Reduction of internal fragmentation in electron-activated dissociation devices and methods

Abstract

An ion isolation apparatus and method or system using one or more auxiliary electrodes in an ion reactor having an RF electrode adapted to direct positively charged precursor ions along a first axis and an electron source for introducing an electron beam along a second axis transverse to the first axis such that electronically activated dissociation of the precursor ions into reaction products can occur, wherein the auxiliary electrode is configured to apply a complementary AC signal to enable selective extraction of the reaction products while isolating the precursor ions along the second central axis. For example, the complementary AC signal can comprise a notched white noise signal with a notch that suppresses frequencies at which precursor ions (and / or reduced charge species having the same molecular mass but a different charge state) would otherwise be excited.

Description

Technical Field

[0001] (Related Application) This application claims the priority of U.S. Provisional Application No. 63 / 076,785, filed on September 10, 2020, entitled "Reduction of Internal Fragmentation in Electron Activated Dissociation Devices and Methods", and U.S. Provisional Application No. 63 / 076,785 is hereby incorporated by reference in its entirety.

[0002] (Field) The teachings herein relate to activated ion reactions for mass spectrometry, and more particularly, to methods and systems for performing electron activated dissociation (EAD).

Background Art

[0003] (Background) Ion reactions typically involve the reaction of ions that are charged either positively or negatively with another ion that is charged either positively or negatively or another charged species that can be an electron. In electron activated dissociation (EAD), for example, the charged species is an electron beam, and the electron collision with the ion results in fragmentation of the ion. EAD has been used to dissociate biomolecules in mass spectrometry (MS), covering a wide range of potential applications from normal proteomics in liquid chromatography mass spectrometry / mass spectrometry (LC-MS / MS) to top-down analysis (undigested), de novo sequencing (discovery of abnormal amino acid sequences), study of post-translational modifications (glycosylation, phosphorylation, etc.), protein-protein interactions (functional study of proteins), and also providing the ability to include the identification of small molecules.

[0004] Mechanisms for EAD (Electron Activation Dissociation) can include, for example, electron capture dissociation (ECD) using electrons with kinetic energies of 0–3 eV, high-temperature ECD (electrons with kinetic energies of 5–10 eV), and high-energy electron ionization dissociation (HEEID) (electrons with kinetic energies exceeding 13 eV). These electron-activated dissociations are considered complementary to conventional collision-induced or activated dissociation (CID or CAD) and have been incorporated into advanced MS devices.

[0005] Hereafter, the use of the term "EAD" in this instruction should be understood to encompass all forms of electron-associated dissociation techniques and not be limited to the use of electrons at any specific degree of kinetic energy.

[0006] In conventional MS systems, electrons are introduced as a transverse beam (or temporarily trapped within the instrument) so that electrons collide with precursor positive ions as ions pass through the instrument in the axial direction. For example, a mass spectrometer may include a branched RF ion trap structure in which an electron beam is injected orthogonally into the analytical ion beam using independent control of both the ion and electron beams. For further details, see PCT application PCT / IB2014 / 00893, filed on 29 May 2014 (which is incorporated herein by reference in its entirety). Such devices can operate in either a "flow" mode or a simultaneous trap mode.

[0007] When a transverse beam of electrons is injected into an MS instrument, the electron beam must be controlled so that it is focused and directed into a region where the electrons can most efficiently interact (i.e., dissociate) with the ions passing through the instrument. Electron-activated dissociation is a very promising technique for top-down sequencing of proteins and other large biomolecules.

[0008] In these situations, the charged precursor molecule typically has a highly protonated charge state of 30+ or ​​higher. Ideally, it would be desirable to induce only one cleavage of the molecule, and in the case of protein analysis, for example, to produce only one N-terminal and C-terminal fragment pair. However, the resulting fragments also have a highly charged state that can easily capture another electron and fragment. For example, when a second electron is captured by the N-terminal fragment, this process not only produces a shorter N-terminal fragment but also a fragment that does not have the N-terminus of the original protein. This type of fragment is called an internal fragment.

[0009] In top-down sequencing of proteins, internal fragments are not useful for sequencing because there are too many possible combinations of start and end amino acid residues in them. Such internal fragments introduce background noise around the precursor m / z. This significantly increases the difficulty of finding highly charged terminal fragments and typically limits the analyzable size of the protein to below about 300 amino acid residues.

[0010] Therefore, there is a need for devices and methods that can reduce internal fragmentation during the electron-activated dissociation of molecules, especially large, highly charged biomolecules. [Overview of the Initiative] [Means for solving the problem]

[0011] (overview) According to this instruction, methods, systems, and devices for ionic reactions that can reduce internal fragmentation during the electronically activated dissociation of molecules, particularly during the dissociation of large, highly charged biomolecules, are disclosed.

[0012] In one aspect of this teaching, a method for carrying out an ionic reaction is disclosed, the method comprising: introducing a plurality of ions into a dissociation apparatus via a first path extending along a first central axis defined by at least one plurality of electrodes, wherein an input lens electrode is positioned close to one end of the first path and an output lens electrode is positioned close to the other end of the first path; introducing electrons from an electron source via a second path extending along a second central axis, wherein the second path intersects the first path in an intersection region so that ions and electrons can interact; and providing at least one auxiliary electrode that can be activated to isolate precursor ions in an isolation region along the second central axis.

[0013] The precursor ions are preferably high molecular weight ions. Separation is preferably achieved by applying a potential to one or more auxiliary electrodes in conjunction with a magnetic field. Separation can be selectively applied to the precursor ions by a linear radio frequency (RF) quadrupole structure using auxiliary electrodes that provide a “wall” potential. The precursor ions are dissociated by the electron beam within the isolation region. When the product ions are excited by a complementary AC signal applied to the RF quadrupole, the dissociated reaction products can be selectively removed from the isolation region. Due to differences in mass and / or charge, the reaction products may overcome the isolation, leaving only the unreacted precursor ions exposed to further electron beam exposure. Thus, almost all of the precursor ions can ultimately be dissociated in a state where substantially fewer internal fragments are formed by reducing the likelihood of a second electron interaction.

[0014] The method according to this teaching may further include providing at least two auxiliary electrodes, namely one auxiliary electrode parallel to the first axis and positioned on one side of the first axis, and another auxiliary electrode parallel to the first axis and positioned on the opposite side of the first axis. The method further includes controlling the precursor ions by applying a DC potential to at least one of the auxiliary electrodes so that the precursor ions remain confined to a second path in which they can interact with the electron beam.

[0015] In some embodiments, one or more auxiliary electrodes may be elongated structures extending parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens. For example, one or more auxiliary electrodes may each have an elongated T-shape with a stem portion closest to the first axis. Alternatively, one or more auxiliary electrodes may have a notched T-shape.

[0016] The method of this instruction may further include selectively exciting reaction product ions following the electron-activated dissociation of precursor ions by driving at least one set of RF electrodes with a complementary AC signal that excites ions having a response m / z value. Selective extraction can be achieved by varying the frequency of the complementary AC signal, for example by the fixed ion-trap RF frequency and amplitude of the driving signal, while suppressing the frequency that would excite the precursor ions, thereby inducing resonant excitation of the reaction product ions. The method may further include selectively extracting the excited reaction product ions by lowering the potential of the extraction lens electrode at the extraction end of the first axis.

[0017] In another aspect of the present invention, one or more auxiliary electrodes for use in an ion reactor having an RF electrode adapted to guide a positively charged precursor ion along a first axis and an electron source for introducing an electron beam along a path transverse to the first axis such that electron-activated dissociation of the ion may occur, wherein the auxiliary electrodes are adapted with respect to an arrangement parallel to the first axis to drive the precursor ion into the electron beam path when a potential is applied to the electrode.

[0018] In one embodiment, the auxiliary electrode may be an elongated electrode extending along at least 50 percent of the length of the first path (ion path), preferably more than 75 percent of the first path, and more preferably along substantially the entire length of the first path, for example, an auxiliary electrode terminating at one end near the ion inlet lens and at the other end near the ion extraction lens. In one embodiment, two auxiliary electrodes may be deployed in the ion reaction cell: one electrode extending upward parallel to the first path and the other electrode extending downward parallel to the first path. (The terms “upward” and “downward” are used simply for the sake of clarity; for example, in a different orientation, one of the auxiliary electrodes may extend to the left parallel to the first path, while the other electrode extends to the left parallel to the first path.)

[0019] In some embodiments, one or both of the auxiliary electrodes may have an elongated "T" shape, as described with further reference to the drawings. The elongated electrode may be straight, curved, or form an inverted "V" with respect to the first path. Alternatively, the elongated electrode may be notched to provide a more open region at the intersection of the first (ionic) and second (electron) paths.

[0020] During use, the auxiliary electrode(s) act to isolate ions (e.g., precursor ions) within the isolation region along the second central axis, in accordance with the activation of the electrode(s).

[0021] In another aspect, the auxiliary electrodes of this teaching may be deployed, for example, in a system for performing electron-activated dissociation comprising a first set of electrodes in which at least a first segment thereof is arranged in a quadrupole orientation around a first central axis, the first segment of the first set of electrodes extending axially along the first central axis from a proximal inlet end to a distal end, such that it defines a first portion of a first pathway extending along the first central axis, with a proximal inlet end for receiving precursor ions from an ion source.

[0022] The system also includes a second set of electrodes, at least a first segment thereof arranged in a quadrupole orientation around a first central axis so as to define a second portion of a first path, the first segment of the second set of electrodes extending axially along the first central axis from the proximal end to the distal exit end, such that a short-lateral path extends between the proximal end of the second set of electrodes and the distal end of the first set of electrodes, the proximal end of the second set of electrodes being separated from the distal end of the first set of electrodes, and the short-lateral path extending from the first axis end to the second axis end along a second central axis substantially perpendicular to the first central axis and intersecting the first path in the cross region.

[0023] In one embodiment, the electrodes of the first and second sets of electrodes are L-shaped electrodes having longitudinal and transverse sections, where the longitudinal section of each electrode in the first and second sets of electrodes defines the first section of the first and second sets of electrodes, each, and the transverse section of each electrode in the first and second sets of electrodes defines a transverse path, where two transverse sections of electrodes from the first set of electrodes and two transverse sections of electrodes from the second set of electrodes are directed to define a set of transverse electrodes arranged in a quadrupole orientation around a second central axis between the first axial end and the crossing region of the transverse path.

[0024] The system may further include an electron source disposed proximate to a first axial end of the short-axis path for introducing a plurality of electrons along a second central axis such that the electrons travel through the short-axis path in a first short-axis direction toward the intersection region, and at least one auxiliary electrode disposed parallel to the first axis for driving precursor ions into the electron beam path when a potential is applied to the auxiliary electrode.

[0025] In some embodiments, the auxiliary electrode may include a first electrode disposed on one side of the first axis parallel to the first axis and a second auxiliary electrode disposed on the opposite side of the first axis parallel to the first axis.

[0026] In the system of the present teachings, one or more auxiliary electrodes are also elongated structures extending parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens. For example, the auxiliary electrode(s) may have an elongated T-shape with a stem portion closest to the first axis. Alternatively, one or more auxiliary electrodes may have a T-shape with a notch.

[0027] The system may further include a drive circuit for selectively exciting reaction product ions following electron-activated dissociation of precursor ions by driving at least one set of quadrupole electrodes using a complementary AC signal that excites ions having a response m / z value.

[0028] These and other features of the present applicant's teachings are described herein. This specification also provides, for example, the following items: (Item 1) An ion isolation device, At least a first auxiliary electrode for use in an ionic reaction apparatus, the ionic reaction apparatus comprising an RF electrode adapted to guide a positively charged precursor ion along a first axis, and an electron source for introducing an electron beam along a path transverse to the first axis such that electron-activated dissociation of the precursor ion into a reaction product may occur, wherein the auxiliary electrode comprises at least a first auxiliary electrode adapted with respect to an arrangement parallel to the first axis to drive the precursor ion into the electron beam path when a potential is applied to the auxiliary electrode, A drive circuit for applying a complementary AC signal to at least one auxiliary electrode to confine precursor ions within the electron beam path while the reaction product is selectively extracted from the apparatus, A device equipped with the following features. (Item 2) The apparatus according to item 1, wherein the drive circuit further comprises a notch filter, the drive circuit is configured to apply a notched white noise signal to the at least one auxiliary electrode, so that the notch filter suppresses the frequency at which the precursor ion would otherwise be excited. (Item 3) The apparatus according to item 1, wherein the drive circuit further comprises a digital waveform generator that generates a notched white noise waveform, and the drive circuit is configured to apply the notched white noise signal to the at least one auxiliary electrode, thereby suppressing the frequency at which the notch filter would otherwise excite the precursor ion. (Item 4) The apparatus according to item 1, wherein the first auxiliary electrode is adapted with respect to an arrangement parallel to the first axis and on one side of the first axis, and the apparatus further comprises a second auxiliary electrode adapted with respect to an arrangement parallel to the first axis and on the opposite side of the first axis. (Item 5) The apparatus according to item 1, wherein the at least one auxiliary electrode is an elongated structure extending parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens. (Item 6) The apparatus according to item 1, wherein the at least one auxiliary electrode has an elongated T shape with a stem portion closest to the first axis, and optionally, the at least one auxiliary electrode has a notched T shape. (Item 7) A method for carrying out an ionic reaction, The method involves introducing multiple ions into a dissociation apparatus via a first path extending along a first central axis, defined by at least one or more electrodes, wherein an input lens electrode is positioned close to one end of the first path, and an output lens electrode is positioned close to the other end of the first path. The method involves introducing electrons from an electron source via a second path extending along a second central axis, wherein the second path intersects with the first path in an intersection region so that ions and electrons can interact. To provide at least one auxiliary electrode that can be activated to isolate ions in one or more isolation regions along the second central axis, Applying a complementary AC signal to at least one auxiliary electrode to enable selective extraction of reaction products from the apparatus, A method that includes this. (Item 8) The method according to item 7, further comprising providing at least two auxiliary electrodes, namely one auxiliary electrode parallel to the first axis and located on one side of the first axis, and another auxiliary electrode parallel to the first axis and located on the opposite side of the first axis. (Item 9) The method of item 7, wherein the step of applying a complementary AC signal to the at least one auxiliary electrode further comprises applying the complementary AC signal to the at least one auxiliary electrode to selectively excite the reaction products, such that precursor ions remain confined in the second pathway from which they can interact with the electron beam while the reaction products can be extracted. (Item 10) The method according to item 7, wherein the complementary AC signal further comprises a notched white noise signal, the notches in the white noise signal suppress the frequencies at which the precursor ions would otherwise be excited. (Item 11) The method according to item 7, wherein the drive circuit further comprises a digital waveform generator that generates a notched white noise waveform, and the drive circuit is configured to apply the notched white noise signal to the at least one auxiliary electrode, so that the digitally generated white noise has a suppressed frequency that would otherwise excite the precursor ion. (Item 12) The method according to item 10, wherein the white noise signal is notched at the resonance frequency between the precursor ion and a reduced charge species having the same molecular mass but a different charge state. (Item 13) The method according to item 7, wherein the at least one auxiliary electrode is an elongated structure extending parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens. (Item 14) The method according to item 7, wherein the at least one auxiliary electrode has an elongated T shape with a stem portion closest to the first axis. (Item 15) The method according to item 7, wherein the at least one auxiliary electrode has a notched T shape. (Item 16) The method according to item 7, further comprising selectively exciting a reaction product ion following the electron-activated dissociation of the precursor ion by driving at least one set of RF electrodes with a complementary AC signal that excites an ion having a response m / z value. (Item 17) The method according to item 7, further comprising selectively extracting excited reaction product ions by lowering the potential of the extraction lens electrode at the extraction end of the first axis. (Item 18) The method according to item 7, wherein the step of applying a complementary AC signal further comprises selectively exciting the reaction products such that the precursor ions remain confined to the second pathway through which they can interact with the electron beam, while the reaction products can be extracted. (Item 19) The method according to item 7, wherein the step of applying a complementary AC signal further includes applying a notched white noise signal to the at least one auxiliary electrode, so that the notch filter suppresses the frequencies at which the precursor ion would otherwise be excited. (Item 20) The method according to item 7, wherein the step of applying a complementary AC signal further includes applying a notched white noise signal to the at least one auxiliary electrode, thereby causing the digital waveform generator to produce a white noise wave with a suppressed frequency that would otherwise excite the precursor ion. (Item 21) The method according to item 10, wherein the white noise signal is notched at the resonance frequency between the precursor ion and a reduced charge species having the same molecular mass but a different charge state. (Item 22) A system for performing electron-activated dissociation, A first set of electrodes, wherein at least a first segment of the first set of electrodes is arranged in a quadrupole orientation around a first central axis, the first segment of the first set of electrodes extends axially along the first central axis from a proximal inlet end to a distal end so as to define a first portion of a first path extending along the first central axis, the proximal inlet end being for receiving precursor ions from an ion source, A second set of electrodes, wherein at least a first segment of the second set of electrodes is arranged in a quadrupole orientation around a first central axis to define a second portion of the first path, the first segment of the second set of electrodes extends axially along the first central axis from a proximal end to a distal exit end, the proximal end of the second set of electrodes is separated from the distal end of the first set of electrodes such that a short-axis path extends between the proximal end of the second set of electrodes and the distal end of the first set of electrodes, the short-axis path extends from a first axis end to a second axis end along a second central axis substantially perpendicular to the first central axis and intersecting the first path in the intersection region, The electrodes of the first and second sets of electrodes are L-shaped electrodes having longitudinal and transverse divisions, wherein the longitudinal division of each electrode in the first and second sets of electrodes defines the first division of the first and second sets of electrodes, respectively, and the transverse division of each electrode in the first and second sets of electrodes defines the transverse path, and two of the transverse divisions of the electrodes from the first set of electrodes and two of the transverse divisions of the electrodes from the second set of electrodes are oriented to define a set of transverse electrodes arranged in a quadrupole orientation around a second central axis between the first axial end of the transverse path and the intersection region. A second set of electrodes, An electron source positioned near the first axial end of the short-direction path for introducing a plurality of electrons along the second central axis such that the electrons travel through the short-direction path in the first short-direction toward the cross region, At least one auxiliary electrode, positioned parallel to the first axis, to drive precursor ions into the electron beam path when a potential is applied to the auxiliary electrode, A drive circuit for applying a complementary AC signal to at least one auxiliary electrode to confine precursor ions within the electron beam path while the reaction product is selectively extracted from the apparatus, A system equipped with these features. (Item 23) The system according to item 22, further comprising a first electrode adapted with respect to placement on one side of the first axis, parallel to the first axis, and a second auxiliary electrode adapted with respect to placement on the opposite side of the first axis, parallel to the first axis. (Item 24) The system according to item 22, wherein the at least one auxiliary electrode is an elongated structure extending parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens. (Item 25) The system according to item 22, wherein the at least one auxiliary electrode has an elongated T shape with a stem portion closest to the first axis. (Item 26) The system according to item 25, wherein the at least one auxiliary electrode has a notched T-shape. (Item 27) The system according to item 22, wherein the drive circuit further comprises a circuit for selectively exciting a reaction product ion following the electron-activated dissociation of the precursor ion by driving at least one set of quadrupole electrodes with a drive signal that excites an ion having a response m / z value. (Item 28) The system according to item 27, wherein the drive circuit further comprises a notch filter, the drive circuit is configured to apply a notched white noise signal to the at least one auxiliary electrode, so that the notch filter suppresses the frequency at which the precursor ion would otherwise be excited. (Item 29) The system according to item 27, wherein the drive circuit further comprises a digital waveform generator, the drive circuit being configured to apply a notched white noise signal to the at least one auxiliary electrode, thereby causing the digital waveform generator to produce a white noise signal with a suppressed frequency that would otherwise excite the precursor ion. [Brief explanation of the drawing]

[0029] Those skilled in the art will understand that the drawings described below are for illustrative purposes only. The drawings are not intended to limit the scope of the applicant's teachings in any way.

[0030] [Figure 1] Figure 1 shows a general schematic diagram of an ionic reaction cell.

[0031] [Figure 2] Figure 2 shows a cross-sectional view according to one embodiment of this teaching.

[0032] [Figure 3A] Figure 3A depicts a cross-sectional view of Figure 2 along line II.

[0033] [Figure 3B] Figure 3B depicts a cross-sectional view of Figure 2 along line II-II.

[0034] [Figure 4] Figure 4 shows a simplified side view of an electron injection embodiment according to one embodiment of this teaching.

[0035] [Figure 5] Figure 5 shows a simplified side view of the electron beam focusing and defocusing effects according to one embodiment of this teaching.

[0036] [Figure 6] Figure 6 illustrates the implantation and trapping of ions into the apparatus according to one embodiment of this instruction.

[0037] [Figure 7] Figure 7 illustrates the discharge of ions or reaction products of an ionic reaction from an apparatus according to one embodiment of this teaching.

[0038] [Figure 8] Figure 8 illustrates continuous-mode operation in one embodiment of this teaching, in which ions and electrons are continuously injected and a flow of product ions as a result of ion-electron interactions is continuously discharged.

[0039] [Figure 9] Figure 9 shows a cross-sectional view of one embodiment of this teaching illustrating the orientation of the magnetic field.

[0040] [Figure 10]Figure 10 is a schematic perspective view of an ion reaction cell with auxiliary electrodes according to this instruction.

[0041] [Figure 11A] Figure 11A is a schematic perspective view of one embodiment of an auxiliary electrode for use in the apparatus of Figure 10.

[0042] [Figure 11B] Figure 11B is a schematic perspective view of another embodiment of the auxiliary electrode for use in the apparatus of Figure 10.

[0043] [Figure 12] Figure 12 is a schematic perspective view of an ion reaction cell with auxiliary electrodes, showing an exemplary quadrupole RF-driven signal for inducing ion resonance excitation according to this instruction.

[0044] [Figure 13] Figure 13 shows an exemplary circuit for generating the drive signal shown in Figure 12.

[0045] [Figure 14A] Figure 14A is a schematic diagram of the positively charged precursor ions confined according to this instruction at the upper branch 95 of the electron beam path in the apparatus shown in Figure 10.

[0046] [Figure 14B] Figure 14B is a schematic diagram of the positively charged precursor ions confined according to this instruction at the lower branch 95 of the electron beam path in the apparatus shown in Figure 10.

[0047] [Figure 15] Figure 15 is a schematic diagram of the reaction product ions selectively extracted from the apparatus shown in Figure 10.

[0048] [Figure 16] Figure 16 is a schematic diagram of a drive circuit for one or more auxiliary electrodes to confine precursor ions within the electron beam path while selectively enabling the extraction of reaction products. [Modes for carrying out the invention]

[0049] (Detailed explanation) For clarity, please understand that the following discussion details various aspects of embodiments of the applicant's teachings, while omitting certain specific details whenever it is convenient or appropriate. For example, discussions of similar or analogous features in alternative embodiments may be somewhat abbreviated. Well-known concepts or ideas may also not be discussed in detail for the sake of brevity. Those skilled in the art will recognize that some embodiments of the applicant's teachings may not require some of the details specifically described in all implementations described herein, solely to provide a thorough understanding of the embodiments. Similarly, it will be apparent that the embodiments described may be susceptible to modification or alteration by common general knowledge without departing from the scope of this disclosure. The following detailed descriptions of embodiments should not be considered to limit the scope of the applicant's teachings in any way.

[0050] Referring to Figure 1, a general schematic diagram of one embodiment of this teaching is depicted. The ionic reaction cell 1 receives a set of reactants, which are ions 2 and charged species 3, as input. Optionally, energy in the form of photons or light 4 is added. Light 4 can be obtained from a laser source and is preferably light in either the ultraviolet or infrared spectrum. Ion 2 can be any ion that is positively (cationic) or negatively (anionic). Charged species 3 can be electrons or ions that are either positively or negatively charged. In one preferred embodiment, as will be described in more detail below, the charged species is a beam of electrons that is transmitted in the short direction to ion 2, passes through the reaction cell 1, and induces collisions and reactions. When the charged species is electrons, the electron source can be a filament such as a tungsten or thorium-treated tungsten filament or another electron source such as a Y2O3 cathode. The reaction device may also include a cooling gas such as helium (He) and nitrogen (N2). A typical pressure of the cooling gas is 10-2 ~10 -4 It can be a toll. Filament electron sources are typically used because they are inexpensive, but they are not very robust in the presence of residual oxygen gas. On the other hand, cathodes made from Y2O3 are more expensive electron sources, but they are more robust in oxygen and can therefore be useful for de novo sequencing using radical-oxygen reactions. When operating, a current of 1 to 3 amperes is typically applied to heat the electron source, which generates 1 to 10 watts of thermal power. If a magnet is used, a heat sink system for the electron source can be provided to keep its temperature below its Curie temperature, at which the magnetization of a permanent magnet is lost. Other known methods for cooling the magnet can also be used.

[0051] Inside the ionic reaction cell 1, ions 2 and charged species 3 all interact with each other, along with the optional addition of photons 4. Depending on the properties of the reactants used, the interactions can produce several phenomena that result in the formation of product ions 5, which can then potentially be extracted or discharged from the ionic reaction cell 1 along with other unreacted ions 2 and / or, depending on the circumstances, possibly charged species 3.

[0052] When ion 2 is a cation and charged species 3 is an electron, the cation can capture electrons, and the interaction between ion 2 and charged species 3 can undergo electron capture dissociation, resulting in the formation of product ion 5, which is a fragment of the original ion 2. When ion 2 is a cation and charged species 3 is an anion, the interaction between ion 2 and charged species 3 can be electron transfer dissociation, in which electrons are transferred from charged species 3 to ion 2, causing ion 2 to fragment. The stream of species discharged from the ionic reaction cell can consist of one or more ions 2 and / or their fragments, or mixtures thereof.

[0053] In addition, with respect to electron-related fragmentation, high-temperature ECD, high-energy electron ionization dissociation (HEEID), active ion ECD (AI-ECD), electron-electron-electron-ionization excitation (EIEIO) of ions from organic materials, electron-desorption dissociation (EDD), negative ETD, and negative ion ECD can be implemented. For example, when ion 2 is a cation, ECD, ETD, and high-temperature ECD can be implemented, while when ion 2 is an anion, EDD, negative ETD, and negative ion ECD can be used. Proton transfer reactions can also be implemented if the charged species 3 is appropriately selected.

[0054] Referring now to Figure 2, a side view of an ion reactor 10 in a certain aspect of one embodiment of this teaching is depicted. Shown as a cutaway section, the outer cylindrical housing 29 and the inner cylindrical housing 30 enclose a first path 11 having a first central axis 12, a first axis end 13, and a second axis end 14. This path provides a passage for ions 2 to enter the ion reactor 10.

[0055] Lens electrodes (15, 16) are installed at each end of the first path 11. Lens electrode 15 allows ions 2 to enter the apparatus 10, and lens electrode 16 controls the discharge of unreacted ions 2 or product ions 5 from the apparatus 10. The lens electrodes do not need to be installed directly on the shaft end, but can be installed in close proximity just outside the shaft end. As can be understood, due to the symmetrical nature of the device, the direction of the ions can be reversed as ions 2 enter through lens electrode 16 and exit through lens electrode 15, provided that the surrounding ion transport devices are properly configured.

[0056] The apparatus 10 comprises a first set 17 of quadrupole electrodes mounted in an inner cylindrical housing 30, the electrodes 17 arranged around a first central axis 12 in a quadrupole configuration. Here, a quadrupole is specifically embodied for preferred operation, but any multipole configuration, including hexupoles, octupoles, etc., may also be used. In the figure, only two of the four quadrupole electrodes are depicted, with the other two electrodes behind the depicted electrodes. For the two electrodes depicted within the quadrupole electrode 17, the electrodes have opposite polarities. These first set 17 of quadrupole electrodes are connected to an RF voltage source and controller (not shown) which provides the electrodes with an RF voltage to generate an RF field capable of inducing ions 2 toward the first central axis 12, which is the midpoint of the quadrupole.

[0057] Furthermore, the second set 18 of quadrupole electrodes (only two are depicted, the other two are in the background) mounted in the inner cylindrical housing 30 is positioned a short distance away from the first set 17 of quadrupole electrodes, creating a roughly cylindrical gap 19 between the first set 17 and the second set 18. The first and second quadrupoles 17 and 18 share the same central axis 12, and the rods of the first set 17 of quadrupoles are aligned linearly with those of the second set 18. Although depicted as cylindrical, it should be understood that the important thing is not the shape of the gap itself, but the existence of a gap between the first set 17 and the second set 18 of quadrupoles. For example, even if the quadrupoles have the same configuration, this shape could also be described as a rectangular box shape. The second set 18 of this quadrupole electrode is also attached to an RF voltage source and controller (not shown) which is responsible for supplying an RF voltage to the electrodes to generate an RF field that can serve to guide ions 2 and / or product ions 5 toward the central axis 12, which is the midpoint of the second set 18 of the quadrupole electrode.

[0058] The inner and outer cylindrical housings have notches for the insertion of a second path 20 having a second central axis 21 with a first shaft end 22 and a second shaft end 23. This second path 20 provides a passage for transporting charged species 3 into the device 10. The first and second paths are substantially orthogonal to each other and meet at an intersection 24, which lies along the first central axis 12 and the second central axis 21. Each of the four electrodes in the first set 17 of quadrupole electrodes, which are briefly illustrated in Figures 3A and 3B, which are cross-sectional views obtained in lines II and II-II of Figure 2 respectively, can be paired with one of the four electrodes in the second set 18 of electrodes, for example, each electrode (25a, 25b) in each electrode pair having opposite polarity and each being directly opposite across the intersection of the other electrodes (25b, 25a) in the electrode pair. A similar relationship exists for electrode pairs with electrodes (26a, 26b).

[0059] The same relationship applies to the two remaining electrodes in the first set of electrodes 17, which are paired with the two remaining electrodes in the second set of electrodes 18. This orientation of the electrodes results in the RF field generated between the intersection 24 and the first axial end 22 of the second path 20 being out of phase with respect to the RF field generated between the intersection 24 and the second axial end 23 of the second path 20. Due to this configuration of the electrodes, the RF field is essentially absent on the central axis 21.

[0060] The first shaft end 22 of the second path 20 includes, or has in close proximity to, an electron filament 27, which is to be used to generate electrons for transmission into the second path 20 toward the intersection 24. The first shaft end 22 may also include, or have in close proximity to, one or more suitable electrode gates 28 for controlling the entry of electrons into the apparatus 10. A magnetic field source (not shown), such as a permanent magnet, is configured to implement a magnetic field parallel to the second path 20. This magnetic field is useful when ECD, high-temperature ECD, HEEID, EDD, and negative-ion ECD are implemented when the charged species is electrons. When the charged species is reagent anions, including scenarios where the reaction taking place is, for example, an ETD reaction, the magnetic field source and magnetic field are not required.

[0061] The presence of gaps can lead to ion leakage through the weaker side of the cell within the gap area due to the quadrupole RF field. This can typically be mitigated by the use of "polar" electrodes, which are flat plates positioned to prevent this leakage. The polar electrodes are aligned vertically and separated from the other electrodes. A positive electrical bias on the polar electrodes repels charged ions and reaction products from the opening. As is understood, these blocking electrodes are electrically connected to a suitable voltage source.

[0062] Referring again to Figure 2, in one embodiment, the RF frequency applied to the quadrupole is in the range of approximately 400 kHz to 1.2 MHz, and preferably the RF frequency is approximately 800 kHz.

[0063] Referring here to Figure 4, a depiction of another embodiment in a side view of the ion reaction device 40 is shown, where only charged species 3, specifically electrons, are injected. The ion reaction device 40 includes a first path 41 having a first central axis 42, the path 41 having a first axis end 43 and a second axis end 44. Electrode lenses (45, 46) that enable control of the entry and exit of ions from the ion reaction device 40 are mounted at each end of the first path 41. The device 41 is generally L-shaped and comprises a first set 47 of quadrupole electrodes arranged around the first central axis 42. In the figure, only two of the four quadrupole electrodes are depicted, with the other two electrodes behind the depicted electrodes. Of the two electrodes depicted within the quadrupole electrodes 47, the electrodes have opposite polarities. Similarly, a second set 48 of quadrupole electrodes, which are generally L-shaped (only two are depicted, the other two are in the background), is set at a small distance from the first set 47 of quadrupole electrodes, the distance forming a tightly formed, nearly cylindrical gap 49 between the first set 47 and the second set 48 of electrodes.

[0064] With respect to the two electrodes depicted within the quadrupole electrode 48, the electrodes have opposite polarities. The electrodes depicted at the top in each of the first set 47 and the second set 48 of the quadrupole electrode are opposite to each other in polarity. As will be understood by those skilled in the art, the two unshown electrodes in each set of quadrupole electrodes have polarities that match the polarity of the quadrupole electrode, such as in the configurations shown in Figures 3A and 3B.

[0065] The second path 50 has a second central axis 51 having a first axis end 52 and a second axis end 53. This second path provides a passage for transporting charged types into the device 40. This orientation of the electrodes results in an RF field generated between the intersection (of the first path 41 and the second path 50) and the first axis end 52 of the second path 50 being out of phase with respect to the RF field generated between the intersection (of the first path 41 and the second path 50) and the second axis end 53 of the second path 50. The first axis end 52 of the second path 50 includes, or is mounted in close proximity to, an electron filament 57 to be used to generate electrons 60 for transmission into the second path 50. The first axis end 52 also includes, or can be mounted in close proximity to, a suitable electrode gate 63 which serves to direct electrons into the device along the second path.

[0066] The polar electrode 58 also serves to further control the entry of electrons 60 into the apparatus 40 and to block the escape of ions and reaction products. Another polar electrode 59 is located at or near the second axis end 53 of the second path 50. A magnetic field generator (not shown) is positioned and directed in such a manner that it produces a magnetic field parallel to the second path. The direction of the magnetic field can be either from the first axis end 52 to the second axis end 53 or vice versa. This magnetic field is useful when ECDs, high-temperature ECDs, HEEIDs, EIEIOs, EDDs, and negative-ion ECDs are implemented, when the charged species is electrons. A grid 61 can be positioned to act as a gate to switch electrons 60 that are near or in the vicinity of the electron filament 57. The RF field causes the electrons 60, which are focused as they enter the apparatus 40, to become defocused as they approach the intersection of the first path 41 and the second path 50. As electron 60 passes through the intersection, the reversal of the RF field polarity causes electron 60 to become focused again. This results in a more uniform distribution of electrons in the direction normal to the first path, increasing the opportunity for ion-electron interactions within the apparatus 40, which can also lead to better sensitivity. The electron beam then produces a local induced potential.

[0067] A clearer illustration of the electron defocusing effect is shown in Figure 5, where the apparatus 70 is configured in a manner similar to apparatus 40, with a first set of quadrupole electrodes 71 and a second set of quadrupole electrodes 72. In one embodiment, electron lenses with a potential of +1V are placed at the inlet and outlet of the electron beam path, and these are used to assist in focusing the electron beam. For brevity, other parts are not repeated. It can be seen that the flow of electrons 60 into apparatus 70 defocuses as they approach the center point 74, but is focused again when they pass through the center point. A magnetic field of 0.1T (not shown) is aligned parallel to and along the electron-direction path. Again, this magnetic field is useful when ECD, high-temperature ECD, HEEID, EIEIO, EDD, and negative-ion ECD are implemented, when the charged species is electrons. The RF field can have a maximum amplitude of 100V, and the electron beam energy can be 0.2eV at the center.

[0068] Figures 6 and 7 depict side views of the ion trapping effect generated by the apparatus 100 according to one embodiment of the present invention in a conventional trapping manner. A first path 101, comprising a first shaft end 103 and a second shaft end 104, provides a channel for ions to be injected from the first shaft end 103. A second path 110, comprising a first shaft end 112 and a second shaft end 113, also provides a path for the electron beam generated by the filament 114. A set of quadrupole electrodes 107 (only two are depicted, the other two are in the background) attached to a suitable set of RF voltage sources is oriented with respect to the central axis 102 to guide ions to the midpoint in the quadrupole electrodes 107, and plays a role in guiding the ions. The second set 108 of quadrupole electrodes (only two are depicted, the other two are behind) is set at a small distance from the first set 107 of quadrupole electrodes, and the distance between the first set 107 and the second set 108 of quadrupole electrodes forms a gap 109 between the sets of electrodes. This second set 108 of quadrupole electrodes serves to guide ions to the midpoint between the quadrupole electrodes 108 with respect to the central axis 102. For the two electrodes depicted in quadrupole electrode 107, the electrodes have opposite polarities. For the two electrodes depicted in quadrupole electrode 108, the electrodes have opposite polarities. The electrodes depicted at the top in each of the first set 107 and the second set 108 of quadrupole electrodes are opposite in polarity to each other. As will be understood by those skilled in the art, the two unshown electrodes in each set of quadrupole electrodes have polarities that match the polarity of the quadrupole electrodes, such as in the configurations shown in Figures 3A and 3B. A magnetic field generator (not shown) provides a magnetic field oriented parallel to the direction of the second path and in line with the second central axis 111. Here again, this magnetic field is useful when ECD, high-temperature ECD, EIEIO, HEEID, EDD, and negative-ion ECD are implemented, when the charged species is electrons. The inlet lens electrode 105 and the outlet lens gate electrode 106 control the inflow and outflow of ions into and out of the device 100, respectively.In this embodiment, the inlet lens electrode 105 is set to a potential that allows ions to flow into the device 100, while the outlet lens electrode 106 has a sufficiently high potential to temporarily prevent ions from flowing out of the device.

[0069] The second path also includes, or is installed in close proximity to, positively biased polar electrodes 115, 116 that prevent ion outflow through the axial ends 112, 113 of the second path 110. In this embodiment, when ions are implanted, the electron beam is initially turned off so that charged species do not enter the apparatus 100 through the second path 110. Thus, the apparatus 100 functions as an ion trap where the implanted ions accumulate at the intersection between the first path 101 and the second path 110.

[0070] When sufficient ions have accumulated, the potential of the lens electrode 105 is increased to prevent ions from flowing into the device 100, thereby preventing ions from entering and leaving. The electron beam can then be turned on so that electrons can pass through the aperture of the electrode 115 into the device 100. At this time, the electrons interact with the ions, undergo EAD, and may result in fragmentation of the product ions. Once sufficient fragmentation has occurred, the filament 114 can be turned off, the potential of the lens electrode 105 can be increased, and the potential of the lens electrode 106 can be decreased, thereby allowing the product ions to exit through the second shaft end 104 as depicted in Figure 7. To obtain more efficient trapping, a cooling gas, such as helium or nitrogen gas, may be introduced into the device 100. Each electrode from the first quadrupole 107 and the second quadrupole 108 has a first portion of the electrode oriented substantially parallel to the first central axis 102, while the second portion is oriented substantially parallel to the second central axis. Since each portion of each electrode has the same polarity with respect to a given electrode, the electrodes can collectively act as a trap directing ions toward both the central axis 102 and the central axis 111. Thus, the apparatus 100 acts as a two-dimensional trap, more precisely, a linear trap in two directions. In Figure 6, it is depicted with a smooth, rounded transition between the first and second portions, but other configurations, such as sharp angles, can also be used. Shown below the apparatus in each of Figures 6 and 7 are graphs of the spatial potential for positive ions in the horizontal direction within the apparatus along the central axis 102.

[0071] In Figure 6, the potential at the inlet is approximately equal to that of the incident isolated ions, thus allowing the ions to pass through and enter the apparatus. The potential at the outlet is higher than that of the isolated ions entering the apparatus, so the ions are trapped and do not exit through the right side of the apparatus. In Figure 7, the inlet potential is higher, thereby preventing the ions from exiting by returning through the inlet, while the potential at the outlet is lower than that of the product ions, thereby allowing the ions to exit the apparatus.

[0072] Figure 8 depicts a side view of the operation of the apparatus 100 in a simultaneous trapping mode in which ions continuously enter through lens 105 and electrons 117 continuously enter into the polar electrode 115 through the aperture. The interaction between ions and electrons 117 can induce EAD, resulting in the fragmentation and formation of product ions. These product ions and unreacted ions are extracted from the apparatus through lens electrode 106 in a semi-continuous manner in which lens electrode 106 switches between open and closed positions. When in the closed position, the potential located within the lens electrode is higher than that of the ions contained in the apparatus, thereby allowing ions to accumulate and increasing residence and reaction time so that the EAD reaction can occur. When ions are to be extracted, lens electrode 106 is opened by lowering the potential within the lens, allowing the product ions to be removed. Shown below apparatus 100 in Figure 8 is a horizontal spatial representation of the potential with respect to positive ions, showing the exit potential oscillating between high and low potentials representing the closed and open positions of lens 106.

[0073] Referring here to Figure 9, another system 200 according to this instruction is depicted in a side view inserted in series between two quadrupoles. A quadrupole filter Q1 having a quadrupole rod 218 is installed upstream of the apparatus 200 and serves to trap / induct / otherwise ions and provide an ion source at the inlet of the apparatus 200. A quadrupole Q2 having a quadrupole rod 219 is installed downstream of the apparatus 200 for further analysis or processing and can receive product ions and unreacted ions and serve to trap / induct / isolate / otherwise these species within the quadrupole. The apparatus is similar to the apparatus described above and will not be described in detail for the sake of brevity. The apparatus 200 has a first path 201 and a second path 210. The apparatus 200 includes two filaments, each one located at either the first shaft end 212 or the second shaft end 213 of the second path 210. This configuration allows for the independent operation of the filaments so that if one filament is being used and suddenly becomes inoperable, the other filament can be used as a spare and activated, resulting in little to no downtime.

[0074] While the use of an additional quadrupole is specifically illustrated, it should be understood that other types of devices may also be installed either before or after the apparatus according to this teaching. For example, the devices may include various ion guides, filters, traps, ion mobility devices including differential mobility and field-asymmetric ion mobility analyzers, as well as other mass spectrometry devices such as time-of-flight mass spectrometers. In various embodiments, the electron-controlled optics and ion-controlled optics are completely separated, so that independent operation with respect to both charged particles is possible. With respect to electrons, the electron energy can be controlled by the potential difference between the electron source and the intersection of the ion path and the charged species path. The charged species path can be controlled in an on / off manner by the use of a gate electrode. A lens may be positioned at or near the axial end of either of the second paths and, when positively biased, focuses the charged species when such species are electrons. Ions introduced through the other paths are positively biased and therefore stable in the vicinity of the lens. It should also be understood that the design of the present invention is applicable to higher-order multipole structures such as hexupole or octupole RF electrode structures.

[0075] For further teachings regarding electron-activated dissociation, see U.S. Patent Application Publication No. 20180005810, filed December 21, 2015, entitled "Electron Induced Dissociation Devices and Methods," PCT Application No. PCT / IB2014 / 00893, filed May 29, 2014, entitled "Inline Ion Reaction Device Cell And Method of Operation," and PCT Application No. PCT / IB2012 / 002621, filed December 6, 2012, entitled "Ion Extraction Method For Ion Trap Mass Spectrometry" (each of which is incorporated herein by reference in its entirety).

[0076] Figure 10 shows a schematic perspective view of the ion reactor 10A, which is similar to the one depicted in the plan view in Figure 2. Accompanying components are omitted for clarity of explanation. The ion reactor 10A includes a first path 11 having a first central axis 12, a first axis end 13, and a second axis end 14. This path provides a route for ions 2 to enter the ion reactor 10.

[0077] Lens electrodes are installed at each end of the first path 11. The inlet lens electrode 15 allows ions to enter the apparatus 10A and the second (outlet) lens electrode at the opposite end of the path (not shown), and controls the discharge of unreacted or reacted product ions from the apparatus 10A. The lens electrodes do not need to be installed directly on the shaft end, but can be installed in close proximity just outside the shaft end. As can be understood, due to the symmetrical nature of the device, the direction of ions can be reversed as ions enter through lens electrode 16 and exit through lens electrode 15, provided that the surrounding ion transport devices are properly configured.

[0078] The apparatus 10A comprises a first set 17 of quadrupole electrodes mounted in an inner cylindrical housing (not shown), the electrodes 17 arranged around a first central axis 12 in a quadrupole configuration. Here, a quadrupole is specifically embodied, but any multipole configuration, including sextupoles, octupoles, etc., can also be used, although in most cases, a quadrupole configuration is preferred. In the figure, only two of the four quadrupole electrodes are depicted, with the other two electrodes behind the depicted electrodes. For the two electrodes 17A and 17B depicted within the quadrupole electrode 17, the electrodes have opposite polarities. These first set of quadrupole electrodes 17 are connected to an RF voltage source and controller (not shown) which provides an RF voltage to the electrodes to generate an RF field capable of inducing ions toward the first central axis 12, which is the midpoint of the quadrupole.

[0079] Similarly, the second set 18 of quadrupole electrodes mounted in the inner cylindrical housing 30 is positioned a short distance away from the first set 17 of quadrupole electrodes, creating a roughly cylindrical gap between the first set 17 and the second set 18. The first quadrupole 17 and the second quadrupole 18 share the same central axis 12, and the rods of the first set 17 of quadrupoles are aligned linearly with those of the second set 18. Although described as cylindrical, it should be understood that the important thing is not the shape of the gap itself, but the existence of a gap between the first set 17 and the second set 18 of quadrupoles. For example, even if the quadrupoles have the same configuration, this shape can also be described as a rectangular box shape. This second set of quadrupole electrodes 18A, 18B, 18C, and 18D are also attached to an RF voltage source and controller (not shown) which serve to provide the electrodes with an RF voltage to generate an RF field that can serve to guide precursor ions and / or reaction product ions toward the central axis 12, which is the midpoint of the second set of quadrupole electrodes 18.

[0080] The inner and outer cylindrical housings have notches for the insertion of a second path 20 having a second central axis 21. This second path 20 provides a path for transporting charged species (e.g., electrons) into the device 10. The first and second paths are substantially orthogonal to each other and meet at an intersection inside the device 10A, which lies along the first central axis 12 and the second central axis 21. Each of the four electrodes in the first set 17 of quadrupole electrodes can be paired with one of the four electrodes in the second set 18 of electrodes, for example, each electrode (17A, 17B) in each electrode pair having opposite polarity and each directly opposite across the intersection of the other electrodes (18B, 18A) in the electrode pair. Similar relationships exist with respect to electrode pairs with electrodes.

[0081] The same relationship applies to the two remaining electrodes in the first set of electrodes 17 (not shown) that are paired with the two remaining electrodes in the second set of electrodes 18C and 18D. This orientation of the electrodes results in the RF field generated between the intersection point 24 and the first axis end 22 of the second path 20 being out of phase with respect to the RF field generated between the intersection point 24 and the second axis end 23 of the second path 20. Due to this configuration of the electrodes, the RF field is essentially absent on the central axis 21.

[0082] The first shaft end of the second path 20 includes, or is adjacent to, an electron filament (as described above) to be used to generate electrons for transmission into the second path 20 toward the intersection in the apparatus 10A. The first shaft end also includes, or may be adjacent to, one or more suitable electrode gates for controlling the entry of electrons into the apparatus 10A. A magnetic field source (not shown), such as a permanent magnet, is configured to implement a magnetic field parallel to the second path 20. This magnetic field is useful when an ECD, high-temperature ECD, HEEID, EDD, and negative-ion ECD are implemented, when the charge species is electrons.

[0083] The presence of gaps can lead to ion leakage through the weaker side of the cell within the gap area due to the quadrupole RF field. This can typically be mitigated by the use of "polar" electrodes, which are planar electrodes positioned to prevent this leakage. The polar electrodes are aligned vertically and separated from the other electrodes. The positive charge on the polar electrodes repels charged ions and reaction products, etc., from the opening. As is understood, these blocking electrodes are electrically connected to a suitable voltage source.

[0084] The two auxiliary electrodes 90 and 92 described in this instruction are also shown in Figure 10. These auxiliary electrodes are adapted with respect to a configuration parallel to the first axis to drive precursor ions into the electron beam path when a potential is applied to the auxiliary electrodes, as will be described in more detail below.

[0085] In Figure 11A, the auxiliary electrodes are shown alone with all other elements of the apparatus 10A removed. In some embodiments, the auxiliary electrodes 90 and 922 are generally elongated structures extending parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens. In some embodiments, as shown in Figure 11A, electrodes 90 and 92 may have an elongated T-shape with a stem portion 21 closest to the first axis. In an alternative embodiment illustrated in Figure 11B, the auxiliary electrodes 90A and 90B are T-shaped but have central notches 94 and 96 in the ion crossing region and electron path.

[0086] Figure 12 is another perspective view of the apparatus according to this teaching, similar to that shown in Figure 10. Parts of the upper and lower auxiliary electrodes 90 and 92 have been removed to allow a clear view of the quadrupole electrodes. By applying a potential (position bias) to one or both of the auxiliary electrodes 90, 92, positively charged precursor ions are driven out of the ion path along axis 12 and pushed into the electron beam path (along axis 21), if they remain either (or both) in front of or behind the electron beam path. Once the precursor ions are isolated, the electron beam is activated (as described above) to deliver a stream of electrons along a second axis 21 (labeled "B"), which may induce electron-activated dissociation of the precursor ions.

[0087] Figure 12 also illustrates the signals applied to the quadrupole electrodes that can extract reaction product ions. Essentially, a deformation of the excitation signal can be applied to the upstream L-shaped electrodes (17A-17D) of the first quadrupole 17 and the L-shaped downstream electrodes (18A-18D) of the second quadrupole.

[0088] Figure 13 is an illustrative schematic of an embodiment of a circuit useful for driving a quadrupole electrode. The net effect of these signals is to provide resonant excitation to types of ions present in apparatus 12A, depending on their mass / charge ratio. Ions with a response m / z are excited to a point where they can overcome the isolation potentials of auxiliary electrodes 90 and / or 92. By opening an ion extraction lens (not shown), these excited ions can be selectively extracted from apparatus 12A, while other less excited ions remain isolated within the electron beam path 20 (along the axis 21). By sweeping the frequency of the excitation signal, ions with various m / z characteristics can be selectively excited.

[0089] Therefore, according to this teaching, by modulating the frequency according to a pattern having one or more notches (a subset of frequencies in which the signal is suppressed), all ions present in the isolation region, except for ions with a specific m / z, can be excited and escape isolation. For example, a white noise signal may be applied using frequency notches corresponding to frequencies in which precursor ions would otherwise be excited, and the white noise-compensated AC can selectively extract reaction product ions while retaining the precursor ions so that they can further interact with the electron beam. If the notches further correspond to frequencies in which reduced charge species, which otherwise have the same molecular mass but different charges, would be excited, the white noise-compensated AC can selectively extract fragment ions while retaining the precursor ions and reduced charge species so that they can further interact with the electron beam.

[0090] As a result of this instruction, while the precursor ions remain isolated for further EAD treatment, the reaction product ions generated by electron-activated dissociation (EAD) are rapidly removed from the apparatus before further internal fragmentation can occur, thereby increasing the overall yield of the reaction product ions.

[0091] The isolation process is further illustrated in Figures 14A and 14B. In these cross-sectional views of the apparatus, precursor ions are allowed to enter the apparatus along axis 12 (by temporarily lowering the potential of the input lens electrode 15). When the potential is increased on the lens electrode 15 and a similar bias is applied to the extraction lens electrode 16, the auxiliary electrode 92, and the combined auxiliary electrode 90 (not shown in this figure), the positively charged precursor ions are propelled into the upper branch 95 or lower branch 97 (or both) of the electron beam path.

[0092] Figure 15 illustrates the selective extraction of reaction product ions 99 from segregation at the lower branch of the electron beam path. As described above, when the frequency of the quadrupole drive signal is tuned to a specific value, reaction product ions having a specific m / z can be excited, allowed to escape segregation, and extracted by lowering the potential on the extraction lens electrode 16.

[0093] Figure 16 is a schematic diagram of a drive circuit 150 configured to generate a notched white noise signal. The circuit 150 may include a frequency modulator 152 (e.g., a frequency mixer capable of generating a white noise signal) and a notch filter 154. The notch filter 154 is configured to suppress the resonance frequencies of precursor ions (preferably reduced charge species having the same molecular mass but different charge states) before applying a signal to one or more auxiliary electrodes 92 and / or 94. Alternatively, the same functionality of notching can be achieved by digital waveform generation. A digital waveform generator is programmed to generate white noise, but certain frequency components are removed from the white noise.

[0094] It should be understood that numerous modifications are made to the disclosed embodiments without departing from the scope of this teaching. The aforementioned figures and examples refer to specific elements, but are intended to be examples and illustrations only, and not limitations. Those skilled in the art should understand that various modifications may be made in form and detail to the disclosed embodiments without departing from the scope of this teaching as encompassed by the accompanying claims.

Claims

1. An ion isolation device, the ion isolation device, At least a first auxiliary electrode for use in an ionic reaction apparatus, the ionic reaction apparatus comprising an RF electrode adapted to guide a positively charged precursor ion along a first axis, and an electron source for introducing an electron beam along a path transverse to the first axis such that electron-activated dissociation of the precursor ion into a reaction product may occur, wherein the auxiliary electrode comprises at least a first auxiliary electrode adapted with respect to an arrangement parallel to the first axis to drive the precursor ion into the electron beam path when a potential is applied to the auxiliary electrode, A drive circuit for applying a complementary AC signal to at least one auxiliary electrode to confine precursor ions within the electron beam path while the reaction product is selectively extracted from the ion reaction apparatus, An ion isolation device equipped with the following features.

2. The apparatus according to claim 1, wherein the drive circuit further comprises a notch filter, the drive circuit is configured to apply a notched white noise signal to the at least one auxiliary electrode, thereby suppressing the frequency at which the precursor ion would be excited.

3. The apparatus according to claim 2, wherein the drive circuit further comprises a digital waveform generator that generates a notched white noise waveform, and the drive circuit is configured to apply the notched white noise signal to the at least one auxiliary electrode, thereby suppressing the frequency at which the notch filter would excite the precursor ion.

4. The apparatus according to claim 1, wherein the first auxiliary electrode is adapted with respect to an arrangement parallel to the first axis and on one side of the first axis, and the apparatus further comprises a second auxiliary electrode adapted with respect to an arrangement parallel to the first axis and on the opposite side of the first axis.

5. The apparatus according to claim 1, wherein the at least one auxiliary electrode has an elongated structure that extends parallel to the first axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens.

6. The apparatus according to claim 1, wherein the at least one auxiliary electrode has an elongated T shape with a stem portion closest to the first axis, and optionally, the at least one auxiliary electrode has a notched T shape.

7. A method for carrying out an ionic reaction, wherein the method is The method involves introducing multiple ions into a dissociation apparatus via a first path extending along a first central axis, defined by at least one or more electrodes, wherein an input lens electrode is positioned close to one end of the first path, and an output lens electrode is positioned close to the other end of the first path. The method involves introducing electrons from an electron source via a second path extending along a second central axis, wherein the second path intersects the first path in an intersection region such that the ions and electrons can interact. To provide at least one auxiliary electrode that can be activated to isolate ions in one or more isolation regions along the second central axis, Applying a complementary AC signal to at least one auxiliary electrode to enable selective extraction of reaction products from the dissociation device, Methods that include...

8. The method according to claim 7, further comprising providing at least two auxiliary electrodes, namely one auxiliary electrode positioned parallel to the first central axis and on one side of the first central axis, and another auxiliary electrode positioned parallel to the first central axis and on the opposite side of the first central axis.

9. The method according to claim 7, further comprising applying the complementary AC signal to the at least one auxiliary electrode to selectively excite the reaction products, such that the precursor ions remain confined in the second pathway through which they can interact with the electron beam while the reaction products can be extracted.

10. The method according to claim 7, wherein the application of the complementary AC signal further includes the application of a notched white noise signal, the notch in the white noise signal suppresses the frequency at which precursor ions would be excited.

11. The method according to claim 10, wherein the white noise signal is notched at the resonance frequency between the precursor ion and a reduced charge species having the same molecular mass but a different charge state.

12. The method according to claim 7, wherein the at least one auxiliary electrode has an elongated structure that extends parallel to the first central axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens.

13. The method according to claim 7, wherein the at least one auxiliary electrode has an elongated T shape with a stem portion closest to the first central axis.

14. The method according to claim 7, wherein the at least one auxiliary electrode has a notched T shape.

15. The method according to claim 7, further comprising selectively exciting a reaction product ion following the electron-activated dissociation of a precursor ion by driving at least one set of RF electrodes with a complementary AC signal that excites an ion having a response m / z value.

16. The method according to claim 7, further comprising selectively extracting excited reaction product ions by lowering the potential of the extraction lens electrode at the extraction end of the first central axis.

17. The method according to claim 7, further comprising applying the complementary AC signal to selectively excite the reaction products such that the precursor ions remain confined to the second pathway through which they can interact with the electron beam while the reaction products can be extracted.

18. The method according to claim 7, wherein the application of the complementary AC signal further includes applying a notched white noise signal to the at least one auxiliary electrode using a drive circuit comprising a digital waveform generator, thereby the digital waveform generator generates a white noise wave with a suppressed frequency from which precursor ions will be excited.

19. The method according to claim 10, wherein the white noise signal is notched at the resonance frequency between the precursor ion and a reduced charge species having the same molecular mass but a different charge state.

20. A system for performing electron-activated dissociation, wherein the system is A first set of electrodes, wherein at least a first segment of the first set of electrodes is arranged in a quadrupole orientation around a first central axis, and the first segment of the first set of electrodes extends axially along the first central axis from a proximal inlet end to a distal end so as to define a first portion of a first path extending along the first central axis, the proximal inlet end being for receiving precursor ions from an ion source, A second set of electrodes, wherein at least a first portion of the second set of electrodes is arranged in a quadrupole orientation around a first central axis so as to define a second portion of the first path, the first portion of the second set of electrodes extends axially along the first central axis from a proximal end to a distal exit end, the proximal end of the second set of electrodes is separated from the distal end of the first set of electrodes such that a short-axis path extends between the proximal end of the second set of electrodes and the distal end of the first set of electrodes, the short-axis path extends from a first axis end to a second axis end along a second central axis substantially perpendicular to the first central axis and intersecting the first path in the intersection region, The electrodes of the first and second sets of electrodes are L-shaped electrodes having longitudinal and transverse divisions, the longitudinal division of each electrode in the first and second sets of electrodes respectively defines the first division of the first and second sets of electrodes, the transverse division of each electrode in the first and second sets of electrodes defines the transverse path, and two of the transverse divisions of the electrodes from the first set of electrodes and two of the transverse divisions of the electrodes from the second set of electrodes are oriented to define a set of transverse electrodes arranged in a quadrupole orientation around a second central axis between the first axial end of the transverse path and the intersection region. A second set of electrodes, An electron source positioned near the first axial end of the short-direction path for introducing a plurality of electrons along the second central axis such that electrons travel through the short-direction path in the first short-direction toward the cross region, At least one auxiliary electrode, the at least one auxiliary electrode being positioned parallel to the first central axis to drive precursor ions into the electron beam path when a potential is applied to the auxiliary electrode, A drive circuit for applying a complementary AC signal to at least one auxiliary electrode to confine precursor ions within the electron beam path while the reaction product is selectively extracted from the system, A system that includes these features.

21. The system according to claim 20, further comprising a first electrode adapted with respect to an arrangement on one side of the first central axis, parallel to the first central axis, and a second auxiliary electrode adapted with respect to an arrangement on the opposite side of the first central axis, parallel to the first central axis.

22. The system according to claim 20, wherein the at least one auxiliary electrode has an elongated structure that extends parallel to the first central axis from one end proximal to the precursor ion inlet lens to a second end proximal to the reaction product extraction lens.

23. The system according to claim 20, wherein the at least one auxiliary electrode has an elongated T shape with a stem portion closest to the first central axis.

24. The system according to claim 23, wherein the at least one auxiliary electrode has a notched T shape.

25. The system according to claim 20, wherein the drive circuit further comprises a circuit for selectively exciting a reaction product ion following the electron-activated dissociation of the precursor ion by driving at least one set of quadrupole electrodes with a drive signal that excites an ion having a response m / z value.

26. The system according to claim 25, wherein the drive circuit further comprises a notch filter, the drive circuit is configured to apply a notched white noise signal to the at least one auxiliary electrode, so that the notch filter suppresses the frequency at which the precursor ion would be excited.

27. The system according to claim 25, wherein the drive circuit further comprises a digital waveform generator, the drive circuit is configured to apply a notched white noise signal to the at least one auxiliary electrode, thereby causing the digital waveform generator to produce a white noise signal with a suppressed frequency that will excite the precursor ion.

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