axial path, and a transition portion configured to urge ions from the first axial path onto the second axial path.

The high and low attenuation modes may be effected by changing the peak-to- peak amplitude of the AC or RF voltage applied to the first and/or second and/or transition portions of the ion guide.

The spectrometer may be operated in the fragmentation modes described herein, e.g. in relation to the above aspect of the present invention. Accordingly, a downstream electrode may be arranged downstream of the ion guide and the spectrometer may comprise a voltage supply arranged and configured to apply a potential difference between the ion guide and the downstream electrode, in a fragmentation mode, so as to accelerate ions therebetween; wherein the spectrometer is configured to maintain the gas pressure between the ion guide and downstream electrode such that when the voltage supply causes the ions to be accelerated, in the fragmentation mode, the ions collide with gas and fragment to form fragment ions

The second aspect of the present invention also provides a method of mass spectrometry comprising: providing a spectrometer as described above in relation to the first aspect;

guiding ions along the longitudinal axis of the ion guide; and

operating the voltage supply in: (i) a low-attenuation mode, in which a relatively high peak-to-peak amplitude AC or RF voltage is applied to the electrodes so as to provide relatively strong radial confinement of the ions; and (ii) a high-attenuation mode, in which a lower peak-to-peak amplitude AC or RF voltage is applied to the electrodes so as to provide weaker radial confinement of the ions.

From a third aspect the present invention also provides a mass spectrometer comprising:

an ion guide comprising a plurality of axially spaced electrodes;

a downstream electrode arranged downstream of the ion guide;

a voltage supply arranged and configured to apply a potential difference between the ion guide and the downstream electrode; and

a time of flight mass analyser having a time of flight region and a pusher assembly, and configured to apply a voltage pulse to the pusher assembly so as to pulse ions into the time of flight region;

wherein the spectrometer is configured to operate the voltage supply so as to switch between: (i) an ion trapping mode, in which a potential difference is applied between the ion guide and the downstream electrode for trapping ions therebetween; and (ii) an ejection mode, in which a potential difference is applied between the ion guide and the downstream electrode for pulsing ions from the region therebetween towards the pusher assembly; and

wherein the spectrometer is configured to synchronise the timing that it switches from the ion trapping mode to the ejection mode with the timing at which the voltage pulse is applied to the pusher assembly for accelerating ions into the time of flight region.

This enhances the duty cycle of the spectrometer, since fewer ions reach and pass through the extraction region of the pusher assembly whilst it is not being pulsed.

In the ion trapping mode, the potential applied to the downstream electrode may be higher than the potential applied to the end of the ion guide, so as to trap ions and prevent the passing downstream. In the ejection mode, the potential applied to the end of the ion guide may be higher than the potential applied to the downstream electrode so as to pulse ions towards the pusher assembly. The voltage supply may then switch back to the ion trapping mode so as to trap ions that are subsequently received in the region between the ion guide and the downstream electrode. This cycle may be repeated multiple times during each experimental run, e.g. periodically, and the pulsing of the pusher assembly may be synchronised each of with the ejection modes.

The potential applied to an electrode of the pusher assembly may initially be low, but then raised in a pulsed manner after a delay period from when the ejection mode has started. The duration of the delay period is set such that at least some of the ions pulsed towards the pusher assembly arrive at the pusher assembly at the same time that an electrode of the pusher assembly is pulsed. The spectrometer may be configured to switch between the ion trapping mode and the ejection mode multiple times in a single experimental run.

The voltage supply may be configured to apply a pulsed voltage to an electrode of the ion guide and/or said downstream electrode so as to switch from the trapping mode to the ejection mode and pulse ions towards the pusher assembly.

An electric field-free region may be provided between the downstream electrode and the mass analyser for allowing ions pulsed in the ejection mode to spatially separate as they travel towards the mass analyser.

The spectrometer may comprise an upstream vacuum chamber, a downstream vacuum chamber adjacent the upstream vacuum chamber, and a differential pumping aperture separating these vacuum chambers; wherein the ion guide is located in the upstream vacuum chamber and the downstream electrode is an electrode in which the differential pumping aperture is formed.

The electric fields from the downstream end of the ion guide may focus the ions through the downstream aperture and into the downstream vacuum chamber.

The upstream vacuum chamber may be the second vacuum chamber described herein and the downstream vacuum chamber may be the third vacuum chamber described herein.

The ion guide may be the second ion guide described herein.

The ion guide may comprise a plurality of axially spaced electrodes and one or more voltage supply configured to apply a plurality of different DC potentials to different respective ones of the axially spaced electrodes so as to generate a DC gradient for urging ions through and out of the second ion guide.

The axially spaced electrodes may be connected by a resistor chain, except for the electrodes at the downstream end of the ion guide, and the voltage supply may be arranged and configured to apply a potential difference between the ion guide and the downstream electrode is connected to the electrodes at the downstream end of the ion guide.

Said voltage supply may be configured to increase the DC potential of an electrode at the downstream end of the ion guide and/or decrease the potential applied to the downstream electrode when switching from the trapping mode to the ejection mode. Additionally, or alternatively; said voltage supply may be configured to decrease the DC potential of an electrode at the downstream end of the ion guide and/or increase the potential applied to the downstream electrode when switching from the ejection mode to the trapping mode.

The ion guide is desirably not operated as a resolving RF/DC mass filter, but instead may be operated so as to transmit all ions. However, at a given RF voltage amplitude, such ion guides may still only be capable of transmitting ions above a certain mass to charge ratio, i.e. a low mass cut off. In order to optimise the transmission of all ions, at least during part of an experiment run, the amplitude of the RF radial confinement voltage applied to the second ion guide may be scanned with time. The spectrometer may comprise an AC or RF voltage supply for applying an AC or RF voltage to the electrodes of the ion guide for radially confining ions to an axis therethrough, and may be configured to vary the peak-to-peak amplitude of the AC or RF voltage applied to the electrodes as a function of time.

The AC or RF amplitude may be ramped up or down as a function of time, e.g. in a linear manner.

Although the mass analyser has been described as a Time of Flight mass analyser, it may alternatively be another type of discontinuous mass analyser that is synchronised with the pulsing of ions towards it.

The third aspect the present invention also provides a method of mass

spectrometry comprising:

providing a spectrometer as described above in relation to the third aspect;

applying a potential difference between the ion guide and the downstream electrode;

operating the voltage supply so as to switch between: (i) an ion trapping mode, in which a potential difference is applied between the ion guide and the downstream electrode so as to trap ions therebetween; and (ii) an ejection mode, in which a potential difference is applied between the ion guide and the downstream electrode so as to pulse ions from the region therebetween towards the pusher assembly; and

synchronising the timing of the switch from the ion trapping mode to the ejection mode with the timing at which the voltage pulse is applied to the pusher assembly so that at least some of the ions pulsed towards the pusher assembly in the ejection mode arrive at the pusher assembly at the time the voltage pulse is applied to the pusher assembly such that these ions are accelerated into the time of flight region.

From a fourth aspect the present invention also provides a mass spectrometer comprising:

an upstream vacuum chamber, a downstream vacuum chamber adjacent the upstream vacuum chamber, and a differential pumping aperture separating these vacuum chambers;

a time of flight mass analyser having a time of flight region and a pusher assembly arranged to receive ions and pulse the ions orthogonally into the time of flight region; and ion transfer optics for guiding ions towards and into said pusher assembly, said ion transfer optics having a plurality of axially spaced electrodes that include an electrode in which said differential pumping aperture is located and one or more other electrode downstream of the differential pumping aperture that comprises a slotted aperture through which ions pass in use.

The transfer optics is also referred to elsewhere herein as a transfer lens.

The slotted aperture is elongated and so has a maximum size in a first dimension and a greater maximum size in a second orthogonal dimension. The slotted aperture is completely surrounded by the electrode that it is located within.

The slotted aperture may be rectangular, substantially rectangular but with curved edges at its longitudinal ends, or ovoid. The one or more electrode having the slotted aperture may be arranged downstream of the differential pumping aperture of the transfer optics.

Said differential pumping aperture may have a circular cross-sectional shape.

The pusher assembly may be configured to pulse the ions in a first dimension into the time of flight region; and the slotted aperture may be configured so as to cause an ion beam passing therethrough to attain a maximum size in the first dimension that is smaller than a maximum size in a second orthogonal dimension, wherein the first and second dimensions are orthogonal to the longitudinal axis of the ion beam passing through the slotted aperture.

This ensures that the ions enter the pusher assembly relatively well confined in the first dimension and relatively spread out in the second dimension. It is desired that the ion beam enters the pusher assembly having a relatively small size (and velocity spread) parallel to the axis in which the ions are accelerated into the time of flight region (i.e. the first dimension), so as to provide high mass resolution, and spreading the ion beam in the second dimension as described above enables this, e.g. without space-charge effects becoming problematic.

Conventionally, separate electrodes have been provided either side of the ion beam axis for restricting the size of the ion beam in the direction parallel to the axis in which the ions are accelerated into the time of flight region, i.e. the first dimension.

However, such electrodes do not control the size of the ion beam in its radially orthogonal dimension, i.e. the second dimension. The slotted aperture(s) in the embodiments of the present invention allow control of the ion beam in both orthogonal dimensions.

Furthermore, the slotted electrode(s) enables the size of the ion beam to be controlled in multiple dimensions using a single electrode and therefore reduces complexity and may improve mechanical alignment and tolerance.

The pusher assembly may comprise an entrance plate having a slotted entrance aperture therein, wherein this slotted aperture has substantially the same shape and/or orientation as the slotted aperture in said one or more electrode of the transfer optics.

The entrance plate may be maintained at ground potential; and/or may be electrically and/or mechanically connected to a downstream end electrode of the transfer optics.

The transfer optics may comprise axially spaced electrodes arranged upstream and/or downstream of its differential pumping aperture.

The transfer optics may comprise at least one acceleration electrode arranged upstream of its differential pumping aperture, wherein the spectrometer further comprise an upstream electrode arranged upstream of the transfer optics, and wherein the spectrometer is configured to maintain the at least one acceleration electrode at a potential that is lower than the potential of the upstream electrode such that ions are accelerated by the acceleration electrode.

The upstream vacuum chamber may include a second differential pumping aperture at its downstream end, wherein this second differential pumping aperture is in said upstream electrode. Each of the at least one acceleration electrode may have an aperture through which the ions pass, wherein the aperture is circular.

The aperture(s) may have a diameter that is greater than the diameter of the differential pumping aperture in the transfer optics.

The differential pumping aperture of the transfer optics may have an axial length therethrough that is selected from: ³ 5 mm; ³ 6 mm; ³ 7 mm; ³ 8 mm; ³ 9 mm; ³ 10 mm; ³ 11 mm; ³ 12 mm; ³ 13 mm; ³ 14 mm; or ³ 15 mm; and/or wherein the axial length of the differential pumping aperture in the transfer optics is selected from: £ 15 mm; £ 14 mm; £ 13 mm; £ 12 mm; £ 11 mm; or £ 10 mm.

A relatively long differential pumping aperture provides a relatively low fluid conductance through the aperture, since an aperture of a given diameter will have a lower fluid conductance the longer the axial path through it is. The lower fluid conductance through the differential pumping aperture helps maintain the upstream and downstream vacuum chambers at their pressure differential. However, if the axial length of the differential pumping aperture is too long then field-free regions may occur within the differential pumping aperture, which may result in ions being lost if they have a significant component of velocity orthogonal to the axis of the aperture, e.g. by being scattered by the background gas molecules.

The axial length of the differential pumping aperture in the transfer optics may be in the range between 8 to 13 mm; 9 to 12 mm; or 10-11 mm.

The above lengths are significantly longer than the length of a conventional differential pumping aperture.

The differential pumping aperture may be formed in a planar/sheet portion of an electrode of the transfer optics.

The electrode forming the differential pumping aperture of the transfer optics may be maintained at a higher potential than the one or more acceleration electrode.

The electrode forming the differential pumping aperture of the transfer optics may be grounded. This, along with the diameter and length of the aperture, may reduce the transmission of electric fields between the third and fourth vacuum chambers.

The transfer optics, at each of one or more axial location, may comprise two separate electrodes between which the ions pass in use, and the spectrometer may be configured to apply a potential difference between these separate electrodes so as to steer the ion beam passing therethrough.

For example, this steering may be used to optimise the transmission of the ions into the aperture in the entrance plate to the pusher assembly. A relatively small, potential difference may be applied between the electrodes such as, for example, £ 5V.

The separate electrodes may have radially inner edges that are substantially parallel to each other.

The radially inner edges may be arranged in the same orientation as the longitudinal edges of the slots in the slotted electrode(s) of the transfer optics and/or entrance plate of the pusher assembly. A first electrode (or a first electrode portion) of the transfer optics downstream of its differential pumping aperture electrode may be maintained at the same potential as the electrode (portion) in which the differential pumping aperture is provided, e.g. at ground potential.

The transfer optics may comprise a second electrode downstream of the first electrode (or first electrode portion), which may be maintained at a higher potential than the first electrode (or first electrode portion). The transfer optics may comprise a third electrode downstream of the second electrode, which may be maintained at a lower potential than the second electrode, and optionally at a lower potential than the differential pumping aperture electrode of the transfer optics. The transfer optics may comprise a fourth electrode downstream of the third electrode, which may be maintained at the same potential as the differential pumping aperture electrode. This enables the ion beam to be conditioned for TOF mass analysis.

The transfer optics may comprise an elongated tubular electrode through which the ions travel in use.

The tubular electrode may have a length selected from: ³ 2 cm; ³ 3 cm; ³ 4 cm; ³

5 cm; ³ 6 cm; ³ 7cm; ³ 8 cm; ³ 9 cm; or ³ 10 cm.

The spectrometer may be configured to maintain the tubular electrode at ground potential.

The tubular electrode may be at a downstream end of the transfer optics.

The tubular electrode may have an apertured plate portion at its upstream end and/or downstream end, optionally wherein the aperture in the apertured plate is slotted.

The tubular electrode may be electrically and/or mechanically connected to a grounded chassis of the spectrometer.

As such, no power supply to the tubular portion is required, reducing cost and complexity of the instrument.

The time of flight mass analyser may be arranged in the downstream vacuum chamber.

The upstream and downstream vacuum chambers may be the third and fourth vacuum chambers described herein.

It is contemplated that the mass analyser may be an ion analyser other than a TOF mass analyser. Alternatively, or additionally, it is contemplated that the transfer optics need not necessarily have one or more electrode with a slotted aperture.

From a fifth aspect, the present invention provides a mass spectrometer comprising:

a mass analyser or ion mobility analyser; and

ion transfer optics for guiding ions towards and into said mass analyser or ion mobility analyser, said ion transfer optics having a plurality of axially spaced electrodes that include an electrode in which said differential pumping aperture is located, wherein the differential pumping aperture of the transfer optics has an axial length therethrough that is selected from: ³ 5 mm; ³ 6 mm; ³ 7 mm; ³ 8 mm; ³ 9 mm; ³ 10 mm; ³ 11 mm; ³ 12 mm; ³ 13 mm; ³ 14 mm; or ³ 15 mm.

The transfer optics of this aspect may have any of the features described hereinabove in relation to the fourth aspect.

For example, the differential pumping aperture of the transfer optics may have an axial length therethrough that is selected from: £ 15 mm; £ 14 mm; £ 13 mm; £ 12 mm; £ 11 mm; or £ 10 mm.

The mass analyser may be a TOF mass analyser.

From a sixth aspect the present invention provides a mass spectrometer comprising:

a mass analyser or ion mobility analyser; and

ion transfer optics for guiding ions towards and into said mass analyser or ion mobility analyser, said ion transfer optics having a plurality of axially spaced electrodes that include an electrode in which said differential pumping aperture is located and a tubular electrode having a length x arranged downstream of the differential pumping aperture, wherein x is selected from: ³ 2 cm; ³ 3 cm; ³ 4 cm; ³ 5 cm; ³ 6 cm; ³ 7cm; ³ 8 cm; ³ 9 cm; or ³ 10 cm.

The transfer optics of this aspect may have any of the features described hereinabove in relation to the fourth and fifth aspects.

The tubular electrode may be at a downstream end of the transfer optics.

From another aspect, the present invention provides a mass spectrometer comprising:

a mass analyser or ion mobility analyser; and

ion transfer optics for guiding ions towards and into said mass analyser or ion mobility analyser, said ion transfer optics having a plurality of axially spaced electrodes that include an electrode which is electrically grounded for preventing electric fields from being transmitted through the ion transfer optics. The present invention also provides a method of mass spectrometry comprising: providing a spectrometer as described herein in relation to the fourth, fifth, or sixth aspects, or said another aspect; and

guiding ions through said transfer optics into said mass analyser or ion mobility analyser.

From a seventh aspect, the present invention provides a mass spectrometer comprising:

a vacuum housing having an opening through a wall thereof;

a plurality of electrodes arranged inside the vacuum housing; and

a printed circuit board (PCB) mounted to the vacuum housing over the opening and in a gas-tight manner for maintaining a vacuum within the vacuum housing;

wherein the PCB has an inner surface facing towards the vacuum housing that is electrically connected to said one or more electrodes, and an outer surface facing away from the vacuum housing having one or more electrical connections thereon that are in electrical communication with said one or more electrodes.

The spectrometer may further comprise an AC or RF and/or DC voltage supply and/or voltage controller arranged outside of said vacuum housing and electrically connected to said one or more electrical connections on the outer surface of the PCB.

Said one or more electrical connections on the outer surface of the PCB may be provided in an electrical socket or plug; and wherein the voltage supply and/or voltage controller may be connectable, or connected, to the electrical socket or plug via a complementary electrical plug or socket, respectively.

The plug and socket may be configured to be repeatedly connectable and disconnectable so as to form and disconnect an electrical connection therebetween.

The voltage supply and/or voltage controller may be housed in a module having said electrical plug or socket mounted to a casing of the module.

This allows the module to be arranged closer to the PCB and hence reduces the length of electric cables therebetween, and RF pickup or interference associated therewith.

The plurality of electrodes may be ion optics, such as one or more ion guide or transfer optics.

The PCB may have a central portion covering the opening in the vacuum housing and a peripheral portion arranged over the vacuum housing wall, wherein fixing members are arranged through the peripheral portion of the PCB and secured into the vacuum housing wall so as to hold the PCB against the vacuum housing wall.

A resilient seal may be provided at the interface between the PCB and the vacuum housing wall.

The thickness of the vacuum housing wall may be stepped so that the wall is relatively thin around the opening, in the region on which the peripheral portion of the PCB is located, and is thicker laterally adjacent to and outwards of the peripheral portion of the PCB. The peripheral portion of the PCB may therefore be embedded in the vacuum housing wall. This embedded configuration of the PCB may help maintain the vacuum seal.

The PCB may have had one or more of its layers removed, at least in its peripheral region that contacts the wall of the vacuum housing, for allowing better surface contact between the PCB and vacuum housing wall; or the PCB may have fewer layers in its peripheral region that contacts the wall of the vacuum housing than in its central region arranged directly over said opening in the vacuum housing wall.

For example, the outer resistive layer of the PCB may have been removed, at least in the peripheral region of the PCB.

The vacuum housing may comprise a Time of Flight mass analyser.

The PCB may be sized and configured to withstand a pressure differential across it of: ³ 1 x 10⁴ mbar, ³ 5 x 10⁴ mbar, ³ 1 x 10⁵ mbar, ³ 5 x 10⁵ mbar, ³ 1 x 10⁶ mbar, ³ 5 x 10⁶ mbar, ³ 1 x 10⁷ mbar, ³ 5 x 10⁷ mbar, ³ 1 x 10⁸ mbar, ³ 5 x 10⁸ mbar, ³ 1 x 10⁹ mbar,

³ 5 x 10⁹ mbar, ³ 1 x 10¹⁰ mbar, ³ 5 x 10¹⁰ mbar, ³ 1 x 10¹¹ mbar, ³ 5 x 10¹¹ mbar, ³ 1 x 10¹² mbar, or ³ 5 x 10¹² mbar.

The vacuum housing may have a plurality of openings through said wall thereof and a respective plurality of PCBs mounted to the vacuum housing over the openings in a gas-tight manner for maintaining a vacuum within the vacuum housing, wherein each PCB has an inner surface facing towards the vacuum housing that is electrically connected to said one or more electrodes, and an outer surface facing away from the vacuum housing having one or more electrical connections thereon that are in electrical communication with said one or more electrodes.

The use of multiple PCBs enables each PCB, and each corresponding vacuum housing wall aperture, to be made relatively small. This enables the PCBs to withstand the pressure differential across them without being damaged. However, it is contemplated that all of the ion optics may be connected to a single PCB.

The first ion guide and/or second ion guide and/or transfer optics described herein may be connected to one PCB or different respective ones of the PCBs.

The vacuum housing may define an upstream vacuum chamber configured to be maintained at a relatively high pressure and a downstream vacuum chamber configured to be maintained at a relatively low pressure, wherein a first of the PCBs is located in a wall of the upstream vacuum chamber and a second of the PCBS is located in a downstream vacuum chamber.

The cross-sectional area of the opening in the wall of the upstream vacuum chamber may be greater than the cross-sectional area of the opening in the wall of the downstream vacuum chamber and/or wherein the first PCB is larger than the second PCB.

The second PCB may be configured to be able to withstand a greater pressure differential across it than the first PCB.

The seventh aspect of the present invention also provides a method of mass spectrometry comprising: providing a spectrometer as described in relation to the seventh aspect;

pumping the region inside the vacuum housing down to a pressure below atmospheric pressure; and

supplying a voltage or electrical signal to the one or more electrical connections on the outer surface of the PCB such that the voltage or signal is transmitted to one or more of the plurality of electrodes arranged inside the vacuum housing.

According to various embodiments a relatively small footprint or compact Time of Flight (“TOF”) mass spectrometer (“MS”) or analytical instrument is provided which has a relatively high resolution. The mass spectrometer may have particular application in the biopharmaceutical industry and in the field of general analytical Electrospray Ionisation (“ESI”) and subsequent mass analysis. The mass spectrometer according to various embodiments is a high performance instrument wherein manufacturing costs have been reduced without compromising performance.

The instrument according to various embodiments is particularly user friendly compared with the majority of other conventional instruments. The instrument may have single button which can be activated by a user in order to turn the instrument ON and at the same time initiate an instrument self-setup routine. The instrument may, in particular, have a health diagnostics system which is both helpful for users whilst providing improved diagnosis and fault resolution.

According to various embodiments the instrument may have a health diagnostics or health check which is arranged to bring the overall instrument, and in particular the mass spectrometer and mass analyser, into a state of readiness after a period of inactivity or power saving. The same health diagnostic system may also be utilised to bring the instrument into a state of readiness after maintenance or after the instrument switches from a maintenance mode of operation into an operational state. Furthermore, the health diagnostics system may also be used to monitor the instrument, mass spectrometer or mass analyser on a periodic basis in order to ensure that the instrument in operating within defined operational parameters and hence the integrity of mass spectral or other data obtained is not compromised.

The health check system may determine various actions which either should automatically be performed or which are presented to a user to decide whether or not to proceed with. For example, the health check system may determine that no corrective action or other measure is required i.e. that the instrument is operating as expected within defined operational limits. The health check system may also determine that an automatic operation should be performed in order, for example, to correct or adjust the instrument in response to a detected error warning, error status or anomaly. The health check system may also inform the user that the user should either take a certain course of action or to give approval for the control system to take a certain course of action. Various embodiments are also contemplated wherein the health check system make seek negative approval i.e. the health check system may inform a user that a certain course of action will be taken, optionally after a defined time delay, unless the user instructs otherwise or cancels the proposed action suggested by the control system. Embodiments are also contemplated wherein the level of detail provided to a user may vary dependent upon the level of experience of the user. For example, the health check system may provide either very detailed instructions or simplified instructions to a relatively unskilled user.

The health check system may provide a different level of detail to a highly skilled user such as a service engineer. In particular, additional data and/or instructions may be provided to a service engineer which may not be provided to a regular user. It is also contemplated that instructions given to a regular user may include icons and/or moving graphical images. For example, a user may be guided by the health check system in order to correct a fault and once it is determined that a user has completed a step then the control system may change the icon and/or moving graphical images which are displayed to the user in order to continue to guide the user through the process.

The instrument according to various embodiments has been designed to be as small as possible whilst also being generally compatible with existing UPLC systems. The instrument is easy to operate and has been designed to have a high level of reliability. Furthermore, the instrument has been designed so as to simplify diagnostic and servicing thereby minimising instrument downtime and operational costs.

According to various embodiments the instrument has particular utility in the health services market and may be integrated with Desorption Electrospray Ionisation (“DESI”) and Rapid Evaporative Ionisation Mass Spectrometry (“REIMS”) ion sources in order to deliver commercially available In Vitro Diagnostic Medical Device (“IVD”)/Medical Device (“MD”) solutions for targeted applications.

The mass spectrometer may, for example, be used for microbe identification purposes, histopathology, tissue imaging and surgical (theatre) applications.

The mass spectrometer has a significantly enhanced user experience compared with conventional mass spectrometers and has a high degree of robustness. The instrument is particularly easy to use (especially for non-expert users) and has a high level of accessibility.

The mass spectrometer has been designed to integrate easily with liquid chromatography (“LC”) separation systems so that a LC-TOF MS instrument may be provided. The instrument is particularly suited for routine characterisation and monitoring applications in the biopharmaceutical industry. The instrument enables non-expert users to collect high resolution accurate mass data and to derive meaningful information from the data quickly and easily. This results in improved understanding of products and processes with the potential to shorten time to market and reduce costs.

The instrument may be used in biopharmaceutical last stage development and quality control (“QC”) applications. The instrument also has particular application in small molecule pharmaceutical, food and environmental (“F&E”) and chemical materials analyses.

The instrument has enhanced mass detection capabilities i.e. high mass resolution, accurate mass and an extended mass range. The instrument also has the ability to fragment parent ions into daughter or fragment ions so that MS/MS type experiments may be performed.

BRIEF DESCRIPTION OF THE DRAWINGS

Various embodiments together with other arrangements given for illustrative purposes only will now be described, by way of example only, and with reference to the accompanying drawings in which:

Fig. 1 shows a perspective view of a bench-top Time of Flight mass spectrometer according to various embodiments coupled to a conventional bench-top liquid

chromatography (“LC”) separation system;

Fig. 2A shows a front view of a bench-top mass spectrometer according to various embodiments showing three solvent bottles loaded into the instrument and a front display panel, Fig. 2B shows a perspective view of a mass spectrometer according to various embodiments and Fig. 2C illustrates in more detail various icons which may be displayed on the front display panel in order to highlight the status of the instrument to a user and to indicate if a potential fault has been detected;

Fig. 3 shows a schematic representation of mass spectrometer according to various embodiments, wherein the instrument comprises an Electrospray Ionisation (“ESI”) or other ion source, a conjoined ring ion guide, a segmented quadrupole rod set ion guide, one or more transfer lenses and a Time of Flight mass analyser comprising a pusher electrode, a reflectron and an ion detector;

Fig. 4 shows a known Atmospheric Pressure Ionisation (“API”) ion source which may be used with the mass spectrometer according to various embodiments;

Fig. 5 shows a first known ion inlet assembly which shares features with an ion inlet assembly according to various embodiments;

Fig. 6A shows an exploded view of the first known ion inlet assembly, Fig 6B shows a second different known ion inlet assembly having an isolation valve, Fig. 6C shows an exploded view of an ion inlet assembly according to various embodiments, Fig. 6D shows the arrangement of an ion block attached to a pumping block upstream of a vacuum chamber housing a first ion guide according to various embodiments, Fig. 6E shows in more detail a fixed valve assembly which is retained within an ion block according to various embodiments, Fig. 6F shows the removal by a user of a cone assembly attached to a clamp to expose a fixed valve having a gas flow restriction aperture which is sufficient to maintain the low pressure within a downstream vacuum chamber when the cone is removed and Fig. 6G illustrates how the fixed valve may be retained in position by suction pressure according to various embodiments;

Fig. 7A shows a pumping arrangement according to various embodiments, Fig. 7B shows further details of a gas handling system which may be implemented, Fig. 7C shows a flow diagram illustrating the steps which may be performed following a user request to the turn the Atmospheric Pressure Ionisation (“API”) gas ON and Fig. 7D shows a flow chart illustrating a source pressure test which may be performed according to various embodiments;

Fig. 8 shows in more detail a mass spectrometer according to various

embodiments;

Fig. 9 shows a Time of Flight mass analyser assembly comprising a pusher plate assembly having mounted thereto a pusher electronics module and an ion detector module and wherein a reflectron assembly is suspended from an extruded flight tube which in turn is suspended from the pusher plate assembly;

Fig. 10A shows in more detail a pusher plate assembly, Fig. 10B shows a monolithic pusher plate assembly according to various embodiments and Fig. 10C shows a pusher plate assembly with a pusher electrode assembly or module and an ion detector assembly or module mounted thereto;

Fig. 11 shows a flow diagram illustrating various processes which occur upon a user pressing a start button on the front panel of the instrument according to various embodiments;

Fig. 12A shows in greater detail three separate pumping ports of a turbo molecular pump according to various embodiments and Fig. 12B shows in greater detail two of the three pumping ports which are arranged to pump separate vacuum chambers;

Fig. 13 shows in more detail a transfer lens arrangement;

Fig. 14A shows details of a known internal vacuum configuration and Fig. 14B shows details of a new internal vacuum configuration according to various embodiments;

Fig. 15A shows a schematic of an arrangement of ring electrodes and conjoined ring electrodes forming a first ion guide which is arranged to separate charged ions from undesired neutral particles, Fig. 15B shows a resistor chain which may be used to produce a linear axial DC electric field along the length of a first portion of the first ion guide and Fig. 15C shows a resistor chain which may be used to produce a linear axial DC electric field along the length of a second portion of the first ion guide;

Fig. 16A shows in more detail a segmented quadrupole rod set ion guide according to various embodiments which may be provided downstream of the first ion guide and which comprises a plurality of rod electrodes, Fig. 16B illustrates how a voltage pulse applied to a pusher electrode of a Time of Flight mass analyser may be

synchronised with trapping and releasing ions from the end region of the segmented quadrupole rod set ion guide, Fig. 16C illustrates in more detail the pusher electrode geometry and shows the arrangement of grid and ring lenses or electrodes and their relative spacing, Fig. 16D illustrates in more detail the overall geometry of the Time of Flight mass analyser including the relative spacings of elements of the pusher electrode and associated electrodes, the reflectron grid electrodes and the ion detector, Fig. 16E is a schematic illustrating the wiring arrangement according to various embodiments of the pusher electrode and associated grid and ring electrodes and the grid and ring electrodes forming the reflectron, Fig. 16F illustrates the relative voltages and absolute voltage ranges at which the various ion optical components such as the Electrospray capillary probe, differential pumping apertures, transfer lens electrodes, pusher electrodes, reflectron electrodes and the detector are maintained according to various embodiments, Fig. 16G is a schematic of an ion detector arrangement according to various embodiments and which shows various connections to the ion detector which are located both within and external to the Time of Flight housing and Fig. 16H shows an illustrative potential energy diagram;

Fig. 17A schematically illustrates the vacuum chambers of the mass spectrometer in the preferred embodiments; Fig. 17B shows a cross-sectional view through parts of the spectrometer shown in Fig. 8 and illustrates the ion optics in more detail; Fig. 17C shows a cross-sectional view through the embodiment at a point where a printed circuit board is located; and Fig. 17D shows voltage controller modules connected to the printed circuit boards;

Fig. 18A shows a schematic of a first ion guide according to an embodiment of the present invention, and Fig. 18B shows cross-sectional views through the ion guide at different locations; and

Fig. 19 shows an embodiment in which the amplitude of the RF radial confinement voltage applied to the second ion guide is scanned with time during an experimental run.

DETAILED DESCRIPTION

Various aspects of a newly developed mass spectrometer are disclosed. The mass spectrometer comprises a modified and improved ion inlet assembly, a modified first ion guide, a modified quadrupole rod set ion guide, improved transfer optics, a novel cantilevered time of flight arrangement, a modified reflectron arrangement together with advanced electronics and an improved user interface.

The mass spectrometer has been designed to have a high level of performance, to be highly reliable, to offer a significantly improved user experience compared with the majority of conventional mass spectrometers, to have a very high level of EMC

compliance and to have advanced safety features.

The instrument comprises a highly accurate mass analyser and overall the instrument is small and compact with a high degree of robustness. The instrument has been designed to reduce manufacturing cost without compromising performance at the same time making the instrument more reliable and easier to service. The instrument is particularly easy to use, easy to maintain and easy to service. The instrument constitutes a next-generation bench-top Time of Flight mass spectrometer.

Fig. 1 shows a bench-top mass spectrometer 100 according to various

embodiments which is shown coupled to a conventional bench-top liquid chromatography separation device 101. The mass spectrometer 100 has been designed with ease of use in mind. In particular, a simplified user interface and front display is provided and instrument serviceability has been significantly improved and optimised relative to conventional instruments. The mass spectrometer 100 has an improved mechanical design with a reduced part count and benefits from a simplified manufacturing process thereby leading to a reduced cost design, improved reliability and simplified service procedures. The mass spectrometer has been designed to be highly electromagnetic compatible (“EMC”) and exhibits very low electromagnetic interference (“EMI”).

Fig. 2A shows a front view of the mass spectrometer 100 according to various embodiments and Fig. 2B shows a perspective view of the mass spectrometer according to various embodiments. Three solvent bottles 201 may be coupled, plugged in or otherwise connected or inserted into the mass spectrometer 100. The solvent bottles 201 may be back lit in order to highlight the fill status of the solvent bottles 201 to a user.

One problem with a known mass spectrometer having a plurality of solvent bottles is that a user may connect a solvent bottle in a wrong location or position. Furthermore, a user may mount a solvent bottle but conventional mounting mechanisms will not ensure that a label on the front of the solvent bottle will be positioned so that it can be viewed by a user i.e. conventional instruments may allow a solvent bottle to be connected where a front facing label ends up facing away from the user. Accordingly, one problem with conventional instruments is that a user may not be able to read a label on a solvent bottle due to the fact that the solvent bottle ends up being positioned with the label of the solvent bottle facing away from the user. According to various embodiments conventional screw mounts which are conventionally used to mount solvent bottles have been replaced with a resilient spring mounting mechanism which allows the solvent bottles 201 to be connected without rotation.

According to various embodiments the solvent bottles 201 may be illuminated by a LED light tile in order to indicate the fill level of the solvent bottles 201 to a user. It will be understood that a single LED illuminating a bottle will be insufficient since the fluid in a solvent bottle 201 can attenuate the light from the LED. Furthermore, there is no good single position for locating a single LED.

The mass spectrometer 100 may have a display panel 202 upon which various icons may be displayed when illuminated by the instrument control system.

A start button 203 may be positioned on or adjacent the front display panel 202. A user may press the start button 203 which will then initiate a power-up sequence or routine. The power-up sequence or routine may comprise powering-up all instrument modules and initiating instrument pump-down i.e. generating a low pressure in each of the vacuum chambers within the body of the mass spectrometer 100.

According to various embodiments the power-up sequence or routine may or may not include running a source pressure test and switching the instrument into an Operate mode of operation.

According to various embodiments a user may hold the start button 203 for a period of time, e.g. 5 seconds, in order to initiate a power-down sequence.

If the instrument is in a maintenance mode of operation then pressing the start button 203 on the front panel of the instrument may initiate a power-up sequence.

Furthermore, when the instrument is in a maintenance mode of operation then holding the start button 203 on the front panel of the instrument for a period of time, e.g. 5 seconds, may initiate a power-down sequence. Fig. 2C illustrates in greater detail various icons which may be displayed on the display panel 202 and which may illuminated under the control of instrument hardware and/or software. According to various embodiments one side of the display panel 202 (e.g. the left-hand side) may have various icons which generally relate to the status of the instrument or mass spectrometer 100. For example, icons may be displayed in the colour green to indicate that the instrument is in an initialisation mode of operation, a ready mode of operation or a running mode of operation.

In the event of a detected error which may require user interaction or user input a yellow or amber warning message may be displayed. A yellow or amber warning message or icon may be displayed on the display panel 202 and may convey only relatively general information to a user e.g. indicating that there is a potential fault and a general indication of what component or aspect of the instrument may be at fault.

According to various embodiments it may be necessary for a user to refer to an associated computer display or monitor in order to get fuller details or gain a fuller appreciation of the nature of the fault and to receive details of potential corrective action which is recommended to perform in order to correct the fault or to place the instrument in a desired operational state.

A user may be invited to confirm that a corrective action should be performed and/or a user may be informed that a certain corrective action is being performed.

In the event of a detected error which cannot be readily corrected by a user and which instead requires the services of a skilled service engineer then a warning message may be displayed indicating that a service engineer needs to be called. A warning message indicating the need for a service engineer may be displayed in the colour red and a spanner or other icon may also be displayed or illuminated to indicate to a user that an engineer is required.

The display panel 202 may also display a message that the power button 203 should be pressed in order to turn the instrument OFF.

According to an embodiment one side of the display panel 202 (e.g. the right-hand side) may have various icons which indicate different components or modules of the instrument where an error or fault has been detected. For example, a yellow or amber icon may be displayed or illuminated in order to indicate an error or fault with the ion source, a fault in the inlet cone region, a fault with the fluidic systems, an electronics fault, a fault with one or more of the solvent or other bottles 201 (i.e. indicating that one or more solvent bottles 201 needing to be refilled or emptied), a vacuum pressure fault associated with one or more of the vacuum chambers, an instrument setup error, a communication error, a problem with a gas supply or a problem with an exhaust.

It will be understood that the display panel 202 may merely indicate the general status of the instrument and/or the general nature of a fault. In order to be able to resolve the fault or to understand the exact nature of an error or fault a user may need to refer to the display screen of an associated computer or other device. For example, as will be understood by those skilled in the art an associated computer or other device may be arranged to receive and process mass spectral and other data output from the instrument or mass spectrometer 100 and may display mass spectral data or images on a computer display screen for the benefit of a user.

According to various embodiments the status display may indicate whether the instrument is in one of the following states namely Running, Ready, Getting Ready, Ready Blocked or Error.

The status display may display health check indicators such as Service Required, Cone, Source, Set-up, Vacuum, Communications, Fluidics, Gas, Exhaust, Electronics, Lock-mass, Calibrant and Wash.

A“Hold power button for OFF” LED tile is shown in Fig. 2C and may remain illuminated when the power button 203 is pressed and may remain illuminated until the power button 203 is released or until a period of time (e.g. 5 seconds) has elapsed whichever is sooner. If the power button 203 is released before the set period of time (e.g. less than 5 seconds after it is pressed) then the“Hold power button for OFF” LED tile may fade out over a time period of e.g. 2 s.

The initialising LED tile may be illuminated when the instrument is started via the power button 203 and may remain ON until software assumes control of the status panel or until a power-up sequence or routine times out.

According to various embodiments an instrument health check may be performed and printer style error correction instructions may be provided to a user via a display screen of a computer monitor (which may be separate to the front display panel 202) in order to help guide a user through any steps that the user may need to perform.

The instrument may attempt to self-diagnose any error messages or warning status alert(s) and may attempt to rectify any problem(s) either with or without notifying the user.

Depending upon the severity of any problem the instrument control system may either attempt to correct the problem(s) itself, request the user to carry out some form of intervention in order to attempt to correct the issue or problem(s) or may inform the user that the instrument requires a service engineer.

In the event where corrective action may be taken by a user then the instrument may display instructions for the user to follow and may provide details of methods or steps that should be performed which may allow the user to fix or otherwise resolve the problem or error. A resolve button may be provided on a display screen which may be pressed by a user having followed the suggested resolution instructions. The instrument may then run a test again and/or may check if the issue has indeed been corrected. For example, if a user were to trigger an interlock then once the interlock is closed a pressure test routine may be initialised as detailed below.

Fig. 3 shows a high level schematic of the mass spectrometer 100 according to various embodiments wherein the instrument may comprise an ion source 300, such as an Electrospray Ionisation (“ESI”) ion source. However, it should be understood that the use of an Electrospray Ionisation ion source 300 is not essential and that according to other embodiments a different type of ion source may be used. For example, according to various embodiments a Desorption Electrospray Ionisation (“DESI”) ion source may be used. According to yet further embodiments a Rapid Evaporative Ionisation Mass Spectrometry (“REIMS”) ion source may be used.

If an Electrospray ion source 300 is provided then the ion source 300 may comprise an Electrospray probe and associated power supply.

The initial stage of the associated mass spectrometer 100 comprises an ion block 802 (as shown in Fig. 6C) and a source enclosure may be provided if an Electrospray Ionisation ion source 300 is provided.

If a Desorption Electrospray Ionisation (“DESI”) ion source is provided then the ion source may comprise a DESI source, a DESI sprayer and an associated DESI power supply. The initial stage of the associated mass spectrometer may comprise an ion block 802 as shown in more detail in Fig. 6C. However, according to various embodiments if a DESI source is provided then the ion block 802 may not enclosed by a source enclosure.

It will be understood that a REIMS source involves the transfer of analyte, smoke, fumes, liquid, gas, surgical smoke, aerosol or vapour produced from a sample which may comprise a tissue sample. In some embodiments, the REIMS source may be arranged and adapted to aspirate the analyte, smoke, fumes, liquid, gas, surgical smoke, aerosol or vapour in a substantially pulsed manner. The REIMS source may be arranged and adapted to aspirate the analyte, smoke, fumes, liquid, gas, surgical smoke, aerosol or vapour substantially only when an electrosurgical cutting applied voltage or potential is supplied to one or more electrodes, one or more electrosurgical tips or one or more laser or other cutting devices.

The mass spectrometer 100 may be arranged so as to be capable of obtaining ion images of a sample. For example, according to various embodiments mass spectral and/or other physico-chemical data may be obtained as a function of position across a portion of a sample. Accordingly, a determination can be made as to how the nature of the sample may vary as a function of position along, across or within the sample.

The mass spectrometer 100 may comprise a first ion guide 301 such as a

StepWave (RTM) ion guide 301 having a plurality of ring and conjoined ring electrodes. The mass spectrometer 100 may further comprise a segmented quadrupole rod set ion guide 302, one or more transfer lenses 303 and a Time of Flight mass analyser 304. The quadrupole rod set ion guide 302 may be operated in an ion guiding mode of operation and/or in a mass filtering mode of operation. The Time of Flight mass analyser 304 may comprise a linear acceleration Time of Flight region or an orthogonal acceleration Time of Flight mass analyser.

If the Time of Flight mass analyser comprises an orthogonal acceleration Time of Flight mass analyser 304 then the mass analyser 304 may comprise a pusher electrode 305, a reflectron 306 and an ion detector 307. The ion detector 307 may be arranged to detect ions which have been reflected by the reflectron 306. It should be understood, however, that the provision of a reflectron 306 though desirable is not essential.

According to various embodiments the first ion guide 301 may be provided downstream of an atmospheric pressure interface. The atmospheric pressure interface may comprises an ion inlet assembly. The first ion guide 301 may be located in a first vacuum chamber or first differential pumping region.

The first ion guide 301 may comprise a part ring, part conjoined ring ion guide assembly wherein ions may be transferred in a generally radial direction from a first ion path formed within a first plurality of ring or conjoined ring electrodes into a second ion path formed by a second plurality of ring or conjoined ring electrodes. The first and second plurality of ring electrodes may be conjoined along at least a portion of their length. Ions may be radially confined within the first and second plurality of ring electrodes.

The second ion path may be aligned with a differential pumping aperture which may lead into a second vacuum chamber or second differential pumping region.

The first ion guide 301 may be utilised to separate charged analyte ions from unwanted neutral particles. The unwanted neutral particles may be arranged to flow towards an exhaust port whereas analyte ions are directed on to a different flow path and are arranged to be optimally transmitted through a differential pumping aperture into an adjacent downstream vacuum chamber.

It is also contemplated that according to various embodiments ions may in a mode of operation be fragmented within the first ion guide 301. In particular, the mass spectrometer 100 may be operated in a mode of operation wherein the gas pressure in the vacuum chamber housing the first ion guide 301 is maintained such that when a voltage supply causes ions to be accelerated into or along the first ion guide 301 then the ions may be arranged to collide with background gas in the vacuum chamber and to fragment to form fragment, daughter or product ions. According to various embodiments a static DC voltage gradient may be maintained along at least a portion of the first ion guide 301 in order to urge ions along and through the first ion guide 301 and optionally to cause ions in a mode of operation to fragment. The ions may fragment in the ion guide or downstream of the ion guide.

However, it should be understood that it is not essential that the mass

spectrometer 100 is arranged so as to be capable of performing ion fragmentation in the first ion guide 301 in a mode of operation.

The mass spectrometer 100 may comprise a second ion guide 302 downstream of the first ion guide 302 and the second ion guide 302 may be located in the second vacuum chamber or second differential pumping region.

The second ion guide 302 may comprise a segmented quadrupole rod set ion guide or mass filter 302. However, other embodiments are contemplated wherein the second ion guide 302 may comprise a quadrupole ion guide, a hexapole ion guide, an octopole ion guide, a multipole ion guide, a segmented multipole ion guide, an ion funnel ion guide, an ion tunnel ion guide (e.g. comprising a plurality of ring electrodes each having an aperture through which ions may pass or otherwise forming an ion guiding region) or a conjoined ring ion guide.

The mass spectrometer 100 may comprise one or more transfer lenses 303 located downstream of the second ion guide 302. One of more of the transfer lenses 303 may be located in a third vacuum chamber or third differential pumping region. Ions may be passed through a further differential pumping aperture into a fourth vacuum chamber or fourth differential pumping region. One or more transfer lenses 303 may also be located in the fourth vacuum chamber or fourth differential pumping region.

The mass spectrometer 100 may comprise a mass analyser 304 located downstream of the one or more transfer lenses 303 and may be located, for example, in the fourth or further vacuum chamber or fourth or further differential pumping region. The mass analyser 304 may comprise a Time of Flight (“TOF”) mass analyser. The Time of Flight mass analyser 304 may comprise a linear or an orthogonal acceleration Time of Flight mass analyser.

According to various embodiments an orthogonal acceleration Time of Flight mass analyser 304 may be provided comprising one or more orthogonal acceleration pusher electrode(s) 305 (or alternatively and/or additionally one or more puller electrode(s)) and an ion detector 307 separated by a field free drift region. The Time of Flight mass analyser 304 may optionally comprise one or more reflectrons 306 intermediate the pusher electrode 305 and the ion detector 307.

Although highly desirable, it should be recognised that the mass analyser does not have to comprise a Time of Flight mass analyser 304. More generally, the mass analyser 304 may comprise either: (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; or (xiv) a linear acceleration Time of Flight mass analyser.

Although not shown in Fig. 3, the mass spectrometer 100 may also comprise one or more optional further devices or stages. For example, according to various

embodiments the mass spectrometer 100 may additionally comprise one or more ion mobility separation devices and/or one or more Field Asymmetric Ion Mobility

Spectrometer (“FAIMS”) devices and/or one or more devices for separating ions temporally and/or spatially according to one or more physico-chemical properties. For example, the mass spectrometer 100 according to various embodiments may comprise one or more separation stages for temporally or otherwise separating ions according to their mass, collision cross section, conformation, ion mobility, differential ion mobility or another physico-chemical parameter.

The mass spectrometer 100 may comprise one or more discrete ion traps or one or more ion trapping regions. However, as will be described in more detail below, an axial trapping voltage may be applied to one or more sections or one or more electrodes of either the first ion guide 301 and/or the second ion guide 302 in order to confine ions axially for a short period of time. For example, ions may be trapped or confined axially for a period of time and then released. The ions may be released in a synchronised manner with a downstream ion optical component. For example, in order to enhance the duty cycle of analyte ions of interest, an axial trapping voltage may be applied to the last electrode or stage of the second ion guide 302. The axial trapping voltage may then be removed and the application of a voltage pulse to the pusher electrode 305 of the Time of Flight mass analyser 304 may be synchronised with the pulsed release of ions so as to increase the duty cycle of analyte ions of interest which are then subsequently mass analysed by the mass analyser 304. This approach may be referred to as an Enhanced Duty Cycle (“EDC”) mode of operation.

Furthermore, the mass spectrometer 100 may comprise 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.

The mass spectrometer 100 may comprise 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.

The fourth or further vacuum chamber or fourth or further differential pumping region may be maintained at a lower pressure than the third vacuum chamber or third differential pumping region. The third vacuum chamber or third differential pumping region may be maintained at a lower pressure than the second vacuum chamber or second differential pumping region and the second vacuum chamber or second differential pumping region may be maintained at a lower pressure than the first vacuum chamber or first differential pumping region. The first vacuum chamber or first differential pumping region may be maintained at lower pressure than ambient. Ambient pressure may be considered to be approx. 1013 mbar at sea level.

The mass spectrometer 100 may comprise an ion source configured to generate analyte ions. In various particular embodiments, the ion source may comprise an

Atmospheric Pressure Ionisation (“API”) ion source such as an Electrospray Ionisation (“ESI”) ion source or an Atmospheric Pressure Chemical Ionisation ("APCI") ion source.

Fig. 4 shows in general form a known Atmospheric Pressure Ionisation ("API") ion source such as an Electrospray Ionisation ("ESI") ion source or an Atmospheric Pressure Chemical Ionisation ("APCI") ion source. The ion source may comprise, for example, an Electrospray Ionisation probe 401 which may comprise an inner capillary tube 402 through which an analyte liquid may be supplied. The analyte liquid may comprise mobile phase from a LC column or an infusion pump. The analyte liquid enters via the inner capillary tube 402 or probe and is pneumatically converted to an electrostatically charged aerosol spray. Solvent is evaporated from the spray by means of heated desolvation gas.

Desolvation gas may be provided through an annulus which surrounds both the inner capillary tube 402 and an intermediate surrounding nebuliser tube 403 through which a nebuliser gas emerges. The desolvation gas may be heated by an annular electrical desolvation heater 404. The resulting analyte and solvent ions are then directed towards a sample or sampling cone aperture mounted into an ion block 405 forming an initial stage of the mass spectrometer 100.

The inner capillary tube 402 is preferably surrounded by a nebuliser tube 403. The emitting end of the inner capillary tube 402 may protrude beyond the nebuliser tube 403. The inner capillary tube 402 and the nebuliser tube 403 may be surrounded by a desolvation heater arrangement 404 as shown in Fig. 4 wherein the desolvation heater 404 may be arranged to heat a desolvation gas. The desolvation heater 404 may be arranged to heat a desolvation gas from ambient temperature up to a temperature of around 600°C. According to various embodiments the desolvation heater 404 is always OFF when the API gas is OFF.

The desolvation gas and the nebuliser gas may comprise nitrogen, air or another gas or mixture of gases. The same gas (e.g. nitrogen, air or another gas or mixture of gases) may be used as both a desolvation gas, nebuliser gas and cone gas. The function of the cone gas will be described in more detail below.

The inner probe capillary 402 may be readily replaced by an unskilled user without needing to use any tools. The Electrospray probe 402 may support LC flow rates in the range of 0.3 to 1.0 mL/min.

According to various embodiments an optical detector may be used in series with the mass spectrometer 100. It will be understood that an optical detector may have a maximum pressure capability of approx. 1000 psi. Accordingly, the Electrospray

Ionisation probe 401 may be arranged so as not to cause a back pressure of greater than around 500 psi, allowing for back pressure caused by other system components. The instrument may be arranged so that a flow of 50:50 methanol/water at 1.0 mL/min does not create a backpressure greater than 500 psi.

According to various embodiments a nebuliser flow rate of between 106 to 159 L/hour may be utilised.

The ESI probe 401 may be powered by a power supply which may have an operating range of 0.3 to 1.5 kV.

It should, however, be understood that various other different types of ion source may instead be coupled to the mass spectrometer 100. For example, according to various embodiments, the ion source may more generally comprise either: (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 ("SAII") ion source; (xxvii) a Desorption Electrospray Ionisation (“DESI”) ion source; (xxviii) a Laser Ablation Electrospray Ionisation (“LAESI”) ion source; (xxix) a Surface Assisted Laser Desorption Ionisation (“SALDI”) ion source; or (xxx) a Low Temperature Plasma (“LTP”) ion source.

A chromatography or other separation device may be provided upstream of the ion source 300 and may be coupled so as to provide an effluent to the ion source 300. The chromatography separation device may comprise a liquid chromatography or gas chromatography device. Alternatively, 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 mass spectrometer 100 may comprise an atmospheric pressure interface or ion inlet assembly downstream of the ion source 300. According to various embodiments the atmospheric pressure interface may comprise a sample or sampling cone 406,407 which is located downstream of the ion source 401. Analyte ions generated by the ion source 401 may pass via the sample or sampling cone 406,407 into or onwards towards a first vacuum chamber or first differential pumping region of the mass spectrometer 100. However, according to other embodiments the atmospheric pressure interface may comprise a capillary interface.

As shown in Fig. 4, ions generated by the ion source 401 may be directed towards an atmospheric pressure interface which may comprise an outer gas cone 406 and an inner sample cone 407. A cone gas may be supplied to an annular region between the inner sample cone 407 and the outer gas cone 406. The cone gas may emerge from the annulus in a direction which is generally opposed to the direction of ion travel into the mass spectrometer 100. The cone gas may act as a declustering gas which effectively pushes away large contaminants thereby preventing large contaminants from impacting upon the outer cone 406 and/or inner cone 407 and also preventing the large

contaminants from entering into the initial vacuum stage of the mass spectrometer 100.

Fig. 5 shows in more detail a first known ion inlet assembly which is similar to an ion inlet assembly according to various embodiments. The known ion inlet assembly as shown and described below with reference to Figs. 5 and 6A is presented in order to highlight various aspects of an ion inlet assembly according to various embodiments and also so that differences between an ion inlet assembly according to various embodiments as shown and discussed below with reference to Fig. 6C can be fully appreciated.

With reference to Fig. 5, it will be understood that the ion source (not shown) generates analyte ions which are directed towards a vacuum chamber 505 of the mass spectrometer 100.

A gas cone assembly is provided comprising an inner gas cone or sampling cone 513 having an aperture 515 and an outer gas cone 517 having an aperture 521. A disposable disc 525 is arranged beneath or downstream of the inner gas cone or sampling 513 and is held in position by a mounting element 527. The disc 525 covers an aperture 511 of the vacuum chamber 505. The disc 525 is removably held in position by the inner gas cone 513 resting upon the mounting element 527.

As will be discussed in more detail below with reference to Fig. 6C, according to various embodiments the mounting element 527 is not provided in the preferred ion inlet assembly.

The disc 525 has an aperture or sampling orifice 529 through which ions can pass.

A carrier 531 is arranged underneath or below the disc 525. The carrier 531 is arranged to cover the aperture 511 of the vacuum chamber 505. Upon removal of the disc 525, the carrier 531 may remain in place due to suction pressure.

Fig. 6A shows an exploded view of the first known ion inlet assembly. The outer gas cone 517 has a cone aperture 521 and is slidably mounted within a clamp 535. The clamp 535 allows a user to remove the outer gas cone 517 without physically having to touch the outer gas cone 517 which will get hot during use.

An inner gas cone or sampling cone 513 is shown mounted behind or below the outer gas cone 517. The known arrangement utilises a carrier 531 which has a 1 diameter aperture. The ion block 802 is also shown having a calibration port 550. However, the calibration port 550 is not provided in an ion inlet assembly according to various embodiments.

Fig. 6B shows an second different known ion inlet assembly as used on a different instrument which has an isolation valve 560 which is required to hold vacuum pressure when the outer cone gas nozzle 517 and the inner nozzle 513 are removed for servicing. The inner cone 513 has a gas limiting orifice into the subsequent stages of the mass spectrometer. The inner gas cone 513 comprises a high cost, highly precisioned part which requires routine removal and cleaning. The inner gas cone 513 is not a disposable or consumable item. Prior to removing the inner sampling cone 513 the isolation valve 560 must be rotated into a closed position in order to isolate the downstream vacuum stages of the mass spectrometer from atmospheric pressure. The isolation valve 560 is therefore required in order to hold vacuum pressure whilst the inner gas sampling cone 513 is removed for cleaning.

Fig. 6C shows an exploded view of an ion inlet assembly according to various embodiments. The ion inlet assembly according to various embodiments is generally similar to the first known ion inlet assembly as shown and described above with reference to Figs. 5 and 6A except for a few differences. One difference is that a calibration port 550 is not provided in the ion block 802 and a mounting member or mounting element 527 is not provided.

Accordingly, the ion block 802 and ion inlet assembly have been simplified.

Furthermore, importantly the disc 525 may comprise a 0.25 or 0.30 mm diameter aperture disc 525 which is substantially smaller diameter than conventional arrangements.

According to various embodiments both the disc 525 and the vacuum holding member or carrier 531 may have a substantially smaller diameter aperture than conventional arrangements such as the first known arrangement as shown and described above with reference to Figs. 5 and 6A.

For example, the first known instrument utilises a vacuum holding member or carrier 531 which has a 1 mm diameter aperture. In contrast, according to various embodiments the vacuum holding member or carrier 531 according to various

embodiments may have a much smaller diameter aperture e.g. a 0.3 mm or 0.40 mm diameter aperture.

Fig. 6D shows in more detail how the ion block assembly 802 according to various embodiments may be enclosed in an atmospheric pressure source or housing. The ion block assembly 802 may be mounted to a pumping block or thermal interface 600. Ions pass through the ion block assembly 802 and then through the pumping block or thermal interface 600 into a first vacuum chamber 601 of the mass spectrometer 100. The first vacuum chamber 601 preferably houses the first ion guide 301 which as shown in Fig. 6D and which may comprise a conjoined ring ion guide 301. Fig. 6D also indicates how ion entry 603 into the mass spectrometer 100 also represents a potential leak path. A correct pressure balance is required between the diameters of the various gas flow restriction apertures in the ion inlet assembly with the configuration of the vacuum pumping system.

Fig. 6E shows the ion inlet assembly according to various embodiments and illustrates how ions pass through an outer gas cone 517 and an inner gas cone or sampling cone 513 before passing through an apertured disc 525. No mounting member or mounting element is provided unlike the first known ion inlet assembly as described above.

The ions then pass through an aperture in a fixed valve 690. The fixed valve 690 is held in place by suction pressure and is not removable by a user in normal operation. Three O-ring vacuum seals 692a, 692b, 692c are shown. The fixed valve 690 may be formed from stainless steel. A vacuum region 695 of the mass spectrometer 100 is generally indicated.

Fig. 6F shows the outer cone 517, inner sampling cone 513 and apertured disc 525 having been removed by a user by withdrawing or removing a clamp 535 to which at least the outer cone 517 is slidably inserted. According to various embodiments the inner sampling cone 513 may also be attached or secured to the outer cone 517 so that both are removed at the same time.

Instead of utilising a conventional rotatable isolation valve, a fixed non-rotatable valve 690 is provided or otherwise retained in the ion block 802. An O-ring seal 692a is shown which ensures that a vacuum seal is provided between the exterior body of the fixed valve 690 and the ion block 802. An ion block voltage contact 696 is also shown. O- rings seals 692b, 692c for the inner and outer cones 513,517 are also shown.

Fig. 6G illustrates how according to various embodiments a fixed valve 690 may be retained within an ion block 802 and may form a gas tight sealing therewith by virtue of an O-ring seal 692a. A user is unable to remove the fixed valve 690 from the ion block 802 when the instrument is operated due to the vacuum pressure within the vacuum chamber 695 of the instrument. The direction of suction force which holds the fixed valve 690 in a fixed position against the ion block 802 during normal operation is shown.

The size of the entrance aperture into the fixed valve 690 is designed for optimum operation conditions and component reliability. Various embodiments are contemplated wherein the shape of the entrance aperture may be cylindrical. However, other embodiments are contemplated wherein there may be more than one entrance aperture and/or wherein the one or more entrance apertures to the fixed valve 690 may have a non-circular aperture. Embodiments are also contemplated wherein the one or more entrance apertures may be angled at a non-zero angle to the longitudinal axis of the fixed valve 690.

It will be understood that total removal of the fixed valve 690 from the ion block 802 will rapidly result in total loss of vacuum pressure within the mass spectrometer 100.

According to various embodiments the ion inlet assembly may be temporarily sealed in order to allow a vacuum housing within the mass spectrometer 100 to be filled with dry nitrogen for shipping. It will be appreciated that filling a vacuum chamber with dry nitrogen allows faster initial pump-down during user initial instrument installation. It will be appreciated that since according to various embodiments the internal aperture in the vacuum holding member or carrier 531 is substantially smaller in diameter than conventional arrangements, then the vacuum within the first and subsequent vacuum chambers of the instrument can be maintained for substantially longer periods of time than is possible conventionally when the disc 525 is removed and/or replaced.

Accordingly, the mass spectrometer 100 according to various embodiments does not require an isolation valve in contrast with other known mass spectrometers in order to maintain the vacuum within the instrument when a component such as the outer gas cone 517, the inner gas cone 513 or the disc 525 are removed.

A mass spectrometer 100 according to various embodiments therefore enables a reduced cost instrument to be provided which is also simpler for a user to operate since no isolation valve is needed. Furthermore, a user does not need to be understand or learn how to operate such an isolation valve.

The ion block assembly 802 may comprise a heater in order to keep the ion block 802 above ambient temperature in order to prevent droplets of analyte, solvent, neutral particles or condensation from forming within the ion block 802.

According to an embodiment when a user wishes to replace and/or remove either the outer cone 517 and/or the inner sampling cone 513 and/or the disc 525 then both the source or ion block heater and the desolvation heater 404 may be turned OFF. The temperature of the ion block 802 may be monitored by a thermocouple which may be provided within the ion block heater or which may be otherwise provided in or adjacent to the ion block 802.

When the temperature of the ion block is determined to have dropped below a certain temperature such as e.g. 55°C then the user may be informed that the clamp 535, outer gas cone 517, inner gas sampling cone 513 and disc 525 are sufficiently cooled down such that a user can touch them without serious risk of injury.

According to various embodiment a user can simply remove and/or replace the outer gas cone 517 and/or inner gas sampling cone 513 and/or disc 525 in less than two minutes without needing to vent the instrument. In particular, the low pressure within the instrument is maintained for a sufficient period of time by the aperture in the fixed valve 690.

According to various embodiments the instrument may be arranged so that the maximum leak rate into the source or ion block 802 during sample cone maintenance is approx. 7 mbar L/s. For example, assuming a backing pump speed of 9 m³/hour (2.5 L/s) and a maximum acceptable pressure of 3 mbar, then the maximum leak rate during sampling cone maintenance may be approx. 2.5 L/s x 3 mbar = 7.5 mbar L/s.

The ion block 802 may comprise an ion block heater having a K-type thermistor.

As will be described in more detail below, according to various embodiments the source (ion block) heater may be disabled to allow forced cooling of the source or ion block 802. For example, desolvation heater 404 and/or ion block heater may be switched OFF whilst API gas is supplied to the ion block 802 in order to cool it down. According to various embodiments either a desolvation gas flow and/or a nebuliser gas flow from the probe 401 may be directed towards the cone region 517,513 of the ion block 802. Additionally and/or alternatively, the cone gas supply may be used to cool the ion block 802 and the inner and outer cones 513,517. In particular, by turning the desolvation heater 404 OFF but maintaining a supply of nebuliser and/or desolvation gas from the probe 401 so as to fill the enclosure housing the ion block with ambient temperature nitrogen or other gas will have a rapid cooling effect upon the metal and plastic components forming the ion inlet assembly which may be touched by a user during servicing. Ambient temperature (e.g. in the range 18-25 °C) cone gas may also be supplied in order to assist with cooling the ion inlet assembly in a rapid manner. Conventional instruments do not have the functionality to induce rapid cooling of the ion block 802 and gas cones 521 ,513.

Liquid and gaseous exhaust from the source enclosure may be fed into a trap bottle. The drain tubing may be routed so as to avoid electronic components and wiring. The instrument may be arranged so that liquid in the source enclosure always drains out even when the instrument is switched OFF. For example, it will be understood that an LC flow into the source enclosure could be present at any time.

An exhaust check valve may be provided so that when the API gas is turned OFF the exhaust check valve prevents a vacuum from forming in the source enclosure and trap bottle. The exhaust trap bottle may have a capacity ³ 5L.

The fluidics system may comprise a piston pump which allows the automated introduction of a set-up solution into the ion source. The piston pump may have a flow rate range of 0.4 to 50 mL/min. A divert/select valve may be provided which allows rapid automated changeover between LC flow and the flow of one or two internal set-up solutions into the source.

According to various embodiments three solvent bottles 201 may be provided. Solvent A bottle may have a capacity within the range 250-300 mL, solvent B bottle may have a capacity within the range 50-60 mL and solvent C bottle may have a capacity within the range 100-125 mL. The solvent bottles 201 may be readily observable by a user who may easily refill the solvent bottles.

According to an embodiment solvent A may comprise a lock-mass, solvent B may comprise a calibrant and solvent C may comprise a wash. Solvent C (wash) may be connected to a rinse port.

A driver PCB may be provided in order to control the piston pump and the divert/select valve. On power-up the piston pump may be homed and various purge parameters may be set.

Fluidics may be controlled by software and may be enabled as a function of the instrument state and the API gas valve state in a manner as detailed below:

When software control of the fluidics is disabled then the valve is set to a divert position and the pump is stopped.

Fig. 7 A illustrates a vacuum pumping arrangement according to various embodiments.

A split-flow turbo molecular vacuum pump (commonly referred to as a“turbo” pump) may be used to pump the fourth or further vacuum chamber or fourth or further differential pumping region, the third vacuum chamber or third differential pumping region, and the second vacuum chamber or second differential pumping region. According to an embodiment the turbo pump may comprise either a Pfeiffer (RTM) Splitflow 310 fitted with a TC110 controller or an Edwards (RTM) nEXT300/100/100D turbo pump. The turbo pump may be air cooled by a cooling fan.

The turbo molecular vacuum pump may be backed by a rough, roughing or backing pump such as a rotary vane vacuum pump or a diaphragm vacuum pump. The rough, roughing or backing pump may also be used to pump the first vacuum chamber housing the first ion guide 301. The rough, roughing or backing pump may comprise an Edwards (RTM) nRV14i backing pump. The backing pump may be provided external to the instrument and may be connected to the first vacuum chamber which houses the first ion guide 301 via a backing line 700 as shown in Fig. 7A.

A first pressure gauge such as a cold cathode gauge 702 may be arranged and adapted to monitor the pressure of the fourth or further vacuum chamber or fourth or further differential pumping region. According to an embodiment the Time of Flight housing pressure may be monitored by an Inficon (RTM) MAG500 cold cathode gauge 702.

A second pressure gauge such as a Pirani gauge 701 may be arranged and adapted to monitor the pressure of the backing pump line 700 and hence the first vacuum chamber which is in fluid communication with the upstream pumping block 600 and ion block 802. According to an embodiment the instrument backing pressure may be monitored by an Inficon (RTM) PSG500 Pirani gauge 701.

According to various embodiments the observed leak plus outgassing rate of the Time of Flight chamber may be arranged to be less than 4 x 10⁵ mbar L/s. Assuming a 200 L/s effective turbo pumping speed then the allowable leak plus outgassing rate is 5 x 10⁷ mbar x 200 L/s = 1 x 10⁴ mbar L/s.

A turbo pump such as an Edwards (RTM) nEXT300/100/100D turbo pump may be used which has a main port pumping speed of 400 L/s. As will be detailed in more detail below, EMC shielding measures may reduce the pumping speed by approx. 20% so that the effective pumping speed is 320 L/s. Accordingly, the ultimate vacuum according to various embodiments may be 4 x 10⁵ mbar L/s / 320 L/s = 1.25 x 10⁷ mbar. According to an embodiment a pump-down sequence may comprise closing a soft vent solenoid as shown in Fig. 7B, starting the backing pump and waiting until the backing pressure drops to 32 mbar. If 32 mbar is not reached within 3 minutes of starting the backing pump then a vent sequence may be performed. Assuming that a pressure of 32 mbar is reached within 3 minutes then the turbo pump is then started. When the turbo speed exceeds 80% of maximum speed then the Time of Flight vacuum gauge 702 may then be switched ON. It will be understood that the vacuum gauge 702 is a sensitive detector and hence is only switched ON when the vacuum pressure is such that the vacuum gauge 702 which not be damaged.

If the turbo speed does not reach 80% of maximum speed within 8 minutes then a vent sequence may be performed.

A pump-down sequence may be deemed completed once the Time of Flight vacuum chamber pressure is determined to be < 1 x 10⁵ mbar.

If a vent sequence is to be performed then the instrument may be switched to a Standby mode of operation. The Time of Flight vacuum gauge 702 may be switched OFF and the turbo pump may also be switched OFF. When the turbo pump speed falls to less than 80% of maximum then a soft vent solenoid valve as shown in Fig. 7B may be opened. The system may then wait for 10 seconds before then switching OFF the backing pump.

It will be understood by those skilled in the art that the purpose of the turbo soft vent solenoid valve as shown in Fig. 7B and the soft vent line is to enable the turbo pump to be vented at a controlled rate. It will be understood that if the turbo pump is vented at too fast a rate then the turbo pump may be damaged.

The instrument may switch into a maintenance mode of operation which allows an engineer to perform service work on all instrument sub-systems except for the vacuum system or a subsystem incorporating the vacuum system without having to vent the instrument. The instrument may be pumped down in maintenance mode and conversely the instrument may also be vented in maintenance mode.

A vacuum system protection mechanism may be provided wherein if the turbo speed falls to less than 80% of maximum speed then a vent sequence is initiated.

Similarly, if the backing pressure increases to greater than 10 mbar then a vent sequence may also be initiated. According to an embodiment if the turbo power exceeds 120 W for more than 15 minutes then a vent sequence may also be initiated. If on instrument power-up the turbo pump speed is > 80% of maximum then the instrument may be set to a pumped state, otherwise the instrument may be set to a venting state.

Fig. 7B shows a schematic of a gas handling system which may be utilised according to various embodiments. A storage check valve 721 may be provided which allows the instrument to be filled with nitrogen for storage and transport. The storage check valve 721 is in fluid communication with an inline filter.

A soft vent flow restrictor may be provided which may limit the maximum gas flow to less than the capacity of a soft vent relief valve in order to prevent the analyser pressure from exceeding 0.5 bar in a single fault condition. The soft vent flow restrictor may comprise an orifice having a diameter in the range 0.70 to 0.75 mm.

A supply pressure sensor 722 may be provided which may indicate if the nitrogen pressure has fallen below 4 bar.

An API gas solenoid valve may be provided which is normally closed and which has an aperture diameter of not less than 1.4 mm.

An API gas inlet is shown which preferably comprises a Nitrogen gas inlet.

According to various embodiments the nebuliser gas, desolvation gas and cone gas are all supplied from a common source of nitrogen gas.

A soft vent regulator may be provided which may function to prevent the analyser pressure exceeding 0.5 bar in normal condition.

A soft vent check valve may be provided which may allow the instrument to vent to atmosphere in the event that the nitrogen supply is OFF.

A soft vent relief valve may be provided which may have a cracking pressure of 345 mbar. The soft vent relief valve may function to prevent the pressure in the analyser from exceeding 0.5 bar in a single fault condition. The gas flow rate through the soft vent relief valve may be arranged so as not to be less than 2000 L/h at a differential pressure of 0.5 bar.

The soft vent solenoid valve may normally be in an open position. The soft vent solenoid valve may be arranged to restrict the gas flow rate in order to allow venting of the turbo pump at 100% rotational speed without causing damage to the pump. The maximum orifice diameter may be 1.0 mm.

The maximum nitrogen flow may be restricted such that in the event of a catastrophic failure of the gas handling the maximum leak rate of nitrogen into the lab should be less than 20% of the maximum safe flow rate. According to various

embodiments an orifice having a diameter of 1.4 to 1.45 mm may be used.

A source pressure sensor may be provided.

A source relief valve having a cracking pressure of 345 mbar may be provided.

The source relief valve may be arranged to prevent the pressure in the source from exceeding 0.5 bar in a single fault condition. The gas flow rate through the source relief valve may be arranged so as not to be less than 2000 L/h at a differential pumping pressure of 0.5 bar. A suitable valve is a Ham-Let (RTM) H-480-S-G-1/4-5psi valve.

A cone restrictor may be provided to restrict the cone flow rate to 36 L/hour for an input pressure of 7 bar. The cone restrictor may comprise a 0.114 mm orifice.

The desolvation flow may be restricted by a desolvation flow restrictor to a flow rate of 940 L/hour for an input pressure of 7 bar. The desolvation flow restrictor may comprise a 0.58 mm orifice.

A pinch valve may be provided which has a pilot operating pressure range of at least 4 to 7 bar gauge. The pinch valve may normally be open and may have a maximum inlet operating pressure of at least 0.5 bar gauge.

When the instrument is requested to turn the API gas OFF, then control software may close the API gas valve, wait 2 seconds and then close the source exhaust valve. In the event of an API gas failure wherein the pressure switch opens (pressure < 4 bar) then software control of the API gas may be disabled and the API gas valve may be closed. The system may then wait 2 seconds before closing the exhaust valve.

In order to turn the API gas ON a source pressure monitor may be turned ON except while a source pressure test is performed. An API gas ON or OFF request from software may be stored as an API Gas Request state which can either be ON or OFF. Further details are presented below:

Fig. 7C shows a flow diagram showing an instrument response to a user request to turn the API gas ON. A determination may be made as to whether or not software control of API gas is enabled. If software control is not enabled then the request may be refused. If software control of API gas is enabled then the open source exhaust valve may be opened. Then after a delay of 2 seconds the API gas valve may be opened. The pressure is then monitored. If the pressure is determined to be between 20-60 mbar then a warning message may be communicated or issued. If the pressure is greater than 60 mbar then then the API gas valve may be closed. Then after a delay of 2 seconds the source exhaust valve may be closed and a high exhaust pressure trip may occur.

A high exhaust pressure trip may be reset by running a source pressure test.

According to various embodiments the API gas valve may be closed within 100 ms of an excess pressure being sensed by the source pressure sensor.

Fig. 7D shows a flow diagram illustrating a source pressure test which may be performed according to various embodiments. The source pressure test may be commenced and software control of fluidics may be disabled so that no fluid flows into the Electrospray probe 401. Software control of the API gas may also be disabled i.e. the API is turned OFF. The pressure switch may then be checked. If the pressure is above 4 bar for more than 1 second then the API gas valve may be opened. However, if the pressure is less than 4 bar for more than 1 second then the source pressure test may move to a failed state due to low API gas pressure.

Assuming that the API gas valve is opened then the pressure may then be monitored. If the pressure is in the range 18-100 mbar then a warning message may be output indicating a possible exhaust problem. If the warning status continues for more than 30 seconds then the system may conclude that the source pressure test has failed due to the exhaust pressure being too high.

If the monitored pressure is determined to be less than 18 mbar then the source exhaust valve is closed. The pressure may then again be monitored. If the pressure is less than 200 mbar then a warning message indicating a possible source leak may be issued.

If the pressure is determined to be greater than 200 mbar then the API gas valve may be closed and the source exhaust valve may be opened i.e. the system looks to build pressure and to test for leaks. The system may then wait 2 seconds before determining that the source pressure test is passed.

If the source pressure test has been determined to have been passed then the high pressure exhaust trip may be reset and software control of fluidics may be enabled. Software control of the API gas may then be enabled and the source pressure test may then be concluded.

In the event of a source pressure test failure, the divert valve position may be set to divert and the valve may be kept in this position until the source pressure test is either passed or the test is over-ridden.

It is contemplated that the source pressure test may be over-ridden in certain circumstances. Accordingly, a user may be permitted to continue to use an instrument where they have assessed any potential risk as being acceptable. If the user is permitted to continue using the instrument then the source pressure test status message may still be displayed in order to show the original failure. As a result, a user may be reminded of the continuing failed status so that the user may continually re-evaluate any potential risk.

In the event that a user requests a source pressure test over-ride then the system may reset a high pressure exhaust trip and then enable software control of the divert valve. The system may then enable software control of the API gas before determining that the source pressure test over-ride is complete.

The pressure reading used in the source pressure test and source pressure monitoring may include a zero offset correction.

The gas and fluidics control responsibility may be summarised as detailed below:

A pressure test may be initiated if a user triggers an interlock.

The instrument may operate in various different modes of operation. If the turbo pump speed falls to less than 80% of maximum speed whilst in Operate, Over-pressure or Power save mode then the instrument may enter a Standby state or mode of operation. If the pressure in the Time of Flight vacuum chamber is greater than 1 x 10⁵ mbar and/or the turbo speed is less than 80% of maximum speed then the instrument may be prevented from operating in an Operate mode of operation.

According to various embodiments the instrument may be operated in a Power save mode. In a Power save mode of operation the piston pump may be stopped. If the instrument is switched into a Power save mode while the divert valve is in the LC position, then the divert valve may change to a divert position. A Power save mode of operation may be considered as being a default mode of operation wherein all back voltages are kept ON, front voltages are turned OFF and gas is OFF.

If the instrument switches from a Power save mode of operation to an Operate mode of operation then the piston pump divert valves may be returned to their previous states i.e. their states immediately before a Power save mode of operation was entered.

If the Time of Flight region pressure rises above 1.5 x 10⁵ mbar while the instrument is in an Operate mode of operation then the instrument may enter an Over pressure mode of operation or state.

If the Time of Flight pressure enters the range 1x1 O ⁸ to 1x1 O ⁵ mbar while the instrument is in an Over-pressure mode of operation then the instrument may enter an Operate mode of operation.

If the API gas pressure falls below its trip level while the instrument is in an Operate mode of operation then the instrument may enter a Gas Fail state or mode of operation. The instrument may remain in a Gas Fail state until both: (i) the API gas pressure is above its trip level; and (ii) the instrument is operated in either Standby or Power save mode.

According to an embodiment the instrument may transition from an Operate mode of operation to an Operate with Source Interlock Open mode of operation when the source cover is opened. Similarly, the instrument may transition from an Operate with Source Interlock Open mode of operation to an Operate mode of operation when the source cover is closed.

According to an embodiment the instrument may transition from an Over-pressure mode of operation to an Over-pressure with Source Interlock Open mode of operation when the source cover is opened. Similarly, the instrument may transition from an Over pressure with Source Interlock Open mode of operation to an Over-pressure mode of operation when the source cover is closed.

The instrument may operate in a number of different modes of operation which may be summarised as follows:

Reference to front end voltages relates to voltages which are applied to the Electrospray capillary electrode 402, the source offset, the source or first ion guide 301 , aperture #1 (see Fig. 15A) and the quadrupole ion guide 302.

Reference to analyser voltages relates to all high voltages except the front end voltages.

Reference to API gas refers to desolvation, cone and nebuliser gases.

Reference to Not Pumped refers to all vacuum states except pumped.

If any high voltage power supply loses communication with the overall system or a global circuitry control module then the high voltage power supply may be arranged to switch OFF its high voltages. The global circuitry control module may be arranged to detect the loss of communication of any subsystem such as a power supply unit (“PSU”), a pump or gauge etc.

According to various embodiments the system will not indicate its state or mode of operation as being Standby if the system is unable to verify that all subsystems are in a Standby state.

As is apparent from the above table, when the instrument is operated in an Operate mode of operation then all voltages are switched ON. When the instrument transitions to operate in an Operate mode of operation then the following voltages are ON namely transfer lens voltages, ion guide voltages, voltages applied to the first ion guide 301 and the capillary electrode 402. In addition, the desolvation gas and desolvation heater are all ON.

If a serious fault were to develop then the instrument may switch to a Standby mode of operation wherein all voltages apart from the source heater provided in the ion block 802 are turned OFF and only a service engineer can resolve the fault. It will be understood that the instrument may only be put into a Standby mode of operation wherein voltages apart from the source heater in the ion block 802 are turned OFF only if a serious fault occurs or if a service engineer specifies that the instrument should be put into a Standby mode operation. A user or customer may (or may not) be able to place an instrument into a Standby mode of operation. Accordingly, in a Standby mode of operation all voltages are OFF and the desolvation gas flow and desolvation heater 404 are all OFF. Only the source heater in the ion block 802 may be left ON.

The instrument may be kept in a Power Save mode by default and may be switched so as to operate in an Operate mode of operation wherein all the relevant voltages and gas flows are turned ON. This approach significantly reduces the time taken for the instrument to be put into a useable state. When the instrument transitions to a Power Save mode of operation then the following voltages are ON - pusher electrode 305, reflectron 306, ion detector 307 and more generally the various Time of Flight mass analyser 304 voltages.

The stability of the power supplies for the Time of Flight mass analyser 304, ion detector 307 and reflectron 306 can affect the mass accuracy of the instrument. The settling time when turning ON or switching polarity on a known conventional instrument is around 20 minutes.

It has been established that if the power supplies are cold or have been left OFF for a prolonged period of time then they may require up to 10 hours to warm up and stabilise. For this reason customers may be prevented from going into a Standby mode of operation which would switch OFF the voltages to the Time of Flight analyser 304 including the reflectron 306 and ion detector 307 power supplies.

On start-up the instrument may move to a Power save mode of operation as quickly as possible as this allows the power supplies the time they need to warm up whilst the instrument is pumping down. As a result, by the time the instrument has reached the required pressure to carry out instrument setup the power supplies will have stabilised thus reducing any concerns relating to mass accuracy.

According to various embodiments in the event of a vacuum failure in the vacuum chamber housing the Time of Flight mass analyser 304 then power may be shut down or turned OFF to all the peripherals or sub-modules e.g. the ion source 300, first ion guide 301 , the segmented quadrupole rod set ion guide 302, the transfer optics 303, the pusher electrode 305 high voltage supply, the reflectron 306 high voltage supply and the ion detector 307 high voltage supply. The voltages are primarily all turned OFF for reasons of instrument protection and in particular protecting sensitive components of the Time of Flight mass analyser 307 from high voltage discharge damage.

It will be understood that high voltages may be applied to closely spaced electrodes in the Time of Flight mass analyser 304 on the assumption that the operating pressure will be very low and hence there will be no risk of sparking or electrical discharge effects. Accordingly, in the event of a serious vacuum failure in the vacuum chamber housing the Time of Flight mass analyser 304 then the instrument may remove power or switch power OFF to the following modules or sub-modules: (i) the ion source high voltage supply module; (ii) the first ion guide 301 voltage supply module; (iii) the quadrupole ion guide 302 voltage supply module; (iv) the high voltage pusher electrode 305 supply module; (v) the high voltage reflectron 306 voltage supply module; and (vi) the high voltage detector 307 module. The instrument protection mode of operation is different to a Standby mode of operation wherein electrical power is still supplied to various power supplies or modules or sub-modules. In contrast, in an instrument protection mode of operation power is removed to the various power supply modules by the action of a global circuitry control module. Accordingly, if one of the power supply modules were faulty it would still be unable in a fault condition to turn voltages ON because the module would be denied power by the global circuitry control module.

Fig. 8 shows a view of a mass spectrometer 100 according to various

embodiments in more detail. The mass spectrometer 100 may comprise a first vacuum PCB interface 801a having a first connector 817a for directly connecting the first vacuum interface PCB 801a to a first local control circuitry module (not shown) and a second vacuum PCB interface 801b having a second connector 817b for directly connecting the second vacuum interface PCB 801b to a second local control circuitry module (not shown).

The mass spectrometer 100 may further comprise a pumping or ion block 802 which is mounted to a pumping block or thermal isolation stage (not viewable in Fig. 8). According to various embodiments one or more dowels or projections 802a may be provided which enable a source enclosure (not shown) to connect to and secure over and house the ion block 802. The source enclosure may serve the purpose of preventing a user from inadvertently coming into contact with any high voltages associated with the Electrospray probe 402. A micro-switch or other form of interlock may be used to detect opening of the source enclosure by a user in order to gain source access whereupon high voltages to the ion source 402 may then be turned OFF for user safety reasons.

Ions are transmitted via an initial or first ion guide 301 , which may comprise a conjoined ring ion guide, and then via a segmented quadrupole rod set ion guide 302 to a transfer lens or transfer optics arrangement 303. The transfer optics 303 may be designed in order to provide a highly efficient ion guide and interface into the Time of Flight mass analyser 304 whilst also reducing manufacturing costs.

Ions may be transmitted via the transfer optics 303 so that the ions arrive in a pusher electrode assembly 305. The pusher electrode assembly 305 may also be designed so as to provide high performance whilst at the same time reducing

manufacturing costs.

According to various embodiments a cantilevered Time of Flight stack 807 may be provided. The cantilevered arrangement may be used to mount a Time of Flight stack or flight tube 807 and has the advantage of both thermally and electrically isolating the Time of Flight stack or flight tube 807. The cantilevered arrangement represents a significant design departure from conventional instruments and results in substantial improvements in instrument performance.

According to an embodiment an alumina ceramic spacer and a plastic (PEEK) dowel may be used.

According to an embodiment when a lock mass is introduced and the instrument is calibrated then the Time of Flight stack or flight tube 807 will not be subjected to thermal expansion. The cantilevered arrangement according to various embodiments is in contrast to known arrangements wherein both the reflectron 306 and the pusher assembly 305 were mounted to both ends of a side flange. As a result conventional arrangements were subjected to thermal impact.

Ions may be arranged to pass into a flight tube 807 and may be reflected by a reflectron 306 towards an ion detector 811. The output from the ion detector 811 is passed to a pre-amplifier (not shown) and then to an Analogue to Digital Converter (“ADC”) (also not shown). The reflectron 306 is preferably designed so as to provide high performance whilst also reducing manufacturing cost and improving reliability.

As shown in Fig. 8 the various electrode rings and spacers which collectively form the reflectron subassembly may be mounted to a plurality of PEEK support rods 814. The reflectron subassembly may then be clamped to the flight tube 807 using one or more cotter pins 813. As a result, the components of the reflectron subassembly are held under compression which enables the individual electrodes forming the reflectron to be maintained parallel to each other with a high level of precision. According to various embodiments the components may be held under spring loaded compression.

The pusher electrode assembly 305 and the detector electronics or a discrete detector module may be mounted to a common pusher plate assembly 1012. This is described in more detail below with reference to Figs. 10A-10C.

The Time of Flight mass analyser 304 may have a full length cover 809 which may be readily removed enabling extensive service access. The full length cover 809 may be held in place by a plurality of screws e.g. 5 screws. A service engineer may undo the five screws in order to expose the full length of the time of flight tube 807 and the reflectron 306.

The mass analyser 304 may further comprise a removable lid 810 for quick service access. In particular, the removable lid 810 may provide access to a service engineer so that the service engineer can replace an entrance plate 1000 as shown in Fig. 10C. In particular, the entrance plate 1000 may become contaminated due to ions impacting upon the surface of the entrance plate 1000 resulting in surface charging effects and potentially reducing the efficiency of ion transfer from the transfer optics 303 into a pusher region adjacent the pusher electrode 305.

A SMA (SubMiniature version A) connector or housing 850 is shown but an AC coupler 851 is obscured from view.

Fig. 9 shows a pusher plate assembly 912, flight tube 907 and reflectron stack 908. A pusher assembly 905 having a pusher shielding cover is also shown. The flight tube 907 may comprise an extruded or plastic flight tube. The reflectron 306 may utilise fewer ceramic components than conventional reflectron assemblies thereby reducing manufacturing cost. According to various embodiments the reflectron 306 may make greater use of PEEK compared with conventional reflectron arrangements.

According to other embodiments the reflectron 306 may comprise a bonded reflectron. According to another embodiment the reflectron 306 may comprise a metalised ceramic arrangement. According to another embodiment the reflectron 306 may comprise a jigged then bonded arrangement.

According to alternative embodiments instead of stacking, mounting and fixing multiple electrodes or rings, a single bulk piece of an insulating material such as a ceramic may be provided. Conductive metalised regions on the surface may then be provided with electrical connections to these regions so as to define desired electric fields. For example, the inner surface of a single piece of cylindrical shaped ceramic may have multiple parallel metalised conductive rings deposited as an alternative method of providing potential surfaces as a result of stacking multiple individual rings as is known conventionally. The bulk ceramic material provides insulation between the different potentials applied to different surface regions. The alternative arrangement reduces the number of components thereby simplifying the overall design, improving tolerance build up and reducing manufacturing cost. Furthermore, it is contemplated that multiple devices may be constructed this way and may be combined with or without grids or lenses placed in between. For example, according to one embodiment a first grid electrode may be provided, followed by a first ceramic cylindrical element, followed by a second grid electrode followed by a second ceramic cylindrical element.

Fig. 10A shows a pusher plate assembly 1012 comprising three parts according to various embodiments. According to an alternative embodiment a monolithic support plate 1012a may be provided as shown in Fig. 10B. The monolithic support plate 1012a may be made by extrusion. The support plate 1012a may comprise a horse shoe shaped bracket having a plurality (e.g. four) fixing points 1013. According to an embodiment four screws may be used to connect the horse shoe shaped bracket to the housing of the mass spectrometer and enable a cantilevered arrangement to be provided. The bracket may be maintained at a voltage which may be the same as the Time of Flight voltage i.e. 4.5 kV. By way of contrast, the mass spectrometer housing may be maintained at ground voltage i.e. 0V.

Fig. 10C shows a pusher plate assembly 1012 having mounted thereon a pusher electrode assembly and an ion detector assembly 1011. An entrance plate 1000 having an ion entrance slit or aperture is shown.

The pusher electrode may comprise a double grid electrode arrangement having a 2.9 mm field free region between a second and third grid electrode as shown in more detail in Fig. 16C.

Fig. 11 shows a flow diagram illustrating various processes which may occur once a start button has been pressed.

According to an embodiment when the backing pump is turned ON a check may be made that the pressure is < 32 mbar within three minutes of operation. If a pressure of < 32 mbar is not achieved or established within three minutes of operation then a rough pumping timeout (amber) warning may be issued.

Fig. 12A shows the three different pumping ports of the turbo molecular pump according to various embodiments. The first pumping port H1 may be arranged adjacent the segmented quadrupole rod set 302. The second pumping port H2 may be arranged adjacent a first lens set of the transfer lens arrangement 303. The third pumping port (which may be referred to either as the H port or the H3 port) may be directly connected to Time of Flight mass analyser 304 vacuum chamber.

Fig. 12B shows from a different perspective the first pumping port H1 and the second pumping port H2. The user clamp 535 which is mounted in use to the ion block 802 is shown. The first ion guide 301 and the quadrupole rod set ion guide 302 are also indicated. A nebuliser or cone gas input 1201 is also shown. An access port 1251 is provided for measuring pressure in the source. A direct pressure sensor is provided (not fully shown) for measuring the pressure in the vacuum chamber housing the initial ion guide 301 and which is in fluid communication with the internal volume of the ion block 802. An elbow fitting 1250 and an over pressure relief valve 1202 are also shown.

One or more part-rigid and part-flexible printed circuit boards (“PCBs”) may be provided. According to an embodiment a printed circuit board may be provided which comprises a rigid portion 1203a which is located at the exit of the quadrupole rod set region 302 and which is optionally at least partly arranged perpendicular to the optic axis or direction of ion travel through the quadrupole rod set 302. An upper or other portion of the printed circuit board may comprise a flexible portion 1203b so that the flexible portion 1203b of the printed circuit board has a stepped shape in side profile as shown in Fig.

12B.

According to various embodiments the H1 and H2 pumping ports may comprise EMC splinter shields.

It is also contemplated that the turbo pump may comprise dynamic EMC sealing of the H or H3 port. In particular, an EMC mesh may be provided on the H or H3 port.

Fig. 13 shows in more detail the transfer lens arrangement 303 and shows a second differential pumping aperture (Aperture #2) 1301 which separates the vacuum chamber housing the segmented quadrupole rod set 302 from first transfer optics which may comprise two acceleration electrodes. The relative spacing of the lens elements, their internal diameters and thicknesses according to an embodiment are shown.

However, it should be understood that the relative spacing, size of apertures and thicknesses of the electrodes or lens elements may be varied from the specific values indicated in Fig. 13.

The region upstream of the second aperture (Aperture #2) 1301 may be in fluid communication with the first pumping port H1 of the turbo pump. A third differential pumping aperture (Aperture #3) 1302 may be provided between the first transfer optics and second transfer optics.

The region between the second aperture (Aperture #2) 1301 and the third aperture (Aperture #3) 1302 may be in fluid communication with the second pumping port H2 of the turbo pump.

The second transfer optics which is arranged downstream of the third aperture 1302 may comprises a lens arrangement comprising a first electrode which is electrical connection with the third aperture (Aperture #3) 1302. The lens arrangement may further comprise a second (transport) lens and a third (transport/steering) lens. Ions passing through the second transfer optics then pass through a tube lens before passing through an entrance aperture 1303. Ions passing through the entrance aperture 1303 pass through a slit or entrance plate 1000 into a pusher electrode assembly module.

The lens apertures after Aperture #3 1302 may comprise horizontal slots or plates. Transport 2/steering lens may comprise a pair of half plates.

The entrance plate 1000 may be arranged to be relatively easily removable by a service engineer for cleaning purposes.

One or more of the lens plates or electrodes which form a part of the overall transfer optics 303 may be manufactured by introducing an overcompensation etch of 5%. An additional post etch may also be performed. Conventional lens plates or electrodes may have a relatively sharp edge as a result of the manufacturing process. The sharp edges can cause electrical breakdown with conventional arrangements. Lens plates or electrodes which may be fabricated according to various embodiments using an overcompensation etching approach and/or additional post etch may have significantly reduced sharp edges which reduces the potential for electrical breakdown as well as reducing manufacturing cost.

Fig. 14A shows details of a known internal vacuum configuration and Fig. 14B shows details of a new internal vacuum configuration according to various embodiments.

A conventional arrangement is shown in Fig. 14A wherein the connection 700 from the backing pump to the first vacuum chamber of a mass spectrometer makes a T- connection into the turbo pump when backing pressure is reached. However, this requires multiple components so that multiple separate potential leak points are established. Furthermore, the T-connection adds additional manufacturing and maintenance costs.

Fig. 14B shows an embodiment wherein the backing pump 700 is only directly connected to the first vacuum chamber i.e. the T-connection is removed. A separate connection 1401 is provided between the first vacuum chamber and the turbo pump.

A high voltage supply feed through 1402 is shown which provides a high voltage (e.g. 1.1 kV) to the pusher electrode module 305. An upper access panel 810 is also shown. A Pirani pressure gauge 701 is arranged to measure the vacuum pressure in the vacuum chamber housing the first ion guide 301. An elbow gas fitting 1250 is shown through which desolvation/cone gas may be supplied. With reference to Fig. 14B, behind the elbow gas fitting 1250 is shown the over pressure relief valve 1202 and behind the over pressure relief valve 1202 is shown a further elbow fitting which enables gas pressure from the source to be directly measured.

Fig. 15A shows a schematic of the ion block 802 and source or first ion guide 301. According to an embodiment the source or first ion guide 301 may comprise six initial ring electrodes followed by 38-39 open ring or conjoined electrodes. The source or first ion guide 301 may conclude with a further 23 rings. It will be appreciated, however, that the particular ion guide arrangement 301 shown in Fig. 15A may be varied in a number of different ways. In particular, the number of initial ring electrodes (e.g. 6) and/or the number of final stage (e.g. 23) ring electrodes may be varied. Similarly, the number of intermediate open ring or conjoined ring electrodes (e.g. 38-39) may also be varied.

It should be understood that the various dimensions illustrated on Fig. 15A are for illustrative purposes only and are not intended to be limiting. In particular, embodiments are contemplated wherein the sizing of ring and/or conjoined ring electrodes may be different from that shown in Fig. 15A.

A single conjoined ring electrode is also shown in Fig. 15A.

According to various embodiment the initial stage may comprise 0-5, 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50 or > 50 ring or other shaped electrodes. The intermediate stage may comprise 0-5, 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35- 40, 40-45, 45-50 or > 50 open ring, conjoined ring or other shaped electrodes. The final stage may comprise 0-5, 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50 or > 50 ring or other shaped electrodes.

The ring electrodes and/or conjoined ring electrodes may have a thickness of 0.5 mm and a spacing of 1.0 mm. However, the electrodes may have other thicknesses and/or different spacings.

Aperture #1 plate may comprise a differential pumping aperture and may have a thickness of 0.5 mm and an orifice diameter of 1.50 mm. Again, these dimensions are illustrative and are not intended to be limiting.

A source or first ion guide RF voltage may be applied to all Step 1 and Step 2 electrodes in a manner as shown in Fig. 15A. The source or first ion guide RF voltage may comprise 200 V peak-to-peak at 1.0 MHz.

Embodiments are contemplated wherein a linear voltage ramp may be applied to Step 2 Offset (cone).

The Step 2 Offset (cone) voltage ramp duration may be made equal to the scan time and the ramp may start at the beginning of a scan. Initial and final values for the Step 2 Offset (cone) ramp may be specified over the complete range of Step 2 Offset (cone).

According to various embodiments a resistor chain as shown in Fig. 15B may be used to produce a linear axial field along the length of Step 1. Adjacent ring electrodes may have opposite phases of RF voltage applied to them.

A resistor chain may also be used to produce a linear axial field along the length of Step 2 as shown in Fig. 15C. Adjacent ring electrodes may have opposite phases of RF voltage applied to them.

Embodiments are contemplated wherein the RF voltage applied to some or substantially all the ring and conjoined ring electrodes forming the first ion guide 301 may be reduced or varied in order to perform a non-mass to charge ratio specific attenuation of the ion beam. For example, as will be appreciated, with a Time of Flight mass analyser 304 the ion detector 307 may suffer from saturation effects if an intense ion beam is received at the pusher electrode 305. Accordingly, the intensity of the ion beam arriving adjacent the pusher electrode 305 can be controlled by varying the RF voltage applied to the electrodes forming the first ion guide 301. Other embodiments are also contemplated wherein the RF voltage applied to the electrodes forming the second ion guide 302 may additionally and/or alternatively be reduced or varied in order to attenuate the ion beam or otherwise control the intensity of the ion beam. In particular, it is desired to control the intensity of the ion beam as received in the pusher electrode 305 region.

Fig. 16A shows in more detail the quadrupole ion guide 302 according to various embodiments. The quadrupole rods may have a diameter of 6.0 mm and may be arranged with an inscribed radius of 2.55 mm. Aperture #2 plate which may comprise a differential pumping aperture may have a thickness of 0.5 mm and an orifice diameter of 1.50 mm. The various dimensions shown in Fig. 16A are intended to be illustrative and non-limiting.

The ion guide RF amplitude applied to the rod electrodes may be controllable over a range from 0 to 800 V peak-to-peak.

The ion guide RF voltage may have a frequency of 1.4 MHz. The RF voltage may be ramped linearly from one value to another and then held at the second value until the end of a scan.

As shown in Fig. 16B, the voltage on the Aperture #2 plate may be pulsed in an Enhanced Duty Cycle mode operation from an Aperture 2 voltage to an Aperture 2 Trap voltage. The extract pulse width may be controllable over the range 1-25 ps. The pulse period may be controllable over the range 22-85 ps. The pusher delay may be controllable over the range 0-85 ps.

Fig. 16C shows in more detail the pusher electrode arrangement. The grid electrodes may comprise 0 60 parallel wire with 92% transmission (0 0.018 mm parallel wires at 0.25 mm pitch). The dimensions shown are intended to be illustrative and non limiting.

Fig. 16D shows in more detail the Time of Flight geometry. The region between the pusher first grid, reflectron first grid and the detector grid preferably comprises a field free region. The position of the ion detector 307 may be defined by the ion impact surface in the case of a MagneTOF (RTM) ion detector or the surface of the front MCP in the case of a MCP detector.

The reflectron ring lenses may be 5 mm high with 1 mm spaces between them.

The various dimensions shown in Fig. 16D are intended to be illustrative and non-limiting.

According to various embodiments the parallel wire grids may be aligned with their wires parallel to the instrument axis. It will be understood that the instrument axis runs through the source or first ion guide 301 through to the pusher electrode assembly 305.

A flight tube power supply may be provided which may have an operating output voltage of either +4.5 kV or -4.5 kV depending on the polarity requested.

A reflectron power supply may be provided which may have an operating output voltage ranging from 1625 ± 100 V or -1625 ± 100 V depending on the polarity requested.

Fig. 16E is a schematic of the Time of Flight wiring according to an embodiment. The various resistor values, voltages, currents and capacitances are intended to be illustrative and non-limiting. According to various embodiments a linear voltage gradient may be maintained along the length of the reflectron 306. In a particular embodiment a reflectron clamp plate may be maintained at the reflectron voltage.

An initial electrode and associated grid 1650 of the reflectron 306 may be maintained at the same voltage or potential as the flight tube 807 and the last electrode of the pusher electrode assembly 305. According to an embodiment the initial electrode and associated grid 1650 of the reflectron 306, the flight tube 807 and the last electrode and associated grid of the pusher electrode assembly 305 may be maintained at a voltage or potential of e.g. 4.5 kV of opposite polarity to the instrument or mode of operation. For example, in positive ion mode the initial electrode and associated grid 1650 of the reflectron 306, the flight tube 807 and the last electrode and associated grid of the pusher electrode assembly 305 may be maintained at a voltage or potential of -4.5 kV.

The second grid electrode 1651 of the reflectron 306 may be maintained at ground or OV.

The final electrode 1652 of the reflectron 306 may be maintained at a voltage or potential of 1.725 kV of the same polarity as the instrument. For example, in positive ion mode the final electrode 1652 of the reflectron 306 may be maintained at a voltage or potential of +1.725 kV.

It will be understood by those skilled in the art that the reflectron 306 acts to decelerate ions arriving from the time of flight region and to redirect the ions back out of the reflectron 306 in the direction of the ion detector 307.

The voltages and potentials applied to the reflectron 306 according to various embodiments and maintaining the second grid electrode 1651 of the reflectron at ground or 0V is different from the approach adopted in conventional reflectron arrangements.

The ion detector 307 may always be maintained at a positive voltage relative to the flight tube voltage or potential. According to an embodiment the ion detector 307 may be maintained at a +4 kV voltage relative to the flight tube.

Accordingly, in a positive ion mode of operation if the flight tube is maintained at an absolute potential or voltage of -4.5 kV then the detector may be maintained at an absolute potential or voltage of -0.5 kV.

Fig. 16F shows the DC lens supplies according to an embodiment. It will be understood that Same polarity means the same as instrument polarity and that Opposite polarity means opposite to instrument polarity. Positive means becomes more positive as the control value is increased and Negative means becomes more negative as the control value is increased. The particular values shown in Fig. 16F are intended to be illustrative and non-limiting.

Fig. 16G shows a schematic of an ion detector arrangement according to various embodiments. The detector grid may form part of the ion detector 307. The ion detector 307 may, for example, comprise a MagneTOF (RTM) DM490 ion detector. The inner grid electrode may be held at a voltage of +1320 V with respect to the detector grid and flight tube via a series of zener diodes and resistors. The ion detector 307 may be connected to a SMA 850 and an AC coupler 851 which may both be provided within or internal to the mass analyser housing or within the mass analyser vacuum chamber. The AC coupler 851 may be connected to an externally located preamp which in turn may be connected to an Analogue to Digital Converter (“ADC”) module.

Fig. 16H shows a potential energy diagram for an instrument according to various embodiments. The potential energy diagram represents an instrument in positive ion mode. In negative ion mode all the polarities are reversed except for the detector polarity. The particular voltages/potentials shown in Fig. 16H are intended to be illustrative and non-limiting.

The instrument may include an Analogue to Digital Converter (“ADC”) which may be operated in peak detecting ADC mode with fixed peak detecting filter coefficients. The ADC may also be run in a Time to Digital Converter (“TDC”) mode of operation wherein all detected ions are assigned unit intensity. The acquisition system may support a scan rate of up to 20 spectra per second. A scan period may range from 40 ms to 1 s. The acquisition system may support a maximum input event rate of 7x10⁶ events per second.

According to various embodiments the instrument may have a mass accuracy of 2- 5 ppm may have a chromatographic dynamic range of 10⁴. The instrument may have a high mass resolution with a resolution in the range 10000-15000 for peptide

mapping. The mass spectrometer 100 is preferably able to mass analyse intact proteins, glycoforms and lysine variants. The instrument may have a mass to charge ratio range of approx. 8000.

Instrument testing was performed with the instrument fitted with an ESI source 401. Sample was infused at a flow rate of 400 mL/min. Mass range was set to m/z 1000. The instrument was operated in positive ion mode and high resolution mass spectral data was obtained.

According to various embodiments the instrument may have a single analyser tune mode i.e. no sensitivity and resolution modes.

According to various embodiments the resolution of the instrument may be in the range 10000-15000 for high mass or mass to charge ratio ions such as peptide mapping applications. The resolution may be determined by measuring on any singly charged ion having a mass to charge ratio in the range 550-650.

The resolution of the instrument may be around 5500 for low mass ions. The resolution of instrument for low mass ions may be determined by measuring on any singly charged ion having a mass to charge ratio in the range 120-150.

According to various embodiments the instrument may have a sensitivity in MS positive ion mode of approx. 11 ,000 counts/second. The mass spectrometer 100 may have a mass accuracy of approx. 2-5 ppm

Mass spectral data obtained according to various embodiments was observed as having reduced in-source fragmentation compared with conventional

instruments. Adducts are reduced compared with conventional instruments. The mass spectral data also has cleaner valleys (<20%) for mAb glycoforms.

As disclosed in US 2015/0076338 (Micromass), the contents of which are incorporated herein by reference, the instrument according to various embodiment may comprise a plurality of discrete functional modules. The functional modules may comprise, for example, electrical, mechanical, electromechanical or software components. The modules may be individually addressable and may be connected in a network. A scheduler may be arranged to introduce discrete packets of instructions to the network at predetermined times in order to instruct one or more modules to perform various operations. A clock may be associated with the scheduler.

The functional modules may be networked together in a hierarchy such that the highest tier comprises the most time-critical functional modules and the lowest tier comprises functional modules which are the least time time-critical. The scheduler may be connected to the network at the highest tier.

For example, the highest tier may comprise functional modules such as a vacuum control system, a lens control system, a quadrupole control system, an electrospray module, a Time of Flight module and an ion guide module. The lowest tier may comprise functional modules such as power supplies, vacuum pumps and user displays.

The mass spectrometer 100 according to various embodiments may comprise multiple electronics modules for controlling the various elements of the spectrometer. As such, the mass spectrometer may comprise a plurality of discrete functional modules, each operable to perform a predetermined function of the mass spectrometer 100, wherein the functional modules are individually addressable and connected in a network and further comprising a scheduler operable to introduce discrete packets of instructions to the network at predetermined times in order to instruct at least one functional module to perform a predetermined operation.

The mass spectrometer 100 may comprise an electronics module for controlling (and for supplying appropriate voltage to) one or more or each of: (i) the source; (ii) the first ion guide; (iii) the quadrupole ion guide; (iv) the transfer optics; (v) the pusher electrode; (vi) the reflectron; and (vii) the ion detector.

This modular arrangement may allow the mass spectrometer to be reconfigured straightforwardly. For example, one or more different functional elements of the spectrometer may be removed, introduced or changed, and the spectrometer may be configured to automatically recognised which elements are present and to configure itself appropriately.

The instrument may allow for a schedule of packets to be sent onto the network at specific times and intervals during an acquisition. This reduces or alleviates the need for a host computer system with a real time operating system to control aspects of the data acquisition. The use of packets of information sent to individual functional modules also reduces the processing requirements of a host computer.

The modular nature conveniently allows flexibility in the design and/or

reconfiguring of a mass spectrometer. According to various embodiments at least some of the functional modules may be common across a range of mass spectrometers and may be integrated into a design with minimal reconfiguration of other modules.

Accordingly, when designing a new mass spectrometer, wholesale redesign of all the components and a bespoke control system are not necessary. A mass spectrometer may be assembled by connecting together a plurality of discrete functional modules in a network with a scheduler.

Furthermore, the modular nature of the mass spectrometer 100 according to various embodiments allows for a defective functional module to be replaced easily. A new functional module may simply be connected to the interface. Alternatively, if the control module is physically connected to or integral with the functional module, both can be replaced.

Fig. 8 shows a schematic perspective view of an embodiment of the present invention, with some of the outer cover panels removed. The spectrometer comprises an ion block 802 having an ion sampling cone arranged thereon, an orthogonal acceleration Time of Flight (TOF) mass analyser 304, and ion optics for transferring ions from the sampling cone to the TOF mass analyser. The ion optics for transferring ions from the sampling cone to the TOF mass analyser comprises a first ion guide 301 , a second ion guide 302 and a transfer lens 303. The TOF mass analyser comprises a pusher assembly 805 for orthogonally accelerating ions, a flight tube 807, an ion mirror (i.e. reflectron 306) and an ion detector.

As shown more clearly in the schematic of Fig. 17A, the ion optics and TOF mass analyser 304 are housed in vacuum chambers of a vacuum housing that, in use, are evacuated by gas pumps. More specifically, the first ion guide 303 is arranged in a first vacuum chamber 1701 that has the ion sampling cone 513 and an apertured wall 1710 at its axial ends for allowing ions to pass therethrough. This first chamber 1701 may be evacuated, e.g. by a backing pump (or roughing pump), through gas line 700. The second ion guide 302 is arranged in a second vacuum chamber 1702 that has apertured walls 1710, 1301 at its axial ends for allowing ions to pass therethrough. This second vacuum chamber 1702 may be evacuated through gas port H1. The transfer lens 303 comprises an apertured electrode that forms a differential pumping aperture, thereby defining a third vacuum chamber 1703 and a fourth vacuum chamber 1704. The third vacuum chamber 1703 may be evacuated through gas port H2, and the fourth vacuum chamber 1704 may be evacuated through gas port H3. The transfer lens 303 may extend into both the third and fourth vacuum chambers, for transferring ions into the pusher assembly 305 of the TOF mass analyser 304. In the depicted embodiment, the second, third and fourth vacuum chambers 1702,1703, 1704 are evacuated by the same pump, which may be a split-flow turbopump 1700 connected to gas exhaust ports H1 , H2 and H3. However, it is contemplated that multiple pumps could be used to evacuate gas through the ports H1 , H2, H3. Fig. 17A also schematically shows an ion source located over the ion sampling orifice 1705.

Fig. 14B shows a schematic perspective view of the embodiment shown in Fig. 8, except from the opposite side. This view better illustrates the gas line 700 that is connected to the backing pump (not shown) for evacuating the first vacuum chamber 1701. The instrument also comprises a gas line 1401 between the turbopump 1700 and first vacuum chamber 1701 , such that the turbopump 1700 is in fluid communication with the backing pump via the gas line 700 and first vacuum chamber 1701. This allows the backing pump to pump down the pressure of the turbopump 1700 before the turbopump is activated.

As shown in Fig. 8 and 17C, the vacuum housing has apertures 1730 arranged through its wall, proximate the ion optics 301 , 302, 303, and printed circuit boards (PCBs) 801 a, 801 b are arranged in these apertures for providing electrical communications through the vacuum housing wall to the ion optics.

Figs. 12B and 17B show schematic, cross-sectional views through parts of the spectrometer shown in Fig. 8 and illustrate the ion optics 301 , 302, 303 in more detail. More specifically, Fig. 12B shows the ion block 802, first ion guide 301 , second ion guide 302 and transfer lens 303 in more detail. Fig. 17B shows the second ion guide 302, transfer lens 303 and pusher assembly 305 of the TOF mass analyser in more detail. Fig. 17C shows a schematic cross-sectional view in the plane orthogonal to the longitudinal axis of the ion optics 301 , 302, 303, and at a point where a PCB 801a (or 801 b) is located.

The general operation of the spectrometer will now be described. In operation, the vacuum pumps are switched on, which evacuate gas from the vacuum chambers 1701 , 1702, 1703, 1704 through the above described vacuum ports until the vacuum chambers are at the desired pressure. More specifically, the backing pump may be activated so as to evacuate the first vacuum chamber 1701 and the turbopump 1700 via the gas line 700. The turbopump 1700 may then be activated so as to evacuate the second 1701 , third 1702 and fourth 1704 vacuum chambers. As each vacuum chamber is pumped, the gas load decreases for successive vacuum chambers, in the downstream direction. The vacuum pumps may therefore cause the successive vacuum chambers to have successively decreasing gas pressures. This enables the TOF mass analyser to be maintained at the low pressure desired for TOF mass analysis. For example, the ion source 300 may be at around atmospheric pressure, the first vacuum chamber 1701 may be pumped down to around T¹⁰ mbar, the second vacuum chamber 1702 may be pumped down to around 10² mbar, the third vacuum chamber 1703 may be pumped down to around 10⁴ mbar, and the fourth vacuum chamber 1704 may be pumped down to around 10⁶ mbar. However, the chambers 1701 , 1702, 1703, 1704 may be maintained at other pressures.

As described above, an ion source 300 is arranged adjacent to the ion sampling cone 513. This may be an atmospheric pressure ion source such as an electrospray ion source, although ion sources of other types and/or that operate at other pressures may be used. The ion source outlet may be provided inside of an ion source housing (not shown), which may be secured over the ion sampling block so that the ion source is enclosed between the ion source housing and the ion block.

Ions generated from the ion source pass 300 towards and through the ion sampling orifice 1705 and into the first ion guide 301. RF voltages are applied to the electrodes of the first ion guide 301 so as to radially confine the ions therein. The first ion guide 301 guides ions along its longitudinal axis so that they pass through the aperture 1713 in the downstream wall 1710 of the first vacuum chamber and into the second ion guide 302 in the second vacuum chamber 1702. The first ion guide 301 may be configured in a manner that allows it to transmit ions through to the second ion guide 302, whilst allowing neutral or relatively large cluster species to be pumped out of the vacuum housing by the vacuum pump. As such, the ion sampling orifice 1705 may be made relatively large, enabling the sensitivity of the instrument to be relatively high. Modes are also contemplated in which the ions are fragmented, or are not fragmented, in or downstream of the first ion guide 301. The form of the ion guide will be described in more detail further below.

Ions transmitted by the first ion guide 301 pass into the second ion guide 302, which may be of any form, although a multiple rod set ion guide such as a quadrupole rod set ion guide is contemplated in the embodiments. RF voltages are applied to the electrodes of the second ion guide so as to radially confine the ions therein. The second ion guide 302 may be segmented into a plurality of axial segments that are maintained at different DC voltages such that ions are urged through the second ion guide 302 by a DC voltage gradient and towards aperture 1301 in the downstream wall of the second vacuum chamber 1702. The ions then pass through the aperture and into the transfer lens 303 arranged in the third vacuum chamber 1703. The ions are transmitted by the transfer lens 303 into the fourth vacuum chamber 1704 and into the pusher assembly 305 of the TOF mass analyser. The pusher assembly 305 is an orthogonal accelerator that receives the ions along a first dimension and which has electrodes and a pulsed voltage supply that pulse the ions in a second dimension that is orthogonal to the first dimension, and into a field-free flight region inside the flight tube. The ions travel through the flight region 804 and into the ion mirror 306, in which they are reflected back in the second dimension. The ions maintain a component of velocity in the first dimension and as such they are reflected back by the ion mirror 306 onto the ion detector 307. As is known to the skilled person, the ions separate according to their mass to charge ratio as they travel through the field- free region. The spectrometer is therefore able to determine the mass to charge ratio of a given ion from the duration of time that has elapsed between that ion being pulsed by the pusher assembly and the time that it has been detected at the ion detector.

Various components of the spectrometer will now be described in more detail.

As described above, PCBs 801a, 801b are provided for supplying the electrodes of the ion optics 301 , 302, 303 with the desired voltages, e.g. RF and/or DC voltages. The vacuum housing wall 1733 has apertures 1730 (i.e. windows) therethrough that are proximate the ion optics. PCBs 801a, 801 b are provided over the apertures for providing electrical communication through the wall of the vacuum housing. The PCB 801a, 801 b and vacuum housing wall 1733 are configured so that a vacuum seal is provided between each PCB and the vacuum housing wall, thereby preventing gas from leaking passed the PCB and into the vacuum housing when the vacuum pump is operating. Each PCB 801a, 801 b may be arranged so that it has it central portion 1731 covering its respective aperture 1730 in the vacuum housing and a peripheral portion 1732 arranged over the vacuum housing wall 1733. As best seen in Figs. 12B and 17B, fixing members 1734, such as screws or bolts, may be arranged through the peripheral portion 1732 of the PCB and secured into the vacuum housing wall 1733 so as to hold the PCB against the vacuum housing wall 1733 in a gas tight manner. A resilient seal 1735 may be provided between the PCB and the vacuum housing wall 1733 (e.g. surrounding the aperture 1730 in the vacuum housing) to assist the gas-tight seal, as shown in Fig. 17C. The thickness of the vacuum housing wall 1733 may be stepped so that the wall is relatively thin around the aperture 1730, in the region on which the peripheral portion 1732 of the PCB is located, and is thicker laterally adjacent to and outwards of the peripheral portion 1732 of the PCB, e.g. as shown in Fig. 12B. The peripheral portion 1732 of the PCB may therefore be embedded in the vacuum housing wall 1733, and the external surface 1736 of the PCB may be substantially flush with the vacuum housing wall 1733. The fixing members 1734 may be fixed through the peripheral portion 1732 of the PCB into the thinner portion of the vacuum housing wall. This embedded configuration of the PCB may help maintain the vacuum seal.

A conventional PCB substrate may be used in the PCBs 801 a, 802b. However, it is also contemplated that the PCB used may have had one or more of its external layers removed such that the surface 1737 of the PCB facing the vacuum housing makes better surface contact with the housing wall 1733. For example, the outer resistive layer of the PCB may have been removed, at least in the peripheral region 1732 of the PCB.

The electrodes of the first ion guide 301 are electrically connected to the internal side 1373 of a first of the PCBs 801 a (i.e. the side facing the vacuum housing), and the electrodes of the second ion guide 302 and transfer lens 303 are electrically connected to the internal side 1373 of a second of the PCBs 801 b. However, it is contemplated that a third PCB may be provided in a further aperture through the vacuum housing wall and that the second ion guide 302 and transfer lens 303 may be electrically connected to the internal sides of the second and third PCBS, respectively, i.e. to separate PCBs. The use of multiple PCBs enables each PCB, and each corresponding vacuum housing wall aperture, to be made relatively small. This enables the PCBs to withstand the pressure differential across them without being damaged. However, it is contemplated that all of the ion optics may be connected to a single PCB.

The vacuum chambers in TOF mass spectrometers are maintained at relatively low pressures in use. Each PCB 801a, 801 b must therefore be sized and configured to withstand a relatively high pressure differential across it, due to the low pressure vacuum chamber on its inner surface and atmospheric pressure region (or other higher pressure region) on its outer surface. For example, each PCB may be sized and configured such that when arranged in its respective aperture 1730 in the vacuum housing wall 1733 it is able to withstand a pressure differential across it of: ³ 1 x 10⁴ mbar, ³ 5 x 10⁴ mbar, ³ 1 x 10⁵ mbar, ³ 5 x 10⁵ mbar, ³ 1 x 10⁶ mbar, ³ 5 x 10⁶ mbar, ³ 1 x 10⁷ mbar, ³ 5 x 10⁷ mbar,

³ 1 x 10⁸ mbar, ³ 5 x 10⁸ mbar, ³ 1 x 10⁹ mbar, ³ 5 x 10⁹ mbar, ³ 1 x 10¹° mbar, ³ 5 x 10¹° mbar, ³ 1 x 10¹¹ mbar, ³ 5 x 10¹¹ mbar, ³ 1 x 10¹² mbar, or ³ 5 x 10¹² mbar. PCBs along different parts of the instrument may be sized and configured such that when arranged in their respective apertures 1730 in the vacuum housing wall 1733 they are able to withstand different pressure differentials across them. For example, the vacuum pressure in the spectrometer may be greater in a downstream region than an upstream region, as the TOF mass analyser must be at low pressure, and therefore a first PCB 804a arranged at the upstream region in the spectrometer may be arranged and configured to withstand a lower pressure differential across it than a second PCB 804b arranged at the downstream region.

RF and/DC voltage supplies and voltage controllers may be located outside of the vacuum housing and connected to the external sides 1736 of the PCBs, i.e. the sides facing away from the vacuum housing. These RF and/DC voltage supplies and voltage controllers may be connected to the PCBs by plug in connectors, such as the pin connectors shown 817a, 817b. This allows easy connection and disconnection of the voltage supplies and voltage controllers. Embodiments are contemplated wherein the voltage controllers and/or voltage supplies are arranged in a voltage controller module 1740a, 1740b (shown in Figs. 17C and 17D) and are electrically connected to an external connector 1741a, 1741 b on the outer surface 1742a, 1742b of the housing module. The external connector 1741a, 1741 b of the housing module may be complementary to the connector 817a, 817b on the PCB such that the housing module connector can be directly plugged into the PCB connector, i.e. without the use of intermediate cables. This allows the voltage source and controller to be arranged closer to the ion optics 301 , 302, 303 and hence reduces the length of electric cables therebetween, and RF pickup or interference associated therewith.

Although the PCBs 801a, 801 b have been described as supplying voltages through the vacuum housing wall to the ion optics 301 , 302, 303, they may also supply voltages or electrical signals to other components. For example, the ion source 300 may include an electrical heater and the PCB may supply power to the heater.

The first ion guide 301 may be an ion guide that guides ions along a first axial path

1801 and then onto and along a second axial path 1802 that is displaced from the first axial path.

Fig. 18A shows a schematic of the first ion guide 301 arranged in the first vacuum chamber 1701 that is between the ion sampling orifice 1705 and the second ion guide 302. The first ion guide 301 may comprise a first portion 1811 for guiding ions along a first axial path 1801 , a second portion 1812 for guiding ions along a second axial path

1802 (which may be parallel to and displaced the first axial path), and a transition portion 1813 for transferring ions from the first axial path to the second axial path. In the depicted embodiment , each of the first 1811 and second 1812 ion guide portions may comprise a plurality of axially separated apertured electrodes 1821 , 1822, 1841 , 1842 (e.g. ring electrodes) for radially confining the ions along their respective axial paths. RF voltages are applied to these electrodes so as to radially confine the ions. For example, different (e.g. opposite) phases of an RF voltage supply may be applied to adjacent apertured electrodes in the known manner so as to radially confine the ions.

Fig. 18B shows three cross-sectional views of the electrode arrangement in the first ion guide 301 at different axial points along the ion guide. View 1 shows the electrode arrangement proximate the sampling cone 513, where the ions are confined in the first portion 1811 of the first ion guide to the first axial path by the apertured electrodes 1821. View 3 shows the electrode arrangement proximate the differential pumping aperture 1713, where the ions are confined in the second portion 1812 of the ion guide 301 to the second axial path by the apertured electrodes 1842. View 2 shows the electrode arrangement in the transition region 1813 of the ion guide, in which the ions are transferred from the first axial path of the first ion guide portion 1811 to the second axial path of the second ion guide portion 1812. The transition region 1813 may comprise a plurality of such electrodes 1831 , 1832 at axially spaced locations. The ion transfer between the first and second axial paths in the transition region 1813 may be achieved by: providing one or more electrodes 1831 in the transition region, each of which only partially encircles the first axial path and has a radial opening 1833 in its side that is directed towards the second axial path (e.g. an arc-shaped electrode); providing one or more electrodes 1832 in the transition region, each of which only partially encircles the second axial path and has a radial opening 1834 in its side that is directed towards the first axial path (e.g. an arc-shaped electrode); and urging ions from the first axial path, through the radial openings 1833, 1834 in the electrodes 1831 , 1832 , and onto the second axial path. This urging of the ions may be performed by providing an electrical potential difference, e.g. by applying voltages to the electrodes 1831 , 1832 in the transition region 1813 so as to provide a potential difference in the radial direction.

Referring back to Fig. 18A, the first ion guide portion 1801 may be arranged in the first vacuum chamber 1701 such that the gas path from the sampling cone 513 is aligned (e.g. coaxial) with the first axial path 1801 defined by the first ion guide portion 1811. The second ion guide portion 1812 may be arranged in the first vacuum chamber 1701 such that the differential pumping aperture 1713 between the first and second vacuum chambers 1701 , 1702 is aligned (e.g. coaxial) with the second axial path 1802 defined by the second ion guide portion 1812. The axis of the second ion guide 302 may be aligned (e.g. coaxial) with the second axial path 1802 defined by the second ion guide portion 1812 of the first ion guide 301.

As described above, a vacuum pump is provided for evacuating the first vacuum chamber 1701 through a gas pumping port 1855. The opening 1706 of the gas pumping port 1855 may be arranged in the wall of the first vacuum chamber 1701 at a point downstream of the first ion guide portion 1811. For example, the opening 1706 of the gas pumping port may be aligned (e.g. coaxial) with the first axial path 1801 of the first ion guide portion 1811. The end of the ion guide formed by the second portion 1812 may be physically shielded from the gas pumping port 1855 by a barrier. However, although the gas pumping port 1855 is shown schematically in Fig. 18A as being adjacent the first ion guide 301 , it may be located at another location in the first vacuum chamber.

In operation, ions from the ion source 300 pass through the sampling cone 513 and into the first vacuum chamber 1701 , whereby the gas and ions tend to expand into the lower pressure region. The ions enter into the first portion 1811 of the ion guide and are radially confined thereby, but may be relatively diffuse, as shown by ion cloud 1850. The ions are driven axially along the first portion 1811 of the ion guide, which may be achieved by a voltage gradient and/or the gas flow towards the gas pumping port 1855. When ions reach the transition portion 1813 of the ion guide, they are urged in the radial direction and onto the second axial path 1802 defined by the second portion 1812 of the ion guide, as shown by ion trajectories 1851. As described above, this may be caused by applying a potential difference in the radial direction. As a result, ions are caused to migrate from the first ion guide portion 1811 to the second ion guide portion 1812. In contrast, the majority of the gas flow continues towards and through the gas pumping port 1855, e.g. substantially along the axis defined by the first ion guide portion 1811 , as shown by arrow 1852. Ions are therefore radially confined in the second ion guide portion 1812 and travel along the second axial path 1802 towards the differential pumping aperture 1713, whereas the majority of the gas is routed in a different direction towards the gas pumping port 1855. At least part of the second portion 1812 of the ion guide may be shielded from the pumping port 1855 by a barrier 1853, so that the gas flow towards the pumping port 1855 is directed away from the second axial path 1802 of the second ion guide portion 1812.

The second ion guide portion 1812 may have a smaller radial cross-section than the first portion 1811 so that the ions are radially compressed in the second portion as compared to the first portion, as shown by ion beam 1854. Ions are then guided by the second ion guide portion 1812 through the differential pumping aperture 1713 and into the second vacuum chamber 1702.

The ion guide 301 in the above-described arrangement is able to handle relatively high gas loads (e.g. since the ion guide initially conveys the ions with the gas flow towards the pumping port 1855 and then moves the ions out of the gas flow), and the first ion guide therefore enables the first vacuum chamber 1701 to be operated at relatively high pressures. The ion sampling aperture 1705 may therefore be relatively large, thereby increasing the ion transmission into the first ion guide and ultimately through to the mass analyser. The signal to noise ratio of the instrument may therefore be relatively high.

As described above, one or more potential gradient may be provided along the first ion guide 301 in order to urge ions through the first vacuum chamber 1701. Different DC voltages may be applied to the axially spaced electrodes 1821 , 1822, 1831 , 1832, 1841 , 1842 of the first ion guide 301 in order to provide such one or more potential gradient. Different voltages may be applied to different ones of the electrodes 1821 , 1831 forming the first axial path 1801 (e.g. to electrodes of both the first ion guide portion 1811 and transition portion 1813) so as to provide a first potential gradient that urges ions through the first vacuum chamber 1701 and towards the second vacuum chamber 1702. Different voltages may be applied to different ones of the electrodes forming the second axial path 1832, 1842 (e.g. to electrodes of both the transition portion 1813 and the second portion of the ion guide 1812) so as to provide a second potential gradient that urges ions through the first vacuum chamber 170 and towards the second vacuum chamber 1702. At least some of the voltages applied to the first ion guide 301 for forming the first potential gradient may be greater in magnitude than at least some of the voltages applied to the first ion guide 301 for forming the second potential gradient. The differential pumping aperture 1713 between the first and second vacuum chambers may be maintained at a DC voltage that is lower than the DC voltages applied to the first ion guide to form the potential gradients, such that ions are urged towards this aperture 1713.

It may be desired to operate the spectrometer in a first mode in which the ions are not fragmented as they are transmitted to the mass analyser and/or in a second mode in which the ions are fragmented as they are transmitted to the mass analyser. The fragmentation in the second mode may be achieved using dedicated fragmentation cells. However, fragmentation of the ions may alternatively be performed by controlling the voltages applied to the ion optics 301 , 302, 303 so as to accelerate the ions to collide with the background gas in the vacuum chamber(s) 1701 , 1702, 1703 and fragment, i.e. via Collisionally Induced Dissociation (CID).

In embodiments, such fragmentation may be achieved by controlling the voltages applied to the first ion guide 301 , relative to the voltage of an adjacent downstream electrode such as the differential pumping aperture 1713, so as to accelerate the ions to fragment. For example, the electrode at the downstream end of the first ion guide may be maintained at a higher potential than the said adjacent electrode (e.g. electrode differential pumping aperture 1713) so as to cause such acceleration and fragmentation.

In contrast, in the first mode the voltages applied to the first ion guide 301 , relative to the voltage of said downstream electrode 1713 (e.g. differential pumping aperture), may be controlled such that the ions are not accelerated to the extent that they are fragmented in the first mode. It will therefore be appreciated that the voltages applied to the first ion guide 301 may be varied with time so as to change between the first and second modes. When the spectrometer switches from the first mode to the second mode, the electric potential applied to electrode at the downstream end of the first ion guide may be increased so as to cause the ions to be accelerated into fragmentation. In these embodiments, the potentials applied to the other upstream electrodes of the first ion guide may also be increased, e.g. by the same or a proportional amount, as the spectrometer switches from the first mode to the second mode. This ensures that the potential gradient(s) for urging ions through and out of the first ion guide 301 are maintained even when the spectrometer is in the second, fragmentation mode. Conversely, when the spectrometer switches from the second mode to the first mode, the electric potential applied to electrode at the downstream end of the first ion guide may be decreased so that the ions are not accelerated into fragmentation. The potentials applied to the other upstream electrodes of the first ion guide 301 may also be decreased, e.g. by the same or a proportional amount, as the spectrometer switches from the second mode to the first mode.

Although embodiments have been described in which the potential(s) applied to the first ion guide 301 are increased when switching from the non-fragmentation mode to the fragmentation mode, and vice-versa, it is contemplated that alternatively (or additionally) the potential applied to said adjacent downstream electrode (e.g. differential pumping aperture 1713) may be decreased when switching from the non-fragmentation mode to the fragmentation mode, and vice versa.

As described herein, the first ion guide 301 is able to handle relatively high gas loads, which enables the first vacuum chamber 1701 to be operated at relatively high pressures. When the spectrometer is operated in the fragmentation mode, this enables efficient CID fragmentation to be performed in this region.

Less preferred embodiments are contemplated wherein ions may be accelerated into CID fragmentation with the background gas by travelling one or more DC potential barrier along the first and/or second and/or transition ion guide portions so as to urge the ions to collide with the gas molecules. This may be performed by successively applying one or more transient DC voltage to successive electrodes along the ion guide 301.

It has been recognised that it may be desirable to attenuate the ions being transmitted to the time of flight mass analyser, e.g. in order to prevent detector saturation if the ion source is particularly intense. For example, if the analyte is provided to the ion source 300 in a particularly dirty solvent then contaminant ions may be generated in relatively high abundancy and may obscure the analyte ion signal. This has not been problematic in previous instruments, such as those having quadrupole mass analysers, as the quadrupole mass filter therein filters out ions other than those in a narrow range of mass to charge ratios that are desired to be transmitted.

According to the embodiments of the present invention, the spectrometer may be operated in a high attenuation mode in which the first ion guide 301 attenuates the ion beam passing therethrough by a relative high amount, and a low attenuation in which the first ion guide 301 attenuates the ion beam passing therethrough by lower amount (e.g. substantially no attenuation). The spectrometer may switch from the low attenuation mode to the high attenuation mode by varying the amplitude and/or frequency of the RF voltage applied to the electrodes of the first ion guide such that the radial confinement of the ions within the first ion guide 301 by the RF voltage is less efficient than in the low attenuation mode. In the high attenuation mode the ions will therefore be radially confined less well than in the low attenuation mode and hence ions will be lost to the electrodes of the first ion guide 301 or to the first vacuum chamber 1701 at a higher rate. This approach may allow all species of ions to be attenuated, e.g. in a substantially

proportional manner, and hence may provide a relatively high signal to noise ratio at the ion detector as compared to other attenuation techniques.

The spectrometer may also switch from the high attenuation mode to the low attenuation mode by varying the amplitude and/or frequency of the RF voltage applied to the electrodes of the first ion guide such that the radial confinement of the ions within the first ion guide 301 by the RF voltage is more efficient than in the high attenuation mode.

The spectrometer may be configured to switch from the low attenuation mode to the high attenuation mode when the detector electronics detect an ion signal above a threshold intensity or threshold ion impact rate. Similarly, the spectrometer may be configured to switch from the high attenuation mode to the low attenuation mode when the detector electronics detect an ion signal below a threshold intensity or threshold ion impact rate.

Although two attenuation modes have been described, it is contemplated that three or more attenuation modes may be provided by varying the amplitude and/or frequency of the RF voltage applied to the electrodes of the first ion guide between three or more respective values.

It is contemplated that such attenuation may be performed in regions of the spectrometer other than the first ion guide 301. However, performing the attenuation using the first ion guide 301 is preferred, e.g. since the RF voltages applied to the electrodes of the first ion guide may not be varied in (peak-to-peak) amplitude other than in the attenuation mode.

As described above, ions transmitted by the first ion guide 301 pass into the second ion guide 302 in the second vacuum chamber 1702. The second ion guide 302 is used to guide the ions through the second vacuum chamber 1702 and into the transfer optics 303 in the third vacuum chamber 1703. In order to assist in maintaining the third vacuum chamber 1703 at a lower pressure than the second vacuum chamber 1702, the differential pumping aperture 1301 in the wall between the second and third vacuum chambers may be smaller than the differential pumping aperture1713 in the wall between the first and second vacuum chambers. For example, the differential pumping apertures 1713, 1301 may have diameters of 3 mm and 1.5 mm respectively. The second ion guide 302 may be a multipole rod set ion guide, such as a quadrupole rod set ion guide.

Fig. 16A shows a schematic of an embodiment of the second ion guide 302 arranged between the differential pumping apertures 1713, 1301 of the second vacuum chamber. In the depicted embodiment the second ion guide 302 is an axially segmented quadrupole rod set ion guide. The second ion guide has four rods 1900 (only two of which are shown), each of which is axially segmented into a plurality of coaxially aligned electrodes 1901. RF voltages are applied to the electrodes 1901 in the rods 1900 of the second ion guide so as to radially confine the ions therebetween. Different phases on an RF voltage supply may be applied to adjacent rods (in the circumferential direction) of the multipole ion guide in order to achieve this. For example, opposite phases on the RF voltage supply may be applied to circumferentially adjacent rods.

As described above, the second ion guide 302 may be segmented into a plurality of axial segments 1901 that may be maintained at different DC voltages such that ions are urged through the second ion guide by a DC voltage gradient and towards the transfer lens. This may be achieved by connecting the axially spaced electrodes 1901 to a voltage supply via a series of resistors 1902.

Embodiments are contemplated wherein the ion optics 301 , 302, 303 trap the ions and then pulse them into the pusher assembly 305 of the TOF mass analyser, e.g. in an Enhanced Duty Cycle (EDC) mode. The pusher assembly 305 is then pulsed so as to orthogonally accelerate these ions into the time of flight region 804 of the TOF mass analyser. The timing of the pulsing of the ion optics 301 , 302, 303 may be synchronised with the timing of the pulsing of the pusher assembly 305 such that ions pulsed by the ion optics reach the pusher assembly at the time the pusher assembly is pulsed. This enhances the duty cycle of the spectrometer, since fewer ions reach and pass through the extraction region of the pusher assembly 305 whilst it is not being pulsed. For example, the time at which an ion of interest will reach the pulsed region of the ion optics may be known and the spectrometer may control the ion optics so as to pulse the ion optics at this time such that the ions of interest reach the pusher assembly 305 at the time the pusher assembly is orthogonally pulsed.

The above may be achieved by applying a potential difference between the second ion guide 302 and an adjacent downstream electrode, such as the differential pumping aperture 1301 leading to the third vacuum chamber 1703, so as to trap the ions and prevent them from passing downstream. The potential difference between the second ion guide 302 and the adjacent downstream electrode 1301 may be altered at the desired time so as to pulse the ions towards the pusher assembly. For example, the electrode forming the downstream end of the second ion guide 302 may be pulsed at a higher potential than said adjacent electrode (e.g. the differential pumping aperture 1301) so as to cause such pulsing of the ions. The timing of this pulsing may be synchronised with the timing of the pulsing of the pusher assembly 305 such that ions pulsed by the second ion guide 302 reach the pusher assembly 305 at the time the pusher assembly is pulsed. In contrast, when ions of interest are not at the downstream end of the second ion guide 302, the voltage applied to the end of the second ion guide 302 may be controlled such that the ions are not pulsed towards the pusher assembly 305. It will therefore be appreciated that the voltage applied to the end of the second ion guide 302 may be varied with time so as to selectively pulse ions towards the pusher assembly 305. The electrodes at the downstream end of the second ion guide 302 may not be connected to the resistor chain 1902 that supplies an axial DC voltage gradient to the portion of the second ion guide that is upstream.

Although embodiments have been described in which the voltage applied to the end of the second ion guide 802 is pulsed, it is contemplated that alternatively (or additionally) the voltage applied to said adjacent downstream electrode (e.g. differential pumping aperture 1301) may be pulsed.

Fig.16B shows an example of an Enhanced Duty Cycle mode in which the potential applied to the differential pumping aperture 1301 directly downstream of the second ion guide is controlled so as to provide an enhanced duty cycle. The upper plot illustrates the potential applied to the differential pumping aperture 1301 as a function of time and the lower plot illustrates the potential applied to an electrode of the pusher assembly 305 as a function of time. Referring to the upper plot, the differential pumping aperture 1301 may initially be maintained at a potential that is higher than the potential applied to the downstream end of the second ion guide 302, so as to trap ions and prevent the passing downstream. When it is desired to pulse ions towards the pusher assembly of the TOF mass analyser, the potential applied to the differential pumping aperture 1301 is dropped below that of the downstream end of the second ion guide 302 for an extraction pulse period . The ions are therefore pulsed towards the pusher assembly. The potential applied to the differential pumping aperture 1301 is then raised again to be above the potential applied to the downstream end of the second ion guide 302 so as to trap ions that are subsequently received in the region upstream of the differential pumping aperture. Referring to the lower plot in Fig. 16B, the potential applied to the electrode of the pusher assembly 305 is initially low, but is raised in a pulsed manner after a delay period t₂ from the lowering of the potential applied to the differential pumping aperture 1301. The duration of the delay period t₂ is set such that at least some of the ions pulsed towards the pusher assembly arrive at the pusher assembly at the same time that the electrode 305 of the pusher assembly is pulsed. These ions are therefore orthogonally accelerated into the TOF mass analyser. As shown in Fig. 16B, the above process is then subsequently repeated.

The second ion guide 302 is desirably not operated as a resolving RF/DC mass filter, but instead may be operated so as to transmit all ions. However, at a given RF voltage amplitude, such ion guides may still only be capable of transmitting ions above a certain mass to charge ratio, i.e. a low mass cut off. In order to optimise the transmission of all ions, at least during part of an experiment run, the amplitude of the RF radial confinement voltage applied to the second ion guide may be scanned with time.

Fig. 19 shows an example of how the amplitude of the RF radial confinement voltage may be scanned with time during an experimental run from a relatively low initial value to a relatively high final value. This may result in a reasonable transmission by the second ion guide 302 for ions of all mass to charge ratios in the desired range. The RF amplitude may be ramped up with time in a linear manner. Although the RF amplitude is shown as being ramped up with time, it may alternatively be ramped down with time. The RF amplitude may be maintained constant with time, after being ramped up or down.

The RF field from the second ion guide may focus the ions through the aperture between the second and third vacuum chambers.

As described above, ions transmitted by the second ion guide 302 pass through the aperture 1301 at the downstream wall of the second vacuum chamber 1702 and into the third vacuum chamber 1703, in which the upstream portion of the transfer optics 303 are located. The transfer optics has an apertured electrode 2003 defining a differential aperture 1302 between the third and fourth vacuum chambers 1703, 1704, and a downstream portion of the transfer optics extends into the fourth vacuum chamber 1704. The transfer optics 303 initially accelerates the ions and guides them through its differential pumping aperture 1302 and into the fourth vacuum chamber 1704, and then steers and focuses the ions so as to pass through the apertured entrance plate 1000 into the pusher assembly 305. The transfer optics conditions the ion beam such that it is optimised for the TOF mass analysis.

Fig. 13 shows a schematic of a cross-sectional view through the transfer optics 303, which is arranged between the differential pumping aperture 1301 at the downstream end of the second vacuum chamber 1703 and the apertured entrance plate 1000 into the pusher assembly 305 of the TOF mass analyser. The forms of the individual electrodes in the transfer optics are best seen in Fig. 17B. The transfer optics 303 comprises two acceleration electrodes 2001 , 2002 arranged between of its differential pumping aperture 1302 and the differential pumping aperture 1301 of the second vacuum chamber 1702, although it is contemplated that fewer or more acceleration electrodes may be provided. The first, more upstream, acceleration electrode 2001 may be maintained at a potential that is lower than the potential of the differential pumping aperture 1301 at the downstream end of the second vacuum chamber 1702, such that ions are accelerated between this differential pumping aperture 1301 and the first acceleration electrode 2001. The second, more downstream, acceleration electrode 2002 may be maintained at a potential that is lower than the first acceleration electrode 2001 such that ions are accelerated between the first and second acceleration electrodes. The first and/or second acceleration electrodes may comprise an aperture (e.g. a circular aperture) 2004, 2005 through which the ions are transmitted. The aperture 2004, 2005 may have a cross-sectional area (e.g. diameter) that is greater than the cross-sectional area (e.g. diameter) of the differential pumping aperture 1301 at the downstream end of the second vacuum chamber 1702. For example, this differential pumping aperture 1301 may have a diameter of 1.5 mm, whereas the first and/or second acceleration electrodes apertures 2004, 2005 may have a diameter of 5 mm.

The differential pumping aperture 1302 in the transfer optics may have a cross- sectional area (e.g. diameter) that is greater than the cross-sectional area (e.g. diameter) of the differential pumping aperture 1301 at the downstream end of the second vacuum chamber. The differential pumping aperture 1302 defined by the transfer optics may be circular and may have, for example, a diameter of 2.5 mm. The portion of the electrode 2006 of the transfer optics that defines the differential pumping aperture 1302 may be relatively thick, such that the axial length of the differential pumping aperture 1302 is relatively long. This provides a relatively low fluid conductance through the aperture 1302, since an aperture of a given diameter will have a lower fluid conductance the longer the axial path through it is. The lower fluid conductance through the differential pumping aperture 1302 helps maintain the third 1703 and fourth 1704 vacuum chambers at their pressure differential. However, if the axial length of the differential pumping aperture 1302 is too long then field-free regions may occur within the differential pumping aperture 1302, which may result in ions being lost if they have a significant component of velocity orthogonal to the axis of the aperture 1302, e.g. by being scattered by the background gas molecules. The axial length of the differential pumping aperture 1302 is therefore not made too long and the transfer optics may be configured such that the ions are focussed through the differential pumping aperture 1302. For example, the axial length of the differential pumping aperture 1302 may be 10.5 mm, which is significantly longer than a conventional differential pumping aperture. The differential pumping aperture 1302 may be formed in a planar/sheet portion of an electrode 2006. This portion may be thicker than the planar acceleration electrodes and/or the (planar portions of the) downstream electrodes 2007-2011.

The electrode 2006 forming the differential pumping aperture 1302 may be maintained at a higher potential than at least some of the acceleration electrodes 2001 , 2002. For example, the electrode 2006 forming the differential pumping aperture 1302 may be grounded. This, along with the diameter and length of the aperture 1302, may reduce the transmission of electric fields between the third and fourth vacuum chambers 1703, 1704. This also avoids the need for electronics such as a flux capacitance PCB.

The depicted transfer lens 303 comprises five axially spaced electrodes 2007- 2011 (or electrode portions), through which the ions travel, arranged downstream of its differential pumping aperture 1302. However, it is contemplated that fewer or more such electrodes may be provided. The apertured entrance plate 1000 into the pusher assembly 305 may have a slotted aperture 1303 such as a substantially rectangular aperture, as best seen in Fig. 17B. This enables ions to enter the pusher assembly 305 spread over a greater area (transverse to the beam axis) than if the entrance plate aperture 1303 was circular. It is desired that the ion beam enters the pusher assembly 305 having a relatively small dimension (and velocity spread) parallel to the axis in which the ions are accelerated into the time of flight region, so as to provide high mass resolution, and spreading the ion beam as described above enables this without space-charge effects becoming problematic. Accordingly, at least one or at least some of the axially spaced electrodes 2007-2011 of the transfer optics 303 that are arranged downstream of its differential pumping aperture 1302 may comprise slotted apertures 2012-2016, e.g. so as to cause the cross-sectional shape of the ion beam to match that of the aperture in the entrance plate to the pusher assembly. These slotted apertures may be oriented in a corresponding manner to the slotted aperture 1303 in the entrance plate 1000 to the pusher assembly 305 and/or may have a corresponding size and/or shape to the slotted aperture 1303 in the entrance plate 1000 to the pusher assembly.

Conventionally, separate electrodes have been provided either side of the ion beam axis for restricting the size of the ion beam in the direction parallel to the axis in which the ions are accelerated into the time of flight region. However, such electrodes do not control the size of the ion beam in its radially orthogonal dimension. The slotted apertures 2012-2016, 1303 in the embodiments of the present invention allow control of the ion beam in both orthogonal dimensions. Furthermore, the slotted apertures enable the size of the ion beam to be controlled in multiple dimensions using a single electrode and therefore reduces complexity and may improve mechanical alignment and tolerance.

The electrodes of the transfer optics 303 at one (or more) axial location of the transfer optics may be provided in the form of two separate electrodes, between which the ions pass. A potential different may be applied between the separate electrodes so as to steer the ion beam passing therethrough, e.g. in order to optimise the transmission of the ions into the aperture in the entrance plate to the pusher assembly. A relatively small, potential difference may be applied between the electrodes such as, for example, £ 5V. The electrodes may have radially inner edges that are parallel to each other. In embodiments in which the transfer optics 303 includes slotted electrodes, the parallel inner edges may be arranged in the same orientation as the longitudinal edges of the slots in the slotted electrodes. A first of the electrodes 2007 (or a first electrode portion) of the transfer optics downstream of its differential pumping aperture electrode 2006 may be maintained at the same potential as the electrode 2007 (portion) in which the differential pumping aperture 1302 is provided, e.g. at ground potential. A second of the electrodes 2008 of the transfer optics downstream of the first electrode 2007 (or first electrode portion) may be maintained at a higher potential than the first electrode 2007 (or first electrode portion). A third of the electrodes 2009 of the transfer optics downstream of the second electrode 2008 (or first electrode portion) may be maintained at a lower potential than the second electrode 2008, and optionally at a lower potential than the differential pumping aperture electrode 2006. This enables the ion beam to be conditioned for TOF mass analysis.

A fourth of the electrodes 2010 of the transfer optics downstream of the third electrode 2009 may be maintained at the same potential as the differential pumping aperture electrode 2006. The fourth electrode 2010 may have an elongated tubular portion 2015 having its longitudinal axis arranged along the ion path. The tubular portion 2015 may be maintained at ground potential, e.g. by being electrically connected or mechanically connected to the grounded chassis of the spectrometer. As such, no power supply to the tubular portion 2015 is required, reducing cost and complexity of the instrument. The tubular portion provides a drift region for the ions.

The aperture 2012-2016 in any one, or all, of the electrodes 2008-2011 downstream of the differential pumping aperture 1302 in the transfer optics may have a diameter that is larger than that of the differential pumping aperture 1302 in at least one dimension. For example, the apertures 2012-2016 in the downstream electrodes may have a minimum diameter of 4 mm, e.g. in the smaller dimension for a slotted aperture.

It is contemplated that the first electrode 2007 (or electrode portion) may be omitted.

In the embodiment shown in Fig. 20, the transfer optics 303 has a first electrode portion 2007 downstream of its differential pumping aperture electrode 2006 which is maintained at the same potential, e.g. at ground potential. This first electrode portion

2007 has a slotted aperture 2012 for transmitting ions therethrough. A second electrode

2008 is provided downstream of the first electrode portion 2007 and is maintained at a higher potential than the first electrode portion 2007. This second electrode 2008 has a slotted aperture 2013 for transmitting ions therethrough. A third electrode 2009 is provided downstream of the second electrode 2008 and that is formed from two separate electrode parts, between which the ions pass. The electrode parts may have radially inner edges that are parallel to each other and arranged in the same orientation as the longitudinal edges of the slots in the slotted electrodes. The third electrode 2009 may be maintained at a lower potential than the second electrode 2008, and optionally at a lower potential than the differential pumping aperture electrode 2006. A fourth electrode 2010 is provided downstream of the third electrode 2009 and is maintained at the same potential as the differential pumping aperture electrode 2006, e.g. ground. The fourth electrode 2010 has an upstream portion having a slotted aperture 2015 for transmitting ions therethrough and a downstream tubular portion 2017 that provides a drift region for the ions to travel through. The downstream end of the tubular portion 2017 may or may not have an apertured wall 2011 through which the ions pass on the way to the pusher assembly 305. The elongated tubular portion 2017 may be maintained at ground potential, e.g. by being electrically connected or mechanically connected to the grounded chassis of the spectrometer.

As mentioned above, the entrance plate 1000 to the pusher assembly 305 may have a rectangular slotted ion entrance aperture 1303. This entrance plate 1000 may be maintained at ground potential, e.g. by being electrically or mechanically connected to the fourth electrode 2010, such as at the tubular portion 2017. Each dimension of the aperture 1303 in the entrance plate may be larger than those of the differential pumping aperture 1302 provided by the transfer optics and/or smaller than the dimensions of the apertures 2012-2016 in the transfer optics electrodes downstream of this differential pumping aperture 1302. For example, the slotted aperture 1303 in the entrance plate 1000 may have a minimum dimension of 2 mm.

The centre line of each electrode opening (or aperture) may be within ± 0.2 mm of the differential pumping aperture 1302 axis.

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:

an ion guide comprising a first portion configured to guide ions along a first axial path, a second portion configured to guide ions along a second different axial path, and a transition portion configured to urge ions from the first axial path onto the second axial path;

a downstream electrode arranged downstream of the ion guide; and

a voltage supply arranged and configured to apply a potential difference between the ion guide and the downstream electrode, in a fragmentation mode, so as to accelerate ions therebetween; wherein the spectrometer is configured to maintain the gas pressure between the ion guide and downstream electrode such that when the voltage supply causes the ions to be accelerated, in the fragmentation mode, the ions collide with gas and fragment to form fragment ions.

2. The spectrometer of claim 1 , wherein the spectrometer is configured to operate the voltage supply in: (i) a high-fragmentation mode, in which a relatively high potential difference is applied between the ion guide and the downstream electrode such that ions collide with the gas and fragment to form said fragment ions; and (ii) a low-fragmentation mode, in which a lower or no potential difference is applied between the ion guide and the downstream electrode.

3. The spectrometer of claim 2, wherein the spectrometer is configured to switch between the high-fragmentation mode and low-fragmentation mode in a single

experimental run.

4. The spectrometer of claim 2 or 3, wherein the voltage supply is configured to apply a pulsed voltage to an electrode of the ion guide and/or said downstream electrode so as to switch from the low-fragmentation mode to the high-fragmentation mode.

5. The spectrometer of claim 2, 3 or 4, wherein the ion guide comprises a plurality of axially spaced electrodes and one or more voltage supply configured to apply a plurality of different DC potentials to different respective ones of the axially spaced electrodes so as to generate a DC gradient for urging ions through and out of the ion guide; and wherein said one or more voltage supply is configured to increase the DC potential of an electrode at the downstream end of the ion guide when switching from the low-fragmentation mode to the high-fragmentation mode and also to increase at least some of the DC potentials in said plurality of different DC potentials so as to maintain a potential gradient along the ion guide that urges ions along and out of the ion guide.

6. The spectrometer of claim 5, wherein the spectrometer is configured to control the voltage supplies so as to maintain substantially the same voltage gradient along the ion guide in both the high and low fragmentation modes.

7. The spectrometer of any preceding claim,

wherein the first portion and transition portion of the ion guide each comprise a plurality of axially spaced electrodes arranged about said first axial path and through which ions are transmitted in use, and wherein the spectrometer is configured to apply different DC voltages to different respective ones of these electrodes so as to maintain a first voltage gradient along the first portion and transition portion for driving ions through the ion guide; and

wherein the transition portion and second portion of the ion guide each comprise a plurality of axially spaced electrodes arranged about said second axial path and through which ions are transmitted in use, and wherein the spectrometer is configured to apply different DC voltages to different respective ones of these electrodes so as to maintain a second voltage gradient along the transition portion and second portion for driving ions through the ion guide; and

wherein at any given axial location along the transition region of the ion guide, the potential of the first gradient is higher than the potential of the second gradient.

8. The spectrometer of any preceding claim, comprising an AC or RF voltage supply connected to said electrodes for applying an AC or RF voltage to the electrodes for radially confining ions within the ion guide to said axis; wherein the spectrometer is configured to operate the voltage supply in: (i) a low- attenuation mode, in which a relatively high peak-to-peak amplitude AC or RF voltage is applied to the electrodes for providing relatively strong radial confinement of the ions; and (ii) a high-attenuation mode, in which a lower peak-to-peak amplitude AC or RF voltage is applied to the electrodes for providing weaker radial confinement of the ions.

9. The spectrometer of any preceding claim, comprising a first vacuum chamber, a second vacuum chamber adjacent the first vacuum chamber, and a differential pumping aperture separating the first and second vacuum chambers; wherein the ion guide is located in the first vacuum chamber and the downstream electrode is an electrode in which the differential pumping aperture is formed.

10. The spectrometer of claim 9, wherein the first vacuum chamber has an ion sampling orifice, or other ion inlet aperture, at an upstream end thereof which separates the first vacuum chamber from an atmospheric pressure region in which the ion source may be located.

11. The spectrometer of claim 10, wherein the ion sampling orifice, or other ion inlet aperture, has a diameter of: ³ 0.5 mm; ³ 0.55 mm; ³ 0.6 mm; ³ 0.65 mm; ³ 0.7 mm; ³

0.75 mm; ³ 0.8 mm; ³ 0.85 mm; ³ 0.9 mm; ³ 0.95 mm; or ³ 1 mm.

12. A method of mass spectrometry comprising:

providing a mass spectrometer as claimed in any preceding claim;

13. A mass spectrometer comprising:

14. The spectrometer of claim 13, wherein substantially all species of ions passing through the ion guide are attenuated substantially proportionally in the high attenuation mode, relative to the low-attenuation mode.

15. The spectrometer of claim 13 or 14, comprising an ion detector downstream of the ion guide, and wherein the spectrometer is configured to switch from the low attenuation mode to the high attenuation mode when the detector detects an ion signal above a threshold intensity or threshold ion impact rate; and/or wherein the spectrometer is configured to switch from the high attenuation mode to the low attenuation mode when the detector detects an ion signal below a threshold intensity or threshold ion impact rate.

16. The spectrometer of claim 13, 14 or 15, comprising a time of flight mass analyser arranged downstream of the ion guide for receiving ions transmitted by the ion guide, or ions derived therefrom.

17. The spectrometer of any one of claims 13-16, wherein the ion guide comprises a first portion configured to guide ions along a first axial path, a second portion configured to guide ions along a second different axial path, and a transition portion configured to urge ions from the first axial path onto the second axial path.

18. A method of mass spectrometry comprising:

providing a spectrometer as claimed in any one of claims 13-17;

guiding ions along the longitudinal axis of the ion guide; and

19. A mass spectrometer comprising:

an ion guide comprising a plurality of axially spaced electrodes;

a downstream electrode arranged downstream of the ion guide;

20. A mass spectrometer comprising:

21. The spectrometer of claim 20, wherein the pusher assembly is configured to pulse the ions in a first dimension into the time of flight region; and wherein the slotted aperture is configured so as to cause an ion beam passing therethrough to attain a maximum size in the first dimension that is smaller than a maximum size in a second orthogonal dimension, wherein the first and second dimensions are orthogonal to the longitudinal axis of the ion beam passing through the slotted aperture.

22. A mass spectrometer comprising:

a mass analyser or ion mobility analyser; and

23. A mass spectrometer comprising:

a mass analyser or ion mobility analyser; and

24. A mass spectrometer comprising:

a mass analyser or ion mobility analyser; and

ion transfer optics for guiding ions towards and into said mass analyser or ion mobility analyser, said ion transfer optics having a plurality of axially spaced electrodes that include an electrode which is electrically grounded for preventing electric fields from being transmitted through the ion transfer optics.

25. A mass spectrometer comprising:

a vacuum housing having an opening through a wall thereof;

a plurality of electrodes arranged inside the vacuum housing; and