Quadrupole mass filter and mass analyzer

Abstract

A method of mass spectrometry is provided, the method comprising: supplying ions having an initial axial kinetic energy range to a mass filter; and mass filtering the ions by applying different voltages to the electrodes of the mass filter during different respective residence times so as to provide different mass transfer windows during different residence times; wherein the method comprises increasing, during at least one of the residence times, the range of axial kinetic energy that the ions have when they pass through and / or through the mass filter.

Description

[0001] Cross-reference to related applications

[0002] This application claims priority and the benefit of UK Patent Application No. 2218772.8, filed on December 13, 2023, the entire content of which is incorporated herein by reference. Technical field

[0003] The present invention generally relates to mass spectrometers, and more particularly to quadrupole mass filters or mass analyzers for such mass spectrometers. Background art

[0004] Resolution quadrupole mass filters and mass analyzers are well-known devices in which RF and DC voltages are applied to the electrodes of the device in order to select the mass-to-charge ratios that can be transmitted by it. Typically, in order to achieve optimal mass resolution, the ions entering the mass filter or mass analyzer have been collisionally cooled in an upstream device such as an ion guide, so that the ions have as low an average energy and energy spread as possible. Summary of the invention

[0005] According to a first aspect, the present invention provides a method of mass spectrometry, the method comprising: supplying ions having an initial axial kinetic energy range to a mass filter; and mass filtering the ions by applying different voltages to the electrodes of the mass filter during different respective residence times so as to provide different mass transmission windows during different residence times; wherein the method comprises increasing the axial kinetic energy range that the ions have as they travel towards and / or through the mass filter during at least one of the residence times.

[0006] In other words, the method comprises providing, during a given one of the residence times, an axial kinetic energy range greater than the said initial axial kinetic energy range to the ions passing through the mass filter.

[0007] The step of increasing the axial kinetic energy range causes ions of a given mass-to-charge ratio to exit the mass filter with a relatively wide range of radial displacements relative to the central axis of the mass filter during the duration of that residence time. This helps to ensure that the proportion of ions leaving the mass filter and being transmitted downstream through the mass spectrometer is relatively insensitive to small shifts in the nominal mass transmission window of the mass filter for that residence time.

[0008] For the avoidance of doubt, axial kinetic energy is the kinetic energy of the ions in the downstream direction from the ion source to the mass filter (e.g., along the central axis of the mass filter).

[0009] It should be understood that the step of increasing the axial kinetic energy range of the ions as they travel towards the mass filter causes these ions to enter the mass filter with an increased axial kinetic energy range.

[0010] The mass filter can be a quadrupole set mass filter for DC resolution.

[0011] The step of applying different voltages to the mass filter during different respective residence times can include applying different combinations of RF voltage amplitudes and DC voltage amplitudes to the mass filter during different respective residence times.

[0012] The RF voltage amplitude and the DC voltage amplitude can remain constant during any given residence time.

[0013] Ions can enter the mass filter substantially at the central longitudinal axis of the mass filter. The voltage applied to the mass filter during any given residence time radially confines the ions within the mass transfer window of that residence time towards the central axis. Within the mass transfer window, ions of any given mass-to-charge ratio oscillate radially around the central axis at substantially the same (time) frequency.

[0014] As the axial kinetic energy range of the ions increases, during at least one of the residence times, ions of the same mass-to-charge ratio will exit the mass filter (for each of the at least one of the residence times) with a wider radial displacement range relative to the central axis compared to the case where the energy of the ions has not increased.

[0015] Thus, for each of the at least one of the residence times, the step of increasing the axial kinetic energy range can cause ions of a given mass-to-charge ratio to exit the mass filter with a wider radial displacement range relative to the central axis of the mass filter during the duration of the residence time compared to the radial displacement range completed by the ions when their axial kinetic energy has not increased.

[0016] The method can include providing, downstream of the mass filter, a physical aperture or ion optical device for receiving the ions transmitted by the mass filter, the ion optical device having an ion acceptance aperture defined by the electric field of the ion optical device.

[0017] The physical aperture can be an aperture in an electrode or an aperture in the wall of the spectrometer, such as a differential pumping aperture between two chambers (e.g., two vacuum chambers) of the spectrometer. The ion acceptance aperture can be an entrance aperture of an ion optical device (such as an ion lens, an ion guide, or a mass filter, etc.).

[0018] The method can include detecting, downstream of the mass filter, the ions or their fragments or product ions transmitted during the different residence times in order to generate mass spectrometry data, and summing the mass spectrometry data obtained during the different residence times; optionally in order to form at least one mass peak corresponding to the ions or their fragments or product ions transmitted by the mass filter during the different residence times.

[0019] The fragment or product ions can be generated by fragmenting or reacting the ions transmitted by the mass filter.

[0020] It should be understood that the mass filter can be coupled to an ion detector to form a mass analyzer.

[0021] The step of increasing the axial kinetic energy range can include performing a plurality of cycles during each of the at least one dwell time in the dwell time, where each cycle includes modulating the axial kinetic energy of the ions leading to and / or passing through the mass filter between a minimum axial kinetic energy and a maximum axial kinetic energy.

[0022] During each cycle, the axial kinetic energy can change continuously and progressively (e.g., linearly) between a maximum value and a minimum value, or it can step discontinuously between a plurality of values.

[0023] The method can include performing at least 5 cycles during each of the at least one dwell time in the dwell time. Optionally, at least 10 cycles can be performed during each of the at least one dwell time in the dwell time.

[0024] It is also contemplated that for each of the one or more dwell times, only a single cycle can be performed. Alternatively, during each of the at least one dwell time in the dwell time, for example, for a short dwell time where there may not be time to perform a complete cycle of modulating the axial kinetic energy, only a part of one cycle of the cycle can be performed.

[0025] For example, the method can include performing a plurality of mass scan cycles, where in each mass scan cycle, the mass transmission window of the mass filter is scanned over a mass range; and the cycle of modulating the axial kinetic energy of the ions can be performed asynchronously with the mass scan cycles. The ion signals of the plurality of mass scan cycles can be summed to form a mass peak.

[0026] The step of increasing the axial kinetic energy range that the ions have can include: providing a first axial kinetic energy range centered around a first average axial kinetic energy to the ions arriving at the outlet of the mass filter during the course of one dwell time in the dwell time; and providing a second axial kinetic energy range centered around a second average axial kinetic energy to the ions arriving at the outlet of the mass filter during the course of another dwell time in the dwell time; where the second axial kinetic energy range is wider than the first axial kinetic energy range, and the second average axial kinetic energy is higher than the first average axial kinetic energy.

[0027] This ensures that the ions arriving at the outlet of the mass filter during the course of a given dwell time have a relatively wide axial kinetic energy range relative to their average kinetic energy. Therefore, these ions leave the mass filter with a relatively large radial displacement range relative to the central axis of the mass filter during the course of a given dwell time.

[0028] The step of increasing the axial kinetic energy range may include providing a DC potential difference along the axial region of the mass filter or along the axial region upstream of the mass filter, and varying the DC potential difference during each of the at least one dwell time within the dwell time such that ions entering the axial region at different times are imparted with different axial kinetic energies.

[0029] For example, ion optics (such as an ion guide) may be provided upstream of the mass filter, and a DC voltage may be applied to these devices such that a potential difference is provided between the ion optics and the mass filter. One or both of these DC voltages may be varied during each of the one or more dwell times such that ions entering the axial region at different times are imparted with different axial kinetic energies.

[0030] During each of the one or more dwell times, the DC potential difference may cycle one or more times between a maximum value and a minimum value. Alternatively, as described above, only a portion of one cycle of the cycle may be performed during each of the at least one dwell time within the dwell time. For example, if multiple mass scan cycles are performed, the cycle modulating the DC potential difference may be performed asynchronously with the mass scan cycles. The ion signals of multiple mass scan cycles may be summed to form a mass peak.

[0031] The inventors have recognized that for the mass transfer window for transporting ions having a relatively low mass-to-charge ratio, the diffusion of the axial kinetic energy of the ions can be increased without degrading the mass resolution of the mass filter. This is because although such devices are typically operated such that they have a high mass resolution for the mass transfer window for transporting ions having a relatively high mass-to-charge ratio, they tend to have a lower mass resolution for the mass transfer window for transporting ions having a relatively low mass-to-charge ratio. This is especially the case when all mass transfer windows within the mass transfer window have the same width (i.e., the same mass-to-charge ratio range), since the mass resolution is defined by the mass-to-charge ratio being transported divided by the width of the mass transfer window.

[0032] Thus, the method can include increasing the range of axial kinetic energy of ions as they travel to and / or through the mass filter such that the ions have a first range of axial kinetic energy during a first dwell time of the dwell times, during which the mass transfer window of the mass filter is set to transmit ions in a first mass-to-charge ratio range; wherein the method further includes: (i) increasing the range of axial kinetic energy of ions as they travel to and / or through the mass filter such that the ions have a second range of axial kinetic energy, which is narrower than the first range of axial kinetic energy, during a second dwell time of the dwell times, during which the mass transfer window of the mass filter is set to transmit ions in a second mass-to-charge ratio range that is higher than the first mass-to-charge ratio range; and / or (ii) not increasing the range of axial kinetic energy of ions as they travel to and / or through the mass filter during a dwell time when the mass transfer window of the mass filter is set to transmit ions in a mass-to-charge ratio range that is higher than the first mass-to-charge ratio range and / or the second mass-to-charge ratio range.

[0033] The methods described herein can be performed during a single experimental run. For example, while scanning the mass filter, ions can be supplied to the mass filter substantially continuously so as to have different mass transfer windows at different dwell times.

[0034] All of the dwell times in the dwell times can be of the same duration.

[0035] All of the mass transfer windows in the mass transfer windows can have the same width, i.e., the same mass-to-charge ratio range. For example, the mass transfer windows can each have a width of ≤1 Da, ≤0.8 Da, ≤0.6 Da, ≤0.4 Da, or ≤0.2 Da.

[0036] To obtain a relatively high mass resolution, it is desirable to provide ions having a relatively long transit time through the mass filter such that the ions are under the influence of the electric field for a longer time. The inventors have recognized that since the mass resolution of the mass filter tends to be relatively low for ions with low mass-to-charge ratios, the average energy of these ions can be increased (i.e., the transit time through the mass filter can be reduced) without negatively affecting the mass resolution achieved by the mass filter. In contrast, since the mass resolution of the mass filter is relatively high for higher mass-to-charge ratios, it is desirable to minimize the average kinetic energy of these ions in order to maintain the relatively high mass resolution achievable by the mass filter.

[0037] Thus, the method may include providing a first average axial kinetic energy for ions passing through the mass filter during a residence time when the mass transmission window of the mass filter is set to transmit ions in a range of mass-to-charge ratios; and providing a second average axial kinetic energy for ions passing through the mass filter that is lower than the first average axial kinetic energy during a residence time when the mass transmission window of the mass filter is set to transmit ions in a range of mass-to-charge ratios higher than the one range of mass-to-charge ratios.

[0038] The method may include collisionally cooling the ions before providing the ions to the mass filter. Thus, the ions may be collisionally cooled before performing the step of increasing the range of axial kinetic energy of the ions.

[0039] A first aspect of the present invention also provides a mass spectrometer that includes: a mass filter having electrodes; at least one voltage source for applying a voltage to the electrodes; and a control circuit configured to control the mass spectrometer to: supply ions having an initial range of axial kinetic energy to the mass filter; control the at least one voltage source to apply different voltages to the electrodes of the mass filter during different respective residence times so as to provide different mass transmission windows to the mass filter during different residence times; and increase the range of axial kinetic energy that the ions have as they travel to and / or through the mass filter during at least one of the residence times.

[0040] The spectrometer may have any of the features described above with respect to the method according to the first aspect of the present invention, or be configured to perform any of the methods described above with respect to the method according to the first aspect of the present invention.

[0041] For example, the mass filter may be a DC resolving quadrupole set mass filter.

[0042] The mass spectrometer may include a physical aperture or ion optics downstream of the mass filter for receiving ions transmitted by the mass filter, the ion optics having an ion acceptance aperture defined by the electric field of the ion optics.

[0043] The physical aperture may be an aperture in the electrodes, or an aperture in the wall of the spectrometer, such as a differential pumping aperture between two chambers (e.g., two vacuum chambers) of the spectrometer. The ion acceptance aperture may be an entrance aperture of ion optics (such as an ion lens, an ion guide, or a mass filter, etc.).

[0044] The spectrometer has an ion detector and may be configured to: detect ions or their fragments or product ions transmitted during the different residence times; generate mass spectrometry data; and sum the mass spectrometry data obtained during the different residence times.

[0045] The mass filter may be coupled to the ion detector to form a mass analyzer.

[0046] The spectrometer may have a fragmentation or reaction device downstream of the mass filter for fragmenting or reacting the ions transmitted by the mass filter to form the fragment or product ions.

[0047] The mass spectrometer includes electrodes and one or more voltage sources configured to provide a DC potential difference along an axial region of the mass filter or along an axial region upstream of the mass filter, wherein the control circuit is configured to control the mass spectrometer by controlling the one or more voltage sources to increase the axial kinetic energy range so as to change the DC potential difference during each of the at least one dwell time in the dwell time, such that ions entering the axial region at different times are imparted with different axial kinetic energies.

[0048] For example, ion optical devices (such as ion guides) may be provided upstream of the mass filter, and a DC voltage may be applied to these devices such that a potential difference is provided between the ion optical devices and the mass filter. One or both of these DC voltages may be changed during each of the one or more dwell times such that ions entering the axial region at different times are imparted with different axial kinetic energies.

[0049] During each of the one or more dwell times, the DC potential difference may cycle one or more times (or only partially cycle) between a maximum value and a minimum value.

[0050] Although the mass filter has been described as being operated to apply different voltages to the electrodes of the mass filter during different dwell times to provide different corresponding mass transmission windows during different dwell times, it is also contemplated that the present invention need not be limited thereto. For example, even if the mass filter is not scanned between different mass transmission windows, the step of increasing the axial kinetic energy range of the ions as they travel to and / or through the mass filter will result in the ions leaving the mass filter with a relatively wide range of radial displacements relative to the central axis, and thus ensure a minimum level of transmission of the ions through the downstream or ion acceptance apertures. For example, when the mass filter is parked at a particular MRM transition, the techniques described herein may be used.

[0051] Accordingly, in a second aspect, the present invention also provides a method of mass spectrometry, the method comprising: supplying ions to a mass filter having a mass transmission window; and increasing the axial kinetic energy range of the ions as they travel to and / or through the mass filter.

[0052] The method according to the second aspect may have any of the features described with respect to the method of the first aspect, except that it need not necessarily be limited to a mass filter having different mass transmission windows during different dwell times.

[0053] A second aspect of the present invention also provides a mass spectrometer, which comprises: a mass filter having electrodes; at least one voltage source for applying a voltage to the electrodes to provide a mass transmission window to the mass filter; and a control circuit configured to control the mass spectrometer to: supply ions to the mass filter; and increase the range of axial kinetic energy that the ions have as they travel to and / or through the mass filter.

[0054] The mass spectrometer according to the second aspect may have any of the features described with respect to the first aspect, except that it is not necessarily limited to a mass filter having different mass transmission windows during different residence times.

[0055] It has been recognized that alternative techniques can be used to mitigate the problems discussed herein. Thus, it is not necessarily required to increase the range of axial kinetic energy that the ions have as they travel to and / or through the mass filter, and other techniques can be used alternatively.

[0056] Accordingly, in a third aspect, the present invention provides a method of mass spectrometry, which comprises: (i) mass filtering ions using a mass filter having a mass transmission window; (ii) repeatedly scanning the mass transmission window across a mass-to-charge ratio range having a width of less than 1 Da.

[0057] The third aspect of the present invention may have any of the features described with respect to the first and second aspects of the present invention, except that it is not necessarily required to increase the range of axial kinetic energy that the ions have as they travel to and / or through the mass filter.

[0058] To avoid doubt, according to the third aspect, the mass transmission window has a width less than the mass-to-charge ratio range. For example, the mass transmission window may have a width of ≤0.8 Da, ≤0.7 Da or ≤0.6 Da.

[0059] The repeated scanning step may be performed during a single experimental run, such as during a period when ions are supplied to the mass filter substantially continuously and / or when an analyte is supplied to the mass spectrometer including the mass filter continuously.

[0060] The repeated scanning step may be performed over a certain period of time, and ions transmitted by the mass filter or ions derived therefrom during said period are detected in order to obtain mass spectrometry data; and the mass spectrometry data may be summed or averaged.

[0061] The method may include associating the summed or averaged mass spectrometry data with the mass-to-charge ratios within the mass-to-charge ratio range.

[0062] For example, the mass spectrometry data may be associated with the mass-to-charge ratio at the center of the mass-to-charge ratio range across which the mass transmission window is repeatedly scanned.

[0063] It should be understood that the mass transfer window is set by selecting the voltages applied to the electrodes of the mass filter (i.e., the RF voltage and / or the DC voltage).

[0064] The repeated scanning step can be performed by varying the amplitude of the RF voltage and / or the DC voltage applied to the electrodes of the mass filter.

[0065] The repeated scanning step can include scanning the mass transfer window back and forth in opposite directions across the mass-to-charge ratio range.

[0066] Alternatively, and less preferably, the repeated scanning step can repeatedly scan the mass transfer window across the mass-to-charge ratio range in the same direction (e.g., in the direction of increasing or decreasing mass-to-charge ratio).

[0067] The method can include selecting a target mass-to-charge ratio to be transmitted by the mass filter and then performing the mass filtering and repeated scanning steps, wherein the mass-to-charge ratio range across which the mass transfer window is repeatedly scanned includes the target mass-to-charge ratio.

[0068] For example, the method can form part of a multiple reaction monitoring experiment for analyzing target ions of interest having the target mass-to-charge ratio, and the mass filtering and repeated scanning steps can be performed to cause the mass filter to transmit the target ions of interest.

[0069] Alternatively, step (ii) can be repeated a plurality of times, wherein each time step (ii) is performed, the mass-to-charge ratio range across which the mass transfer window is repeatedly scanned is changed. Step (ii) can be repeated the plurality of times during a single experimental run, such as during a period in which ions are supplied to the mass filter substantially continuously and / or during a period in which an analyte is supplied to a mass spectrometer including the mass filter.

[0070] The mass-to-charge ratio range can be changed such that once step (ii) has been repeated the plurality of times, the mass filter has scanned within a total mass-to-charge ratio range (such as a total mass-to-charge ratio range having a width, for example, ≥2 Da, ≥5 Da, ≥10 Da, ≥15 Da, ≥20 Da, ≥30 Da, ≥40 Da, or ≥50 Da) sufficient to transmit a plurality of different ion species.

[0071] The method can include detecting the ions transmitted by the mass filter or ions derived therefrom during the single experimental run in order to obtain a mass spectrum.

[0072] A third aspect of the present invention also provides a mass spectrometer, which includes: a mass filter having electrodes; at least one voltage source for applying a voltage to the electrodes to provide a mass transfer window to the mass filter; and a control circuit configured to control the mass spectrometer to: (i) supply ions to the mass filter; and (ii) repeatedly scan the mass transfer window across a mass-to-charge ratio range having a width of less than 1 Da.

[0073] A mass spectrometer according to the third aspect may be configured to perform any of the methods described herein with respect to the third aspect.

[0074] According to a fourth aspect, the present invention provides a method of mass spectrometry, the method comprising: (i) mass filtering ions using a mass filter having a mass transmission window; (ii) changing the width of the mass transmission window while the center of the mass transmission window remains at a constant mass-to-charge ratio.

[0075] Step (ii) includes optionally changing the width of the mass transmission window a plurality of times between a minimum width and a maximum width. The minimum width and / or the maximum width may have a width of less than 1 Da (such as ≤0.5 Da, ≤0.4 Da, ≤0.3 Da, ≤0.2 Da or ≤0.1 Da).

[0076] Step (ii) is performed during a single experimental run, such as during a period when ions are substantially continuously supplied to the mass filter and / or during a period when an analyte is continuously supplied to a mass spectrometer including the mass filter.

[0077] Step (ii) may be performed over a certain period of time, and ions transmitted by the mass filter or ions derived therefrom during said period are detected in order to obtain mass spectrometry data; and wherein the mass spectrometry data is summed or averaged.

[0078] The method may include correlating the summed or averaged mass spectrometry data with the mass-to-charge ratio within the window. For example, the mass spectrometry data may be correlated with the value of the constant mass-to-charge ratio.

[0079] It should be understood that the mass transmission window is set by selecting the voltage applied to the electrodes of the mass filter (i.e., the RF voltage and / or the DC voltage).

[0080] The step of changing the width of the window may be performed by changing the amplitude of the RF voltage and / or the DC voltage applied to the electrodes of the mass filter.

[0081] The method may include selecting a target mass-to-charge ratio desired to be transmitted by the mass filter, and then performing steps (i) and (ii), wherein the target mass-to-charge ratio remains within the window during step (ii).

[0082] For example, the target mass-to-charge ratio may be the constant mass-to-charge ratio.

[0083] The method may form part of a multiple reaction monitoring experiment for analyzing target ions of interest having the target mass-to-charge ratio, and wherein steps (i) and (ii) are performed so that the mass filter transmits the target ions of interest.

[0084] Alternatively, step (ii) can be repeated multiple times, where each time step (ii) is performed, the value of the constant mass-to-charge ratio is changed.

[0085] Step (ii) can be repeated the multiple times during a single experimental run, such as during a period when ions are supplied to the mass filter substantially continuously and / or when an analyte is supplied to a mass spectrometer including the mass filter continuously.

[0086] Each time step (ii) is performed, the value of the constant mass-to-charge ratio can be changed such that once step (ii) has been repeated the multiple times, the mass filter has scanned within a total mass-to-charge ratio range sufficient to transmit multiple different ion species (such as a total mass-to-charge ratio range having a width of, for example, ≥2 Da, ≥5 Da, ≥10 Da, ≥15 Da, ≥20 Da, ≥30 Da, ≥40 Da, or ≥50 Da).

[0087] The method can include detecting ions transmitted by the mass filter or ions derived therefrom during the single experimental run in order to obtain a mass spectrum.

[0088] A fourth aspect of the present invention also provides a mass spectrometer including: a mass filter having electrodes; at least one voltage source for applying a voltage to the electrodes to provide a mass transmission window to the mass filter; and a control circuit configured to control the mass spectrometer to: (i) supply ions to the mass filter; and (ii) change the width of the mass transmission window while the center of the mass transmission window remains at a constant mass-to-charge ratio value.

[0089] The mass spectrometer according to the fourth aspect can be configured to perform any of the methods described herein with respect to the fourth aspect. Description of the Drawings

[0090] Various embodiments of the present invention will now be described by way of example only and with reference to the drawings, in which:

[0091] Figures 1A to 1D Shows how ion species having a single axial kinetic energy oscillate as they are transmitted through a mass filter when different voltages are applied to the mass filter;

[0092] Figure 2 Shows mass spectrometry data detected by scanning a mass filter when the ions being analyzed have a single axial kinetic energy;

[0093] Figure 3 Shows ions having a wide axial kinetic energy range that are transmitted through a mass filter;

[0094] Figure 4 Shows mass spectrometry data detected by scanning a mass filter when the ions being analyzed have a wide axial kinetic energy range;

[0095] Figures 5A to 5B Shows ions with a narrow axial kinetic energy range that are transmitted through a mass filter when different voltages are applied to the mass filter;

[0096] Figure 6A And Figure 6B Correspond to respectively Figure 4 And Figure 2 Illustrates how the intensity value changes with small changes in the mass-to-charge ratio;

[0097] Figure 7 Shows a schematic diagram of a mass spectrometer according to an embodiment of the present invention;

[0098] Figures 8A to 8C Shows exemplary improved mass spectrometry data provided by an embodiment of the present invention;

[0099] Figure 9 In a manner similar to Figure 2 Shows simulated mass peaks exhibiting peaks and valleys; and

[0100] Figure 10 Shows three mass peaks obtained using a mass filter with three different widths of the mass transfer window. Detailed Description

[0101] Figure 1A And Figure 1B Each shows a schematic diagram of a DC resolution quadrupole set mass filter 2 according to an embodiment of the present invention, which is followed downstream by a perforated electrode 4. The mass filter 2 has quadrupole electrodes 6 to which an RF voltage and a DC voltage are applied. These voltages radially confine ions having a certain mass-to-charge ratio range within a range called the mass transfer window in the mass filter, such that these ions can be transmitted from the inlet to the outlet of the mass filter. Ions with a mass-to-charge ratio outside this range have unstable trajectories in the mass filter and thus are not transmitted to the outlet of the mass filter. The RF voltage and the DC voltage can be changed over time such that different mass-to-charge ratio ranges can be transmitted by the mass filter at different corresponding times, i.e., such that the mass transfer window moves. For example, the mass transfer window of the mass filter can be scanned by progressively stepping up or down the amplitudes of the RF voltage and the DC voltage applied to the mass filter. During the scan of the mass filter, the amplitude ratio of the RF voltage and the DC voltage can be kept constant. Each time the amplitudes of the RF voltage and the DC voltage are stepped to a new value, the amplitudes can be kept constant for a period of time called the dwell time before the amplitudes are stepped again.

[0102] As described above, ions having a mass-to-charge ratio within the mass transfer window of the mass filter are radially confined by the mass filter. These ions oscillate radially between the electrodes as they travel along the longitudinal central axis of the mass filter, as will be described with respect to Figure 1C AndFigure 1D is described in more detail.

[0103] Figure 1A shows how the maximum oscillation amplitude 8 of ions changes with distance along the ion guide for a single ion species having the same mass-to-charge ratio, the same axial kinetic energy along the central axis, and the same starting position at the upstream end of the mass filter. In other words, Figure 1A shows Figure 1C and Figure 1D the envelope shown in. The envelope 8 can be considered to have nodes and antinodes, at the nodes, the ions have an oscillation amplitude close to the central axis of the mass filter, and at the antinodes, the oscillation amplitude of the ions is at the maximum radial distance relative to the central axis.

[0104] Figure 1C and Figure 1D show an example of the trajectory of ions stable within the mass filter. Figure 1C shows the amplitude of the radial oscillation of ions about the central axis in the dimension (i.e., the x-dimension) between a pair of electrodes of a quadrupole mass filter, which varies with the axial distance along the mass filter. More specifically, Figure 1B shows the trajectory 3 of ions entering the mass filter traveling in the +x direction, and the trajectory 5 of ions entering the mass filter traveling in the -x direction. As can be seen from Figure 1C , the amplitude of the ion oscillation changes as they travel along the mass filter. Although the detailed ion motion may be complex and the amplitude of any given ion will depend on its starting conditions when entering the mass filter (such as its spatial position, velocity, and the phase of the RF voltage), the envelope 8 around these amplitudes can be considered to have nodes and antinodes arranged at a specific spatial frequency.

[0105] Similarly, Figure 1D shows the amplitude of the radial oscillation of ions about the central axis in the other dimension (i.e., the y-dimension) between a pair of electrodes of a quadrupole mass filter, which varies with the axial distance along the mass filter. More specifically, Figure 1D shows the trajectory 7 of ions entering the mass filter traveling in the +y direction, and the trajectory 9 of ions entering the mass filter traveling in the -y direction. As has been described with respect to Figure 1C , the amplitude of the ion oscillation changes as they travel along the mass filter, and the envelope 8 around these amplitudes can be considered to have nodes and antinodes arranged at the said specific spatial frequency.

[0106] It should be understood that if the nodes are located at the exit of the mass filter, as Figure 1AAs shown, when the ions have substantially no radial displacement relative to the central axis, a relatively large proportion of the ions will leave the mass filter. In this scenario, a relatively high proportion of the ions will be transmitted through the pores 10 of the downstream perforated electrode 4 because the central axis through the pores is aligned with the central axis of the mass filter.

[0107] In contrast, as Figure 1B shown, if an antinode is located at the exit of the mass filter, a relatively large proportion of the ions will leave the mass filter when the ions have a relatively large radial displacement relative to the central axis of the mass filter. Thus, only a relatively low proportion of the ions will be transmitted through the downstream pores 10, and the remaining ions will be lost to the system, such as by striking the electrode 4 in which the pores are formed.

[0108] The frequency at which the ions oscillate radially and thus the spacing of the nodes and antinodes in the envelope 8 (assuming the ions have the same velocity in the axial direction) depends on the values of the parameters a and q in the Mathieu stability diagram in which the ions are located. In other words, this depends on the amplitudes of the RF voltage and DC voltage applied to the mass filter and also on the mass-to-charge ratio of the ions (assuming the mass filter has a constant inscribed radius and a constant RF frequency). When the mass transmission window of a DC resolving quadrupole mass filter is scanned over time to be able to transmit different mass-to-charge ratios at different times, the amplitudes of the RF voltage and DC voltage change. Thus, the values of the parameters a and q will also change, resulting in a change in the frequency at which the ions oscillate radially and thus a change in the spacing between the nodes and antinodes. Therefore, the average radial displacement of the ions at the point where the ions leave the mass filter and thus the proportion of the ions transmitted through the downstream pores will change as the mass filter is scanned. Thus, it should be understood that if the ions have substantially the same mass-to-charge ratio and the same axial kinetic energy, the proportion of the ions transmitted through the pores will change cyclically in an up and down manner as the mass filter is scanned.

[0109] Figure 2 Shows an example of mass spectrometry data detected for a single species of ions by scanning the mass filter in the manner described above with respect to Figures 1A to 1B As described. Typically, the y-axis represents the intensity of the detected ions, and the x-axis represents the mass-to-charge ratio. Since only a single ion species is transmitted in this example, it is expected that the mass peak will exhibit a Gaussian distribution. However, the mass spectrometry data appears to exhibit multiple mass peaks. This is because the transmission level of the ions changes as the mass filter is scanned, as described above. The relatively high-intensity portion 12 in the mass spectrometry data corresponds to the ions transmitted at a relatively high transmission level (i.e., when the node of the envelope is located at the exit of the mass filter), while the relatively low-intensity valley 14 corresponds to the ions transmitted at a relatively low intensity (i.e., when the antinode is located at the exit of the mass filter).

[0110] Although it is generally desirable for ions to have the smallest possible energy spread so that the mass filter has high mass resolution, in practice, not all ions passing through the mass filter have the same axial energy along the central axis. Instead, the ions have an axial energy spread. For example, ions are typically collisionally cooled to an average kinetic energy of about 0.5 eV before entering the mass filter. At the point of entry into the mass filter, such ions typically have an average axial kinetic energy of 0.5 eV and an axial kinetic energy spread of up to 1 eV. In this case, the axial kinetic energy spread of the ions is relatively large in the direction along the central axis of the mass filter. Although ions of the same mass-to-charge ratio will oscillate radially at the same frequency within the mass filter, ions with different axial kinetic energies will have different transit times through the mass filter and will thus arrive at the exit of the mass filter with different radial displacements relative to the central axis of the mass filter. In other words, ions with different axial kinetic energies can be considered to have different envelopes 8, where the nodes of those envelopes are at different spacings along the mass filter, such as as Figure 3 shown.

[0111] Figure 3 shows an embodiment corresponding to the Figures 1A to 1B embodiment, except that the ions have a relatively wide axial kinetic energy range compared to their average axial kinetic energy. As can be seen, even though the ions have the same mass-to-charge ratio, ions with different axial kinetic energies have different envelopes 8 such that the nodes of these different envelopes can be considered to be at different axial positions along the mass filter. Ions with different axial kinetic energies leave the mass filter at different corresponding radial displacements relative to the central axis. In fact, because the ions have a relatively wide axial kinetic energy range compared to their average axial kinetic energy, the ions at the exit of the mass filter have a wide range of radial displacements relative to the central axis. Thus, at any given time, only a moderate proportion of the ions leaving the mass filter are transmitted through the downstream aperture 10, with other ions being lost, for example, by hitting the surface surrounding the aperture. This is the case even when scanning the mass transmission window of the mass filter, assuming the ions have a relatively wide axial kinetic energy range compared to their average axial kinetic energy.

[0112] For example, at any given moment, ions with a first axial kinetic energy may have a relatively small average radial displacement when they leave the mass filter and thus have a relatively high level of transmission through the downstream pores, while ions with a second different axial kinetic energy may have a relatively high average radial displacement when they leave the mass filter and thus have a lower level of transmission through the downstream pores. At a subsequent time when the mass transmission window has been scanned to enable the transmission of a new mass-to-charge ratio range, ions with the first axial kinetic energy may have a relatively large average radial displacement when they leave the mass filter and thus have a relatively low level of transmission through the downstream pores, while ions with the second axial kinetic energy may have a relatively low average radial displacement when they leave the mass filter and thus have a higher level of transmission through the downstream pores. Thus, the proportion of ions transmitted at any given time may remain relatively constant when scanning the mass filter, and thus significant peaks and valleys do not occur in the mass peaks detected for such ions.

[0113] Figure 4 Shows an example of mass spectrometry data detected for a single ion species by scanning a mass filter when the ions have a relatively wide axial kinetic energy range relative to their average axial kinetic energy. It can be seen that the mass peaks do not have Figure 2 the significant peaks 12 and valleys 14 shown in

[0114] However, if the ions have a relatively small axial kinetic energy range relative to their average axial kinetic energy, the transmission level may change as the mass filter is scanned, as will be described with respect to Figure 5A and Figure 5B as described.

[0115] Figure 5A and Figure 5B show embodiments corresponding to the embodiments in Figure 3 except that the ions have a relatively narrow axial kinetic energy range relative to their average axial kinetic energy. Since the ions have a relatively narrow axial kinetic energy range relative to their average axial kinetic energy, the ions at the outlet of the mass filter have a narrow range of radial displacements relative to the central axis. In other words, ions with different axial kinetic energies can be considered to have different envelopes 8 that have nodes that are relatively close to each other in the axial direction.

[0116] As Figure 5A shown, when a certain combination of RF voltage and DC voltage is applied to the mass filter, all of the ions in the ions will have a relatively low radial displacement relative to the central axis when they leave the mass filter because the ions only have slightly different axial kinetic energies. In other words, the nodes of all of the envelopes in the envelope 8 will be at or relatively close to the outlet of the mass filter. Thus, a large proportion of these ions will be transmitted through the downstream pores. In contrast, as Figure 5BAs shown, when the scanning filter is applied with different combinations of RF voltage and DC voltage, all ions in the ion beam will have a relatively high radial displacement relative to the central axis when they leave the filter, because the ions only have slightly different axial kinetic energies. In other words, the antinodes of all envelopes in envelope 8 will be located at the exit of the filter or relatively close to the exit of the filter. Therefore, a lower proportion of ions will be transmitted through the downstream pores. Thus, if the ions have a relatively small range of axial kinetic energies relative to their average axial energy, the adverse effects described with respect to FIGS. 1 to Figure 2 may occur.

[0117] Although ions with different mass-to-charge ratios are transmitted during the mass transfer window when the filter has different mass transfer windows, the ions transmitted during the mass transfer window can oscillate radially at approximately the same frequency within the filter (when the ratio of the q and a parameters in the Mathieu stability diagram remains constant). However, as described above, ions with different axial kinetic energies will have different spacings between the nodes (and between the antinodes) in their envelopes. For example, ions with a lower mass-to-charge ratio tend to have a higher average kinetic energy, and thus the spacing between the nodes (and between the antinodes) in their envelopes is relatively large, and the adverse effects described with respect to FIGS. 1 to Figure 2 will be more prominent. Embodiments of the present invention recognize that for ions with a relatively large spacing between nodes (or antinodes), a relatively high ratio of kinetic energy diffusion to average kinetic energy is required to mitigate the effects described with respect to FIGS. 1 to Figure 2 Conversely, for ions with a smaller spacing between nodes (or antinodes), the ratio of kinetic energy diffusion to average kinetic energy can be controlled to be lower to mitigate the effects described with respect to FIGS. 1 to Figure 2 described.

[0118] For various reasons, it is generally desirable to provide the ions with a relatively high average axial kinetic energy. Since the spectrometer is set in such a way that the axial kinetic energy diffusion tends to remain approximately constant for all average axial kinetic energies, when the average axial kinetic energy increases, the axial kinetic energy diffusion becomes a smaller proportion of the average axial kinetic energy. Therefore, increasing the average axial kinetic energy may cause the adverse effects described with respect to FIGS. 1 to Figure 2 to occur.

[0119] For example, it may be desirable to provide the ions with an axial kinetic energy above a threshold, but it is also desirable to keep the axial kinetic energy as low as possible, resulting in a small axial kinetic energy range relative to the average axial kinetic energy. For example, it may be necessary for the ions to have an axial kinetic energy above the threshold to avoid the effects caused by contaminants that accumulate on the electrodes of the mass filter over time. Such contamination may occur because the ions filtered out by the mass filter impinge on its electrodes. Although the ions are neutralized when they impinge on the electrodes, they can leave an electrically insulating deposit on the electrodes, and additional ions can impinge on this electrically insulating deposit. This can lead to the accumulation of charge on the insulating deposit and thus to the formation of a potential barrier. To minimize the effect of the potential barrier on the movement of unfiltered ions through the mass filter, it may be necessary to provide the ions with a minimum threshold axial kinetic energy. However, for high mass resolution, it is desirable for the ions to experience as many RF field cycles of the mass filter as possible, and thus it is desirable for the ions to have the lowest possible axial kinetic energy, but above the threshold axial kinetic energy described above. Thus, there is a tendency to provide the ions such that they have only a small axial kinetic energy range, and for the reasons discussed above, this can be problematic when this range represents a relatively small fraction of the average axial kinetic energy.

[0120] Figure 6A and Figure 6B correspond respectively to Figure 4 and Figure 2 and help to further illustrate the problems encountered when increasing the average axial kinetic energy of the ions. As compared with Figure 6A in which the average axial kinetic energy of the ions is used to obtain mass spectrometry data, Figure 6B shows the mass spectrometry data obtained when the average axial kinetic energy of the ions is increased by 3 eV. The spread of the axial kinetic energy of the ions is substantially the same for Figure 6A and Figure 6B which means that the spread of the axial kinetic energy of Figure 6B represents a larger fraction of the average axial kinetic energy as compared with Figure 6A .

[0121] As illustrated by the vertical lines in Figure 6A , if the mass position below drifts slightly, for example due to thermal effects, the intensity of the detected ion signal changes only a relatively small amount, as illustrated by the horizontal dashed line. In contrast, as illustrated by the vertical lines in Figure 6B , if the mass position below drifts slightly, the intensity of the detected ion signal can change a relatively large amount, as illustrated by the horizontal dashed line.

[0122] The inventors have recognized the above problems and may desire to provide the ions with an axial kinetic energy spread above a threshold fraction of the average axial kinetic energy such that the transmission level of the ions downstream of the mass filter remains relatively constant across the mass peak, for example even when scanning the mass transmission window of the mass filter.

[0123] Figure 7 A schematic diagram of a mass spectrometer according to an embodiment of the present invention is shown. The spectrometer includes an ion source 16, a first vacuum chamber 18 that is pumped down to a first pressure during use, a second vacuum chamber 20 that is pumped down to a lower pressure during use, and a third vacuum chamber 22 that is pumped down to an even lower pressure during use. The first vacuum chamber 18 includes an ion guide 24. The second vacuum chamber 20 includes a DC resolving quadrupole filter 2 that can be operated in the manner described above. The second vacuum chamber may also include a fragmentation or reaction unit 26. The unit 26 may have a housing 28 with an inlet opening and an outlet opening. The housing 28 may be configured to maintain the region therein at a higher pressure than the region in the remainder of the second vacuum chamber 20, for example for collision-induced fragmentation of ions entering the unit. For example, a gas may be supplied to the unit 26 to maintain it at a higher pressure. Alternatively, reactant molecules or ions may be supplied to the unit 26 to react with the analyte ions entering the unit, for example to cause fragmentation of the analyte ions; or to undergo other reactions with the analyte ions to produce product ions. The unit 26 may include an ion guide 30 for guiding the analyte ions from the inlet of the unit 26 to the outlet, and / or for guiding the fragment or product ions generated from the analyte ions within the unit 26 to the outlet of the unit. The third vacuum chamber 22 may include a mass analyzer, such as a time-of-flight mass analyzer.

[0124] During use, analyte ions are generated in the ion source 16 and enter the first vacuum chamber 18 through an inlet aperture, where the analyte ions may be received in the ion guide 24. A voltage source 32 applies one or more voltages (such as an RF voltage) to the electrodes of the ion guide 24 to radially confine the ions therein. The first vacuum chamber may be maintained at a relatively high pressure such that the ions are collisionally cooled via collisions with background gas molecules in the first vacuum chamber. The ions are pushed in the downstream direction, for example by an air flow and / or an electric field, to pass through a differential pumping aperture in the wall between the first vacuum chamber 18 and the second vacuum chamber 20. The ions then enter the filter 2, which has an RF voltage and a DC voltage applied to its electrodes by a voltage source 34 to provide a mass transmission window for the filter. Ions with a mass-to-charge ratio within the mass transmission window are transmitted through the filter and exit its outlet, while ions with a mass-to-charge ratio outside the mass transmission window are filtered out by the filter.

[0125] The ions that are transmitted to the outlet of the mass filter then travel downstream and can enter the inlet aperture to enter the fragmentation or reaction cell 26. These ions are directed through cell 26 and are directed by the ion guide 30 therein to the outlet aperture. A voltage source 36 applies one or more voltages (such as an RF voltage) to the electrodes of the ion guide 30 in order to radially confine the ions therein. If the fragmentation or reaction cell is activated, at least some of the ions are fragmented or reacted in order to form fragment or product ions. For example, if cell 26 is a collision-induced dissociation (CID) cell, the ions can be accelerated into or within cell 26 for fragmentation. Alternatively, if cell 26 is a reaction cell, the ions can react with reactants in the cell in order to fragment or produce other product ions, such as adduct ions. On the other hand, if the fragmentation or reaction cell 26 is deactivated, the analyte ions pass through it and exit the outlet aperture with substantially no fragmentation or reaction occurring.

[0126] The ions exiting cell 26 can then pass to the detector or mass analyzer 23, enabling mass analysis of the ions.

[0127] The DC voltage and the amplitude of the RF voltage applied to the mass filter 2 to generate the mass transmission window can be stepped over time such that the value of the mass-to-charge ratio that can be transmitted by the mass filter changes over time. For example, the mass transmission window of the mass filter can be scanned by progressively stepping up or down the amplitude of the RF voltage and the DC voltage applied to the mass filter. During the scan of the mass filter, the amplitude ratio of the RF voltage and the DC voltage can be kept constant. Each time the amplitude of the RF voltage and the DC voltage is stepped to a new value, the amplitude can be kept constant for a period of time called the dwell time before the amplitude is stepped again. The spectrometer includes control circuitry that controls the various ion optical devices and voltage sources discussed above.

[0128] However, as described above, it has been recognized that during each dwell time, if the ions transmitted by the mass filter 2 have a relatively narrow axial kinetic energy spread relative to their average axial kinetic energy, the proportion of ions transmitted through the spectrometer (e.g., through the inlet aperture in cell 26) can change as the mass filter is scanned. It has also been recognized that it may be desirable to increase the axial kinetic energy spread of the ions transmitted by the mass filter 2 during each dwell time, such that the level of ion transmission downstream of the mass filter is relatively constant as the mass filter is scanned.

[0129] The axial kinetic energy spread of the ions can be increased before the ions enter the mass filter and / or within the mass filter itself, and can be achieved by applying an electric field to the ions. For example, the ions can be subjected to an electric field whose amplitude in the axial direction is modulated in order to increase the axial energy spread of the ions. The electric field can be generated by a DC voltage.

[0130] For example, ions may travel through a region across which there is a DC potential difference on their way to the mass filter 2, and the DC potential difference may be modulated over time. As an approximation, the ions will pick up the energy of the potential difference through which they pass. Thus, ions entering this region at different times will experience different DC potential differences and will thus be provided with different kinetic energies.

[0131] Reference Figure 7 , for example, the DC voltage applied to the ion guide 24 and / or the mass filter 2 may be modulated such that the DC potential difference between the ion guide 24 and the mass filter 2 is modulated over time. Thus, ions leaving the ion guide 24 at different times will be provided with different axial kinetic energies and will enter the mass filter 2 with those different kinetic energies.

[0132] The RF voltage and the DC voltage applied to the mass filter 2 are fixed during any given dwell time such that the mass filter has a mass transmission window that can only transmit a certain range of mass-to-charge ratios. Ions of a particular mass-to-charge ratio will oscillate radially in the mass filter at a certain frequency as they travel downstream through the mass filter. The embodiments modulate the DC potential difference within a range of values during each dwell time such that the ions transmitted by the mass filter during that dwell time have different axial kinetic energies and thus different transit times from the inlet to the outlet of the mass filter. Thus, within the duration of any given dwell time, the ions will leave the mass filter with a relatively large range of radial displacements relative to the central axis of the mass filter. Thus, when the mass filter is scanned such that the mass transmission window is held at different mass-to-charge ratio positions at different dwell times, the proportion of ions that can be transmitted through a downstream aperture (e.g., the inlet aperture of cell 26) of the mass filter is relatively constant for all dwell times in the dwell time. Thus, scanning the mass filter does not result in significantly different proportions of ions being transmitted through the downstream aperture during different dwell times.

[0133] The modulation may involve performing a cycle in which the DC potential difference changes between a maximum value and a minimum value. During this cycle, the DC potential difference may change in a continuous and progressive manner (e.g., in a linear manner) between the maximum and minimum values, or it may step discontinuously between multiple values. Ideally, the modulation may involve performing multiple such cycles during each dwell time. This helps to avoid different average transmission levels for different dwell times. For example, it may be desirable to provide ≥5 or ≥10 cycles during each dwell time. For example, if each dwell time has a duration of 1 ms, it may be desirable to modulate the DC potential difference at a frequency of ≥10 kHz.

[0134] Although the axial kinetic energy of ions has been described as being modulated by modulating the DC potential difference between the mass filter 2 and the upstream ion guide 24, it is contemplated that the axial kinetic energy can be modulated in other ways. For example, the axial kinetic energy of ions can be modulated within the mass filter 2 and / or the ion guide 24 rather than between them. This can be achieved, for example, by providing a DC potential difference along the mass filter 2 and / or the ion guide 24 and modulating this DC potential difference. The mass filter and / or the ion guide can include axially segmented electrodes, and different DC voltages can be applied to different segments to form an axial DC potential difference. The DC voltage applied to each segment can be changed over time to perform the modulation discussed. Alternatively, rod electrodes angled with respect to the central axis can be provided in the mass filter and / or the ion guide to form an axial DC potential difference, and the DC voltage applied to those electrodes can be changed over time to modulate the axial DC potential difference.

[0135] As an alternative or supplement to modulating the DC potential difference, different axial kinetic energies can be provided to ions by repetitively traveling one or more DC potentials in the downstream direction along an axial region of the spectrometer. To modulate the energy of ions during each dwell time, the speed at which one or more DC potentials travel along the axial region can be changed during each dwell time. For example, ions entering the axial region at one time can be pushed downstream by one or more DC potentials at a first speed so as to have a relatively low axial kinetic energy, while ions entering the axial region at another time can be pushed downstream by one or more DC potentials at a second different speed so as to have a higher axial kinetic energy. The speed of the DC potential can be modulated during each dwell time by performing a cycle in which the speed of the DC potential changes between a maximum and a minimum or vice versa. Desirably, the modulation can involve performing multiple such cycles during each dwell time. The axial region can be an axial region of the mass filter 2 and / or an axial region of the ion guide 24 and / or an axial region between the ion guide 24 and the mass filter 2.

[0136] Although the axial kinetic energy of ions has been described as being modulated by modulating the potential, it is contemplated that the axial kinetic energy can be modulated in other ways. For example, an air flow can be provided through a region for pushing ions in the upstream or downstream axial direction. The speed of the air flow can be adjusted such that ions passing through the region at different times will experience different air flow speeds and will thus leave the region with different kinetic energies.

[0137] Alternatively or additionally, ions can pass through a region in which the gas pressure is modulated such that ions passing through the region at different times will experience different gas pressures and will thus leave the region with different kinetic energies.

[0138] Figures 8A to 8C Illustrated is exemplary mass spectrometry data provided by embodiments of the present invention.

[0139] Figure 8A shows mass spectrometry data indicating how the intensity of an ion signal changes as the mass filter 2 is scanned over four different mass ranges when the ions being analyzed by the mass filter have a relatively low average axial kinetic energy and a relatively high proportion of axial kinetic energy spread relative to the average axial kinetic energy. In this example, the four mass ranges correspond to mass peaks centered at 42.1 Da, 74.1 Da, 183.0 Da, and 455.3 Da. As can be seen, each of the mass peaks has a relatively Gaussian shape and its intensity does not change significantly for small changes in the mass-to-charge ratio relative to the peak center. However, as described above, it may not be desirable to perform mass analysis on ions with such a low average axial kinetic energy, for example because their transport is more susceptible to the effects of charges that may accumulate on contaminated electrodes of the mass filter.

[0140] Figure 8B shows the mass spectrometry data for an experiment corresponding to the experiment used to obtain the data in Figure 8A , except that the average axial kinetic energy of the ions being mass analyzed is 2 eV higher (i.e., the axial kinetic energy spread is substantially the same as in Figure 8A and Figure 8B . By comparing Figure 8A and Figure 8B , it can be seen that increasing the average axial kinetic energy of the ions, without significantly increasing the axial kinetic energy spread, results in the appearance of peaks and valleys in each of the mass peaks. This is particularly prominent for the leftmost mass peak (centered at 42.1 Da) in Figure 8B , which shows significant intensity variations and only small changes in the mass position relative to the center of the mass peak. Although the FWHM of the low-mass mass peaks does not change as the average axial kinetic energy increases, the appearance of peak shape aberrations means that mass drifts can lead to large signal intensity variations. This can be particularly problematic in, for example, multiple reaction monitoring (MRM) or selective reaction monitoring (SRM).

[0141] Figure 8C shows the mass spectrometry data for an experiment corresponding to the experiment used to obtain the data in Figure 8B (i.e., ions having substantially the same average axial kinetic energy as in Figure 8B ), except that before mass analysis in the mass filter, the ions are subjected to a DC field that is modulated at a frequency of 10 kHz in the manner described above such that the spread of the axial kinetic energy of the ions is + / - 1.2 eV relative to the average axial kinetic energy. As by comparing Figure 8B and Figure 8CIt can be seen that increasing the spread of the axial kinetic energy of the ions in this way significantly smooths the intensity distribution of each mass peak in the mass spectrum, i.e., reduces the presence of peaks and valleys in each mass peak in the mass spectrum. Therefore, it should be understood that this technique enables mass analysis of ions having a relatively high average axial energy (e.g., in order to reduce or avoid the effects of surface charging in a mass filter), while maintaining the reproducibility of the mass analysis for small mass-to-charge ratio variations.

[0142] It is generally considered undesirable to increase the energy spread of ions prior to mass analysis because this reduces the mass resolution of the ions, where mass resolution is defined as the mass-to-charge ratio divided by the mass-to-charge ratio peak width. However, the inventors have recognized that the spread of the axial kinetic energy of the ions can be increased at relatively low mass-to-charge ratios without compromising the mass resolution of a quadrupole mass analyzer or a quadrupole mass filter because, although such devices are typically operated such that they have a high mass resolution at high mass-to-charge ratios, they tend to have a lower mass resolution at lower mass-to-charge ratios. More specifically, quadrupole mass filters and mass analyzers are typically operated to have a mass transmission window that remains constant in size when scanned. Thus, although such devices will have a high mass resolution when transmitting high mass-to-charge ratio ions, they will have a lower mass resolution when transmitting lower mass-to-charge ratio ions. For example, if the mass transmission window is set to have a width of 0.5 Da, the mass resolution of 1000 Da ions will be 1000 / 0.5 = 2000, while the mass resolution of 100 Da ions will be only 100 / 0.5 = 200.

[0143] The inventors have recognized that since the mass resolution of the mass filter or mass analyzer is relatively low for low mass-to-charge ratios, the average energy of these ions and their energy spread can be increased without affecting the mass resolution achieved by the mass filter or mass analyzer. In contrast, since the mass resolution of the mass filter or mass analyzer is relatively high for high mass-to-charge ratios, it is desirable that the average kinetic energy of these ions and their energy spread be minimized in order to maintain the high mass resolution that can be achieved by the mass filter or mass analyzer. Thus, the modulation can be applied in a mass-to-charge ratio-dependent manner.

[0144] Although the invention has been described with reference to various embodiments, those skilled in the art will understand that various changes can be made in form and detail without departing from the scope of the invention as set forth in the appended claims.

[0145] For example, the mass filter can have a post-filter at its downstream end.

[0146] The mass filter need not be a DC resolving filter. For example, the mass filter can be an RF-only filter.

[0147] Although embodiments of a quadrupole filter have been described, the invention extends to quadrupole mass analyzers, i.e., where an ion detector detects ions transmitted by the quadrupole and determines the mass-to-charge ratio of the detected ions based on the voltage applied to the quadrupole when the detected ions are transmitted by the quadrupole.

[0148] Although embodiments have been described where ions are transmitted through pores in electrodes or other surfaces, it is contemplated that the pores can be acceptance pores defined by the electric field of a device downstream of the filter.

[0149] The filter or mass analyzer can include a set of quadrupole rods having continuous rod electrodes, or alternatively, the quadrupole electrodes can be axially segmented, such as by including plate electrodes whose main surfaces are arranged in a plane orthogonal to the central axis.

[0150] Additionally or alternatively, the cross-sectional shape of each electrode in the quadrupole electrodes in a plane orthogonal to the central axis can be circular, hyperbolic, bow-shaped, or any other shape.

[0151] Although various embodiments have been described, it should be understood that the spectrometer need not have all of the components shown or can have different components. For example, the spectrometer can have fewer or more vacuum chambers than those described above. Additionally or alternatively, the spectrometer need not have a fragmentation or reaction unit. Additionally or alternatively, an alternative type of mass analyzer can be used in place of the TOF mass analyzer, and this mass analyzer need not be provided in its own vacuum chamber. For example, the mass spectrometer can be a tandem quadrupole mass spectrometer, where filter 2 is used as a filter that selectively transmits precursor ions or as a filter that selectively transmits product ions.

[0152] Although the problem of the appearance of peak 12 and valley 14 within a mass peak has been described in the context of a scanning filter, such as as shown in Figure 2 it should be understood that the same problem can occur even if the filter is not scanned. For example, during an experiment (such as a multiple reaction monitoring (MRM) experiment), the filter can be parked such that its mass transmission window is at a fixed position within the mass peak of an ion species. If the filter is parked such that the mass transmission window is mainly within one of the peaks 12 in the mass peak, then an ion signal with a high intensity will be transmitted, while if the filter is parked such that the mass transmission window is within one of the valleys 14 in the mass peak, then an ion signal with a significantly lower intensity will be transmitted. Therefore, the present invention can be used to reduce the effect of placing the mass transmission window at slightly different positions within a mass peak on the ion transmission level.

[0153] Although embodiments have been described in which the axial energy spread of the ions is relatively high compared to the average axial energy in order to smooth the peaks and valleys that would otherwise appear in the mass peaks, it is contemplated that other techniques may be performed to achieve this purpose.

[0154] As described above, it has been recognized that when the axial energy spread of the ions is relatively low compared to the average axial energy of the ions, peaks and valleys may appear in the mass peaks because the transmission level of the ions changes as the mass transmission window of the mass filter is located at different mass-to-charge ratio positions within the mass peak. Due to the reasons discussed above, these peaks and valleys in transmission occur at specific mass-to-charge ratio positions.

[0155] More specifically, for a given ion species having a specific average axial kinetic energy, the peaks and valleys in the mass spectrometry data will occur at positions corresponding to specific q and a values in the Mathieu stability diagram, i.e., at a specific combination of the amplitudes of the RF voltage and DC voltage applied to the mass filter. For example, referring to Figure 2 , if the mass transmission window is located within one of the peaks in peak 12 (e.g., at approximately m / z = 74.2), the intensity of the ion signal detected downstream of the mass filter will be relatively high, while if the mass transmission window is located within one of the valleys in valley 14 (e.g., at approximately m / z = 74.0), the intensity of the ion signal detected downstream of the mass filter will be significantly lower, even though peak 12 and valley 14 are located relatively close to the center of the mass peak.

[0156] As described above, this is problematic when scanning the mass filter, for example because the mass spectrometry data for a single ion species may appear to have multiple different mass peaks. Additionally, this can be problematic when the mass transmission window of the mass filter is parked (i.e., held within a specific mass-to-charge ratio range) because the ion transmission level through the mass filter will vary depending on the mass-to-charge ratio range at which the mass filter is parked. For example, this is problematic in multiple reaction monitoring (MRM) experiments.

[0157] To overcome this problem, when it is desired for the mass filter to transmit a specific ion species (e.g., in an MRM experiment), rather than holding the mass transmission window within a fixed mass-to-charge ratio range, the mass transmission window can be scanned back and forth within the mass-to-charge ratio range. This scanning is performed by changing the amplitudes of the RF voltage and DC voltage applied to the mass filter while keeping their ratio constant or changing their ratio. For example, the RF voltage and DC voltage applied to the mass filter can be changed in order to change the q and a values in the Mathieu stability diagram, which changes the frequency at which the ions transmitted by the mass filter oscillate radially. For a given axial kinetic energy, this changes the axial position of the nodes (and antinodes) in the envelope and thus changes the ion transmission level.

[0158] For example, referring to Figure 2, if a conventional MRM technique is used, the mass filter can be parked such that the mass transfer window only transmits ions having a mass-to-charge ratio of 74.0, which will provide a low level of ion transmission. In contrast, embodiments of the present invention scan the mass transfer window back and forth across a preselected mass range that is expected to correspond to some or all of the mass-to-charge ratio values of the ion species of interest that will be transmitted by the mass filter. For example, in the example shown in Figure 2 , the mass transfer window can be scanned back and forth between a mass-to-charge ratio of 73.8 and a mass-to-charge ratio of 74.8. Ions transmitted by the mass filter or ions derived therefrom are detected downstream of the mass filter in order to obtain mass spectrometry data. The mass spectrometry data associated with the ions transmitted during the period of scanning the mass transfer window back and forth can be summed in order to form a mass peak of the ion of interest. For example, this can associate the average intensity of the ions with the mass-to-charge ratio within the mass range.

[0159] Figure 9 In a manner similar to Figure 2 , another simulated mass peak exhibiting a peak 12 and a valley 14 is shown. Figure 9 The mass peak shown in is for ions having a nominal mass-to-charge ratio of 42 and an average axial kinetic energy of 4 eV. As can be seen, the mass peak has a width of approximately 0.7 Da. In this example, if the mass filter is parked such that its mass transfer window is fixed to only transmit ions having a mass-to-charge ratio of 42.1, the ion signal of the transmitted ions will be approximately twice that of the case where the mass transfer window is fixed to only transmit ions having a mass-to-charge ratio of 42.0. To overcome this problem, embodiments of the present invention modulate the position of the mass transfer window back and forth within the mass peak, for example, between mass-to-charge ratios of 41.9 and 42.2, as indicated by the arrows. As described above, the mass spectrometry data associated with the ions transmitted during the period of scanning the mass transfer window back and forth can be summed in order to form a mass peak of the ion of interest. For example, this can associate the average intensity of the ions with the mass-to-charge ratio within the mass range.

[0160] This technique is not only useful when the mass filter is parked at a specific mass-to-charge ratio, but can also be used in embodiments where the mass transfer window of the mass filter is scanned, for example, when scanning the mass filter across a relatively large mass-to-charge ratio range in order to transmit different ion species at different times. In such embodiments, rather than continuously and progressively scanning the mass transfer window in one direction (i.e., increasing or decreasing m / z), the mass transfer window is scanned back and forth within a relatively narrow mass-to-charge ratio range centered on a center mass-to-charge ratio, and the value of the center mass-to-charge ratio is scanned within the wider mass-to-charge ratio range.

[0161] In addition to the above techniques, or alternatively, the resolution of the mass filter can be modulated in order to overcome the problems discussed herein. This is possible because changing the resolution of the mass filter will change the mass-to-charge ratio positions where the peak 12 and the valley 14 are located, as will be referencedFigure 10 as described

[0162] Figure 10 Three mass peaks are shown, each of which is obtained by scanning a mass filter across the shown mass-to-charge ratio range, but the resolution of the mass filter used in each scan (i.e., the width of the mass transmission window) is different. Mass peak 40 is obtained under the same conditions as shown in Figure 9 and has a mass peak width of 0.7 Da. Mass peak 42 is a mass peak obtained under the same conditions as mass peak 40, except that the width of the mass transmission window used to obtain the mass peak is increased, resulting in a mass peak with a width of 0.8 Da. Mass peak 44 is a mass peak obtained under the same conditions as mass peak 40, except that the width of the mass transmission window used to obtain the mass peak is further increased, resulting in a mass peak with a width of 0.9 Da. As can be seen from Figure 10 changing the width of the mass transmission window (i.e., the resolution of the mass filter) causes a change in the positions of peaks 12 and valleys 14 within the mass peak.

[0163] As described above, if the mass filter is set such that its mass transmission window is at any particular mass-to-charge ratio (such as in an MRM experiment), the intensity of the transmitted ions may vary significantly depending on the mass-to-charge ratio at which the window is set. This is because the window can be located within peak 12 or valley 14 of the mass peak. However, it has been recognized that by setting the mass transmission window to be centered at a particular mass-to-charge ratio and then changing the width of the mass transmission window over time, the above problems can be alleviated. Mass spectrometry data related to the ions transmitted while changing the width of the window can be summed to form a mass peak. For example, this can associate the average intensity of the ions with the mass-to-charge ratio within the window. This effectively averages the ion signals obtained with different mass transmission window widths, making the measurement less susceptible to intensity variations that might otherwise occur depending on the location of the mass transmission window.

Claims

1. A method of mass spectrometry, the method comprising: Supplying ions having an initial axial kinetic energy range to a mass filter; And Mass filtering the ions by applying different voltages to the electrodes of the mass filter during different respective residence times so as to provide different mass transmission windows during the different residence times; Wherein the method includes increasing the axial kinetic energy range that the ions have as they travel to and / or through the mass filter during at least one of the residence times.

2. The method according to claim 1, wherein the mass filter is a quadrupole set mass filter for DC resolution.

3. The method according to claim 1 or 2, wherein for each of the at least one of the residence times, the step of increasing the axial kinetic energy range causes ions of a given mass-to-charge ratio to exit the mass filter during the duration of the residence time with a radial displacement range that is wider than the radial displacement range that the ions would have completed relative to the central axis of the mass filter if their axial kinetic energy had not been increased.

4. The method according to any one of the preceding claims, the method including providing a physical aperture or ion optical device downstream of the mass filter for receiving the ions transmitted by the mass filter, the ion optical device having an ion acceptance aperture defined by the electric field of the ion optical device.

5. The method according to any one of the preceding claims, the method including detecting, downstream of the mass filter, the ions or their fragments or product ions transmitted during the different residence times so as to generate mass spectrometry data and summing the mass spectrometry data obtained during the different residence times; optionally so as to form at least one mass peak corresponding to the ions or their fragments or product ions transmitted by the mass filter during the different residence times.

6. The method according to any one of the preceding claims, wherein the step of increasing the axial kinetic energy range includes performing a plurality of cycles during each of the at least one of the residence times, wherein each cycle includes modulating the axial kinetic energy of the ions traveling to and / or through the mass filter between a minimum axial kinetic energy and a maximum axial kinetic energy.

7. The method according to claim 6, the method including performing at least 5 cycles during each of the at least one of the residence times.

8. The method according to any one of the preceding claims, wherein the step of increasing the axial kinetic energy range that the ions have includes: Providing, during the course of one of the residence times, a first axial kinetic energy range about a first average axial kinetic energy distribution to the ions arriving at the exit of the mass filter; and Providing, during the course of another of the residence times, a second axial kinetic energy range about a second average axial kinetic energy distribution to the ions arriving at the exit of the mass filter; Wherein the second axial kinetic energy range is wider than the first axial kinetic energy range and the second average axial kinetic energy is higher than the first average axial kinetic energy.

9. The method according to any one of the preceding claims, wherein the step of increasing the axial kinetic energy range comprises providing a DC potential difference along an axial region of the mass filter or along an axial region upstream of the mass filter, and varying the DC potential difference during each of the at least one dwell time of the dwell times such that ions entering the axial region at different times are imparted with different axial kinetic energies.

10. The method according to any one of the preceding claims, the method comprising increasing the axial kinetic energy range of the ions as they travel to and / or through the mass filter such that the ions have a first axial kinetic energy range during a first dwell time of the dwell times, during which the mass transmission window of the mass filter is set to transmit ions in a first mass-to-charge ratio range; wherein the method further comprises: (i) increasing the axial kinetic energy range of the ions as they travel to and / or through the mass filter such that the ions have a second axial kinetic energy range, which is narrower than the first axial kinetic energy range, during a second dwell time of the dwell times, during which the mass transmission window of the mass filter is set to transmit ions in a second mass-to-charge ratio range higher than the first mass-to-charge ratio range; and / or (ii) not increasing the axial kinetic energy range of the ions as they travel to and / or through the mass filter during a dwell time during which the mass transmission window of the mass filter is set to transmit ions in a mass-to-charge ratio range higher than the first mass-to-charge ratio range and / or the second mass-to-charge ratio range.

11. The method according to any one of the preceding claims, the method comprising providing a first average axial kinetic energy for the ions to pass through the mass filter during a dwell time during which the mass transmission window of the mass filter is set to transmit ions in a mass-to-charge ratio range; and providing a second average axial kinetic energy for the ions to pass through the mass filter, which is lower than the first average axial kinetic energy, during a dwell time during which the mass transmission window of the mass filter is set to transmit ions in a mass-to-charge ratio range higher than the one mass-to-charge ratio range.

12. A mass spectrometer, the mass spectrometer comprising: a mass filter having electrodes; at least one voltage source for applying a voltage to the electrodes; and a control circuit configured to control the mass spectrometer to: supply ions having an initial axial kinetic energy range to the mass filter; control the at least one voltage source to apply different voltages to the electrodes of the mass filter during different respective dwell times so as to provide different mass transmission windows for the mass filter during the different dwell times; and increase the axial kinetic energy range of the ions as they travel to and / or through the mass filter during at least one of the dwell times.

13. The mass spectrometer according to claim 12, wherein the mass spectrometer includes an electrode and one or more voltage sources configured to provide a DC potential difference along an axial region of the mass filter or along an axial region upstream of the mass filter, and wherein the control circuit is configured to control the mass spectrometer to increase the axial kinetic energy range by controlling the one or more voltage sources so as to change the DC potential difference during each of at least one dwell time of the dwell time, such that ions entering the axial region at different times are imparted with different axial kinetic energies.

14. A method of mass spectrometry, the method comprising: supplying ions to a mass filter having a mass transport window; and increasing the axial kinetic energy range that the ions have as they travel to and / or through the mass filter.

15. A mass spectrometer, the mass spectrometer comprising: a mass filter having an electrode; at least one voltage source for applying a voltage to the electrode to provide a mass transport window to the mass filter; and a control circuit configured to control the mass spectrometer to: supply ions to the mass filter; and increase the axial kinetic energy range that the ions have as they travel to and / or through the mass filter.

16. A method of mass spectrometry, the method comprising: (i) mass filtering ions using a mass filter having a mass transport window; (ii) repeatedly scanning the mass transport window across a mass-to-charge ratio range less than 1 Da.

17. The method according to claim 16, wherein the repeated scanning step is performed during a single experimental run, such as during a period when ions are supplied to the mass filter substantially continuously and / or during a period when an analyte is supplied to a mass spectrometer including the mass filter.

18. The method according to claim 16 or 17, wherein the repeated scanning step is performed over a period of time, and ions transmitted by the mass filter or ions derived therefrom during the period are detected to obtain mass spectrometry data; and wherein the mass spectrometry data is summed or averaged.

19. The method according to claim 18, the method comprising correlating the summed or averaged mass spectrometry data with the mass-to-charge ratios within the mass-to-charge ratio range.

20. The method according to any one of claims 16 to 19, wherein the repeated scanning step includes scanning the mass transport window back and forth in opposite directions across the mass-to-charge ratio range.

21. The method according to any one of claims 16 to 20, the method comprising selecting a target mass-to-charge ratio to be transmitted by the mass filter, and then performing the mass filtering and repeated scanning steps, wherein the mass-to-charge ratio range across which the mass transport window is repeatedly scanned includes the target mass-to-charge ratio.

22. A method of mass spectrometry, the method comprising: (i) mass filtering ions using a mass filter having a mass transport window; (ii) changing the width of the mass transport window while the center of the mass transport window remains at a constant mass-to-charge ratio value.

23. The method according to claim 22, wherein step (ii) is performed over a period of time, and ions transmitted by the mass filter or ions derived therefrom during said period of time are detected in order to obtain mass spectrometry data; and wherein said mass spectrometry data is summed or averaged.

24. The method according to claim 22 or 23, the method comprising selecting a target mass-to-charge ratio that is desired to be transmitted by the mass filter, and then performing steps (i) and (ii), wherein the target mass-to-charge ratio remains within the window during step (ii).

25. The method according to claim 22, 23 or 24, wherein the method forms part of a multiple reaction monitoring experiment for analyzing target ions of interest having the target mass-to-charge ratio, and wherein steps (i) and (ii) are performed so as to cause the mass filter to transmit the target ions of interest.

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