Mass spectrometer with high duty cycle

Abstract

A method of mass spectrometry comprising the steps of: a) providing a mass spectrometer having a time-of-flight (TOF) mass analyzer; b) performing a survey scan including isolating a packet of precursor ion species and mass analyzing the ions to obtain a first mass spectral data; c) determining a time window during which one of the precursor ion species, or fragment or product ions derived therefrom, was mass analyzed; and d) isolating another packet of precursor ion species and mass analyzing the ions to obtain a second mass spectral data, wherein a pusher of the TOF mass analyzer is pulsed according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence comprising a pulse sequence period. f) selecting from the second mass spectral data that was acquired during a time period corresponding to a time window of the survey scan to acquire selected data; g) repeating steps d) to f) at least one further time to obtain a plurality of sets of selected data; and combining the plurality of sets of selected data and decoding the combined data to acquire mass spectral data indicative of the mass-to-charge ratios of ions detected by the TOF mass analyzer.

Description

[Technical field]

[0001] (CROSS REFERENCE TO RELATED APPLICATIONS) This application claims priority to and the benefit of UK Patent Application No. 2204104.0, filed March 23, 2022, the entire contents of which are incorporated herein by reference.

[0002] FIELD OF THEINVENTION The present invention relates generally to mass spectrometers in which ions are repeatedly pulsed into a separation region causing the ions to be separated according to their mass-to-charge ratio. [Background technology]

[0003] In both Data Dependent Acquisition (DDA) and tandem (MSMS) mass spectrometry, precursor ions are filtered so that only selected species of precursor ions are transmitted downstream for analysis at any given time. The mass spectrometer therefore selects different species of precursor ions to be transmitted downstream for analysis. This process continues until the desired species of precursor ions are analyzed. In general, it is desirable to sequentially select and transmit as many precursor ions per unit time as possible in order to analyze the sample as quickly as possible. 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 the sensitivity of the ions detected. For example, if the spectrometer settings are changed to increase the number of transmitted precursor species from 25 different precursors per second to 50 different precursors per second, this results in half the number of ions in each fragment ion scan.

[0004] It would be desirable to increase the overall duty cycle of such equipment. Summary of the Invention

[0005] A first aspect of the present disclosure is a method of mass spectrometry comprising: a) providing a mass spectrometer having an ion separator for separating ions according to a physicochemical property, and a time-of-flight (TOF) mass analyzer having an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region to the detector; b) performing a survey scan, where a separation cycle is performed in which packets of precursor ion species are separated in the ion separator such that precursor ion species having different values ​​of the physicochemical property elute from the ion separator at different times, and then mass analyzing the separated precursor ion species, or fragment or product ions derived therefrom, in the TOF mass analyzer to obtain first mass spectral data; c) determining from the first mass spectral data a time window during which one of the precursor ion species, or fragment or product ions derived therefrom, was mass analyzed by the TOF mass analyzer; and d) performing a survey scan, where a packet of precursor ion species is separated in the ion separator such that precursor ion species having different values ​​of the physicochemical property elute from the ion separator at different times, and then mass analyzing the separated precursor ion species, or fragment or product ions derived therefrom, in the TOF mass analyzer to obtain first mass spectral data. performing another separation cycle in which another packet of precursor ion species is separated in an ion separator; then e) mass analysing in a TOF mass analyser the precursor ion species separated in step d), or fragment or product ions derived therefrom, to obtain second mass spectral data, the mass analysis comprising pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence; f) selecting from the second mass spectral data mass spectral data acquired during a period corresponding to the time window of the survey scan to obtain selected data; g) repeating steps d) to f) at least one further time such that a plurality of sets of selected data are obtained; h) combining the plurality of sets of selected data to obtain combined data;i) decoding the combined data to obtain mass spectral data indicative of the mass-to-charge ratios of the ions detected by the TOF mass analyzer;

[0006] As mass spectral data for the same precursor ion species (or fragment or product ions derived therefrom) are selected and combined from multiple separation cycles, the number of ions occurring at a given flight time (i.e., having a given mass-to-charge ratio) is more likely to reach the level required by the decoding process to determine that a mass peak is present. This is in contrast to known techniques in which mass spectral data obtained from a single separation cycle is decoded. In such known techniques, ions may not be determined to be associated with a mass peak if they have low abundance. The new technique disclosed herein can avoid such shortcomings because it decodes the data only after it is combined.

[0007] Step c) may include determining a first time delay between a start time of a separation cycle in the survey scan and a start time of the time window, while the method may include setting the period in step f) to start after a second time delay from a start time of another separation cycle in step d), the first time delay being the same as the second time delay.

[0008] The time window may have the same duration as the period in step f).

[0009] The step of selecting mass spectral data in step f) may include selecting only a portion of the mass spectral data obtained in step e), where other unselected mass spectral data obtained in step e) may be discarded or not selected for combination with the other data.

[0010] The selected mass spectral data obtained in step f) may include mass spectral data obtained during a plurality of different ones of the pulse sequence periods of step e).

[0011] The different pulse sequence periods may be consecutive (ie immediately adjacent) pulse sequence periods.

[0012] The combined data may be decoded based on knowledge of the pulse sequence used in each of the multiple pulse sequence periods.

[0013] All of the multiple pulse sequences may consist of the same pulse sequence, ie, the same pattern of pulses may be used in each one of the pulse sequences.

[0014] The decoding may involve assigning data corresponding to detected ions to a mass-to-charge ratio and determining that a mass-to-charge ratio peak is detected only if more than a threshold number of ions are assigned to a given mass-to-charge ratio.

[0015] If less than a threshold number of ions are assigned to a given mass-to-charge ratio, the data for those ions (from the combined data) may be discarded.

[0016] Optionally, determining a time window in step c) comprises determining a time window during which only a single one of the precursor ion species, or fragment or product ions derived therefrom, reaches the TOF mass analyzer and is mass analyzed by the TOF mass analyzer, and thus the selected mass spectral data in step f) may consist of only mass spectral data for that single one of the precursor ion species, or fragment or product ions derived therefrom.

[0017] The method may comprise fragmenting or reacting precursor ion species in a fragmentation or reaction device between steps d) and e), and said mass analysing in step e) comprises mass analysing the resulting fragment or product ions.

[0018] It should be understood that fragmenting or reacting any given precursor ion species may result in multiple different fragment or product ion species being formed, and a TOF mass analyzer may simultaneously mass analyze all of the different fragment or product species derived from any given precursor species.

[0019] The analyzer can associate mass spectral data representing the mass-to-charge ratios of the fragment or product ions with their precursor ions. This may be done by associating the fragment or product ions with precursor ions detected by the TOF mass analyzer at the same time as, or with the same intensity profile as, these fragment or product ions (as some precursor ions may remain even after the fragmentation or reaction step). Alternatively, if the precursor ions are mass filtered such that different precursor ions are transmitted to the fragmentation or reaction device at different times, the fragment or product ions may be associated with their precursor ions based on their detection times.

[0020] The method may thus include the steps of separating precursor ions according to physicochemical properties, fragmenting or reacting the precursor ions to produce fragment or product ions, transmitting the fragment or product ions into a mass analyzer such that fragment or product ions derived from different precursor ions are transmitted into the mass analyzer over different time windows, and performing mass analysis on the fragment or product ions.

[0021] The method may include providing a mass filter for filtering ions between the ion separator and the fragmentation or reaction device, the mass filter filtering ions to transmit only ions having a restricted value or range of values ​​of mass to charge ratio at any given time, and controlling the mass filter to change the value or range of values ​​as ions elute from the ion separator to transmit different species of ions towards the fragmentation or reaction device at different times.

[0022] The mass filter may be controlled to vary the value, or range of values, over a cycle time that is synchronised with the separation cycle of step d).

[0023] The mass filter may be controlled in synchronism with the elution times of ions from the ion separator such that at any given time the mass filter is set to transmit the mass to charge ratios expected to arrive at the mass filter from the ion separator. For example, if the ion separator is an ion mobility separator, the transit time of a given mass to charge ratio ion through the ion separator can be estimated (as mobility and mass to charge ratio are related) and used to control the mass filter to selectively transmit that mass to charge ratio as it exits the ion separator.

[0024] Thus, the mass filter can be controlled to transmit one or more ion species, while other ion species that are desired to be transmitted later for analysis are still traveling through the ion separator towards the mass filter. Thus, relatively few ions are discarded at the mass filter, and the sensitivity of the analysis is relatively high. However, separating ions in this way can result in relatively few ions reaching the TOF mass analyzer per unit time, which can lead to the problems described herein when using coded frequent pulsing (EFP) techniques. The present disclosure overcomes this by combining EFP data in a new manner.

[0025] If ions are fragmented or reacted, separation of the precursor ions by the ion separator may be preserved in the fragment or product ions such that fragment or product ions of different precursor ion species may arrive at the TOF mass analyzer over different respective time periods.

[0026] Each of the separation cycles described herein may be initiated by pulsing a packet of ions containing the precursor ion species of interest into the ion separator.

[0027] For example, ions may be accumulated in an ion accumulator and periodically pulsed to an ion separator which performs a separation cycle between each pulse, and the mass filter may be changed during each separation cycle as described above, for example in synchronism with the ion separator.

[0028] The first physicochemical property may be ion mobility.

[0029] For example, the ion separator may be a drift-time ion mobility separator having electrodes and a voltage source that maintains a static DC gradient that urges ions through or against a background gas such that the ions separate according to their mobility through the gas. Alternatively, the ion separator may have electrodes and a voltage source configured to repeatedly move a DC or pseudo-potential barrier along the ion separator to urge ions through or against a gas within the ion separator such that the ions separate according to their mobility through the gas.

[0030] Alternatively, the first physicochemical property may be, for example, mass-to-charge ratio.

[0031] The step of mass analyzing during that survey scan in step b) may include pulsing the pusher in a manner such that the duration between any pair of adjacent pusher pulses is equal to or greater than the flight time from the pusher to the ion detector of the largest mass-to-charge ratio ion pushed by the pusher. Thus, data acquired by the TOF mass analyzer in a multiple-push survey scan is not multiplexed and does not require decoding.

[0032] It will be appreciated that the survey scan may process ions in the same manner as the (non-survey scan) mode described as being performed following the survey scan, except that the TOF mass analyzer and TOF data are used differently in the two modes. In other words, if the non-survey scan mode includes the above-mentioned mass filtering and / or fragmentation / reaction steps, the survey scan mode may also include corresponding steps. This ensures that the time window identified in the survey scan corresponds to the duration during which that one of the precursor ion species, or fragment or product ions derived therefrom, is mass analyzed in the TOF mass analyzer during the non-survey scan.

[0033] A first aspect of the present disclosure also provides a mass spectrometer comprising a time-of-flight (TOF) mass analyzer having an ion separator for separating ions according to physicochemical properties, an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region to the detector, and control circuitry configured to carry out the methods described herein.

[0034] The mass spectrometer may be configured to perform any of the methods described herein.

[0035] A second aspect of the disclosure provides a method of mass analysis that may include providing a time-of-flight (TOF) mass analyzer having an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region and toward the detector; mass analyzing the ions in the TOF mass analyzer to obtain data about the ions, the mass analyzing including pulsing the pusher according to a pulse sequence of successive pushes arranged such that a duration between any pair of pushes in the pulse sequence is different from a duration between any other pair of pushes in the pulse sequence; determining that one or more ion species arrive at the TOF mass analyzer during only a portion of one or more of the pulse sequence periods; combining only data acquired by the mass analyzer during the portion of the one or more pulse sequence periods; and decoding the combined data.

[0036] It is recognized that if an ion species arrives at the TOF mass analyzer over a period shorter than the pulse sequence period, it may not be desirable to combine all of the TOF data acquired over that period prior to the decoding step, for example combining TOF data acquired over the entire pulse sequence period would result in combining more noise data than necessary since the ion is not present in the TOF mass analyzer for the entire pulse sequence period.

[0037] The method may include, prior to the step of mass analyzing the ions, performing a survey scan, wherein the one or more ion species are mass analyzed by a TOF mass analyzer, determining from the survey scan a time window during which the one or more ion species reach the TOF mass analyzer, and using the time window to determine a portion of one or more of the pulse sequence periods during which the one or more ion species reach the TOF mass analyzer.

[0038] A second aspect of the disclosure also provides a TOF mass analyzer including an ion detector, a pusher that, when pulsed, pushes ions into a time-of-flight region and towards the detector, and a control circuit configured to mass analyze the ions to acquire data relating to the ions by pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that a duration between any pair of pushes in the pulse sequence is different from a duration between any other pair of pushes in the pulse sequence, and configured to determine that one or more ion species arrive at the TOF mass analyzer during only a portion of one or more of the pulse sequence periods, combine only data acquired by the mass analyzer during that portion of the one or more pulse sequence periods, and decode the combined data to acquire mass spectral data indicative of the mass-to-charge ratio of the one or more species.

[0039] The TOF mass analyser may be configured to carry out any of the methods described in relation to the second aspect of the present disclosure.

[0040] The present disclosure also provides a mass spectrometer comprising a TOF mass analyzer according to a second aspect of the present disclosure.

[0041] A third aspect of the present invention provides a method of mass spectrometry comprising the steps of: (i) providing a time-of-flight (TOF) mass analyzer having an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region towards the detector; (ii) mass analysing ions in the TOF mass analyzer to obtain data relating to the ions, the mass analysing comprising pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence; (iii) combining data obtained during different ones of the pulse sequence periods to obtain combined data; and (iv) decoding the combined data to obtain mass spectral data indicative of the mass-to-charge ratio of the ions.

[0042] Because data from multiple pulse sequence periods are combined, the number of ions occurring at a given flight time (i.e., having a given mass-to-charge ratio) is more likely to reach the level required by the decoding process to determine that a mass peak exists. This is in contrast to known techniques in which data obtained in a single pulse sequence period is decoded. In such known techniques, ions may not be determined to be associated with a mass peak if they have low abundance. The new technique disclosed herein can avoid such shortcomings because it decodes the data only after it is combined.

[0043] The combined data may be decoded based on knowledge of the pulse sequence used in each of the multiple pulse sequence periods.

[0044] All of the multiple pulse sequences may consist of the same pulse sequence, ie, the same pattern of pulses may be used in each one of the pulse sequences.

[0045] The decoding may assign data corresponding to detected ions to a mass-to-charge ratio, and determine that a mass-to-charge ratio peak is detected only if more than a threshold number of ions are assigned to a given mass-to-charge ratio.

[0046] If less than a threshold number of ions are assigned to a given mass-to-charge ratio, the data for those ions (from the combined data) may be discarded.

[0047] At least one ion species is allowed to reach and be mass analyzed by the TOF mass analyzer over a time window that includes the duration of the plurality of different pulse sequences.

[0048] The different pulse sequence periods may be consecutive (ie immediately adjacent) pulse sequence periods.

[0049] The method may combine data acquired during all (i.e., not only some) of the pulse sequence periods during which at least one ion species arrives at the TOF mass analyzer, and then perform a decoding step on the resulting combined data.

[0050] At least one ion species may arrive at the TOF mass analyzer over a time window corresponding to at least one pulse sequence period, and data acquired by the mass analyzer during the at least one pulse sequence period may be combined with data acquired by the mass analyzer during a first pulse sequence period beginning after the time that the at least one ion species stops entering the TOF mass analyzer.

[0051] The method may include a step of fragmenting or reacting precursor ions upstream of the TOF mass analyzer, and the step of mass analysing the ions in the TOF mass analyzer may include mass analysing the resulting fragment or product ions.

[0052] It should be understood that fragmenting or reacting any given precursor species may result in multiple different fragment or product ion species being formed, and a TOF mass analyzer may simultaneously analyze all of the different fragment or product species derived from any given precursor species.

[0053] The analyzer can associate mass spectral data representing the mass-to-charge ratios of the fragment or product ions with their precursor ions. This may be done by associating the fragment or product ions with precursor ions detected by the TOF mass analyzer at the same time as, or with the same intensity profile as, these fragment or product ions (as some precursor ions may remain even after the fragmentation or reaction step). Alternatively, if the precursor ions are mass filtered such that different precursor ions are transmitted to the fragmentation or reaction device at different times, the fragment or product ions may be associated with their precursor ions based on their detection times.

[0054] The method may include the steps of separating ions according to physicochemical properties, feeding the resulting separated ions to a mass analyzer and performing the mass analysing step on these ions.

[0055] The method may include separating precursor ions according to physicochemical properties, fragmenting or reacting the precursor ions to produce fragment or product ions, transmitting the fragment or product ions to a mass analyzer such that fragment or product ions derived from different precursor ions are transmitted to the mass analyzer over different time windows, and performing mass analysis on the fragment or product ions.

[0056] The physicochemical property may be, for example, ion mobility or mass-to-charge ratio. For example, the separator may be a drift-time ion mobility separator having electrodes and a voltage source that maintains a static DC gradient that forces ions through a background gas to separate according to mobility. Alternatively, the separator may have electrodes and a voltage source configured to repeatedly move a DC or pseudo-potential barrier along the ion separator to force ions through or against a gas in the ion separator such that the ions separate according to their mobility through the gas.

[0057] The method may include providing a mass filter between the separator and the TOF mass analyzer for filtering ions such that at any given time it transmits only ions having a restricted value or range of values ​​of mass to charge ratio, and controlling the mass filter to change the value or range of values ​​as ions elute from the ion separator to transmit different species of ions towards the mass analyzer at different times.

[0058] The mass filter may be controlled in synchronism with the elution time of ions from the separator.

[0059] For example, the mass filter may be controlled in synchronism with the elution time of ions from the separator such that at any given time the mass filter is set to transmit the mass to charge ratio expected to arrive at the mass filter from the separator. For example, if the separator is an ion mobility separator, the transit time of a given mass to charge ratio ion through the separator can be estimated (as mobility and mass to charge ratio are related) and used to control the mass filter to selectively transmit that mass to charge ratio as it exits the separator.

[0060] Thus, the mass filter can be controlled to transmit one or more ion species, while other ion species that are desired to be transmitted later for analysis are still traveling through the separator towards the mass filter. Thus, relatively few ions are discarded at the mass filter, and the sensitivity of the analysis is relatively high. However, separating ions in this way can result in relatively few ions reaching the TOF mass analyzer per unit time, which can lead to the problems described herein when using coded frequent pulsing (EFP) techniques. The present disclosure overcomes this by combining EFP data in a new manner.

[0061] A mass filter may be placed between the separator and a fragmentation or reaction device that performs the fragmentation or reaction described above.

[0062] If ions are fragmented or reacted, separation of the precursor ions by the separator may be preserved in the fragment or product ions such that fragment or product ions of different precursor ions may arrive at the TOF mass analyzer at different times.

[0063] The method may include pulsing a packet of ions comprising different species of ions into the separator to initiate the step of separating the ions.

[0064] For example, ions may be accumulated in an ion accumulator and periodically pulsed into a separator which performs a separation cycle between each pulse, and the mass filter may be changed during each separation cycle as described above, for example in synchronism with the separator.

[0065] The method may include, prior to the step of mass analyzing the ions, performing a survey scan in which one or more ion species are mass analyzed by a TOF mass analyzer, determining from the survey scan a time window during which the one or more ion species reach the TOF mass analyzer, and selecting the plurality of different pulse sequence periods based on the time window determined in the survey scan.

[0066] For example, at least a portion of each of the plurality of different pulse sequence periods may overlap with the time window. Alternatively, the method may include selecting at least one pulse sequence period during which one or more species arrive at the TOF mass analyzer as one or more of the plurality of different pulse sequence periods, and selecting a first pulse sequence period that begins after a time at which the one or more species stop entering the TOF mass analyzer as another of the one of the plurality of different pulse sequence periods.

[0067] These techniques, which use survey scan data, ensure that data for the desired ion species is combined.

[0068] The method comprises the steps of mass analysing one or more further ion species using a TOF mass analyser in a survey scan, determining a further time window during which the one or more further ion species arrive at the TOF mass analyser from the survey scan, and determining from the further time window that the one or more further ion species arrive at the TOF mass analyser during only a portion of one or more of the pulse sequence periods during step (ii) of claim 1, combining only data acquired by the mass analyser during the portion of the one or more pulse sequence periods, and decoding the combined data.

[0069] It is recognized that if an ion species arrives at the TOF mass analyzer over a period shorter than the pulse sequence period, it may not be desirable to combine all of the TOF data acquired over that period prior to the decoding step, for example combining TOF data acquired over the entire pulse sequence period would result in combining more noise data than necessary since the ion is not present in the TOF mass analyzer for the entire pulse sequence period.

[0070] During a survey scan, the TOF mass analyzer may be operated in a mode such that the duration between any pair of adjacent pusher pulses is greater than or equal to the flight time from the pusher to the detector of the largest mass-to-charge ratio ion pushed by the pusher.

[0071] Thus, the data acquired by the TOF mass analyzer in a multiple push survey scan is not multiplexed and does not require decoding.

[0072] In embodiments where a survey scan is used, it will be understood that the survey scan may process ions in the same manner as the non-survey scan mode described above, except that the TOF mass analyzer and TOF data are used differently in the two modes. In other words, if the non-survey scan separates and / or filters and / or fragments ions, the survey scan may also include corresponding steps. This ensures that the time at which an ion is determined to arrive at the TOF mass analyzer in a survey scan corresponds to the time at which an ion would arrive at the TOF mass analyzer in a non-survey scan. This information can then be used to select which data to combine in the non-survey mode.

[0073] A third aspect of the disclosure also provides a TOF mass analyzer having an ion detector, a pusher that when pulsed pushes ions into a time-of-flight region to the detector, and control circuitry configured to mass analyze the ions and acquire data related to the ions by pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence, combine data acquired during different ones of the pulse sequence periods to obtain combined data, and then decode the combined data to obtain mass spectral data indicative of the mass-to-charge ratio of the ions.

[0074] The TOF mass analyser may be configured to carry out any of the methods described herein, for example in relation to the third aspect.

[0075] The present disclosure also provides a mass spectrometer comprising an ion separator for separating ions according to physicochemical properties, a mass filter for mass filtering separated ions received from the ion separator, the mass filter being configured to transmit ions of different mass-to-charge ratios as the ions elute from the ion separator, a fragmentation or reaction device for fragmenting or reacting the ions received from the mass filter to produce fragment or product ions, and a TOF mass analyzer as described above for mass analysing the fragment or product ions.

[0076] The mass spectrometer may be configured to perform any of the methods described herein, for example in relation to the third aspect. [Brief description of the drawings]

[0077] [Figure 1]1 shows a schematic diagram of an embodiment of a mass spectrometer according to one embodiment of the present disclosure. [Diagram 2] 13 illustrates how a mass filter can be controlled as a function of time to transmit precursor ions according to one embodiment of the present disclosure. [Diagram 3] 2, except that the fragment or product ion species that may be produced from the precursor ions are also shown. [Figure 4] 1 shows an example of how ions can be mass analyzed by a TOF mass analyzer according to a non-encoded high frequency pulsing technique. [Diagram 5] 1 shows an example of how ions can be mass analyzed by a TOF mass analyzer according to the coded high frequency pulsing technique. [Figure 6] 1 illustrates a technique according to one embodiment of the present disclosure in which data acquired by a TOF mass analyzer during multiple pulse sequences is combined prior to decoding the data. [Figure 7] 1 illustrates a technique according to one embodiment of the present disclosure in which only data acquired by a TOF mass analyzer during a portion of a pulse sequence period is combined before decoding the data. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0078] Various embodiments of the present invention will now be described, by way of example only, with reference to the accompanying drawings, in which: 1 shows a schematic diagram of an embodiment of a mass spectrometer according to the present disclosure. The spectrometer comprises an ion source 1, an ion accumulator 2, an ion separator 3, a mass filter 4, a fragmentation or reaction device 5, and a time-of-flight (TOF) mass analyzer 6. It will be appreciated that other ion optical devices may also be provided within the spectrometer, such as, for example, one or more RF ion guides, electrostatic lenses, or collisionally cooled RF ion guides, which are configured to urge ions therethrough, such as by using an axial electric field or by moving a potential barrier therealong.

[0079] In use, ions are provided from an ion source 1, which may be an ion source that generates ions from an analytical sample or may be an ion optical device that provides ions. Ions from the ion source 1 may be accumulated in an ion accumulator 2 and then released as ion packets into the separator 3. The accumulator 2 may accumulate ions and periodically pulse them into the separator 3. The accumulator 2 may be configured to allow ions to enter the accumulator 2 continuously, or may prevent ions from entering the accumulator 2 when packets of ions are being pulsed into the separator 3. In either case, the accumulator 2 accumulates ions from the ion source 1 between the times that packets of ions are pulsed into the separator 3. However, it is contemplated that the accumulator 2 may be omitted and the ion source 1 may instead pulse ions into the separator 3, for example, by being a pulsed ion source or by providing an ion gate between the ion source 1 and the separator 3.

[0080] The separator 3 is controlled to cause each packet of ions received within it, for example from the accumulator 2, to separate according to one or more physicochemical properties. For example, the separator 3 may separate the ions according to ion mobility or mass-to-charge ratio, or a combination of both of these physicochemical properties. For example, the separator 3 may be an ion mobility separator that drives the ions against a gas so that the ions separate according to their mobility through the gas and elute from the separator at a time that depends on their mobility through the gas. The separator 3 may drive the ions through the gas using an electric field, such as that generated by a static DC gradient or that generated by moving a DC potential barrier along the device, in a known manner. The gas may be substantially static or the gas may flow in a direction opposite to the direction in which the ions are forced by the electric field.

[0081] The separated ions then pass from the separator 3 to a mass filter 4. The mass filter 4 is controlled to only allow a single mass to charge ratio (or a limited range of mass to charge ratios) to pass at any given time, and the single mass to charge ratio (or limited range) changes over time as the separated ions from the ion packet elute from the separator 3. The mass filter 4 may be altered to be synchronized with the separation cycle of the separator 3.

[0082] Figure 2 represents an example of how the mass filter 4 may be controlled as a function of time as ions separated from an ion packet elute from the separator 3. More specifically, Figure 2 shows a plot of the mass to charge ratio transmitted by the mass filter 4 as a function of time since an ion packet is pulsed into the separator 3. In this example, the mass filter 4 is controlled to transmit only ions having a first, relatively low mass to charge ratio at a first time. The mass filter is then controlled at a second, later time to transmit only ions having a second, higher mass to charge ratio. The mass filter is then controlled at a third, later time to transmit only ions having a third, higher mass to charge ratio. The mass filter is then controlled at a fourth, later time to transmit only ions having a fourth, lower mass to charge ratio. The mass filter is then controlled at a fifth, later time to transmit only ions having a fifth, higher mass to charge ratio.

[0083] The mass filter 4 may be, for example, a resolving quadrupole mass filter, although it is contemplated that other types of mass filters may be used. It will also be appreciated that the mass filter 4 may be controlled to transmit different mass to charge ratios at different times in ways other than those shown in the example of Figure 2.

[0084] After a delay time after the ion packet is pulsed into the separator 3, another packet of ions may be pulsed into the separator 3 and the above process may be repeated to separate and filter the ions in this next packet. The delay time may be the time it takes for all of the ions of interest in an ion packet (i.e., those that the filter 4 is set to transmit at one point in time) to pass through the separator 3 and reach the filter 4, but may be set to a shorter or longer delay time if desired. Any desired number of ion packets may be sequentially separated and then filtered in the manner described above.

[0085] Separated ions transmitted by the filter 4 (i.e., not removed by the filter) may be transferred to a fragmentation or reaction device 5 where they may be fragmented or reacted to produce fragment or product ions. 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 technique. For example, the device may react ions with reagent ions or molecules to fragment the ions, 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.

[0086] FIG. 3 shows the same plot as FIG. 2, except that the fragment or product ion species generated from the precursor ions are superimposed. In the illustrated example, a first precursor species transmitted by mass filter 4 is shown as a first dark oval, and fragments or reacts to generate two species of fragment or product ions, which are shown by lighter colored ovals above and below the first dark oval. 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 through fifth precursor species (represented by dark ovals) fragments or reacts to generate three species of fragment or product ions (represented by lighter ovals).

[0087] It should be understood that different precursor ions arrive at the fragmentation or reaction device 5 at different times due to their separation in the separator 3, and therefore different precursor ions fragment or react at different times to produce their fragment or product ions at different times. Although Figure 3 shows that the fragment or product ion species are produced over a time that precisely matches the time that their precursor ion species are transmitted by the filter 4, it should be understood that this may not be the case, and the time that any given fragment or product ion species is produced may deviate from the time that the precursor ion species was transmitted by the filter 4 due, for example, to the transmission time of the precursor ion species to (or through) the fragmentation or reaction device 5 and / or the time it takes for the precursor species to undergo fragmentation or reaction within the device 5.

[0088] The separation of precursor ion species induced by the separator 3 may preserve between the fragment or product ion species derived from these precursor ion species. In particular, different precursor ion species arrive at the fragmentation or reaction device 5 at different times and therefore their respective fragment or product ion species are generated at corresponding different times. The fragment or product ion species may be forced out of the fragmentation or reaction device 5 such that the fragment or product ion species derived from the different precursor species arrive at the TOF mass analyzer 6 at different respective times.

[0089] Assuming loss-free accumulation in accumulator 2 and loss-free ion transmission, the duty cycle and therefore sensitivity for both precursor ions, and therefore fragment or product ions, for the example shown in Figures 2 and 3 is more than five times better than conventional MSMS approaches that mass filter precursor ions without accumulating and separating ions upstream of the mass filter.

[0090] As described above, the fragment or product ions generated in the fragmentation or reaction device 5 are transferred to a TOF mass analyzer 6. As is well known in the art, the TOF mass analyzer 6 has a pusher that pulses ion packets into a time-of-flight region (e.g., a field-free region) and towards an ion detector. As the ions pass through the time-of-flight region, they separate according to their mass-to-charge ratio and then impinge on the ion detector. Thus, the separated ions arrive at the ion detector at different times, and the time at which an ion arrives at the detector is related to its mass-to-charge ratio. The mass-to-charge ratio of a given ion can be determined from the duration between the time the ion is pulsed into the time-of-flight region and the time it is detected by the ion detector. Thus, the TOF mass analyzer 6 can obtain data from the signal detected at the detector to determine the mass-to-charge ratio of the ions pulsed into the mass analyzer 6 and their intensities to form a mass spectrum.

[0091] The 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 time-of-flight region. This allows ions of different mass-to-charge ratios to be separated to a greater extent as they travel through the time-of-flight region, thus providing the TOF mass analyzer 6 with higher mass resolution. Thus, the TOF mass analyzer 6 may be a Multi-Reflecting TOF (MRTOF) mass analyzer that uses ion mirrors to reflect ions multiple times as they drift from the pusher towards the ion detector.

[0092] Fragment or product ions derived from any given species of precursor ions reach the TOF mass analyzer 6 within a limited time period related to the time period when those precursor species exit the separator 3 .

[0093] FIG. 4 shows an example of how fragment or product ions are mass analyzed by a TOF mass analyzer according to a conventional (non-encoded high frequency pulsing) approach. In this example, three fragment or product ions with three different mass-to-charge ratios are generated from a single precursor species in a fragmentation or reaction device 5 and then sent to a TOF mass analyzer 6 over the same period of time. The three fragment or product ions arrive at the pusher of the TOF mass analyzer 6 over a time window 8 shown in FIG. 4. The TOF mass analyzer 8 periodically pulses the pusher so that it repeatedly samples the fragment or product ions throughout the time window 8 and mass analyzes them. The times at which the TOF pusher is pulsed are indicated by vertical lines 10 on the x-axis. These multiple pulses 10 of the TOF pusher during the duration 8 cause multiple TOF mass spectra to be generated for the fragment or product ions derived from each precursor ion. 4 shows only fragment or product ions from one of the precursor species transmitted by the filter 4, it should be understood that fragment or product ions from other precursor ion species transmitted by the filter 4 (at a later or earlier time, respectively, for that one of the species) will also be mass analyzed in a corresponding manner (at a later or earlier time, respectively) in the TOF mass analyzer 6. This conventional data acquisition scheme has proven useful, for example, as it allows precise 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 the processing software to group together fragment or product ions that are common to the same precursor species.

[0094] However, the approach illustrated by FIG. 4 provides a relatively low TOF sampling duty cycle for the TOF mass analyzer 6. 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 ions pushed by a given pusher pulse to arrive at the ion detector of the TOF analyzer 6 before another packet of ions is pushed towards the ion detector by the next pusher pulse. This means that the duration between pusher pulses 10 is equal to or greater than the flight time from pusher to detector of the largest mass-to-charge ratio desired to be detected. Thus, the sampling duty cycle decreases with the square root of the largest mass-to-charge ratio desired to be detected. TOF sampling duty cycles with such techniques are typically in the range of 0.1% to 50%. These values ​​are typical maximum duty cycles.

[0095] To increase the sampling duty cycle of the TOF mass analyzer 6, it is known to use an encoded frequent pulsing (EFP) technique in which the pusher is operated such that the duration between adjacent pulses 10 of the pusher is less than the flight time of the heaviest mass-to-charge ratio desired to be analyzed. In such a technique, the pusher is controlled to perform a sequence of successive pushes, which are arranged in time such that the duration between any pair of pushes in the sequence is different from the duration between any other pair of pushes in the sequence. The sequence of pushes may be repeated one or more times during the mass analysis. Although the ions of interest pulsed into the TOF mass analyzer 6 by different pushes arrive at the TOF detector in overlapping periods according to this EFP technique, the TOF mass analyzer can decode the resulting data using a decoding algorithm to determine which data is associated with each push by using the timing of the pushes in the sequence of pushes (as the duration between any pair of pushes in the sequence is unique). The TOF mass analyzer 6 can thus convert the data into mass spectral data representing the mass spectrum of the detected ions.

[0096] FIG. 5 shows the same example as shown in FIG. 4, but for controlling the pusher of a TOF mass analyzer 6 using EFP technology. The times at which the pusher is pulsed are indicated by vertical lines 12 on the x-axis. The pusher is controlled to perform a pulse sequence of successive pushes during a pulse sequence period 14, all of which are arranged in time such that the duration between any pair of pushes within a pulse sequence (i.e. within a pulse sequence period 14) is different from the duration between any other pair of pushes within the pulse sequence. The same pulse sequence may be repeated in successive pulse sequence periods 14. In FIG. 5, the first push in each pulse sequence is highlighted by being shown as a thicker vertical line than the other pushes in the pulse sequence. In this example, the pusher is controlled to perform a pulse sequence of eight successive pushes within each pulse sequence period 14. However, it will be understood that each pulse sequence may consist of more or less than eight pushes.

[0097] It is contemplated that the starting pushes of adjacent pulse sequences may be closer together than shown, or may be further apart. For example, the first push of each pulse sequence in FIG. 5 is selected to coincide with one of the pushes 10 shown in FIG. 4, but this is for illustrative purposes only and need not be the case. However, desirably, the starting pushes of adjacent pulse sequences are spaced apart in time by an amount that corresponds to or is greater than the flight time from the pusher to the detector of the largest mass-to-charge ratio desired to be mass analyzed by the TOF mass analyzer (e.g., pulsed by the pusher).

[0098] It will be appreciated that in the example shown in Figure 5 there is eight times more push than in the example shown in Figure 4. This therefore increases the sampling duty cycle of the TOF mass analyzer by a factor of eight.

[0099] As mentioned above, each sequence of pushes 12 is executed over a pulse sequence period 14. Data acquired by the TOF mass analyzer 6 during this pulse sequence period 14 may later be decoded by a decoding algorithm to obtain mass spectral data representative of the mass spectrum of the ions detected by the detector.

[0100] Although EFP techniques are useful for increasing the sampling duty cycle of the TOF mass analyzer 6, it has been recognized that problems may arise due to the manner in which the decoding algorithm operates to obtain mass spectral data representative of the mass spectrum. More specifically, the decoding algorithm defines a minimum threshold for the number of ions that must be detected at any particular flight time (from pusher to detector) before it is determined that a mass-to-charge ratio peak exists. Otherwise, the number of ions detected may not be statistically meaningful. For example, the decoding algorithm may define the minimum threshold as 10 ions. Then, if the decoding algorithm determines that less than 10 ions are detected at any given flight time within the pulse sequence time, the data for those ions are rejected and not assigned to a mass-to-charge ratio.

[0101] An embodiment of the present disclosure improves upon such techniques by combining (i.e., summing) data acquired by the TOF mass analyzer 6 from multiple pulse sequence periods 14 and then applying a decoding algorithm to the combined data. The combined data may then be decoded using a decoding algorithm to generate mass spectral data representative of the mass spectrum of the detected ions. Thus, ions representing mass peaks are less likely to be discarded even if they are present within each pulse sequence period 14 at levels below a minimum threshold set by the decoding algorithm. This is because when data from multiple pulse sequence periods 14 is combined, it is more likely that the number of ions occurring at a given flight time (i.e., having a given mass-to-charge ratio) will increase to above the minimum threshold required by the decoding algorithm to determine that a mass peak is present.

[0102] 6 illustrates a technique according to one embodiment of the present disclosure. This technique is the same as that described in connection with FIG. 5, except that data acquired by the TOF mass analyzer 6 during multiple pulse sequence periods 14 are combined (i.e., summed) and then decoded to obtain mass spectral data representative of the mass spectrum of the detected ions. Data acquired during multiple pulse sequence periods 14 can be combined to generate a single set of summed mass spectral data, such as a single set of histogrammed data. In the illustrated example, data from five pulse sequence periods 14 is combined before decoding, although it will be understood that data from a different number of pulse sequence periods may be combined.

[0103] 6 shows that fragment or product ions pass through the TOF mass analyzer 6 over a time window 8 spanning at least a portion of four successive pulse sequence periods 14, and that these ions no longer enter the TOF mass analyzer 6 during the illustrated fifth pulse sequence period 14. However, since ions sampled by the push in the fourth pulse sequence period 14 reach the TOF ion detector during the fifth pulse sequence period 14, it may still be desirable to combine data acquired during the fifth pulse sequence period 14 with data acquired in all (or a subset) of the first through fourth pulse sequence periods 14. In more general terms, TOF data acquired during at least one or at least some of the pulse sequence periods 14 occurring when a first species of fragment or product ion is received (and mass analyzed) by the TOF mass analyzer may be combined with TOF data acquired during a first pulse sequence period 14 beginning after the first species of fragment or product ion stops entering the TOF mass analyzer 6. This combined data is then decoded.

[0104] When summing TOF data acquired during a pulse sequence period 14, before decoding it, it may be desirable not to include TOF data acquired in the last pulse sequence period 14 of the pulse sequence period 14 that ends before that first species of fragment or product ion begins to enter the TOF mass analyzer 6. This helps to ensure that TOF data relating to ions other than the first species of fragment or product ion is not included in the combined data. Although data relating to a first species of fragment or product ion has been described as being acquired and combined, it will be appreciated from the above that multiple fragment or product ions may be generated from the same precursor species and that these multiple fragment or product ions may arrive at the TOF mass analyzer 6 during the same time window 8. Thus, data relating to all of these multiple species of fragment or product ions may be acquired and combined in the manner described above.

[0105] 6 shows one example of how fragment or product ions derived from a precursor ion of a first species may be mass analyzed in a TOF mass analyzer 6, it will be understood that the TOF mass analyzer 6 may also mass analyze in a corresponding manner fragment or product ions derived from precursor ions of other species received (at earlier or later times) at the TOF mass analyzer 6. For example, fragment or product ions derived from a second, different precursor ion will arrive at the TOF mass analyzer over a different, later time window (e.g., as represented by FIG. 3). These fragment or product ions may then be analyzed in a manner corresponding to that described in connection with FIG. 6.

[0106] To determine which pulse sequence period 14 should be used when summing TOF data for fragment or product ions from a precursor species, the method disclosed herein may first identify the time window during which these fragment or product ions enter the TOF mass analyzer 6. This may be done by performing a survey scan to determine the time windows during which the various different fragment or product ions reach the TOF mass analyzer 6. For example, the survey scan may include an MS scan to determine which precursor ions are present in the analytical sample. The survey scan may then perform the method described in connection with Figures 1-4, with the filter 4 being controlled to transmit different ones of the precursor ions detected at different times in the MS scan. Alternatively, the survey scan may perform the method described in connection with Figures 1-4 without first performing an MS scan to determine which precursor ions are present in the analytical sample. Furthermore, it is envisioned that ions do not need to be fragmented or reacted during the survey scan, but instead precursor ions may be detected by the TOF mass analyzer, since the time window during which precursor ions are detected will correspond to the time window over which those fragment or product ions are detected.

[0107] During a survey scan, the TOF mass analyzer 6 may be operated in a non-EFP mode, i.e. the duration between successive pusher pulses is equal to or greater than the pusher-to-detector flight time of the largest mass-to-charge ratio desired to be mass analyzed, for example as described in relation to Figure 4. The resulting TOF data can then be used to determine the time window during which fragment or product ions derived from each precursor ion transmitted by the filter 4 reach the TOF mass analyzer 6.

[0108] The method described in relation to Figures 1-3 can then be carried out again, and the resulting fragment or product ions can be mass analysed according to the EFP technique described in relation to Figure 6, i.e. the TOF data acquired during multiple pulse sequence periods 14 can be combined and then decoded. Since the time window during which each species of fragment or product ions arrives at the TOF mass analyser 6 is known from the survey scan, the mass analyser 6 can use this information to determine the timing of the pulse sequence periods 14 occurring during which fragment or product ion species of any given precursor ion species arrive at the TOF mass analyser 6. The mass analyser 6 then selects and combines the TOF data acquired during all or a subset of these pulse sequence periods 14. The mass analyser 6 may also combine this data with TOF data acquired during a first pulse sequence period 14 beginning after the time at which these fragment or product ion species stop entering the TOF mass analyser 6. The combined data is then decoded as described herein.

[0109] The technique described above is that the TOF data that is combined (before decoding) is TOF data obtained from product or fragment ions eluted from only a single precursor ion species transmitted during only a single separation cycle of the separator 3. In other words, the TOF data that is summed (before decoding) is TOF data obtained during the elution of a single precursor species from a single separation cycle of the separator 3. However, it is also contemplated that the TOF data that is combined (before decoding) may be TOF data obtained during the elution time of the same single precursor ion species during multiple separation cycles of the separator 3. This TOF data obtained from multiple separation cycles can be combined and then decoded. This serves to combine a relatively large amount of spectral data before the combined data is decoded using a decoding algorithm, thereby overcoming the above-mentioned problem with a minimum threshold set by the decoding algorithm.

[0110] According to these techniques, a survey scan may be performed, for example, in the same manner as described above. The survey scan may be used to determine the time window during which a precursor species of interest will arrive at the TOF mass analyzer 6 relative to the start of the separator's separation cycle (e.g., relative to the time that an ion packet is pulsed into the separator 3). Alternatively, the scan may be used to determine the time window during which fragment / product ions of a precursor ion species of interest will arrive at the TOF mass analyzer 6 (e.g., relative to the start of the separator's separation cycle).

[0111] The method described in relation to Figures 1-3 can then be carried out and the resulting fragment or product ions can be mass analyzed according to the EFP technique described in relation to Figure 6. In other words, the packets of precursor ions are separated in the separator 3, filtered by the mass filter 4, fragmented or reacted in the fragmentation or reaction device 5, and the resulting fragment or product ions are then mass analyzed by the TOF mass analyzer 6. Since the time window during which fragment or product ions from the precursor ion species of interest reach the TOF mass analyzer 6 is known from the survey scan, the mass analyzer 6 can use this information to determine the timing of the pulse sequence periods 14 occurring during which these fragment or product ion species reach the TOF mass analyzer 6. The mass analyzer 6 then selects the TOF data acquired during all or a subset of these pulse sequence periods 14 for combination with other data. As mentioned above, the mass analyzer 6 may also select the TOF data acquired during the first pulse sequence period 14 beginning after the time at which these fragment or product ion species stop entering the TOF mass analyzer 6 for summation with other data.

[0112] The above method is then repeated by pulsing another packet of precursor ions into the separator 3, separating the precursor ions therein, filtering the ions eluting from the separator 3 using mass filter 4, fragmenting or reacting the filtered ions in fragmentation or reaction device 5, and then mass analyzing the resulting fragment or product ions in TOF mass analyzer 6. The mass analyzer 6 then again selects a portion of the TOF data that corresponds to fragment or product ions derived from the precursor ion species of interest and combines it with the previously selected TOF data.

[0113] The above method may be repeated as many times as desired, each time combining TOF data corresponding to fragment or product ions derived from a precursor ion species of interest with previously selected TOF data, which may then be decoded to obtain mass spectral data.

[0114] In the above embodiments, each species of fragment or product ion has been described as arriving at the TOF mass analyzer 6 over a time window longer than the pulse sequence period 14, e.g., longer than the pusher-to-detector flight time of the largest mass-to-charge ratio desired to be mass analyzed by the TOF mass analyzer 6. However, some species of fragment or product ions may arrive at the TOF mass analyzer 6 over a time window shorter than the pulse sequence period 14. This may occur, for example, because a precursor species of such fragment or product species elutes from the separator 3 over a relatively short duration.

[0115] 7 shows an example in which fragment or product ions of three species (derived from the same precursor) arrive at the TOF mass analyzer 6 over a time window 8 shorter than the pulse sequence period 14. As described above, the TOF mass analyzer 6 operates according to the EFP technique. The number of pushes 12 within each pulse sequence period 14 differs from that shown in FIG. 6, but this is for illustrative purposes only and, as explained above, each pulse sequence period 14 may include any desired number of pushes 12.

[0116] It has been recognised that where ion species arrive at the TOF mass analyser 6 over a time window 8 that is shorter than the pulse sequence period 14, not only may it be desirable not to combine TOF data acquired during multiple pulse sequence periods 14 prior to the decoding step, but it may also be undesirable to combine all of the TOF data acquired during a single pulse sequence period 14 prior to the decoding step. For example, combining TOF data acquired over the entire pulse sequence period 14 would include more noise data than necessary, since ions are not present in the TOF mass analyser 6 for the entire pulse sequence period 14.

[0117] According to an embodiment of the present disclosure, in such a situation, TOF data acquired during only a portion of a pulse sequence period 14 is combined before decoding. For example, TOF data acquired during a portion of a pulse sequence period 14 corresponding to at least a portion of the duration that an ion species enters the TOF mass analyzer 6 may be combined and then decoded. Less preferably, TOF data acquired during a pulse sequence period 14 after an ion species has stopped entering the TOF mass analyzer 6 may be combined before the decoding step, since the ion species may still be received at the TOF detector during at least a portion of this time.

[0118] The duration at which an ion species enters the TOF mass analyzer 6 can be determined from the survey scan in a manner corresponding to the survey scan described above. The mass analyzer 6 can then use this information to determine the pulse sequence period 14 within which the species will arrive at the TOF detector and the duration over which the data should be summed.

[0119] Although the present invention has been described with reference to preferred embodiments, it will be understood by those skilled in the art that various changes in form and detail may be made therein without departing from the scope of the invention as set forth in the appended claims.

[0120] For example, although the mass filter 4 has been described as being stepped between different discrete mass transmission windows as ions elute from the separator 3, it is contemplated that the mass filter 4 may instead have a mass transmission window that is progressively scanned. For example, the mass transmission window may increase one mass-to-charge ratio unit at a time. Alternatively, the mass filter 4 may have a mass transmission window that is configured to be capable of simultaneously transmitting a range of mass-to-charge ratios (e.g., a range of multiple Da). This mass transmission window may be progressively scanned such that each time the mass transmission window moves to transmit a new mass range, the new mass range still partially overlaps with the previous mass range that the filter 4 was configured to transmit.

[0121] Alternatively or additionally, although filter 4 has been described as a mass-to-charge ratio filter, it is contemplated that the filter may filter ions according to another physicochemical property, such as ion mobility or FAIMS.

[0122] Alternatively or additionally, although separator 3 has been described as an ion mobility separator, it is contemplated that the separator may separate ions according to another physicochemical property, such as mass-to-charge ratio.

[0123] Additionally, although the techniques described herein are described in connection with summing and decoding TOF data associated with detected fragment or product ions, it is contemplated that the TOF data may instead relate to precursor ions (i.e., analyte ions that have not been fragmented or reacted to form distinct ions). Alternatively, or in addition, it is contemplated that the techniques described herein may be performed without isolating and / or filtering ions.

Claims

1. 1. A method of mass spectrometry comprising: a) providing a time-of-flight (TOF) mass analyzer having an ion separator for separating ions according to physicochemical properties, and an ion detector, and a pusher that, when pulsed, pushes ions into a time-of-flight region to the detector; b) performing a survey scan, comprising a separation cycle in which packets of precursor ion species are separated in the ion separator such that precursor ion species having different values ​​of said physicochemical property elute from the ion separator at different times, and then mass analysing the separated precursor ion species, or fragment or product ions derived therefrom, in the TOF mass analyser to obtain first mass spectral data; c) determining from the first mass spectral data a time window during which one of the precursor ion species, or fragment or product ions derived therefrom, was mass analyzed by the TOF mass analyzer; d) performing another separation cycle in which another packet of precursor ion species is separated in the ion separator such that precursor ion species having different values ​​of said physicochemical property elute from the ion separator at different times; and e) mass analysing the precursor ion species separated in step d), or fragment or product ions derived therefrom, in the TOF mass analyser to obtain second mass spectral data, the mass analysis comprising pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence; f) selecting from said second mass spectral data mass spectral data acquired during a period of time corresponding to said time window of said survey scan to acquire selected data; g) repeating steps d) through f) at least one additional time to obtain a plurality of sets of the selected data; and h) combining the sets of selected data to obtain combined data; and i) decoding the combined data to obtain mass spectral data indicative of the mass-to-charge ratios of the ions detected by the TOF mass analyzer; A method comprising:

2. 2. The method of claim 1, wherein step c) comprises determining a first time delay between a start time of the separation cycle in the survey scan and a start time of the time window, and wherein the method comprises setting the period in step f) to start after a second time delay from a start time of the another separation cycle in step d), the first time delay being the same as the second time delay.

3. The method according to claim 1 or 2, wherein the time window has the same duration as the period in step f).

4. 4. The method of claim 1, 2 or 3, wherein the selected mass spectral data acquired in step f) comprises mass spectral data acquired during a plurality of different ones of the pulse sequence periods of step e).

5. The method of any one of claims 1 to 4, wherein the combined data is decoded based on knowledge of the pulse sequence used in each of the plurality of pulse sequence periods.

6. 6. The method of claim 1, wherein the decoding comprises assigning data corresponding to detected ions to a mass-to-charge ratio and determining that a mass-to-charge ratio peak is detected only if more than a threshold number of ions are assigned to a given mass-to-charge ratio.

7. 7. The method of any one of claims 1 to 6, wherein between steps d) and e), precursor ion species are fragmented or reacted in a fragmentation or reaction device, and said mass analysing in step e) comprises mass analysing the resulting fragment or product ions.

8. 10. A method according to claim , comprising the steps of: providing a mass filter for filtering ions between the ion separator and the fragmentation or reaction device, the mass filter filtering ions to transmit only ions having a restricted value or range of values ​​of mass to charge ratio at any given time; and controlling the mass filter to vary the value or range of values ​​as ions elute from the ion separator to transmit different species of ions towards the fragmentation or reaction device at different times.

9. 9. The method of claim 8, wherein the mass filter is controlled to vary the value or range of values ​​over a cycle time that is synchronized with the separation cycle of step d).

10. The method according to any one of claims 1 to 9, wherein the first physicochemical property is ion mobility.

11. 11. The method of claim 1, wherein during the survey scan of step b), the mass analysing step comprises pulsing the pusher in a manner such that the duration between any pair of adjacent pusher pulses is equal to or greater than the flight time from the pusher to the ion detector of the highest mass-to-charge ratio ion pushed by the pusher.

12. 1. A mass spectrometer comprising: an ion separator for separating ions according to their physicochemical properties; a time-of-flight (TOF) mass analyzer having an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region and onto the detector; and A control circuit configured to carry out the method according to any one of claims 1 to 11. A mass spectrometer comprising:

13. 1. A method of mass spectrometry comprising: providing a time-of-flight (TOF) mass analyzer having an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region toward the detector; mass analysing ions in the TOF mass analyser to obtain data relating to the ions, the mass analysing comprising pulsing the pusher according to a pulse sequence of successive pushes, the successive pushes being arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence; determining that one or more ion species arrive at the TOF mass analyzer during only a portion of one or more of the pulse sequence periods; combining only data acquired by the mass analyzer during the portion of the one or more pulse sequence periods; Decrypting the combined data; A method comprising:

14. performing a survey scan prior to said step of mass analyzing ions, in which said one or more ion species are mass analyzed by said TOF mass analyzer; determining from the survey scan a time window during which the one or more ion species reach the TOF mass analyzer; using the time window to determine the portion of the one or more pulse sequence periods during which the one or more ion species reach the TOF mass analyzer; The method of claim 13, comprising:

15. 1. A TOF mass analyzer comprising: an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region onto the detector; A control circuit comprising: mass analyzing ions to obtain data relating to the ions by pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence; determining that one or more ion species arrive at the TOF mass analyzer during only a portion of one or more of the pulse sequence periods; combining only data acquired by the mass analyzer during the portion of the one or more pulse sequence periods; decoding the combined data to obtain mass spectral data representative of the mass-to-charge ratio of the one or more species; A control circuit configured as follows: A TOF mass analyzer comprising:

16. 1. A method of mass spectrometry comprising: (i) providing a time-of-flight (TOF) mass analyzer having an ion detector and a pusher that, when pulsed, pushes ions into a time-of-flight region towards the detector; (ii) mass analysing ions in the TOF mass analyser to obtain data relating to the ions, the mass analysing comprising pulsing the pusher according to a plurality of respective successive pulse sequences during a plurality of pulse sequence periods, each pulse sequence consisting of successive pushes arranged such that the duration between any pair of pushes in the pulse sequence is different from the duration between any other pair of pushes in the pulse sequence; (iii) combining the data acquired during different ones of the pulse sequence periods to obtain combined data; and then (iv) decoding the combined data to obtain mass spectral data indicative of the mass-to-charge ratios of the ions; A method comprising:

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