Mass spectrometry method, mass spectrometer and computer software

Abstract

The invention provides a mass spectrometry method. The method comprises the following steps for each sub-range of a plurality of sub-ranges selected from a total m / z range: configuring an ion beam switch to direct ions to a first ion storage device; a sample of precursor ions to be analyzed is accumulated in the first ion storage device, the precursor ions having an m / z value within the sub-range. In option a), the method further includes configuring the ion beam switch (for each sub-range of the plurality of sub-ranges) to direct ions toward a first mass analyzer and inject a sample of fragmented precursor ions into the first mass analyzer, wherein the sample of fragmented precursor ions is formed from fragmentation of precursor ions having an m / z value within the sub-range. In option b), the method further includes configuring the ion beam switch (for each sub-range of the plurality of sub-ranges) to direct ions to a second ion storage device and to accumulate a sample of fragmented precursor ions in the second ion storage device for analysis in a first mass analyzer, wherein the fragmented precursor ions are formed by fragmentation of precursor ions having an m / z value within the sub-range.

Description

Field of the Invention

[0001] The field of the present invention is liquid chromatography - mass spectrometry (LC - MS). Specifically, the present invention relates to tandem mass spectrometry in which precursor ions and fragment ions are analyzed. More specifically, the present invention relates to improving the dynamic range of MS1 scans in tandem mass spectrometry. The present invention relates specifically but not exclusively to advanced hybrid mass spectrometers having multiple analyzers. Background Art

[0002] Standard tandem liquid chromatography - mass spectrometry (LC - MS) methods involve performing an "MS1" scan, in which ions having a wide m / z range are analyzed by a mass analyzer to produce an MS1 spectrum (containing information about precursor ions). Methods of operating an LC - MS also involve isolating and fragmenting ions from eluted analyte species to perform an "MS2" scan, in which ions within a narrow m / z range are isolated (e.g., using a quadrupole mass filter), those ions are fragmented, and the fragment ions are mass - analyzed to produce an MS2 spectrum, which contains structural and quantitative information about the fragment ions.

[0003] In LC - MS methods, multiple MS2 scans are typically performed during chromatographic separation, where the m / z isolation range is different for each MS2 scan. The MS2 (or "MS / MS") spectrum is supported by an MS1 (or "MS" or "full MS") survey scan, which provides high - quality peak information such as accurate mass data and precursor intensities of a wide range of unfragmented precursor ions.

[0004] For data - independent acquisition (DIA) methods, the MS1 scan is optional and can be skipped to allow time to generate additional MS2 spectra. The list of m / z targets for each of the multiple MS2 scans can be a step - increasing / decreasing m / z list across the m / z range of interest. One such example is described in EP 3,410,463, which is incorporated herein by reference. The resulting precursor information can be used for quantification, while the fragment information can be used for identification.

[0005] In data - dependent acquisition (DDA), an MS1 step is required to generate a list of precursor targets for MS2 analysis. The list of m / z targets for each of the multiple MS2 scans corresponds to the list of precursor ions identified in the MS1 scan.

[0006] To perform mass analysis of ions, the ions (fragment ions or precursor ions) are typically first accumulated in an ion trap and then the accumulated ions are ejected as a group into a mass analyzer for mass analysis. Accumulation improves the sensitivity of the instrument, but care is required during the fill time of the ion trap for the ions (so - called "automatic gain control" AGC) to avoid harmful space - charge effects.

[0007] One problem with existing methods is that the dynamic range of the MS1 spectrum is limited. Depending on the sample, the concentration of digested peptides varies by more than 10 orders of magnitude, but in a single-shot spectrum in, for example, a Fourier transform mass analyzer such as an electrostatic orbitrap mass analyzer (e.g., Orbitrap TM manufactured by Thermo Fisher Scientific TM FT mass analyzer), the dynamic range may be limited to approximately 4 orders of magnitude. Additionally, the number of ions that can be injected into an orbitrap mass analyzer is limited to approximately 10 5 by the capacity of the accumulation C-trap. Thus, low-intensity peptide precursor signals may be suppressed. For DDA experiments, these problems are significant and can lead to precursor targets being missed. For DIA experiments, the lack of good precursor data hinders identification and quantification.

[0008] One way to improve the dynamic range of the MS1 spectrum is the "Boxcar" method (as described in Meier et al., Nature Methods, 2018, Vol. 15, pp. 440-448) and the high dynamic range (HDR) method described in UK Patent Application No. 2211790.7, which is incorporated herein by reference. In these methods, the wide mass range being analyzed is subdivided into multiple narrower isolation windows. For each isolation window, a separate injection is performed in the C-trap, with different fill times depending on the ion current. By this method, densely populated m / z regions are attenuated while sparsely populated m / z regions are amplified. Thus, the detection sensitivity of relatively weak peaks is improved, and the effective dynamic range of the scan is increased. However, the use of these methods significantly increases the time required to accumulate ions, especially when a large number of isolation windows are needed. Due to the long fill times for low-level windows and the time required to switch the quadrupole and ion source voltages, HDR scans may require a large amount of additional time and affect the rate at which MS2 scans can be performed. Thus, these methods can reduce the time available for MS2 scans in fast LC-MS methods, which is limited by the time it takes for the sample to elute from the column.

[0009] The multi-window HDR method also has the disadvantage of discarding a large number of ions due to quadrupole isolation. The loss of ions can be addressed via a pre-accumulation process. For example, a trapped ion mobility device can be used to pre-accumulate ions before the quadrupole and release the ions in a mass / mobility-dependent manner synchronized with the mass filter, thus greatly reducing ion loss (as described in Meier et al., Molecular Cellular Proteomics, 2018, Vol. 17, pp. 2524-2545).

[0010] Differential mobility filtering can be used to improve proteomics performance by removing analytically less useful singly charged ions from an aggregated population (as described in Hebert et al., Anal. Chem., 2018, Vol. 90, pp. 9529-9537). This can be advantageous in low sample or single cell experiments where the analyte signal is small compared to the singly charged solvent background signal.

[0011] In a DIA experiment, the MS2 spectrum can retain a proportion of unfragmented precursor ions (in an amount insufficient to be analytically useful). Some instruments provide an optional feature called "stepped collision energy" described in US 9,536,717. This feature provides multiple separate injections into the collision cell (also known as the "fragmentation chamber") at a range of collision energies, and then the summed ion population is transferred to a C-trap / Fourier transform mass analyzer and analyzed together. This variation in energy increases the probability that one of the energies used is optimal for fragmenting the precursor ions. However, this method also uses many collision energies that are not optimal for fragmenting the precursor ions, along with the associated cost of ion beam time. The actual act of changing the collision energy and making a second or third injection in the collision cell may not be overly time-intensive, and in some cases, there may be an additional 1-3 ms overhead on a scan cycle of >40 ms.

[0012] US 8,686,350 describes a method in which different types of ions can be aggregated in an ion trap before being ejected into a mass analyzer. In one example, a combination of two types of ions having the same narrow mass range is injected into the ion trap, one ion being fragmented and one ion remaining as an intact precursor. This allows for greater confidence that the precursor ion can be detected and precisely mass measured. However, quantification may be affected by the proportion of unfragmented precursors left by the MS2 injection. SUMMARY OF THE INVENTION

[0013] The present invention provides a mass spectrometry method. The method includes the following steps for each of a plurality of sub-ranges selected from a total m / z range:

[0014] Configuring an ion beam switch to direct ions to a first ion storage device;

[0015] Aggregating a sample of precursor ions to be analyzed in the first ion storage device, the precursor ions having m / z values within the sub-range.

[0016] In option a), the method further includes (for each of the plurality of sub-ranges) configuring the ion beam switch to direct ions to a first mass analyzer and injecting a sample of fragmented precursor ions into the first mass analyzer, wherein the sample of fragmented precursor ions is formed by fragmentation of precursor ions having m / z values within the sub-range.

[0017] In option b), the method further includes (for each of the plurality of sub-ranges) configuring the ion beam switch to direct ions to a second ion storage device and accumulating a sample of fragmented precursor ions in the second ion storage device for analysis in a first mass analyzer, wherein the fragmented precursor ions are formed by fragmentation of precursor ions having m / z values within the sub-range.

[0018] In the DIA method that interleaves MS2 and SIM injection, the proposed method uses a branched ion beam path provided by an ion beam switch such that when generating an MS / MS spectrum (by analyzing fragment ions), precursor ions for HDR scanning are established in a first ion storage device. Beam switching in a vacuum enables rapid transitions and short duty cycles, which are advantageous for strong ion peaks. Although ion optics are known, no method has been found in the prior art for parallel accumulation of different ion populations generated on the basis of the same quadrupole isolation using these devices.

[0019] Advantageously, the proposed method facilitates high-quality HDR scanning by accumulating precursor ions from multiple injections. The injection time for each sub-range can be customized individually to improve resolution. Compared to separate MS1 and MS2 analyses, the total time spent obtaining MS / MS spectra and HDR precursor scan data can be reduced.

[0020] The proposed method is suitable for quantification of a wide dynamic range of analyte ions. Normally performing separate MS1 and MS2 scans would involve extended delays to switch the ion source and quadrupole to scan through the mass range independently of the DIA cycle scan used to obtain fragment data. The number of ions to be processed for HDR scanning is high, and thus always consumes a significant proportion of the ion beam time.

[0021] The fragmented precursor ions in the sample of fragmented precursor ions can be formed by fragmentation of precursor ions having m / z values within the sub-range. More specifically, the sample of fragmented precursor ions can consist of fragmented precursor ions formed by fragmentation of precursor ions having m / z values within the sub-range.

[0022] The sample of precursor ions can consist of precursor ions having m / z values within the sub-range.

[0023] Samples of precursor ions for each sub-range of a plurality of sub-ranges can be combined together in a first ion storage device such that the first ion storage device contains precursor ions having m / z values from the total m / z range. In other words, ions from each sub-range may be present in the first ion storage device.

[0024] The method may also include analyzing a combined sample of precursor ions having m / z values from the total m / z range in a first mass analyzer or a second mass analyzer. In other words, multiple SIM injections can be combined together in a first ion storage device and analyzed together in a mass analyzer. Although the precursor accumulation step is performed for each sub-range, the step of analyzing the combined sample of precursor ions may be performed once for the total m / z range.

[0025] In a first example, the method further includes ejecting ions from the first ion storage device into a second mass analyzer. In other words, there may be two mass analyzers in series, both of which are downstream of the ion beam switch.

[0026] In a second example, the first ion storage device is an intermediate ion storage device, where the method further includes configuring the ion beam switch to transfer the precursor ions accumulated in the first ion storage device to a third ion storage device for analysis in a second mass analyzer.

[0027] The third ion storage device may be between an ion filter and the ion beam switch. Ions can be transferred from the ion filter to the ion beam switch via the third ion storage device.

[0028] The method may further include ejecting ions from the third ion storage device into the second mass analyzer.

[0029] The precursor ions transferred from the first ion storage device to the third ion storage device may include samples of the precursor ions for each sub-range of the plurality of sub-ranges.

[0030] In other words, in the second example, there may be two mass analyzers in series, the first mass analyzer being downstream of the ion beam switch (for analyzing the fragment ions, such as a time-of-flight mass analyzer), and the second mass analyzer being upstream of the ion beam switch (for analyzing the precursor ions, such as a Fourier transform mass analyzer).

[0031] After the sample of fragmentation precursor ions in each of the plurality of sub-ranges has been accumulated in the second ion storage device, the precursor ions can be transferred from the first ion storage device to the third ion storage device. In other words, after all the fragment ions have been accumulated or analyzed, the precursor ions can be transferred away from the intermediate ion storage device. This prevents the precursor ions accumulated in the intermediate ion storage device from mixing with other ions in the ion beam switch during the transfer.

[0032] The third ion storage device can be a curved linear ion trap (also known as a "c-trap").

[0033] To minimize overhead, the beam switching device preferably exhibits relatively rapid voltage transitions. Compared to the accumulation times of the precursor ions and fragment ions, the time taken to switch between ion destinations can be small. In some examples, the switching time is about 1 millisecond or less.

[0034] The ion beam switch can provide sufficient ion transmission to eliminate ion mixing between sub-ranges.

[0035] In some examples, the third ion storage device is disposed upstream of the ion beam switch. In this case, ions can first be accumulated in the third ion storage device (such as in the c-trap) before the switching region. This configuration can allow accumulation (in the c-trap) to be parallel with ion transmission through the ion beam switch for the immediately preceding sub-range. In other words, after all the precursor ions from the first sub-range have been ejected from the third ion storage device, the accumulation of precursor ions from the next sub-range in the third ion storage device can begin while the precursor ions from the first sub-range are being transmitted through the ion beam switch. This improves overall performance even if the switching process is relatively slow.

[0036] The second mass analyzer can be a Fourier transform mass analyzer. This applies to the first and second examples above.

[0037] In a third example, the first ion storage device can be an intermediate ion storage device. The method can further include configuring the ion beam switch to transfer the precursor ions accumulated in the first ion storage device to the first mass analyzer (in option a) or the second ion storage device (in option b).

[0038] In the case where the ion beam switch is configured to direct ions to the second ion storage device, the sample of precursor ions is accumulated in the second ion storage device and the precursor ions are transferred to the second ion storage device (option b), the method can further include ejecting the precursor ions from the second ion storage device into the first mass analyzer.

[0039] The precursor ions transferred from the first ion storage device (transferred to the first mass analyzer or the second ion storage device) may include a sample of the precursor ions for each of the plurality of sub-ranges.

[0040] The transferred precursor ions may include precursor ions having m / z values from the total m / z range. In other words, the transferred precursor ions may include a combined sample from each sub-range.

[0041] In the case where the ion beam switch is configured to direct ions to the second ion storage device and a sample of the fragmented precursor ions is accumulated in the second ion storage device (option b), the method may further include ejecting the sample of the fragmented precursor ions from the second ion storage device into the first mass analyzer.

[0042] After each accumulation (before accumulating fragment ions formed by fragmentation of precursor ions from the next sub-range), a sample of the fragmented precursor ions may be ejected from the second ion storage device.

[0043] A sample of the fragmented precursor ions may be ejected from the second ion storage device before the precursor ions are transferred to the second ion storage device.

[0044] After samples of the fragmented precursor ions for each of the plurality of sub-ranges have been ejected from the second ion storage device into the first mass analyzer, the precursor ions may be transferred from the first ion storage device to the second ion storage device.

[0045] In some examples, the ion beam switch is between the ion filter and the first ion storage device and between the ion filter and the second ion storage device, and is configured to (alternately) direct ions from the ion filter to the first ion storage device and the second ion storage device.

[0046] For each sub-range, the step of accumulating the sample of the precursor ions may be performed before the step of accumulating the sample of the fragmented precursor ions.

[0047] Alternatively, for each sub-range, the step of accumulating the sample of the fragmented precursor ions may be performed before the step of accumulating the sample of the precursor ions.

[0048] The method may further include analyzing a sample of the precursor ions in the first mass analyzer or the second mass analyzer for each of the plurality of sub-ranges. In this alternative, the precursor ions of each sub-range are analyzed separately in a SIM scan, rather than all SIM injections being accumulated together in one scan and analyzing the precursor ions from the total m / z range. The SIM scan may be interleaved with a fragmentation scan, which may advantageously mean that no reconfiguration of the ion filter is required between the SIM scan and the fragmentation scan for each sub-range. The method may further include obtaining scan data associated with the precursor ions of each sub-range. The method may further include combining the scan data associated with the precursor ions for each sub-range to form a high-definition scan for the total m / z range. In other words, the SIM scan data is stitched together to provide a high-resolution MS scan. In this case, a pre-scan may not be required (since the sub-ranges are contiguous and cover the total m / z range).

[0049] In another example, an HDR MS scan may be sliced into a plurality of scans, each of the plurality of scans being associated with precursor ions from a plurality of contiguous sub-ranges. In this alternative, each scan includes simultaneously analyzing multiple SIM injections. The method may further include combining the scan data from each of the plurality of scans to form a high-definition scan of the total m / z range. In this case, a pre-scan may not be required because a) the sub-ranges are contiguous and cover the total m / z range, and b) each sub-range is analyzed in a corresponding one of the plurality of scans.

[0050] The ion beam switch may be configured to operate under pure molecular flow conditions. Pure molecular flow conditions (also known as free molecular flow or Knudsen diffusion) are observed when the Knudsen number Kn is greater than 20 or more preferably Kn > 10.

[0051] The method may further include fragmenting the precursor ions to produce a sample of the fragmented precursor ions.

[0052] In the case where the ion beam switch is configured to direct ions to the second ion storage device and the sample of the fragmented precursor ions is accumulated in the second ion storage device (option b), the ions may be fragmented in the second ion storage device.

[0053] In other words, the precursor ions may be directed by the ion beam switch to the second ion storage device, and then once the ions have been accumulated in the second ion storage device, they may be fragmented.

[0054] Alternatively, a multipole collision cell (e.g., an IRM collision cell) may be used to fragment the ions.

[0055] The multipole collision cell can be upstream of the ion beam switch such that the ion beam switch directs the fragmented precursor ions to the first mass analyzer (in option a) or the second ion storage device (in option b). In some examples, the multipole collision cell can be between the ion filter (if present) and the ion beam switch.

[0056] Alternatively, the multipole collision cell can be downstream of the ion beam switch such that the ion beam switch directs the precursor ions to the multipole collision cell, which then transfers the fragmented ions to the first mass analyzer (in option a) or the second ion storage device (in option b). In other words, in option a), the multipole collision cell can be between the ion beam switch and the first mass analyzer, or in option b), the multipole collision cell can be between the ion beam switch and the second ion storage device.

[0057] In option b), the fragmented ions can accumulate in the second ion storage device and then be ejected from the second ion storage device into the first mass analyzer.

[0058] The method can also include configuring the ion filter for each of a plurality of sub-ranges to transmit precursor ions having m / z values within that sub-range. A sample of precursor ions can be received from the configured ion filter. The sample of fragmented precursor ions can be formed by fragmentation of the precursor ions received from the configured ion filter.

[0059] In other words, the ion filter may not be reconfigured between filling the first ion storage device and the second ion storage device.

[0060] The sample of fragmented precursor ions can be formed by fragmentation of the precursor ions received via the ion beam switch from the configured ion filter (where fragmentation occurs downstream of the ion beam switch). Alternatively, the sample of fragmented precursor ions can be formed by fragmentation of the precursor ions received from the configured ion filter, and then the sample of fragmented precursor ions can be transferred via the ion beam switch (where fragmentation occurs upstream of the ion beam switch).

[0061] Configuring the ion filter can include setting the transmission window of the ion filter. The transmission window can be adjusted between each of the plurality of sub-ranges. For each sub-range, the transmission window for the step of accumulating the sample of precursor ions can be the same as the transmission window for the step of injecting the sample of fragmented precursor ions into the first mass analyzer (in option a) or accumulating the sample of fragmented precursor ions in the second ion storage device (in option b).

[0062] A front-end accumulation device, such as an ion mobility separator, such as a trapped ion mobility separator (as incorporated in the Bruker TIMS-ToF series mass spectrometers) (and would be advantageous for the methods described herein), can be used. Such devices can release ions within an m / z range synchronized with the quadrupole isolation window. Thus, ion transport is greatly facilitated. Also thereby, the required injection time can be reduced (due to the brighter isolated ion beam). This reduction in injection time can be used to offset the additional time overhead of SIM injection.

[0063] The method can further include configuring the ion mobility separator to transfer precursor ions having m / z values within the sub-range to an ion filter.

[0064] The method can further include, for each of a plurality of sub-ranges within the total m / z range, controlling the ion mobility separator such that the precursor ions transferred to the ion filter correspond to the transmission window of the ion filter.

[0065] A sample accumulating precursor ions can include controlling the fill time of the precursor ions based on the relative abundances of the precursor ion species within the corresponding sub-range.

[0066] In the case where the ion beam switch is configured to direct ions to the second ion storage device and the sample of fragmented precursor ions is accumulated in the second ion storage device (option b), the method can further include: for each of the plurality of sub-ranges, ejecting the sample of fragmented precursor ions into the first mass analyzer and analyzing the sample of fragmented precursor ions in the first mass analyzer.

[0067] The plurality of sub-ranges can include a first sub-range and a second sub-range.

[0068] The step of analyzing the sample of fragmented precursor ions from the first sub-range can at least partially overlap (in time) with the step of accumulating in the second ion storage device the sample of fragmented precursor ions formed by fragmentation of precursor ions having m / z values within the second sub-range.

[0069] In the case where the ion beam switch is configured to direct ions to the first mass analyzer (option a), the method can further include analyzing the sample of fragmented precursor ions in the first mass analyzer.

[0070] The step of analyzing the sample of fragmented precursor ions from the first sub-range can at least partially overlap (in time) with the step of accumulating in the first ion storage device the sample of precursor ions having m / z values within the second sub-range.

[0071] The first mass analyzer can be a time-of-flight ToF analyzer.

[0072] The first mass analyzer can be a multi-reflection time-of-flight (MR-ToF) analyzer.

[0073] The first ion storage device can be a curved linear trap (e.g., a c-trap).

[0074] In the case where the ion beam switch is configured to direct ions to the second ion storage device and a sample of the fragmented precursor ions is accumulated in the second ion storage device (option b), the second ion storage device can be a linear trap (e.g., a DP-R trap).

[0075] The method may further include ionizing the sample to produce precursor ions.

[0076] A sample of fragmented precursor ions can be formed by fragmentation of precursor ions having m / z values within the sub-range at multiple different collision energies.

[0077] The method may further include:

[0078] Configuring an ion filter to transmit precursor ions having m / z values from the total m / z range;

[0079] Transferring an initial sample of precursor ions having m / z values from the total m / z range to the first mass analyzer or the second mass analyzer;

[0080] Analyzing the initial sample of the precursor ions; and

[0081] Obtaining scan data for the total m / z range from the analysis of the initial sample of the precursor ions.

[0082] In other words, the method can include a pre-scan (e.g., an AGC pre-scan) of the total m / z range before analyzing ions from multiple sub-ranges. Optionally, the method can include accumulating (in a single fill and in the first ion storage device or the second ion storage device) an initial sample of precursor ions having m / z values from the total m / z range. Alternatively, the initial sample can be directed to the first mass analyzer or the second mass analyzer. Analyzing an initial sample of precursor ions having m / z values from the total m / z range can include obtaining scan data for the total m / z range (which can be low-resolution, full MS scan data rather than SIM scan data).

[0083] The method may further include determining the multiple sub-ranges from the total m / z range based on scan data obtained from the analysis of an initial sample of precursor ions (having m / z values from the total m / z range). This can be referred to as a data-dependent acquisition (DDA) method.

[0084] Each of the multiple sub-ranges can have the same width.

[0085] The multiple sub - ranges can be consecutive.

[0086] The method can be carried out during a time period based on the chromatographic peak width when the sample elutes from the chromatographic system.

[0087] In another example, a mass spectrometry method is also provided. The method includes the following steps for each of a plurality of sub - ranges selected from a total m / z range:

[0088] Configure an ion beam splitter to direct ions to a first ion destination and a second ion destination, where the first ion destination is a first ion storage device;

[0089] Accumulate a sample of precursor ions to be analyzed in the first ion storage device, where the precursor ions have an m / z value within the sub - range.

[0090] In option a), the second ion destination is a first mass analyzer, and the method further includes (for each of the plurality of sub - ranges) injecting a sample of fragmented precursor ions into the first mass analyzer, where the sample of fragmented precursor ions is formed by fragmentation of precursor ions having an m / z value within the sub - range.

[0091] In option b), the second ion destination is a second ion storage device, and the method further includes (for each of the plurality of sub - ranges) accumulating a sample of fragmented precursor ions in the second ion storage device for analysis in a first mass analyzer, where the sample of fragmented precursor ions is formed by fragmentation of precursor ions having an m / z value within the sub - range.

[0092] The proposed method helps to slice an ion beam proportionally based on the spatial distribution of the ion beam. The sliced ion beam can be used to generate parallel accumulation regions for simultaneously accumulating precursor ions for HDR MS1 scans (SIM injection) alongside a series of MS2 scans.

[0093] The methods described herein can be used to establish high - quality HDR scans (or equivalent precursor data from multiple MS1 scans, where each scan spans multiple sub - ranges) using a Fourier transform mass analyzer.

[0094] The proposed method is suitable for the quantification of a wide dynamic range of analyte ions. Normally performing separate MS1 and MS2 scans would involve extended delays to switch the ion source and quadrupole to scan through the mass range independently of the DIA cycle scan used to obtain fragment data. The number of ions to be processed for HDR scans is high, and thus it always consumes a significant proportion of the ion beam time.

[0095] Fragmented precursor ions in a sample of fragmented precursor ions can be formed by fragmentation of precursor ions having m / z values within a sub-range. More specifically, a sample of fragmented precursor ions can consist of fragmented precursor ions formed by fragmentation of precursor ions having m / z values within that sub-range.

[0096] A sample of precursor ions can consist of precursor ions having m / z values within a sub-range.

[0097] Samples of precursor ions for each of a plurality of sub-ranges can be combined together in a first ion storage device such that the first ion storage device contains precursor ions having m / z values from a total m / z range. In other words, ions from each sub-range can be present in the first ion storage device.

[0098] The method can also include analyzing a combined sample of precursor ions having m / z values from the total m / z range in a first mass analyzer or a second mass analyzer. In other words, multiple SIM injections can be combined together in the first ion storage device and analyzed together in the mass analyzer. Although the precursor accumulation step is performed for each sub-range, the step of analyzing the combined sample of precursor ions can be performed once for the total m / z range.

[0099] In a first example, the method also includes ejecting ions from the first ion storage device into a second mass analyzer. In other words, there can be two mass analyzers in series, both of which are downstream of the ion beam splitter.

[0100] In a second example, the first ion storage device is an intermediate ion storage device, wherein the method also includes configuring the ion beam splitter to transfer precursor ions accumulated in the first ion storage device to a third ion storage device for analysis in the second mass analyzer.

[0101] The third ion storage device can be between an ion filter and the ion beam splitter (specifically, the input region of the ion beam splitter). Ions can be transferred from the ion filter to the ion beam splitter via the third ion storage device.

[0102] In this case, ions can be transferred from a first “exit” region to an “entrance” region. Thus, in the step of transferring precursor ions accumulated in the first ion storage device to the third ion storage device, the first exit region can be used as an entrance, and the first entrance region can be used as an exit. In other words, the ions travel in a direction opposite to the normal.

[0103] The method can also include ejecting ions from the third ion storage device into the second mass analyzer.

[0104] The precursor ions transferred from the first ion storage device to the third ion storage device may include a sample of the precursor ions for each of the plurality of sub-ranges.

[0105] In other words, in a second example, there may be two mass analyzers in series, a first mass analyzer downstream of the ion beam splitter (for analyzing the fragment ions, such as a time-of-flight mass analyzer), and a second mass analyzer upstream of the ion beam splitter (for analyzing the precursor ions, such as a Fourier transform mass analyzer).

[0106] After a sample of the fragmented precursor ions for each of the plurality of sub-ranges has been accumulated in the second ion storage device, the precursor ions may be transferred from the first ion storage device to the third ion storage device. In other words, after all of the fragment ions have been accumulated or analyzed, the precursor ions may be transferred out of the intermediate ion storage device. This prevents the precursor ions accumulated in the intermediate ion storage device from mixing with other ions in the ion beam splitter during the transfer.

[0107] The third ion storage device may be a curved linear ion trap (also referred to as a "c-trap").

[0108] The ion beam splitter may provide sufficient ion transport to eliminate ion mixing between sub-ranges.

[0109] In some examples, the third ion storage device is disposed upstream of the ion beam splitter. In this case, ions may first be accumulated in the third ion storage device (such as in the c-trap) before the ion beam splitter. This configuration may allow accumulation (in the c-trap) to be parallel to ion transport through the ion beam splitter for the immediately preceding sub-range. In other words, after all of the precursor ions from the first sub-range have been ejected from the third ion storage device, accumulation of precursor ions from the next sub-range in the third ion storage device may begin while the precursor ions from the first sub-range are being transported through the ion beam splitter. This improves overall performance even if the time taken to clear ions out of the ion beam splitter is relatively slow.

[0110] The second mass analyzer may be a Fourier transform mass analyzer. This applies to both the first and second examples described above.

[0111] In a third example, the first ion storage device may be an intermediate ion storage device. The method may further include configuring the ion beam splitter to transfer precursor ions accumulated in the first ion storage device to a second ion destination (e.g., the first mass analyzer in option a or the second ion storage device in option b).

[0112] In this case, ions can be transferred from the first "exit" region to the second exit region. Thus, in the step of transferring the precursor ions accumulated in the first ion storage device to the second ion destination, the first exit region can be used as an inlet.

[0113] In the case where the second ion destination is a second ion storage device (option b), the method may further include ejecting the precursor ions from the second ion storage device into the first mass analyzer.

[0114] The precursor ions transferred (transferred to the first mass analyzer or the second ion storage device) from the first ion storage device may include a sample of the precursor ions of each sub-range of the plurality of sub-ranges.

[0115] The transferred precursor ions may include precursor ions having m / z values from the total m / z range. In other words, the transferred precursor ions may include a combined sample from each sub-range.

[0116] In the case where the second ion destination is a second ion storage device (option b), the method may further include ejecting a sample of the fragmented precursor ions from the second ion storage device into the first mass analyzer.

[0117] After each accumulation (before accumulating the fragment ions formed by the fragmentation of the precursor ions from the next sub-range), a sample of the fragmented precursor ions can be ejected from the second ion storage device.

[0118] A sample of the fragmented precursor ions can be ejected from the second ion storage device before the precursor ions are transferred to the second ion storage device.

[0119] After a sample of the fragmented precursor ions of each sub-range of the plurality of sub-ranges has been ejected from the second ion storage device into the first mass analyzer, the precursor ions can be transferred from the first ion storage device to the second ion storage device.

[0120] The first ion storage device can be provided by a DC barrier adjacent to the first output region. In other words, the first ion storage device (intermediate ion storage device) can be integrated into the ion beam splitter.

[0121] In some examples, the ion beam splitter is between the ion filter and the first ion destination and between the ion filter and the second ion destination, and is configured to direct ions (simultaneously) from the ion filter to the first ion destination and the second ion destination.

[0122] For each sub-range, the step of accumulating a sample of the precursor ions can be performed before the step of accumulating a sample of the fragmented precursor ions.

[0123] Alternatively, for each sub-range, the step of accumulating the sample of the fragmented precursor ions can be performed before the step of accumulating the sample of the precursor ions.

[0124] The method may also include, for each sub-range of the plurality of sub-ranges, analyzing the sample of the precursor ions in the first mass analyzer or the second mass analyzer. In this alternative, the precursor ions of each sub-range are analyzed separately in a SIM scan, rather than injecting all SIM accumulations together in one scan and analyzing the precursor ions from the total m / z range. The SIM scan can be interleaved with the fragmentation scan, which can advantageously mean that no reconfiguration of the ion filter is required between the SIM scan and the fragmentation scan for each sub-range. The method may also include obtaining scan data related to the precursor ions of each sub-range. The method may also include combining the scan data related to the precursor ions for each sub-range to form a high-definition scan for the total m / z range. In other words, the SIM scan data is stitched together to form a high-resolution MS scan. In this case, a pre-scan may not be required (since the sub-ranges are continuous and cover the total m / z range).

[0125] In another example, an HDR MS scan can be sliced into a plurality of scans, each of the plurality of scans being related to precursor ions from a plurality of consecutive sub-ranges. In this alternative, each scan includes simultaneously analyzing multiple SIM injections. The method may also include combining the scan data from each of the plurality of scans to form a high-definition scan of the total m / z range. In this case, a pre-scan may not be required because a) the sub-ranges are continuous and cover the total m / z range, and b) each sub-range is analyzed in a corresponding one of the plurality of scans.

[0126] The ion beam splitter can be configured to operate under pure molecular flow conditions. Pure molecular flow conditions (also known as free molecular flow or Knudsen diffusion) are observed when the Knudsen number Kn is greater than 20 or more preferably Kn > 10.

[0127] The method may also include fragmenting the precursor ions to produce a sample of the fragmented precursor ions.

[0128] In the case where the second ion destination is the second ion storage device (option b), the ions can be fragmented in the second ion storage device.

[0129] In other words, the precursor ions can be directed by the ion beam splitter to the second ion storage device, and then once the ions have been accumulated in the second ion storage device, they can be fragmented.

[0130] Alternatively, a multipole collision cell (e.g., an IRM collision cell) can be used to fragment the ions.

[0131] The multipole collision cell can be downstream of the ion beam splitter such that the ion beam splitter directs precursor ions to the multipole collision cell which then transfers the fragmented ions to the second ion destination (the first mass analyzer in option a or the second ion storage device in option b). In other words, the multipole collision cell can be between the ion beam switch and the second ion destination.

[0132] In option b), the fragmented ions can be accumulated in the second ion storage device and then ejected from the second ion storage device into the first mass analyzer.

[0133] The method can further include configuring an ion filter for each of a plurality of sub-ranges to transmit precursor ions having m / z values within that sub-range. A sample of precursor ions can be received from the configured ion filter. The sample of fragmented precursor ions can be formed by fragmentation of the precursor ions received from the configured ion filter.

[0134] In other words, the ion filter can be configured once for each sub-range and the configuration is adapted to fill the first ion storage device with precursor ions and send the fragmented precursor ions to the second ion destination (while using the ion beam splitter).

[0135] The sample of fragmented precursor ions can be formed by fragmentation of the precursor ions received from the configured ion filter via the ion beam splitter.

[0136] Configuring the ion filter can include setting the transmission window of the ion filter. The transmission window can be adjusted between each of the plurality of sub-ranges. For each sub-range, the transmission window for the step of accumulating the sample of precursor ions can be the same as the transmission window for the step of injecting the sample of fragmented precursor ions into the first mass analyzer (in option a) or accumulating the sample of fragmented precursor ions in the second ion storage device (in option b).

[0137] A front-end accumulation device such as an ion mobility separator such as a trapped ion mobility separator (as incorporated in the Bruker TIMS-ToF series of mass spectrometers) (and would be advantageous for the methods described herein) can be used. Such devices can release ions in an m / z range synchronized with the quadrupole isolation window. Thus, ion transmission is greatly facilitated. Also thus, the required injection time can be reduced (due to a brighter isolated ion beam). This reduction in injection time can be used to offset the additional time overhead of SIM injection.

[0138] The method may further include configuring an ion mobility separator to transfer precursor ions having m / z values within the sub-range to an ion filter.

[0139] The method may further include, for each of a plurality of sub-ranges within the total m / z range, controlling the ion mobility separator such that the precursor ions transferred to the ion filter correspond to the transmission window of the ion filter.

[0140] The sample accumulating the precursor ions may include controlling the filling time of the precursor ions based on the relative abundances of precursor ion species within the corresponding sub-range.

[0141] In the case where the second ion destination is a second ion storage device and the sample of fragmented precursor ions is accumulated in the second ion storage device (option b), the method may further include: for each of the plurality of sub-ranges, ejecting the sample of fragmented precursor ions from the second ion storage device into the first mass analyzer and analyzing the sample of fragmented precursor ions in the first mass analyzer.

[0142] The plurality of sub-ranges may include a first sub-range and a second sub-range.

[0143] The step of analyzing the sample of fragmented precursor ions from the first sub-range may at least partially overlap (in time) with the step of accumulating in the second ion storage device the sample of fragmented precursor ions formed by fragmentation of precursor ions having m / z values within the second sub-range.

[0144] In the case where the second ion destination is a first mass analyzer and the sample of fragmented precursor ions is injected into the first mass analyzer (option a), the method may further include analyzing the sample of fragmented precursor ions in the first mass analyzer.

[0145] The step of analyzing the sample of fragmented precursor ions from the first sub-range may at least partially overlap (in time) with the step of accumulating in the first ion storage device the sample of precursor ions having m / z values within the second sub-range.

[0146] The first mass analyzer may be a time-of-flight ToF analyzer.

[0147] The first mass analyzer may be a multi-reflection time-of-flight MR-ToF analyzer.

[0148] The first ion storage device may be a curved linear trap (e.g., c-trap).

[0149] In the case where the second ion destination is a second ion storage device and a sample of the fragmented precursor ions is accumulated in the second ion storage device (option b), the second ion storage device can be a linear trap (e.g., a DP-R trap).

[0150] The method may also include ionizing a sample to generate precursor ions.

[0151] A sample of fragmented precursor ions can be formed by fragmentation of precursor ions having m / z values within the sub-range at multiple different collision energies.

[0152] The method may also include:

[0153] Configuring an ion filter to transmit precursor ions having m / z values from the total m / z range;

[0154] Transferring an initial sample of precursor ions having m / z values from the total m / z range to the first mass analyzer or the second mass analyzer;

[0155] Analyzing the initial sample of the precursor ions; and

[0156] Obtaining scan data for the total m / z range from the analysis of the initial sample of the precursor ions.

[0157] In other words, the method can include a pre-scan (e.g., an AGC pre-scan) of the total m / z range before analyzing ions from multiple sub-ranges. Optionally, the method can include accumulating (in a single fill and in the first ion storage device or the second ion storage device) an initial sample of precursor ions having m / z values from the total m / z range. Alternatively, the initial sample can be directed to the first mass analyzer or the second mass analyzer. To transfer the initial sample of ions, the ion beam splitter can be configured such that substantially all of the ions are directed to one exit region (and a negligible amount of ions are directed to the other exit region). Analyzing the initial sample of precursor ions having m / z values from the total m / z range can include obtaining scan data for the total m / z range (which can be low-resolution, full MS scan data, rather than SIM scan data).

[0158] The method may also include determining the multiple sub-ranges from the total m / z range based on scan data obtained from the analysis of the initial sample of precursor ions (having m / z values from the total m / z range). This can be referred to as a data-dependent acquisition (DDA) method.

[0159] Each of the multiple sub-ranges can have the same width.

[0160] The multiple sub-ranges can be continuous.

[0161] This method can be carried out within a time period based on the chromatographic peak width when the sample elutes from the chromatographic system.

[0162] In yet another example, a mass spectrometry method is provided, including the following steps for each of a plurality of sub-ranges selected from a total m / z range:

[0163] Configure an ion guide to direct ions to a first ion destination and / or a second ion destination, where the first ion destination is a first ion storage device;

[0164] Accumulate a sample of precursor ions to be analyzed in the first ion storage device, where the precursor ions have an m / z value within the sub-range.

[0165] In option a), the second ion destination is a first mass analyzer, and the method further includes (for each of the plurality of sub-ranges) injecting a sample of fragmented precursor ions into the first mass analyzer, where the sample of fragmented precursor ions is formed by fragmentation of precursor ions having an m / z value within the sub-range.

[0166] In option b), the second ion destination is a second ion storage device, and the method further includes accumulating a sample of fragmented precursor ions to be analyzed in the second ion storage device, where the sample of fragmented precursor ions is formed by fragmentation of precursor ions having an m / z value within the sub-range.

[0167] The ion guide can be an ion beam splitter or an ion beam switch.

[0168] The ion guide can have an inlet region for receiving ions, a first outlet region for directing ions to the first ion destination, and a second outlet region for directing ions to the second ion destination.

[0169] A mass spectrometer configured to perform the above method is also provided.

[0170] The mass spectrometer can include an ion guide, a first ion destination, and a second ion destination.

[0171] A computer software including instructions is also provided, where the instructions, when executed by a processor of a computer, cause the computer to perform the above method.

[0172] The instructions can be executed by a processor of a controller of the mass spectrometer, so that the mass spectrometer performs the method.

[0173] In yet another example, an ion guide for a mass spectrometer with a switchable ion path is provided. The ion guide includes: a first ion transport aperture configured to receive an ion beam. The ion guide further includes: a radio frequency (RF) surface including a plurality of RF electrodes disposed on a first surface such that the plurality of RF electrodes are parallel to each other. The ion guide further includes: an RF voltage source configured to apply an alternating RF phase to each of the plurality of RF electrodes. The ion guide further includes: a DC potential source configured to apply a DC gradient across the RF surface, wherein the DC gradient is configured to direct the ion beam via a first ion path or a second ion path. The ion guide further includes a second ion transport aperture and a third ion transport aperture. Ions traveling in the first ion path are directed between the first ion transport aperture and the second ion transport aperture, and ions traveling in the second ion path are directed between the first ion transport aperture and the third ion transport aperture.

[0174] In this way, ions can be trapped within a large volume on the RF surface. The ions can be gently directed by the DC gradient to follow either the first ion path (between the first ion transport aperture and the second ion transport aperture) or the second ion path (between the first ion transport aperture and the third ion transport aperture).

[0175] Due to the low mean free path of ions, a DC gradient is particularly desirable in systems operating at higher pressures (or lower vacuum). Ions can stop flying due to excessive collisions with the background gas. Then, these ions may not reach the analyzer in a timely manner, resulting in losses or leading to incorrect measurements when the ions reach the analyzer. Ions remaining in the ion guide can create an unwanted space charge effect on other ions in flight. The DC gradient can help ensure that ions are removed from the ion guide and reach the analyzer, thereby reducing transmission losses and transit time losses.

[0176] The DC gradient can include an orthogonal component and an axial component.

[0177] In this way, the DC gradient can use the orthogonal component to direct the ion beam to follow the first ion path or the second ion path, and can use the axial component to direct the ion beam from one end of the ion guide to the other end.

[0178] The second ion transport aperture and the third ion transport aperture can be in a first plane, and the orthogonal component of the DC gradient can be parallel to the first plane, and the axial component of the DC gradient can be parallel to the direction of the shortest distance from the first ion transport aperture to the first plane.

[0179] In this way, the DC gradient can use the orthogonal component to direct the ion beam to follow the first ion path or the second ion path, and can use the axial component to direct the ion beam from one end of the ion guide to the other end (i.e., between the first ion transport hole and the plane intersecting the second ion transport hole and the third ion transport hole).

[0180] The radio frequency electrodes can include elongated electrode plates that are arranged such that the plane of each plate is parallel to the plane of an adjacent plate.

[0181] Advantageously, the electrode plates can prevent ions from approaching the first surface.

[0182] The radio frequency electrodes can be arranged in a grid.

[0183] In this way, the radio frequency electrodes can be used to apply a DC gradient or a traveling wave in the axial direction and the orthogonal direction.

[0184] The ion guide can include: a top plate that is configured to apply a repulsive voltage that repels the ion beam toward the radio frequency surface.

[0185] In this way, these ions can be compressed close to the radio frequency surface.

[0186] The top plate can include a DC voltage source, where the DC voltage source can be configured to apply a DC gradient to the top plate.

[0187] In this way, the top plate can be configured to apply a DC gradient.

[0188] The top plate can include a PCB and a plurality of DC electrodes printed on the PCB.

[0189] Advantageously, the DC electrodes can be printed in a shape that allows the application of a DC gradient. If the top plate is configured to apply a repulsive voltage and the top plate includes DC electrodes printed on the PCB, the repulsive voltage prevents ions from approaching the PCB.

[0190] The plurality of DC electrodes can be arranged in a grid.

[0191] In this way, a two-dimensional DC gradient can be applied.

[0192] The plurality of DC electrodes can be arranged in a horseshoe configuration, where the prongs of the horseshoe are adjacent to the second ion transport hole and the third ion transport hole.

[0193] In this way, the shape of the DC electrodes can help define the first ion path and the second ion path.

[0194] The plurality of DC electrodes can be connected by resistors.

[0195] In this way, a DC gradient can be applied.

[0196] The DC potential source may include a plurality of auxiliary DC electrodes, each of which is positioned between the RF electrodes.

[0197] In this way, both the RF electrodes and the DC potential source can be arranged on the first surface or adjacent to the first surface.

[0198] The plurality of auxiliary DC electrodes may include elongate electrode plates, and the RF electrodes may include elongate electrode plates that are arranged such that the plane of each plate is parallel to the plane of an adjacent plate, wherein the plane of the plates of the DC electrodes is parallel to the plane of the plates of the adjacent RF electrodes.

[0199] In this way, the DC electrodes can be mounted between the RF electrodes and a DC gradient strong enough to reach the center of the ion guide can be applied.

[0200] The auxiliary DC electrodes may include elongate electrode plates that are wedge-shaped in the plane of the plates.

[0201] In this way, the DC electrodes can apply a DC gradient.

[0202] Each of the plurality of DC electrodes may include peaks and valleys located in the top of the plate.

[0203] In this way, the ion beam can be spatially focused as the ions travel along the first ion path or the second ion path.

[0204] The RF electrodes may include: elongate electrode plates that are arranged such that the plane of each plate is parallel to the plane of an adjacent plate, and the first surface may include a PCB, wherein the auxiliary DC electrodes include printed electrodes located between the RF electrodes.

[0205] In this way, the DC electrodes can be printed between the RF electrodes.

[0206] The ion guide may include a top surface facing the RF surface, the top surface including: a plurality of RF electrodes arranged on the top surface; and a plurality of auxiliary DC electrodes, each of the plurality of auxiliary DC electrodes being mounted between the RF electrodes.

[0207] In this way, both the first surface and the top surface can include electrodes that provide a pseudo-potential surface and apply a DC gradient.

[0208] The radio frequency electrode may include: an elongated electrode plate, which is arranged such that the plane of each plate is parallel to the plane of an adjacent plate, wherein each radio frequency electrode of the radio frequency electrodes may include a first notch and a second notch in the top of the radio frequency electrode, wherein the first notch and the second notch coincide with the positions of the first ion path and the second ion path, and wherein the depths of the first notch and the second notch increase towards the second ion transport hole and the third ion transport hole.

[0209] In this way, when ions travel along the first ion path or the second ion path, the ion beam can be spatially focused.

[0210] The ion guide may further include: a first side guard plate positioned on the first side of the radio frequency surface; and a second side guard plate positioned on the second side of the radio frequency surface.

[0211] In this way, leakage of ions from the sides of the ion guide can be prevented. The first side guard plate and the second side guard plate may be configured to prevent ions from leaving the ion guide via the first side or the second side, and / or to shape the ion cloud.

[0212] The first side guard plate and the second side guard plate may include a first wall and a second wall.

[0213] In this way, leakage of ions from the sides of the ion guide can be physically prevented.

[0214] The first side guard plate and the second side guard plate may include a first protection electrode and a second protection electrode, wherein the first protection electrode and the second protection electrode are configured to receive a repulsive DC voltage or an attractive DC voltage.

[0215] In this way, if a repulsive DC voltage is applied, then when ions travel between the first ion transport hole and the second ion transport hole or the third ion transport hole, ions can be repelled from the sides of the ion guide to keep the ions within the main volume of the ion guide. If an attractive DC voltage is applied, the ion cloud can be pulled towards the edge of the radio frequency electrode, thereby helping to focus the ion beam.

[0216] The first surface may be configured to form the first side guard plate and the second side guard plate.

[0217] In this way, separate side guard plates may not be required.

[0218] The radio frequency electrode may be configured to form the first side guard plate and the second side guard plate.

[0219] Advantageously, the radio frequency electrode can repel ions away from the sides of the ion guide.

[0220] The first surface may be inclined relative to the top plate or the top surface such that the distance between the first surface and the top plate or the top surface decreases as it approaches the second ion transport hole and the third ion transport hole.

[0221] In this way, when ions travel from the first ion transport hole to the second ion transport hole or the third ion transport hole, the ion beam can be spatially focused.

[0222] The ion guide may further include: a chamber opposite the first ion transport hole, wherein the chamber is configured to receive the undeflected component of the ion beam.

[0223] In this way, neutral particles, droplets or other unwanted materials can be removed from the ion guide. Description of the Drawings

[0224] The present invention can be implemented in various ways, and specific embodiments will now be described by way of example only and with reference to the following drawings.

[0225] Figure 1 A schematic diagram of a mass spectrometer suitable for performing the method according to an embodiment is shown.

[0226] Figure 2 An example of a branched RF multipole that can be used as an ion beam switch is illustrated.

[0227] Figure 3 A schematic diagram of an ion guide according to an embodiment of the present disclosure including a radio frequency (RF) surface, the RF surface including a plurality of RF electrodes, the plurality of RF electrodes including elongated electrode plates, is shown.

[0228] Figure 4 A schematic diagram of an RF electrode of an ion guide according to an embodiment of the present disclosure is shown, wherein the RF electrode includes a notch forming a channel.

[0229] Figure 5 shows a schematic cross-sectional view of an ion guide according to an embodiment of the present disclosure. Figure 5A The RF electrode, the top plate, the first side guard plate and the second side guard plate are shown. Figure 5B The RF electrode and the top plate are shown, wherein the RF electrode includes the first side guard plate and the second side guard plate. Figure 5C The RF electrode and the top plate are shown, wherein the RF electrode includes the first side guard plate, the second side guard plate, the first notch and the second notch. Figure 5D The RF electrode, the top plate, the first DC electrode and the second DC electrode are shown, wherein the RF electrode includes the first side guard plate and the second side guard plate.

[0230] Figure 6A schematic diagram of an ion guide according to an embodiment of the present disclosure is shown, where the ion guide includes a radio frequency (RF) surface and a top plate, the RF surface includes a plurality of RF electrodes, and the top plate includes a DC electrode structure.

[0231] Figure 7 A schematic diagram of a DC electrode structure according to an embodiment of the present disclosure is shown, where the DC electrode structure includes a grid of printed electrodes.

[0232] Figure 8 A schematic diagram of a DC electrode structure according to an embodiment of the present disclosure is shown, where the DC electrode structure includes a printed electrode in a horseshoe shape.

[0233] Figure 9 A schematic diagram of an ion guide according to an embodiment of the present disclosure is shown, where the ion guide includes a radio frequency (RF) surface, the RF surface includes a plurality of RF electrodes and a plurality of auxiliary DC electrodes mounted between the RF electrodes.

[0234] Figure 10 A schematic diagram of an ion guide according to an embodiment of the present disclosure is shown, where the ion guide includes a radio frequency (RF) surface, the RF surface includes a plurality of RF electrodes and a plurality of auxiliary DC electrodes mounted between the RF electrodes, and where the ion guide further includes a top surface, the top surface includes a plurality of RF electrodes and a plurality of auxiliary DC electrodes mounted between the RF electrodes.

[0235] Figure 11 A schematic diagram of a cross-section of an auxiliary DC electrode according to an embodiment of the present disclosure is shown.

[0236] Figure 12 A schematic diagram of an ion guide according to an embodiment of the present disclosure is shown, where the ion guide includes a radio frequency (RF) surface, the RF surface includes a plurality of RF electrodes and a plurality of auxiliary DC electrodes printed between the RF electrodes.

[0237] Figure 13 A schematic diagram of a mass spectrometer incorporating an ion guide according to an embodiment of the present disclosure is shown.

[0238] Figure 14 illustrates two alternative configurations of a hybrid mass spectrometer incorporating a beam switching device. Figure 14A A configuration is illustrated where the beam switch is located after the quadrupole mass filter. Figure 14B A configuration is illustrated where the beam switching device is located after the curved linear ion storage device.

[0239] Figure 15 An ion beam splitting device based on an RF carpet ion guide is illustrated.

[0240] FIG. 16 illustrates two alternative configurations of a hybrid mass spectrometer incorporating a beam splitting device.

[0241] Figure 17 Illustrated is a DIA method for parallel accumulation of SIM injections in a curved linear ion storage device, which uses a Fourier transform mass analyzer constructed as a single HDR scan, interleaved between a series of MS2 scans in a time-of-flight mass analyzer. DETAILED DESCRIPTION

[0242] Figure 1 Shown is a schematic arrangement of a mass spectrometer 1 suitable for performing the method according to an embodiment. The mass spectrometer 1 can be a hybrid Fourier transform / multi-reflection time-of-flight mass spectrometer (MR-ToF) as described in US 10,699,888, which is incorporated by reference. Details of the mass analyzer are described in US 9,136,101, which is incorporated by reference herein.

[0243] In Figure 1 , a sample to be analyzed (e.g., from an autosampler) is supplied to a chromatographic device such as a liquid chromatography (LC) column ( Figure 1 not shown in). One such example of an LC column is the ProSwift TM monolithic column from Thermo Fisher Scientific, Inc., which provides high performance liquid chromatography (HPLC) by forcing a sample transported in a mobile phase through a stationary phase of irregular or spherical shaped particles that make up the stationary phase under high pressure. In an HPLC column, sample molecules elute at different rates depending on their degree of interaction with the stationary phase.

[0244] Chromatography can be generated by measuring the number of sample molecules eluting from the HPLC column over time using a detector (e.g., a mass spectrometer). Sample molecules eluting from the HPLC column will be detected as peaks above the baseline measurement on the chromatogram. When different sample molecules have different elution rates, multiple peaks on the chromatogram can be detected. Preferably, individual sample peaks are separated in time from other peaks in the chromatogram such that different sample molecules do not interfere with each other.

[0245] In chromatography, the presence of a chromatographic peak corresponds to the period of time during which a sample molecule is present at the detector. Thus, the width of a chromatographic peak is equal to the period of time during which a sample molecule is present at the detector. Preferably, the chromatographic peak has a Gaussian shape distribution, or can be assumed to have a Gaussian shape distribution. Therefore, the width of a chromatographic peak can be determined based on multiple standard deviations calculated from the peak. For example, the peak width can be calculated based on 4 standard deviations of the chromatographic peak. Alternatively, the peak width can be calculated based on the width at half the maximum height of the peak. Other methods known in the art for determining peak width may also be suitable.

[0246] Then, an electrospray ionization source (ESI source) 2 under atmospheric pressure is used to ionize the sample molecules separated by liquid chromatography.

[0247] The sample ions then enter the vacuum chamber of the mass spectrometer 1 and are guided by a capillary 25 into a radio-frequency-only S lens 3 (also known as an ion funnel). The ions are focused by the S lens 3 into an injection flat electrode 4 (also known as a quadrupole prefilter), which injects the ions into a curved flat electrode 5 with an axial field. The curved flat electrode 5 guides (charged) ions along a curved path passing through it, while unwanted neutral molecules (such as entrained solvent molecules) are not guided along the curved path and are lost. For example, the curved path can be bent at 90 degrees or have an S-shaped swing.

[0248] The TK lens 6 is located at the distal end of the curved flat electrode 5. The ions enter a downstream mass selector in the form of a quadrupole mass filter 7 from the curved flat electrode 5. The TK lens serves as an edge field corrector for the quadrupole mass filter 7. The quadrupole mass filter 7 is usually but not necessarily segmented and serves as a bandpass filter, allowing selected mass numbers or a limited mass range to pass while excluding ions of other mass-to-charge ratios (m / z). The filter can also be operated in a radio-frequency-only mode, in which the filter has no mass selectivity, i.e., it transmits substantially all m / z ions. For example, the quadrupole mass filter 7 can be controlled by a controller to select precursor ions within a certain range of mass-to-charge ratios allowed to pass through while filtering out (attenuating) other ions in the precursor ion stream. Alternatively, the S lens 3 can operate as an ion gate, and the ion gate (TK lens) 6 can be an electrostatic lens.

[0249] Although Figure 1 a quadrupole mass filter is shown, those skilled in the art should understand that other types of mass selection devices may also be suitable for selecting precursor ions within the mass range of interest. For example, the ion separator depicted in US-A-2015287585, the ion trap depicted in WO-A-2013076307, the ion mobility separator described in US-A-2012256083, the ion gate mass selection device described in WO-A-2012175517, or the charged particle trap described in US799223, which is incorporated herein by reference. Those skilled in the art should understand that other methods of selecting precursor ions based on ion mobility, differential mobility, and / or transverse modulation are also suitable.

[0250] The method called synchronous precursor scan (SPS) can also be used to perform isolation of multiple ions of different masses or mass ranges in an ion trap. In addition, in some embodiments, more than one ion selection device or mass selection device can be provided. For example, another mass selection device can be provided downstream of the fragmentation chamber 12. In this way, MS 3 or MSn Scanning (usually using a ToF mass analyzer for mass analysis).

[0251] Then, the ions pass through a quadrupole exit lens / split lens arrangement 8, which acts as an ion gate to control the passage of ions into the first transfer multipole 9 optionally via a charge detector (not illustrated). The first transfer multipole 9 guides the mass-filtered ions from the quadrupole mass filter 7 into a curved linear ion trap (C-trap) 10. The C-trap (first ion storage device) 10 has a longitudinally extending curved electrode supplied with an RF voltage and end caps supplied with a DC voltage. As a result, a potential well extends along the curved longitudinal axis of the C-trap 10. In a first operating mode, a DC end cap voltage is set for the C-trap such that ions arriving from the first transfer multipole 9 are trapped in the potential well of the C-trap 10, where the ions are cooled. The injection time (IT) of the ions into the C-trap determines the number of ions (ion packet) subsequently ejected from the C-trap into the mass analyzer.

[0252] The cooled ions accumulate as a cloud towards the bottom of the potential well and are then orthogonally ejected from the C-trap towards the second mass analyzer 11. As Figure 1 shown, the second mass analyzer is a Fourier transform mass analyzer, such as an Orbitrap mass analyzer 11, e.g., Orbitrap sold by Thermo Fisher Scientific Inc. TM mass analyzer. The Fourier transform mass analyzer 11 has an off-center injection hole, and the ions are injected into the Orbitrap mass analyzer 11 as a coherent group through the off-center injection hole. Then, the ions are trapped in the Orbitrap mass analyzer by a super-logarithmic electric field, and the ions move back and forth in the longitudinal direction while orbiting around the inner electrode.

[0253] The moving axial (z) component of the ion packet in the Orbitrap mass analyzer is (more or less) defined as a simple harmonic motion, where the angular frequency in the z direction is related to the square root of the mass-to-charge ratio of a given ion species. Thus, over time, the ions are separated according to their mass-to-charge ratio.

[0254] The ions in the Orbitrap mass analyzer are detected by using an image current detector (not shown), which generates a "transient" containing information about all ion species in the time domain as the ion species pass through the image current detector. Then, this transient is subjected to a fast Fourier transform (FFT), thereby generating a series of peaks in the frequency domain. Based on these peaks, a mass spectrum representing the abundance / ion intensity versus m / z can be generated.

[0255] In the above configuration, in the absence of fragmentation, sample ions (more specifically, a mass range segment of sample ions within the mass range of interest selected by the quadrupole mass filter 7) are analyzed by the orbital trap mass analyzer 11. The resulting mass spectrum is denoted as MS1.

[0256] Although Figure 1 the orbital trap mass analyzer 11 is shown in, alternatively, other mass analyzers can be used, including other Fourier transform mass analyzers. For example, a Fourier transform ion cyclotron resonance (FTICR) mass analyzer can be used as the mass analyzer for MS1 scans. Mass analyzers such as orbital trap mass analyzers and ion cyclotron resonance mass analyzers can be used in embodiments even in cases where other types of signal processing different from Fourier transform are used to obtain mass spectrometry information from transient signals (see, for example, WO 2013 / 171313, Thermo Fisher Scientific).

[0257] In the second operating mode of the C-trap 10, ions that pass through the quadrupole exit lens / skimmer arrangement 8 and the first transfer multipole 9 and enter the C-trap 10 can also continue their path through the C-trap and enter the fragmentation chamber 12, which can be an "ion routing multipole" (IRM) collision cell. Thus, the C-trap effectively acts as an ion guide in the second operating mode. Alternatively, the cooled ions in the C-trap 10 can be ejected axially from the C-trap into the fragmentation chamber 12. In Figure 1 the mass spectrometer 1 of, the fragmentation chamber 12 is a high energy collision dissociation (HCD) device to which collision gas is supplied. The precursor ions that reach the fragmentation chamber 12 collide with the collision gas molecules, thereby fragmenting the precursor ions into fragment ions.

[0258] Although the HCD fragmentation chamber 12 is shown in Figure 1 , alternatively, other fragmentation devices employing methods such as collision induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), photodissociation, etc. can be used. In addition, ion fragmentation can be performed in the high pressure region of the extraction trap 14.

[0259] The fragmented ions can be ejected from the fragmentation chamber 12 into the C-trap 10 at the relatively axial end. The ejected fragmented ions enter the second transfer multipole 13. The second transfer multipole 13 guides the fragmented ions from the fragmentation chamber 12 into the extraction trap (second ion trap) 14. The extraction trap 14 is a radio frequency voltage controlled trap containing buffer gas. For example, a suitable buffer gas is at a pressure of 5×10 -4 mBar to 1×10 -2Argon within the range of mBar. The extraction trap is capable of quickly cutting off the applied RF voltage and applying a DC voltage to extract the trapped ions. A suitable planar extraction trap, also known as a rectangular ion trap, is further described in US 9,548,195, which is incorporated herein by reference. Alternatively, a C-trap is also suitable for use as the second ion trap.

[0260] An extraction trap 14 is provided to form an ion packet of fragmented ions before the fragmented ions are injected into a time-of-flight mass analyzer 15. The extraction trap 14 accumulates the fragmented ions before injecting them into the time-of-flight mass analyzer 15.

[0261] Although an extraction trap (ion trap) is shown in the Figure 1 embodiment, those skilled in the art will appreciate that other methods of forming an ion packet of fragmented ions will be equally suitable for the embodiment. For example, the relatively slow transfer of ions through a multipole can be utilized to affect the aggregation of ions, and the ions can then be ejected as a single group into the ToF mass analyzer. Alternatively, the orthogonal displacement of ions can be utilized to form groups. Other details of these alternatives can be found in US2003 / 0001088, which describes a traveling wave ion aggregation method and is incorporated herein by reference.

[0262] In Figure 1 the time-of-flight mass analyzer 15 shown is a multi-reflection time-of-flight mass analyzer (MR-ToF) 15. The MR-ToF 15 is constructed around two opposing ion mirrors 16, 162 that are elongated in the drift direction. The mirrors face each other in a direction orthogonal to the drift direction. The extraction trap 14 injects ions into the first mirror 16, and then the ions oscillate between the two mirrors 16, 162. The ejection angles of the ions from the extraction trap 14 and additional deflectors 17, 172 allow control of the ion energy in the drift direction such that the ions are guided along the length of the mirrors 16, 162 during oscillation, thereby producing a Z-shaped trajectory. The mirrors 16, 162 are tilted relative to each other, thereby creating a potential gradient that delays the drift velocity of the ions and causes the ions to be reflected back and focused onto the detector 18 in the drift dimension. The tilting of the opposing mirrors generally has the negative side effect of changing the oscillation period of the ions as they travel along the drift dimension. This is corrected using a strip electrode 19 (as a compensation electrode) that changes the flight potential of the portion of the space between the mirrors that varies along the length of the opposing mirrors 16, 162. The combined variation in the width of the strip electrode 19 and the change in the distance between the mirrors 16, 162 allows for ion reflection and spatial focusing onto the detector 18 as well as maintaining good time focusing. A suitable MR-ToF 15 for use in the embodiment is further described in US2015028197(A1), which is incorporated herein by reference.

[0263] In one example, an MS1 scan can be performed by a second mass analyzer (Orbitrap mass analyzer 11). In a second example, precursor ions can be fragmented and an MS2 scan can be performed by the second mass analyzer (Orbitrap mass analyzer 11) or the first mass analyzer (time-of-flight mass analyzer), depending on whether the fragmentation chamber is controlled to eject the ions back towards the C-trap 10 or forward into the second transfer multipole 13. In additional operating modes, a second mass analyzer (time-of-flight mass analyzer 15) can perform an MS1 scan of the ions. In this operating mode, the ions are axially guided through the C-trap 10 to the fragmentation chamber, but do not have sufficient kinetic energy to cause fragmentation and the ions are guided to the second transfer multipole 13 without fragmentation. Then, the ions can be accumulated in groups in the extraction trap 14, as described above.

[0264] Once a predetermined number of ions have accumulated in the extraction trap, the ions accumulated in the extraction trap are injected into the MR-ToF analyzer 15 as ion packets. By ensuring that each packet of ions injected into the MR-ToF 15 has at least a predetermined (minimum) number of ions, the resulting ion packets reaching the detector will represent the entire mass range of interest of the MS1 or MS2 spectrum. A single packet of precursor ions or fragmented ions is sufficient to obtain the MS1 or MS2 spectrum of the corresponding ions. For MS2, this represents increased sensitivity compared to the conventional acquisition of time-of-flight spectra, in which multiple spectra are typically acquired and summed for each given mass range segment. Preferably, the minimum total ion current (TIC) in each mass window is accumulated in the extraction trap before injection into the time-of-flight mass analyzer. In some examples, the time-of-flight mass analyzer acquires at least N spectra (scans) per second in the MS2 domain, where N = 50, or more preferably 100 or 200 or more.

[0265] Preferably, at least X% of the MS2 scans contain more than Y ion counts (where X = 30 or 50 or 70 or most preferably 90 or more, and Y = 200 or 500 or 1000 or 2000 or 3000 or 5000 or more). Most preferably, at least 90% of the MS2 scans contain more than 500 ion counts, or more preferably more than 1000 ion counts, and desirably more than 5000 ion counts. This provides an increased dynamic range of the MS2 spectrum. The desired ion count for each MS2 scan can be provided by adjusting the number of ions included in each packet of fragmented ions. For example, in Figure 1In embodiments, the accumulation time of the extraction trap can be adjusted to ensure that a sufficient number of ions have been accumulated. Thus, the controller can be configured to determine that a suitable fragmented ion packet has been formed when a predetermined number of ions are present in the extraction trap or when a predetermined period of time has elapsed. The predetermined period of time can be specified to ensure that the time-of-flight mass analyzer operates at the desired frequency when the ion current to the extraction trap is relatively low.

[0266] The mass spectrometer 1 is under the control of a controller which is configured, for example, to control the ejection timing of the trapping assembly; set appropriate potentials on the electrodes of a quadrupole, etc. to focus and filter ions; acquire mass spectrometry data from the orbitrap device 11; acquire mass spectrometry data from the MR-ToF 15; control the sequence of MS1 scans and MS2 scans, etc. It should be understood that the controller can include a computer which can operate according to a computer program which contains instructions for causing the mass spectrometer to perform the steps of the method according to the embodiments.

[0267] It should be understood that Figure 1 the specific arrangement of the components shown in is not necessary for the methods described subsequently. In fact, other arrangements for performing the methods of the embodiments are also suitable. In some examples, all scans (MS1, MS2, and / or SIM) are performed by the MR-ToF analyzer, which is faster than the orbitrap analyzer.

[0268] A front-end accumulation device, such as an ion mobility separator (e.g., a trapped ion mobility separator TIMS), can be configured to release ions in the m / z range corresponding to the quadrupole isolation window. As a result, the ion transmission of the quadrupole filter is improved. Due to the ion mobility separator, the injection time required can also be reduced (since the isolated ion beam is brighter). This reduction in injection time can be used to at least partially offset the additional time overhead of SIM injection.

[0269] The ion mobility separator can include a stacked-ring ion guide which applies a DC gradient in one direction to push ions and, conversely, passes them through a gas wind in the opposite direction.

[0270] In one example of the ion mobility separator, an electric field barrier in the gas flow is used to block ions according to their ion mobility. As the ion mobility increases, the field barrier decreases and the ions are released.

[0271] TIMS is described in detail in U.S. Patent 7,838,826, U.S. Patent 9,891,194, and Meier et al. (2018, Molecular Cellular Proteomics, Vol. 17, pp. 2534-2545), which are incorporated herein by reference.

[0272] The extended ion funnel consists of a plurality of segmented electrodes assembled around a common axis. The extended ion guide can be considered in three sections:

[0273] An inlet focusing section,

[0274] a mobility analysis section, and

[0275] an outlet focusing section.

[0276] In the focusing section, the distance between adjacent electrodes is approximately equal to the thickness of the electrodes. The diameter of the orifice in the electrode is a function of the position of the electrode in the ion funnel assembly. For example, the segmented electrode with the largest orifice is located at the inlet end of the ion funnel, and the segmented electrode with the smallest orifice is located at the outlet end of the ion funnel.

[0277] In some examples, the orifice diameter can be a linear function of the position of the segmented electrode. In other examples, the function can be non-linear. The angle formed between the common axis and the inner boundary of the ion funnel (i.e., formed by the inner edges of the segmented electrodes) can be approximately 19°. However, any angle between 0° and 90° can be used.

[0278] In the mobility analysis section of the ion funnel, the segmented electrodes can all have the same inner diameter. The space between adjacent electrodes can be filled with a dielectric or resistive liner. The thickness of the segmented electrode should be less than its inner diameter, and the spacing between the electrodes should be less than the thickness of the segmented electrode to maintain a uniform RF field such that the axial DC field is uniform near the axis.

[0279] The liner or O-ring between the electrodes forms a substantially airtight seal such that the orifices in the electrodes form airtight channels through which gas can flow. Gas enters the channels in the inlet focusing section, forms a laminar flow that uniformly passes through the mobility analysis section, contracts through the outlet focusing section, and then exits through the orifices in the final electrode. The orifices are substantially cylindrically symmetric to maintain a cylindrically symmetric flow profile. In operation, the symmetric laminar flow of the gas means that all ions of a given type at a given position along the axis will experience a given force due to the gas flow, substantially independent of their lateral position relative to the axis.

[0280] The quadrupole ion filter includes four rods spaced equidistantly at a predetermined radius around a central axis. A radio frequency (RF) (e.g., 1 MHz sine wave) electric potential is applied between these rods. The electric potentials on adjacent rods are 180° out of phase. The rods on opposite sides of the axis of the quadrupole are electrically connected such that the quadrupole is formed into two pairs of rods. Ions travel along the axis of the quadrupole and exit the quadrupole through an orifice. The RF electric potential applied between these rods tends to radially confine the ions. When only RF is applied between these rods, substantially all ions are transmitted through the quadrupole. Applying DC as well as RF electric potential between the pairs of rods allows only ions within a limited mass range to be transmitted through the quadrupole. Ions outside this mass range are filtered out and do not reach the exit end.

[0281] The DC electric field strength varies as a function of position along the axis. However, at some positions in the analysis section, the field strength reaches a maximum, forming a potential barrier that ions must overcome to reach the exit end of the funnel. Near the position of this maximum field strength, the uniformity of the DC field is important because this is the point at which ions are selected based on their mobility. Therefore, the DC field should be cylindrically symmetric.

[0282] An example method of operation includes the following steps:

[0283] Form a DC potential barrier in the analysis section;

[0284] Apply an RF field for focusing ions towards the axis;

[0285] Generate ions in an ion source;

[0286] Introduce ions in a carrier gas into an extended ion funnel;

[0287] Introduce ions into a focusing section by applying an electric potential to the electrodes of the focusing section and / or deflection electrodes;

[0288] Transfer ions into the analysis section by applying a DC electric potential to the electrodes of the focusing section;

[0289] Optionally, prevent additional ions from entering the analysis section by applying a DC electric potential to the deflection electrodes and / or the electrodes of the focusing section;

[0290] Use a pump located downstream of the exit end of the funnel to induce a carrier gas flow through the channel;

[0291] Gradually reduce the DC potential barrier in the analysis section to allow the carrier gas flow to push ions from the ion group over the DC potential barrier in order of ion mobility; and

[0292] Focus the ions through an orifice in the exit electrode.

[0293] In another example, a DC gradient is used to push the ions out, contrary to the gas wind. As the DC potential increases, the ions are released in order of mobility.

[0294] In one example method, a full mass scan is performed using a Fourier transform mass analyzer 11 with a long acquisition transient to generate a high-resolution MS1 spectrum. At the same time, the MR-ToF 15 analyzer performs a series of MS2 acquisitions at a very fast scan rate and high sensitivity.

[0295] Example methods for combining ion implantation and analysis are described in US 8,686,350, which is incorporated herein by reference.

[0296] The example methods described herein utilize two injections to accumulate different types of ions: the first injection is of fragmented ions, and the second injection is of intact precursor ions (the first and second ion injections can be performed in either order). The ions can be from the same ion source and have the same quadrupole isolation window but different fragmentation energies (the collision energy for the precursor injection is zero). The fragment ions are analyzed in a mass analyzer to provide a fragment spectrum. The precursor ions are accumulated in an ion storage device and combined with precursor ions from other quadrupole isolation windows. The combined precursor ions are then analyzed in a mass analyzer to provide analysis scan data. Such scan data provides precursor information in addition to the fragment spectrum. The precursor ion accumulation can be performed quickly together with normal MS2 fragmentation analysis because there is no additional quadrupole switching time, and the additional injection time for the precursor ion (SIM) component should be lower than the time for the fragmentation injection.

[0297] In the case of analysis using a hybrid instrument (such as Figure 1 the instrument shown), it is preferred to measure the SIM component (the unfragmented precursor ions for each sub-range) in a high-resolution MS1 scan. To do this, the unfragmented SIM component needs to be separated from the fragmented MS2 component and then collected for separate analysis. The path to the fragment analyzer (the first analyzer) must not be blocked by the accumulated SIM injection ions. One way to achieve this is to create a branched ion path such that the SIM ions can be separated and sent to one area while acquiring the MS2 scan in parallel.

[0298] In some examples, the ions can be switched between two separate ion destinations using a beam switching device to create a branched ion path. A switchable path ion guide is described in UK Patent Application No. 2209555.8, which is incorporated herein by reference. Other suitable devices are described in Patent Publications US7829850B2, US20190103261A1, US8581181B2, and US9984861B2.

[0299] Ion beam switching devices exist in the prior art. Many of these involve switching in RF gas-filled multipoles, which is slow due to ion diffusion in the gas and cannot operate with transition times in the low microsecond range. Such devices can be compatible with the proposed method. In such a case, the ions are preferably decelerated before entering the RF gas-filled deflector to reduce unwanted fragmentation in the deflector. However, preferably, an ion beam switch operating under pure molecular flow conditions (Kn > 10 - 20) is provided instead.

[0300] In one example, a double plate gate can be used for switching, preferably after ion acceleration in the range of 10V to 50V to reduce ion losses. Preferably, such a gate is located in the pressure region of 10 -4 mbar to 10 -5 mbar and is spatially separated from the RF gas-filled deflector. This reduces the probability of ion-molecule collisions and corresponding losses while providing a reduced switching time that is important for strong ion beams from modern ion sources.

[0301] The branched RF multipole described in US7829850B2 may be suitable as an ion beam switch. As Figure 2 shown, the device is an RF quadrupole that can move ions down one channel or the other by switching the RF phase, amplitude, or by applying a DC gradient. The device is compatible with high vacuum, and thus ions can be transferred quickly without diffusion and thus have a minimum time loss due to path switching or ion transit.

[0302] Figure 2 A perspective view of the branched radio frequency multipole system described in US7829850B2 is illustrated. The branched radio frequency multipole system 50 includes branched electrodes 55A and 55B arranged parallel to each other. The branched radio frequency multipole system also includes orthogonal electrodes 60A, 60B, 60C, 60D, 60E, 60F, 65A, and 65B. The orthogonal electrodes 60A to 60F, 65A, and 65B are arranged orthogonal to the branched electrodes 55A and 55B such that the branched radio frequency multipole 50 includes a first ion channel between ports 70 and 75 of the branched radio frequency multipole 50 and a second ion channel between ports 70 and 80. Port 70 is an opening defined by the branched electrodes 55A and 55B and the orthogonal electrodes 60A and 60D. Port 75 is an opening defined by the branched electrodes 55A and 55B and the orthogonal electrodes 60C and 65A. Port 80 is an opening defined by the branched electrodes 55A and 55B and the orthogonal electrodes 60F and 65B. The first ion channel and the second ion channel overlap in a portion of the branched radio frequency multipole 50 adjacent to port 70 and diverge at a branch point 85 before continuing to port 75 and port 80, respectively.

[0303] The RF voltages applied to the orthogonal electrodes 60B, 60C, and 65A can be controlled such that a first ion channel including the path between port 70 and port 75 is opened. Alternatively, the RF voltages applied to the orthogonal electrodes 60E, 60F, and 65B can be controlled such that a second ion channel including the path between port 70 and port 80 is opened. Thus, the path of ions through the branched radiofrequency multipole 50 can be controlled by selecting an appropriate voltage.

[0304] In another example, as described in UK Patent Application No. 2209555.8, an ion guide having a switchable ion path includes a first ion transport aperture configured to receive an ion beam. The ion guide includes: a radiofrequency (RF) surface including a plurality of radiofrequency electrodes arranged on a first surface such that the plurality of RF electrodes are parallel to each other. The RF surface may also be referred to as a radiofrequency blanket. The ion guide further includes: a radiofrequency voltage source configured to apply an alternating radiofrequency phase to each of the plurality of RF electrodes. The ion guide further includes: a DC potential source configured to apply a DC gradient across the RF surface, wherein the DC gradient is configured to direct the ion beam via a first ion path or a second ion path. The ion guide further includes: a second ion transport aperture and a third ion transport aperture, wherein ions traveling in the first ion path are directed to the second ion transport aperture, and ions traveling in the second ion path are directed to the third ion transport aperture.

[0305] Hereinafter, the term "DC potential source" refers to any DC potential source. A voltage can be applied to the DC potential source to generate an electric potential (or an electric field). A DC voltage source can be used to apply the voltage. The DC potential source can include electrodes to which a voltage can be applied to generate a DC potential. A DC gradient can be applied by using radiofrequency electrodes (such that the RF electrodes include the DC potential source) by applying a DC voltage gradient to the radiofrequency electrodes. In addition, a DC gradient can be applied by using auxiliary DC electrodes (wherein the auxiliary DC electrodes include the DC potential source).

[0306] In use, the ion guide may be configured to receive an ion beam via a first ion transport aperture. The DC gradient may be configured to direct the ion beam via a first ion path or a second ion path such that ions of the ion beam exit the ion guide via a second ion transport aperture or a third ion transport aperture. The DC gradient may be configured to separate the ion beam into a first portion and a second portion and direct the first portion of the ion beam along the first ion path (such that the first portion exits the ion guide via the second ion transport aperture) and direct the second portion of the ion beam along the second ion path (such that the second portion exits the ion guide via the third ion transport aperture). Additionally, the ion guide may be configured to receive an ion beam via the second ion transport aperture and / or the third ion transport aperture. The DC gradient may be configured to direct ions entering the ion guide via the second ion transport aperture along the first ion path such that the ions are directed to the first ion transport aperture and exit the ion guide via the first ion transport aperture. The DC gradient may be configured to direct ions entering the ion guide via the third ion transport aperture along the second ion path such that the ions are directed to the first ion transport aperture and exit the ion guide via the first ion transport aperture.

[0307] For simplicity, most of the following description assumes that the ion guide is configured to receive an ion beam via a first ion transport aperture and the ion beam exits the ion guide via a second ion transport aperture and / or a third ion transport aperture. The first ion transport aperture is referred to as the inlet, the second ion transport aperture is referred to as the first exit aperture, and the third ion transport aperture is referred to as the second exit aperture. However, any of the examples described below may be used in two directions (such that the ion beam travels from the first ion transport aperture to the second ion transport aperture and / or the third ion transport aperture, or used in the opposite direction such that one or more ion beams travel from the second ion transport aperture and / or the third ion transport aperture to the first ion transport aperture). Additionally, a downstream (or upstream) stage may be adjacent to the ion guide such that the "ion transport apertures" of the ion guide will more accurately be regarded as "ion transport regions", such as an inlet region or an outlet region. For example, if a path leads to a trapping region built into the ion guide, a "hole" may not be provided. However, for simplicity, specific examples will be described below with reference to holes.

[0308] Reference Figure 3 , shows an ion guide 100 according to an embodiment of the present disclosure. The ion guide 100 will be described with reference to the Figure 3 axis shown. The ion guide includes a front end that includes a first ion transport aperture (inlet); and a rear wall 140 that includes a second ion transport aperture (first exit aperture) 120 and a third ion transport aperture (second exit aperture) 130. The front end may be open (such that the first ion transport aperture covers the entire front end) or may include a wall that includes the first ion transport aperture.

[0309] The RF surface 110 includes a plurality of RF electrodes arranged parallel to each other. In use, opposite radio frequency phases can be applied to alternating RF electrodes in series (such that each RF electrode has an RF phase opposite to that of its adjacent electrode), thereby forming a repulsive pseudopotential surface. In Figure 3 the illustrated embodiment, the RF electrodes include elongated electrode plates, wherein the planes of each of the plurality of plates are parallel to each other (and parallel to the z-x plane indicated by the Figure 3 axis in). The first three RF electrodes are labeled 111, 112, and 113 to illustrate this arrangement. The remaining RF electrodes are not labeled. There may be more or fewer RF electrodes than Figure 3 shown. In one embodiment, the RF surface 110 may include 50 RF electrodes, which include elongated electrode plates. The first surface may be perpendicular to the plane of each of the plurality of plates (and thus parallel to the x-y plane) or may be at an angle A with the plane of each of the plurality of plates (such that the first surface is at an angle (90 - A)° with the x-y plane). The angle A may be, for example, between 45° and 90°, or may be any other angle.

[0310] In another embodiment, the RF surface may include a plurality of printed RF electrodes on a PCB. In another embodiment, the RF electrodes may include electrodes formed, for example, by lithography on a substrate.

[0311] In a specific example where the RF electrodes include elongated plates, the RF electrodes may include a thickness between 0.5 mm and 1.5 mm and a spacing between 0.5 mm and 1.5 mm. The RF electrodes may include other thicknesses or spacings. The applied RF voltage may be between 20 V and 2000 V, where the frequency is between 1 MHz and 3 MHz. The applied RF voltage may have other magnitudes or frequencies. The internal volume of the ion guide may be approximately 100 cm 3 , where the dimensions are approximately 10 cm × 10 cm × 1 cm. However, this is a specific example and the ion guide may have any internal volume. In some embodiments where the RF electrodes include PCB printed electrodes (or electrodes formed on a substrate by means such as lithography), the electrodes may be smaller and closer spaced than the above-described electrodes. The thickness and spacing of the RF electrodes may be about 10 μm, where the applied RF voltage may have a frequency of at least 10 MHz. The thickness and spacing of the RF electrodes may be greater than 10 μm, for example, between 10 μm and 1 mm.

[0312] The ion guide 100 further includes a first exit hole 120 and a second exit hole 130. The ion guide may include a rear wall 140 that includes the first exit hole 120 and the second exit hole 130. In use, an ion beam may enter the ion guide 100 via an entrance at the front end of the ion guide 100 opposite the rear wall (the front end may be open or may include a hole through which the ion beam enters the ion guide 100). Ions may be directed to the first exit hole 120 or the second exit hole 130 by a DC gradient applied by a DC potential source. The RF surface 110 acts as an ion trapping region while the DC gradient is superimposed on the RF field to direct the ions to the selected exit hole such that the ions are trapped and directed within a large volume. The DC gradient may include a component (referred to as orthogonal DC) that directs the ion beam left or right (i.e., in either x direction) to follow a first ion path or a second ion path, but may also include a component that accelerates the ion beam from the front end of the ion guide towards the rear wall of the ion guide (referred to as axial DC).

[0313] The first exit hole 120 and the second exit hole 130 may include physical holes to define the maximum extent of the output channels of the ion beam. The first exit hole 120 and the second exit hole 130 may include physical holes and may be further defined by an electric field such that the first exit hole 120 and the second exit hole 130 are defined by the physical holes and the electric field. The first exit hole 120 and the second exit hole 130 may be defined by an electric field in the absence of physical holes. In an embodiment where the first exit hole 120 and the second exit hole 130 are defined by an electric field in the absence of physical holes, the rear wall may include an opening, where the opening may extend across all or part of the rear wall. The first exit hole 120 and the second exit hole 130 may also have a DC voltage applied to them. The DC voltage applied to the first exit hole 120 and the second exit hole 130 may be equal or different. The DC voltage may be configured to trap or admit ions, for example, according to the requirements of downstream elements of a mass spectrometer. The DC voltage may be variable.

[0314] The ion guide 100 may further include a top plate 150 opposite the RF surface 110. The top plate 150 may be parallel to the RF surface 110 or at an angle to the RF surface 110. The top plate 150 may be parallel to the x - y plane or at an angle to the x - y plane. The top plate 150 may include a ground plate or a repelling plate. In the case where the top plate 150 includes a repelling plate, the repelling plate may be configured to confine the ion beam close to the RF surface. The repelling plate may include a repelling DC electrode (i.e., a DC electrode to which a DC voltage may be applied to repel the ion beam). The repelling plate may be configured to prevent the ion beam from approaching the repelling plate, thereby avoiding contamination and charging effects on the repelling plate. In one embodiment, the ion beam may be kept at least 5 mm away from the repelling plate.

[0315] The rear wall 140 may optionally further include a chamber 160. The chamber 160 may be positioned between the first exit hole 120 and the second exit hole 130. In the case where an ion beam is received into the ion guide 100 together with a stream of neutral particles and / or charged droplets or other unwanted materials, the chamber 160 may be configured to receive the stream of neutral particles and / or charged droplets or other unwanted materials. The chamber 160 may include a cylinder that is open at the ion guide end of the cylinder and closed at the opposite end of the cylinder, such that the chamber 160 is configured to receive unwanted materials and retain the unwanted materials within the chamber 160. Additionally, the chamber 160 may include a hole or other outlet component configured to receive unwanted materials and allow the unwanted materials to exit the ion guide 100. A pump may be used to assist in removing unwanted materials from the ion guide via the chamber 160.

[0316] In some embodiments, the ion guide 100 may include a first side guard and a second side guard. The first side guard and the second side guard may be configured to prevent ions from exiting the ion guide 100 via the first (left) side or the second (right) side. The first side and the second side each extend between the front end and the rear wall 140, and each of the first side and the second side may be open, closed, or partially open. The first side and the second side may be parallel to each other or at an angle to each other. The first side and the second side may be parallel to the z-axis. The first side guard and the second side guard may respectively include a first protection electrode and a second protection electrode. The first protection electrode and the second protection electrode may be mounted at the first side and the second side of the ion guide 100. A small repulsive DC voltage may be applied to the first protection electrode and the second protection electrode to repel ions from the first side and the second side. The voltage applied to the first side guard and the second side guard may be used in combination with a DC gradient to define the maximum lateral displacement of the ion guide. The first side guard and the second side guard may include the first protection electrode and the second protection electrode, or may include a series of PCB printed electrodes separated by a resistor chain. The first side guard and the second side guard may be physically close to the first side and the second side to prevent gas from exiting the ion guide 100 via the first side and the second side. In other embodiments, the first side and the second side may be open, and the first side guard and the second side guard may use only electrodes to prevent ions from exiting. In some embodiments, the first side guard and the second side guard may be configured to prevent leakage using only physical closures, or only electrodes, or a combination of physical closures and electrodes. Figure 3 The illustrated embodiment shows the first side guard 170 and the second side guard 180 physically enclosing the first side and the second side.

[0317] In some embodiments, the ion guide may be configured to increase the spatial focusing of the ion beam near the first exit hole and the second exit hole. For example, downstream elements of a mass spectrometer may have a narrow spatial acceptance, so it may be beneficial to focus the ion beam exiting the ion guide. The ion guide may be configured to gradually increase the spatial focusing of the ion beam as the ion beam approaches the first exit hole or the second exit hole.

[0318] In embodiments where the RF surface including the RF electrode includes an elongated electrode plate, the RF electrode may include channels configured to increase the spatial focusing (i.e., reduce the spatial spread) of the ion beam closer to the first exit hole and the second exit hole. Referring Figure 4 , the RF electrode may include notches with increasing depth closer to the rear wall of the ion guide. For simplicity, only a proportion of the RF electrode is shown. In Figure 4 the electrodes shown, the RF electrode 210 is closest to the front end of the ion guide, and the RF electrode 260 is closest to the rear wall of the ion guide. The front RF electrode 210 includes an elongated electrode plate without notches. Each of the RF electrodes 220, 230, 240, 250, and 260 includes two notches (221, 222, 231, 232, 241, 242, 251, 252, 261, 262) in the top edge of the elongated electrode plate. The depth of the notches increases with the distance from the front end of the ion guide. The width of the notches may also increase with the distance from the front end of the ion guide. The notches follow the first ion path and the second path. The DC gradient is configured to direct the ion beam to follow the first ion path or the second path. In Figure 4 the example shown, the ion beam follows the left path. The direction of the orthogonal DC that directs the ion beam to the left path is indicated by arrow 270. The direction of the axial DC that accelerates the ion beam towards the rear wall is indicated by arrow 280. The ion beam, shown by the dashed region, passes through the notches of the RF electrode and is compressed into the notches by a repulsive DC field that confines the ion beam close to the RF surface. As the ion beam passes over the larger notches, the focus of the ion beam thus narrows, and more of the ion beam is accommodated within the notches. The ion beam 213 passing over the RF electrode 210 is the widest, having a relatively flat cross-section. The ion beam 223 passing over the RF electrode 220 is slightly narrower. The ion beam 233 passing over the RF electrode 230 is narrower, and as the ion beam is compressed into the notch, the lower portion of the ion beam 233 has begun to assume the shape of the notch. The ion beam 233 still retains a wider and flatter portion above the RF electrode. The ion beams 243 and 253 passing over the RF electrodes 240 and 250 have a larger lower proportion located within the notches, and the size of the upper portion wider than the notch decreases. The ion beam 263 passing over the RF electrode 260 is the narrowest and does not have a portion wider than the notch. In Figure 4There may be more RF electrodes between those electrodes shown, such that the size of the notch gradually increases. The notch is shown as an arc, but may be other shapes.

[0319] In some embodiments, in addition to or instead of being shaped to provide a channel, the RF electrodes may be shaped to provide a first side guard and a second side guard. Figure 5A A cross-section of an ion guide is shown, showing RF electrode 311 and DC repelling plate 312. The DC repelling plate 312 may be further configured to apply a DC gradient. The first side guard and the second side guard include a first DC side guard 313 and a second DC side guard 314. A repelling DC voltage may be applied to the first DC side guard 313 and the second DC side guard 314. Figure 5B A cross-section of an ion guide is shown, showing RF electrode 321 and DC repelling plate 322. The RF electrode 321 bends upward at the ends to form a first side guard 323 and a second side guard 324. The first side guard 323 and the second side guard 324 may be perpendicular to the central portion of the RF electrode 321, angled with respect to the central portion of the RF electrode, or the RF electrode may bend at the ends to form the first side guard and the second side guard. Figure 5C A cross-section is shown of a Figure 5B similar configuration, where the ends of RF electrode 331 form a first side guard 333 and a second side guard 334. As in Figure 5C , the ion guide also includes a DC repelling plate 332. The RF electrode 331 also includes a first notch 335 and a second notch 336. The first notch 335 and the second notch 336 are configured to focus the ion beam, as referenced in Figure 4 . Figure 5D A cross-section of an ion guide including a DC repelling plate 342 and an RF electrode 341 is shown, the RF electrode bending at the ends to meet (or approach) the edges of the DC repelling plate 342. The ion guide also includes attracting DC electrodes 343 and 344. The attracting DC electrodes 343 and 344 may be configured to apply an attracting DC field that pulls the ion cloud towards the edges or corners of the RF electrode (advantageously, strongly pulling the ion cloud), which improves the focusing of the ion beam.

[0320] In some embodiments, a DC gradient can be applied by applying a DC voltage gradient to the RF electrodes. In other embodiments, an auxiliary DC electrode can be used to apply the DC gradient. As will be described below, in some embodiments, the top plate can include an auxiliary DC electrode configured to apply a DC gradient. In other embodiments, the auxiliary DC electrode can be mounted between the RF electrodes. Both the axial and orthogonal components of the DC gradient can be applied using the auxiliary DC electrode, or both the axial and orthogonal components of the DC gradient can be applied using the RF electrodes, or one component can be applied using the auxiliary DC electrode and the other component can be applied using the RF electrodes.

[0321] In one embodiment, referring to Figure 6 , the top plate 150 includes a repulsion plate. In Figure 2 the example shown, the configuration of the RF surface is the same as in Figure 3 , where the RF electrodes include elongated electrode plates. As described above, the repulsion plate can include a repulsion DC electrode. The repulsion plate can also be configured to apply one or both components of the DC gradient. The repulsion plate can include a repulsion PCB 410 having a series of printed electrodes configured to act as a repulsion plate and apply a guiding DC gradient. The DC gradient can be superimposed on the repulsion field such that ions are directed to the first exit hole 120 or the second exit hole 130. The DC gradient includes an orthogonal component and can also include an axial component. The orthogonal DC gradient can be configured to provide a guiding force in two orthogonal directions (left and right). Optionally, the DC gradient can be configured to provide a guiding force in only one orthogonal direction (e.g., push ions to the left or right), while the other direction can be provided by a DC series (by linking the RF electrode series with resistors and applying a DC voltage between the electrodes such that a series of DC steps between the RF electrodes forms a gradient), a traveling wave applied to the RF electrodes, or a pulsed DC. The guiding force of the RF electrodes can depend on the direction in which the RF electrodes are mounted. The RF electrodes can be mounted such that the plane of the elongated electrode plate is parallel to the z-x plane. Optionally, the RF electrodes can alternatively be mounted such that the plane of the elongated electrode plate is parallel to the z-y plane. The RF electrodes can be configured to provide the orthogonal component of the DC gradient, and the top plate can be configured to provide the axial component of the DC gradient. In another embodiment, the RF electrodes can be arranged in a grid including rows of electrodes parallel to the z-y plane and columns of electrodes parallel to the z-x plane such that a DC gradient or a traveling wave can be applied in the orthogonal and axial directions.

[0322] A repulsive PCB configured to apply a DC gradient may include a series of printed electrodes separated by a resistor chain. Voltages may be applied at each end. A linear DC gradient may be generated by a linear one-dimensional series of electrodes. An ion guide may require DC gradients in two dimensions, providing an orthogonal DC gradient in one dimension to direct an ion beam to a first ion path or a second ion path, and providing an axial DC gradient in a second dimension to accelerate ions from the front end of the ion guide to the back wall. Refer to Figure 7 , a grid of printed electrodes separated by resistors may be used to generate a diagonal DC gradient. The electrodes are shown as squares (e.g., 510). Each electrode in a row is separated by a resistor (e.g., 520), and the electrodes at the ends of each row are separated from the electrodes at the ends of adjacent rows by resistors (e.g., 530). A two-dimensional DC gradient requires four voltage inputs, one at each corner of the grid (V1, V2, V3, and V4).

[0323] In another embodiment, the top plate 150 may include a repulsive plate 600 that includes DC electrodes arranged in a shape that defines a first ion path and a second ion path. Refer to Figure 8 , the top plate 150 may include a horseshoe configuration of DC electrodes. The back wall 140 is indicated to show the positions of the first exit hole 120 and the second exit hole 130. The bottom of the repulsive plate 600 corresponds to the front end of the ion guide. In use, an ion beam enters the ion guide via the front end, and the polarity of the DC gradient determines which of the first exit hole 120 and the second exit hole 130 the ion beam is directed to. The DC electrodes may be printed. The DC electrodes are indicated by white rectangles and triangles (three of the DC electrodes 610, 620, and 630 are marked as examples in Figure 8 . The DC electrodes may be segmented differently to form a horseshoe shape. The remaining space around the horseshoe (indicated by the shading) is configured to repel ions. This may be achieved by using DC side guards and / or by other printed electrodes. The width of the channel narrows towards the first exit hole 120 and the second exit hole 130, thereby focusing the ion beam close to the exit holes and allowing a wide channel close to the front end of the ion guide. The repulsive plate 600 may further be configured to accept ions transmitted back to the ion guide from a downstream element (e.g., ion optics) via one of the exit holes. The ions may be directed to another exit hole without changing the DC gradient while storing the ions within the ion guide.

[0324] As described above, the top plate 150 may include a repulsive plate configured to apply a DC gradient in addition to applying a repulsive field. Refer to Figure 9 , in one embodiment, the ion guide 700 may include a top plate 750 that includes a ground plate or a repulsive plate but does not apply a DC gradient. The ion guide includes Figure 3A similar RF surface 710, where the RF electrodes include elongated electrode plates (three example RF electrodes are labeled 711, 712, and 713). The ion guide 700 includes a rear wall 740, which includes a first exit hole 720 and a second exit hole 730. The ion guide also includes auxiliary DC electrodes (three example DC electrodes are labeled 761, 762, and 763) indicated by the shading and mounted between the RF electrodes. The static potential experienced by the ion beam is a combination of the DC applied to the RF electrodes and the DC applied to the auxiliary DC electrodes. The axial DC gradient can be achieved by varying the height of successive DC electrodes or by connecting the auxiliary electrodes with a resistor chain. The orthogonal DC gradient can be achieved by having wedge-shaped auxiliary DC electrodes, as Figure 9 shown.

[0325] In one embodiment, Figure 9 the top plate 750 shown can be replaced by a second RF surface. Referring to Figure 10 , the ion guide 800 includes the same first RF surface 810 as Figure 9 shown. The first RF surface includes RF electrodes that include elongated electrode plates (three example RF electrodes are labeled 811, 812, and 813). The ion guide also includes auxiliary DC electrodes (three example DC electrodes are labeled 861, 862, and 863) indicated by the shading and mounted between the RF electrodes of the first RF surface. The ion guide 800 includes a rear wall 840, which includes a first exit hole 820 and a second exit hole 830. The ion guide 800 includes a second RF surface 870 located at the top of the ion guide. The second RF surface includes RF electrodes that include elongated electrode plates (three example RF electrodes are labeled 871, 872, and 873). The ion guide also includes auxiliary DC electrodes (three example auxiliary DC electrodes are labeled 881, 882, and 883) indicated by the shading and mounted between the RF electrodes of the second RF surface. The static potential experienced by the ion beam is a combination of the DC applied to the RF electrodes of the first RF surface and the second RF surface and the DC applied to the auxiliary DC electrodes mounted between the RF electrodes of the first RF surface and the second RF surface. The axial DC gradient can be achieved by varying the height of successive DC electrodes or by connecting the auxiliary electrodes with a resistor chain. The orthogonal DC gradient can be achieved by having wedge-shaped auxiliary DC electrodes.

[0326] Figure 10The illustrated embodiments do not include repelling plates, so ions are not compressed towards the top RF surface or the bottom RF surface. This arrangement increases the volume available for ions under space charge. However, as described above, it may be beneficial to focus the ion beam near the exit aperture. In an embodiment, this can be achieved by tilting one or both RF surfaces such that the distance between the first RF surface 810 and the second RF surface 870 decreases the closer to the rear wall 840. In other embodiments, the DC gradient can be configured to more strongly attract to an auxiliary DC electrode in the first RF surface or an auxiliary DC electrode in the second RF surface, thereby pulling the ions towards the surface with the more attractive DC gradient.

[0327] Figure 4 and Figure 5C An RF electrode including notches to form channels in the RF surface is shown. In a similar manner, in embodiments where a DC gradient is applied by auxiliary DC electrodes mounted between the RF electrodes, the auxiliary DC electrodes can include peaks or valleys to define channels that are configured to improve the spatial focusing of the ion beam near the exit aperture. This can be in addition to or in place of the notches in the RF electrodes. Referring to Figure 11 , an auxiliary DC electrode 900 is shown that includes a peak 910, a valley 920, and a ramp 930 between the peak and the valley to provide an orthogonal DC gradient. The peak 910 can correspond to the position of a first ion path and the valley 920 can correspond to the position of a second ion path. By selecting the polarity of the DC applied to the auxiliary DC electrode, the ions are directed to the first ion path or the second ion path.

[0328] Note that any of the above features related to the spatial focusing of the ion beam can be used for the spatial focusing of an ion beam traveling from a first ion transport aperture to a second ion transport aperture or a third ion transport aperture, or for the spatial focusing of an ion beam traveling from a second ion transport aperture or a third ion transport aperture to a first ion transport aperture.

[0329] Referring to Figure 9 and Figure 10 the illustrated embodiments include auxiliary DC electrodes that include elongated electrode plates. The elongated electrode plates are mounted between the RF electrodes. In other embodiments, the ion guide can include auxiliary DC electrodes printed between the RF electrodes. Referring to Figure 12, the ion guide 1000 may include an RF surface 1010, a rear wall 1040 including a first exit hole 1020 and a second exit hole 1030, and a top plate 1050. The top plate 1050 may include a repelling plate or a ground plate. The ion guide 1000 may further include a plurality of auxiliary DC electrodes printed on a PCB 1070. The RF surface 1010 may include an RF electrode mounted between the printed auxiliary DC electrodes. Three RF electrodes 1011, 1012, and 1013 are marked as examples, and three auxiliary DC electrodes 1061, 1062, and 1063 are marked as examples. The auxiliary DC electrodes may be separated by a resistor chain, for example, to form a two-dimensional grid similar to Figure 7 shown. To reduce contamination, the RF electrode may be suspended above the exposed portion of the PCB 1070 located between the RF electrode and the auxiliary DC electrode (where the exposed portion of the PCB 1070 may include a dielectric material).

[0330] For an embodiment including auxiliary DC electrodes mounted between RF electrodes, where the auxiliary DC electrodes include elongated electrode plates, the height of the auxiliary DC electrodes relative to the RF electrodes may affect the performance of the ion guide. Preferably, the auxiliary DC electrodes may not protrude into the trapping volume of the ion guide above the RF electrodes. In the case where the auxiliary DC electrodes are recessed below the RF electrodes, as the degree of recess of the DC electrodes relative to the RF electrodes increases, the proportion of the applied DC voltage reaching the center of the trapping region decreases.

[0331] Referring to Figure 13 , the ion guide as described above may be used near the front of a complex hybrid mass spectrometer to separate a fast region from a slow region or a lossy region. Figure 13An example is illustrated in which a schematic of an instrument is shown that combines rapid MS2 operation on a fast path to a multi-reflection time-of-flight (MR-ToF) analyzer 1263 with a slow path to a Fourier transform mass analyzer 1274 for MS1, or with complex ion processing within an adjacent resolving ion trap (where MS1 can include analysis of unfragmented precursor ions and MS2 can include analysis of fragmented precursor ions). The instrument can include an electrospray ionization (ESI) source 1210, a lens 1220 (such as an S-lens including an ion funnel with an increasing interpolation spacing between rings), an ion guide 1230, and a 90° ion guide 1240. The ion beam can then pass through a beam-switching ion guide 1250 according to an embodiment of the present disclosure, and the ion beam can be directed to either the fast path or the slow path. The fast path can include a quadrupole mass filter 1261, a collision cell 1262, and an MR-ToF analyzer 1263. The slow path can include a C-trap 1271, a collision cell or resolving ion trap 1272, an ion guide 1273, and a Fourier transform mass analyzer 1274. The ion guides 1230, 1240, and 1273 are not beam-switching ion guides according to the present disclosure, but rather direct the ion beam along a single path. Although the analyzers can be arranged in a single path, ion losses through the chain can reduce the sensitivity of the MR-ToF analyzer. The chain is blocked whenever the ion trap performs slower ion manipulations such as MS3 (involving fragmentation of fragment ions) or electron transfer dissociation (ETD). The MR-ToF analyzer also blocks the rear of the ion trap, thereby preventing a laser that may be installed for photodissociation fragmentation. At least for these reasons, the ability to switch between the fast path and the slow path is beneficial. Additionally, the fast path and the slow path can be arranged side by side to make the instrument more compact than a single long path.

[0332] Two possible configurations for an instrument (e.g., a hybrid Fourier transform mass / MR-ToF mass spectrometer) incorporating a branched ion path are illustrated in FIG. 14. These configurations illustrate how a beam-switching device can be incorporated into the instrument.

[0333] In a first example, an ion beam switch is used to select between a path to a first mass analyzer (e.g., a time-of-flight mass analyzer) or a second mass analyzer (e.g., a Fourier transform mass analyzer). Precursor ions from SIM injection are accumulated in a curved linear ion storage device (e.g., a C-trap) without blocking the ion beam path to a linear ion storage device (e.g., a DP-R trap).

[0334] In a second example, a parallel trapping region is provided for accumulating precursor ions from SIM injection. An ion beam switch is used to select between the paths to the parallel trapping region and the first mass analyzer (e.g., a time-of-flight mass analyzer). Precursor ions from SIM injection are accumulated in the parallel trapping region without blocking the ion beam path to the linear ion storage device (e.g., a DP-R trap). The precursor ions from the combined SIM injection are then returned via the ion beam switch to the second mass analyzer (e.g., a Fourier transform mass analyzer).

[0335] In one method of operation, the beam switching device toggles between two routes and for each mass window in a DIA sequence, injects into the path leading to the first mass analyzer (e.g., a time-of-flight mass analyzer) for MS / MS analysis and into the path leading to the second mass analyzer (e.g., a Fourier transform mass analyzer) or the parallel trapping region to accumulate ions for a HDR full MS scan.

[0336] In Figure 14A the example shown, the beam switch is located after the quadrupole mass filter and operates to send the MS2 injection (of fragmented precursor ions) to the time-of-flight mass analyzer (optionally via a linear ion storage device) and the SIM injection (of precursor ions) to the first ion storage device and then to the Fourier transform mass analyzer. In parallel with performing multiple MS2 injections and scans, the SIM injections are accumulated together in the first ion storage device (e.g., a C-trap). After a series of SIM injections have been accumulated in the C-trap, the ions can then be ejected into the Fourier transform mass analyzer for long acquisition times.

[0337] In Figure 14B the example shown, the beam switching device is located after the curved linear ion storage device (e.g., a C-trap) and thus alternatively switches the path between the linear trap and a new parallel trapping region such as an ion trap or an IRM-like device. Ions accumulated in the parallel trapping region can be transferred back to the C-trap / Fourier transform mass analyzer for analysis.

[0338] Alternatively, ions accumulated in the parallel trapping region can be transferred to the linear trap / MR-ToF for analysis.

[0339] To further improve efficiency, it is preferred to eliminate the overhead due to the need for active beam path switching. One way to do this is to isolate a portion of the ion implantation. This can be achieved by differentiating the properties of the ions (such as position or energy). Then, a single (longer) implantation can be split and used to supply two ion destinations. Even more preferably, the conditions are set such that a certain proportion of the ion beam is split, either as a function of collision cooling or spatial distribution, and the chopped ion beam is delivered to separate ion destinations. This then further saves the time overhead between implantations. Thus, a method of beam splitting via a section of a broad ion packet is provided. The chopped ion beam is formed by passing the ions through a wedge electrode. The ions are separated based on the spatial distribution of the ion packet.

[0340] Figure 15 An ion beam splitter is illustrated. In this particular example, the ion beam splitter includes a pair of RF surfaces or a single RF blanket, with side guards and a wedge-shaped DC electrode (also known as a beam splitting electrode or "beam pliers") positioned between the entry hole and the exit hole. Ions are injected through the entry hole and the distribution allows for broadening across the width of the waveguide. The ions can be trapped during this time, for example, by the direction of the DC gradient applied across the RF electrodes. After the ions have spread in width, the DC gradient or traveling wave pulls the ions towards the exit hole. The ions are repelled by the wedge electrode electric field but still attracted, causing the wedge to split the ion distribution into two parts, and the resulting different ion groups are attracted to their nearest exit hole.

[0341] The proposed ion beam splitter is based on the principle of previously proposed beam switching devices (such as those described in UK Patent Application No. 2209555.8 or Patent Publications US7829850B2, US20190103261A1, US8581181B2 or US9984861B2) to create branched ion paths. Instead of switching the ion beam between destinations, the proposed beam splitter provides a proportional splitting of the ion beam on the wedge electrode. Figure 15 The device can be used to replace Figure 1 the ion routing multipole / fragmentation chamber 12 in a

[0342] Once a portion of the precursor ions has been separated using the ion beam splitter, the separated ions must be stored somewhere. Therefore, further changes to the Figure 1 configuration of the instrument are needed to incorporate additional ion storage devices.

[0343] Two possible configurations of an instrument (e.g., a hybrid Fourier transform / MR-ToF mass spectrometer) for incorporating a branched ion path are illustrated in Figure 16. These configurations illustrate how the beam splitting device can be incorporated into a Figure 1 instrument. Both configurations provide for storage in a C-trap (Figure 16A ) or an additional trapping region Figure 16B ) to perform parallel ion trapping at a first ion destination without blocking the ion beam path to a second ion destination (e.g., a linear trap or a time-of-flight mass analyzer).

[0344] In a first configuration, as Figure 16A shown, the ion beam splitter is located after the quadrupole mass filter and operates to send MS2 injection via a first ion storage device (e.g., a linear ion storage device) to a first mass analyzer (e.g., a time-of-flight mass analyzer) and send SIM injection via a second ion storage device (e.g., a curved linear ion storage device) to a second mass analyzer (e.g., a Fourier transform mass analyzer). In parallel with performing multiple MS2 injections and scans, SIM injections will accumulate together in the first ion storage device. After a series of SIM injections have accumulated in the first ion storage device, the ions can then be ejected into the second mass analyzer (e.g., for long acquisition times). Advantageously, since the precursor ions from SIM card injections accumulate in the curved linear ion storage device (e.g., a C-trap), they do not block the ion beam path to the linear ion storage device (e.g., a DP-R trap).

[0345] In a second configuration, the ion beam splitter device is located after the curved linear ion storage device (e.g., a C-trap) and thus alternatively chops the ions between a second ion storage device (e.g., a linear trap) and an intermediate ion storage device (also referred to as the "parallel trapping region"). The intermediate ion storage device can be an ion trap or an IRM-type device. Alternatively, the intermediate ion storage device can be provided by a DC barrier, instead of the first exit aperture of the ion beam splitter, such that ions accumulate at the first exit region (e.g., at the end of the wedge of the ion beam splitter).

[0346] Once SIM ions from multiple sub-ranges have accumulated in the parallel trapping region, the precursor ions can return through the ion beam splitter to a third ion storage device (e.g., a C-trap) and be ejected from the third ion storage device into the second mass analyzer (e.g., a Fourier transform mass analyzer).

[0347] Alternatively, once SIM ions from multiple sub-ranges have accumulated in the parallel trapping region, the precursor ions can pass through the ion beam splitter to the second ion destination (e.g., a linear trap / MR-ToF).

[0348] To minimize overhead, it is advantageous for the beam splitting device and / or beam switching device to be relatively fast, with voltage transitions and sufficient ion transport to eliminate mixing, preferably taking about 1 millisecond or less. If the process is relatively slow, ions can first accumulate before the switching region, such as in a C-trap, to allow accumulation to be parallel to subsequent ion transport.

[0349] In the DIA method, when a series of MS2 scans are performed, most ions will be sent for analysis while a certain proportion will be separated and can be accumulated. The Fourier transform mass analyzer can be used to analyze such ion accumulation in a manner similar to the "Boxcar" method described in the background art to provide an HDR scan.

[0350] Figure 17 Shows that it can be in Figure 1 、 Figure 13 、FIG. 14 or FIG. 16 of the mass spectrometer to achieve a graphical illustration of the DIA method. In the DIA method according to some specific examples, for each injection performed with fragmentation, there is an additional injection with the same quadrupole isolation window and reduced collision energy or no collision energy. As normal for DIA, the target mass is scanned through a predetermined range and isolation step. Figure 17 Shows such a scan sequence from m / z 300 Th to 900 Th, with a 5 Th isolation window, as can be used for "bottom-up" measurements of protein samples for digestion. An optional AGC (automatic gain control) pre-scan (preferably in a time-of-flight mass analyzer) can be performed to help determine the appropriate ion injection time in subsequent scans. Alternatively, a Fourier transform mass analyzer (e.g., Orbitrap TM mass analyzer) can be used to perform an optional MS1 full scan. The MS2 injection is transferred to a linear trap and extracted to a time-of-flight (e.g., MR-ToF) mass analyzer for a series of scans (T1 to T61). SIM injections are accumulated together in an ion storage device, such as a curved linear ion storage device (C-trap) or other ion trapping device. An HDR MS1 scan can be generated by analyzing the combined precursor ions (e.g., in a Fourier transform mass analyzer).

[0351] SIM and MS2 injections are interleaved to minimize quadrupole and source switching time overhead, which otherwise could significantly reduce the time available for ion accumulation. At the end of the cycle, the accumulated series of SIM injections are then extracted into a Fourier transform mass analyzer for a long transient analysis, e.g., at 240K resolution.

[0352] Advantageously, AGC is used to control the number of ions in a curved linear ion storage device and a Fourier transform mass analyzer such that the total number of ions in each SIM injection does not add up to a level that overwhelms the ion storage device. For example, if there are 60 SIM injections per cycle, the number of ions from each SIM injection can be limited to about 1500 ions.

[0353] For longer cycles, additional scans using the Fourier transform mass analyzer can be performed in the middle of the cycle to increase the dynamic range of the precursor scan data at the cost of reducing the maximum transient time by half. In other words, the first half of the SIM injections from multiple sub-ranges can be analyzed together in the first scan, and the second half of the SIM injections from multiple sub-ranges can be analyzed together in the second scan.

[0354] More generally, rather than performing one scan on the precursor ions from the total m / z range, the method can include multiple scans of the precursor ions, where each scan includes precursor ions from multiple sub-ranges.

[0355] Figure 17 The method can be performed on Figure 1 the combined Fourier transform mass analyzer and MR-ToF instrument shown, as modified according to FIG. 14. Alternatively, the method can be performed on a single mass analyzer instrument, such as a ToF instrument only or a Fourier transform mass analyzer only (and potentially taking longer).

[0356] The timing of the different operations can be configured such that certain operations are performed in parallel to reduce the total time taken. Figure 1 The Fourier transform / MR-ToF instrument shown in is capable of running single injections at approximately 200 Hz, with an injection time (also referred to as the "fill time") of 3 ms and an overhead of 2 ms. Additional overhead will deplete the duty cycle and reduce the instrument sensitivity.

[0357] Ions are transported from the ion source to the analyzer. Multiple separate ion packets can be processed simultaneously in different components.

[0358] SIM / MS2 injections can be interleaved, depending on whether fragmentation occurs in the IRM 120 or in the high-pressure region of the extraction trap 140. The injection (also referred to as "loading") can be performed and directed by the branching ion path to an ion storage device (also referred to as the "extraction trap") or a mass analyzer, thereby minimizing additional overhead. Additional injections can involve precursor ions from an ion filter having the same m / z characteristics. During operation according to some example methods, the collision energy of the fragmentation chamber can be adjusted. The fragmentation energy is adjusted from a preset MS2 level for the sample that produces the fragmented precursor ions to a reduced level (such as zero) so that the precursor ions pass through the fragmentation chamber without fragmentation.

[0359] Ions from different injections should not be mixed before the fragmentation step. If fragmentation is performed upstream of the ion beam switch (e.g., in the IRM collision cell), then after a short delay required to change the IRM offset, the second injection follows the first injection. Since the ions transmitted in the ion beam switch are of different types (precursor ions transmitted to a first ion destination and fragment ions transmitted to a second ion destination), the ion beam switch should clear the first ion packet before allowing the second ion packet.

[0360] If fragmentation is performed downstream of the ion beam switch (e.g., through the high-pressure region of the extraction trap), then the first ion packet in the ion beam switch should be cleared before allowing the second ion packet to enter. However, since the second injection has the same m / z range as the first injection (the ion beam switch transmits precursor ions to two destinations), the need to thoroughly clear the ion region between injections is reduced.

[0361] In Figure 17 Another variant of the DIA process shown, a stepped fragmentation energy can be applied to each MS2 scan. In other words, MS2 ions are added to the second ion storage device in multiple injections, each injection having a different fragmentation energy.

[0362] In some variants of the method, in the case of performing a pre-scan, it may be preferred not to perform SIM injections on the m / z sub-ranges of the total precursor mass range that have been densely populated. This can be determined based on a full MS pre-scan, and the full MS scan should collect sufficient data for such regions. Omitting SIM injections for these sub-ranges can further reduce the time required for the entire method and improve the resolution of the scans for the combined SIM injections. The HDR MS1 scan can be obtained by combining the full MS pre-scan with the scans for the combined SIM injections.

[0363] In this document, the term "mass" may be used to refer to the mass-to-charge ratio m / z. Unless otherwise specified, the resolution of a mass analyzer is understood to refer to the mass analyzer resolution determined at a mass-to-charge ratio of 200.

[0364] In the description of the present invention herein, it should be understood that, unless otherwise implicitly or explicitly understood or stated, words in the singular form encompass their plural counterparts, and words in the plural form encompass their singular counterparts. Further, it should be understood that, unless otherwise implicitly or explicitly understood or stated, for any given component or embodiment described herein, any possible candidates or alternatives listed for that component may generally be used individually or in combination with each other. Additionally, it should be understood that the drawings shown herein are not necessarily drawn to scale, where only some elements may be drawn for the clarity of the present invention. Also, reference numerals may be repeated in the various drawings to indicate corresponding or similar elements. Further, it should be understood that any such listing of candidates or alternatives is merely illustrative and not restrictive, unless implicitly or explicitly understood or stated otherwise.

[0365] Unless otherwise defined, all other technical and scientific terms used herein have the meanings commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present specification (including definitions) shall prevail. It should be understood that there is an implied "about" before quantitative terms mentioned in this specification, such that minor and non-substantive deviations are within the scope of this teaching. In this application, unless otherwise specifically specified, the use of the singular includes the plural. Also, the use of "comprising", "including" and "containing" is not intended to be limiting and does not exclude the possibility of also including other elements. In the case of using the word "consisting", this is intended to mean excluding other elements. As used herein, "a" or "an" may also refer to "at least one" or "one or more". Additionally, the use of "or" is inclusive, such that the phrase "A or B" is true when A is true, B is true, or both A and B are true.

[0366] As used in this document, when used as a noun, the term "scan" means a mass spectrum, regardless of the type of mass analyzer used to generate and acquire the mass spectrum. When used as a verb in this document, the term "scan" refers to generating and acquiring a mass spectrum by a mass analysis method, regardless of the type of mass analyzer or mass analysis used to generate and acquire the mass spectrum. As used herein, the term "full scan" refers to a mass spectrum that covers a range of mass-to-charge (m / z) values including multiple mass spectral peaks.

[0367] As used in this document, each of the terms "liquid chromatography" and "liquid chromatography method" (both abbreviated as "LC") and the term "liquid chromatography mass spectrometry" (abbreviated as "LC-MS") is intended to apply to any type of liquid separation system capable of separating a liquid sample carrying multiple analytes into various "fractions" or "isolates", where the chemical composition of each such "fraction" or "isolate" is different from that of each other such fraction or isolate, and where the term "chemical composition" refers to the quantity, concentration, and / or type of the various analytes in the fraction or isolate. Thus, the terms "liquid chromatography", "liquid chromatography method", "liquid chromatography mass spectrometry", "LC", and "LC-MS" are intended to include and refer to, but not be limited to, liquid chromatography, high performance liquid chromatography, ultra high performance liquid chromatography, size exclusion chromatography, and capillary electrophoresis devices.

[0368] In addition to LC devices, any other separation device, including ion mobility devices, HPLC, GC, or ion chromatography, can be connected to a mass spectrometer. Any known fragmentation method (including collision-activated dissociation, photon-induced dissociation, electron capture, or electron transfer dissociation) also produces data suitable for use in the present invention.

[0369] Although embodiments in accordance with the present disclosure have been described with reference to specific types of devices and applications (specifically, mass spectrometers) and such embodiments have certain advantages in such cases, as discussed herein, the methods in accordance with the present disclosure can be applied to other types of devices and / or applications. Specific manufacturing details and associated uses of ion guides are not only potentially advantageous (especially considering known manufacturing constraints and capabilities), but can also vary significantly to obtain devices with similar or identical operations. Unless otherwise stated, each feature disclosed in this specification can be replaced by an alternative feature for the same, equivalent, or similar purpose. Thus, unless otherwise stated, each feature disclosed is only one example of a series of equivalent or similar property features.

[0370] Unless otherwise stated, the use of any and all examples or exemplary language ("for example", "such as", and similar language) herein is intended only to better illustrate the invention and does not limit the scope of the invention. No language in the specification should be construed as indicating that any non-claimed element is essential for practicing the invention.

[0371] Unless otherwise stated or the context otherwise requires, any steps described in this specification can be performed in any order or simultaneously.

[0372] All aspects and / or features disclosed in this specification can be combined in any combination, except for combinations where at least some of such features and / or steps are mutually exclusive. As described herein, there can be specific combinations of aspects with additional benefits, such as aspects of ion guides for mass spectrometers and / or ion mobility spectrometers. Specifically, the preferred features of the present invention apply to all aspects of the present invention and can be used in any combination. Similarly, features described in non-essential combinations can be used individually (not in combination).

Claims

1. A mass spectrometry method, comprising the following steps: For each of a plurality of sub-ranges selected from a total m / z range: Configure an ion beam switch to direct ions to a first ion storage device; Accumulate a sample of precursor ions to be analyzed in the first ion storage device, the precursor ions having m / z values within the sub-range; Or: a) Configure the ion beam switch to direct ions to a first mass analyzer and inject a sample of fragmented precursor ions into the first mass analyzer, or b) Configure the ion beam switch to direct ions to a second ion storage device and accumulate a sample of fragmented precursor ions in the second ion storage device for analysis in a first mass analyzer, wherein the sample of fragmented precursor ions is formed by fragmentation of precursor ions having m / z values within the sub-range.

2. The method according to claim 1, wherein samples of the precursor ions for each of the plurality of sub-ranges are combined together in the first ion storage device such that the first ion storage device contains precursor ions having m / z values from the total m / z range.

3. The method according to claim 1 or claim 2, wherein the first ion storage device is an intermediate ion storage device, and wherein the method further comprises configuring the ion beam switch to transfer the precursor ions accumulated in the first ion storage device to a third ion storage device for analysis in a second mass analyzer.

4. The method according to claim 3, wherein the precursor ions transferred from the first ion storage device to the third ion storage device include samples of the precursor ions for each of the plurality of sub-ranges.

5. The method according to claim 3 or claim 4, wherein the precursor ions are transferred from the first ion storage device to the third ion storage device after samples of the fragmented precursor ions for each of the plurality of sub-ranges have been accumulated in the second ion storage device.

6. The method according to claim 1 or claim 2, wherein the first ion storage device is an intermediate ion storage device, and wherein the method further comprises configuring the ion beam switch to transfer the precursor ions accumulated in the first ion storage device to a) the first mass analyzer or b) the second ion storage device.

7. The method according to claim 6, wherein the precursor ions transferred from the first ion storage device include samples of the precursor ions for each of the plurality of sub-ranges.

8. The method according to claim 6 or claim 7, wherein the ion beam switch is configured to direct ions to the second ion storage device and a sample of the fragmented precursor ions is accumulated in the second ion storage device, the method further comprising ejecting the sample of the fragmented precursor ions accumulated in the second ion storage device into the first mass analyzer, wherein after the sample of the fragmented precursor ions in each of the plurality of sub-ranges has been ejected from the second ion storage device into the first mass analyzer, the precursor ions are transferred from the first ion storage device to the second ion storage device.

9. The method according to any one of the preceding claims, wherein the ion beam switch is configured to operate under pure molecular flow conditions.

10. The method according to any one of the preceding claims, wherein the method further comprises fragmenting the precursor ions to produce a sample of the fragmented precursor ions, wherein alternatively: the ion beam switch is configured to direct ions to the second ion storage device, and a sample of the fragmented precursor ions is accumulated in the second ion storage device, wherein the ions are fragmented in the second ion storage device; or a multipole collision cell is used to fragment the ions.

11. The method according to any one of the preceding claims, further comprising, for each of the plurality of sub-ranges: configuring an ion filter to transmit precursor ions having m / z values within the sub-range; wherein the sample of the precursor ions is received from the configured ion filter, wherein the sample of the fragmented precursor ions is formed by fragmentation of the precursor ions received from the configured ion filter.

12. The method according to claim 11, wherein configuring the ion filter comprises setting a transmission window of the ion filter, wherein the transmission window is adjusted between each of the plurality of sub-ranges, and wherein for each sub-range, the transmission window for the step of accumulating the sample of the precursor ions is the same as the transmission window for the step of injecting the sample of the fragmented precursor ions into the first mass analyzer or accumulating the sample of the fragmented precursor ions in the second ion storage device.

13. The method according to claim 11 or claim 12, further comprising configuring an ion mobility separator to transfer precursor ions having m / z values within the sub-range to the ion filter.

14. The method according to claim 13, further comprising, for each of the plurality of sub-ranges in the total m / z range, controlling the ion mobility separator such that the precursor ions transferred to the ion filter correspond to the transmission window of the ion filter.

15. The method according to any one of the preceding claims, wherein accumulating the sample of the precursor ions comprises controlling the fill time of the precursor ions based on the relative abundances of the precursor ion species in the corresponding sub-range.

16. The method according to any one of the preceding claims, wherein the ion beam switch is configured to direct ions to the second ion storage device and a sample of the fragmented precursor ions is accumulated in the second ion storage device, the method further comprising: For each of the plurality of sub-ranges, a sample of the fragmented precursor ions is injected into the first mass analyzer and the sample of the fragmented precursor ions is analyzed in the first mass analyzer, wherein the plurality of sub-ranges includes a first sub-range and a second sub-range, and wherein the step of analyzing the sample of the fragmented precursor ions from the first sub-range at least partially overlaps with the step of accumulating in the second ion storage device the sample of the fragmented precursor ions formed by fragmentation of precursor ions having m / z values within the second sub-range.

17. The method according to claim 16, wherein the plurality of sub-ranges includes a first sub-range and a second sub-range, and wherein the step of analyzing the sample of the fragmented precursor ions from the first sub-range at least partially overlaps with the step of accumulating in the first ion storage device the sample of the precursor ions having m / z values within the second sub-range.

18. The method according to any one of the preceding claims, wherein the first mass analyzer is a time-of-flight ToF analyzer.

19. The method according to any one of the preceding claims, wherein the first ion storage device is a curved linear ion trap.

20. The method according to any one of the preceding claims, wherein the ion beam switch is configured to direct ions to the second ion storage device, and the sample of the fragmented precursor ions is accumulated in the second ion storage device, wherein the second ion storage device is a linear ion trap.

21. The method according to any one of the preceding claims, further comprising: configuring an ion filter to transmit precursor ions having m / z values from the total m / z range; transferring an initial sample of precursor ions having m / z values from the total m / z range to the first mass analyzer or the second mass analyzer; analyzing the initial sample of the precursor ions; and obtaining scan data for the total m / z range from the analysis of the initial sample of the precursor ions.

22. The method according to claim 21, further comprising selecting the plurality of sub-ranges from the total m / z range based on the scan data obtained from the analysis of the initial sample of the precursor ions.

23. A mass spectrometry method, comprising the steps of: for each of a plurality of sub-ranges selected from a total m / z range: configuring an ion beam splitter to direct ions to a first ion destination and a second ion destination, wherein the first ion destination is a first ion storage device; accumulating in the first ion storage device a sample of precursor ions to be analyzed, the precursor ions having m / z values within the sub-range; wherein alternatively: a) the second ion destination is a first mass analyzer, and wherein the method further comprises injecting a sample of fragmented precursor ions into the first mass analyzer, or b) the second ion destination is a second ion storage device, and wherein the method further comprises accumulating in the second ion storage device a sample of fragmented precursor ions for analysis in the first mass analyzer. The sample of the fragmented precursor ions is formed by fragmentation of precursor ions having m / z values within the sub-range.

24. A mass spectrometer configured to perform the method according to any one of the preceding claims.

25. A computer software comprising instructions which, when executed by a processor of a computer, cause the computer to perform the method according to any one of claims 1 to 23.

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