Mass spectrometer with high duty cycle

Abstract

As a method of mass spectrometry: a) accumulating precursor ions in a first ion accumulator; b) performing a separation cycle comprising pulses a packet of the precursor ions from the first ion accumulator into an ion separator, and separating the precursor ions such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times; c) mass filtering the precursor ions eluted from the ion separator to deliver a selected precursor ion species; d) fragmenting or reacting the selected precursor ion species to generate a set of fragments or product ion species therefrom; e) accumulating the set of fragments or product ion species in a second ion accumulator; f) releasing the set of fragments or product ion species from the second ion accumulator into a TOP mass spectrometer, wherein the operation of the TOP mass spectrometer is synchronized with the release of ions from the second ion accumulator, so that a plurality of different species of the set of fragments or product ion species are simultaneously pulsed into the TOF region of the TOP mass spectrometer by a pusher electrode; and g) repeat steps c) to f) at least once during the separation cycle, wherein the selected precursor ion species are different each time steps c) to f) are performed.

Description

Technology Field

[0001] Cross-reference regarding related applications

[0002] This application claims priority and interest to UK Patent Application No. 2204106.5 filed on March 23, 2022. The full contents of this application are incorporated herein by reference a.

[0003] Technology field

[0004] The present invention generally relates to a mass spectrometer that repeatedly pulses ions into a separation region so that the ions are separated according to their mass-to-charge ratio. Background Technology

[0005] In both Data-Dependent Acquisition (DDA) and Tandem Mass Spectrometry (MSMS), precursor ions are filtered so that only selected species of precursor ions are delivered downstream for analysis at any given time. The mass spectrometer then selects different species of precursor ions to be delivered downstream for analysis. This process continues until the precursor ions of the desired species are analyzed. To analyze the sample as quickly as possible, it is generally desirable to sequentially select and deliver as many precursor ions as possible per unit time. However, in conventional instruments such as Quadrupole-Time-of-Flight (QToF) mass spectrometers, simply increasing the rate at which precursor species are selected results in a linear decrease in sensitivity to the detected ions. For example, if the analyzer settings are changed to increase the number of delivered precursor species from 25 different precursors per second to 50 different precursors per second, this results in the number of ions in each fragment ion scan being halved.

[0006] It is desired to increase the overall duty cycle of such mechanisms.

[0007] A first aspect of the present disclosure provides a mass spectrometry method comprising the following:

[0008] a) a step of accumulating precursor ions in a first ion accumulator;

[0009] b) performing a separation cycle comprising the steps of: pulse a packet of the precursor ions from the first ion accumulator into an ion separator; and separating the precursor ions such that precursor ions having different values ​​of first physicochemical properties are eluted from the ion separator at different times;

[0010] c) a step of mass filtering the precursor ions eluted from the ion separator to transmit selected precursor ion species;

[0011] d) a step of fragmenting or reacting the selected precursor ion species to generate a set of fragment or product ion species therefrom;

[0012] e) a step of accumulating a set of the fragment or product ion species in a second ion accumulator;

[0013] f) releasing the set of fragment or product ion species from the second ion accumulator into the TOF mass analyzer, wherein the operation of the TOF mass analyzer is synchronized with the release of ions from the second ion accumulator, so that a plurality of different species of the set of fragment or product ion species are simultaneously pulsed into the time of flight region of the TOF mass analyzer by a pusher electrode; and

[0014] g) steps c) to f) are repeated at least once during the separation cycle, wherein the selected precursor ion species are different each time steps c) to f) are performed.

[0015] The inventors recognized that the period during which a second ion accumulator can accumulate fragment or product ions and release them for analysis in a TOF mass spectrometer is comparable to the period during which any given precursor ion is eluted from an upstream separator. Thus, fragment or product ion species derived from a first precursor ion species eluted from the ion separator during a given separation cycle of the ion separator can be accumulated, captured, and released to the TOF mass spectrometer before the second precursor ion species is eluted from the ion separator within the same separation cycle of the ion separator. The present method provides a relatively high duty cycle because, rather than the other precursor ion species being discarded while the selected precursor ion species is fragmented, the other precursor ion species remains in a delayed state in the ion separator. Furthermore, the duty cycle is relatively high because the synchronization between the second ion accumulator and the TOF mass spectrometer allows multiple fragment or product ion species of the selected precursor to be analyzed simultaneously.

[0016] An ion separator can be an ion mobility separator, and its physicochemical properties can be ion mobility.

[0017] For example, the ion separator may be an ion mobility separator configured to drive ions through a background gas arranged internally. Ions may be driven through the background gas by an electric field to be separated according to mobility. For example, ions may be driven by applying a static DC potential gradient along the ion separator and / or by repeatedly shifting the DC potential along the ion separator. The electric field may be arranged to pressurize ions in a downstream direction (toward the TOF mass spectrometer) through the ion separator. Alternatively, the background gas may flow downstream, and the electric field may be arranged to pressurize ions in an upstream direction relative to the gas flow to cause ions to be separated according to mobility.

[0018] Other embodiments are considered in which the ion separator is a Field Asymmetric Ion Mobility Separator (FAIMS) device or a Differential Mobility Separator (DMS). Less preferably, the ion separator mass may be a mass-to-charge ratio separator and the physicochemical properties may be a mass-to-charge ratio.

[0019] Whenever step c) is performed, only the selected precursor ion species may be delivered, and other precursor ion species may not be delivered.

[0020] Alternatively, whenever step c) is performed, the mass filter may deliver precursor ions having a mass-to-charge ratio within a limited range, so that multiple precursor ion species are delivered simultaneously, while precursor ions having a mass-to-charge ratio outside this limited range are filtered out. Then, step d) may include a step of simultaneously fragmenting or reacting the delivered multiple precursor ion species to generate a set of multiple fragments or product ion species therefrom. Step e) may include a step of simultaneously accumulating a set of fragments or product ion species in a second ion accumulator. Step f) may include a step of simultaneously releasing a set of fragments or product ion species from the second ion accumulator to a TOF mass spectrometer, wherein the operation of the TOF mass spectrometer is synchronized with the release of ions from the second ion accumulator so that multiple different species of the set of fragments or product ion species are simultaneously pulsed into the TOF region of the TOF mass spectrometer by a pusher electrode. Step g) repeats steps c) to f) at least once during the separation cycle, wherein the range of the mass-to-charge ratio delivered by the mass filter may include different steps each time steps c) to f) are performed.

[0021] A voltage is applied to the electrodes of the mass filter to transfer a limited range of mass-to-charge ratios, such as only a single precursor ion species or multiple precursor ion species, at any given time. According to step g), the voltage varies over time during the separation cycle so that at least one different precursor ion species is transferred by the mass filter whenever steps c) to f) are performed.

[0022] The mass filter may be a quadrupole mass filter, such as, for example, a quadrupole rod set mass filter or an axially segmented quadrupole rod set mass filter. However, it is considered that other types of mass filters may be used in the present disclosure.

[0023] The fragment or product ion species may be pressurized into the second ion accumulator: (i) fragment or product ion species derived from the same precursor ion species reach the second ion accumulator over substantially the same period and accumulate in the second ion accumulator for at least part of this period, and / or (ii) fragment or product ion species derived from the precursor species delivered by the mass filter at different times reach the second ion accumulator over different respective periods.

[0024] Whenever the sequence of steps c) through e) is performed, the fragment or product ion species may be accumulated in a second ion accumulator over a period equal to or corresponding to the period during which their precursor ion species are transferred by the mass filter.

[0025] For example, fragment or product ion species may be accumulated in a second ion accumulator over a period substantially equal to or correlated with the duration between the start time when the voltage applied to the mass filter to initiate the transfer of the precursor ion species is switched and the end time when the voltage applied to the mass filter to terminate the transfer of the precursor ion species.

[0026] Accordingly, the second ion accumulator can be synchronized with the mass filter so that substantially all fragment or product ions derived from any given precursor ion species accumulate within the second ion accumulator. This, along with the way the second ion accumulator and the TOF mass spectrometer are synchronized, allows the duty cycle of the analytical system to be relatively high.

[0027] It is also considered that whenever the sequence of steps c) through e) is performed, the fragment or product ion species may be accumulated in the second ion accumulator over a period shorter than the period during which their precursor ion species are transferred by the mass filter. For example, the fragment or product ion species may be accumulated in the second ion accumulator over a period shorter than the duration between the start time when the voltage applied to the mass filter to initiate the transfer of the precursor ion species is switched and the end time when the voltage applied to the mass filter to terminate the transfer of the precursor ion species.

[0028] Optionally, whenever the sequence of steps c) through e) is performed, only fragments or product ions derived from the selected precursor ion species, and optionally some ions of the selected precursor ion species itself, are accumulated in the second ion accumulator; whereas other precursor ion species and fragments or product ions derived therefrom are not accumulated in the second ion accumulator.

[0029] Accordingly, embodiments of the present disclosure release fragment or product ions into a TOF mass spectrometer without simply capturing them in order to improve the duty cycle. Rather, the period during which the fragment or product ions accumulate is set to coincide with the period during which their precursor ion species are transferred by a mass filter. Consequently, the period during which the precursor ion species are transferred by a mass filter can be set to coincide with the period during which the precursor ion species are eluted from a separator. In this way, embodiments of the present disclosure provide a very high duty cycle.

[0030] Therefore, whenever the sequence of steps b) and c) is performed, the mass filter can be controlled to deliver the precursor ion species of interest over a period that is equal to, correlated with, or shorter than the period during which the corresponding precursor ion species is eluted from the ion separator.

[0031] For example, the mass filter can be controlled to deliver the precursor species of interest over a period substantially equal to, correlated with, or shorter than the duration between the start time when the precursor ion species begins to elute from the ion separator and the end time when the precursor ion stops eluting from the ion separator.

[0032] Step f) may include releasing fragment or product ion species from a second ion accumulator in reverse order of mass-to-charge ratio, starting with ions with a relatively high mass-to-charge ratio and gradually releasing ions with a lower mass-to-charge ratio, so that different species of fragment or product ion species reach the pusher electrode simultaneously and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode.

[0033] A transfer region may be provided between the second ion accumulator and the TOF mass spectrometer, wherein the pressure within the transfer region and the energy released from the second ion accumulator cause fragment or product ions having a relatively low mass-to-charge ratio to catch up with fragment or product ions having a higher mass-to-charge ratio, so that the ions simultaneously reach the pusher electrode and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode.

[0034] Optionally, substantially all fragment or product ion species emitted from the second ion accumulator arrive at the pusher electrode at substantially the same time whenever step f) is performed, and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode.

[0035] Step f) may include the step of substantially simultaneously releasing all fragment or product ion species from the second ion accumulator, wherein a transfer zone is provided between the second ion accumulator and the TOF mass spectrometer, and the ions are separated in the transfer zone according to the second physicochemical properties so that the fragment or product ion species reach the TOF mass spectrometer at a time depending on their second physicochemical property values, and the operation of the TOF mass spectrometer is synchronized with the release of ions from the second ion accumulator so that the fragment or product ion species having a value of a selected range of the second physicochemical property values ​​are simultaneously pulsed into the TOF zone of the TOF mass spectrometer by the pusher electrode.

[0036] The above method may include the step of receiving an input signal representing a value of the selected range of a second physicochemical characteristic in a mass spectrometer performing the above method, wherein the operation of the TOF mass spectrometer is synchronized with the emission of ions from a second ion accumulator so that a fragment or product ion paper having a value of the selected range of the second physicochemical characteristic value is simultaneously pulsed into the TOF region of the TOF mass spectrometer by a pusher electrode.

[0037] A second physicochemical property may be the mass-to-charge ratio, causing ions to be separated in the transport zone according to this ratio. For example, the operating conditions in the transport zone may cause fragment or product ion species with a relatively low mass-to-charge ratio to move through it more quickly than fragment or product ion species with a higher mass-to-charge ratio. For instance, the product of the pressure (P) in the transport zone and the length of the ion flight path (L) through the transport zone (i.e., PxL) may be at a level where the ions substantially do not collide with background gas molecules in the transport zone.

[0038] Alternatively, the second physicochemical property may be ion mobility, and ions are separated in the transfer zone according to ion mobility. For example, the transfer zone may function as an ion mobility separator configured to drive ions through a background gas arranged within it. Ions may be driven through the background gas by an electric field to be separated according to mobility. For example, ions may be driven by applying a static DC potential gradient along the transfer zone and / or by repeatedly shifting the DC potential along the transfer zone. The electric field may be positioned to pressurize ions in a downstream direction through the transfer zone. Alternatively, the background gas may flow downstream, and the electric field may be positioned to pressurize ions in an upstream direction relative to the gas flow to cause ions to be separated according to mobility.

[0039] Steps a) through g) may be repeated during a single experimental run. To avoid doubt, the term “during a single experimental run” means during the continual analysis of an analytical sample. For example, steps a) through g) may be repeated while ions are generated from the analytical sample substantially continuously (e.g., in a substantially continuous or pulsed manner) and / or during a single liquid or gas chromatography run.

[0040] The present disclosure also provides a mass spectrometer configured to perform the method described herein.

[0041] Accordingly, a first aspect of the present invention also provides a mass spectrometer comprising the following:

[0042] First ion accumulator;

[0043] Ion separator;

[0044] Mass filter;

[0045] Fragmentation or reaction device;

[0046] Second ion accumulator;

[0047] TOF mass spectrometer having a TOF region and a pusher electrode; and

[0048] It includes a control circuit configured to control a mass spectrometer, and the mass spectrometer is:

[0049] a) accumulating precursor ions in the first ion accumulator;

[0050] b) performing a separation cycle comprising the steps of pulse a packet of the precursor ions from the first ion accumulator into the ion separator, and separating the precursor ions in the ion separator such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times;

[0051] c) mass filtering the precursor ions eluted from the ion separator using the mass filter to deliver selected precursor ion species;

[0052] d) fragmenting or reacting the selected precursor ion species in the fragmentation or reaction apparatus to produce a set of fragmented or product ion species therefrom;

[0053] e) accumulating the set of fragment or product ion species in the second ion accumulator;

[0054] f) releasing the set of fragment or product ion species from the second ion accumulator into the TOF mass spectrometer, wherein the operation of the TOF mass spectrometer is synchronized with the release of ions from the second ion accumulator, so that a plurality of different species of the set of fragment or product ion species are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode;

[0055] g) Steps c) to f) are repeated at least once during the separation cycle, wherein the mass filter is controlled such that the selected precursor ion species is different each time steps c) to f) are performed.

[0056] A control circuit may be configured to control a mass spectrometer, such that step f) includes releasing fragment or product ion species from a second ion accumulator in reverse order of mass-to-charge ratio, starting with ions of a relatively high mass-to-charge ratio and gradually releasing ions of a lower mass-to-charge ratio, so that different species of fragment or product ion species reach the pusher electrode simultaneously and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode.

[0057] The mass spectrometer may include a transfer region between a second ion accumulator and a TOF mass spectrometer, wherein the spectrometer is configured to maintain pressure in the transfer region and release ions from the second ion accumulator with energy, so that fragment or product ions having a relatively low mass-to-charge ratio catch up with fragment or product ions having a higher mass-to-charge ratio, causing the ions to simultaneously reach the pusher electrode and be pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode.

[0058] The mass spectrometer may include a transfer region between a second ion accumulator and a TOF mass spectrometer; wherein a control circuit is configured to control the mass spectrometer, so as to include a step f) in which all fragment or product ion species are substantially simultaneously released from the second ion accumulator into the transfer region, so as to be separated in the transfer region according to a second physicochemical property and reach the TOF mass spectrometer at a time depending on the value of the second physicochemical property, and the operation of the TOF mass spectrometer is synchronized with the release of ions from the second ion accumulator so as to simultaneously pulse fragment or product ion species having a value of a selected range of the second physicochemical property value into the TOF region of the TOF mass spectrometer by a pusher electrode.

[0059] The mass spectrometer may include a user interface configured to input a selected range of values ​​for a second physicochemical characteristic; wherein the analyzer is configured such that a control circuit controls the operation of the TOF mass spectrometer based on the values ​​of the selected range to synchronize the operation of the TOF mass spectrometer with the emission of ions from a second ion accumulator, so that fragment or product ion paper having values ​​of the selected range of values ​​for the second physicochemical characteristic is simultaneously pulsed into the TOF region of the TOF mass spectrometer by a pusher electrode.

[0060] The mass spectrometer includes an ion source. The mass spectrometer may also include a liquid or gas chromatography separator for separating the sample for analysis upstream of the ion source.

[0061] The mass spectrometer may be configured to repeat steps a) through g) during a single experimental run, for example, while ions are generated substantially continuously (e.g., in a substantially continuous or pulsed manner) by an ion source and / or during a single liquid or gas chromatography separation run.

[0062] It is considered that the second ion accumulator may be omitted. In these embodiments, the second ion accumulator is not synchronized with the TOF mass spectrometer to control the fragment or product ion (from any given precursor ion species) that is simultaneously analyzed by the TOF mass spectrometer. Rather, this is accomplished by synchronizing the operation of the TOF mass spectrometer with the time at which the fragment or product ion is generated. Thus, the time at which the mass filter delivers the selected precursor ion species to the fragmentation or reaction zone is synchronized with the TOF mass spectrometer to control the fragment or product ion from the selected precursor ion species that is simultaneously mass analyzed.

[0063] Accordingly, from a second aspect, the present disclosure provides a mass analysis method comprising the following:

[0064] a) A step of accumulating precursor ions in a first ion accumulator;

[0065] b) performing a separation cycle comprising the steps of pulse a packet of the precursor ions from the first ion accumulator into the ion separator, and separating the precursor ions such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times;

[0066] c) a step of switching a mass filter that mass filters the precursor ions eluted from the ion separator to initiate the transfer of the selected precursor ion species;

[0067] d) a step of fragmenting or reacting the selected precursor ion species to generate a set of fragments or product ion species therefrom;

[0068] e) a step of initiating the delivery of the selected precursor ion species, wherein the set of fragment or product ion species is delivered through a delivery region to a TOF mass spectrometer having a pusher electrode and a TOF region, wherein the ions are separated in the delivery region according to a second physicochemical property, so that the fragment or product ion species reach the TOF mass spectrometer at a time dependent on their second physicochemical property value, and the operation of the TOF mass spectrometer is synchronized with the time at which the mass filter is switched, so that the fragment or product ion species having a value of a selected range of the second physicochemical property reaching the pusher electrode substantially simultaneously are pulsed simultaneously by the pusher electrode within the flight time of the TOF mass spectrometer; and

[0069] f) repeat steps c) to e) at least once during the separation cycle, wherein the selected precursor ion species are different each time steps c) to e) are performed.

[0070] Any given selected fragment of a precursor ion species or product ion species undergoes a separation cycle in a transfer zone, where the separation cycle is triggered based on the time when the mass filter switches to begin the transfer of the corresponding precursor ion species.

[0071] The above method may include, in a mass spectrometer performing the above method, receiving an input signal representing a value of a selected range of the second physicochemical property, and controlling the operation of the TOF mass spectrometer so that a fragment or product ion species having a value of the selected range of the second physicochemical property reaches the pusher electrode substantially simultaneously and is pulsed simultaneously into the TOF region of the TOF mass spectrometer by the pusher electrode.

[0072] Fragments or product ions of any given precursor ion species may reach the TOF mass spectrometer at a time corresponding to the time when the mass filter begins to deliver its precursor ion species. For example, the selected precursor ion species delivered in step c) may not be axially captured before fragmentation or reaction in step d); and the fragments or product ions generated in step d) may not be axially captured before reaching the TOF mass spectrometer.

[0073] The method according to the second embodiment of the present disclosure may have any of the features described in relation to the first embodiment of the present disclosure, except that it is not necessary to use a second ion accumulator.

[0074] For example, whenever step c) is performed, only selected precursor ion species may be delivered, and other precursor ion species are not delivered. Alternatively, whenever step c) is performed, the mass filter may deliver precursor ions having a limited range of mass-to-charge ratios, so that multiple precursor ion species are delivered simultaneously, while precursor ions having a mass-to-charge ratio outside this limited range are filtered out. Then, step d) may include the step of simultaneously fragmenting or reacting the delivered multiple precursor ion species to generate a set of multiple fragments or product ion species therefrom. Step e) may include the step of delivering the set of multiple fragments or product ion species through a delivery region to a TOF mass spectrometer, wherein the operation of the TOF mass spectrometer is synchronized with the time at which the mass filter is switched to initiate the delivery of said precursor ion species such that fragments or product ion species having a selected range of values ​​of a second physicochemical property reach the pusher electrode substantially simultaneously and are pulsed simultaneously by the pusher electrode within the flight time of the TOF mass spectrometer. Step f) repeats steps c) to e) at least once during the separation cycle, wherein the range of the mass-to-charge ratio delivered by the mass filter may include different steps each time steps c) to e) are performed.

[0075] The present disclosure also provides a mass spectrometer configured to perform the method described in connection with a second aspect of the present disclosure.

[0076] Accordingly, the present disclosure provides a mass spectrometer comprising the following:

[0077] First ion accumulator;

[0078] Ion separator;

[0079] Mass filter;

[0080] Fragmentation or reaction device;

[0081] TOF mass spectrometer having a TOF region and a pusher electrode;

[0082] A transfer region between the fragmentation or reaction device and the TOF mass spectrometer; and

[0083] It includes a control circuit configured to control a mass spectrometer, and the mass spectrometer is:

[0084] a) accumulating precursor ions in the first ion accumulator;

[0085] b) performing a separation cycle comprising the steps of pulse a packet of the precursor ions from the first ion accumulator into the ion separator, and separating the precursor ions in the ion separator such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times;

[0086] c) to initiate the transfer of selected precursor ion species, switch a mass filter that mass filters the precursor ions eluted from the ion separator;

[0087] d) fragmenting or reacting the selected precursor ion species in the fragmentation or reaction apparatus to produce a set of fragmented or product ion species therefrom;

[0088] e) transfer the set of fragment or product ion species through the transfer region to the TOF mass spectrometer, wherein the ions are separated in the transfer region according to a second physicochemical property, so that the fragment or product ion species reach the TOF mass spectrometer at a time dependent on their second physicochemical property value, and the operation of the TOF mass spectrometer is synchronized with the time at which the mass filter is switched, so as to initiate the transfer of the selected precursor ion species such that the fragment or product ion species having a value of a selected range of the second physicochemical property reaching the pusher electrode substantially simultaneously are pulsed simultaneously by the pusher electrode within the flight time of the TOF mass spectrometer;

[0089] f) Steps c) to e) are repeated at least once during the separation cycle, provided that the selected precursor ion species are different each time steps c) to e) are performed. Brief explanation of the drawing

[0090] Various embodiments of the present invention will now be described, only by way of example, with reference to the accompanying drawings. FIG. 1 shows a schematic diagram of an embodiment of a mass spectrometer according to the present disclosure. Figure 2 illustrates an example of a method in which a mass filter can be controlled as a function of time to selectively deliver different precursor ion species over different periods. Figure 3 shows the same plot as Figure 2, except for the overlapping fragment or product ion species. Figure 4 shows an example of a method in which fragments or product ions can be mass analyzed by a TOF mass spectrometer. FIG. 5 shows a method by which the mass spectrometer of FIG. 1 can be operated according to an embodiment of the present disclosure. Figure 6 illustrates a method in which the process described in relation to Figure 5 can be repeated multiple times for different precursor ion species eluted from the ion separator during the same separation cycle. FIG. 7 shows a method in which the mass spectrometer of FIG. 1 can be operated according to another embodiment of the present disclosure. Figure 8 illustrates a method in which the process described in relation to Figure 7 can be repeated multiple times for different precursor ion species eluted from the ion separator during the same separation cycle. Specific details for implementing the invention

[0091] FIG. 1 shows a schematic diagram of an embodiment of a mass spectrometer according to the present disclosure. The spectrometer comprises an ion source (1), a first ion accumulator (2), an ion separator (3), a mass filter (4), a fragmentation or reaction device (5), a second ion accumulator (6), a transfer zone (7), and a time-of-flight (TOF) mass spectrometer (8). Other ion-optical devices may also be provided within the spectrometer, such as one or more RF ion guides, electrostatic lenses, or impact-cooled RF ion guides, which are configured to pressurize ions through them by using an axial electric field or by moving a potential barrier along them.

[0092] When in use, ions are supplied from an ion source (1), which may be an ion source that generates ions from an analysis sample or an ion-optical device that supplies ions. Ions from the source (1) can be accumulated in a first ion accumulator (2) and then released into a separator (3) as packets of ions. The ion accumulator (2) can accumulate ions and periodically pulse them into the separator (3). The accumulator (2) can be configured so that ions can continuously enter it, or the entry of ions into the accumulator (2) can be blocked at the time when packets of ions are pulsed into the separator (3). In either case, the accumulator (2) accumulates ions from the source (1) during the period between the time packets of ions are pulsed into the separator (3).

[0093] The separator (3) is controlled so that each ion packet received from the accumulator (2) is separated according to one or more physicochemical properties. For example, the separator (3) may separate ions according to ion mobility or mass-to-charge ratio, or a combination of both of these physicochemical properties. The separated ions are then passed from the separator (3) to a mass filter (4). The mass filter (4) is controlled to deliver only a single mass-to-charge ratio (or a limited range of mass-to-charge ratios) at any given time, wherein the single mass-to-charge ratio (or limited range) changes over time as the separated ions from the ion packet are eluted from the separator (3).

[0094] FIG. 2 illustrates an example of a method in which a mass filter (4) can be controlled as a function of time when ions separated from an ion packet are eluted from a separator (3). More specifically, FIG. 2 shows a plot of the mass-to-charge ratio delivered by the mass filter (4) as a function of time because the packet of ions is pulsed into the separator (3). In this example, the mass filter (4) is controlled to deliver only ions having a relatively low first mass-to-charge ratio at a first time. Then, the mass filter is controlled to deliver only ions having a higher second mass-to-charge ratio at a later second time. Then, the mass filter is controlled to deliver only ions having a higher third mass-to-charge ratio at a later third time. Then, the mass filter is controlled to deliver only ions having a lower fourth mass-to-charge ratio at a later fourth time. Then, the mass filter is controlled to deliver only ions having a higher second mass-to-charge ratio at a later fifth time.

[0095] It is considered that the mass filter (4) may be, for example, a decomposition quadrupole mass filter, but other types of mass filters may be used. It will also be recognized that the mass filter (4) may be controlled to deliver different mass-to-charge ratios at different times in a manner other than that shown in the example of FIG. 2.

[0096] After a delay time, another packet of ions may be pulsed from the ion accumulator (2) to the separator (3), and the process may be repeated to separate and filter ions from this new packet. The delay time may be set to a shorter or longer delay time if desired, but may be the time it takes for all ions of interest from one packet of ions (i.e., those set to be delivered by the mass filter (4) at some point) to pass through the separator (3) and then through the filter (4). Any desired number of packets of ions may be separated sequentially and then filtered in the manner described above.

[0097] The separated ions delivered by the filter (4) (i.e., rather than being filtered by the filter (4)) are delivered to a fragmentation or reaction device (5). The fragmentation or reaction device (5) may be a collision-induced dissociation (CID) device, an electron capture dissociation (ECD) device, an electron transfer dissociation (ETD) device, a surface-induced dissociation (SID) device, or a device that fragments ions according to any other technology. For example, the device may fragment ions by reacting ions with reagent ions or molecules, or the device may be used to react ions with reagent ions or molecules to form other types of product ions, such as adduct ions.

[0098] FIG. 3 shows the same plot as FIG. 2, except for the fragment or product ion species generated from the superimposed precursor ions. In the illustrated example, the first precursor species delivered by the mass filter (4) is illustrated as the first dark ellipse and is fragmented or reacted to produce two species of fragment or product ions, which are illustrated by the bright ellipses above and below the first dark ellipse. In this example, one of the fragment or product ion species has a higher mass-to-charge ratio than the first precursor species, and the other has a lower mass-to-charge ratio. In this example, each of the second to fifth precursor species (represented by the dark ellipse) is fragmented or reacted to produce three species of fragment or product ions (represented by the bright ellipse).

[0099] It will be recognized that different precursor ions, due to their separation in the separator (3), reach the fragmentation or reaction device (5) at different times, and thus different precursor ions are fragmented or reacted at different times to produce their fragment or product ions at different times. FIG. 3 shows that the fragment or product ion species are produced over a period that is precisely aligned with the period during which their precursor ion species are delivered by the filter (4), but in reality this may not be the case, and it will be recognized that the period during which any given fragment or product ion species is produced may be offset from the time delivered by its precursor ion species filter (4) due, for example, the time of passage of the precursor ion species to (or through) the fragmentation or reaction device (5), and / or the time it takes for the precursor ion species to undergo fragmentation or reaction in the device (5).

[0100] The separation of precursor ion species induced by the separator (3) can be preserved between fragment or product ion species derived from these precursor ion species. In particular, different precursor ion species reach the fragmentation or reaction device (5) at different times, and thus their respective fragment or product ion species are generated at corresponding different times. The fragment or product ion species can be pressurized out through the fragmentation or reaction device (5) so that the fragment or product ion species derived from different precursor species reach the second ion accumulator (6) at different times. Thus, fragment or product ion species derived from the same precursor species reach the second ion accumulator (6) and accumulate in the second ion accumulator over substantially the same period.

[0101] The second ion accumulator (6) accumulates ions and periodically pulses them into the transfer area (7). The second ion accumulator (6) may be configured so that ions continuously enter it, or ions may be blocked from entering the accumulator (6) at the time when packets of ions are pulsed into the transfer area (7). In either case, the accumulator accumulates ions from the fragmentation or reaction device (5) during the period between the time packets of ions are pulsed from the accumulator (6) into the transfer area (6). However, the second ion accumulator (6) may be omitted, and the fragmentation or reaction device (5) may instead pulse ions into the transfer area (7), for example, by providing an ion gate between the fragmentation or reaction device (5) and the transfer area (7). Alternatively, the second ion accumulator (6) and the fragmentation or reaction device (5) may be two parts of the same device.

[0102] Fragment or product ions are delivered through the delivery area (7) to the TOF mass spectrometer (8). As is well known in the art, the TOF mass spectrometer (8) has a pusher that pulses the ion packet into the TOF area (e.g., an electric field-free area) and toward the ion detector. As the ions pass through the TOF area, they are separated according to their mass-to-charge ratio and then strike the ion detector. Thus, the separated ions arrive at the ion detector at different times, where the time the ions reach the detector is related to the mass-to-charge ratio. The mass-to-charge ratio of any given ion can be determined from the duration between the time it is pulsed into the TOF area and the time it is detected by the ion detector. Thus, the TOF mass spectrometer (8) can acquire data from the signal detected by the detector, determine the mass-to-charge ratio of the ions pulsed into the mass spectrometer (8) and their intensity, and form a mass spectrum.

[0103] Ions may be reflected by one or more ion mirrors between the pusher and the ion detector to provide a relatively long flight path through the TOF region. This allows ions with different mass-to-charge ratios to be separated to a greater degree as they travel through the TOF region, thus providing higher mass resolution to the TOF mass spectrometer (8). Thus, the TOF mass spectrometer (8) may be a multi-reflection TOF (MTROF) mass spectrometer that uses ion mirrors to reflect ions multiple times as they drift from the pusher toward the ion detector.

[0104] Fragment or product ion derived from any given species of precursor ion arrives at the TOF mass spectrometer (8) within a limited period associated with the time it takes for its precursor species to exit the separator (3).

[0105] FIG. 4 illustrates an example of a method in which fragment or product ions are mass analyzed by a TOF mass spectrometer (8) according to a conventional (non-EFP (Encoded Frequent Pulsing)) approach. In this example, three species of fragment or product ions having three different mass-to-charge ratios are generated from a single precursor species within a fragmentation or reaction device (5) and then transferred from a second ion accumulator (6) through a transfer zone (7) to the TOF mass spectrometer (8) over the same period. The three species of fragment or product ions reach the pusher of the TOF mass spectrometer (8) over the time window (9) shown in FIG. 4. The TOF mass spectrometer (8) pulses the pusher periodically, thereby repeatedly sampling the fragment or product ions and mass analyzing them over the entire time window (9). The time at which the TOF pusher pulses is indicated by a vertical line (10) on the x-axis. During the duration (9), these multiple pulses (10) of the TOF pusher cause multiple TOF mass spectra to be generated for each fragment or product ion derived from the respective precursor ion.

[0106] FIG. 4 shows only fragment or product ions from one precursor species delivered by the filter (4), but it will be recognized that fragment or product ions derived from other precursor ion species delivered by the filter (4) (at later or earlier times, respectively) will also be mass analyzed in the corresponding manner by the TOF mass spectrometer (8). This conventional method of data acquisition has proven useful, for example, because it allows accurate measurements to be made in the separation time domain of the separator (3), and thus ultimately allows physicochemical properties such as ion mobility and collision cross-section to be determined. This approach also allows processing software to group fragment or product ions common to the same precursor species together.

[0107] However, the approach illustrated by FIG. 4 provides a relatively low sampling duty cycle to the TOF mass spectrometer (8). This is because a relatively long duration is provided between any given pusher pulse (10) and the next pusher pulse, which allows time for the heaviest mass-to-charge ratio ion pushed by the given pusher pulse to reach the ion detector of the TOF analyzer (8) before another packet of ions is pushed toward the ion detector by the next pusher pulse. This means that the duration between pusher pulses (10) is longer than the flight time from the pusher to the detector of the maximum mass-to-charge ratio to be detected. As such, the sampling duty cycle is reduced by the square root of the maximum mass-to-charge ratio to be detected. The TOF sampling duty cycle according to this technique is typically within the range of 0.1% to 50%. These values ​​are typical maximum duty cycles.

[0108] To improve the overall experimental duty cycle of the analytical system, ion transfer between the various components of the analytical system is synchronized.

[0109] FIG. 5 illustrates how the mass spectrometer of FIG. 1 can be operated according to an embodiment of the present disclosure. The upper part of FIG. 5 schematically illustrates a part of the analyzer of FIG. 1, while the lower part of FIG. 5 shows a plot illustrating how an ion precursor species is analyzed in the analyzer. The plot shows an example of the mass-to-charge ratio (y-axis) of ions present in different regions of the illustrated analyzer, namely at different times (x-axis).

[0110] As described above in relation to FIG. 1, the separator (3) performs a separation cycle in which different ion species are pulsed from the first accumulator (2) to the separator (3), separated according to physicochemical properties, and then eluted at different times according to physicochemical properties. The ions eluted from the separator (3) are received by the mass filter (4). At any given time during the separation cycle of the ion separator (3), the mass filter (4) may be configured to deliver a selected mass-to-charge ratio, or a selected range of mass-to-charge ratios, for example, only a single precursor ion species. In FIG. 5, this is illustrated by a dark ellipse under the mass filter (4), which represents a first precursor ion species having a specific mass-to-charge ratio delivered by the mass filter over a period of time. The precursor species are then delivered to a fragmentation or reaction device (5), where they are fragmented or reacted to form fragment or product ions. This process is illustrated in FIG. 5 by six ellipses arranged in a column below the fragmentation or reaction device (5). The dark ellipses represent precursor species, while the five brighter ellipses represent different species of fragments or product ions generated from the precursor species. It will be recognized that five or more different types of fragments or product ions may be generated. Additionally, some of the precursor ions may or may not be present after fragmentation or reaction.

[0111] Next, the fragment or product ion is transferred into the second ion accumulator (6) during the ion accumulation period. After this ion accumulation period, fragment or product ions of different species are released from the second ion accumulator (6) into the transfer zone (7) at different times. More specifically, the fragment or product ions are released from the ion accumulator (6) in reverse order of mass-to-charge ratio. That is, the fragment or product ion species with the highest mass-to-charge ratio are released first, followed by fragment or product ions with progressively lower mass-to-charge ratios in sequence. This is illustrated by the five fragment or product species shown below the transfer zone (7) in FIG. 5. The intervals of the five fragment or product species along the time axis illustrate that the fragment or product ion species with the highest mass-to-charge ratio are released first, followed by fragment or product ion species with progressively lower mass-to-charge ratios at progressively later times.

[0112] The manner in which fragment or product ion species are emitted from the second ion accumulator (6) and the manner in which the transfer zone (7) is configured are selected so that at least some of the different fragment or product ion species reach the TOF mass spectrometer (8) substantially simultaneously. This is illustrated in FIG. 5 by the column of five fragment or product ion species shown below the TOF mass spectrometer (8). For example, different fragment or product species may be emitted from the ion accumulator (6) having substantially the same energy, and the transfer zone (7) may be maintained at a relatively low pressure so that there is relatively little collision between the ions and the background gas as the ions move to the TOF mass spectrometer (8). Under these conditions, it will be seen that the transfer zone (7) operates as a time of flight such that ions having a relatively low mass-to-charge ratio move faster than ions having a higher mass-to-charge ratio. In this way, fragment or product ion species having a relatively low mass-to-charge ratio, emitted from the ion accumulator (6) after heavier fragment or product ion species (i.e., having a higher mass-to-charge ratio), catch up with the heavier fragment or product ion species and reach the TOF mass spectrometer (8) substantially simultaneously with them. The pusher of the TOF mass spectrometer (8) pulses the pusher at the time when a number of different types of fragment or product ions reach the pusher of the TOF mass spectrometer (8) simultaneously, synchronized with the emission of ions from the ion accumulator (6). In this way, the TOF mass spectrometer has a relatively high duty cycle.

[0113] The second ion accumulator (6) may be a mass-selective ion trap. The ion trap may be a 3D quadrupole field ion trap or a linear ion trap. Ions may be ejected from the ion trap into the transfer zone (7) and toward the TOF mass spectrometer (8) in reverse order of mass-to-charge ratio. This can be achieved in various ways as known in the art. For example, an RF voltage and / or DC voltage applied to the electrodes of the ion trap may be varied over time (e.g., scanned) to cause ions with a sequentially decreasing mass-to-charge ratio to become destabilized in the ion trap and thus ejected into the transfer zone (7) and toward the TOF mass spectrometer (8). Alternatively, or additionally, an AC voltage may be applied to the electrodes of the ion trap to resonantly excite and eject ions of a specific mass-to-charge ratio from the ion trap into the transfer zone (7) and toward the TOF mass spectrometer (8). The frequency of such AC voltage can be changed over time (e.g., scanned) to sequentially emit ions with a decreasing mass-to-charge ratio. For example, the accumulator (6) can mass-selectively emit ions in a decreasing mass-to-charge ratio as described in US 6770872 incorporated herein by reference.

[0114] The inventors recognized that the period during which the second ion accumulator (6) can accumulate fragment or product ions and release them in reverse order of mass-to-charge ratio is comparable to the period during which any given precursor ion is eluted from the upstream separator (3). For example, in an example, the second ion accumulator (6) accumulates and releases fragment or product ion species from any given precursor ion species over a period of approximately 1 ms, which is approximately the same period as the precursor ion species being eluted from the separator (3). Thus, fragment or product ion species derived from the first precursor ion species eluted from the ion separator (3) during a given separation cycle of the separator (3) can be accumulated, captured, and released (in reverse order of mass-to-charge ratio) before being eluted from the ion separator (3) within the same separation cycle of the second precursor ion species separator (3). This is explained in more detail in relation to FIG. 6. As such, the mass spectrometer has a relatively high duty cycle because the precursor ions are fragmented and analyzed while they are delayed in the separator without being discarded by other precursor ions.

[0115] FIG. 6 illustrates a method in which the process described in relation to FIG. 5 can be repeated multiple times for different precursor ion species eluted from the separator (3) during the same separation cycle.

[0116] The lower plot of FIG. 6 corresponds to the process described in relation to FIG. 5, where the first precursor ion species eluted from the separator (3) is fragmented or reacted, and the resulting fragment or product ion is accumulated in the accumulator (6) and then released to the TOF mass spectrometer (8) in reverse order of mass-to-charge ratio.

[0117] The intermediate plot of FIG. 6 shows the same process performed for a second precursor ion species eluted from separator (3) during the same separation cycle as the first precursor ion species, but at a shorter time. More specifically, according to the intermediate plot of FIG. 6, the mass filter (4) is set to deliver the second precursor ion species represented by the dark ellipse in the intermediate plot. The second precursor ion species is then delivered to a fragmentation or reaction device (5), where it is fragmented or reacted to form fragment or product ions. This is illustrated by five brighter ellipses arranged in a column with a dark ellipse, but it will be recognized that five or more different types of fragment or product ions may be produced. The fragment or product ions derived from the second precursor ion species are then delivered to a second ion accumulator (6) and released from it in reverse order of mass to charge ratio, so that at least some of the different fragment or product ion species reach the TOF mass spectrometer (8) substantially simultaneously.

[0118] The upper plot of FIG. 6 illustrates the same process performed for a third precursor ion species eluted from separator (3) during the same separation cycle as the first and second precursor ion species, but at a shorter time. More specifically, according to the upper plot of FIG. 6, the mass filter (4) is set to deliver the third precursor ion species, represented by a dark ellipse. The third precursor ion species is then delivered to a fragmentation or reaction device (5), where it is fragmented or reacted to form fragment or product ions. This is illustrated by five brighter ellipses arranged in a column with a dark ellipse, but it will be recognized that five or more different types of fragment or product ions may be produced. The fragment or product ions are then delivered to a second ion accumulator (6) and released from it in reverse order of mass-to-charge ratio, so that at least some of the different fragment or product ion species reach the TOF mass spectrometer (8) substantially simultaneously.

[0119] The mass spectrometer may be configured so that only fragment or product ions derived from any given precursor ion species enter the accumulator (6) after all fragment or product ions derived from previously analyzed precursor ion species have been discharged from the accumulator. This can be achieved, for example, by an analyzer that controls the time at which the mass filter (4) switches to allow the given precursor ion species to be delivered to be the time or after the accumulator (6) has discharged the fragment or product ion with the lightest mass-to-charge ratio derived from the preceding precursor ion species. Alternatively, an ion gate may be provided upstream of the accumulator (6) controlled by the analyzer to prevent ions from entering the accumulator until the accumulator (6) is controlled to discharge all fragment or precursor ions in reverse order of mass-to-charge ratio.

[0120] Although it is shown that three precursor ions are analyzed during a single separation cycle of the species separator (3), it is considered that only two species of precursor ions, or more than three species of precursor ions, may be analyzed sequentially in the manner described during a single separation cycle.

[0121] Additionally, although the above method has been described so far in the context of a separator (3) performing a single separation cycle, it will be understood that multiple separation cycles may be performed during the same experimental run, and the above method may be repeated for each of these separation cycles during the experimental run.

[0122] The aforementioned method of synchronizing the transfer of ions between various components of the analytical system improves the overall experimental duty cycle of the analytical system. For example, the mass filter (4) is synchronized with the ion separator (3) so that during a single separation cycle of the separator (3), the mass filter (4) switches between transferring different precursor ion species at different times. The precursor ions transferred by the mass filter (4) are fragmented or reacted in the reaction device (5) and then pass to the second ion accumulator (6). The second ion accumulator (6) is synchronized with the mass filter (4) (and thus also synchronized with the ion separator (3)) so that during a single separation cycle of the separator (3): (i) a first set of fragment or product ions derived from the first precursor ion species, eluted from the separator (3), and transferred by the mass filter (4) is accumulated in the second ion accumulator (6) and then released into the transfer zone (7); (ii) A second set of fragment or product ions derived from the second precursor ion species, eluted from the separator (3), and delivered by the mass filter (4) is accumulated in the second ion accumulator (6) and then released into the delivery area (7). In this way, the mass spectrometer has a relatively high duty cycle because the precursor ions are fragmented and analyzed while other precursor ions are delayed in the separator (3) without being discarded. Additionally, the TOF mass spectrometer (8) can be synchronized with the release of ions from the second ion accumulator (6) to pulse the pusher of the TOF mass spectrometer when multiple fragment or product ion species from the same precursor reach the pusher simultaneously. In this way, the TOF mass spectrometer has a relatively high duty cycle.

[0123] FIG. 7 illustrates another method according to the same disclosure as described above in relation to FIG. 5 and FIG. 6, up to the point where fragment or product ion is released from the second ion accumulator (6). In the embodiment illustrated by FIG. 7, different fragment or product ion species are released from the second ion accumulator (6) substantially simultaneously into the transfer zone (7). This is illustrated by the five fragment or product species shown below the transfer zone (7) in FIG. 7.

[0124] The transfer zone (7) is configured to separate fragment or product ion species according to their physicochemical properties. For example, ions in the transfer zone (7) may be separated according to ion mobility or mass-to-charge ratio, or a combination of both of these physicochemical properties. For example, the transfer zone (7) may be maintained at a relatively low pressure so that there are relatively few collisions between the ions and the background gas inside as the ions move to the TOF mass spectrometer (8). Under these conditions, it will be noted that the transfer zone (7) functions as a TOF zone where ions are separated according to their mass-to-charge ratio. As such, fragment or product ion species with a relatively low mass-to-charge ratio will reach the TOF mass spectrometer (8) before ions with a higher mass-to-charge ratio. This is illustrated in FIG. 7 by the five fragment or product ion species shown below the TOF mass spectrometer (8). These species are shown spaced apart on the time axis, showing that the smallest mass-to-charge ratio fragment or product ion species arrives at the TOF mass spectrometer (8) first, followed by progressively higher mass-to-charge ratio fragment or product ion species reaching progressively higher times.

[0125] Alternatively, fragment or product ion species may be pulsed into a transfer zone (7) and separated internally according to their mobility through a background gas arranged within the transfer zone (7). The ions may be driven through the background gas by an electric field to be separated according to mobility. For example, the ions may be driven by applying a static DC potential gradient along the transfer zone (7) and / or by repeatedly shifting the DC potential along the transfer zone (7). The electric field may be arranged so that the ions are pressurized through the transfer zone (7) toward the TOF mass spectrometer (8). Alternatively, the background gas may flow in a direction that pressurizes the ions toward the TOF mass spectrometer (8), while the electric field may be arranged to pressurize the ions against the gas flow so that the ions are separated according to mobility. In these mobility separation embodiments, the ions pulsed into the transfer zone (7) may reach the TOF mass spectrometer (8) in a sequence that increases or decreases mobility.

[0126] In the embodiment described in relation to FIG. 7, the transfer region (7) acts as an ion separator that performs a separation cycle in which different ion species are pulsed into the transfer region (7), separated internally according to their physicochemical properties, and then eluted to a mass spectrometer (8) at different times according to their physicochemical property values. This separation cycle may be shorter than the separation cycle of the ion separator (3).

[0127] After the separation of ions in the transfer region (7) according to their physicochemical properties, the ions can be transferred into an ion guide that guides the separated ions to the TOF mass spectrometer (8) while maintaining the separation. For example, a voltage can be applied to the ion guide to create a series of potential wells (and thus potential barriers) spaced axially along the ion guide. The voltage may be a DC voltage, but it is thought that alternatively, a pseudo-potential well can be formed by using an AC voltage. The voltage applied to the electrodes can be varied over time to cause the series of potential wells to move from the upstream end of the ion guide along the ion guide to the TOF mass spectrometer (8). As ions with different values ​​of physicochemical properties reach the upstream end of the ion guide at different times, ions with different ranges of physicochemical properties are captured in different potential wells and thus transition in said wells to reach the TOF mass spectrometer (8) at different times. The ion guide can operate in the same manner as the ion guide described in US 7829841, which is incorporated herein by reference, for example.

[0128] In the embodiment illustrated in FIG. 7, fragment or product ions having a limited range of physicochemical properties (where the transfer area (7) separates the ions accordingly) simultaneously reach the pusher of the TOF mass spectrometer (8) and can synchronize the pusher with the release of ions from the second ion accumulator (6) so that the pusher pulses ions having this selected range of physicochemical properties into the TOF area of ​​the TOF mass spectrometer (8).

[0129] FIG. 8 illustrates a method in which the process described in relation to FIG. 7 can be repeated multiple times for different precursor ion species eluted from the first ion separator (3) during the same separation cycle.

[0130] The lower plot of FIG. 8 corresponds to the process described in relation to FIG. 7, where the first precursor ion species eluted from the separator (3) is fragmented or reacted, and the resulting fragment or product ion is accumulated and then released all at once into the TOF mass spectrometer (8).

[0131] The intermediate plot of FIG. 8 shows the same process performed for a second precursor ion species eluted from separator (3) during the same separation cycle as the first precursor ion species, but at a shorter time. More specifically, according to the intermediate plot of FIG. 8, the mass filter (4) is set to deliver the second precursor ion species, represented by the dark ellipse in the intermediate plot. The second precursor ion species is then delivered to a fragmentation or reaction device (5), where it is fragmented or reacted to form fragment or product ions. This is illustrated by five brighter ellipses arranged in a column with a dark ellipse, but it will be recognized that five or more different types of fragment or product ions may be produced. The fragment or product ions derived from the second precursor ion species are then delivered to a second ion accumulator (6), from which they are all released at once, causing different fragment or product ion species to reach the TOF mass spectrometer (8) at different times.

[0132] The upper plot of FIG. 8 illustrates the same process performed for a third precursor ion species eluted from separator (3) during the same separation cycle as the first and second precursor ion species, but at a shorter time. More specifically, according to the upper plot of FIG. 8, the mass filter (4) is set to deliver the third precursor ion species, represented by a dark ellipse. The third precursor ion species is then delivered to a fragmentation or reaction device (5), where it is fragmented or reacted to form fragment or product ions. This is illustrated by five brighter ellipses arranged in a column with a dark ellipse, but it will be recognized that five or more different types of fragment or product ions may be produced. The fragment or product ions are then delivered to a second ion accumulator (6), from which they are all released at once, causing the different fragment or product ion species to reach the TOF mass spectrometer (8) at different times.

[0133] The mass spectrometer may be configured so that only fragment or product ions derived from any given precursor ion species enter the second ion accumulator (6) after all fragment or product ions derived from the previously analyzed precursor ion species have been discharged from the accumulator (6). This can be achieved, for example, by an analyzer that controls the time at which the mass filter (4) switches to allow the given precursor ion species to be delivered to be the time at or after the time at which the accumulator (6) discharged the fragment or product ions derived from the preceding precursor ion species. Alternatively, an ion gate may be provided upstream of the accumulator (6) controlled by the analyzer to prevent ions from entering the accumulator until the accumulator (6) is controlled to discharge all fragment or precursor ions.

[0134] Although it is shown that three precursor ions are analyzed during a single separation cycle of the species separator (3), it is considered that only two species of precursor ions, or more than three species of precursor ions, may be analyzed sequentially in the manner described during a single separation cycle.

[0135] Additionally, although the above method has been described so far in the context of a separator (3) performing a single separation cycle, it will be understood that multiple separation cycles may be performed during the same experimental run, and the above method may be repeated for each of these separation cycles during the experimental run.

[0136] Although the present invention has been described with reference to preferred embodiments, it will be understood by those skilled in the art that various modifications in form and detail may be made without departing from the scope of the invention as set forth in the appended claims.

[0137] For example, although an embodiment in which a second ion accumulator (6) is present has been described in relation to FIGS. 7 and 8, it is considered that the second ion accumulator (6) may be omitted. In this embodiment, each precursor ion species may be fragmented or reacted in a fragmentation or reaction device (5) without capturing the ion, and the resulting fragment or product ion generated is transferred into a transfer zone (7) without being captured. In this embodiment, the fragment or product ion of any given precursor ion species will enter the transfer zone (7) at a time corresponding to the time when the mass filter (4) begins to transfer the precursor ion species. Thus, the start of the separation cycle in the transfer zone (7) for the fragment or product ion of any given precursor ion species is triggered by the time when the mass filter (4) switches to begin transferring the precursor ion species. As previously mentioned, fragment or product ions having a limited range of physicochemical properties reach the pusher of the TOF mass spectrometer (8) at different times. The pusher is synchronized with the time when the mass filter (4) switches to deliver a new precursor ion species, causing the pusher to pulse ions having a selected range of physicochemical properties into the TOF region of the TOF mass spectrometer (8).

[0138] An embodiment in which the analyzer comprises a first ion accumulator (2) and / or a second ion accumulator (6) is described herein. An ion attenuation device may be provided upstream of the first and / or second ion accumulators to attenuate ions moving toward them. This may be used to reduce the number of ions entering the ion accumulators (2, 6), for example, to reduce space-charge effects in the ion accumulators and / or to prevent saturation of the detector in the TOF mass spectrometer (8). Additionally or alternatively, an ion attenuation device may be provided downstream of the first and / or second ion accumulators (2, 6) to attenuate ions moving downstream therefrom. This may be used, for example, to prevent saturation of the detector in the TOF mass spectrometer (8).

[0139] Although the mass filter (4) has been described as stepping through different individual mass transfer windows as ions are eluted from the separator (3), the mass filter (4) is considered to have a mass transfer window that is instead scanned progressively. For example, the mass transfer window may increase by one mass-to-charge ratio unit at a time. Alternatively, the mass filter (4) may have a mass transfer window configured to simultaneously transfer a range of mass-to-charge ratios (e.g., a range consisting of multiple Da). Such a mass transfer window can be scanned progressively so that whenever the mass transfer window is moved to transfer a new mass range, the new mass range still partially overlaps with the previous mass range that the filter (4) was configured to transfer.

[0140] Alternatively or additionally, although the filter (4) has been described as a mass-to-charge ratio filter, the filter is considered to be capable of filtering ions based on other physicochemical properties such as ion mobility or FAIMS.

[0141] Alternatively or additionally, although the separator (3) has been described as an ion mobility separator, the separator is considered to be capable of separating ions based on other physicochemical properties such as mass-to-charge ratio.

[0142] In a less preferred embodiment, the first ion accumulator (2) may be omitted, and the source (1) may be, for example, a pulsed ion source, or may instead pulse ions into the separator (3) by providing an ion gate between the source (1) and the separator (3).

Claims

Claim 1 A mass spectrometry method comprising: a) accumulating precursor ions in a first ion accumulator; b) performing a separation cycle comprising pulses a packet of precursor ions from the first ion accumulator into an ion separator, and separating the precursor ions such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times; c) mass filtering the precursor ions eluted from the ion separator to deliver a selected precursor ion species; d) fragmenting or reacting the selected precursor ion species to generate a set of fragments or product ion species therefrom; e) accumulating the set of fragments or product ion species in a second ion accumulator; f) releasing the set of fragments or product ion species from the second ion accumulator into a TOF mass spectrometer, wherein the operation of the TOF mass spectrometer is synchronized with the release of ions from the second ion accumulator, so that a plurality of different species of the set of fragments or product ion species are simultaneously pulsed into the TOF region of the TOF mass spectrometer by a pusher electrode; and g) a mass spectrometry method comprising repeating steps c) to f) at least once during the separation cycle, wherein the selected precursor ion species comprises different steps each time steps c) to f) are performed. Claim 2 A mass spectrometry method according to claim 1, wherein the ion separator is an ion mobility separator and the physicochemical characteristic is ion mobility. Claim 3 A mass spectrometry method according to claim 1, wherein the fragment or product ion species is pressurized into the second ion accumulator: (i) fragment or product ion species derived from the same precursor ion species reach the second ion accumulator over the same period and accumulate in the second ion accumulator for at least part of such period, and / or (ii) fragment or product ion species derived from the precursor species delivered by the mass filter at different times reach the second ion accumulator over different respective periods. Claim 4 A mass spectrometry method according to claim 1, wherein whenever the sequence of steps c) to e) is performed, the fragment or product ion species are accumulated in the second ion accumulator over a period equal to or correlated with the period during which these precursor ion species are transferred by the mass filter. Claim 5 A mass spectrometry method according to claim 1, wherein whenever the sequence of steps c) to e) is performed, only fragment or product ion species derived from the selected precursor ion species, and optionally some ions of the selected precursor ion species itself, are accumulated in the second ion accumulator; but other precursor ion species and fragment or product ions derived therefrom are not accumulated in the second ion accumulator. Claim 6 A mass spectrometry method according to claim 1, wherein, whenever the sequence of steps b) and c) is performed, the mass filter is controlled to deliver the selected precursor ion species only over a period equal to, correlated with, or shorter than the period during which the corresponding precursor ion species is eluted from the ion separator. Claim 7 A mass spectrometry method according to any one of claims 1 to 6, wherein step f) releases the fragment or product ion species from the second ion accumulator in reverse order of mass-to-charge ratio, starting with ions of a relatively high mass-to-charge ratio and gradually releasing ions of a lower mass-to-charge ratio, such that different species of the fragment or product ion species simultaneously reach the pusher electrode and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 8 A mass spectrometry method according to claim 7, wherein a transfer region is provided between the second ion accumulator and the TOF mass spectrometer, and the pressure in the transfer region and the energy released from the second ion accumulator to the ions cause fragment or product ions having a relatively low mass-to-charge ratio to catch up with fragment or product ions having a higher mass-to-charge ratio, so that the ions simultaneously reach the pusher electrode and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 9 A mass spectrometry method according to claim 7, wherein all of the fragment or product ion species emitted from the second ion accumulator arrive at the pusher electrode at the same time whenever step f) is performed and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 10 A mass spectrometry method according to any one of claims 1 to 6, wherein step f) comprises the step of simultaneously releasing all of the fragment or product ion species from the second ion accumulator, providing a transfer zone between the second ion accumulator and the TOF mass spectrometer, separating the ions in the transfer zone according to a second physicochemical property so that the fragment or product ion species reach the TOF mass spectrometer at a time depending on their second physicochemical property value, and synchronizing the operation of the TOF mass spectrometer with the release of the ions from the second ion accumulator so that the fragment or product ion species having a value of a selected range of the second physicochemical property value are simultaneously pulsed into the TOF zone of the TOF mass spectrometer by the pusher electrode. Claim 11 A mass spectrometry method according to claim 10, comprising the step of receiving an input signal representing a value of the selected range of the second physicochemical characteristic in a mass spectrometer performing the above method, and synchronizing the operation of the TOF mass spectrometer with the emission of the ion from the second ion accumulator so that a fragment or product ion species having a value of the selected range of the second physicochemical characteristic value is simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 12 In claim 10, the second physicochemical property is a mass-to-charge ratio, and the mass spectrometry method separates ions in the transfer region according to the mass-to-charge ratio. Claim 13 In item 10, the second physicochemical property is ion mobility, and a mass spectrometry method for separating ions in the transfer region according to ion mobility. Claim 14 A mass spectrometry method according to any one of claims 1 to 6, wherein steps a) to g) are repeated during a single experimental run. Claim 15 In a mass spectrometer, a first ion accumulator; an ion separator; a mass filter; a fragmentation or reaction device; a second ion accumulator; a TOF mass spectrometer having a TOF region and a pusher electrode; and includes a control circuit configured to control a mass spectrometer, wherein the mass spectrometer performs a separation cycle comprising: a) accumulating precursor ions in the first ion accumulator; b) pulse a packet of the precursor ions from the first ion accumulator into the ion separator; and separating the precursor ions in the ion separator such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times; c) mass filtering the precursor ions eluted from the ion separator using the mass filter to deliver a selected precursor ion species; d) fragmenting or reacting the selected precursor ion species in the fragmentation or reaction device to generate a set of fragmented or product ion species therefrom; e) accumulating the set of fragmented or product ion species in the second ion accumulator; and f) releasing the set of fragmented or product ion species from the second ion accumulator into the TOF mass spectrometer, wherein the operation of the TOF mass spectrometer is synchronized with the release of ions from the second ion accumulator, so as to the fragmented or product ion species A mass spectrometer, wherein a plurality of different papers of a set are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode, and steps c) to f) are repeated at least once during the separation cycle, wherein the mass filter is controlled such that the selected precursor ion paper is different each time steps c) to f) are performed. Claim 16 In claim 15, the control circuit is configured to control the mass spectrometer, wherein step f) comprises the step of releasing fragment or product ion species from the second ion accumulator in reverse order of mass-to-charge ratio, starting with ions of a relatively high mass-to-charge ratio and gradually releasing ions of a lower mass-to-charge ratio, so that different species of fragment or product ion species simultaneously reach the pusher electrode and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 17 A mass spectrometer according to claim 16, comprising a transfer region between the second ion accumulator and the TOF mass spectrometer, wherein the spectrometer is configured to maintain pressure in the transfer region and release ions from the second ion accumulator with energy, such that fragment or product ions having a relatively low mass-to-charge ratio catch up with fragment or product ions having a higher mass-to-charge ratio, so that the ions simultaneously reach the pusher electrode and are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 18 A mass spectrometer according to claim 15, comprising a transfer region between the second ion accumulator and the TOF mass spectrometer; wherein the control circuit is configured to control the mass spectrometer, and step f) comprises the step of simultaneously releasing all the fragment or product ion species from the second ion accumulator into the transfer region, so that the fragment or product ion species are separated in the transfer region according to a second physicochemical property and reach the TOF mass spectrometer at a time depending on the value of their second physicochemical property, and synchronizing the operation of the TOF mass spectrometer with the release of the ions from the second ion accumulator so that the fragment or product ion species having a value of a selected range of the second physicochemical property value are simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 19 In claim 18, the analyzer comprises a user interface configured to input a value of a selected range of the second physicochemical characteristic, wherein the analyzer is configured such that the control circuit controls the operation of the TOF mass spectrometer based on the value of the selected range to synchronize the operation of the TOF mass spectrometer with the emission of the ion from the second ion accumulator, thereby causing a fragment or product ion species having a value of the selected range of the second physicochemical characteristic to be simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 20 A mass spectrometry method comprising: a) accumulating precursor ions in a first ion accumulator; b) performing a separation cycle comprising pulses of said precursor ions from the first ion accumulator into an ion separator, and separating said precursor ions such that precursor ions having different values ​​of first physicochemical properties are eluted from said ion separator at different times; c) switching a mass filter that mass filters said precursor ions eluted from said ion separator to initiate the delivery of a selected precursor ion species; d) fragmenting or reacting said selected precursor ion species to generate a set of fragment or product ion species therefrom; e) delivering said set of fragment or product ion species through a delivery region to a TOF mass spectrometer having a pusher electrode and a TOF region, wherein the ions are separated in said delivery region according to a second physicochemical property, so that the fragment or product ion species reach said TOF mass spectrometer at a time dependent on their second physicochemical property value, and the operation of said TOF mass spectrometer is synchronized with the time at which the mass filter is switched so that they reach said pusher electrode simultaneously A mass spectrometry method comprising: a step of initiating the delivery of the selected precursor ion species such that the fragment or product ion species having a value of a selected range of the second physicochemical properties is simultaneously pulsed by the pusher electrode within the flight time of the TOF mass spectrometer; and f) repeating steps c) to e) at least once during the separation cycle, wherein the selected precursor ion species comprises different steps each time steps c) to e) are performed. Claim 21 A mass spectrometry method according to claim 20, comprising the steps of: receiving an input signal representing a value of a selected range of the second physicochemical property in a mass spectrometer performing the above method; and controlling the operation of the TOF mass spectrometer so that a fragment or product ion species having a value of the selected range of the second physicochemical property simultaneously reaches the pusher electrode and is simultaneously pulsed into the TOF region of the TOF mass spectrometer by the pusher electrode. Claim 22 In a mass spectrometer, a first ion accumulator; an ion separator; a mass filter; a fragmentation or reaction device; a TOF mass spectrometer having a TOF region and a pusher electrode; a transfer region between the fragmentation or reaction device and the TOF mass spectrometer; and includes a control circuit configured to control a mass spectrometer, wherein the mass spectrometer performs a separation cycle comprising: a) accumulating precursor ions in the first ion accumulator; b) pulse a packet of the precursor ions from the first ion accumulator into the ion separator; and separating the precursor ions in the ion separator such that precursor ions having first physicochemical properties of different values ​​are eluted from the ion separator at different times; c) switching a mass filter that mass filters the precursor ions eluted from the ion separator to initiate the transfer of a selected precursor ion species; d) fragmenting or reacting the selected precursor ion species in the fragmentation or reaction device to generate a set of fragmented or product ion species therefrom; e) transferring the set of fragmented or product ion species through the transfer region to the TOF mass spectrometer, wherein the ions are separated in the transfer region according to a second physicochemical property, so that the fragmented or product ion species reach the TOF mass spectrometer at a time depending on their second physicochemical property value, and the operation of the TOF mass spectrometer is f) initiating the delivery of the selected precursor ion species so that the fragment or product ion species having a value of a selected range of the second physicochemical properties simultaneously reaching the pusher electrode at the time of switching of the mass filter is pulsed simultaneously by the pusher electrode within the flight time of the TOF mass spectrometer, and repeating steps c) to e) at least once during the separation cycle, wherein the selected precursor ion species are different each time steps c) to e) are performed.

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