Apparatus and method

Abstract

An apparatus comprising: an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes; a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap for trapping ions in a trapping region thereof; an electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD; wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and wherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

Description

[0001] APPARATUS AND METHOD

[0002] FIELD

[0003] The present invention relates to injection of electrons into multipole ion guides and / or ion traps.

[0004] BACKGROUND

[0005] External injection of electrons in radio-frequency (RF) ion traps driven by two-state rectangular waveforms has been presented in the literature for a three-dimensional quadrupole ion trap (3D QIT) [Ding L & Brancia F L, ECD in a DIT MS, Anal Chem, 2006, 78, 1995-2000], and two-dimensional linear ion traps (2D LIT) [Papanastasiou D et al., The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry, J Am Soc Mass Spectrom, 2022, 33(10), 1990-2007], In prior art 3D and 2D quadrupole ion trap configurations, the one or a pair of rectangular waves applied fortrapping ions, respectively, are switched between two discrete voltage levels, while electrons are admitted in the trapping region via simple through holes in the electrodes of the quadrupole, only during the application of the positive voltage level, which corresponds to half the period of the rectangular waveform. In a 3D QIT, a single rectangular waveform is applied to the ring electrode and electrons are injected via a simple through hole in one of the two endcap electrodes. For electron capture dissociation (ECD) reactions to be effective, electron injection is synchronized with the negative excursion of the rectangular trapping waveform while an additional external deflection potential is synchronized with the rectangular waveform for admitting electrons during the appropriate waveform phase. In a 2D LIT, a pair of anti-phase rectangular waveforms is used and, similarly, electrons are injected through round apertures on pole - electrodes receiving the positive voltage level.

[0006] However, such external injection of electrons in RF ion traps may result in severe surface contamination of electrodes and concomitant degradation of performance, often within a short period of time. Surface contamination has a strong negative impact on instrument robustness, especially in high throughput analytical laboratories with back-to-back experiments scheduled over prolonged periods.

[0007] Hence, there remains a need to improve external injection of electrons in RF ion traps, for example to reduce, minimize and / or eliminate surface contamination of electrodes and concomitant degradation of performance and / or to improve efficiency of electron-based fragmentation reactions.

[0008] -Broker Confidential-SUMMARY OF THE INVENTION

[0009] A first aspect provides an apparatus comprising:

[0010] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0011] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0012] an electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0013] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0014] wherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

[0015] A second aspect provides an apparatus comprising:

[0016] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes; and

[0017] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof;

[0018] -Broker Confidential-wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0019] wherein the second set of states provides a substantially field free region in the ion trap or a quadrupole field in the ion trap for mitigating escape of ions from the trapping region, for injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0020] A third aspect provides a method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes, the method comprising:

[0021] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;

[0022] applying the generated RF voltage waveform to the set of electrodes;

[0023] trapping ions in the ion trap during the first set of states; and

[0024] injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0025] A fourth aspect provides a method of an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes, the method comprising:

[0026] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the

[0027] -Broker Confidential-first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states and wherein the second set of states provides a substantially field free region in the ion trap or a quadrupole field in the ion trap for mitigating escape of ions from the trapping region, for injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD; and

[0028] applying the generated RF voltage waveform to the set of electrodes.

[0029] A fifth aspect provides an apparatus comprising:

[0030] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0031] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0032] an electron source, configured to inject electrons into the ion trap for reactions thereof with the trapped ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0033] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0034] wherein the third dimension (z1) of the first section is relatively greater than the third dimension (z2) of the second section.

[0035] A sixth aspect provides an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0036] -Broker Confidential-wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes;

[0037] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section.

[0038] A seventh aspect provides an electrode for an ion trap, wherein the electrode has a first passageway therethrough for electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes;

[0039] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section.

[0040] An eighth aspect provides a method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes; wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0041] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0042] wherein the method comprises:

[0043] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed;

[0044] applying the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof;

[0045] trapping ions in the ion trap during the first set of states; and

[0046] -Broker Confidential-injecting electrons into the ion trap via the first passageway, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0047] wherein injecting the electrons into the ion trap via the first passageway comprises allowing defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0048] A ninth aspect provides an apparatus comprising:

[0049] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0050] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0051] an electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0052] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes;

[0053] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0054] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0055] wherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

[0056] -Broker Confidential-A tenth aspect provides a method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes; wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0057] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0058] wherein the method comprises:

[0059] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;

[0060] applying the generated RF voltage waveform to the set of electrodes;

[0061] trapping ions in the ion trap during the first set of states; and

[0062] injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0063] wherein injecting the electrons into the ion trap via the first passageway comprises allowing defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0064] An eleventh aspect provides an apparatus comprising:

[0065] a multipole ion guide comprising a set of electrodes, for example two or more pairs of rod electrodes; a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of

[0066] -Broker Confidential-electrodes, wherein the first set of states provides a radial confining field in the multipole ion guide for radially confining ions in a radial confining region thereof; and

[0067] an electron source, configured to inject electrons into the multipole ion guide for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0068] characterized by:

[0069] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0070] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0071] and / or

[0072] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0073] wherein the electron source is configured to inject the electrons into the multipole ion guide during the second set of states, for example only during the second set of states.

[0074] A twelfth aspect provides a method of reacting ions with electrons in a multipole ion guide comprising a set of electrodes, for example two or more pairs of rod electrodes;

[0075] optionally wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0076] optionally wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0077] wherein the method comprises:

[0078] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and optionally a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;

[0079] -Broker Confidential-applying the generated RF voltage waveform to the set of electrodes;

[0080] radially confining ions in the multipole ion guide during the first set of states; and

[0081] injecting electrons into the multipole ion guide, optionally during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0082] optionally wherein injecting the electrons into the multipole ion guide via the first passageway comprises allowing defocusing, deflection, divergence and / or spreading of the electrons, for example due to the radial confining field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0083] DETAILED DESCRIPTION OF THE INVENTION

[0084] Apparatus - voltage waveform

[0085] The first aspect provides an apparatus comprising:

[0086] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0087] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0088] an electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0089] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0090] wherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

[0091] -Broker Confidential-In this way, defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field and / or space charge effects, is attenuated and / or avoided since the electrons are injected into the ion trap during the second set of states, for example only during the second set of states, when a trapping field is not provided in the ion trap. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the ion trap improved.

[0092] In more detail, although external injection of electrons in quadrupole ion traps driven by conventional two-state rectangular waveforms (waveforms switched between two-discrete voltage levels) is potentially an efficient process for electron-based fragmentation reactions with analyte ions, the defocusing action of the electron beam inside the quadrupole field during the injection phase can lead to severe electrode surface contamination and degradation of performance within a short period of time. Surface contamination effects have a strong negative impact on instrument robustness, especially in high throughput setups with back-to-back experiments scheduled over a prolonged period. The high-density (pA) low-energy electron beams typically injected in ion traps are extremely difficult to collimate and focus through narrow apertures. The defocusing of electron beams injected in a quadrupole field, together with beam divergence effects due to excessive space charge conditions, require new implementations to reduce or eliminate contamination and charging of both conducting and insulating surfaces.

[0093] Hence, the inventors have developed alternative implementations of rectangular waveforms for trapping ions and / or redesign the inlet and outlet openings in quadrupole ion traps coupled to external electron sources. The new designs described herein minimize or eliminate surface contamination and charging of pole -electrodes, improving robustness and enabling higher density electron beams, which further enhance the efficiency of electron-based fragmentation reactions.

[0094] Ion trap

[0095] The apparatus comprises the ion trap, for example a 2 dimensional, 2D, ion trap such as a linear ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT. In one example, the ion trap comprises and / or is a 2D ion trap such as a LIT comprising a quadrupole, a hexapole, an octapole, a decapole or a dodecapole ion trap, preferably a quadrupole LIT. Suitable ion traps are known.

[0096] -Broker Confidential-In one example, the ion trap comprises and / or is a segmented linear quadrupole ion trap, for example as described in WO 2017 / 134436 A1 , the subject matter of which is incorporated by reference herein in entirety.

[0097] In one example, the segmented linear quadrupole ion trap comprises:

[0098] at least two discrete trapping regions for processing ions;

[0099] a RF electrical potential generator for producing two RF waveforms, and arranged to apply each to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to trap ions radially;

[0100] a multi-output DC electrical potential generator for producing multiple DC field components superimposed to the RF field component and distributed across the length of the linear ion trap to control ions axially;

[0101] a control unit configured to switch the DC electrical potentials and corresponding DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions to alter ion potential energy from a first level to a second level, and to enable a first ion processing step in at least one of the first and second levels; and

[0102] wherein the control unit is configured to switch DC electrical potential(s) at the second level at / of one side of the first trapping region to a value less than the minimum DC electrical potential of the first trapping region thereby permitting the release of ions confined therein for movement along the axis of the linear ion trap by acceleration away from the first trapping region.

[0103] In one example, the segmented linear quadrupole ion trap comprises:

[0104] at least two discrete trapping regions for processing ions;

[0105] a RF electrical potential generator for producing two RF waveforms and arranged to apply each to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to confine ions radially;

[0106] a multi-output DC electrical potential generator (103, 300) for producing multiple DC field components superimposed to the RF field component and distributed across the length of the linear ion trap to control ions axially; and

[0107] a control unit configured to switch the DC electrical potentials and corresponding DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions axially confined therein to alter ion potential energy from a first ion potential energy level to a second ion potential energy level by simultaneously changing the DC electrical potentials of the first trapping region between a first DC electrical potential level and a second DC electrical potential level, and to enable a first ion processing step in at least one of the first and second ion potential energy levels.

[0108] -Broker Confidential-In one example, the segmented linear quadrupole ion trap comprises:

[0109] at least two discrete trapping regions for processing ions;

[0110] a RF electrical potential generator for producing two RF waveforms, and arranged to apply each to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to confine ions radially;

[0111] a multi-output DC electrical potential generator or producing multiple DC field components superimposed to the RF field component and distributed across the length of the linear ion trap to control ions axially;

[0112] a control unit configured to switch the DC electrical potentials and corresponding DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions axially confined therein to alter ion potential energy from a first ion potential energy level to a second ion potential energy level by simultaneously changing the DC electrical potentials of the first trapping region between a first DC electrical potential level and a second DC electrical potential level, and to enable a first ion processing step in at least one of the first and second ion potential energy levels; and

[0113] wherein the control unit is configured to switch one or more of the DC electrical potentials at the second ion potential energy level at one side of the first trapping region to a value less than the minimum DC electrical potential of the first trapping region thereby permitting the release of ions confined therein for movement along the axis of the linear ion trap by acceleration away from the first trapping region.

[0114] In one example, the control unit is further configured to switch at least one DC field component of the multiple DC field components collectively forming the first trapping region between three different DC electrical potential levels.

[0115] In one example, the control unit is further configured to switch at least one DC field component of the multiple DC field components to transfer ions from the first trapping region to a second trapping region of the at least two discrete trapping regions to enable a second processing step.

[0116] In one example, the control unit is further configured to switch a plurality of the DC field components, from among the multiple DC field components, which collectively form a second trapping region of the at least two discrete trapping regions to alter the potential energy of ions stored therein from the first level to the second level.

[0117] -Broker Confidential-In one example, the control unit is further configured to switch at least one DC field component of the multiple DC field components collectively forming the second trapping region between three different DC electrical potential levels.

[0118] In one example, the RF waveforms comprise substantially rectangular voltage pulse trains.

[0119] In one example, the segmented linear quadrupole ion trap comprises a pair of pole electrodes configured to receive a beam of particles that are injected through at least one of the two discrete trapping regions populated with ions at a first potential energy level

[0120] In one example, said particles that are injected in the absence of a collision gas within said at least one of the two discrete trapping regions.

[0121] In one example, the control unit is further configured to switch a plurality of the multiple DC field components to release ions from the first trapping region toward a second trapping region with sufficient kinetic energy to perform collision induced dissociation.

[0122] In one example, the control unit is further configured to switch at least one of the DC field components to eject processed ions toward a mass analyzer for measuring mass-to-charge ratio.

[0123] In one example, the segmented linear quadrupole ion trap is configured with at least two trapping regions and to enable processing of ions in at least one of the two trapping regions. In one example, one of the at least two trapping regions is configured to receive electrons from an external electron source to activate ions trapped therein. In one example, the ion analysis apparatus comprises a power supply configured to drive the segmented linear quadrupole ion trap using a pair of antiphase rectangular waveforms.

[0124] In one example, processing of a first packet of ions ejected from the trapping device, or a mass selected fraction of the first packet of ions (mass selected using the first quadrupole mass filter), is performed downstream of the trapping device in the segmented linear quadrupole ion trap and / or in the collision cell. In one example, in parallel to this processing (i.e. concurrently, simultaneously), the trapping device accumulates a second packet of ions, thus enhancing the duty cycle of the mass spectrometer.

[0125] -Broker Confidential-Set of electrodes

[0126] The ion trap comprises the set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes. Suitable sets of electrodes are known.

[0127] In one example, the ion trap comprises and / or is a 2D ion trap such as a LIT and the set of electrodes comprises N pairs of rod electrodes, wherein N is a natural number greater than or equal to 2, for example 2, 3, 4, 5, 6 or more. It should be understood that N is the order of the multipole.

[0128] In one example, the rod electrodes are hyperbolic and / or comprise hyperbolic electrode surfaces (i.e. hyperbolic rods). In one example, rod electrodes are round and / or comprise round electrode surfaces (i.e. round rods). Hyperbolic rods are generally preferred but relatively more costly than round rods.

[0129] Power supply

[0130] The apparatus comprises the power supply. Suitable power supplies are known.

[0131] The power supply is configured to generate the substantially rectangular radio frequency, RF, voltage waveform. Suitable RF voltage waveform generators are known.

[0132] The power supply is configured to apply the generated RF voltage waveform to the set of electrodes. It should be understood that mutually opposed waveforms are applied to mutually adjacent electrodes i.e. conventionally.

[0133] In one example, the power supply is configured to: apply a DC equipotential to respective electrodes of the set of electrodes during the second set of states. In this way, the same DC potential is applied to the respective electrodes (i.e. all the rods) of the set of electrodes during the second set of states.

[0134] Trapping duty cycle is defined as the percentage of the respective duration of the first set of states relative to the period of the RF voltage waveform.

[0135] Electron injection duty cycle is defined as the percentage of the respective duration of the second set of states relative to the period of the RF voltage waveform.

[0136] -Broker Confidential-In one example, the power supply is configured to: generate the RF voltage waveform, wherein an electron injection duty cycle is in a range from 5% to 95%, preferably in a range from 10% to 90%, more preferably in a range from 25% to 75%, for example 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70% or 75%.

[0137] In one example, the power supply is configured to: generate the RF voltage waveform, wherein respective durations of the respective states of the first set of states and / or the second set of states are equal. In this way, an electron injection duty cycle of 50% may be provided.

[0138] In one example, the power supply is configured to: generate the RF voltage waveform, wherein respective durations of the respective states of the first set of states and / or the second set of states are unequal. In this way, different electron injection duty cycles may be provided, for example in a range from 5% to 95%, preferably in a range from 10% to 90%, more preferably in a range from 25% to 75%, for example 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70% or 75%, for example depending on a type of the electron reaction for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0139] In one example, the power supply is configured to: control, for example individually and / or independently, respective durations of the respective states of the first set of states and / or the second set of states. In this way, different electron injection duty cycles may be provided, for example depending on a type of the electron reaction for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0140] Voltage waveform

[0141] It should be understood that the RF voltage waveform is substantially rectangular (also known as digital), having substantially constant or constant respective voltage levels during the respective durations of the respective states of the first set of states and the second set of states, with fast rise and fall times therebetween. In one example, the RF voltage waveform is rectangular.

[0142] The RF voltage waveform includes the first set of states including the first state having the first voltage level and the second state having the second voltage level, wherein the first state and the second state (i.e. of the first set of states) are mutually opposed (i.e. the first voltage level and the second voltage level are equal in magnitude and duration and opposed in polarity). It should be understood that the first set of states corresponds with or is effectively a conventional RF rectangular two-state

[0143] -Broker Confidential-voltage waveform used for trapping ions in conventional ion traps. In one example, the first set of states includes only the first state and the second state i.e. excludes a third state, for example.

[0144] The RF voltage waveform includes the second set of states including the first state having the first voltage level, as described herein.

[0145] In one example, the RF voltage waveform has a frequency in a range from XXX

[0146] First set of states

[0147] The first set of states provides a trapping field in the ion trap for trapping ions in a trapping region thereof. Suitable trapping fields are known.

[0148] Second set of states

[0149] The first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states. In this way, the first voltage level of the second set of states is an intermediate voltage level, for example that does not provide a trapping field, that provides a quadrupole field in the ion trap for mitigating escape of ions from the trapping region and / or provides a substantially field free region in the ion trap. In this way, an electric field strength in the ion trap due to the second set of states is lowered compared with the first set of states, thereby facilitating injection of electrons therein.

[0150] It should be understood that a duration of the second set of states does not significantly reduce a trapping efficiency of the ion trap. That is, escape of some ions from the trapping region may be acceptable since an efficiency of electron reactions with the remaining ions may be enhanced since defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field and / or space charge effects, is attenuated and / or avoided since the electrons are injected into the ion trap during the second set of states.

[0151] In one example, the second set of states does not provide a trapping field. In this way, an electric field strength in the ion trap due to the second set of states is lowered compared with the first set of states, thereby facilitating injection of electrons therein, while escape of electrons is mitigated. In this way, an efficiency of electron reactions may be improved.

[0152] -Broker Confidential-In one example, the second set of states provides a quadrupole field in the ion trap for mitigating escape of ions from the trapping region. In this way, an electric field strength in the ion trap due to the second set of states is lowered compared with the first set of states, thereby facilitating injection of electrons therein, while escape of electrons is mitigated. In this way, an efficiency of electron reactions may be improved.

[0153] In one example, the second set of states provides a substantially field free region in the ion trap. In this way, injection of electrons therein is facilitated since defocusing, deflection, divergence and / or spreading of the electrons, for example due to a trapping field, is eliminated.

[0154] In one example, the first voltage level, or a magnitude thereof, of the second set of states is based on (for example, calculated using) the first voltage level and / or the second voltage level of the first set of states. For example, the first voltage level, or a magnitude thereof, of the second set of states may be a predetermined level based on (for example, calculated using) the first voltage level and / or the second voltage level of the first set of states, such as a predetermined percentage level or a predetermined absolute level. In one example, the predetermined percentage level is in a range from 0% to 75%, preferably in a range from 5% to 50%, more preferably in a range from 10% to 25%, for example 10%, 15%, 20% or 25%.

[0155] In one example, the first voltage level of the second set of states is based on (for example, calculated using) a mean of the first voltage level and / or the second voltage level of the first set of states. In one example, the first voltage level of the second set of states is a mean of the first voltage level and / or the second voltage level of the first set of states, for example 0 V.

[0156] In one example, the first voltage level, or a magnitude thereof, of the second set of states is based on (for example, calculated using) an energy of the electrons injected into the ion trap. The energy of the electrons is defined by the difference between the DC bias of the RF voltage waveform, for example during the second set of states, and the DC bias of the electron source. In this way, the first voltage level, or a magnitude thereof, of the second set of states may depend on a type of the electron reaction for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0157] In one example, the second set of states includes a second state having a second voltage level. The second state and / or the second voltage level may be as described with respect to the first state and / or the first voltage level mutatis mutandis.

[0158] -Broker Confidential-In one example, the first state and the second state (i.e. of the second set of states) are mutually opposed (i.e. the first voltage level and the second voltage level are equal in magnitude and optionally duration and opposed in polarity). In this way, the second set of states may provide a quadrupole field in the ion trap for mitigating escape of ions from the trapping region.

[0159] In one example, the first set of states and the second sets of states are in series (i.e. successively). In this way, the first set of states precedes, for example, the second set of states in a period of the RF voltage waveform. In other words, the sets of states alternate. For example, a period of the RF voltage waveform may comprise or consist of in series: first set of states, second set of states such as first state of the first set of states, second state of the first set of states, first state of the second set of states, optionally second state of the second set of states.

[0160] In one example, respective states of the first set of states and the second sets of states are in series. In this way, the first state of the first set of states precedes, for example, the first state of the second set of states, and the first state of the second set of states precedes, for example, the second state of the second set of states in a period of the RF voltage waveform. In other words, respective states of the sets of states alternate. For example, a period of the RF voltage waveform may comprise or consist of in series: first state of the first set of states, first state of the second set of states, second state of the first set of states, optionally second state of the second set of states.

[0161] Electron source

[0162] The apparatus comprises the electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD. Suitable electron sources are known.

[0163] The electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states. In one example, the electron source is configured to not inject the electrons into the ion trap during the first set of states.

[0164] In one example, the electron source is configured to deflect, for example using a deflection electrode, the electrons away from the ion trap during the first set of states, for example only during the first set of states. In this way, the electron source may be configured to continuously provide electrons but not inject the electrons into the ion trap during the first set of states.

[0165] -Broker Confidential-In one example, the electron source is configured to deflect, for example using a deflection electrode, the electrons into the ion trap during the second set of states, for example only during the second set of states. In this way, the electron source may be configured to continuously provide electrons and inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

[0166] In one example, the electron source is configured to provide a cylindrical beam of electrons to be injected into the ion trap, for example wherein the electron source comprises a circular electron emitter. Such a circular electron emitter is suitable for a passageway wherein the second section comprises and / or is cylindrical section and / or wherein the third section comprises and / or is a conical section.

[0167] In one example, the electron source is configured to provide a ribbon beam of electrons to be injected into the ion trap, for example wherein the electron source comprises a ribbon electron emitter, such as a coated or an uncoated filament, for example provided by a tape or ribbon filament, two or more mutually parallel wire or tape filaments and / or a zig zag filament, thereby presenting a relatively planar or a planar electron emitter surface. In this way, a volume for ion-electron interaction is increased compared with a circular emitter, thereby increasing efficiency of such interactions. Such a ribbon electron emitter is suitable for a passageway wherein the second section comprises and / or is a rectangular section and / or wherein the third section comprise a triangular prismatic frustum section. In one example, the two or more mutually parallel wire or tape filaments carry counter currents, thereby improving voltage distribution, homogenizing an electric field and / or minimizing a spread in electron energy. In one example, a length Lr of the ribbon electron emitter is greater than or equal to a length LI of legs thereof. In this way, a flatter temperature profile (smaller delta T) is provided along the ribbon electron emitter because a relatively larger temperature drop is seen by the legs, thereby improving voltage distribution, homogenizing an electric field and / or minimizing a spread in electron energy.. In one example, a ratio of a length Lr of the ribbon electron emitter to a length LI of legs thereof is in a range from 1 : 1 to 5 : 1 , preferably 3 : 2 to 4 : 1 , more preferably from 2 : 1 to 3 : 1. In one example, the ribbon electron emitter is disposed whereby only electrons emitted from a surface, for example a relatively planar or a planar surface, thereof are injected into the ion trap, wherein the surface and the ion trap, for example the first passageway of the first electrode, are mutually opposed.

[0168] Gap or passageway

[0169] -Broker Confidential-In one example, the electron source is configured to inject the electrons into the ion trap via a gap between adjacent electrodes of the set of electrodes. In this way, a conventional set of electrodes may be used. It should be understood that a field-free plane is conventionally provided between adjacent electrodes of the set of electrodes during the first set of states. However, the field-free plane is infinitesimal such that there would be defocusing, deflection, divergence and / or spreading of the electrons if injected via the gap during the first set of states.

[0170] In one example, a first electrode of the set of electrodes comprises a passageway therethrough and the electron source is configured to inject the electrons into the ion trap via the passageway. In one example, the passageway comprises and / or is simple through hole. In one example, the passageway is as described with the fifth aspect mutatis mutandis.

[0171] Apparatus - voltage waveform

[0172] The second aspect provides an apparatus comprising:

[0173] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes; and

[0174] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof;

[0175] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0176] wherein the second set of states provides a substantially field free region in the ion trap or a quadrupole field in the ion trap for mitigating escape of ions from the trapping region, for injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0177] -Broker Confidential-The apparatus according to the second aspect may be as described with respect to the apparatus according to the first aspect mutatis mutandis.

[0178] Method - voltage waveform

[0179] The third aspect provides a method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and two optionally end electrodes or wherein the 3D ion trap comprises a ring electrode and optionally two end electrodes, the method comprising:

[0180] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;

[0181] applying the generated RF voltage waveform to the set of electrodes;

[0182] trapping ions in the ion trap during the first set of states; and

[0183] injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.

[0184] The method according to the third aspect may include any step as described with respect to the first aspect and / or the second aspect mutatis mutandis.

[0185] The fourth aspect provides a method of an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes, the method comprising: generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage

[0186] -Broker Confidential-level of the first set of states and wherein the second set of states provides a substantially field free region in the ion trap or a quadrupole field in the ion trap for mitigating escape of ions from the trapping region, for injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD; and

[0187] applying the generated RF voltage waveform to the set of electrodes.

[0188] The method according to the fourth aspect may be as described with respect to the method according to the third aspect mutatis mutandis.

[0189] Apparatus - electrode

[0190] The fifth aspect provides an apparatus comprising:

[0191] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0192] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0193] an electron source, configured to inject electrons into the ion trap for reactions thereof with the trapped ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0194] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0195] wherein the third dimension (z1) of the first section is relatively greater than the third dimension (z2) of the second section.

[0196] That is, z1 > z2 such that the first passageway is not a conventional simple through hole.

[0197] -Broker Confidential-In this way, if the first section is relatively more proximal the trapping region compared with the third section, the first section allows defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section, since the third section is elongated along the third axis (Z) compared with the second section. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the ion trap improved.

[0198] In this way, if the first section is relatively more distal the trapping region compared with the third section, the first section improves collimation, in the third axis (Z) in the first section, for example by collisions of divergent electrons from the electron source with surfaces of the first section. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the ion trap improved because collimation of the electrons is improved.

[0199] The ion trap, the set of electrodes, the power supply, the RF voltage waveform, the first set of states, the trapping field, the trapping region and / or the electron source may be as described with respect to the first aspect, the second aspect, the third aspect and / or the fourth aspect, description of which is not repeated for brevity.

[0200] First electrode

[0201] The first electrode of the set of electrodes has the first passageway therethrough for the electrons. It should be understood that the first passageway is a through passageway (also known as a hole), extending completely through the first electrode, for example diametrically therethrough.

[0202] The first passageway defines the first (X) axis and mutually orthogonal second (Y) and third (Z) axes. The first (X) axis and mutually orthogonal second (Y) and third (Z) axes may be consistent with similar definitions of the first electrode and / or the ion trap.

[0203] Sections

[0204] The first passageway comprises the first section, the third section and the second section therebetween. It should be understood that a section is a length of the first passageway. It should be

[0205] -Broker Confidential-understood that the first section, the second section and the third section are in series, for example wherein the first section and the second section are mutually adjacent and wherein the second section and the third section are mutually adjacent, for example without intermediate sections therebetween. In one example, the first passageway consists of the first section, the third section and the second section therebetween. More generally, the first passageway comprises a set of sections, including the first section, the third section and the second section therebetween.

[0206] In one example, the first section is disposed proximal and / or at one end of the first passageway and the third section is disposed proximal and / or at an opposite end of the first passageway. In one example, the first section intersects a surface, for example a cylindrical surface or a hyperbolic surface, of the first electrode, thereby defining a first opening (also known as a window or port) and the third section intersects an opposite surface, for example a diametrically opposite surface, for example a cylindrical surface or a non-cylindrical surface such as a planar surface, thereby defining a third opening. In one example, the second section defines, provides and / or is a third opening. It should be understood that the first opening is defined as the intersection of the first section of the first passageway and the surface of the first electrode.

[0207] Dimensions

[0208] The first section, the third section and the second section have respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes, which may be denoted respectively length, height and width for convenience though the height and / or width may be denoted as respective diameters. It should be understood that the respective second (y) and third (z) dimensions of the first section, the third section and the second section therebetween may or may not be constant along the first (X) axis, as described herein.

[0209] First section

[0210] The third dimension (z1) of the first section is relatively greater than the third dimension (z2) of the second section. That is, the first section provides an expansion volume, allowing defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section. Additionally and / or alternatively, the second section provides a constriction along the third axis (Z) compared with the first section, improving collimation of the electrons.

[0211] -Broker Confidential-In one example, the third dimension (Z) of the first section increases along the first (X) axis, for example linearly or non-linearly such as convexly and / or concavely, away from the second section. For example, the first section may taper outwardly from the second section. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the first section allows greater defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0212] In one example, the second dimension (y1) of the first section is equal to the second dimension (y2) of the second section. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the first section similarly provides a constriction along the second axis (Y) provided by the second section and / or reduces or minimizes the second dimension (y1) in the first electrode at a surface thereof, thereby diminishing an adverse effect on the electric field due to the first passageway.

[0213] In one example, the second dimension (Y) of the first section is constant along the first (X) axis. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the first section maintains a constriction along the second axis (Y) provided by the second section and / or reduces or minimizes the second dimension (y1) in the first electrode at a surface thereof, thereby diminishing an adverse effect on the electric field due to the first passageway.

[0214] In one example, a cross-sectional area of the first section increases along the first (X) axis, for example linearly or non-linearly such as exponentially, away from the second section. It should be understood that the cross-sectional area is determined orthogonally to the first (X) axis. In one example, a cross-sectional shape of the first section is rectangular or rounded rectangular, for example all cross-sections are rectangular or rounded rectangular. In one example, an aspect ratio of the first section and / or the third section is in a range from 3 : 2 to 5 : 1 , preferably in a range from 2 : 1 to 3 : 1 , for example at the first opening.

[0215] In one example, the first section comprises and / or is a triangular prismatic frustum section, for example having two parallel truncated triangular bases and rectangular or semicylindrical walls therebetween, such as a flared (also known as flare) nozzle (i.e. the third dimension (z1) of the first section increases along the first (X) axis linearly, the second dimension (y1) of the first section is constant and all cross-sections are rectangular or rounded rectangular). In one example, the first section comprises and / or is a circular triangular section, for example having two parallel bell-shaped bases and rectangular or semicylindrical walls therebetween (i.e. the third dimension (z1) of the first

[0216] -Broker Confidential-section increases along the first (X) axis non-linearly such as convexly, the second dimension (y1) of the first section is constant and all cross-sections are rectangular or rounded rectangular).

[0217] In one example, the third dimension (z1) of the first section, for example the first opening, is greater than the effective radius RO of the ion trap and / or the set of electrodes, for example in a range from 101% to 300%, preferably in a range from 150% to 250% for example 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240% or 250% of R0, preferably about 200% R0. Typically, the effective radius R0 of the ion trap and / or the set of electrodes is in a range from 2.5 mm to 5 mm.

[0218] In one example, the second dimension (y1) of the first section, for example the first opening, is less than the effective radius R0 of the ion trap and / or the set of electrodes, for example in a range from 50% to 99%, preferably in a range from 60% to 90% for example 60%, 65%, 70%, 75%, 80%, 85% or 90% of R0, preferably about 80% R0. Typically, the effective radius R0 of the ion trap and / or the set of electrodes is in a range from 2.5 mm to 5 mm.

[0219] In one example, the third dimension (z3) of the third section, for example the third opening, is greater than the effective radius R0 of the ion trap and / or the set of electrodes, for example in a range from 101% to 300%, preferably in a range from 150% to 250% for example 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240% or 250% of R0, preferably about 200% R0. Typically, the effective radius R0 of the ion trap and / or the set of electrodes is in a range from 2.5 mm to 5 mm.

[0220] In one example, the second dimension (y3) of the third section, for example the third opening, is less than the effective radius R0 of the ion trap and / or the set of electrodes, for example in a range from 50% to 99%, preferably in a range from 60% to 90% for example 60%, 65%, 70%, 75%, 80%, 85% or 90% of R0, preferably about 80% R0. Typically, the effective radius R0 of the ion trap and / or the set of electrodes is in a range from 2.5 mm to 5 mm.

[0221] Third section

[0222] In one example, the third dimension (z3) of the third section is relatively greater than the third dimension (z2) of the second section. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the third section improves collimation, in the third axis (Z) in the third section, for example by collisions of divergent electrons from the electron source with surfaces of the third section. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to

[0223] -Broker Confidential-efficiency of electron-based fragmentation reactions in the ion trap improved because collimation of the electrons is improved.

[0224] In one example, the third dimension (z3) of the third section increases along the first (X) axis, for example linearly or non-linearly such as convexly and / or concavely, away from the second section. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the third section improves collimation, in the third axis (Z) in the third section, for example by collisions of divergent electrons from the electron source with surfaces of the third section. In one example, a cross-sectional area of the third section increases along the first (X) axis, for example linearly or non-linearly such as exponentially, away from the second section. It should be understood that the cross-sectional area is determined orthogonally to the first (X) axis. In one example, a cross-sectional shape of the third section is circular, for example all cross-sections are circular.

[0225] In one example, the second dimension (y3) of the third section is relatively greater than the second dimension (y3) of the second section. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the third section improves collimation, in the third axis (Z) in the third section, for example by collisions of divergent electrons from the electron source with surfaces of the third section. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the ion trap improved because collimation of the electrons is improved.

[0226] In one example, the second dimension (y3) of the third section increases along the first (X) axis, for example linearly or non-linearly such as convexly and / or concavely, away from the second section. In this way, if the first section is relatively more proximal the trapping region compared with the third section, the third section improves collimation, in the third axis (Z) in the third section, for example by collisions of divergent electrons from the electron source with surfaces of the third section.

[0227] In one example, the third section comprises and / or is a conical section for example a frustoconical section such as a funnel (i.e. the third dimension (z3) and the second dimension (y3) of the third section increase along the first (X) axis linearly and all cross-sections are circular). In one example, the third section comprises and / or is a trumpet or bell (i.e. the third dimension (z3) and the second dimension (y3) of the third section increase along the first (X) axis non-linearly such as convexly and all cross-sections are circular).

[0228] -Broker Confidential-In one example, the third section comprises and / or is a triangular prismatic frustum section, for example having two parallel truncated triangular bases and rectangular or semicylindrical walls therebetween, such as a flared (also known as flare) nozzle (i.e. the third dimension (z3) of the third section increases along the first (X) axis linearly, the second dimension (y3) of the third section is constant and all cross-sections are rectangular or rounded rectangular). In one example, the third section comprises and / or is a circular triangular section, for example having two parallel bell-shaped bases and rectangular or semicylindrical walls therebetween (i.e. the third dimension (z3) of the third section increases along the first (X) axis non-linearly such as convexly, the second dimension (y3) of the third section is constant and all cross-sections are rectangular or rounded rectangular).

[0229] In one example, the second dimension (y3), the third dimension (z3) and / or a diameter of the third section, for example the third opening, is greater than the effective radius RO of the ion trap and / or the set of electrodes, for example in a range from 101% to 300%, preferably in a range from 150% to 250% for example 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240% or 250% of R0, preferably about 200% R0. Typically, the effective radius R0 of the ion trap and / or the set of electrodes is in a range from 2.5 mm to 5 mm.

[0230] Second section

[0231] In one example, the second section comprises and / or is cylindrical section, for example a circular aperture. In this way, the second section improves providing of a cylindrical beam of electrons.

[0232] In one example, the second section comprises and / or is a rectangular section, for example a rounded rectangular section or a stadium section. In this way, the second section improves providing of a ribbon beam of electrons, for example from a ribbon electron emitter.

[0233] In one example, the second dimension (y2), the third dimension (z2) and / or a diameter of the second section is less than the effective radius R0 of the ion trap and / or the set of electrodes, for example in a range from 50% to 99%, preferably in a range from 60% to 90% for example 60%, 65%, 70%, 75%, 80%, 85% or 90% of R0, preferably about 80% R0. Typically, the effective radius R0 of the ion trap and / or the set of electrodes is in a range from 2.5 mm to 5 mm.

[0234] Lengths

[0235] In one example, the first dimension (x1) of the first section is greater than the first dimension (x2) of the second section. That is, the first section is longer than the second section.

[0236] -Broker Confidential-In one example, the first dimension (x3) of the third section is greater than the first dimension (x2) of the second section. That is, the third section is longer than the second section.

[0237] In one example, x1 > x3 » x2. In one example, x1 = x3 » x2. In one example, x3 > x1 » x2.

[0238] Symmetry

[0239] In one example, the first passageway has at most 1 or 2 planes of symmetry, for example defined by the second axis and / or the third axis. In one example, the second section and / or the third section has / have cylindrical symmetry about the first axis (X). In one example, the first section has rotational symmetry of order 1 or 2 about the first axis (X).

[0240] In one example, the first section comprises a triangular prismatic frustum section, the second section comprises and / or is cylindrical section and the third section comprises and / or is a conical section, such as a slot-to-cone.

[0241] In one example, the first section comprises a triangular prismatic frustum section, the second section comprises and / or is a rectangular section and the third section comprises and / or is a triangular prismatic frustum section, such as a slot-to-slot.

[0242] Second electrode

[0243] In one example, an electrode, for example the first electrode or a second electrode of the set of electrodes, has a second passageway therethrough for the electrons, wherein the first passageway and the second passageway are coaxial. In this way, the respective first axes (X) of the first passageway and the second passageway are coincident or collinear.

[0244] The second passageway may be as described with respect to the first passageway mutatis mutandis.

[0245] In one example, the first electrode comprises the first passageway and the second electrode comprises the second passageway.

[0246] In one example, the first section of the first passageway and the first section of the second passageway are mutually opposed, for example having the same orientation about the first axis (X). In this way, if the first sections are relatively more proximal the trapping region compared with the third section, the first section of the first passageway provides an outlet from the first passageway

[0247] -Broker Confidential-into the trapping region and the first section of the second passageway provides an inlet into the second passageway from the trapping region.

[0248] In one example, a first opening of the first section of the first passageway and a first opening of the first section of the second passageway are mutually opposed. In one example, a first opening of the first section of the first passageway and a first opening of the first section of the second passageway are mutually similar and / or the same.

[0249] In one example, the second electrode is generally as described with respect to the first electrode.

[0250] 2D ion trap

[0251] In one example, the 2D ion trap comprises two or more pairs of rod electrodes, including a first pair of rod electrodes and a second pair of rod electrodes, wherein the first pair of rod electrodes comprises or consists of the first electrode and the second electrode and wherein the second pair of rod electrodes comprises or consists of a first electrode and a second electrode.

[0252] In one example, the first electrode and / or the second electrode of the second pair of rod electrodes are generally as described with respect to the first electrode and / or the second electrode of the first pair of rod electrodes, mutatis mutandis. That is, the first electrode and / or the second electrode of the second pair of rod electrodes comprise respective passageways, for example as described with respect to the first electrode and / or the second electrode of the first pair of rod electrodes, mutatis mutandis. More generally, in one example, the second pair of rod electrodes comprises and / or is electrical analogues of the first pair of rod electrodes, for example by having analogous surfaces. In this way, an electric field provided by the 2D ion trap is symmetric or relatively more symmetric, compared with conventional electrodes not having passageways therethrough, thereby reducing or eliminating defocusing of electrons in the electric field. In one example, the respective passageways of the first electrode and / or the second electrode of the second pair of rod electrodes comprise, for example only comprise, a first section and optionally a second section, as described with respect to the first electrode and / or the second electrode of the first pair of rod electrodes, mutatis mutandis. In this way, these respective passageways are blind passageways (i.e. not through passageways) while an electric field provided by the 2D ion trap is symmetric or relatively more symmetric, as described previously. In this way, complexity (for example, of machining) is reduced. In one example, the respective passageways of the first electrode and / or the second electrode of the second pair of rod electrodes do not comprise a third section and optionally a second section, as described with respect

[0253] -Broker Confidential-to the first electrode and / or the second electrode of the first pair of rod electrodes, mutatis mutandis. In this way, these respective passageways are blind passageways (i.e. not through passageways).

[0254] / on trap

[0255] The sixth aspect provides an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0256] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes;

[0257] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section.

[0258] The ion trap according to the sixth aspect may be as described with respect to the apparatus according to the fifth aspect mutatis mutandis.

[0259] Electrode

[0260] The seventh aspect provides an electrode for an ion trap, wherein the electrode has a first passageway therethrough for electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes;

[0261] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section.

[0262] The electrode according to the seventh aspect may be as described with respect to the apparatus according to the fifth aspect and / or the ion trap according to the sixth aspect mutatis mutandis.

[0263] Method - electrode

[0264] -Broker Confidential-The eighth aspect provides a method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes; wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0265] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0266] wherein the method comprises:

[0267] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed;

[0268] applying the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof;

[0269] trapping ions in the ion trap during the first set of states; and

[0270] injecting electrons into the ion trap via the first passageway, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0271] wherein injecting the electrons into the ion trap via the first passageway comprises allowing defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0272] The method according to the eighth aspect may include any step as described with respect to the sixth aspect, the seventh aspect and / or the eighth aspect mutatis mutandis.

[0273] Apparatus - waveform & electrode

[0274] The ninth aspect provides an apparatus comprising:

[0275] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set

[0276] -Broker Confidential-of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0277] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0278] an electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0279] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes;

[0280] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0281] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0282] wherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

[0283] The apparatus according to the ninth aspect may be as described with respect to the apparatus according to the first aspect, the second aspect, the fifth aspect, the sixth aspect and / or the seventh aspect mutatis mutandis.

[0284] The tenth aspect provides a method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end electrodes; wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y)

[0285] -Broker Confidential-and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0286] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0287] wherein the method comprises:

[0288] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;

[0289] applying the generated RF voltage waveform to the set of electrodes;

[0290] trapping ions in the ion trap during the first set of states; and

[0291] injecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0292] wherein injecting the electrons into the ion trap via the first passageway comprises allowing defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0293] The method according to the tenth aspect may be as described with respect to the method according to the third aspect, the fourth aspect and / or the eighth aspect mutatis mutandis.

[0294] Multipole ion guide - waveform and / or electrode

[0295] The eleventh aspect provides an apparatus comprising:

[0296] a multipole ion guide (more generally ion guide) comprising a set of electrodes, for example two or more pairs of rod electrodes;

[0297] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a radial confining field in the multipole ion guide for radially confining ions in a radial confining region thereof; and

[0298] -Broker Confidential-an electron source, configured to inject electrons into the multipole ion guide for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0299] characterized by:

[0300] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0301] wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0302] and / or

[0303] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0304] wherein the electron source is configured to inject the electrons into the multipole ion guide during the second set of states, for example only during the second set of states.

[0305] In this way, as described with respect to the first aspect mutatis mutandis, defocusing, deflection, divergence and / or spreading of the electrons, for example due to the trapping field and / or space charge effects, may be attenuated and / or avoided since the electrons are injected into the multipole ion guide during the second set of states, for example only during the second set of states, when a radial confining field is not provided in the multipole ion guide. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the multipole ion guide improved.

[0306] In this way, as described with respect to the fifth aspect mutatis mutandis, if the first section is relatively more proximal the radial confining region compared with the third section, the first section allows defocusing, deflection, divergence and / or spreading of the electrons, for example due to the radial confining field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section, since the third section is elongated along the third axis (Z) compared with the second section. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the multipole ion guide improved.

[0307] -Broker Confidential-In this way, as described with respect to the fifth aspect mutatis mutandis, if the first section is relatively more distal the radial confining region compared with the third section, the first section improves collimation, in the third axis (Z) in the first section, for example by collisions of divergent electrons from the electron source with surfaces of the first section. In this way, surface contamination of the set of electrodes and concomitant degradation of performance are reduced, minimized and / or eliminated and / or to efficiency of electron-based fragmentation reactions in the multipole ion guide improved because collimation of the electrons is improved.

[0308] The apparatus according to the eleventh aspect may be as described with respect to the apparatus according to the first aspect, the second aspect, the fifth aspect, the sixth aspect, the seventh aspect and / or the tenth aspect mutatis mutandis.

[0309] The twelfth aspect provides a method of reacting ions with electrons in a multipole ion guide comprising a set of electrodes, for example two or more pairs of rod electrodes;

[0310] optionally wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0311] optionally wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section;

[0312] wherein the method comprises:

[0313] generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and optionally a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;

[0314] applying the generated RF voltage waveform to the set of electrodes;

[0315] radially confining ions in the multipole ion guide during the first set of states; and

[0316] injecting electrons into the multipole ion guide, optionally during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0317] optionally wherein injecting the electrons into the multipole ion guide via the first passageway comprises allowing defocusing, deflection, divergence and / or spreading of the electrons, for example

[0318] -Broker Confidential-due to the radial confining field, along the third axis (Z) in the first section, for example without collisions of the electrons with surfaces the first electrode and / or surfaces of the first section.

[0319] The method according to the twelfth aspect may be as described with respect to the method according to the third aspect, the fourth aspect, the eighth and / or the eleventh aspect mutatis mutandis.

[0320] BRIEF DESCRIPTION OF THE DRAWINGS

[0321] For a better understanding of the invention, and to show how exemplary embodiments of the same may be brought into effect, reference will be made, by way of example only, to the accompanying diagrammatic Figures, in which:

[0322] Figure 1 schematically depicts a conventional apparatus and a method thereof;

[0323] Figure 2 schematically depicts an apparatus according to an exemplary embodiment and a method according to an exemplary embodiment;

[0324] Figure 3 schematically depicts a method according to an exemplary embodiment;

[0325] Figure 4 schematically depicts a method according to an exemplary embodiment;

[0326] Figure 5 shows CAD perspective view and cross-sectional perspective views of an apparatus according to an exemplary embodiment;

[0327] Figure 6 shows CAD cross-sectional views of the apparatus of Figure 5, in use;

[0328] Figure 7A shows a CAD horizontal cross-sectional view of an apparatus according to an exemplary embodiment; and Figure 7B shows a CAD vertical cross-sectional view of the apparatus;

[0329] Figure 8A shows a CAD perspective view of part of an apparatus according to an exemplary embodiment; and Figure 8B shows a CAD perspective view of part of an apparatus according to an exemplary embodiment; and

[0330] Figure 9 shows a CAD vertical cross-sectional view of an apparatus according to an exemplary embodiment.

[0331] -Broker Confidential-DETAILED DESCRIPTION OF THE DRAWINGS

[0332] Figure 1 schematically depicts a conventional apparatus and a method thereof.

[0333] Figure 1 shows XY and XZ cross-sectional views of a 2D linear ion trap 100 designed with round apertures on two opposing quadrupole - electrodes 101 , 102, 103 arranged along the X-direction, also termed the inlet and outlet X-pole - electrodes, for injecting and / or transmitting electrons from an external source 104, 105, 106, into / through the ion trapping region. Typically, the electron source is configured with a system of DC electrodes to confine and focus the beam towards the 2D LIT. Also shown in Figure 1 of the prior art are the two antiphase waveforms applied to the Y-pole - electrodes 107 and to the X-pole - electrodes 108. Electrons are injected from an external source 104, 105, 106 with different energies along the X axis and flow through 109 the inlet X-pole - electrode into the ion trapping region only when the voltage level of the rectangular waveform applied to the X-pole -electrodes is switched to a positive level, or to any positive value above the potential level applied to the electron source.

[0334] In this example of the prior art, three different kinetic energies are considered corresponding to ECD conditions using ~0 eV electrons, hot ECD conditions corresponding to ~5 eV electrons, and electron induced dissociation (EID) conditions corresponding to higher energy ~35 eV electrons. In ECD electrons are coming to a stop at the center of the ion trap 110 and can be redirected backwards along the X-axis. The strong negative potential established by the rectangular waveform applied to the Y-pole - electrodes 107 during the electron injection period results in a strong defocusing action of the electron beam in Z as observed on the XZ plane 111. As a result, the reflected and strongly defocused electrons are directed onto the surface of the inlet X-pole - electrode 114, leading to surface contamination and ultimately to poor ion trapping conditions after prolonged exposure of the surface to the electron beam. Similarly, when increasing the electron kinetic energy to ~5 eV, the electron beam 112 will go over the potential barrier at the center of the ion trap and the same defocusing action established by the rectangular waveform applied to the Y-pole - electrodes 107 will eventually lead to a burn mark on the surface of the outlet X-pole - electrode 115. The exact same phenomenon is observed by further increasing electron energy to ~35 eV. Although faster electrons are less affected by the defocusing action in Z shown on the XZ plane, the electron beam 113 will also contaminate the hyperbolic surface of the outlet X-pole - electrode 116.

[0335] Figure 1 also shows the kinetic energy of electrons as a function of distance travelled along the X-axis during the injection phase, 117 - 119. In this prior art example, the electron source is set to

[0336] -Broker Confidential-ground potential and the rectangular waveforms are switched between 250 V positive and -250 V negative levels. Under ECD conditions 117, electrons are decelerated to ~0 eV at the center of the ion trap and get reflected towards the inlet X-pole - electrode. The deceleration of the electrons is established in the static quadrupole field, with a positive voltage applied to the X-poles (+V) and a negative voltage applied to the Y-poles (-V). Electrons will reaccelerate towards the exit aperture on the X-pole if the kinetic energy is increased to ~5eV 118 to perform hECD orto even higher energies, for example to ~35 eV 119 to perform EID. In all cases, the defocusing effect is observed in the XZ plane as electrons past the inlet X-pole are decelerated and come to a stop until they reach the center of the ion trap or reaccelerated towards the outlet X-pole. The extent of the defocusing depends, in part, on the kinetic energy of the electrons and, in part, on the intrinsic properties of the quadrupole field applied for storing analyte ions in the ion trap.

[0337] Figure 2 schematically depicts an apparatus according to an exemplary embodiment of the first aspect and a method according to an exemplary embodiment of the third aspect.

[0338] The apparatus comprises:

[0339] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0340] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0341] an electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0342] wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; and

[0343] wherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

[0344] -Broker Confidential-The first aspect provides a single tri-state waveform or a pair of antiphase tri-state waveforms for driving 3D and 2D ion traps respectively. The trapping potential is therefore switched between three discrete voltage levels. In a 2D LIT, the antiphase tristate waveforms applied to the X and Y poles as shown in Figure 1 of the prior art are switched between a first positive voltage level, VP, a second negative voltage level, preferably of equal amplitude, Vn, and also a third middle voltage with the voltage level preferably adjusted to the average value of the positive and negative voltage levels, (Vp+Vn) / 2. For example, if the positive voltage level is set to 25OVoP, the negative voltage level is -25OVoP, the corresponding middle voltage level is OV. In a 2D LIT, the middle voltage level is common to both tristate waveforms thereby creating a field-free region inside the ion trap for a predefined time window within a single waveform period. Preferably, an additional DC bias is applied to the rectangular waveform generator, raising the voltage level of the tristate waveforms by the corresponding DC level, thus raising the voltage of the field-free region, from example, from OVto a higher positive DC voltage level.

[0345] The first aspect of the invention also provides configuring the electron source to inject electrons from an external source into the ion trap only when the middle voltage level is applied. Electrons injected during this time window, also termed the zero-phase of the tristate waveform, are transported through the ion trap under field-free conditions, thus, the defocusing action imposed by a static quadrupole field established when applying opposite potentials to the X and Y poles of a 2D LIT configuration is eliminated. A collimated electron beam modulated by the electron source optics can therefore be focused through the entrance and exit apertures on the inlet and outlet pole - electrodes respectively, eradicating surface contamination and other undesired surface charging effects that have a negative impact on instrument robustness and on the overall performance of RF ion traps enabling electronbased fragmentation reactions with analyte ions.

[0346] Figure 2 shows electrons injected through an ion trap during the zero-phase established by two antiphase tristate waveforms applied to the X and Y poles of a 2D LIT configuration. In this example of the present invention 200, three different electron energies are considered corresponding to ECD at ~0 eV, hot ECD at ~5 eV electrons, and EID at ~35 eV. Under ECD conditions, electrons from an external electron source 204 fly through apertures on the X poles of the ion trap 201 with near-zero kinetic energy, as shown in the corresponding kinetic energy diagram 210. With sufficient collimation from the electron source 204 enabled by a system of lens - electrodes, the cross section and the divergence of the electron beam 207 can be kept sufficiently narrow while interactions with pole -electrode surfaces inside the ion trap are minimized or eliminated, as shown in both the XY 213 and XZ 214 planes. Increasing the kinetic energy to ~5 eV, electrons from the external electron source 205 can also be efficiently focused through the round apertures on the X poles of the ion trap 202.

[0347] -Broker Confidential-With appropriate adjustments to the settings of the electron source 205, the cross section of the electron beam 208 traversing the ion trap with a constant kinetic energy of ~5eV, as shown in the kinetic energy diagram 211 , can also be kept sufficiently narrow and below the characteristic dimensions of the entrance and exit apertures 202 on the inlet and outlet poles respectively. Collimation is enhanced as electron energy increases. The cross section of the electron beam 209 is the narrowest in the example where the electron source 206 produces electrons with kinetic energies of ~35 eV. Similarly, the kinetic energy diagram 212 highlights the constant kinetic energy of the electron beam passing through the apertures 203 on the X-pole - electrodes of the ion trap.

[0348] Figure 2 also shows the two tristate waveforms 215 and 216 applied to the X and Y poles of the 2D LIT respectively. The external source of electrons 204 - 206 is configured with a system of lenses and at least one of the lenses is configured to receive a voltage 217 switched between a first level for enabling injection of electrons into the ion trap and a second level for deflecting electrons away from the ion trap. The deflection lens voltage is synchronized with the phases of the tristate waveform, whilst electron injection is enabled only during the zero-phase of the tristate waveforms, that is, only during the time window where both waveforms are at the same middle voltage level. This method of operation prevents electrons from penetrating into the ion trap and being defocused by the quadrupole field formed during the positive voltage phase of the tristate waveform applied to the X-pole - electrodes. Therefore, electrons can be efficiently injected from an external source 204 - 206 over a wide range of kinetic energies and can be focused to flow through the ion trap 218 only during the zero phase of the tristate waveforms and without interacting with the hyperbolic surfaces of the ion trap.

[0349] In this example, the power supply is configured to: control, for example individually and / or independently, respective durations of the respective states of the first set of states and / orthe second set of states. In other words, the apparatus comprises means for controlling the duty cycle of the tristate waveform(s). Adjustments to the duty cycle of a tristate waveform can be used to optimize the reaction time between analyte ions and externally injected electrons, and further adjust the low-mass cut-off (Imco) and consequently the mass-to-charge range of the ions stored in an ion trap. Controlling the Imco and m / z range is advantageous for optimizing the fragmentation information output in experiments between analyte ions and electrons.

[0350] Figure 3 shows tristate waveform examples designed with different duty cycles and their corresponding stability diagrams for 2D LITs. Only one of the two antiphase waveforms is shown in each case. A first example of a tristate waveform 301 is designed with the middle voltage level to account for 60% of the waveform period. The longer the zero-phase time window within the waveform

[0351] -Broker Confidential-period, the lower the Imco becomes, as shown in the stability diagram 302, enabling the trapping of even lower m / z ions. The 60% duration of the middle voltage level is divided in two-half windows within a waveform period T, with each half window established before and after the high voltage levels, either positive or negative ones. A second example of a tristate waveform 303 is shown in Figure 3 where the duty cycle of the middle level voltage is set to 50%. The corresponding stability diagram 304 exhibits a reduced value for the Imco with the stability boundaries crossing the q axis at ~1.0 instead of ~1.2 in the previous stability diagram 302 where the zero-phase duty cycle is set to 60%. Yet another example of a tristate waveform 305 is shown where the zero-phase duty cycle is set to 40%, thus reducing the reaction time between analyte ions and electrons compared to the previous examples discussed with reference to Figure 3. The Imco in this latter case is further reduced with the stability boundary 306 crossing the q axis at ~0.9, however, one of the benefits of shortening the zero-phase window and lowering the duty cycle for ExD reactions is that trapping efficiency for the higher m / z ions is enhanced, which is desirable in ECD experiments with high mass analytes.

[0352] Ultimately, the optimum duty cycle for enabling reactions between analyte ions and electrons in ion traps driven by tristate waveforms will depend on the application and the corresponding m / z range of interest. For example, tristate waveforms designed with a greater zero-phase duty cycle maybe preferrable for performing EID on smaller m / z, lower charge-state analyte species, while ECD performed on multiply-charged higher m / z analytes may require reducing the zero-phase duty cycle since the electron capture cross section is greater and the reaction time window can be traded for enhanced trapping efficiency.

[0353] In one example, the first set of states and the second sets of states are in series (i.e. successively). In one example, respective states of the first set of states and the second sets of states are in series.

[0354] Different types of tristate waveforms can be implemented with modern electronics to further enable new ion trapping methods and electron-based activation - dissociation reactions. In one example where a pair of antiphase tristate waveforms 400 is applied to a 2D LIT shown in Figure 4, the middle voltage level 401 is not divided into two-half windows as disclosed in reference to Figures 2 and 3, but instead is applied continuously within a waveform period. In this example, the zero-phase is set to 50% of the tristate waveform period. Different duty cycles can be considered to optimize ion trapping and ion-electron reaction efficiencies, while a DC bias 402 can also be applied to facilitate tuning the DC offset of the ion trap relative to the DC offset of the external electron source for fine tuning of the electron energy.

[0355] -Broker Confidential-In yet another example of a waveform 410 shown in Figure 4, the one or more middle voltages 411 are set to levels that are asymmetric with respect to the discrete positive and negative voltage levels 412. In such multilevel state waveforms, it is preferable to keep the area under the waveform voltage curve between the positive and negative phases equal in order to store ions in the center of the quadrupole trapping field. Any asymmetry in the waveforms areas will introduce a DC offset, displacing trapped ions off center, which will alter the energy in reactions between analyte ions and electrons. A deflection voltage applied to one of the lens electrodes of the external electron source can be synchronized with the rectangular trapping waveform to enable injection of electrons during the application of the middle voltage levels 411. The advantage of applying such a multilevel waveform would be to inject electrons in a weak quadrupole field where the defocusing action of the electron beam is minimized, while trapping efficiency for analyte ions is improved compared to antiphase waveforms forming a field-free region when the middle voltage level is set to zero.

[0356] In one example, the electron source is configured to inject the electrons into the ion trap via a gap between adjacent electrodes of the set of electrodes. In this way, tristate or other multiple state waveforms also enable efficient injection of electrons between the pole - electrodes of a 2D LIT, as opposed to injecting electrons through apertures or slits in round, hyperbolic or other types of pole -electrode surfaces employed for ion trapping. External injection of electrons between pole -electrodes in a 2D LIT supplied with two-antiphase or two-state waveforms, as those describe in Figure 1 of the prior art is impractical due to the finite thickness of the electron beam and the deflection electrons will experience when passing through the gap while opposite phase waveforms are applied to pole - electrodes. Tristate or other types of multistate waveforms designed with a zerophase or with a weak quadrupole field-phase windows as disclosed here with reference to Figures 2, 3 and 4 of the present invention establish conditions where such a deflection effect or other defocusing fields are eliminated or substantially reduced.

[0357] In one example, the ion trap comprises and / or is a 2D ion trap such as a LIT and the set of electrodes comprises N pairs of rod electrodes, wherein N is a natural number greater than or equal to 2, for example 2, 3, 4, 5, 6 or more. External injection of electrons is also considered in higher order multipole ion guides and / or ion traps, for example hexapole or octapole configurations, supplied with a pair of tristate or other antiphase waveforms disclosed with reference to Figures 2 - 4. Similarly to a 2D LIT disclosed in the present invention, electrons are transported through the higher-order multipole ion guide and / or ion trap under field-free conditions, for example, thus, the defocusing action imposed by a two-state higher-order field established when applying opposite potentials to the two sets of pole-electrodes comprising a higher-order multipole ion guide is eliminated. A collimated electron beam modulated by the electron source optics can therefore be focused through the

[0358] -Broker Confidential-entrance and exit apertures on the inlet and outlet pole - electrodes respectively of the higher-order multipole ion guide, eradicating surface contamination and other undesired surface charging effects that have a negative impact on instrument robustness and on the overall performance.

[0359] Electron-based fragmentation reactions disclosed so far in the present invention are performed with trapped ions to control the reaction time based on the charge state and / or the density of the analyte ion population stored in the trapping field. Radial trapping is enabled by the application of a pair of antiphase rectangular waveforms to the pole - electrodes, while axial trapping is enabled by applying a DC bias to terminal lens - electrodes or pole - electrode segments adjacent to the trapping region. In yet another aspect of the present invention, electron-based fragmentation reactions can also be performed with ions passing through a 2D LIT or a higher order multipole ion guide driven by tristate or other multistate substantially rectangular waveforms disclosed herein. The passthrough mode is enabled by switching off the axial trapping field or by applying appropriate DC signals to terminal lens electrodes and / or to pole - electrode segments, thus directing ions to move forward along the ion optical axis of any RF multipole ion guide configuration.

[0360] The fifth aspect provides an apparatus comprising:

[0361] an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, or a 3 dimensional, 3D, ion trap such as a quadrupole ion trap, QIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes or wherein the 3D ion trap comprises a ring electrode and two end-cap electrodes;

[0362] a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; and

[0363] an electron source, configured to inject electrons into the ion trap for reactions thereof with the trapped ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;

[0364] wherein a first electrode of the set of electrodes has a first passageway therethrough for the electrons, wherein the first passageway defines a first (X) axis and mutually orthogonal second (Y) and third (Z) axes and wherein the first passageway comprises a first section, a third section and a second section therebetween, having respective first (x), second (y) and third (z) dimensions along the first (X), second (Y) and third (Z) axes; and

[0365] -Broker Confidential-wherein the third dimension (Z) of the first section is relatively greater than the third dimension (Z) of the second section.

[0366] In this way, the surface contamination and surface charging effects observed in a 2D LIT driven by two-stage rectangular waveforms receiving electrons from an external source are addressed by appropriately shaping the inlet and outlet openings on the pole - electrodes to accommodate the phase-space transformation of the electron beam traversing the quadrupolar field. Phase space transformations involve changes in the cross-sectional area and the velocity distributions of a charged particle beam under the influence of an external electric field. The defocusing effect in the Z axis imposed by the application of two-state waveforms, and discussed with reference to Figure 1 of the prior art, can be addressed by elongating the inlet and outlet openings on the X-poles along the Z axis. A potential advantage of the two-state waveform implementation with optimized inlet / outlet openings is that the voltage is switched between two discrete levels instead of three levels in tristate waveforms, which may require more advanced electronics to generate and control such signals.

[0367] Figure 5 shows an implementation example 500 of an asymmetric pair of openings realized on the inlet 501 and outlet 502 X-pole - electrodes of a 2D LIT, as described with respect to the fifth aspect. Cross-sectional views are drawn to highlight the shaping of the inlet opening on each of the X-pole electrodes in the XY 503 and XZ 504 planes respectively. The inlet opening, shown in the XZ cross-sectional view 504, is produced with a constriction 505, a narrow passage defining an acceptance area for admitting electrons in the ion trap. The fraction of the electron beam outside of the acceptance area is reflected backwards by a funnel-shaped surface area 506 at the entrance of the inlet opening. The combination of a cylindrically symmetric funnel-shaped entrance terminating at a round constriction facilitates the formation of a quasi-cylindrical electron beam injected into the ion trap along the X-axis 507. The exit of the inlet opening beyond the constriction is designed with a divergence in Z 508, while the vertical dimension Y 509 shown in the XY cross-sectional view 504 is kept equal to the diameter of the round constriction, forming a round-to-slot exit channel guiding electrons into the ion trap volume. The Z-slotted configuration 508 is essential for ingesting the lowest energy electrons employed in ECD, which are reflected by the quadrupole field and get redirected onto the surface of the entrance X-pole - electrode 501 or 114 shown in Figure 1. The Z dimension of the slot on the inlet X-pole electrode 501 is chosen such as to accept all electrons redirected by the quadrupole field back towards the inlet, thus eliminating surface contamination effects on the hyperbolic surfaces of the ion trap establishing the ion trapping field. Any surface contamination will therefore be restricted inside the round-to-slot exit channel of the inlet X-pole 501 , and the effect on the quality of the quadrupole field storing analyte ions will be negligible.

[0368] -Broker Confidential-In the preferred embodiment shown in Figure 5, a similar arrangement is adopted for the outlet opening on the X-pole electrode 502, where a slot entrance 510 is used to accommodate an electron beam with a larger spread in Z, leading to a constriction 511 and ultimately to a short axisymmetric funnel-shaped exit 512. The dimensions of slot 508 at the exit-end of the inlet opening and at the entrance-end of the outlet opening 510 are preferably matched in order to maintain quadrupole field symmetry. Non symmetric slot / aperture configurations in the i n let / o utlet poles can also be considered while the geometrical quadrupole asymmetry can be compensated by adjusting the amplitude and / or duty cycle of the applied rectangular waveforms and associated DC bias signals.

[0369] In this example, the slot-to-round channel 510 at the entrance of the outlet opening guiding electrons out of the ion trap differs from the round-to-slot channel guiding electrons in. Specifically, the depth of the outlet channel before the constriction 511 is greater while the convergence in Z is less to minimize electrons reflecting on surfaces from getting redirected back into the ion trap, this eliminating stray electron trajectories that may lead to ion-electron interactions with undesired electron kinetic energies or to surface contamination effects. The height of the slot-to-round channel in Y 513 is kept the same as in the inlet opening 509, since the electron beam remains focused in this dimension - the defocusing action is manifested always in Z. The dimensions of both constrictions on the inlet and outlet openings are set equal in this example and are defined, in part, by the acceptable amount of cooling gas used for thermalizing ions in the ion trap that is allowed to leak out. Overall, differences in the characteristic dimensions of the inlet and outlet openings are desirable to optimize separately the injection process as we as the way electrons are guided out of the ion trap.

[0370] Figure 6 shows electron trajectory examples in a 2D LIT driven by a pair of antiphase two-state rectangular waveforms. Despite its rather wide incoming angle and inevitable reflection on the pole - electrode wall, trajectory 601 is focused by the quadrupole field in the Y direction and is efficiently guided out of the ion trap through the slot-to-round channel on the outlet opening. Trajectory 602 shows how the slot-to-round channel at the outlet opening can be used to guide electrons out of the ion trap via utilizing surface reflection effects. Trajectory 603 shows how the funnel-shaped entranceend rejects electrons with highly divergent incoming angles. In contrast, a uniform cylindrical inlet opening would direct such electrons into the ion trap leading to surface contamination. Finally, trajectory 604 highlights the importance of introducing a slot at the exit of the inlet opening in order to accept low energy electrons under ECD conditions that come to a stop at the center of the ion trap and get redirected backward towards the inlet.

[0371] -Broker Confidential-Other types or shapes of openings can be realized on the inlet and outlet X-pole - electrodes of a 2D LIT or on opposite pole - electrodes in a higher order multipole ion guide, for example a hexapole or an octapole configuration, driven by two-state, substantially rectangular waveforms. Substantially rectangular waveforms include waveforms switched between two or more discrete voltage levels, characterized by finite rise and fall times of the voltage between each level. The dimensions of the openings can be matched to degree of defocusing electrons undergo with the trapping field. For example, the shape of the openings disclosed in Figure 6 is more appropriate for performing electronbased fragmentation reactions with trapped ions. Operating a system in passthrough mode preferably requires elongating both openings along the Z axis while preserving all the characteristics as described with reference to Figure 6.

[0372] Figure 7A shows a CAD horizontal cross-sectional view of an apparatus according to an exemplary embodiment; and Figure 7B shows a CAD vertical cross-sectional view of the apparatus. In more detail, the electrodes 701 , 702 of a 2D LIT 700 are generally as described with respect to the electrodes 501 , 502 of the 2D LIT 500. However, in contrast, the respective passageways 711 , 712 are slot-to-slot. In this embodiment, the first section is a triangular prismatic frustum section having two parallel truncated triangular bases and semicylindrical walls therebetween, the second section is a stadium section and the third section is a triangular prismatic frustum section having two parallel truncated triangular bases and semicylindrical walls therebetween. In this way, providing of a ribbon beam of electrons, for example from a ribbon electron emitter, is improved for increased efficiency of ion-electron interactions while minimizing electrons reflecting on surfaces from getting redirected back into the ion trap, eliminating stray electron trajectories that may lead to ion-electron interactions with undesired electron kinetic energies and / or to surface contamination effects.

[0373] Figure 8A shows a CAD perspective view of part 801 of an apparatus according to an exemplary embodiment. In this example, the electron source 801 is configured to provide a cylindrical beam of electrons to be injected into an ion trap, wherein the electron source comprises a circular electron emitter 802, supported by legs 803.

[0374] Figure 8B shows a CAD perspective view of part 811 of an apparatus according to an exemplary embodiment. In this example, the electron source 811 is configured to provide a ribbon beam of electrons to be injected into the ion trap, wherein the electron source comprises a ribbon electron emitter 812, provided by a coated ribbon filament. In this example, a length Lr of the ribbon electron emitter 812 is greater than or equal to a length LI of legs 813 thereof. In this example, a ratio of a length Lr of the ribbon electron emitter 812 to a length LI of legs 813 thereof is in a range from 3 : 2 to 4 : 1 .

[0375] -Broker Confidential-Figure 9 shows a CAD vertical cross-sectional view of an apparatus 900 according to an exemplary embodiment.

[0376] In more detail, the electrodes 901 , 902 of a 2D LIT 900 are generally as described with respect to the electrodes 701 , 702 of the 2D LIT 700, wherein the respective passageways 911 , 912 are slot-to-slot.

[0377] In this example, the 2D LIT 900 comprises two pairs of rod electrodes, including a first pair of rod electrodes 901 , 902 and a second pair of rod electrodes 903, 904, wherein the first pair of rod electrodes 901 , 902 consists of the first electrode 901 and the second electrode 902 and wherein the second pair of rod electrodes 903, 904 consists of a first electrode 903 and a second electrode 904.

[0378] In this example, the first electrode 903 and the second electrode 904 of the second pair of rod electrodes 903, 904 are generally as described with respect to the first electrode 901 and the second electrode 902 of the first pair of rod electrodes 901 , 902, mutatis mutandis. In this example, the second pair of rod electrodes 903, 904 comprises and / or is electrical analogues of the first pair of rod electrodes 901 , 902, by having analogous surfaces. In this example, the respective passageways 913, 914 of the first electrode 903 and the second electrode 904 of the second pair of rod electrodes 903, 904 only comprise a first section. In this example, the respective passageways 913, 914 of the first electrode 903 and the second electrode 904 of the second pair of rod electrodes 903, 904 do not comprise a third section and a second section. In this way, these respective passageways 903, 904 are blind passageways (i.e. not through passageways). A more symmetric quadrupole field is therefore produced by introducing the blind passageways 913, 914.

[0379] Notes

[0380] Although a preferred embodiment has been shown and described, it will be appreciated by those skilled in the art that various changes and modifications might be made without departing from the scope of the invention, as defined in the appended claims and as described above.

[0381] At least some of the example embodiments described herein may be constructed, partially or wholly, using dedicated special-purpose hardware. Terms such as ‘component’, ‘module’ or ‘unit’ used herein may include, but are not limited to, a hardware device, such as circuitry in the form of discrete or integrated components, a Field Programmable Gate Array (FPGA) or Application Specific Integrated Circuit (ASIC), which performs certain tasks or provides the associated functionality. In some

[0382] -Broker Confidential-embodiments, the described elements may be configured to reside on a tangible, persistent, addressable storage medium and may be configured to execute on one or more processors. These functional elements may in some embodiments include, by way of example, components, such as software components, object-oriented software components, class components and task components, processes, functions, attributes, procedures, subroutines, segments of program code, drivers, firmware, microcode, circuitry, data, databases, data structures, tables, arrays, and variables. Although the example embodiments have been described with reference to the components, modules and units discussed herein, such functional elements may be combined into fewer elements or separated into additional elements. Various combinations of optional features have been described herein, and it will be appreciated that described features may be combined in any suitable combination. In particular, the features of any one example embodiment may be combined with features of any other embodiment, as appropriate, except where such combinations are mutually exclusive. Throughout this specification, the term “comprising” or “comprises” means including the component(s) specified but not to the exclusion of the presence of others.

[0383] Attention is directed to all papers and documents which are filed concurrently with or previous to this specification in connection with this application and which are open to public inspection with this specification, and the contents of all such papers and documents are incorporated herein by reference.

[0384] All of the features disclosed in this specification (including any accompanying claims, abstract and drawings), and / or all of the steps of any method or process so disclosed, may be combined in any combination, except combinations where at least some of such features and / or steps are mutually exclusive.

[0385] Each feature disclosed in this specification (including any accompanying claims, abstract and drawings) may be replaced by alternative features serving the same, equivalent or similar purpose, unless expressly stated otherwise. Thus, unless expressly stated otherwise, each feature disclosed is one example only of a generic series of equivalent or similar features.

[0386] The invention is not restricted to the details of the foregoing embodiments). The invention extends to any novel one, or any novel combination, of the features disclosed in this specification (including any accompanying claims, abstract and drawings), or to any novel one, or any novel combination, of the steps of any method or process so disclosed.

[0387] -Broker Confidential-

Claims

CLAIMS1. An apparatus comprising:an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes;a power supply configured to: generate a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and apply the generated RF voltage waveform to the set of electrodes, wherein the first set of states provides a trapping field in the ion trap fortrapping ions in a trapping region thereof; andan electron source, configured to inject electrons into the ion trap for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD;wherein the RF voltage waveform includes a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states; andwherein the electron source is configured to inject the electrons into the ion trap during the second set of states, for example only during the second set of states.

2. The apparatus according to claim 1 , wherein the first voltage level, or a magnitude thereof, of the second set of states is based on the first voltage level and / or the second voltage level of the first set of states.

3. The apparatus according to claim 2, wherein the power supply configured to: generate the RF voltage waveform, the first voltage level of the second set of states is based on a mean of the first voltage level and / or the second voltage level of the first set of states.

4. The apparatus according to any previous claim, wherein the first voltage level, or a magnitude thereof, of the second set of states is based on an energy of the electrons injected into the ion trap.

5. The apparatus according to any previous claim, wherein the second set of states provides a substantially field free region in the ion trap.-Broker Confidential-6. The apparatus according to any of claims 1 to 4, wherein the second set of states provides a quadrupole field in the ion trap for mitigating escape of ions from the trapping region.

7. The apparatus according to any previous claim, wherein the power supply is configured to: apply a DC equipotential to respective electrodes of the set of electrodes during the second set of states.

8. The apparatus according to any previous claim, wherein the power supply is configured to: generate the RF voltage waveform, wherein respective durations of the respective states of the first set of states and / or the second set of states are equal.

9. The apparatus according to any previous claim, wherein the power supply is configured to: control, for example individually and / or independently, respective durations of the respective states of the first set of states and / or the second set of states.

10. The apparatus according to any previous claim, wherein the second set of states includes a second state having a second voltage level.

11. The apparatus according to any previous claim, wherein the first set of states and the second sets of states are in series and / or wherein respective states of the first set of states and the second sets of states are in series.

12. The apparatus according to any previous claim, wherein the set of electrodes comprises N pairs of rod electrodes, wherein N is a natural number greater than or equal to 2, for example 2, 3, 4, 5, 6 or more.

13. The apparatus according to any previous claim, wherein the electron source is configured to inject the electrons into the ion trap via a gap between adjacent electrodes of the set of electrodes and / or wherein a first electrode of the set of electrodes comprises a passageway therethrough and wherein the electron source is configured to inject the electrons into the ion trap via the passageway.

14. The apparatus according to any previous claim, wherein the electron source is configured to deflect the electrons into the ion trap during the second set of states, for example only during the second set of states; and / or wherein the electron source is configured to deflect the electrons away from the ion trap during the first set of states, for example only during the first set of states.-Broker Confidential-15. A method of reacting ions with electrons in an ion trap, for example a 2 dimensional, 2D, ion trap such as a linear quadrupole ion trap, LIT, wherein the ion trap comprises a set of electrodes, for example wherein the 2D ion trap comprises two or more pairs of rod electrodes and optionally two end electrodes, the method comprising:generating a substantially rectangular radio frequency, RF, voltage waveform, wherein the RF voltage waveform includes: a first set of states including a first state having a first voltage level and a second state having a second voltage level, wherein the first state and the second state are mutually opposed; and a second set of states including a first state having a first voltage level, wherein the first voltage level of the second set of states is between the first voltage level and the second voltage level of the first set of states;applying the generated RF voltage waveform to the set of electrodes;trapping ions in the ion trap during the first set of states; andinjecting electrons into the ion trap during the second set of states, for reactions thereof with the ions, for example electron capture dissociation, ECD, hot ECD, electron induced dissociation, EID, and / or electron detachment dissociation, EDD.-Broker Confidential-

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