Segmented t-bars

Abstract

In one aspect, an ion guide is disclosed, which includes a plurality of rods arranged in a multipole configuration and configured for application of RF voltages thereto and a first set of auxiliary electrodes interposed between said plurality of rods and configured for application of at least one DC voltage thereto so as to generate a bandpass filter. The ion guide further includes a second set of auxiliary electrodes positioned upstream or downstream of said first set of auxiliary electrodes, where the second set of auxiliary electrodes is DC biased relative to the first set of auxiliary electrodes to generate an axial electric field for imparting energy to ions for overcoming a DC potential barrier caused by contamination of the first set of auxiliary electrodes by charged species.

Description

SEGMENTED T-BARSRELATED APPLICATIONS

[0001] This application claims priority to, and the benefit of, U.S. Provisional Application No. 63 / 740,484 filed on December 31, 2024 and U.S. Provisional Application No. 63 / 818,245 filed on June 5, 2025, the contents of both of which are incorporated herein by reference in their entireties.TECHNICAL FIELD

[0002] The present disclosure relates generally to (A) ion guides to be utilized or installed in mass spectrometers, (B) ion guides including a set of multipole electrodes, and a set of auxiliary electrodes interposed between the multipole electrodes, (C) mass spectrometers having such ion guides, and / or (D) a method thereof.BACKGROUND

[0003] Mass spectrometry (MS) is an analytical technique for determining the structure of chemical substances with both qualitative and quantitative applications. MS can be useful for identifying unknown compounds, determining the composition of atomic elements in a molecule, determining the structure of a compound by observing its fragmentation and quantifying the amount of a particular chemical compound in a mixed sample. Mass spectrometers detect chemical entities as ions, so the analytes must be converted to charged ions.

[0004] In many mass spectrometers, one or more ion guides are positioned upstream of a mass analyzer, such as a time-of-flight (TOF) mass analyzer, and other ion optics (such as a mass filter) to guide the ions to the downstream components, e.g., by forming an ion beam. By way of example, such an ion guide can include a set of rods arranged in a quadrupole configuration to which Radio Frequency (RF) voltages can be applied to generate an electromagnetic field for providing radial confinement of the ions.

[0005] In some ion guides, in addition to the quadrupole rods, a set of auxiliary electrodes, e.g., having a T-shaped profile, is interposed between the quadrupole rod set. For example, such auxiliary electrodes can be utilized to prevent the transmission of unwanted ions to downstream components.14896-9374-9380, v. 1SUMMARY

[0006] It has been observed that undesirable contamination of the auxiliary electrodes due to the deposition of ions (e.g., unwanted (non-target) ions) can adversely affect the transmission of target ions through such ion guides.

[0007] In one aspect, an ion guide is disclosed, which includes a plurality of rods arranged in a multipole configuration and configured for the application of RF voltages thereto and a first set of auxiliary electrodes interposed between said plurality of rods and configured for application of at least one DC voltage thereto to generate a bandpass filter. The ion guide further includes a second set of auxiliary electrodes positioned upstream or downstream of said first set of auxiliary electrodes, where the second set of auxiliary electrodes is DC-biased relative to the first set of auxiliary electrodes to generate an axial electric field for imparting energy to ions for overcoming a DC potential barrier caused by the contamination of the first set of auxiliary electrodes by ions deposited on the electrodes. For example, and without limitation, the multipole rod set can have a quadrupole configuration, though other multipole configurations may also be utilized.

[0008] In various embodiments, each auxiliary electrode of the second set of auxiliary electrodes can have a T-shaped cross-sectional profile.

[0009] In various embodiments, the ion guide can include a third set of auxiliary electrodes, where the first set of auxiliary electrodes is positioned between the second set of auxiliary electrodes and the third set of auxiliary electrodes. In other words, (A) one of the second set of auxiliary electrodes and the third set of auxiliary electrodes can be positioned upstream of the first set of auxiliary electrodes, and (B) the other one of the second set of auxiliary electrodes and the third set of auxiliary electrodes can be positioned downstream of the first set of auxiliary electrodes. In various embodiments, the set of upstream auxiliary electrodes is maintained at a DC potential larger (greater) than that of the first set of auxiliary electrodes and the first set of auxiliary electrodes is maintained at a DC potential larger (greater) than that of the second set of downstream auxiliary electrodes.

[0010] In various embodiments, each auxiliary electrode of the second set of auxiliary electrodes has a T-shaped cross-sectional profile.24896-9374-9380, v. 1

[0011] In a related aspect, a mass spectrometer is disclosed, which includes (A) an ion source for receiving a sample and ionizing one or more target analytes in the sample to generate sample ions, and (B) an ion guide for receiving the sample ions and forming an ion beam for transmission to one or more downstream components of the mass spectrometer. The ion guide can include (A) a plurality of rods arranged in a multipole configuration and configured for application of RF voltages thereto, (B) a first set of auxiliary electrodes interposed between the plurality of rods and configured for the application of at least one DC voltage thereto to generate a bandpass filter configured to permit movement of target (desired) ions into the mass spectrometer and also configured to prevent movement of non-target (undesired) ions into the mass spectrometer, and (C) a second set of auxiliary electrodes positioned upstream or downstream of the first set of auxiliary electrodes, which is DC-biased relative to the first set of auxiliary electrodes to generate an axial electric field for imparting energy to target ions for overcoming a DC potential barrier caused by contamination of the first set of auxiliary electrodes by unwanted ions.

[0012] In a related aspect, a method of operating an ion guide can include: arranging a plurality of rods in a multipole configuration, providing an ion passageway extending along the plurality of rods, the ion passageway having an inlet configured to receive a plurality of ions and also having an outlet through which the plurality of ions can exit the ion passageway; interposing a first set of auxiliary electrodes between the plurality of rods arranged in the multipole configuration; interposing a second set of auxiliary electrodes between the plurality of rods arranged in the multipole configuration; positioning the second set of auxiliary electrodes upstream or downstream of the first set of auxiliary electrodes; and applying DC voltages to the plurality of rods, the first set of auxiliary electrodes, and the second set of auxiliary electrodes so as to generate a DC potential along a longitudinal axis of said ion passageway. The DC voltages can be configured such that the DC potential is any of a substantially uniform potential and an attractive potential along the longitudinal axis in a direction extending from the inlet of the ion passageway to the outlet of the ion passageway.

[0013] In general, a desired DC potential along the longitudinal axis of an ion guide according to various embodiments can be generated by using different DC bias potentials between the T-bar electrode assembly and one or more auxiliary electrode assemblies that have34896-9374-9380, v. 1similar geometry as the T-bar electrodes assembly or using different geometries of the T-bar electrodes assembly and the one or more auxiliary electrode assemblies but maintaining the assemblies at the same DC potential and / or a combination of these two approaches.

[0014] Further understanding of various aspects of the present teachings can be obtained by reference to the following detailed description in conjunction with the associated drawings, which are described briefly below.BRIEF DESCRIPTION OF THE DRAWINGS

[0015] FIG. 1A schematically depicts an ion guide having a set of quadrupole rods and a set of auxiliary electrodes interposed between the quadrupole rods,

[0016] FIG. IB is a schematic depiction of a DC potential along the longitudinal axis of the ion guide shown in FIG. 1A in two operational states: (1) when there is no ion transmission through the ion guide, and (2) when there is ion transmission through the ion guide,

[0017] FIG. 1C schematically depicts pulsing of the relative voltage between an input ion lens and the quadrupole rods of the ion guide illustrated in FIG. 1A to produce two states of “ion transmission” and “ion rejection,”

[0018] FIG.1D shows (A) an example of a DC potential that can be established along the longitudinal axis of the ion guide illustrated in FIG. 1A, during an ion transmission interval, when the T-bar electrodes are clean (uncontaminated), and (B) when the T-bar electrodes are contaminated due to deposition of undesired ions thereon,

[0019] FIG. 2A shows a DC potential established along the longitudinal axis of the ion guide depicted in FIG. 1A via raising the DC potential of the quadrupole rods relative to that of the auxiliary electrodes when the auxiliary electrodes are in a clean state,

[0020] FIG. 2B shows a DC potential established along the longitudinal axis of the ion guide depicted in FIG. 1A via raising the DC potential of the quadrupole rods relative to that of the auxiliary electrodes when the auxiliary electrodes are contaminated by deposition of ions thereon,

[0021] FIG. 3A schematically depicts an ion guide that includes a set of quadrupole rods and two sets of auxiliary electrodes that are interposed between the quadrupole rods,44896-9374-9380, v. 1

[0022] FIG. 3B schematically depicts a DC potential established along the longitudinal axis of the ion guide shown in FIG.3A in two states, in one of which the auxiliary electrodes are clean and in the other the upstream auxiliary electrodes are contaminated due to deposition of ions thereon,

[0023] FIG. 4A is another schematic depiction of the ion guide illustrated in FIG.3A,

[0024] FIG. 4B schematically depicts a DC potential according to an embodiment established along the longitudinal axis of the ion guide illustrated in FIG.4A in a clean state and a contaminated state of the upstream auxiliary electrodes, illustrating that the DC potential allows ions to overcome a potential barrier generated by the contamination of the upstream auxiliary electrodes,

[0025] FIG. 4C is a schematic end view of a set of quadrupole rods and a set of T-bar auxiliary electrodes interposed between the quadrupole rods,

[0026] FIG. 5A schematically illustrates an ion guide according to an embodiment including a set of quadrupole rods and two sets of T-bar auxiliary electrodes that are interspersed among the quadrupole rods,

[0027] FIG. 5B schematically depicts a DC potential according to an embodiment established along the longitudinal axis of the ion guide illustrated in FIG.5A in a clean state and in a contaminated state of the downstream set of the auxiliary electrodes,

[0028] FIG. 6A schematically depicts an ion guide according to an embodiment including a set of quadrupole rods and two sets of T-bar auxiliary electrodes interposed between the quadrupole rods,

[0029] FIG. 6B schematically depicts a DC potential according to an embodiment established along the longitudinal axis of the ion guide illustrated in FIG.6A in a clean and in a contaminated state of the upstream set of the auxiliary electrodes,

[0030] FIG. 7A schematically depicts an ion guide according to an embodiment including a set of quadrupole electrodes, two sets of T-bar auxiliary electrodes, and a set of longitudinally tapered auxiliary electrodes positioned downstream of the two sets of T-bar auxiliary electrodes,54896-9374-9380, v. 1

[0031] FIG. 7B schematically depicts a DC potential according to an embodiment established along the longitudinal axis of the ion guide illustrated in FIG.7A in a clean state and in a contaminated state of the middle set of the auxiliary electrodes,

[0032] FIG. 8A schematically depicts an ion guide according to an embodiment including a set of quadrupole rods, an upstream set of T-bar auxiliary electrodes, a downstream set of longitudinally tapered auxiliary electrodes and a middle set of T-bar auxiliary electrodes interposed between the quadrupole rods, where the middle set of the T-bar auxiliary electrodes has a field radius that is larger than the field radius of the upstream set of the T-bar auxiliary electrodes,

[0033] FIG. 8B schematically depicts a DC potential according to an embodiment established along the longitudinal axis of the ion guide illustrated in FIG.8A in a clean state and in a contaminated state of the middle set of the T-bar auxiliary electrodes,

[0034] FIG. 9 schematically depicts a mass spectrometer that includes an ion guide according to an embodiment, and

[0035] FIG. 10 schematically depicts an example of an implementation of any of the controller and the analysis module of the mass spectrometer illustrated in FIG.9.DETAILED DESCRIPTION

[0036] For clarity, the following discussion will explicate various aspects of embodiments. For example, discussing like or analogous features in alternative embodiments may be somewhat abbreviated. Well-known ideas or concepts may also, for brevity, not be discussed in any great detail. The skilled person will recognize that some embodiments may not require certain of the specifically described details in every implementation, which are set forth herein only to provide a thorough understanding of the embodiments. Similarly, it will be apparent that the described embodiments may be susceptible to alteration or variation according to common general knowledge without departing from the scope of the disclosure. The following detailed description of embodiments is not to be regarded as limiting the scope of the applicant’s teachings in any manner.

[0037] As used herein, the terms "about" and "substantially equal" refer to variations in a numerical quantity that can occur, for example, through measuring or handling procedures in the 64896-9374-9380, v. 1real world, through inadvertent error in these procedures, through differences in the manufacture, source, or purity of compositions or reagents, and the like. Typically, the terms "about" and "substantially" as used herein mean 10% greater or less than the value or range of values stated or the complete condition or state. For instance, a concentration value of about 30% or substantially equal to 30% can mean a concentration between 27% and 33%. The terms also refer to variations that would be recognized by one skilled in the art as being equivalent so long as such variations do not encompass known values practiced by the prior art.

[0038] As used herein the term "and / or" includes any and all combinations of one or more of the associated listed items and may be abbreviated as " / ".

[0039] In many of the following embodiments, the auxiliary electrodes are assumed to have a T-bar configuration (profile). But it should be understood that the auxiliary electrodes can have other configurations (profiles). For example, the auxiliary electrodes may have other shapes such as rectangular or may include tapered surfaces.

[0040] Auxiliary electrodes, e.g., in the form of T-shaped electrodes (hereinafter referred to as T-bar electrodes), can be used in ion guides to create a bandpass filter, to protect downstream components, e.g., a mass filter, from unwanted (non-target) ions. When such auxiliary electrodes are operated as a high-mass cut-off filter, ion debris and / or unwanted ions can accumulate on the electrodes, which can change the electric field propelling the ions through the ion guide. In some cases, this can lead to unwanted ion trapping in a region of the ion guide preceding the auxiliary electrode assembly.

[0041] Such trapping of ions can have deleterious effects, especially if ion beam modulation using pulsing electrodes is used. For example, FIG. 1A shows an ion guide 100 (herein also referred to as the ion guide Q0) having a set of quadrupole rods 102 (only two of the rods are visible in FIG. 1A) that are arranged in a quadrupole configuration providing (A) an inlet 102a for receiving ions into a passageway between the rods, and (B) an outlet 102b through which ions can exit the passageway. The ion guide further includes a set of four (4) auxiliary electrodes 104 (only two of the auxiliary electrodes are visible FIG. 1A) having T-shaped profiles (herein also referred to as T-bar electrodes or T-bar assembly) that are interposed between the quadrupole rods. An input ion lens IQ0 is positioned in proximity to the inlet of the ion guide74896-9374-9380, v. 1and can be DC-biased relative to the quadrupole rods to modulate the introduction of ions into the ion guide and an output ion lens IQ1 is positioned in proximity to the outlet of the ion guide and can be DC-biased relative to the quadrupole rods to modulate the exit of the ions from the ion guide. For example, as discussed in more detail below, the DC potential of the input ion lens IQO relative to the DC potential of the QO rods can be adjusted to provide a potential barrier for inhibiting the transmission of ions into the ion guide. Conversely, the relative DC potentials of the ion lens IQO and the QO rods can be adjusted to facilitate the entry of ions into the ion guide.

[0042] To establish modulation of the ion current introduced into the ion guide, in various embodiments, the ion transmission coefficient (ITC) can be modulated by pulsing a relative voltage to be applied between the input ion lens IQO and the quadrupole rods 102. Such pulsing of the relative voltage can produce two states of “ion transmission” and “ion rejection,” as shown schematically in FIG. 1C, in which (A) during the ion transmission period, the ions can enter and pass through the ion guide, and (B) during the ion rejection period, the input lens IQO inhibits ions from entering the ion guide such that the ions cannot pass through the ion guide.

[0043] Thus, this approach can adjust the ion beam’s intensity by varying the ratio of the durations of the ion transmission period and the ion rejection period. A beneficial property of such an approach is that ion attenuation can be set up using an attenuation factor that is known in advance and remains uniform across a wide mass range.

[0044] As shown in FIG. IB, the ion transmission period (herein also referred to as the ion transmission segment) is typically set up with a neutral or slightly downward potential (see, the plot labelled as “transmission” in FIG. IB) in the region between the input ion lens IQO and the quadrupole rods 102 (e.g., a magnitude of five (5) Volt (V) voltage can be applied between the input ion lens IQO and the quadrupole rods) while the ion rejection period (herein also referred to as the ion rejection segment) is set up by applying a large voltage with an opposite polarity (e.g., 50 V) between the input ion lens IQO and the quadrupole rods 102. Such an electric potential can create an electric field, which is sufficient to pull the incoming ions toward the input ion lens IQO and prevent their transmission downstream during the ion rejection period or segment.

[0045] One unwanted effect of this potential is that the electric field can penetrate the region between the input ion lens IQO and the ion guide Q0, which can lead to the establishment of an electric field in the opposite direction relative to the intended direction of ion movement and can 84896-9374-9380, v. 1be sufficient to pull a fraction of ions that had entered the ion guide during a transmission segment but had not moved sufficiently far from the entrance of the quadrupole rods 102 at the onset of the rejection period or segment. This can make the resultant ion ratio between the ion transmission period or segment and the ion rejection period or segment incorrect, though this can be typically corrected; however, when an ion trapping potential is created due to unwanted charging of the auxiliary electrodes (e.g., T-bar electrodes), a larger fraction of such ions may be extracted from an entrance region of the quadrupole rod set, making the correction inaccurate. Such an undesirable contamination of the electrodes of the T-bar assembly is schematically depicted as charged deposit 10 and charged deposit 12 formed on the upstream portions of the rods of the T-bar electrodes 104. In fact, in certain circumstances in which significant ion trapping potential is present at the auxiliary electrodes, most ions can be lost due to such a mechanism.

[0046] By way of illustration, FIG.1D shows (A) an example of a DC potential that can be established along the longitudinal axis of the ion guide, during an ion transmission interval, when the T-bar electrodes 104 are clean (uncontaminated), and (B) when the T-bar electrodes 104 are contaminated due to deposition of unwanted ions thereon. In the clean state of the T-bar electrodes, the on-axis DC potential shows a ramp in an upstream region of the ion guide 100 close to the input ion lens 106a that can help facilitate the entry of the ions into the ion guide 100 with the rest of the DC potential being substantially flat (constant) along the longitudinal axis of the ion guide. In the contaminated state of the T-bar electrodes 104, the presence of the unwanted ions on the surfaces of the T-bar electrodes 104 can lead to the creation of a potential barrier (PB) in proximity to an upstream end of the T-bar electrodes 104, which, together with the input voltage ramp, can form a potential well in which certain ions can accumulate. In other words, creating such a potential barrier can inhibit the passage of certain ions through the ion guide 100.

[0047] Accordingly, to achieve proper operation of an ion guide having an assembly of auxiliary electrodes, there is a need for approaches that can mitigate ion trapping in an entrance region of the ion guide (e.g., in a region between the ion guide entrance and the upstream end of the auxiliary electrodes assembly that is closest to the inlet of the ion guide).

[0048] With reference to FIGS. 2A and 2B, by raising the potential of the quadrupole rods relative to that of the auxiliary electrodes, the potential barrier can be overcome, however, this94896-9374-9380, v. 1approach results in the generation of a potential barrier at the other end of the auxiliary electrodes (i.e., the downstream end of the auxiliary electrodes) that can, in turn, inhibit the passage of ions through the ion guide.

[0049] FIG. 3A schematically depicts an ion guide 300 that includes a set of quadrupole rods 302, as well as a set of T-bar electrodes 304 that are interposed between the quadrupole rods 302 of the quadrupole rod set. An input ion lens IQ0 is positioned in proximity to an inlet 302a of the quadrupole rod set, and an output ion lens IQ1 is positioned in proximity to an outlet 302b of the quadrupole rod set. In this embodiment, a second set of auxiliary electrodes 306 is positioned downstream of the T-bar electrodes 304, with each of the auxiliary electrodes 306 being interposed between two of the quadrupole rods.

[0050] In various embodiments, the T-bar electrode assembly 304 can include two pairs of electrodes, where each pair contains two electrodes that are positioned radially opposed to one another. The T-bar electrode assembly 304 can be operated in two operational modes: (1) a first operational mode in which all ions can pass through the ion guide, and (2) a second operational mode in which the T-bar electrode assembly 304 can operate as a high-mass cut-off filter (or a bandpass filter). In the first operational mode, the electrodes of each radially-opposed pair of the T-bar electrode assembly 304 are maintained at the same DC potential, but each pair is biased relative to the other pair with a resolving DC bias voltage, which controls the bandpass filter. In this disclosure, a reference to the DC potential of the T-bar electrodes 304 (or the DC voltage of the T-bar electrodes) refers to an average of the potentials of the four (4) rods of the T-bar electrode assembly 304. By way of example, biasing the T-bar electrodes 304 at positive (+5) Volts, e.g., relative to the quadrupole rods 302 or a set of auxiliary electrodes 306, can mean that either all of the four T-bar electrodes 304 are biased at +5 Volts or one pair is biased at positive fifteen (+15 V) and the other pair is biased at negative five (-5) Volts, which results in an average bias of +5 Volts.

[0051] With reference to FIG. 3B, application of a DC voltage between the ion lens IQ0 and the quadrupole rods 302 results in the generation of a first electric potential ramp (PR1) that facilitates entry of ions (herein positive ions) into a passageway formed between the quadrupole rods 302. Further, the second set of auxiliary electrodes 306 is maintained at a lower potential relative to the first set of auxiliary electrodes 304, thereby generating a second downward-104896-9374-9380, v. 1sloping potential ramp (PR2) that accelerates the passage of ions through the ion guide. For example, in some cases, the T-bar electrodes 304 can be maintained at zero voltage, and the second set of auxiliary electrodes can be maintained at negative (-) 150 Volts. However, as shown schematically in FIG. 3B, the contamination of the T-bar electrodes 304 results in the generation of a potential barrier that can generate, with the electric potential ramp (PR1), an electric potential well in which at least some of the ions can be trapped and hence adversely affect the transmission of ions through the ion guide, and also potentially lead to the contamination of the electrodes.

[0052] FIG. 4A schematically depicts an embodiment of an ion guide 400 that includes a set of quadruple rods 401 as well as a set of four (4) auxiliary electrodes 402 that have a T-shaped profile and are interposed between the quadrupole rods 401. With respect to FIG.4C, each T-bar electrode 402 includes a base B from which a stem extends toward the longitudinal axis of the quadrupole rod set. A second set of auxiliary electrodes 404 is positioned downstream of the T-bar electrodes. The second set of auxiliary electrodes 404 has a longitudinally tapered cross section (i.e., a varying cross-sectional width) that increases with increasing distance from the T-bar electrodes. Similar to the previous ion guides, an ion input lens IQ0 is positioned in proximity to an inlet 401a of the quadrupole rod set and an ion output lens IQ1 is positioned in proximity to an outlet 400b of the quadrupole rod set.

[0053] As shown in FIG.4B, similar to the previous ion guides, a DC voltage differential is applied between the input ion lens IQ0 and the quadrupole rod set 401 to establish a first potential ramp (PR1) for facilitating the entry of ions into the ion guide. Further, in this embodiment, the quadrupole rods 401 are maintained at a DC potential greater than the DC potential of the T-bar electrodes. This voltage difference is selected to raise the potential of the quadrupole rods 401 above the height of the potential barrier that is generated due to the contamination of the T-bar electrodes 402 via the deposition of debris and / or unwanted ions. By way of example, the quadrupole rods 401 can be maintained a few volts (e.g., three (3) Volts) above the DC voltage applied to the T-bar electrodes 402 (which can be, in this embodiment, zero (0) Volts, though in other embodiments can be a non-zero DC voltage). Moreover, the second set of auxiliary electrodes can be maintained at a lower electric potential relative to the T-bar electrodes 402 to provide a second electric potential ramp (PR2) to accelerate the ions114896-9374-9380, v. 1(herein positive ions) to expedite their transit through the ion guide. By way of example, the second set of auxiliary electrodes 404 can be maintained at a voltage of -150 V below the voltage applied to the T-bar electrodes 402.

[0054] In various embodiments, such a large voltage differential may be needed because of a relatively large average radial distance of the second auxiliary electrodes 404 from the longitudinal axis of the quadrupole rod set 401. In this manner, the creation of an electric potential well in a region between the inlet of the quadrupole rods 401 and the first end of the T-bar electrodes 402 can be prevented while also providing an accelerating axial field, via the second auxiliary electrodes 404, for expediting the passage of ions through the ion guide 400.

[0055] With continued reference to FIG. 4B, the application of differential DC voltages to the input ion lens IQ0, the quadrupole rods 401, the T-bar electrodes 402 and the auxiliary electrodes 404 as described above results in the generation of a DC potential along the longitudinal axis of the ions guide 400, which either decreases or remains substantially constant along different axial portions of the ion guide 400. In other words, the selection of the DC voltages can eliminate the creation of ion wells along the axial extent of the ion guide 400 and hence facilitate the passage of ions through the ion guide 400.

[0056] FIG. 5A schematically depicts another embodiment 500 of an ion guide according to the present teachings, which is similar to the previous embodiment and includes a set of quadrupole rods 502 and a set of four (4) T-bar electrodes 504 (herein referred to also as T-bar assembly) that are interposed between the quadrupole rods. Further, in this embodiment, another set of auxiliary electrodes 506, which is in the form of another set of T-bar electrodes, is positioned upstream of the first set of T-bar electrodes 504. Further, similar to the previous ion guides, an entrance lens or input ion lens IQ0 is positioned in proximity to an inlet of the set of quadrupole rods 502 and an exit ion lens (or an output ion lens) IQ1 is positioned in proximity to an outlet of the quadrupole rod set.

[0057] With reference to FIG. 5B, in this embodiment, the input ion lens IQ0 is maintained at an electric DC potential above the electric DC potential of the quadrupole rod set 502 to provide an entrance potential ramp for facilitating the entry of the ions into the ion guide 500. The upstream T-bar electrodes 506 are maintained at a higher potential relative to the T-bar electrodes 504, and the T-bar electrodes 504 are maintained, in turn, at a higher potential relative 124896-9374-9380, v. 1to that of the quadrupole rod set 502. In general, the electric potential difference between the T-bar electrodes 506 and 504 is selected to be greater than the height of a potential barrier that can be generated due to contamination of the electrodes of T-bar assembly 504 to prevent such a potential barrier from inhibiting the passage of ions through the passageway between the quadrupole rod set 502. By way of example, and without limitation, the quadrupole rod set 502 is maintained at a zero DC voltage while a voltage of about positive four (+4) volts is applied to the upstream T-bar electrodes 506, and a voltage of about positive (+1) volt is applied to the T-bar electrodes 504.

[0058] As shown in FIG. 5B, the selection of the DC voltages applied to the ion lens IQ0, the quadrupole rods 502, the upstream auxiliary electrodes 506, and the T-bar electrodes 504 results in the generation of a DC potential along the longitudinal axis of the ion guide 500, which either decreases (as a ramp or discrete steps) or remains substantially constant along different axial portions of the ion guide, thereby eliminating the creation of potential wells that could trap ions and hence inhibit their passage through the ion guide 500.

[0059] FIG. 6A schematically depicts another embodiment 600 of an ion guide according to the present teachings, which similar to the previous embodiment, includes a set of quadrupole rods 602 and a set of four (4) T-bar electrodes 604 (herein referred to also as T-bar assembly) that are interposed between the quadrupole rods. Unlike the previous embodiment in which another set of auxiliary electrodes was positioned upstream of the quadrupole rod set, in this embodiment, another set of auxiliary electrodes 606, which is in the form of another set of T-bar electrodes, is positioned downstream of the first set of T-bar electrodes 604. Further, similar to the previous ion guides, an input ion lens IQ0 is positioned in proximity of an inlet of the set of quadrupole rods 602 and an output ion lens IQ1 is positioned in proximity of an outlet of the quadrupole rod set.

[0060] With reference to FIG. 6B, in this embodiment, the input ion lens IQ0 is maintained at an electric DC potential above the electric DC potential of the quadrupole rod set to provide an entrance potential ramp for facilitating the entry of the ions (which are assumed to be positive ions in this embodiment) into the ion guide 600. The downstream T-bar electrodes 606 are maintained at a lower DC potential relative to the T-bar electrodes 604 and the T-bar electrodes 604 are maintained, in turn, at a lower DC potential relative to that of the quadrupole rod set 602.134896-9374-9380, v. 1In general, the potential difference between the T-bar electrodes 606 and 604 is selected to be greater than the height of a potential barrier that can be generated due to the contamination of the electrodes of T-bar assembly 604 to prevent such a potential barrier from inhibiting the passage of ions through the passageway between the quadrupole rod set 602. By way of example, and without limitation, the quadrupole rod 602 set can be maintained at a zero DC voltage while a voltage of about +4 volts is applied to the T-bar electrodes 604 and a voltage of about +1 volt is applied to the downstream T-bar electrodes 606.

[0061] With reference to FIG. 6B, similar to the previous embodiments, the selection of the DC voltages applied to the quadrupole rods 602, the first set of T-bar electrodes 604 and the second set of T-bar electrodes 606 results in the generation of an axial DC potential along the longitudinal axis of the ion guide 600, which either decreases (e.g., as a ramp or in discrete steps) or remains substantially constant along a direction from the inlet of the ion guide 600 to its outlet to facilitate the passage of ions through the ion guide 600.

[0062] FIG. 7A schematically depicts an ion guide 700 that includes a set of quadrupole rods 702, and a first set of four (4) T-bar electrodes 704 that are interposed between the quadrupole rods 702. In this embodiment, the ion guide 700 includes an upstream set of auxiliary electrodes 706 and a downstream set of auxiliary electrodes 708, which are respectively positioned upstream and downstream of the T-bar electrodes 704. In this embodiment, the upstream auxiliary electrodes 706 are in the form of four (4) T-bar electrodes that are interposed between the quadrupole rods while the downstream auxiliary electrodes 708 are in the form of elongated electrodes having an increasing cross-sectional width as a function of increasing distance from the T-bar electrodes 704.

[0063] As shown in FIG. 7B, the upstream T-bar electrodes 706 are maintained at a DC potential that is higher than the DC potential at which the T-bar electrodes 704 are maintained. Further, the downstream auxiliary electrodes 708 are maintained at a lower DC potential relative to the T-bar electrodes 704. In general, the potential difference between the upstream auxiliary electrodes 706 and the T-bar electrodes 704 is selected to be greater than the height of a potential barrier that could be generated due to contamination of the T-bar electrodes 704 to prevent such a potential barrier from inhibiting the passage of ions through the ion guide 700. By way of example, and without limitation, voltages of positive four (+4) Volts and positive one (+1) Volt144896-9374-9380, v. 1can be applied to the auxiliary electrodes 706 and the T-bar electrodes 704, respectively.Further, the downstream auxiliary electrodes 708 can be maintained at a voltage of about 150 Volts below the voltage applied to the T-bar electrodes 704.

[0064] Similar to the previous embodiments, a DC potential generated along the longitudinal axis of the ion guide 700 decreases, either as a ramp or in discrete steps, or remains substantially constant in different portions of the ion guide 700 in a direction from the ion guide’s inlet to its outlet, thus facilitating the passage of ions through the ion guide 700.

[0065] In various embodiments, such as those discussed above, the T-bar electrodes and the other auxiliary electrodes may have different dimensions; for example, their protrusion toward to the center of the quadrupole rod set may differ. For example, the T-bar electrodes and the other auxiliary electrodes can have different field radii. As a result, the DC potentials at which the T-bar electrodes and various auxiliary electrodes, such as the above upstream auxiliary electrodes and downstream auxiliary electrodes, are maintained need to be adjusted to achieve a DC potential along the longitudinal axis of the quadrupole rod set in a manner discussed above to ensure that a potential barrier that may be generated due to the contamination of the T-bar electrodes will not inhibit the passage of the ions through the ion guide.

[0066] It should be noted that one potential undesired effect of applying a DC voltage between the auxiliary electrodes and the T-bar electrodes is that it can lead to unwanted ion fragmentation through collision-induced dissociation mechanisms in the presence of a bath gas. As such, in various embodiments, it is desirable to minimize the charging of the T-bar assembly and to configure the geometry of the T-bar electrodes and the auxiliary electrodes such that a relatively small voltage drop between the T-bar electrodes and the auxiliary electrodes would be sufficient to overcome a potential barrier that could develop due to the contamination of the T-bar assembly. For example, the field radius of the T-bar assembly (such as the T-bar assemblies 504, 604 and 704) and those of the auxiliary electrodes can be adjusted to achieve such a result. In various embodiments, the field radius of the T-bar assembly can be selected to be greater than that of the upstream auxiliary electrodes. For example, the dimensions of the rods of the upstream auxiliary electrodes and those of the T-bar assembly can be selected such that the auxiliary electrodes protrude more toward the central (longitudinal) axis of the quadrupole rod set relative to the protrusion of rods of the T-bar assembly, thereby effectively shielding the154896-9374-9380, v. 1unwanted charging effects in a region preceding the T-bar assembly. Another advantage of such an approach is the mechanical protection of the front surfaces (upstream surfaces) of the electrodes of the T-bar assembly, which can result in a more even distribution of the electric charge across the longitudinal surfaces of the T-bar electrodes.

[0067] By way of illustration, FIG. 8A depicts an ion guide 800 that, similar to the previous embodiment, includes a quadrupole rod set 802, a T-bar assembly 804, as well as an upstream and a downstream set of auxiliary electrodes 806 and 808. However, in this embodiment, a field radius R1 of the rods of the T-bar assembly 804 (where the field radius R1 is defined as the distance from the central / longitudinal axis (LA) of the quadrupole rod set 802 to the nearest surface of the rods of the T-bar assembly 804) is greater than a respective field radius R2 of the rods of the upstream set of auxiliary electrodes 806 (where the field radius R2 is defined as the distance from the central axis of the quadrupole rod set 802 to the nearest surface of the rods of the upstream set of the auxiliary electrodes 806). In other words, the rods of the upstream auxiliary electrodes 806 protrude to a greater extent toward the central axis of the quadrupole rod set 802 compared to the extent by which the rods of the T-bar assembly 804 protrude toward the central axis of the quadrupole rod set 802.

[0068] FIG. 8B shows a DC potential that can be generated in the ion guide depicted in FIG.8A. As noted above, the auxiliary electrodes 806 protrude to a larger extent toward the central axis (LA) of the ion guide than the T-bar electrodes 804. As a result, in some embodiments, the auxiliary electrodes 806 and the T-bar electrodes 804 can be maintained at substantially the same DC potential while biasing both the auxiliary electrodes 806 and the T-bar electrodes 804 significantly higher relative to the quadrupole rods 802 to generate a downward potential gradient.

[0069] An ion guide according to various embodiments of the present teachings can be incorporated into a variety of different mass spectrometers. By way of example, FIG. 9 schematically depicts a mass spectrometric system 900 (herein also referred to as a mass spectrometer) according to an embodiment that includes an LC column 902, which can receive a sample and separate a plurality of analytes in the sample based on their elution times from the LC column. The mass spectrometric system 900 further includes an ion source 904 that receives164896-9374-9380, v. 1an eluate exiting the LC column and ionizes one or more analytes contained in the eluate to generate a plurality of sample ions (herein also referred to as precursor ions).

[0070] In this embodiment, an ion guide 906 according to an embodiment of the present teachings can receive the precursor ions and provide focusing of the ions to generate an ion beam that is received by a mass filter 908. One or more DC voltage sources 924, which operate under the control of a controller 918, can apply DC voltages to the quadrupole rods and various auxiliary electrodes of the ion guide 906 according to various embodiments of the present teachings, such as those discussed above, to ensure that the passage of ions through the ion guide 906 is not impeded by potential barriers generated due to the contamination of the auxiliary electrodes. Further, an RF voltage source 926, which also operates under the control of the controller 918, can apply RF voltages to the quadrupole rods of the ion guide to provide radial confinement of the ions as they pass through the ion guide 906.

[0071] In other embodiments, an ion mobility spectrometer (IMS), such as a differential mobility spectrometer (DMS), can be utilized as a separation device to separate ions based on their mobility with the ions exiting the IMS being received by the guide 906.

[0072] The mass filter 908 provides an ion transmission window that allows transmission of ions having m / z values within a target m / z range through the mass filter. By way of example, the mass filter 908 can include a plurality of rods arranged in a quadrupole configuration to which RF voltages as well as a discriminating DC voltage can be applied via the RF and the DC voltage sources 910 and 912, respectively, to generate an ion transmission window. The RF and DC voltage sources are controlled by the controller 918. In this implementation, the ions passing through the mass filter 908 are received by an ion fragmentation device 914 that causes fragmentation of the precursor ions to generate a plurality of product ions.

[0073] The product ions are received by a time-of-flight (TOF) mass analyzer 920 that detects the ions and generates ion detection signals in response to the detection of the ions. A mass analysis module 922 receives the ion detection signals from the TOF mass analyzer and processes those signals to generate a mass spectrum. Further, in various embodiments, the mass analysis module 922 can be configured to perform a mass correction of the measured mass peaks174896-9374-9380, v. 1in accordance with the present teachings. By way of example, the mass analysis module 922 can perform such mass correction during data acquisition or post data acquisition.

[0074] In various embodiments, the controller 918 and the data analysis module 922 according to the present teachings can be implemented in software, firmware, and / or hardware and combinations thereof. By way of example, a digital data processing system including a digital data processor, one or more random access memory modules and one or more communications buses that allow communication between various components of the system can be configured (programmed) to process ion detection data received from a multi-channel or a single-channel ion detection system and to operate on the received data in accordance with various embodiments to identify single-ion detection events (within a margin error).

[0075] By way of example, FIG. 10 is a block diagram that illustrates an example of an implementation of any of the controller and the analysis module as a computersystem 1000, including a bus 1002 or other communication mechanisms for communicating information, and a processor 1004 coupled with bus 1002 for processing information. Computer system 1000 also includes a memory 1006, which can be a random-access memory (RAM) or other dynamic storage device, coupled to bus 1002 for determining base calls, and instructions to be executed by processor 1004.

[0076] Memory 1006 also may be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor 1004. Computer system 1000 further includes a read only memory (ROM) 1008 or other static storage device coupled to bus 1002 for storing static information and instructions for processor 1004. A storage device 1010, such as a magnetic disk or an optical disk, is provided and coupled to bus 1002 for storing information and instructions.

[0077] Computer system 1000 may be coupled via bus 1002 to a display 1012, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 1014, including alphanumeric and other keys, is coupled to bus 1002 for communicating information and command selections to processor 1004. Another type of user input device is cursor control 1016, such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor 1004 and for184896-9374-9380, v. 1controlling cursor movement on display 1012. The computer system 1000 further includes a communication module 1018 that allows the computer system to communicate with other devices and systems, and in particular, with a database 1020.

[0078] By way of example, in embodiments in which the computer system 1000 provides an implementation of the controller 918, the computer system 1000 can be programmed to cause application of required DC and RF voltages to the quadrupole rods as well as the auxiliary electrodes of the ion guide as well as DC and RF voltages to the quadrupole rods of the mass filter. Further, in embodiments in which the computer system 1000 provides an implementation of the analysis module 922, the computer system 1000 can be programmed to process the ion detection signals generated by a detector of the mass analyzer 920 to generate a mass spectrum of the product ions.

[0079] Instructions for performing a task may be read into memory 1006 from another computer-readable medium, such as storage device 1010. Execution of the sequences of instructions contained in memory 1006 causes processor 1004 to perform the task. Alternatively, hard-wired circuitry may be used in place of or in combination with software instructions to implement the present teachings. Thus, implementations of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0080] The above descriptions of various implementations of the present teachings have been presented for purposes of illustration and description. It is not exhaustive and does not limit the present teachings to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practicing of the present teachings. Additionally, the described implementation includes software but the present teachings may be implemented as a combination of hardware and software or in hardware alone. The present teachings may be implemented with both object-oriented and non-object-oriented programming systems.

[0081] Depending on certain implementation requirements, embodiments of the present teachings, the controller can be implemented in hardware, firmware and / or in software.

[0082] In some embodiments, the instructions for operating the optical system can be stored using a non-transitory storage medium such as a digital storage medium, for example a DVD, a194896-9374-9380, v. 1Blu-Ray, a CD, a ROM, a PROM, and EPROM, an EEPROM or a FLASH memory, having electronically readable control signals stored thereon, which cooperate (or are capable of cooperating) with a programmable computer system such that the respective method is performed. Therefore, the digital storage medium may be computer readable.

[0083] While various embodiments have been illustrated and described in detail in the drawings and foregoing description, such illustration and description are to be considered illustrative or exemplary and not restrictive; embodiments of the present disclosure are not limited to the disclosed embodiments. Other variations to the disclosed embodiments can be understood and effected by those skilled in the art in practicing embodiments of the present disclosure, from a study of the drawings, the disclosure, and the appended claims.

[0084] In the claims, the word “comprising” does not exclude other elements or steps, and the indefinite article “a” or “an” does not exclude a plurality. A single processor or other processing unit may fulfill the functions of several items recited in the claims. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measured cannot be used to advantage. Any reference signs in the claims should not be construed as limiting the scope.

[0085] Those having ordinary skill in the art will appreciate that various changes can be made to the above embodiments without departing from the scope of the present teachings.204896-9374-9380, v. 1

Claims

CLAIMSWhat is claimed is:

1. An ion guide, comprising:a plurality of rods arranged in a multipole configuration and providing an ion passageway having an inlet configured to receive a plurality of ions and an outlet through which ions can exit the passageway,a first set of auxiliary electrodes interposed between said plurality of multipole rods,a second set of auxiliary electrodes interposed between said plurality of multipole rods and positioned upstream or downstream of said first set of auxiliary electrodes, at least one DC voltage source for application of DC voltages to said plurality of rods, and said first set and said set of auxiliary electrodes,wherein said DC voltages are configured so as to generate a DC potential along a longitudinal axis of the ion passageway such that said DC potential is any of substantially uniform and attractive in a direction extending from said inlet of said passageway to said outlet of said passageway.

2. The ion guide of Claim 1 , wherein said DC potential is configured to provide ions with sufficient kinetic energy to overcome a potential barrier generated by contamination of any of said first set of auxiliary electrodes and said second set of auxiliary electrodes.

3. The ion guide of Claim 2, wherein said contamination is caused by deposition of a portion of said plurality of ions on at least one rod of any of said first set of auxiliary electrodes and said second set of auxiliary electrodes.

4. The ion guide of any one of Claims 1-3, wherein said multipole configuration comprises a quadrupole configuration.214896-9374-9380, v.

15. The ion guide of any one of Claims 1-3, wherein at least one electrode of any of said first set of auxiliary electrodes and said second set of auxiliary electrodes has a T-shaped cross-sectional profile.

6. The ion guide of any one of Claims 1-3, wherein at least one electrode of said second set of auxiliary electrodes has a longitudinally tapered profile.

7. The ion guide of Claim 1, wherein said first set of auxiliary electrodes is configured to enable the ion guide to function as a mass filter.

8. The ion guide of Claim 7, wherein said mass filter is any of a bandpass and a high-mass cut-off filter.

9. The ion guide of Claim 1, wherein said multipole rods are configured for application of at least one RF voltage thereto so as to provide radial confinement of the ions transiting through the ion passageway.

10. The ion guide of Claim 1, wherein said DC potential is substantially uniform along at least a first portion of the ion passageway and is attractive along at least a second portion of the ion passageway.

11. An ion guide, comprising:a plurality of rods arranged in a multipole configuration and configured for application of RF voltages thereto,a first set of auxiliary electrodes interposed between said plurality of rods and configured for application of at least one DC voltage thereto so as to generate a bandpass filter,a second set of auxiliary electrodes positioned upstream or downstream of said first set of auxiliary electrodes and DC-biased relative to the first set of auxiliary electrodes to generate an axial electric field to impart kinetic energy to ions sufficient to224896-9374-9380, v. 1overcome a DC potential barrier caused by electrically charged contamination of the first set of auxiliary electrodes.

12. The ion guide of Claim 11, wherein said multipole configuration is a quadrupole configuration.

13. The ion guide of any one of Claims 11 and 12, wherein each of the auxiliary electrodes of said first set of auxiliary electrodes has a T-shaped cross-sectional profile.

14. The ion guide of any one of Claims 11 and 12, wherein said second set of auxiliary electrodes is positioned upstream of the first set of auxiliary electrodes and said ion guide further comprises a third set of auxiliary electrodes positioned downstream of said first set of auxiliary electrodes.

15. The ion guide of Claim 14, wherein said first set of auxiliary electrodes is maintained at progressively lower DC potentials.

16. A mass spectrometer, comprising:an ion source for receiving a sample and ionizing one or more target analytes in the sample to generate sample ions,an ion guide for receiving the sample ions and forming an ion beam for transmission to one or more downstream components of the mass spectrometer,said ion guide including:a plurality of rods configured to be arranged in a multipole configuration, and also configured to provide an ion passageway extending along said plurality of rods, said ion passageway having an inlet configured to receive a plurality of ions and also having an outlet through which the plurality of ions exits the ion passageway,a first set of auxiliary electrodes configured to be interposed between said plurality of rods arranged in said multipole configuration,234896-9374-9380, v. 1a second set of auxiliary electrodes configured to be interposed between said plurality of rods arranged in said multipole configuration, and said second set of auxiliary electrodes being positioned upstream or downstream of said first set of auxiliary electrodes,said plurality of rods, said first set of auxiliary electrodes and said second set of auxiliary electrodes each configured to be electrically connectable to at least one DC voltage source configured to apply DC voltages,wherein said at least one DC voltage source is configured to provide said DC voltages to generate a DC potential along a longitudinal axis of said ion passageway such that said DC potential is any of substantially uniform and attractive in various portions of the ion passageway in a direction extending from said inlet to said outlet thereof.

17. The mass spectrometer of Claim 16, wherein at least one electrode of any of said first set of auxiliary electrodes and said second set of auxiliary electrodes has a T-shaped cross- sectional profile.

18. The mass spectrometer of any one of Claims 16 and 17, wherein said DC potential is configured to provide ions with sufficient kinetic energy to overcome a potential barrier generated due to a contamination of any of said first and said second set of auxiliary electrodes.244896-9374-9380, v. 1

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