Disambiguating cyclic ion analyzer spectra

Abstract

To improve a method of operating an ion analyzer.SOLUTION: The method comprises: comparing a first set of ion data with a second set of ion data; identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining, based on the comparison, the number of passes N of a cyclic segment of an ion path taken by ions associated with the corresponding first and second ion peaks; and using the determined number of passes N to determine a physicochemical property of the ions associated with the corresponding first and second ion peaks.SELECTED DRAWING: Figure 2

Description

[Technical field]

[0001] The present invention relates to methods for analysing ions, and in particular to time-of-flight (ToF) mass analysers and ion mobility analysers. [Background technology]

[0002] In time-of-flight (ToF) and ion mobility analyzers, ions pass through a drift region of the analyzer and are eventually detected by a detector. The physicochemical properties of the ions, such as their mass to charge (m / z) ratio or ion mobility, are determined from the drift time of the ions through the drift region.

[0003] It is often desirable to increase the resolution of the analyzer in order to increase the separation of analyte ions and accurately determine their physicochemical properties, such as mass. The resolution of the instrument is limited (among other things) by the total length of the ion flight path through the analyzer.

[0004] There are several "cyclic" analysis techniques whereby ions are caused to undergo multiple repeated cycles along the ion path within the analyzer. Increasing the number of cycles N increases the length of the ion flight path that the ions take within the analyzer, thereby increasing the resolution of the analyzer.

[0005] However, during multiple cycles N through the analyzer, lighter and faster moving ions may overtake (e.g., wrap) heavier and slower moving ions, which can complicate the resulting spectrum and make it difficult to accurately determine all of the physicochemical properties of the detected ions.

[0006] It is believed that there remains room for improvement in the methods of operating ion analyzers. Summary of the Invention

[0007] A first aspect provides a method of operating an analysis instrument comprising an ion analyzer configured to analyze ions by determining a drift time of ions along an ion path, the ion path including at least a first segment and a cyclic segment, the ion path being configured such that ions pass through the first segment once and pass through the cyclic segment one or more times, the method comprising: operating the analyzer in a first mode of operation, in which (i) a first potential is provided along a first segment of an ion path, (ii) a second potential is provided along a cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a first set of ion data; operating the analyzer in a second mode of operation by varying at least one of (i) the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length; and analyzing the ions by determining drift times of the ions along the ion paths to obtain a second set of ion data; comparing the first set of ion data to the second set of ion data and identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining a number N of passes through a cyclic segment of an ion path taken by an ion associated with the corresponding first and second ion peaks; and using the determined number of passes N to determine physicochemical properties of ions associated with the corresponding first and second ion peaks.

[0008] An embodiment relates to a method of operating a cyclic ion analyzer. The analyzer is configured to analyze ions by determining (e.g., measuring) the drift time of ions along an ion path, where ions may pass a cyclic segment of the ion path multiple times before being detected. In a cyclic analyzer, ions with very different physicochemical properties (e.g., mass-to-charge ratio (m / z) or ion mobility) may have similar drift times through the analyzer, for example due to faster moving ions overtaking (e.g., wrapping) slower moving ions in the cyclic segment of the ion path. This may complicate the resulting spectrum and may make it difficult to accurately determine the physicochemical properties of the detected ions.

[0009] Embodiments provide a method for removing spectral ambiguities caused by cyclic ion analyzers: by comparing two sets of ion data acquired using different analyzer settings, as described in more detail below, the number of passes N through a cyclic segment of the ion path taken by ions contributing to an ion peak can be determined, thereby allowing the physicochemical properties of these ions to be unambiguously assigned to the ion peak.

[0010] The analytical instrument may be a mass spectrometer, an ion mobility spectrometer, or a combination of the two (e.g., a mass spectrometer including an ion mobility separator). The instrument may include an ion source. Ions may be generated from a sample in the ion source. Ions may be passed from the ion source to the analyzer via one or more ion optical devices disposed between the ion source and the analyzer.

[0011] The one or more ion optical devices may comprise any suitable configuration of one or more ion guides, one or more lenses, one or more gates, etc. The one or more ion optical devices may include one or more transport ion guides for transporting ions, and / or one or more mass selectors or filters for mass selecting ions, and / or one or more ion cooling ion guides for cooling ions, and / or one or more collision or reaction cells for fragmenting or reacting ions, etc. The one or more or each ion guide may include a multipole ion guide such as a quadrupole ion guide, a hexapole ion guide, a segmented multipole ion guide, a stacked ring ion guide, etc.

[0012] The ion analyzer is configured to analyze ions by determining the drift time of the ions along the ion path. To this end, the ion analyzer may comprise an ion injector disposed at the beginning of the ion path and an ion detector disposed at the end of the ion path. The ion injector may be configured to receive ions from an ion source via one or more ion optical devices. The ion injector may be configured to inject (receive) ions into the ion path (e.g., by accelerating the ions along the ion path), which then travel along the ion path to the detector. The ion injector may be in any suitable form, such as, for example, an ion trap, or one or more (e.g., orthogonal) accelerating electrodes. Upon reaching the detector, the ions may be detected by the detector, e.g., the arrival time of the ions may be recorded by the detector. From the measured drift times, physicochemical properties of the ions, such as the mass-to-charge ratio and / or ion mobility of the ions, may then be determined.

[0013] The ion analyzer is a cyclic analyzer. As such, the ion path includes a cyclic segment through which ions may pass multiple times (repeatedly) as they travel along the ion path (from the ion injector to the detector). The ion path also includes at least one first (non-cyclic) segment through which ions pass only once as they travel along the ion path (from the ion injector to the detector). The first segment may be immediately adjacent (i.e. directly adjacent to) the cyclic segment of the ion path. The first segment may be upstream or downstream of the cyclic segment.

[0014] The ion path may optionally comprise a second (non-cyclic) segment through which ions pass only once as they travel along the ion path (from the ion injector to the detector). The second segment may be directly adjacent (i.e. directly adjacent to) a cyclic segment of the ion path. The second segment may be upstream or downstream of the cyclic segment, for example, such that the ion path comprises a first (non-cyclic) segment, a cyclic segment disposed downstream of the first segment, and a second (non-cyclic) segment disposed downstream of the cyclic segment.

[0015] Thus, when traveling along the ion path (from the ion injector to the detector), an ion may pass through the first segment once, followed by one or more (e.g., multiple) passes through the cyclic segment, and optionally, followed by a pass through the second segment once, before being detected by the detector.

[0016] The ion analyzer may be a time-of-flight (ToF) mass analyzer configured to determine the mass-to-charge ratio (m / z) of the ions from their drift time, or an ion mobility analyzer configured to determine the ion mobility of the ions from their drift time.

[0017] In an embodiment, the analyzer is a closed-loop multi-reflection ion trap mass analyzer. The analyzer may thus comprise two ion mirrors spaced apart and facing each other in a first direction X, an ion injector for injecting ions into the space between the ion mirrors, and a detector for detecting the ions after they have completed multiple reflections between the ion mirrors. The two ion mirrors may together form an ion trap. The two ion mirrors may be configured such that ions trapped in the ion trap oscillate between the ion mirrors (in the first direction X), for example indefinitely, until they are released for detection. The entry and removal of ions into the ion trap may be controlled by applying suitable voltages to deflectors located in the region between the mirrors.

[0018] In these embodiments, the ion path may be configured such that ions make one pass through a first segment of the ion path between the injector and the deflector, then multiple passes through a cyclic segment of the ion path between the ion mirrors, and then one pass through a second segment of the ion path between the deflector and the detector.

[0019] In certain embodiments, the analyzer is a multi-reflection time-of-flight (MR-ToF) analyzer that may be configured to operate, for example, in a so-called "zoom" mode of operation. To that end, the analyzer may comprise two ion mirrors spaced apart and facing each other in a first direction X, each mirror generally elongated along a drift direction Y between a first end and a second end, the drift direction Y being orthogonal to the first direction X, an ion injector for injecting ions into a space between the ion mirrors, the ion injector being located near the first end of the ion mirrors, and a detector for detecting the ions after they have completed multiple reflections between the ion mirrors, the detector being located near the first end of the ion mirrors.

[0020] The analyzer is (i) injecting ions from an ion injector into a space between the ion mirrors, the ions completing a first cycle in which they (a) drift along a drift direction Y towards a second end of the ion mirror, (b) reverse their drift direction velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having a number K of reflections in a direction X between the ion mirrors while drifting back along the drift direction Y towards the first end of the ion mirror; (ii) reversing the drift directional velocity of the ion near the first end of the ion mirror such that the ion completes a further cycle of (a) drifting along drift direction Y towards the second end of the ion mirror, (b) reversing the drift directional velocity near the second end of the ion mirror, and (c) following a zigzag ion path having a plurality of K reflections in direction X between the ion mirrors while drifting back along drift direction Y towards the first end of the ion mirror; (iii) repeating step (ii) one or more times, and then (iv) analyzing the ions by transferring the ions to a detector for detection.

[0021] The analyzer may further comprise a deflector or lens located near the first end of the ion mirror. (i) injecting ions from an ion injector into a space between the ion mirrors, the ions completing a first cycle in which they (a) drift along a drift direction Y from a deflector or lens towards a second end of the ion mirror, (b) reverse their drift direction velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having a number K of reflections in a direction X between the ion mirrors while drifting back along the drift direction Y towards the deflector or lens; (ii) using a deflector or lens to reverse the drift direction velocity of the ions such that the ions (a) drift along a drift direction Y from the deflector or lens towards a second end of the ion mirror, (b) reverse the drift direction velocity near the second end of the ion mirror, and (c) complete a further cycle following a zigzag ion path having a number K of reflections in direction X between the ion mirrors while drifting along drift direction Y back towards the deflector or lens; (iii) repeating step (ii) one or more times, and then (iv) analyzing the ions by moving the ions through a deflector or lens to a detector for detection.

[0022] The deflector or lens may be located approximately equidistant (in the X-direction) between the first and second ion mirrors. The deflector or lens may be positioned along the ion path after the first ion mirror reflection (at the first ion mirror) that the ion beam undergoes after being injected from the injector, but before the second ion mirror reflection (at the second ion mirror). Correspondingly, the deflector or lens may be positioned along the ion path before the last ion mirror reflection (at the second ion mirror) that the ion beam undergoes before reaching the detector, but after the penultimate ion mirror reflection (at the first ion mirror).

[0023] The multi-reflection time-of-flight (MR-ToF) mass analyzer may include any suitable type of MR-ToF. For example, the analyzer may include an MR-ToF having a set of periodic lenses configured to keep the ion beam focused along its flight path, as described, for example, in A. Verenchikov et al., Journal of Applied Solution Chemistry and Modelling, 2017, 6, 1-22.

[0024] However, in certain embodiments, the analyzer is a tilted mirror type multi-reflecting time-of-flight mass analyzer, for example of the type described in U.S. Pat. No. 9,136,101, the contents of which are incorporated herein by reference. Thus, the ion mirrors may be at a non-constant distance from each other in the X direction along at least a portion of their length in the drift direction Y. The drift direction velocity of the ions towards the second end of the ion mirror may be opposed by an electric field resulting from the non-constant distance of the two mirrors from each other. This electric field may cause the ions to reverse their drift direction velocity near the second end of the ion mirror and drift back along the drift direction towards the deflector.

[0025] Alternatively, the analyzer may be a single focusing lens type multi-reflection time-of-flight mass analyzer, for example of the type described in GB Patent No. 2,580,089, the contents of which are incorporated herein by reference. Thus, the deflector may be a first deflector and the analyzer may comprise a second deflector located near the second end of the ion mirror. The second deflector may be configured to cause the ions to reverse their drift direction velocity near the second end of the ion mirror and drift back along the drift direction towards the deflector. To do this, a suitable voltage may be applied to the second deflector, for example in the manner described in GB Patent No. 2,580,089.

[0026] In an embodiment, the deflector may comprise one or more trapezoidal or prismatic electrodes disposed adjacent to the ion beam. This deflector design has a suitably wide acceptance, so that an ion beam that is relatively widely spread in the drift direction can be adequately received and deflected by the deflector. The deflector may comprise a first trapezoidal or prismatic electrode disposed above the ion beam and a second trapezoidal or prismatic electrode disposed below the ion beam. The electrodes may be angled relative to the ion beam, so that when a suitable (DC) voltage is applied to the electrodes, the resulting electric field induces a deflection of the ion beam. A suitable deflection voltage is on the order of ± a few volts, ± tens of volts, or ± hundreds of volts.

[0027] The deflector should be (and in embodiments is) configured such that it can deflect the ion beam by a desired (selected) angle. The angle at which the ion beam is deflected by the deflector may be adjustable, for example, by adjusting the magnitude of the (DC) voltage applied to the deflector. The deflector may be configured such that it can deflect the ion beam at any desired angle.

[0028] In an embodiment, the method includes injecting ions from an ion injector into a space between the ion mirrors. The ions may then be reflected off a first ion mirror and then travel to a deflector. When the ions reach the deflector, the deflector may be configured not to deflect the ion beam (or to deflect the ion beam by a suitably small angle), e.g., not to substantially change the drift directional velocity of the ions, so that the ions continue beyond the deflector and are reflected off a second ion mirror. This may include, for example, not applying or removing a voltage from the deflector (or applying a suitably small voltage to the deflector). The ions then complete a first cycle in which they (a) drift along drift direction Y from the deflector towards the second end of the ion mirror, (b) reverse their drift direction velocity near the second end of the ion mirror, and (c) drift back along drift direction Y towards the deflector while following a zigzag ion path having multiple (K) reflections in direction X between the ion mirrors.

[0029] After the ions complete this first cycle, the deflector may be used to reverse the drift direction velocity of the ions such that the ions complete a further cycle in which they (a) drift along drift direction Y from the deflector towards the second end of the ion mirror, (b) reverse the drift direction velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having multiple (K) reflections in direction X between the ion mirrors while drifting back along drift direction Y towards the deflector. To do this, the deflector may be configured such that the ion beam is deflected, e.g., such that the drift direction velocity of the ions is reversed. This may include, for example, applying a suitable voltage to the deflector during the period when the ions are expected to return to the deflector. A suitable deflection voltage to reverse the drift direction of the ions is on the order of several hundred volts.

[0030] The step of using the deflector to reverse the drift directional velocity of the ions may be repeated one or more times. Thus, the method may include causing the ions to complete multiple (N) cycles within the analyzer, in which in each cycle the ions (a) drift along a drift direction Y from the deflector toward a second end of the ion mirror, (b) reverse their drift directional velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having multiple (K) reflections in direction X between the ion mirrors while drifting back along drift direction Y toward the deflector. A first cycle may be initiated by injecting the ions into the space between the ion mirrors, and after the ions have completed the first cycle, each further cycle may be initiated by using the deflector to reverse the drift directional velocity of the ions.

[0031] The method may include moving the ions from the deflector to the detector for detection. That is, after the ions have completed a desired number (N) of cycles in the analyzer, the ions may be allowed to move from the deflector to the detector for detection. To do this, the deflector may be configured not to deflect the ion beam (or to deflect the ion beam by a suitably small angle), e.g., to not substantially change the drift directional velocity of the ions, so that the ions continue beyond the deflector, are reflected in a second ion mirror, and continue to the detector. This may include, for example, not applying or removing a voltage from the deflector (or applying a suitably small voltage to the deflector) so that the ions exit the deflector in a direction towards the detector. The ions may be reflected off one of the ion mirrors before moving to the detector.

[0032] Upon reaching the detector, the ions may be detected by the detector, e.g., the arrival time of the ions may be recorded by the detector. The flight time and / or mass to charge ratio of the ions may then be determined and, optionally, combined with flight time and / or mass to charge ratio information of other ions, e.g., to produce a mass spectrum. It should be noted that not all of the ions injected into the analyzer may be detected by the detector, e.g., due to unavoidable losses and / or detector inefficiencies at various points between the injector and the detector. Thus, as used herein, the term "ions" should be understood to mean "some, most, or all of the ions."

[0033] In these embodiments, the ion path may be configured such that ions make one pass through a first segment of the ion path between the injector and the deflector or lens, then multiple passes through a cyclic segment of the ion path between the first and second ends of the ion mirror, and then one pass through a second segment of the ion path between the deflector or lens and the detector.

[0034] The method includes first operating the analyzer in a first mode of operation, ions are analyzed (by determining the drift times of the ions along the ion paths) while the analyzer is operating in the first mode of operation to obtain a first set of ion data, then the analyzer is switched to operate in a second mode of operation, ions are analyzed (by determining the drift times of the ions along the ion paths) while the analyzer is operating in the second mode of operation to obtain a second set of ion data.

[0035] The first set of ion data may include multiple ion peaks. The number N of passes through a cyclic segment of an ion path taken by an ion associated with (i.e., giving rise to) some, most, or all of the ion peaks in the first set of ion data may be ambiguous (itself). Similarly, the second set of ion data may include multiple ion peaks, and the number N of passes through a cyclic segment of an ion path taken by an ion associated with (i.e., giving rise to) some, most, or all of the ion peaks in the second set of ion data may be ambiguous (itself). The first and second sets of ion data may be obtained, for example, by analyzing ions from the same sample (e.g., by analyzing ions generated from adjacent regions of the sample and / or by analyzing ions generated from the sample at nearby (adjacent) time points) such that ion peaks corresponding to some, most, or all of the (significant) ion peaks in the first set of ion data appear in the second set of ion data.

[0036] In a first mode of operation, (i) a first potential is provided along a first segment of the ion path, (ii) a second potential is provided along a cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length. The first potential may be a potential provided along some, most, or all of the first segment of the ion path. Similarly, the second potential may be a potential provided along some, most, or all of the cyclic segment of the ion path. The first path length may be the path length of the entire first segment. The second path length may be the path length taken by an ion in a single cycle (single loop) of the cyclic segment of the ion path.

[0037] In the second mode of operation, at least one of (i) the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length is changed relative to the first mode of operation. Thus, the method may include switching the analyzer from the first mode of operation to the second mode of operation by at least one of (i) changing the first potential, (ii) changing the second potential, (iii) changing the first path length, and (iv) changing the second path length. The changes may be made such that the effect of the changes on the drift time of the ions along the first segment is proportionally different from the effect of the changes on the drift time of the ions along the cyclic segment. Thus, for example, in certain embodiments, only one of (i) the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length is changed relative to the first mode of operation (the others do not change between the first and second modes of operation).

[0038] In certain embodiments, where the analyzer is a multi-reflecting time-of-flight (MR-ToF) mass analyzer (as described above), the method includes varying the second path length in the second mode of operation by changing the number of reflections K that the ions make between ion mirrors as they follow the zigzag ion path. This may be done by changing the angle at which the ion beam is deflected by the deflector, i.e., by changing the voltage applied to the deflector. A suitable deflection voltage shift for varying the angle of the beam in this manner is on the order of a few volts or tens of volts.

[0039] Thus, in a first mode of operation, the analyzer may be configured to make a first number K1 of reflections in direction X between the ion mirrors in each cycle while the ion (a) drifts along drift direction Y from the deflector towards the second end of the ion mirror, (b) reverses its drift direction velocity near the second end of the ion mirror, and (c) drifts along drift direction Y back towards the deflector. In a second mode of operation, the analyzer may be configured to make a second, different number K2 of reflections in direction X between the ion mirrors in each cycle while the ion (a) drifts along drift direction Y from the deflector towards the second end of the ion mirror, (b) reverses its drift direction velocity near the second end of the ion mirror, and (c) drifts along drift direction Y back towards the deflector. The first and second times may differ by a small integer amount, such as by 1, i.e., |K1-K2|=1.

[0040] In an alternative embodiment, the method includes altering some, most, or all of the first electrical potential in the second mode of operation such that in the first mode of operation the analyzer may be configured such that a first electrical potential distribution is provided along a first segment of the ion path and in the second mode of operation the analyzer may be configured such that a different electrical potential distribution is provided along the first segment of the ion path.

[0041] The first potential distribution and the different potential distribution may be different such that an electric field experienced by an ion passing along the first segment in the first mode of operation is different from an electric field experienced by an ion passing along the first segment in the second mode of operation. This difference may cause the flight time of an ion (having a particular m / z) along the first segment in the first mode of operation to be different from the flight time of an ion (having the same particular m / z) along the first segment in the second mode of operation. This difference in flight time may be dependent (e.g., proportional) to the mass-to-charge ratio (m / z) of the ion. Thus, varying the first potential between the first and second modes of operation may result in a mass-to-charge ratio dependent time-of-flight shift of an ion passing along the first segment between the first and second modes of operation.

[0042] The first potential may be varied between the two modes of operation in any suitable manner. For example, the instrument may include a flight tube disposed along at least a portion of the first segment of the ion path, and the method may include varying the first potential in the second mode of operation by varying a voltage applied to the flight tube (relative to a voltage applied to the flight tube in the first mode of operation).

[0043] Alternatively, the method may include modifying the first potential in the second mode of operation by modifying a (pulsed) accelerating field provided by the ion implanter (e.g., by modifying a (pulsed) extraction field provided within the ion implanter if the ion implanter is an ion trap). This may be done by modifying one or more (pulsed) accelerating voltages applied to one or more electrodes of the ion implanter. So, in the first mode of operation the ion implanter may be configured to accelerate ions along the ion path using a first accelerating field (one or more first accelerating voltages) and in the second mode of operation the ion implanter may be configured to accelerate ions along the ion path using a second, different accelerating field (one or more second, different accelerating voltages). Suitable accelerating fields for the ion implanter are on the order of hundreds of V / mm and suitable accelerating field shifts between the first and second modes of operation are on the order of tens of V / mm.

[0044] The method includes, for example, comparing the first set of ion data to the second set of ion data to identify a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data. The method may include identifying a plurality of such pairs of corresponding ion peaks in the first set of ion data and the second set of ion data. An ion peak may correspond to another ion peak in that the ions giving rise to the ion peak may have the same value of a physicochemical property (e.g., may be the same species).

[0045] Identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data may include identifying an ion peak having a value of a physicochemical property that is within an expected (e.g., small) range.

[0046] Alternatively, identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data can include: determining, for each ion peak of the one or more ion peaks in the first set of ion data, a first list of possible values ​​of a physicochemical property that an ion associated with that ion peak may have; determining, for each ion peak of the one or more ion peaks in the second set of ion data, a second list of possible values ​​of a physicochemical property that an ion associated with that ion peak may have; The method may include comparing the first list to the second list and identifying ion peaks in the first set of ion data that correspond to ion peaks in the second set of ion data based on the comparison, which may be done by identifying ion peaks that have an equal value or values ​​of the physicochemical property within an expected error range.

[0047] The method includes determining a number N of passes through a cyclic segment of an ion path taken by ions associated with (i.e., giving rise to) corresponding first and second ion peaks. The determination may be made based on a comparison of the first and second sets of ion data. For example, determining the number N of passes through a cyclic segment of an ion path taken by ions associated with the corresponding first and second ion peaks may include measuring a drift time difference between the first and second ion peaks and using the measured drift time difference to estimate the number N of passes through a cyclic segment of an ion path taken by ions associated with the corresponding first and second ion peaks.

[0048] The method includes determining a value of a physicochemical property of ions associated with (i.e., giving rise to) the corresponding first and second ion peaks using the determined number of passes, N. This process of determining a value of a physicochemical property of a pair of corresponding ion peaks (based on the determined value, N) may be repeated for each identified pair of corresponding ion peaks of interest.

[0049] A further aspect provides a non-transitory computer readable storage medium storing computer software code which, when executed on a processor, performs the above-mentioned method.

[0050] A further aspect provides a control system for an analytical instrument, such as a mass spectrometer and / or an ion mobility spectrometer, the control system configured to cause the analytical instrument to perform the above-mentioned method.

[0051] A further aspect provides an analytical instrument, such as a mass spectrometer and / or an ion mobility spectrometer, comprising the above-mentioned control system.

[0052] A further aspect provides an analytical instrument, such as a mass spectrometer and / or an ion mobility spectrometer, comprising: an ion analyzer configured to analyze ions by determining a drift time of ions along an ion path, the ion path including at least a first segment and a cyclic segment, the ion path being configured such that ions pass through the first segment once and through the cyclic segment one or more times; 1. A control system comprising: analyzing ions by determining drift times of ions along an ion path to obtain a first set of ion data, wherein the analyzer is operated in a first mode of operation, where (i) a first potential is provided along a first segment of the ion path, (ii) a second potential is provided along a cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length; operating the analyzer in a second mode of operation by varying at least one of (i) the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length; and analyzing the ions by determining drift times of the ions along the ion paths to obtain a second set of ion data; comparing the first set of ion data to the second set of ion data and identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining a number N of passes through a cyclic segment of an ion path taken by an ion associated with the corresponding first and second ion peaks; and determining physicochemical properties of ions associated with the corresponding first and second ion peaks using the determined number of passes N.

[0053] These aspects and embodiments may, and in embodiments do, include any one or more, or each, of the optional features described herein.

[0054] For example, the ion analyzer may be a time-of-flight (ToF) mass analyzer and the physicochemical property may be mass-to-charge ratio (m / z).

[0055] Therefore, the analyzer two ion mirrors spaced apart and facing each other in a first direction X, each mirror being elongated generally along a drift direction Y between a first end and a second end, the drift direction Y being orthogonal to the first direction X; an ion injector for injecting ions into a space between the ion mirrors, the ion injector being located near a first end of the ion mirror; A detector for detecting ions after the ions have completed multiple reflections between the ion mirrors, the detector being located near a first end of the ion mirror.

[0056] The analyzer is (i) injecting ions from an ion injector into a space between the ion mirrors, the ions completing a first cycle in which they (a) drift along a drift direction Y towards a second end of the ion mirror, (b) reverse their drift direction velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having a number K of reflections in a direction X between the ion mirrors while drifting back along the drift direction Y towards the first end of the ion mirror; (ii) reversing the drift directional velocity of the ion near the first end of the ion mirror such that the ion completes a further cycle of (a) drifting along drift direction Y towards the second end of the ion mirror, (b) reversing the drift directional velocity near the second end of the ion mirror, and (c) following a zigzag ion path having a plurality of K reflections in direction X between the ion mirrors while drifting back along drift direction Y towards the first end of the ion mirror; (iii) repeating step (ii) one or more times, and then (iv) analyzing the ions by transferring the ions to a detector for detection.

[0057] Alternatively, the analyser may be an ion mobility analyser and the physicochemical property may be ion mobility.

[0058] Various embodiments will now be described in more detail with reference to the accompanying drawings. [Brief description of the drawings]

[0059] [Figure 1] 1 illustrates a schematic diagram of an analytical instrument according to an embodiment; [Diagram 2] 1 illustrates a schematic diagram of a cyclic ion analyzer according to an embodiment; [Diagram 3] 1 illustrates a schematic of a closed-loop multi-reflecting ion trap mass analyzer according to an embodiment; [Figure 4] 1 illustrates a schematic representation of a multi-reflecting time-of-flight mass analyzer according to an embodiment; [Diagram 5] 1 illustrates a schematic representation of a multi-reflecting time-of-flight mass analyzer according to an embodiment; [Figure 6] 1 illustrates a schematic of a method for disambiguating a spectrum obtained from a cyclic ion analyzer, according to an embodiment. [Figure 7] 1 illustrates a schematic of a method for disambiguating a spectrum obtained from a cyclic ion analyzer, according to an embodiment. [Figure 8] 1 illustrates a schematic diagram of a cyclic ion analyzer according to an embodiment; [Figure 9] FIG. 1 illustrates how different m / z ions can undergo different numbers of cycles in a cyclic analyzer and the resulting convoluted time-of-flight spectra. [Figure 10A] The convoluted time-of-flight spectrum is shown. [Figure 10B] 4 shows recovered mass spectra found using a method according to an embodiment. [Figure 11] FIG. 11A shows the measured ion peak of the m / z 524 ion acquired when the instrument of FIG. 4 was operated without zoom mode, and FIGS. 11B-11D show the measured ion peak of the m / z 524 ion acquired when the instrument of FIG. 4 was operated in zoom mode. [Figure 12] 13 shows a mass spectrum of a calibration solution acquired using zoom mode, according to an embodiment. [Figure 13] 1 illustrates data from a disambiguation method according to an embodiment. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0060] 1 illustrates a schematic diagram of an analytical instrument that may be operated in accordance with an embodiment. The analytical instrument may be a mass spectrometer (which may optionally include an ion mobility separator) or an ion mobility spectrometer. As shown in FIG. 1, the analytical instrument includes an ion source 10, one or more ion transmission stages 20, and an analyzer 30.

[0061] The ion source 10 is configured to generate ions from a sample. The ion source 10 may be any suitable continuous or pulsed ion source, such as an electrospray ionisation (ESI) ion source, a MALDI ionisation source, an atmospheric pressure ionisation (API) ionisation source, a plasma ionisation source, an electron ionisation source, a chemical ionisation source, etc. In some embodiments, two or more ion sources may be provided and used. The ions may be any suitable type of ion to be analysed, for example small and large organic molecules, biomolecules, DNA, RNA, proteins, peptides, fragments thereof, etc.

[0062] The ion source 10 may optionally be coupled to a separation device, such as a liquid chromatography or capillary electrophoresis separation device (not shown), whereby the sample that is ionized in the ion source 10 comes from the separation device.

[0063] The ion transport stage 20 is disposed downstream of the ion source 10 and may include an atmospheric pressure interface, as well as one or more ion guides, lenses and / or other ion optical devices configured to enable some or all of the ions generated by the ion source 10 to be transported from the ion source 10 to the analyzer 30. The ion transport stage 20 may include any suitable number and configuration of ion optical devices, for example, optionally including any one or more of one or more RF and / or multipole ion guides, one or more ion guides for cooling ions, one or more mass selective ion guides, etc.

[0064] The analyzer 30 is disposed downstream of the ion transport stage 20 and is configured to receive the ions from the ion transport stage 20. The analyzer is configured to analyze the ions to determine physicochemical properties of the ions, such as their mass to charge ratio, mass, ion mobility and / or collision cross section (CCS). To do this, the analyzer 30 is configured to pass the ions along an ion path in the analyzer 30 and measure the time it takes the ions to pass along the ion path (drift time). To that end, the analyzer 30 may comprise an ion detector disposed at the end of the ion path, the analyzer configured to record the arrival time of the ions at the detector. The instrument may be configured to determine the physicochemical properties of the ions from the measured drift times. The instrument may be configured to produce a spectrum of the analyzed ions, such as a mass spectrum or an ion mobility spectrum.

[0065] In certain embodiments, the analyzer 30 is a time-of-flight (ToF) mass analyzer, e.g., configured to determine the mass-to-charge ratio (m / z) of ions by passing the ions along an ion path in a drift region of the analyzer, which is maintained in a high vacuum (e.g., <1×10 -5 The electric field is maintained at a pressure of 1000 psi (mbar). The ions may be accelerated into the drift region by the electric field and may be detected by an ion detector located at the end of the ion path. The acceleration may cause ions with a relatively low mass to charge ratio to achieve a relatively high velocity and reach the ion detector before ions with a relatively high mass to charge ratio. The ions therefore arrive at the ion detector after a time determined by their velocity and the length of the ion path, thereby allowing the mass to charge ratio of the ion to be determined. Each ion or group of ions that arrive at the detector may be sampled by the detector and the signal from the detector may be digitized. A processor may then determine a value indicative of the time of flight and / or mass to charge ratio ("m / z") of the ion or group of ions. Data for multiple ions may be collected and combined to generate a time of flight ("ToF") spectrum and / or a mass spectrum.

[0066] In an alternative embodiment, the analyzer 30 is an ion mobility analyzer and is configured to determine the ion mobility of ions, for example, by passing ions along an ion path in a drift region of the analyzer, with a buffer gas provided in the drift region. The ions may be forced through the buffer gas by an electric field (or the ions may be forced through the drift region by a gas flow arranged such that the electric field opposes the gas flow) and detected by an ion detector arranged at the end of the ion path. Ions with relatively high mobility will reach the ion detector before ions with relatively low mobility. As such, the ions may separate according to their ion mobility and may reach the ion detector after a time determined by their ion mobility. Each ion or group of ions that reaches the detector may be sampled by the detector and the signal from the detector may be digitized. The processor may then determine a value indicative of the drift time and / or ion mobility of the ion or group of ions. Data for multiple ions may be collected and combined to generate a drift time spectrum and / or an ion mobility spectrum.

[0067] The analyzer 30 may also comprise an ion mobility separator coupled to a mass analyzer, for example a mass analyzer provided at the end of the ion mobility portion of the ion path. In these embodiments, any suitable type of mass analyzer may be provided, for example a time-of-flight mass analyzer or an electrostatic ion trap mass analyzer such as an electrostatic orbital trap, more particularly an Orbitrap™ FT mass analyzer manufactured by Thermo Fisher Scientific.

[0068] 1 is merely schematic, and the analysis instrument can, and in embodiments does, include any number of one or more additional components. For example, in some embodiments the analysis instrument includes a collision or reaction cell for fragmenting or reacting ions, and the ions analyzed by the analyzer 30 can be fragment or product ions resulting from fragmenting or reacting parent ions produced by the ion source 10.

[0069] 1, the instrument is under the control of a control unit 50, such as a suitably programmed computer, which controls the operation of the various components of the instrument, including the analyzer 30. The control unit 50 may also receive and process data from the various components, including the detector according to embodiments described herein.

[0070] According to various embodiments, the analyzer 30 is a cyclic analyzer. As such, the ion path within the analyzer 30 is comprised of at least a first portion and a second cyclic portion, and the ion path is configured such that ions traveling along the ion path pass through the first portion only once and pass through the second cyclic portion one or more times (e.g., multiple times) before being detected. This is illustrated diagrammatically in FIG.

[0071] As shown in FIG. 2, the analyzer 30 includes an ion path 32 disposed between an ion injector 31 and an ion detector 33. The ion injector 31 is configured to inject ions into the ion path 32, and the ions travel along the ion path 32 and are detected by a detector 33 disposed at the end of the ion path 32. As shown in FIG. 2, the ion path 32 is composed of a first segment 32a, a second cyclic segment 32b, and a third segment 32c. An ion traveling along the ion path 32 between the ion injector 31 and the ion detector 33 passes through the first segment 32a only once, then passes through the second cyclic segment 32b one or more times (e.g., multiple times), and then passes through the third segment 32c only once. The ion path 32 may include any number of additional segments. Also, the ion path may include only one of the first segment 32a and the third segment 32c.

[0072] It will be appreciated that the cyclic analyzer advantageously makes it possible to increase the length of the ion path 32 taken by ions within the analyzer 30 (between the injector 31 and the detector 33), thereby increasing the resolution of the analyzer 30.

[0073] The cyclic analyzer 30 may comprise any suitable cyclic ion analyzer having an ion path 32 configured to allow ions to traverse a cyclic segment 32b of the ion path multiple times before being detected. Thus, for example, the analyzer 30 may be a cyclic time-of-flight (ToF) mass analyzer, a cyclic ion mobility analyzer, or a cyclic ion mobility separator coupled to a mass analyzer. Figures 3-5 illustrate various exemplary embodiments of the cyclic analyzer 30.

[0074] FIG. 3 illustrates generally in detail a closed multi-reflecting ion trap time-of-flight mass analyzer according to a first exemplary embodiment of an analyzer 30 .

[0075] As shown in Fig. 3, the analyzer comprises a pair of ion mirrors 34, 35 facing each other and forming together an ion trap. The ion mirrors 34, 35 are configured such that ions trapped in the ion trap oscillate between them on an infinitely extended (cyclic) ion path 32b until they are released. Ions can be introduced into the ion trap from an ion source (injector) 31 and are eventually detected by an ion detector 33. In the embodiment shown in Fig. 3, the entry and removal of ions into the ion trap is controlled by applying suitable voltages to a deflector 36 located in the region between the mirrors 34, 35. Alternatively, the entry and removal of ions can be achieved by one or both of the ion mirrors 34, 35 being switchable between a trapping mode and a transmission mode.

[0076] In the embodiment shown in FIG. 3, the ion path 32 is configured such that ions pass once through a first segment 32a of the ion path (between the injector 31 and the deflector 36), then pass multiple times through a second cyclic segment 32b of the ion path (between ion mirrors 34, 35), and then pass once through a third segment 32c of the ion path (between the deflector 36 and the detector 33).

[0077] In this type of cyclic analyzer, ion flight times can be several milliseconds long, and therefore resolution can typically reach >100,000, or even >500,000. However, space charge within the confined volume can degrade analyzer performance due to strong coalescence effects.

[0078] 4 and 5 illustrate schematic details of further exemplary embodiments of the analyzer 30. In these embodiments, the analyzer 30 is a multi-reflecting time-of-flight (MR-ToF) mass analyzer capable of operating in a so-called multi-pass "zoom" mode of operation.

[0079] 4 and 5, the multi-reflecting time-of-flight analyzer 30 includes a pair of opposing ion mirrors 34, 35 spaced apart in a first direction X. The ion mirrors 34, 35 are elongated along an orthogonal drift direction Y between first and second ends.

[0080] An ion source (injector) 31, which may be in the form of an ion trap, is located at one end (first end) of the analyzer. The ion source 31 may be arranged and configured to receive ions from the ion transport stage 20. Ions may be accumulated in the ion source 31 before being injected into the space between the ion mirrors 34, 35. As shown in Figures 4 and 5, ions may be injected from the ion source 31 with a relatively small injection angle or drift directional velocity, producing zigzag ion trajectories, whereby different oscillations between the mirrors 34, 35 are spatially separated. Compared to the analyzer of Figure 3, this has the effect of reducing space charge effects in the analyzer.

[0081] One or more lenses and / or deflectors may be positioned along the ion path between the ion source 31 and the ion mirror 35 where the ions are first encountered. For example, as shown in Figures 4 and 5, a first out-of-plane lens 37, an injection deflector 38, and a second out-of-plane lens 39 may be positioned along the ion path between the ion source 31 and the ion mirror 35 where the ions are first encountered. Other configurations are possible. In general, the one or more lenses and / or deflectors may be configured to suitably condition, focus, and / or deflect the ion beam, i.e., so that the ion beam takes a desired trajectory through the analyzer.

[0082] The analyzer also includes another deflector 36 positioned along the ion path between the ion mirrors 34, 35. As shown in Figures 4 and 5, the deflector 36 may be positioned approximately equidistant along the ion path between the ion mirrors 34, 35 after its first ion mirror reflection (at ion mirror 35) and before its second ion mirror reflection (at the other ion mirror 34).

[0083] The analyzer also includes a detector 33. The detector 33 may be any suitable ion detector configured to detect ions and, for example, record the intensity and arrival time associated with the arrival of the ions at the detector. Suitable detectors include, for example, one or more conversion dynodes, optionally followed by one or more electron multipliers, etc.

[0084] In its "normal" mode of operation, ions are injected from the ion source 31 into the space between the ion mirrors 34, 35 such that ions take a zigzag ion path with multiple reflections in the X direction between the ion mirrors 34, 35 while (a) drifting along drift direction Y from the deflector 36 towards the opposite (second) ends of the ion mirrors 34, 35, (b) reversing their drift direction velocity near the second ends of the ion mirrors 34, 35, and (c) drifting back along drift direction Y towards the deflector 36. The ions may then be transferred from the deflector 36 to the detector 33 for detection.

[0085] In the analyzer of Fig. 4, both ion mirrors 34, 35 are tilted with respect to the X direction and / or the drift Y direction. Alternatively, it is possible to tilt only one of the ion mirrors 34, 35, for example placing the other one parallel to the drift Y direction. In general, the ion mirrors are at a non-constant distance from each other in the X direction along their length in the drift direction Y. The drift direction velocity of the ions towards the second end of the ion mirror is opposed by an electric field resulting from the non-constant distance of the two mirrors from each other, which causes the ions to reverse their drift direction velocity near the second end of the ion mirror and drift back along the drift direction towards the deflector.

[0086] The analyzer shown in Figure 4 further comprises a pair of correction stripe electrodes 40. Ions travelling down the drift length are slightly deflected each time they pass the mirrors 34, 35, and the additional stripe electrodes 40 are used to correct time-of-flight errors caused by changes in the distance between the mirrors. For example, the stripe electrodes 40 can be electrically energised such that the period of ion oscillation between the mirrors is substantially constant along the entire drift length (despite the fact that the distance between the two mirrors is not constant). The ions are eventually reflected back down the drift space and focused onto the detector 33.

[0087] Further details of the tilted mirror multi-reflecting time-of-flight mass analyzer of FIG. 4 are described in US Pat. No. 9,136,101, the contents of which are incorporated herein by reference.

[0088] In the analyzer of Figure 5, the ion mirrors 34, 35 are parallel to each other. In this embodiment, the analyzer includes a second deflector 41 at the second end of the ion mirrors 34, 35 to cause the ions to reverse their drift direction velocity near the second end of the ion mirror and drift back along the drift direction towards the deflector.

[0089] Also, as shown in Figure 5, in this embodiment a lens may be included in the implant deflector 38 and / or the deflector 36. The ion beam may then expand its short path into the analyzer before impinging on the long focal lens, which has the effect of focusing the ion beam along its length. The lens may be an elliptical drift focusing lens mounted in the deflector 36. A second deflector 41, which may include a lens, is used to reverse the beam direction while maintaining control of the focal properties.

[0090] Further details of the single lens multi-reflecting time-of-flight mass analyser of Figure 5 are described in UK Patent No. 2,580,089, the contents of which are incorporated herein by reference.

[0091] In the analyzers shown in Figures 4 and 5, the ion beam is allowed to spread relatively widely (in the drift direction Y) over most of its flight path. This is in contrast to multi-reflection time-of-flight (MR-ToF) mass analyzers that use a set of periodic lenses to focus the ion beam along its entire flight path, as described, for example, in A. Verenchikov et al., Journal of Applied Solution Chemistry and Modelling, 2017, 6, 1-22. An important advantage of allowing the ion beam to spread widely over most of its flight path is that space charge effects are reduced, which can be a significant issue for time-of-flight analyzers. Nevertheless, the embodiments described herein are also applicable to other MR-ToF analyzer designs, such as Verenchikov-type MR-ToF analyzers.

[0092] In the embodiment shown in Figures 4 and 5, the fact that the ion beam is relatively wide in the drift dimension Y means that the deflector 36 should be able to accommodate such a wide beam without introducing clipping or non-uniform deflection. A suitable deflector design is a trapezoidal or prismatic deflector. As such, the deflector 36 may comprise a trapezoidal or prismatic electrode located above the ion beam and another trapezoidal or prismatic electrode located below the ion beam. The electrodes may be angled with respect to the ion beam. Ions may experience a relatively strong electric field at the edges of the angled electrode, inducing deflection. The electrodes may be located out of the plane of deflection, thereby allowing the electrodes to be easily made wide enough to accommodate a wide ion beam (at least compared to more conventional deflection plates that would be located on either side of the beam).

[0093] In an embodiment, the multi-reflecting time-of-flight (MR-ToF) mass analyzer is operated in a multi-pass "zoom" (cyclic) mode of operation. Ions are made to cycle multiple times in the drift direction Y within the analyzer. Increasing the number of cycles N increases the length of the ion path that the ions take within the analyzer (between the injector and the detector), thereby increasing the resolution of the analyzer. In a Verenchikov analyzer, this can be done by controlling the voltage to the entrance lens. In the case of the analyzer shown in Figures 4 and 5, the deflector 36 at the front of the analyzer, which is usually used to reduce the injection angle and / or optimize the number of oscillations (K) in one drift pass, can also be used to reverse the drift direction velocity of the ions to make them complete additional cycles through the analyzer.

[0094] Thus, in a multi-pass "zoom" (cyclic) mode of operation, ions are made to complete multiple (N) cycles within the analyzer, in which, in each cycle, the ions drift in a drift direction Y from the deflector 36 (or entrance lens) towards the opposite (second) ends of the ion mirrors 34, 35 and then return to the deflector 36 (or entrance lens). In each cycle, the ions also complete multiple (K) reflections in the X direction between the ion mirrors. Thus, in each cycle, the ions take a zigzag ion path 32b through the space between the ion mirrors 34, 35.

[0095] In the analyzer shown in Figures 4 and 5, the first cycle may begin by injecting ions from the injector 31 into the space between the ion mirrors 34, 35. The ions may be reflected by one of the ion mirrors 35 and then travel to the deflector 36. No voltage may be applied to the deflector 36 (or a suitable (e.g., relatively small) voltage may be applied to the deflector) so that the ions exit the deflector 36 in a direction toward the second end of the ion mirror. In the presence of the deflector 36, the ions take a zigzag ion path 32b with multiple (K) reflections in direction X between the ion mirrors 34, 35 while (a) drifting along a drift direction Y from the deflector 36 toward the second end of the ion mirror, (b) reversing the drift direction velocity near the second end of the ion mirror, and (c) drifting back along the drift direction Y toward the deflector 36.

[0096] After the ions have completed this first cycle, each further cycle is initiated by using the deflector 36 to reverse the drift directional velocity of the ions (near the first end of the ion mirror). To do this, an appropriate voltage may be applied to the deflector 36 that causes the ions to exit the deflector 36 with a drift directional velocity opposite to the drift directional velocity with which they originally entered the deflector 36.

[0097] After the ions have completed a desired number (N) of cycles within the analyzer, the ions are allowed to travel from the deflector 36 to the detector 33 for detection. To do this, the voltage may be removed from (or a suitable voltage may be applied to) the deflector 36 such that the ions exit the deflector 36 in a direction towards the detector 33. The ions may be reflected off the (other) one of the ion mirrors 34 before traveling to (and being detected by) the detector 33.

[0098] In the embodiment shown in Figures 4 and 5, the ion path is configured such that ions pass once through a first segment 32a of the ion path (between the injector 31 and the deflector 36 via the ion mirror 35), then pass multiple times through a second cyclic segment 32b of the ion path (between the deflector 36 and the deflector 36 via the opposite (second) ends of the ion mirrors 34, 35), and then pass once through a third segment 32c of the ion path (between the deflector 36 and the detector 33 via the other ion mirror 34).

[0099] 3-5 illustrate an exemplary embodiment of a cyclic analyzer 30, it will be appreciated that various alternative embodiments are possible. For example, the analyzer 30 may instead be a cyclic ion mobility analyzer or a cyclic ion mobility separator coupled to a mass analyzer.

[0100] In these embodiments, the cyclic ion mobility analyzer or separator may comprise a closed loop ion separator, for example of the type described in UK Patent Application No. 2,562,690. Ions may be separated according to their ion mobility over a fixed integer number of cycles around the ion mobility separator. Gates may be provided that may be closed to allow multiple pass operation. Gates may be opened to allow ions to exit the ion mobility separator after they have made one or more circuits of the ion mobility separator. Using a cyclic ion mobility separator may allow higher separation and therefore higher ion mobility resolution.

[0101] In these embodiments, the ion path may be configured such that ions pass once through a first segment of the ion path (before the closed-loop ion separator), then pass multiple times through a second cyclic segment of the ion path (within the closed-loop ion separator), and then pass once through a third segment of the ion path (after the closed-loop ion separator).

[0102] A common advantage among various types of cyclic analyzers in which ions are caused to cycle repeatedly a number N of times along an ion path within the analyzer is that increasing the number of cycles N increases the length of the ion path taken by the ions within the analyzer, thereby increasing the resolution of the analyzer.

[0103] However, a common problem is that faster moving (e.g. lighter) ions may overtake (e.g. wrap) slower moving (e.g. heavier) ions during multiple cycles N through the analyzer. This complicates the resulting spectrum and can make it difficult to accurately determine the desired physicochemical properties (e.g. m / z or ion mobility) of all detected ions because the number of cycles N taken by each ion peak in the spectrum becomes ambiguous.

[0104] Thus, embodiments provide a method for removing spectral ambiguities caused by cyclic ion analyzers: by comparing two sets of ion data obtained under different analyzer settings, the number of passes N through the cyclic segment 32b of the ion path 32 taken by ions contributing to an ion peak can be determined, thereby allowing the physicochemical properties of those ions to be unambiguously determined and assigned to the ion peak.

[0105] Although some of the following discussion is described with respect to the MR-ToF analyzer of Figures 4 and 5, those skilled in the art will understand that similar considerations may apply to various other types of cyclic analyzers, such as cyclic ToF analyzers and cyclic ion mobility separators.

[0106] For example, the ion path shown in Figures 4 and 5 is made up of all ions with mass-to-charge ratios ranging from (m / z)1 to (m / z)2. The deflector 36 is switched from mode 1 (deflection from the ion source 31 to the loop), to mode 2 (deflection from the loop back to the loop), and finally to mode 3 (deflection from the loop to the detector 33). The switching times are t 12 and t 23 Time zero is assumed to be the instant of injection.

[0107] The initial switch between mode 1 and mode 2 should be done so that the heaviest ion (m / z) 2 is not earlier than its first pass through the deflector 36, and the lightest ion (m / z) 1 is not later than a0+K oscillations, where K is the number of oscillations per loop (between the next pass through the deflector 36) and a0 represents the fraction of the oscillation before the first pass through the ion source 31 and the deflector 36. Otherwise the lightest ion will not be properly set for the next loop. This gives rise to the double inequality.

number

number

[0108] The second switch from mode 2 to mode 3 should be made so that the heaviest ion does not oscillate faster than a0+(N-1)K times, where N is the number of loops intended. Otherwise, the heaviest ion will exit the loop before all loops have been built up. On the other hand, the second switch should be made so that the lightest ion does not oscillate faster than a0+NK times, otherwise this ion will remain in the analyzer for the next undesired loop. This double inequality is expressed as follows:

number

[0109] Both inequalities (a) and (b) impose an upper bound on the ratio of T2 and T1, t 12 and t 23 , where the constraint from (b) is stronger (lower) than the constraint from (a) for any N>1.

number

[0110] Because the time of flight is proportional to the square root of m / z, this inequality translates directly to the maximum unambiguous mass range (UMR):

number

[0111] To achieve perfect UMR, the switching time t 23 should be as follows:

number

[0112] The first switching time leaves some freedom to be defined. For example, its minimum possible value t 12 = a0T2, which allows the lightest ions to ripple electrons before reaching the deflector for the next time.

[0113] Table 1 shows a simulation of a mass analyzer with an effective oscillation distance of 1.25 m and 20 oscillations per loop. The resolution is calculated in terms of the peak full width at half maximum. The decay in m / z range is quite noticeable as the number of loops increases.

[0114] [Table 1]

[0115] The m / z range of ions entering the analyzer 30 may be restricted, for example through the use of switchable deflectors, mass filters (e.g. quadrupole mass filters), or otherwise to roughly match their m / z range to the UMR of the zoom method, thereby removing ambiguity in the m / z assignments. However, this is fairly wasteful of ion transmission, and to maintain sensitivity, a more efficient method may be preferred.

[0116] Therefore, disambiguation of complex spectra according to embodiments is generally preferred, whereby the correct number of drift reflections is assigned to each ion peak, from which the correct m / z of each ion peak is determined.

[0117] One possible approach to disambiguation would be to directly assign an accurate cycle number N to each ion peak based on the resolution of that peak. From the resolution shifts observed in Table 1, this seems to be a rather attractive approach at first. Similarly, m / z-dependent characteristics (such as single ion detector response, spacing between different charge states, isotopes, or common fragmentation pathways such as ammonia or water loss) can be used to pre-assign approximate m / z to individual ion peaks and thus cycle numbers. Comparisons with survey scans without zoom mode are also possible, especially in MR-ToF analyzers with drift separation, where even survey scans have very high resolution and mass accuracy. However, in practice, these approaches are significantly complicated by space charge effects for strong ion peaks and statistical problems for small ion peaks.

[0118] According to an embodiment, disambiguation of a cyclic analyzer spectrum (such as a ToF mass analyzer spectrum or an ion mobility analyzer spectrum) is performed by varying the flight time differently on ion path segments that are either included (32b) or not (32a, 32c) within the repeat loop.

[0119] As used herein, "effective ion path" is defined as the product of flight time and ion velocity under a nominal accelerating voltage. The effective ion path can be changed by directly changing the ion path length or by changing the voltage, which changes the flight time.

[0120] Referring again to FIG. 2, the effective ion path along the entire ion trajectory 32 consists of three parts:

number

[0121] Effective ion path L0, L m When L0 + L1 are proportionally modified, the measured flight time changes by the same percentage for each ion, regardless of how many loops N the ion makes. However, if L m ΔL m When we change the time of flight by Δt, the time of flight is corrected by Δt in the following ratio:

number

number

[0122] The sum L0+L1 is changed by ΔL0, and L m In the other case where θ is unchanged, the relative time-of-flight shift becomes

number

number

[0123] Thus, in both cases, the number of loops N can be determined based on the time shift Δt measured for the ion peak detected at a moment t after injection. If the number of oscillations N is known, the flight time t can be converted to mass-to-charge ratio (or ion mobility) using a normal transformation.

[0124] Thus, in an embodiment, a first set of ion data is acquired when operating the analytical instrument in a first mode of operation, and a second set of ion data is acquired when operating the analytical instrument in a second, different mode of operation. The first and second sets of ion data may be acquired by analyzing ions from the same sample (e.g., by analyzing ions generated from adjacent regions of the sample and / or by analyzing ions generated from the sample at close (adjacent) time points), such that ion peaks corresponding to some, most, or all of the (significant) ion peaks in the first set of ion data appear in the second set of ion data.

[0125] The first and second operating modes differ with respect to at least one parameter of the analyzer 30. In practice, the ion path 32 of the analyzer is separated into two regions, one region in which the flight path 32b is affected by a number of passes N, and at least one region 32a, 32c is unaffected. A parameter change is applied between the two operating modes, which changes the drift time through one of these segments disproportionately with respect to the other. Thus, the proportional change in drift time depends on the number of passes N that an ion makes through the cyclic segment 32b. In an embodiment, the loop L m Either the effective ion path within the loop L0+L1 is changed between the two modes of operation, or the effective ion path outside the loop L0+L1 is changed between the two modes of operation.

[0126] The effective ion path can be changed by directly changing the ion path length or by changing a voltage that changes the flight time. Thus, in a first mode of operation, (i) a first potential is provided along a first segment 32a, 32c of the ion path, (ii) a second potential is provided along a cyclic segment 32b of the ion path, (iii) the first segment 32a, 32c of the ion path has a first path length, and (iv) the cyclic segment 32b of the ion path has a second path length. In a second mode of operation, at least one of (i) the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length is changed relative to the first mode of operation, e.g., to change the length of the loop L. m One of the effective ion path within and the effective ion path outside of the loop L0+L1 is altered for the first mode of operation.

[0127] This parameter change will induce a time shift Δt for each ion peak between the two sets of ion data. Therefore, the first set of ion data is compared to the second set of ion data to identify corresponding (matching) ion peaks. For each identified ion peak pair of interest, the time shift Δt for that ion peak pair between the two sets of data is measured. The number of loops N for each peak is then estimated (e.g., using the formula above) from the measured time shift Δt, and N is used to calculate the mass-to-charge ratio (or other physicochemical property) of the ion corresponding to the ion peak.

[0128] Effective ion path in the loop L m Various exemplary embodiments for altering either the effective ion path outside of loop L0+L1 or the effective ion path outside of loop L0+L1 are described below, however, it will be appreciated that various alternatives are possible depending, for example, on the particular design of the cyclic ion analyzer 30.

[0129] In the first exemplary embodiment, the path length of the cyclic segment 32b of the ion path is altered between the first and second modes of operation.

[0130] In the multiple reflection analyzer of Figures 4 and 5, the effective length of the loop can be changed by varying the number of reflections K between the ion mirrors 34, 35 made by an ion per cycle, i.e., by changing the number of reflections K in the X direction made by an ion as it (a) drifts along drift direction Y from the deflector 36 towards the second end of the ion mirror, (b) reverses its drift direction velocity near the second end of the ion mirror, and (c) drifts back along drift direction Y towards the deflector 36. This can be done by suitably changing the voltage applied to the deflector 36 between the two modes of operation, i.e., so that the ions exit the deflector 36 at a slightly different angle between the two modes of operation. A suitable voltage shift is on the order of a few volts or tens of volts. In the case of the tilted mirror analyzer of Figure 4, the change in K can also or instead be done by adjusting the voltage applied to the stripe electrodes 40.

[0131] In an embodiment, the number of reflections K between the ion mirrors 34, 35 is varied by ±1 between the two modes of operation and the corresponding time shift Δt is measured for each ion peak. Because the number of passes N is small (typically <6), the time shift Δt can be measured with reasonable accuracy and the exact number of loops N can be determined by rounding (eq.Na) to the nearest integer.

[0132] Loop L m The effective length of is proportional to K, which means that when the number of vibrations K increases by 1, the relative change ΔL m / L m = 1 / K. In this case, the equation eq.Na becomes:

number

[0133] Table 2 shows an example of this disambiguation algorithm applied to the ToF spectrum of a Flexmix calibration mixture. Low m / z ions were set to reach the detector after making up N=2 loops, each loop containing K1=21 oscillations. The corresponding flight times are shown in the first column. However, some ions with higher m / z (mainly Ultramark ions) make up another loop, N=3, due to their lower propagation speed. In order to assign the correct number of loops to each peak, the system was put into a mode with K2=22 oscillations in each loop and the corresponding flight times for each of the peaks were detected. These are shown in the second column. Applying the equation (eq.N.dk), N was calculated from the flight time difference. * The values ​​of m / z were estimated and rounded to the nearest integer. Finally, the m / z ratio was calculated by the following formula:

number

[0134] [Table 2]

[0135] In an embodiment, N * The decimal part of is due to the limited accuracy of the calibration. Nevertheless, the rounded value N * It is clear to assign an integer N as . The fewer loops that need to be distinguished from one another, the more reliable the disambiguation procedure.

[0136] The advantage of the above-mentioned "zoom" mode in the analyzer of FIG. 4 or FIG. 5 is that the analyzer has a relatively long optical path length L m The advantage of having a large drift area (tens of meters) and a relatively small number of loops (N=1.5) is that the 15× m / z range provided by the ion source 10 can be achieved with a zoom mode configured to give the highest m / z ions two drift passes (N=2), which means that the lowest m / z ions get four passes (N=4), such that the only ambiguity is whether an ion gets N=2, 3 or 4 passes.

[0137] Figure 6 is a flow chart illustrating a disambiguation method according to these embodiments. As shown in Figure 6, in this method, a first mass spectrum and a second mass spectrum are acquired by operating the analyzer with different ion oscillations (numbers K and K+1) per cycle through the analyzer (step 60). Corresponding pairs of ion peaks in the two spectra are then identified (step 61), and the number of passes N through the cyclic segment of the ion path taken by the ion associated with each pair of corresponding ion peaks is estimated (step 62). Finally, N is used to calculate the true m / z of the ion (step 63).

[0138] Another approach to determining the number of loops from the flight time under different oscillations per loop, K, is to calculate a list of possible mass-to-charge ratios for each ion peak (from eq.mz) under different assumptions about the possible number of loops, N. This can be done for several possible values

number

number

number

[0139] As illustrated in Tables 3A and 3B, only one candidate N gives a close candidate for m / z under different values ​​of K. These candidate values ​​are assumed to be correct, and all other m / z calculated with other assumptions about the number of loops are discarded as incorrect.

[0140] [Table 3]

[0141] FIG. 7 is a flow chart illustrating a disambiguation method according to these embodiments. As shown in FIG. 7, in this method, a first mass spectrum and a second mass spectrum are acquired by operating the analyzer with different numbers of ion oscillations (K and K+1) per cycle through the analyzer (step 70). Pairs of corresponding ion peaks are identified (step 71). For each candidate value of N (step 72), a candidate m / z value is calculated for each peak (step 73). In this way, a list of possible m / z values ​​is generated for each ion peak of interest. Matched pairs of ion peaks between the two spectra are then identified to determine the exact N for each pair of corresponding ion peaks (step 74). Finally, the unambiguous m / z of each matched pair of ion peaks is determined and assigned to each ion peak (step 75).

[0142] In some embodiments, it may be beneficial to use more than two values ​​of K, at the expense of overall acquisition speed, since some peaks may disappear due to a shift in K, e.g., due to ions being in the deflector 36 during voltage switching. The disappearance of ion peaks in a spectrum can also or instead be used to provide information for disambiguation, since the missing m / z values ​​can be calculated based on deflector size, switching speed / time, etc.

[0143] In general, embodiments may include analyzing ions in a third mode of operation (by determining the drift time of the ions along the ion path) to obtain a third set of ion data, where at least one of (i) the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length is varied relative to the first and second modes of operation, comparing the third set of ion data to the first and / or second set of ion data, and determining, based on the comparison, the number of passes N through a second portion of the ion path taken by an ion associated with a corresponding ion peak.

[0144] In a second exemplary embodiment, disambiguation is performed by comparing the time of flight between two spectra in which the non-reflective segments of the flight path have been altered by varying the potential of the non-reflective segments of the flight path.

[0145] FIG. 8 shows diagrammatically a simplified (e.g. MR-ToF) analyzer layout incorporating a short section of a flight tube 80 before the detector 33. The flight tube 80 can be easily incorporated into the detector configuration as part of a so-called post-accelerator, for example comprising an array of suitably biased electrodes configured to accelerate ions onto a conversion dynode. The flight tube 80 allows the potential to be changed to shift the flight time of ions in the non-reflected segment of the ion path 32c before the detector 33. FIG. 8 also shows the separation of the ion flight path 32 into several sections, the injection L0, the reflected portion L1, the injection L2, the reflection L3, the reflection L4, the reflection L5, the reflection L6, the reflection L7, the reflection L8, the reflection L9, the reflection L10, the reflection L11, the reflection L22, the reflection L12, the reflection L13, the reflection L14, the reflection L15, the reflection L16, the reflection L17, the reflection L18, the reflection L19, the reflection L21, the reflection L22, the reflection L23, the reflection L24, the reflection L25, the reflection L26, the reflection L27, the reflection L28, the reflection L29, the reflection L31, the reflection L22, the reflection L32, the reflection L33, the reflection L14, the reflection L25, the reflection L26, the reflection L31, the reflection L15, the reflection L26, the reflection L27, the reflection L32, the reflection L16, the reflection L28, the reflection L29, the reflection L31, the reflection L17, the reflection L21, the reflection L22, the reflection L33, the reflection L18, the reflection L21, the reflection L22, the reflection L33, the reflection L14, the reflection L25, the reflection L16, the reflection L26, the reflection L27, the reflection L28, the reflection L m , and the built-in flight tube L t FIG. 1 shows the extraction to a detector L1 having a

[0146] The time-of-flight shift caused by the voltage v applied to the flight tube 70 is

number

[0147] In the schematic diagram of FIG. 8, an ion with mass to charge ratio μ=m / z arrives at the second mirror at the following instant:

number

number

number

number

[0148] When the number of cycles N decreases stepwise with the mass-to-charge ratio μ, the function t D (μ) is non-monotonic. This is because the ToF spectrum t D (μ) is ambiguous, and t D This means that a peak located at may correspond to several different mass to charge ratios μ.

[0149] An interval of μ corresponding to a particular integer N(μ) is called a distinct mass interval. For N cycles, the corresponding distinct interval is M N+1 ~M N The range is.

number

[0150] The distinct mass ranges are correspondingly as follows:

number

[0151] A laser diode of length L is positioned between the second mirror and the detector 33 and is energized with a voltage v ≪ ε0. t Consider a short flight tube 80 with a voltage applied. When a voltage is applied, the peak appears shifted by

number

[0152] As v ≪ ε 0 , the peak width does not broaden significantly and the centroid shift is measurable, which allows us to estimate the inverse ion velocity and mass-to-charge ratio μ as

number

[0153] Although the accuracy is low, it is sufficient to determine the cycle number N for a particular peak. For this purpose, the estimated value μ * , the formula (Nμ)

number

number

[0154] The exact μ is then determined as follows:

number

[0155] Thus, in these embodiments, a first set of ion data is acquired when operating the analytical instrument in a first mode of operation, and a second set of ion data is acquired when operating the analytical instrument in a second mode of operation in which the potential along the first (and / or third) segment 32a, 32c of the ion path is changed relative to the first mode of operation. This change induces a time shift Δt for each ion peak between the two sets of ion data, which is used to estimate the cycle number N for each peak, and thus the mass-to-charge ratio (or other physicochemical property), for example, in the manner described above.

[0156] In the embodiment shown in FIG. 8, a flight tube 80 may instead be positioned in the ion path 32a between the ion source 31 and the first mirror.

[0157] Another embodiment is to modify the acceleration field provided by the ion implanter 31 to accelerate ions along the ion path. Where the ion implanter is an ion trap, this may include modifying an extraction field provided within the ion trap to accelerate ions out of the ion trap and along the ion path (e.g., in this embodiment, at least a portion of the first segment 32a of the ion path can be considered to be within the ion trap). Suitable extraction fields are on the order of hundreds of V / mm, and suitable extraction field shifts between the first and second modes of operation are on the order of tens of V / mm.

[0158] Also, when the voltage applied to the flight tube 80 is relatively small, M N Note that the cycle number N will be retained for most ion peaks, except for ion peaks located near

[0159] These embodiments can also be easily implemented in cyclic ion mobility spectrometry (measuring the time of flight through a gas-filled drift path). For example, UK Patent Application No. 2,562,690 describes an instrument that combines a cyclic ion mobility analyzer with a short linear drift tube, which can be easily adapted to shift the total drift time in a similar manner to that described above.

[0160] While the above exemplary embodiments have been described with respect to varying (between a first and second mode of operation) either (i) the potential along the acyclic segments 32a, 32c of the ion path, or (ii) the path length of the cyclic segment 32b of the ion path, it is possible to instead vary either (iii) the potential along the cyclic segment 32b of the ion path (e.g., by including a flight tube along the cyclic segment 32b of the ion path), or (iv) the path length of the acyclic segments 32a, 32c of the ion path (e.g., by controlling the number of reflections K that an ion makes between two ion mirrors), i.e., the effective ion path L in the loop. m It will be appreciated that it is possible to vary one of the effective ion paths outside of loop L0+L1 such that it is altered for the first mode of operation.

[0161] A numerical example of the configuration shown in Fig. 8 is L m = 0.5m, L0 and L1 = 0.4m, L t = 0.3 m, T2 = 0.5 ms and ε0 = 1000 eV. A voltage shift of 10 V was performed on the flight tube 80 between the two spectra. Flight times were calculated for ions with mass-to-charge ratios ranging from 250 to 3250 every 150 m / z.

[0162] FIG. 9 demonstrates how different m / z ions (top panel) are separated into different numbers of reflections and the resulting convoluted time-of-flight spectrum (left panel).

[0163] FIG. 10A shows the Lt Figure 10B shows two overlapping convoluted time-of-flight spectra showing the small shift between peaks produced by the 10 V offset applied to the region, and Figure 10B shows the recovered mass spectrum found by measuring the shift between peaks and assigning cycle numbers. Information is also reproduced in Table 4.

[0164] [Table 4]

[0165] This example assumes that there is no difficulty in matching the peaks before and after the shift, which may be reasonable for small shifts and uncongested spectra. In more complicated cases, it may be beneficial to have an elaborate calibration for both the shifted and unshifted spectra, assign multiple possible m / z values ​​to each ion peak, and then match the peaks together as described above for the first exemplary disambiguation method.

[0166] A mass spectrometer was constructed incorporating the analyzer design of Figure 4. Analyte ion m / z 524 generated from the electrospray source was isolated by the quadrupole, extracted, stored and cooled in the ion trap, and released into the analyzer by a 330 V / mm pulsed electric field under which it was rapidly accelerated to 4 KV flight energy.

[0167] The dispersion of the ions was controlled by a pair of lenses and the direction of the ions was set by the first prism deflector 38 so that the ions passed through the second prism deflector 36 via reflection from the ion mirror 35. To admit the ions to the analyzer, the second prism deflector 36 was set to -160V. After about 200μs, this prism deflector was switched to +280V trapping mode and held there for 800μs, sufficient for the ions to make a second drift pass. The prism 37 was then switched back to -160V transmission mode and the trapped ions were picked up by the electron multiplier detector 33.

[0168] Figure 11 shows the m / z 524 peak obtained when the instrument was operated in single pass and zoom modes. In 3x zoom mode, much higher resolution was observed without significant loss of signal, but a larger number of drift passes was observed to reduce transmission more significantly.

[0169] Figure 12 shows a zoom mode mass spectrum of a typical calibration mixture containing MRFA and U Ultramark injected with Pierce Flexmix calibration solution. In this example, the ion mass range delivered to the ToF analyzer was first isolated by the resolving quadrupole to remove ambiguous peaks. From the first mass 390, approximately a 1.6x m / z range was observed.

[0170] Figure 13 shows data from a test of the disambiguation method according to the first exemplary embodiment. Flexmix ions were injected into the trap with a much wider m / z isolation window 390-2000 than the unambiguous m / z window 390-625, so that the high m / z ultramark ions with -1 drift pass appeared in the mass spectrum. The number of oscillations per drift pass K was then reduced by 1 and the mass calibration factor was recalculated. The high m / z ultramark peaks were observed to have shifted in m / z by -620 ppm, allowing their easy identification.

[0171] A similar experiment with the second exemplary embodiment was performed by varying the pulsed extraction field of the ion implanter from 330 to 240 V / mm, which shifted the high m / z ions by -40 ppm.

[0172] From the above, it will be appreciated that embodiments provide a method of operating an analysis instrument, such as a time-of-flight mass spectrometer, including an analyzer configured to determine the time-of-flight of ions along a path including a cyclic segment and an acyclic segment, the cyclic segment being configured such that at least some ions make two or more loops therein and the acyclic segment being configured such that all ions make only a single pass along it, and at least one of the cyclic segment and the acyclic segment being controlled, for example, using at least one electrode having a switchable voltage that, when switched, modifies the time-of-flight of ions in that segment.

[0173] The method may include determining a time of flight of a first set of ions upon completion of a cyclic segment and an acyclic segment, varying a voltage of at least one of the control electrodes, and then determining a time of flight of a second set of ions upon completion of the cyclic segment and an acyclic segment. The method may include determining a number of loops in the cyclic segment made by the ions of interest based on a time-of-flight difference between the flight times of the first set and the flight times of the second set. The method may then include determining a mass-to-charge ratio of at least one ion based on a total flight path including the determined number of loops in the cyclic portion.

[0174] The cyclic or acyclic segments may be controlled by voltages that, when applied, modify the ion velocity in at least one section of the path, which in turn modifies the flight time in the cyclic or acyclic segments. The cyclic segment may be controlled by voltages that modify the ion flight length within that segment. An ion may undergo two or more oscillations within a single loop within a cyclic segment, and the number of such oscillations may be controlled by application of a control voltage.

[0175] The relative difference between the first and second set of flight times may depend substantially on the number of loops in the ion trajectory in the cyclic segment, and the number of loops may be estimated from the difference for at least one ion. The mass to charge ratio may be estimated for a set of candidate loop numbers, and the true number of loops may be determined by comparison of the estimated mass to charge ratios for the first and second set of flight times.

[0176] Although the invention has been described with reference to various embodiments, it will be understood that various modifications can be made without departing from the scope of the invention as set forth in the appended claims.

Claims

1. 1. A method of operating an analysis instrument including an ion analyzer configured to analyze ions by determining drift times of ions along an ion path, the ion path including at least a first segment and a cyclic segment, the ion path being configured such that ions pass through the first segment once and pass through the cyclic segment one or more times, the method comprising: operating the analyzer in a first mode of operation, wherein (i) a first potential is provided along the first segment of the ion path, (ii) a second potential is provided along the cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a first set of ion data; (i) operating the analyzer in a second mode of operation by varying at least one of the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a second set of ion data. comparing the first set of ion data to the second set of ion data and identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining a number N of passes through the cyclic segment of the ion path taken by ions associated with corresponding first and second ion peaks; and using the determined number of passes N to determine values ​​of the physicochemical properties of the ions associated with the corresponding first and second ion peaks; the ion analyzer is a time-of-flight (ToF) mass analyzer, and the physicochemical property is mass-to-charge ratio (m / z); The time-of-flight mass analyzer is a multi-reflecting time-of-flight (MR-ToF) mass analyzer, and the multi-reflecting time-of-flight mass analyzer comprises: two ion mirrors spaced apart and facing each other in a first direction X, each mirror being elongated generally along a drift direction Y between a first end and a second end, the drift direction Y being orthogonal to the first direction X; an ion injector for injecting ions into a space between the ion mirrors, the ion injector being located proximate the first end of the ion mirror; a detector for detecting the ions after they have completed multiple reflections between the ion mirrors.

2. The detector is located near the first end of the ion mirror, and the analyzer comprises: (i) injecting ions from the ion injector into the space between the ion mirrors, the ions completing a first cycle in which they (a) drift along the drift direction Y towards the second end of the ion mirror, (b) reverse their drift direction velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having a number K of reflections in the direction X between the ion mirrors while drifting back along the drift direction Y towards the first end of the ion mirror; (ii) reversing the drift directional velocity of the ions near the first end of the ion mirror such that the ions complete a further cycle in which they (a) drift along the drift direction Y towards the second end of the ion mirror, (b) reverse the drift directional velocity near the second end of the ion mirror, and (c) follow a zigzag ion path having a number K of reflections in the direction X between the ion mirrors while drifting back along the drift direction Y towards the first end of the ion mirror; (iii) repeating step (ii) one or more times, and then 2. The method of claim 1 , further comprising: (iv) analyzing the ions by: (a) transferring the ions to the detector for detection.

3. The multi-reflecting time-of-flight (MR-ToF) mass analyzer comprises: a deflector located near the first end of the ion mirror; The analyzer (i) injecting ions from the ion injector into the space between the ion mirrors, wherein the ions (a) drift along the drift direction Y from the deflector towards the second end of the ion mirror, (b) reverse their drift direction velocity near the second end of the ion mirror, and (c) complete a first cycle following a zigzag ion path having a number K of reflections in the direction X between the ion mirrors while drifting along the drift direction Y back towards the deflector; (ii) using the deflector to reverse the drift direction velocity of the ions such that the ions (a) drift along the drift direction Y from the deflector towards the second end of the ion mirror, (b) reverse the drift direction velocity near the second end of the ion mirror, and (c) complete a further cycle of following a zigzag ion path having a number K of reflections in the direction X between the ion mirrors while drifting along the drift direction Y back towards the deflector; (iii) repeating step (ii) one or more times, and then 3. The method of claim 2, further comprising: (iv) analyzing the ions by: (a) transferring the ions from the deflector to the detector for detection.

4. 4. The method of claim 3, wherein the method comprises varying the second path length in the second mode of operation by varying the number of reflections K that ions make between the ion mirrors as they follow the zigzag ion path.

5. the method comprising varying the second path length in the second mode of operation by varying a number K of reflections between the ion mirrors as ions follow the zigzag ion path; The method of claim 4 , wherein the number of reflections K that an ion makes between the ion mirrors as it follows the zigzag ion path is varied by varying the voltage applied to the deflector.

6. 6. The method of claim 3, wherein the ion mirrors are at a non-constant distance from each other in the direction X along at least a portion of their length in the drift direction Y, and the drift directional velocity of ions towards the second end of the ion mirror is opposed by an electric field resulting from the non-constant distance of the two mirrors from each other, the electric field causing the ions to reverse their drift directional velocity near the second end of the ion mirror and drift back along the drift direction towards the deflector.

7. 6. The method of claim 3, wherein the deflector is a first deflector and the analyzer comprises a second deflector located proximate the second end of the ion mirror, the second deflector configured to cause the ions to reverse their drift direction velocity proximate the second end of the ion mirror and drift back along the drift direction towards the deflector.

8. 1. A method of operating an analysis instrument including an ion analyzer configured to analyze ions by determining drift times of ions along an ion path, the ion path including at least a first segment and a cyclic segment, the ion path being configured such that ions pass through the first segment once and pass through the cyclic segment one or more times, the method comprising: operating the analyzer in a first mode of operation, wherein (i) a first potential is provided along the first segment of the ion path, (ii) a second potential is provided along the cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a first set of ion data; (i) operating the analyzer in a second mode of operation by varying at least one of the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a second set of ion data. comparing the first set of ion data to the second set of ion data and identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining a number N of passes through the cyclic segment of the ion path taken by ions associated with corresponding first and second ion peaks; and using the determined number of passes N to determine values ​​of the physicochemical properties of the ions associated with the corresponding first and second ion peaks; The method, wherein the analyzer is an ion mobility analyzer and the physicochemical property is ion mobility.

9. The method of claim 1 or 8, wherein the method comprises modifying the first potential in the second mode of operation.

10. 10. The method of claim 9, wherein the instrument further comprises a flight tube disposed along at least a portion of the first segment of the ion path, the method including varying the first potential in the second mode of operation by varying a voltage applied to the flight tube.

11. 10. The method of claim 9, wherein the ion analyzer comprises an ion injector configured to accelerate ions along the ion path, the method including varying the first potential in the second mode of operation by modifying an accelerating electric field provided by the ion injector for accelerating ions along the ion path.

12. Determining the number N of passes through the cyclic segment of the ion path taken by ions associated with the corresponding first ion peak and the second ion peak comprises: Measuring a drift time difference between the first ion peak and the second ion peak; and using the measured drift time difference to estimate a number N of passes through the cyclic segment of the ion path taken by ions associated with corresponding the first and second ion peaks.

13. A non-transitory computer readable storage medium storing computer software code which, when executed on a processor, performs the method of claim 1 or 8.

14. 10. A control system for an analytical instrument, the control system being configured to cause the analytical instrument to perform the method of claim 1 or 8.

15. 1. An analytical instrument that is a mass spectrometer or an ion mobility spectrometer, an ion analyzer configured to analyze ions by determining a drift time of ions along an ion path, the ion path including at least a first segment and a cyclic segment, the ion path configured such that ions pass through the first segment once and pass through the cyclic segment one or more times; 1. A control system comprising: analyzing ions by determining drift times of ions along the ion path to obtain a first set of ion data by operating the analyzer in a first mode of operation, wherein (i) a first potential is provided along the first segment of the ion path, (ii) a second potential is provided along the cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length; (i) operating the analyzer in a second mode of operation by varying at least one of the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a second set of ion data. comparing the first set of ion data to the second set of ion data and identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining a number N of passes through the cyclic segment of the ion path taken by ions associated with corresponding first and second ion peaks; and determining values ​​of physicochemical properties of the ions associated with corresponding first and second ion peaks using the determined number of passes N; the ion analyzer is a time-of-flight (ToF) mass analyzer and the physicochemical property is mass-to-charge ratio (m / z); The time-of-flight mass analyzer is a multi-reflecting time-of-flight (MR-ToF) mass analyzer, and the multi-reflecting time-of-flight mass analyzer comprises: two ion mirrors spaced apart and facing each other in a first direction X, each mirror being elongated generally along a drift direction Y between a first end and a second end, the drift direction Y being orthogonal to the first direction X; an ion injector for injecting ions into a space between the ion mirrors, the ion injector being located proximate the first end of the ion mirror; a detector for detecting the ions after they have completed multiple reflections between the ion mirrors.

16. the detector is located proximate the first end of the ion mirror; The analyzer comprises: (i) injecting ions from the ion injector into the space between the ion mirrors, the ions (a) drifting along the drift direction Y towards the second end of the ion mirror, (b) reversing drift direction velocity near the second end of the ion mirror, and (c) completing a first cycle following a zigzag ion path having a number K of reflections in the direction X between the ion mirrors while drifting back along the drift direction Y towards the first end of the ion mirror; (ii) reversing the drift directional velocity of the ions near the first end of the ion mirror such that the ions (a) drift along the drift direction Y towards the second end of the ion mirror, (b) reverse the drift directional velocity near the second end of the ion mirror, and (c) complete a further cycle following a zigzag ion path having a number K of reflections in direction X between the ion mirrors while drifting back along the drift direction Y towards the first end of the ion mirror; (iii) repeating step (ii) one or more times, and then 16. The analytical instrument of claim 15, configured to analyze the ions by: (iv) moving the ions to the detector for detection.

17. 1. An analytical instrument that is a mass spectrometer or an ion mobility spectrometer, an ion analyzer configured to analyze ions by determining a drift time of ions along an ion path, the ion path including at least a first segment and a cyclic segment, the ion path configured such that ions pass through the first segment once and pass through the cyclic segment one or more times; 1. A control system comprising: analyzing ions by determining drift times of ions along the ion path to obtain a first set of ion data by operating the analyzer in a first mode of operation, wherein (i) a first potential is provided along the first segment of the ion path, (ii) a second potential is provided along the cyclic segment of the ion path, (iii) the first segment of the ion path has a first path length, and (iv) the cyclic segment of the ion path has a second path length; (i) operating the analyzer in a second mode of operation by varying at least one of the first potential, (ii) the second potential, (iii) the first path length, and (iv) the second path length; and analyzing ions by determining drift times of ions along the ion path to obtain a second set of ion data. comparing the first set of ion data to the second set of ion data and identifying a first ion peak in the first set of ion data that corresponds to a second ion peak in the second set of ion data; determining a number N of passes through the cyclic segment of the ion path taken by ions associated with corresponding first and second ion peaks; and determining values ​​of physicochemical properties of the ions associated with corresponding first and second ion peaks using the determined number of passes N; The analytical instrument wherein the analyzer is an ion mobility analyzer and the physicochemical property is ion mobility.

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