Ion trapping scheme with improved mass range

Abstract

The present invention provides a method of trapping ions in an ion trap assembly 100, 120 and a controller 130 for controlling ion trapping in the ion trap assembly 100, 120. A method of the present invention includes introducing ions into the ion trap assembly 100, 120, applying a first RF trapping amplitude to the ion trap assembly 100, 120 to trap introduced ions having m / z ratios within a first m / z ratio range, and cooling the trapped ions. The method also includes reducing the RF trapping amplitude from the first RF trapping amplitude to a lower second RF trapping amplitude to reduce the low mass cutoff of the ion trap assembly 100, 120, and trapping introduced ions having m / z ratios within a second m / z ratio range at the lower second RF trapping amplitude. The mass lower limit of the second m / z ratio range is lower than the low mass cutoff of the ion trap assembly 100, 120 when the first RF trapping amplitude is applied. The total number of trapped ions in the ion trapping assembly 100, 120 is maintained below a threshold value determined as a function of the first and second RF trapping amplitudes.

Description

Technical Field

[0001] The present invention relates to trapping ions in an ion trap assembly. Background Art

[0002] Mass spectrometry is an important chemical analysis technique. Typically, a mass spectrometer includes an ion source that generates ions from a sample, various lenses, a mass filter, an ion capture / storage device and / or a fragmentation device, and one or more mass analyzers.

[0003] An important component of a mass spectrometer is a linear ion trap. An example of such a linear ion trap is a curved linear ion trap or C-trap, which stores / traps ions in a trapping volume using a potential well, which is created by applying an RF potential to a set of curved elongated rods, typically arranged as a quadrupole, hexapole or octopole.

[0004] One application of linear ion traps is as an intermediate storage device prior to mass analysis. For example, a C-trap can be used to store ions for injection into an orbital capture mass analyzer, such as the one developed by Thermo Fisher Scientific under the name These mass analyzers have high mass accuracy and high mass resolution and are therefore increasingly used for the detection of small organic molecules, such as for food and drug analysis, metabolomics and anti-doping applications. In this article, the term mass may be used to refer to the mass-to-charge ratio m / z.

[0005] One of the difficulties of linear ion traps is the range of masses that can be trapped simultaneously. Ions can be trapped in a linear trap by applying RF voltages to longitudinal electrodes to confine the ions radially, while applying static (DC) potentials to end electrodes placed at the axial ends opposite the longitudinal electrodes to confine the ions axially. The pseudopotential well created by a given applied RF voltage decreases in strength as the mass of the ions increases. However, ions with greater mass have similar kinetic energy to ions with less mass. Therefore, ions with greater mass are more likely to have sufficient energy to escape the pseudopotential well created by a given applied RF trapping amplitude, and are therefore more likely to decay in the trap. As a result, ions with greater mass have lower capture efficiencies, thereby limiting the mass range of the ion trap. In practice, the ratio of the highest trapped mass to the lowest trapped mass in ion traps such as C-traps is often limited to 15-20.

[0006] It is desirable to have as wide a range of masses trapped inside a linear ion trap as possible. One way to define the mass range (i.e., m / z ratio range) of ions in a linear ion trap is as the ratio of the highest mass to the lowest mass that can be captured in the ion trap. For small molecule applications, common desired mass ranges may be 1200 / 15 (80), 1500 / 15 (100), or 2000 / 15 (133).

[0007] Figure 1 is a graph of the RF trapping amplitude (volts peak-to-peak, Vpp) applied to the linear ion trap during injection and storage versus the relative intensity of the ions trapped in the linear ion trap. For this graph, the same RF amplitude was applied to the linear ion trap for injection and storage. Each line of the graph represents an ion of a different mass. It can be seen that ions with greater mass have lower intensities at lower RF amplitudes.

[0008] The present invention seeks to increase the trapped mass range of ion trapping assemblies such as linear ion traps and particularly, but not exclusively, curved linear ion traps (C-traps). SUMMARY OF THE INVENTION

[0009] According to a first aspect of the present invention, there is provided a method for trapping ions in an ion trap assembly as described in Embodiment 1.

[0010] The method of embodiment 1 includes: (a) introducing ions into an ion trap assembly; (b) applying a first RF trapping amplitude to the ion trap assembly, thereby trapping introduced ions having m / z ratios within a first m / z ratio range; (c) cooling the trapped ions; (d) reducing the RF trapping amplitude from the first RF trapping amplitude to a second, lower RF trapping amplitude, thereby reducing a low mass cutoff value of the ion trap assembly; and (e) at the second, lower RF trapping amplitude, trapping introduced ions having m / z ratios within a second m / z ratio range, wherein the lower mass limit of the second m / z ratio range is below the low mass cutoff value of the ion trap assembly when the first RF trapping amplitude is applied, wherein the total number of trapped ions in the ion trap is maintained below a threshold value determined as a function of the first and second RF trapping amplitudes.

[0011] This approach improves the mass range (m / z ratio range) of ions trapped in the ion trap assembly. The ion trap assembly may include an ion trap such as a C-trap or other linear ion trap. In the first stage of operation, by applying a relatively high RF trapping potential / amplitude, ions with larger masses are trapped. Although this higher RF trapping potential / amplitude allows the capture of relatively high m / z ions, ions below a low mass cutoff are not trapped.

[0012] By cooling the ions before reducing the RF trapping amplitude to a lower second RF trapping amplitude, the energy of the ions inside the ion trapping assembly is attenuated by collisions with inert gas molecules and the ions relax toward the bottom of the potential well. For example, the kinetic energy of ions entering the ion trapping assembly is typically in the range of 1-200 eV, while the kinetic energy of such ions after cooling is typically less than 100 meV (0.1 eV). The ions can be cooled so that they thermalize in the well. Thus, the pseudopotential well required for trapping the ions during injection is higher than the pseudopotential well required for subsequent storage of the cooled ions. When the RF amplitude is reduced, the cooled, more massive ions remain inside the ion trapping assembly because they do not have enough kinetic energy to escape the potential well created by the lower second RF trapping amplitude.

[0013] The lower second RF trapping amplitude applied in the second stage of operation of the ion trap assembly produces a lower low mass cutoff than the low mass cutoff produced by the higher first RF trapping amplitude applied in the first stage of operation of the ion trap assembly. Thus, once the more massive ions have cooled, the less massive ions can be introduced into the ion trap assembly and trapped by reducing the RF trapping amplitude applied to the ion trap assembly while retaining the more massive ions because they have cooled. In other words, the lower RF trapping amplitude generates an RF field that is sufficient to retain the cooled more massive ions within the ion trap assembly while allowing less massive ions to be introduced and trapped within the same ion trap assembly. This in turn increases the usable mass range of the ion trap assembly relative to methods in which a single RF amplitude or increasing RF amplitudes are used to introduce and trap ions. A wider range of ion masses can be stored in the trap by improving the mass range of ions that can be trapped together in the ion trap assembly compared to previous methods.

[0014] In some embodiments, step (e) comprises introducing ions into an ion capture assembly.

[0015] In some embodiments, the ion trapping assembly can be configured to eject ions from the ion trapping assembly. For example, the ion trapping assembly can be configured to eject ions from the ion trapping assembly to a mass analyzer, which can perform a mass analysis on the ejected ions. The ions can thus be analyzed by the analyzer in a mass scan. A common scan type is a "full scan", which can be used as a survey scan and should cover as wide a mass range as possible. Compared to previous methods, the present invention makes it possible to increase the available mass range and thus can improve one of the fundamental limitations of a full scan in which ions have been trapped.

[0016] In some embodiments, the method may include applying n additional RF trapping amplitudes to the ion trapping assembly, each of which is an intermediate trapping amplitude between the first and second RF trapping amplitudes, wherein n ≥ 1, the n additional RF trapping amplitudes each causing the capture of incoming ions having a corresponding nth m / z ratio range, each of which has a lower mass limit; the method further includes cooling the incoming ions captured at a relatively high RF trapping amplitude before reducing the RF trapping amplitude to a relatively low trapping amplitude. This may be desirable because the RF trapping amplitude may vary less from one run to the next.

[0017] In some embodiments, ions within a selected m / z ratio range can be introduced into the ion trapping assembly from an upstream ion device that transmits ions within the selected m / z ratio range. The method further includes adjusting the upstream ion device to reduce a lower mass limit for the selected m / z ratio range and simultaneously or substantially simultaneously reducing an RF trapping amplitude from a first RF trapping amplitude to a lower second RF trapping amplitude while the lower mass limit for the selected m / z ratio range of the upstream ion device is reduced.

[0018] By adjusting the mass transmission of the upstream ion device, ions in the first mass range can be selected upstream of the ion trap assembly and then trapped by the ion trap assembly, thereby improving the efficiency of the mass spectrometer.

[0019] The upstream ion device can transmit ions within a first m / z ratio range during step (a) of embodiment 1, so that the introduced ions of step (a) have m / z ratios within the first m / z ratio range. The upstream ion device can transmit ions within a second m / z ratio range during step (e) of embodiment 1, so that step (e) further includes introducing ions having m / z ratios within the second m / z ratio range into the ion trap assembly.

[0020] Although the method of embodiment 1 adjusts the low mass cutoff of the ion trap assembly by adjusting the RF trapping amplitude, it is also possible to adjust the low mass cutoff of the ion trap assembly by adjusting the RF trapping frequency. Therefore, according to a second aspect of the present invention, a method for trapping ions in an ion trap assembly as described in embodiment 19 is provided.

[0021] The method of embodiment 19 comprises (a) introducing ions into an ion trap assembly;

[0022] (b) applying a first RF trapping frequency to the ion trap assembly to thereby trap incoming ions having m / z ratios within a first m / z ratio range;

[0023] (c) cooling the trapped ions;

[0024] (d) increasing the RF trapping frequency from a first RF trapping frequency to a second RF trapping frequency, thereby reducing a low mass cutoff of the ion trapping assembly; and

[0025] (e) trapping incoming ions having m / z ratios within a second m / z ratio range at a second RF trapping frequency;

[0026] wherein a lower mass limit of the second m / z ratio range is below a low mass cutoff of the ion trap assembly when the first RF trapping frequency is applied, wherein a total number of trapped ions in the ion trap assembly is maintained below a threshold determined as a function of the first and second RF trapping frequencies.

[0027] Product ions generated by collisional dissociation generally have additional kinetic energy. In addition, the mass range of product ions generated from precursors is wide, generally 100–(mz), where m is the mass of the precursor ion and z is the charge of the precursor ion (and (mz) is the product of the mass of the precursor ion and the charge of the charged precursor ion).

[0028] Therefore, it would also be desirable to improve the mass range (m / z ratio range) of product ions that can be generated and trapped in an ion trapping assembly.

[0029] According to a third aspect of the present invention, there is provided a method of trapping product ions in an ion trap assembly configured to fragment ions as described in embodiment 20. The method of embodiment 20 is advantageous because it improves the mass range of product ions that can be generated and trapped in an ion trap assembly (such as a fragmentation cell, C-trap or other ion trap).

[0030] The method of embodiment 20 includes (a) introducing precursor ions into an ion trap assembly; (b) fragmenting the introduced precursor ions to generate product ions; (c) applying a first RF trapping amplitude to the ion trap assembly to capture product ions having m / z ratios within a first m / z ratio range; (d) cooling the trapped product ions; (e) reducing the RF trapping amplitude from the first RF trapping amplitude to a lower second RF trapping amplitude to reduce a low mass cutoff of the ion trap assembly; and (f) trapping product ions having m / z ratios within a second m / z ratio range at the lower second RF trapping amplitude, wherein the lower mass limit of the second m / z ratio range is lower than the low mass cutoff of the ion trap assembly when the first RF trapping amplitude is applied.

[0031] Product ions are generated from precursor ions introduced into the ion trap assembly. This can occur continuously or intermittently. In the first stage of operation, by applying a relatively high RF trapping potential / amplitude, the more massive product ions are trapped. While this higher RF trapping potential / amplitude allows the capture of relatively high m / z ions, ions below the low mass cutoff are not trapped.

[0032] By cooling the ions before reducing the RF trapping amplitude to a lower second RF trapping amplitude, the energy of the product ions inside the ion trap assembly is attenuated by collisions with inert gas molecules and the ions relax toward the bottom of the potential well. The product ions can be cooled so that they are thermalized in the ion trap assembly. Thus, the pseudopotential well required to capture the product ions during fragmentation is higher than the pseudopotential well required to subsequently store the cooled product ions. When the RF trapping amplitude is reduced, the cooled, more massive product ions remain inside the ion trap assembly because they do not have enough kinetic energy to escape the potential well created by the lower second RF trapping amplitude.

[0033] The lower second RF trapping amplitude applied in the second stage of the ion trapping assembly operation produces a lower low mass cutoff than the low mass cutoff produced by the higher first RF trapping amplitude applied in the first stage of the ion trapping assembly operation. Thus, once the more massive product ions have cooled, the less massive product ions can be trapped in the ion trapping assembly by reducing the RF trapping amplitude applied to the ion trapping assembly while retaining the more massive product ions because they have cooled. In other words, the lower RF trapping amplitude generates an RF field that is sufficient to retain the cooled more massive product ions within the ion trapping assembly while allowing less massive ions to be trapped within the same ion trap. This in turn increases the usable mass range of the ion trapping assembly relative to methods in which a single RF amplitude or increasing RF amplitudes are used to generate and trap product ions.

[0034] According to a fourth aspect of the present invention, there is provided a controller for controlling ion trapping in an ion trapping assembly as described in Embodiment 30.

[0035] According to a fifth aspect of the present invention, there is provided a further controller for controlling ion trapping in an ion trap assembly as described in Embodiment 36.

[0036] According to a sixth aspect of the present invention, there is provided a further controller for controlling ion fragmentation and trapping in an ion trap assembly as described in Embodiment 37.

[0037] According to a seventh aspect of the present invention, an ion trapping assembly as described in Embodiment 39 is provided.

[0038] According to an eighth aspect of the present invention, a mass spectrometer as described in Embodiment 40 is provided. BRIEF DESCRIPTION OF THE DRAWINGS

[0039] The invention may be put into practice in many ways and some specific embodiments will now be described by way of example only and with reference to the accompanying drawings, in which:

[0040] Figure 1is a graph of the relative intensity of ions inside an ion trap versus the RF amplitude applied to the ion trap for injection and storage according to known methods.

[0041] Figure 2 is a schematic diagram of a first embodiment of a mass spectrometer having an ion trap according to the present invention.

[0042] Figure 3 A flow chart is shown which illustrates a method for operating according to a first embodiment of the present invention. Figure 2 The mass spectrometer method.

[0043] Figure 4 yes Figure 3 Schematic diagram of a graph of RF trapping amplitude applied to an ion trap versus time for the method described in FIG.

[0044] Figure 5 A flow chart is shown which illustrates a method for operating according to a second embodiment of the present invention. Figure 2 The mass spectrometer method.

[0045] Figure 6 yes Figure 5 Schematic diagram of a graph of RF trapping amplitude applied to an ion trap versus time for the method described in FIG.

[0046] Figure 7 is a graph of relative intensity of ions versus the amplitude of a second RF trapping applied to the ion trap according to a first embodiment of the present invention.

[0047] Figure 8 is a plot of the observed trapped mass range (MR) versus the automatic gain control (AGC) target (ie, target trapped particle number) obtained using a calibration sample (Calmix).

[0048] FIG. 9( a ) is a mass spectrum obtained according to the prior art method using a calibration sample (Calmix) and a single RF amplitude.

[0049] FIG. 9( b ) is a mass spectrum obtained using a calibration sample (Calmix) and different first and second RF amplitudes according to the first embodiment of the present invention.

[0050] Fig.10 A flow chart is shown which illustrates a method for operating according to a third embodiment of the present invention. Figure 2 The mass spectrometer method.

[0051] Fig.11 yes Fig.10 Schematic diagram of a graph of RF trapping amplitude versus time applied to an ion trapping assembly according to the method described in FIG.

[0052] Figure 12(a) is a mass spectrum obtained when ions in the first and second mass ranges are trapped in the fragmentation cell and transferred from the fragmentation cell to the ion trap while applying a second RF trapping amplitude according to the first embodiment of the method.A calibration sample (Calmix) is used.

[0053] FIG. 12( b ) is a mass spectrum obtained using a calibration sample (Calmix) according to the third embodiment of the present invention.

[0054] Fig.13 FIG. 1 is a schematic diagram of a second embodiment of a mass spectrometer having an ion trap and an ion cooling device according to the present invention. DETAILED DESCRIPTION OF THE INVENTION

[0055] Figure 2 A schematic layout of a mass spectrometer 10 suitable for carrying out methods according to embodiments of the present invention is shown. Figure 2 The schematic layout represents Thermo Fisher Scientific, Inc's Q Quadrupole- Layout of the mass spectrometer.

[0056] The mass spectrometer 10 includes an ion source 20 for generating gas phase ions to be analyzed. The ion source 20 is generally an atmospheric pressure electrospray ion source. Those ions then enter the vacuum chamber of the mass spectrometer 10 and are guided by a capillary 25 into an S-lens 30.

[0057] The S-lens 30 is also known as a stacked ring ion guide (SRIG) or RF lens. Application of an RF amplitude to the S-lens 30 establishes an RF field that confines and focuses the ions as they traverse the S-lens 30. The ions are focused into the implantation flat rods 40 which implant the ions into the curved flat rods 50. The curved flat rods 50 guide the (charged) ions along a curved path through themselves, while unwanted neutral molecules such as entrained solvent molecules are not guided along the curved path and are lost.

[0058] The TK lens 60 is located at the far end of the curved flat rod 50. Ions pass from the curved flat rod 50 into the downstream quadrupole mass filter 70. The quadrupole mass filter 70 can be operated in conjunction with a mass selection window so that the mass filter 70 only extracts those ions inside the desired mass selection window, which contains ions with those target m / z ratios (i.e., a window containing the target isotope). The mass filter is generally but not necessarily segmented and acts as a bandpass filter. In some operating modes, the quadrupole mass filter 70 can be operated in essentially only RF mode, thereby transmitting ions with as wide a mass range as possible. For example, this mode is used when a "full scan" is required and the mass range should be as wide as possible.

[0059] The ions then pass through the quadrupole exit lens / splitter lens arrangement 80 that controls the ions to the transmission multipole 90. The transmission multipole 90 guides the mass-filtered ions from the quadrupole mass filter 70 into the ion trap, which is a curved trap (C-trap) 100. The C-trap 100 has an electrode assembly that includes a curved curved rod extending longitudinally, wherein an RF voltage with an RF capture amplitude is supplied to the curved rod electrode, and an end lens to which a DC voltage is supplied. The result is a potential well extending along the curved longitudinal axis of the C-trap 100. By applying the RF capture amplitude to the rod electrodes (generally quadrupoles, hexapole rods or octopole rods), the C-trap 100 stores ions in the capture volume. In other words, the C-trap 100 can be operated in an "RF only mode" for storing ions, i.e., there is no DC bias between the RF voltages. In some operating modes, a small DC bias can be applied to the rod electrodes. In some embodiments, the C-trap can be replaced with a rectangular ion trap with flat, longitudinally extending electrodes. C-traps used in accordance with embodiments of the present invention typically have an inscribed radius of 3 mm, a length of 25 to 30 mm, an injection slit of 0.8 mm width and 12 mm length, a thickness of 1 mm, and an end aperture of 2-2.5 mm inscribed diameter.

[0060] The cooled ions remain in a cloud toward the bottom of the potential well and are subsequently ejected orthogonally from the C-trap 100 to an orbital capture device 110 (such as the one sold by Thermo Fisher Scientific, Inc. Mass analyzer). For example, by turning off the RF trap voltage / amplitude and applying a DC pulse to one or more elongated longitudinal electrodes of the C-trap 100 to radially eject ions from the trap (e.g., a push-pull DC voltage can be applied to the elongated electrodes on opposite sides of the trap), the ions leave the C-trap 100. The ions are injected into the orbital trapping device 110 as a coherent packet-through an eccentric injection aperture. The ions are then trapped by the hyperlogarithmic electric field inside the orbital trapping device 110 and orbit around the inner electrode in the coherent packet. As the skilled person will appreciate, the ion packet is detected by imaging current and then a mass spectrum is obtained by fast Fourier transform.

[0061] Figure 2 Also shown is a fragmentation cell 120 which allows MS / MS analysis of the ions. WO-A-2006 / 103412 describes the method in more detail. Figure 2 A "dead-end" layout of the fragmentation cell 120 in which precursor ions are ejected axially from the C-trap 100 to the fragmentation cell 120 in a first direction, and the generated fragment ions are returned to the C-trap 100 in the opposite direction.

[0062] The mass spectrometer 10 is under the control of a controller 130, which is configured, for example, to set appropriate potentials to the electrodes of the quadrupole mass filter 70 to focus and filter ions; to set appropriate voltages to the electrode assemblies of the ion trap 100 to capture, store and eject ions; to collect mass spectral data from the orbital capture device 110, control the order of MS1 scans and MS2 scans, etc. It will be understood that the controller 130 may include a computer that operates according to a computer program containing instructions that cause the mass spectrometer 10 to perform the steps of the method of the present invention. The controller 130 may include a trigger circuit to initiate the application of an RF capture amplitude to the electrode assemblies of the ion trap 100. The controller 130 may include a clock for controlling the duration of each RF capture amplitude applied to the electrode assemblies of the ion trap 100. Information related to the mass range of ions to be collected by the ion trap 100 may be input into the controller 130.

[0063] Now combine Figure 3 and Figure 4 An exemplary first embodiment of the method is described. Figure 3 and Figure 4 In an embodiment of the present invention, the ion trapping component is Figure 2 1. The ion trap 100 is a C-trap. However, it will be appreciated that in other embodiments the ion trapping assembly may be a fragmentation cell 120, for example.

[0064] In step 401, sample molecules are ionized using the ESI source 20. The sample ions then enter the vacuum chamber of the mass spectrometer 10. The sample ions are directed by the capillary 25 to the S-lens 30 downstream of the ion source.

[0065] In step 402, ions are selected according to a first mass range (first m / z ratio range) (MR1). The first mass range (MR1) has a mass lower limit value and a mass upper limit value. The mass filter 70 is set to a wide pass mode by the controller 130. Ions are selected by an upstream ion device, which transmits ions of a selected mass range. The upstream ion device can be, for example, one or more of the RF components of the mass spectrometer 10 upstream of the ion trap 100, such as the S-lens 30, the injection flat rod 40, and the curved flat rod 50. If so, the RF amplitude applied to one or more of the RF components is adjusted so that the ions (MR1) in the first mass range pass through the S-lens 30, the injection flat rod 40, the curved flat rod 50, the quadrupole mass filter 70, the quadrupole exit lens / dividing lens layout 80 and pass through the transmission multipole 90 to the ion trap 100, as discussed above.

[0066] In step 403, ions within a first mass range (MR1) are introduced / injected into the ion trap 100, while a first RF amplitude (V1) is applied to the ion trap 100 by the controller 130. The ions within the first mass range (MR1) are trapped inside the ion trap 100 by a potential well generated by the first RF amplitude (V1). The potential well extends along a curved longitudinal axis of the ion trap, which is a C-trap 100. The first RF amplitude (V1) is relatively high, for example, 950 V. The first RF trapping amplitude (V1) is calculated based on the mass lower limit value of the first mass range (MR1).

[0067] In step 404, the ions in the first mass range (MR1) trapped in the ion trap 100 are cooled for a period of time. The trapped ions are cooled for a period of time sufficient for the trapped ions to reduce their kinetic energy so that they remain trapped when the RF trapping amplitude is reduced. The period of time may be, for example, 6 milliseconds. While the ions are being cooled, the controller 130 maintains the first RF trapping amplitude (V1) applied to the ion trap 100. The ions cool over this period of time by colliding with the inert gas inside the ion trap 100. As a result of the cooling, the kinetic energy of the ions decays and they relax toward the bottom of the potential well. In general, the ions become substantially thermalized in the ion trap by cooling.

[0068] In step 405, the RF trapping amplitude applied to the ion trap 100 is reduced from the first RF trapping amplitude (V1) to a lower second RF trapping amplitude (V2). By reducing the RF trapping amplitude, the potential well generated in the ion trap 100 has a lower potential barrier (the energy required for the ions to escape the potential well). However, as the ions in the first mass range have cooled and their kinetic energy has decayed, these ions still do not have enough energy to overcome the potential barrier. Therefore, when the RF trapping amplitude is reduced, the ions in the first mass range (MR1) remain trapped inside the ion trap 100. However, the lower second RF amplitude (V2) results in a smaller low mass cutoff (LMCO) of the ion trap compared to the first RF trapping amplitude that makes it possible to capture and store ions of smaller masses.

[0069] In step 406, ions within a second mass range (MR2) (a second m / z ratio range) are selected by an upstream ion device that transmits ions of the selected mass range. As discussed above, the upstream ion device can be, for example, one or more of the RF components of the mass spectrometer 10 upstream of the ion trap 100, such as the S-lens 30, the injection flat rod 40, and the bent flat rod 50. If so, the RF amplitude applied to one or more of the RF components is reduced so that the ions within the second mass range (MR2) pass through the S-lens 30, the injection flat rod 40, the bent flat rod 50, the quadrupole mass filter 70, the quadrupole exit lens / dividing lens layout 80 and pass through the transmission multipole 90 to the ion trap 100, as discussed above. The second mass range (MR2) has a lower mass limit value and an upper mass limit value. The lower mass limit value of the second mass range is lower than the low mass cutoff value (LMCO) of the ion trap 100 when the first RF capture amplitude (V1) is applied.

[0070] In step 407, ions in the second mass range (MR2) are introduced / injected while the controller 130 maintains the application of the lower second RF trapping amplitude (V2). The ions in the second mass range (MR2) are trapped inside the ion trap by the potential well generated by the second RF trapping amplitude (V2). The ions in the first mass range (MR1) have been sufficiently cooled in step 404 so that they do not have enough kinetic energy to escape the potential well generated by the second RF trapping amplitude (V2). Therefore, the ions in the first mass range (MR1) remain trapped inside the ion trap 100.

[0071] In step 408, the ions inside the ion trap 100 are cooled for a period of time while the second RF amplitude is maintained applied to the ion trap by the controller 130. The cooled ions remain in a cloud toward the bottom of the potential well.

[0072] In step 409, the RF trapping amplitude applied to the ion trap 100 may be automatically turned off and a DC pulse may be applied to the ion trap 100 to cause both ions in the first mass range (MR1) and ions in the second mass range (MR2) to be ejected from the ion trap 100 and into the orbital trap mass analyzer 110. Ejection of ions from an ion trap is well known.

[0073] In one example, the following RF amplitudes may be applied to select and trap ions in the first mass range (MR1): Figure 3 and Figure 4 402 and 403), the first mass range (MR1) has a mass lower limit of 155 m / z:

[0074] The RF amplitude applied to the S-lens (30) may be 98V;

[0075] The RF amplitude applied to the injection flat rod 40 may be 25V;

[0076] The RF amplitude applied to the quadrupole mass filter 70 may be 44V; and

[0077] The RF amplitude applied to the ion trap (C-trap) 100 may be 950V.

[0078] The following RF amplitudes may be applied for selecting and trapping ions in the second mass range (MR2): Figure 3 and Figure 4 406 and 407), the second mass range (MR2) has a mass lower limit of 40 m / z:

[0079] The RF amplitude applied to the S-lens (30) may be 51V;

[0080] The RF amplitude applied to the injection flat rod 40 may be 25V;

[0081] The RF amplitude applied to the quadrupole mass filter 70 may be 44V; and

[0082] The RF amplitude applied to the ion trap (C-trap) 100 may be 400V.

[0083] Figure 4 yes Figure 3 Graph of RF capture amplitude versus time for the method described in . Figure 4 In the embodiment of the present invention, the first RF trapping amplitude (V1) and the second RF trapping amplitude (V2) are applied for the same duration. Therefore, the injection and capture of ions in the first mass range (MR1) and the ion capture and injection of ions in the second mass range (MR2) occur for the same duration. Therefore, the intensity of ions measured for the first mass range (MR1) is proportional to the intensity of ions measured for the second mass range (MR2). Therefore, the mass spectrum obtained by the mass analyzer 110 is not distorted. Figure 4 As shown in , the RF capture amplitude is reduced from a first RF capture amplitude (V1) to a second RF capture amplitude (V2) discontinuously, ie, as a step change.

[0084] although Figure 3 and Figure 4The method shown in has been described for two different mass ranges, but the invention may be implemented using three, four, five or more different mass ranges. In practice, the method may include applying n additional RF trapping amplitudes to the ion trap 100, n being one or more. Each of these RF trapping amplitudes may be between the first and second RF trapping amplitudes. By applying n additional trapping amplitudes to the ion trap 100, each of the introduced ions having a corresponding nth mass range (m / z ratio range) will be trapped. The controller 130 maintains the current RF trapping amplitude for a period of time, which is sufficient for the ions inside the ion trap 100 to cool before reducing the RF trapping amplitude to a relatively lower trapping amplitude. The trapped ions are cooled for a period of time, which is sufficient for the trapped ions to reduce their kinetic energy so that they remain trapped when the RF trapping amplitude is reduced.

[0085] For example, the first and second RF trapping amplitudes (V1, V2) can be the same as those used in the method of the first embodiment. Thus, the mass range of ions ultimately trapped within ion trap 100 will be the same as in the first embodiment. However, each of the n additional RF trapping amplitudes can be an intermediate RF trapping amplitude, i.e., one between the first and second RF trapping amplitudes (V1, V2). According to Figure 5 and Figure 6 This arrangement is discussed in more detail. In this arrangement, instead of decreasing the RF capture amplitude directly from a first capture amplitude to a second capture amplitude, the RF capture amplitude is decreased stepwise through intermediate RF capture amplitudes. Thus, the RF capture amplitude varies less each time it is performed.

[0086] Alternatively, compared to the method of the first embodiment, n additional RF trapping amplitudes can be used to increase the mass range of ions ultimately trapped inside the ion trap 100. For example, one or more of the n additional RF trapping amplitudes may not be between the first and second RF trapping amplitudes. One or more of the n additional RF trapping amplitudes may be greater than the first RF trapping amplitude (V1). Therefore, before reducing the RF trapping amplitude to the first RF trapping amplitude (V1), by applying this larger RF trapping amplitude, it will be possible to capture ions with a larger mass than the upper mass limit of the first mass range (MR1). Alternatively or additionally, one or more of the n additional RF trapping amplitudes may be less than the second RF trapping amplitude (V2). By applying this lower RF trapping amplitude, the low mass cutoff of the ion trap 100 will be reduced. Therefore, by reducing the RF trapping amplitude to this lower RF trapping amplitude after applying the second RF trapping voltage (V2), it will be possible to trap ions having a smaller mass than the low mass cutoff of the ion trap (100) when applying the second RF trapping amplitude (V2).

[0087] In addition to applying an RF trapping amplitude greater than V1 and / or less than V2, as discussed above, one or more RF trapping amplitudes between V1 and V2 may also be applied.

[0088] Now combine Figure 5 and Figure 6 An exemplary second embodiment of the method is described, wherein ions are introduced and trapped in Figure 2 In the ion trap 100, the ion trap is a C-trap. The second embodiment method requires five different mass ranges and five corresponding RF trapping amplitudes.

[0089] Steps 601, 602, 603 and 604 are respectively Figure 3 Steps 401, 402, 403 and 404 are the same.

[0090] In step 605, the RF trapping amplitude applied to ion trap 100 is reduced from a first RF trapping amplitude (V1) to a relatively lower third RF trapping amplitude (V3).

[0091] In step 606, ions are selected according to a third mass range (MR3) (third m / z ratio range) having a lower mass limit value and an upper mass limit value. The lower mass limit value of the third m / z ratio range is lower than a low mass cutoff value of the ion trap 100 when the first RF trapping amplitude (V1) is applied. The low mass cutoff value (LMCO) of the ion trap 100 when the third RF trapping amplitude is applied is lower than the low mass cutoff value of the ion trap 100 when the first RF trapping amplitude (V1) is applied.

[0092] In step 607 , ions in the third mass range ( MR3 ) are introduced / injected and trapped inside the ion trap while the controller 130 maintains the application of the third RF trapping amplitude ( V3 ).

[0093] In step 608 , the ions inside the ion trap are cooled for a period of time while the third RF trapping amplitude ( V3 ) is maintained applied to the ion trap by the controller 130 .

[0094] In step 609, the RF trapping amplitude applied to ion trap 100 is reduced from the third RF trapping amplitude (V3) to a relatively lower fourth RF trapping amplitude (V4).

[0095] In step 610, ions are selected according to a fourth mass range (MR4) (fourth m / z ratio range) having a lower mass limit value and an upper mass limit value. The lower mass limit value of the fourth m / z ratio range is lower than the LMCO of the ion trap 100 when the third RF trapping amplitude (V3) is applied. The LMCO of the ion trap 100 when the fourth RF trapping amplitude (V4) is applied is lower than the LMCO of the ion trap 100 when the third RF trapping amplitude (V3) is applied.

[0096] In step 611 , ions in a fourth mass range ( MR4 ) are introduced / injected and trapped inside the ion trap while the controller 130 maintains application of a fourth RF trapping amplitude ( V4 ).

[0097] In step 612 , ions inside the ion trap are cooled for a period of time while a fourth RF trapping amplitude ( V4 ) is maintained applied to the ion trap by the controller 130 .

[0098] In step 613, the RF trapping amplitude applied to the ion trap is reduced from the fourth RF trapping amplitude to a relatively lower fifth RF trapping amplitude (V5).

[0099] In step 614, ions are selected according to a fifth mass range (MR5) (fifth m / z ratio range) having a lower mass limit value and an upper mass limit value. The fifth mass range (MR5) has a lower mass limit value and an upper mass limit value. The lower mass limit value of the fifth m / z ratio range is lower than the LMCO of the ion trap 100 when the fourth RF trapping amplitude (V4) is applied. The LMCO of the ion trap 100 when the fifth RF trapping amplitude (V5) is applied is lower than the LMCO of the ion trap 100 when the fourth RF trapping amplitude (V4) is applied.

[0100] In step 615, ions in the fifth mass range (MR5) are introduced / injected and trapped in the ion trap while the controller 130 maintains application of the fifth RF trapping amplitude (V5).

[0101] In step 616 , ions inside ion trap 100 are cooled for a period of time while the fifth RF trapping amplitude ( V5 ) is maintained applied to ion trap 100 by controller 130 .

[0102] In step 617, the RF trapping amplitude applied to the ion trap is reduced from the fifth RF trapping amplitude (V5) to a relatively lower second RF trapping amplitude (V2).

[0103] In step 618, ions are selected according to a second mass range (MR2) having a lower mass limit and an upper mass limit, similar to step 406. The lower mass limit of the second m / z ratio range is lower than the LMCO of the ion trap (100) when the fifth RF trapping amplitude (V5) is applied. The LMCO of the ion trap (100) when the second RF trapping amplitude (V2) is applied is lower than the LMCO of the ion trap 100 when the fifth RF trapping amplitude (V5) is applied.

[0104] In step 619, ions in the second mass range (MR2) are introduced / injected and trapped in the ion trap while the controller 130 maintains application of the lower second RF trapping amplitude (V2).

[0105] In step 620 , ions inside ion trap 100 are cooled for a period of time while a second RF trapping amplitude ( V2 ) is maintained applied to ion trap 100 by controller 130 .

[0106] In step 621, the RF trapping amplitude applied to the ion trap 100 may be automatically turned off and a DC pulse may be applied to the ion trap 100 to cause ions in the first, second, third, fourth and fifth mass ranges (MR1, MR2, MR3, MR4, MR5) to be ejected from the ion trap 100 and into the orbital trapping mass analyzer 110. The ejection of ions from the ion trap 100 is well known.

[0107] Steps 605, 609, 613 and 617 are similar to Figure 3 Step 405. By reducing the RF trapping amplitude, the potential well generated in the ion trap 100 has a lower potential barrier. However, as the ions inside the ion trap have cooled and their kinetic energy decays, these ions still do not have enough energy to overcome the potential barrier. Therefore, when the RF trapping amplitude is reduced, the ions remain trapped inside the ion trap 100.

[0108] Steps 606, 610, 614 and 618 are similar to Figure 3 Step 406. Ions are selected by an upstream ion device. The upstream ion device can be, for example, one or more of the RF components of the mass spectrometer 10 upstream of the ion trap 100, such as the S-lens 30. If so, the RF amplitude applied to one or more of the RF components is adjusted so that ions within the selected mass range pass through the S-lens 30, the injection flat rod 40, the bent flat rod 50, the quadrupole mass filter 70, the quadrupole exit lens / splitter lens arrangement 80 and through the transmission multipole 90 to the ion trap 100, as discussed above.

[0109] Steps 607, 611, 615 and 619 are similar to Figure 3 Step 407.

[0110] Steps 608, 612, 616 and 620 are similar to Figure 3 Step 404. By cooling the trapped ions before lowering the RF trapping amplitude, the cooled ions do not have enough kinetic energy to escape the potential well generated by the relatively low RF trapping amplitude. Therefore, the trapped ions remain trapped inside ion trap 100.

[0111] Figure 6 yes Figure 5 RF capture amplitude versus time for the method described in . Figure 6In the embodiment of the present invention, the first, second, third, fourth and fifth RF trapping amplitudes (V1, V2, V3, V4, V5) are each applied for the same duration. Therefore, the injection and trapping of ions in each mass range occur for the same duration. Therefore, the intensities of ions measured for each mass range are proportional to each other. Figure 6 As shown in , each reduction in the RF capture amplitude is performed discontinuously. Figure 6 , the third, fourth and fifth RF capture amplitudes (V3, V4, V5) are each equally spaced between the first and second RF capture amplitudes (V1, V2).

[0112] As discussed above, Figure 1 is a graph of the RF amplitude applied during injection and storage versus the ion intensity inside the C-trap according to the prior art method. For this graph, the same RF amplitude is applied to the C-trap used for injection and storage of ions. Each line of the graph represents an ion of different mass. It can be seen that ions with greater mass have lower intensities at lower RF trapping amplitudes. As discussed in the background section above, the pseudopotential generated by a certain RF voltage decreases in intensity with increasing mass.

[0113] Figure 7 is a graph of the second RF trapping amplitude (V2) applied to the C-trap 100 versus the ion intensity according to the method of the first embodiment of the present invention. For this graph, ions are introduced and trapped in the C-trap 100 at a first RF trapping amplitude (V1) of 1500V. The ions are then cooled. Subsequently, the RF trapping amplitude is reduced to a second RF trapping amplitude (V2) (as shown on the x-axis of the graph) before the ions are ejected from the C-trap 100. Each line represents an ion of a different mass. Compare Figure 1 and Figure 7 By trapping more massive ions (e.g., m / z 1722) at a relatively high RF trapping amplitude (1500 V) and cooling them prior to storage at a lower RF trapping amplitude (e.g., 500 V), the intensity of these ions is greater than that achieved by trapping and storing more massive ions at a single RF trapping amplitude (e.g., 500 V). Figure 7 It is also confirmed that the pseudowell depth required to trap ions is indeed greater than the pseudowell depth required to store ions (ie after the ions have been cooled).

[0114] Figure 8is a plot of the observed trapped mass range (MR) versus the automatic gain control (AGC) target (i.e., target number of trapped particles) obtained using a calibration sample (Calmix). Calmix includes solutions of caffeine (m / z 195), MRFA peptides (m / z 524), and Ultramark polymers (m / z 1122, 1222, ... 1722). MR is the ratio of the highest (last) mass (lm) / lowest (first) mass (fm) trapped in the ion trap. The AGC target represents the space charge (total number of ions) inside the ion trap. In the plot, the expected MR (Exp.MR) at a given RF setting is marked for comparison with the experimentally observed value. The second RF trapping amplitude applied to the ion trap in all measurements was 300 V, corresponding to a first mass (fm) of 40. Figure 8 It is shown that for a given expected mass range above a threshold, the observed trapped mass range (MR) decreases as the total number of ions in the ion trap increases. Figure 8 It is thus shown that the mass range of the trapping (using multiple RFs during trapping according to the invention) depends on the space charge and that this dependence is different for different mass ranges (different RF settings). Since the mass range of the trapped ions depends on the first and second RF amplitudes and / or the first and second RF frequencies applied to the ion trap, in embodiments the total number of trapped ions in the ion trap is kept below a threshold value determined as a function of the first and second RF trapping amplitudes and / or the first and second RF trapping frequencies applied to the ion trap (e.g. as a function of the ratio of the first and second RF trapping amplitudes and / or the first and second RF trapping frequencies). Thus, Figure 8 Shows how the user might weigh the trade-off between the widest mass range in a spectrum and the highest signal-to-noise (S / N) ratio. The latter is very important for depth of analysis and quantitation. For example, if the desired mass range is 40, then the total number of random ions could be 1x10 6 If, on the other hand, a mass range of only 30 is required, the total number of ions can be further increased to 1.25x10 6 And the S / N of trace components can be improved.

[0115] Figures 9(a) and 9(b) show that the method of the present invention achieves an increased usable mass range for the ion trap. Figure 9(a) describes the mass spectrum of a sample obtained using the prior art method, wherein the ions were injected and trapped at a single RF capture amplitude (300V) using the calibration sample Calmix discussed above. Figure 9(b) describes the mass spectrum of the same sample as Figure 9(a) obtained according to the method of the present invention, wherein the first RF capture amplitude (V1) is 1000V and the second RF capture amplitude (V2) is 300V. The time period for changing the electronics to reduce the RF capture amplitude from the first RF capture amplitude (V1) to the second RF capture amplitude (V2) can be 0.5 to 2 milliseconds. The ions are collisionally cooled during the time it takes to change the electronics to reduce the RF capture amplitude and also within a time period similar to the time required to change the electronics (several milliseconds). It can be seen in Figure 9(a) that the mass spectrum contains ions up to m / z 200, i.e., ions of greater mass have decayed. 9(b), the mass spectrum contains ions up to m / z=540, ie ions of greater mass have been trapped and thus detected by the analyser 110. Thus, the method of the invention increases the usable mass range of the ion trap 100.

[0116] Although it has been described with respect to a single ion trap Figures 3 to 6 Although the method used in the present invention is particularly advantageous, in a particularly advantageous embodiment of the present invention, multiple ion traps and / or ion cooling devices can be used in an ion trap assembly.

[0117] Now we will use the ion cooling device ( Figure 2 fragmentation cell 120) and ion trap ( Figure 2 ion trap 100, which is a C-trap), combined with Fig.10 and Fig.11 An exemplary third embodiment of the method is described. The fragmentation cell 120 includes an RF trapping device, such as an RF multipole, so that the fragmentation cell 120 can be operated according to the present invention. The fragmentation cell 120 is operated at a higher pressure than the ion trap 100 and in a low fragmentation mode (low fragmentation includes a mode without fragmentation).

[0118] In step 1001, sample molecules are ionized using the ESI source 20. The sample ions then enter the vacuum chamber of the mass spectrometer 10. The sample ions are guided by the capillary 25 to the S-lens 30 downstream of the ion source.

[0119] In step 1002, ions are selected according to a first mass range (first m / z ratio range) (MR1). The first mass range (MR1) has a lower mass limit and an upper mass limit. The mass filter 70 is set to a wide pass mode by the controller 130. Ions are selected by an upstream ion device, which transmits ions of a selected mass range. The upstream ion device can be, for example, one or more of the RF components of the mass spectrometer 10 upstream of the ion trap 100, such as the S-lens 30, the injection flat rod 40, and the curved flat rod 50. If so, the RF amplitude applied to one or more of the RF components is adjusted so that the ions (MR1) in the first mass range pass through the S-lens 30, the injection flat rod 40, the curved flat rod 50, the quadrupole mass filter 70, the quadrupole exit lens / dividing lens layout 80 and pass through the transmission multipole 90 to the ion trap 100, as discussed above.

[0120] In step 1003, ions within the first mass range (MR1) are introduced / injected into the ion trap 100. The introduced ions within the first mass range (MR1) pass through the ion trap 100 to the fragmentation cell 120, and at the same time, a first RF trapping amplitude (V1) is applied to the fragmentation cell 120 and a corresponding first RF trapping amplitude (V1) is applied to the ion trap 100 by the controller 130. The corresponding first RF trapping amplitude is applied to the ion trap 100 by the controller 130, so that the low mass cutoff value of the ion trap 100 is the same as the low mass cutoff value of the fragmentation cell in step 1003. The ion trap 100 acts as an ion guide, so that ions within the first mass range (MR1) are not trapped in the ion trap 100, but are transmitted through the ion trap 100 to the fragmentation cell 120. The controller 130 can control the RF trapping amplitude applied to the ion trap 100 independently of the RF trapping amplitude applied to the fragmentation cell 120. Alternatively, the RF trapping amplitude can control the RF trapping amplitude applied to the fragmentation cell 120 and the ion trap 100 simultaneously. In step 1003, ions in the first mass range (MR1) are transmitted to the fragmentation cell 120 with minimal additional energy to prevent fragmentation of the transmitted ions. In practice, the difference in DC voltage applied to the ion trap 100 and to the fragmentation cell 120 is minimized to prevent fragmentation during transmission. For example, the DC bias of the ion trap 100 can be 0V and the DC bias of the fragmentation cell 120 can be -2V. In step 1003, once transmitted to the fragmentation cell 120, the ions in the first mass range (MR1) are trapped in the fragmentation cell 120 by the potential well generated by the first RF trapping amplitude (V1) applied to the fragmentation cell 120. The first RF trapping amplitude (V1) is relatively high, for example, 950V. The first RF trapping amplitude (V1) is calculated based on the mass lower limit value of the first mass range (MR1).

[0121] In step 1004, ions in the first mass range (MR1) trapped in the fragmentation cell 120 are cooled for a period of time inside the fragmentation cell 120 while a first RF trapping amplitude (V1) is applied to the fragmentation cell 120. During step 1004, a corresponding first RF trapping amplitude may optionally be applied to the ion trap 100.

[0122] In step 1005, ions in the first mass range (MR1) trapped inside the fragmentation cell 120 are transferred from the fragmentation cell 120 to the ion trap 100 while applying a first RF trapping amplitude (V1) to the fragmentation cell 120 and a corresponding first RF trapping amplitude to the ion trap 100. The ions in the first mass range (MR1) are transferred to the ion trap 100 with minimal additional energy, thereby preventing fragmentation of the transferred ions.

[0123] In step 1006, ions within the first mass range (MR1) that have been transported back to the fragmentation cell 100 are trapped in the ion trap 100 by the potential well generated by the corresponding first RF trapping amplitude applied to the ion trap 100. During step 1006, the first RF trapping amplitude (V1) may optionally be applied to the fragmentation cell 120.

[0124] In step 1007, the ions in the first mass range (MR1) that have been transported back to the fragmentation cell 100 and trapped therein are cooled for a period of time inside the ion trap 100 while a corresponding first RF trapping amplitude is applied to the ion trap 100. The trapped ions are cooled for a period of time that is sufficient for the trapped ions to reduce their kinetic energy so that they remain trapped when the RF trapping amplitude is reduced. This period of time can be, for example, 6 milliseconds. While the ions are being cooled, the controller 130 maintains the application of the corresponding first RF trapping amplitude (V1) to the ion trap 100. The ions cool over this period of time by colliding with the inert gas inside the ion trap 100. As a result of the cooling, the kinetic energy of the ions decays and they relax toward the bottom of the potential well. In general, the ions become substantially thermalized in the ion trap 100 by cooling. During step 1007, the first RF trapping amplitude (V1) can optionally be applied to the fragmentation cell 120.

[0125] In step 1008, the RF trapping amplitude applied to the ion trap 100 is reduced from a corresponding first RF trapping amplitude (V1) to a lower second RF trapping amplitude (V2). By reducing the RF trapping amplitude, the potential well generated in the ion trap 100 has a lower potential barrier (the energy required for the ions to escape the potential well). However, as the ions in the first mass range have cooled and their kinetic energy has decayed, these ions still do not have enough energy to overcome the potential barrier. Therefore, when the RF trapping amplitude is reduced, the ions in the first mass range (MR1) remain trapped inside the ion trap 100. However, compared to the first RF trapping amplitude that makes it possible to capture and store ions of smaller masses, the lower second RF amplitude (V2) results in a smaller low mass cutoff (LMCO) of the ion trap 100. The RF trapping amplitude applied to the fragmentation cell 120 can be controlled independently of the RF trapping amplitude applied to the ion trap. For example, during step 1008, the RF trapping amplitude applied to the fragmentation cell 120 may be maintained at the first RF trapping amplitude (V1). Alternatively, in step 1008, the RF trapping amplitude applied to the fragmentation cell 120 may be decreased synchronously with the RF trapping amplitude applied to the ion trap 100. For example, in step 1008, the RF trapping amplitude applied to the fragmentation cell 120 may be decreased from the first RF trapping amplitude (V1) to a corresponding second RF trapping amplitude. The low mass cutoff value of the fragmentation cell 120 when the corresponding second RF trapping amplitude is applied to the fragmentation cell 120 is the same as the low mass cutoff value of the ion trap 100 when the second RF trapping amplitude (V2) is applied to the ion trap 100.

[0126] In step 1009, ions in a second mass range (MR2) (a second m / z ratio range) are selected by an upstream ion device that transmits ions in the selected mass range. As discussed above, the upstream ion device can be, for example, one or more of the RF components of the mass spectrometer 10 upstream of the ion trap 100, such as the S-lens 30, the injection flat rod 40, and the bent flat rod 50. If so, the RF amplitude applied to one or more of the RF components is reduced so that the ions in the second mass range (MR2) pass through the S-lens 30, the injection flat rod 40, the bent flat rod 50, the quadrupole mass filter 70, the quadrupole exit lens / dividing lens layout 80 and pass through the transmission multipole 90 to the ion trap 100, as discussed above. The second mass range (MR2) has a lower mass limit value and an upper mass limit value. The lower mass limit value of the second mass range is lower than the low mass cutoff value (LMCO) of the ion trap 100 when the first RF capture amplitude (V1) is applied.

[0127] In step 1010, ions in the second mass range (MR2) are introduced / injected into the ion trap 100 while the controller 130 maintains the application of the lower second RF trapping amplitude (V2). The ions in the second mass range (MR2) are trapped inside the ion trap 100 by the potential well generated by the second RF trapping amplitude (V2). The ions in the first mass range (MR1) have been sufficiently cooled in step 1007 so that they do not have enough kinetic energy to escape the potential well generated by the second RF trapping amplitude (V2). Therefore, the ions in the first mass range (MR1) remain trapped inside the ion trap 100.

[0128] In step 1011, the ions inside the ion trap 100 are cooled for a period of time while the second RF amplitude is maintained to the ion trap 100 by the controller 130. The cooled ions remain in a cloud toward the bottom of the potential well. The cooling of the ions inside the ion trap 100 can occur due to collisions between trapped ions in the first mass range (MR1) and trapped ions in the second mass range (MR2).

[0129] In step 1012, the RF trapping amplitude applied to the ion trap 100 may be automatically turned off and a DC pulse may be applied to the ion trap 100 to cause both ions within the first mass range (MR1) and ions within the second mass range (MR2) to be ejected from the ion trap 100 and into the orbital capture mass analyzer 110. It is well known that ions are ejected from the ion trap 100. Therefore, the trapped ions within the first mass range (MR1) and the trapped ions within the second mass range (MR2) may be analyzed together to generate a single mass spectrum having a mass range spanning both the first and second mass ranges (MR1, MR2).

[0130] The low mass cutoff of an ion trap or fragmentation cell depends on the RF trapping amplitude applied to it and on the inscribed radius of the ion trap / fragmentation cell. Fig.10 In the embodiment of FIG. 1 , when the same RF trapping amplitude is applied to the ion trap 100 and the fragmentation cell 120, they have the same low mass cutoff value. Fig.10 In the embodiment of , the corresponding first RF capture amplitude and the first RF capture amplitude (V1) are the same. Similarly, in Fig.10 In an alternative embodiment, the ion trap 100 and the fragmentation cell 120 may have different inscribed radii. In such an embodiment, in order to achieve the same low mass cutoff value for the ion trap 100 as for the fragmentation cell 120, a different RF trapping amplitude needs to be applied to the ion trap. Therefore, the corresponding first RF trapping amplitude and the first RF trapping amplitude (V1) will be different. Similarly, the corresponding second RF trapping amplitude and the second RF trapping amplitude (V2) will be different.

[0131] Typically, the ion trap (ion trap 100) is maintained at a lower pressure than the ion cooling device (fragmentation cell 120), for example, at least 1 or at least 2 orders of magnitude lower. More typically, the pressure in the fragmentation cell 120 times the length of the fragmentation cell 120 is significantly higher than the pressure of the ion trap 100 times the length of the ion trap 100. This ensures efficient capture and transfer of high-m / z ions, such as intact proteins or protein complexes.

[0132] Fig.11 yes Fig.10 FIG. 1 is a graph of the RF trapping amplitude versus time applied to the fragmentation cell 120 and the ion trap 100 for the method described in FIG. 1 . As discussed above, in Fig.10 In an embodiment of the present invention, the corresponding first RF capture amplitude and the first RF capture amplitude (V1) are the same. Similarly, the corresponding second RF capture amplitude and the second RF capture amplitude (V2) are the same. Fig.11 In the embodiment of the present invention, the first RF trapping amplitude (V1) and the second RF trapping amplitude (V2) are applied for the same duration for injecting and trapping ions. Therefore, the injection and trapping of ions in the first mass range (MR1) and the injection and trapping of ions in the second mass range (MR2) occur for the same duration. Therefore, the intensity of ions measured for the first mass range (MR1) is proportional to the intensity of ions measured for the second mass range (MR2). Therefore, the mass spectrum obtained by the mass analyzer 110 is not distorted. Fig.11 It is also shown that the transfer of ions in the first mass range (MR1) from the fragmentation cell 120 to the ion trap 100 occurs before the RF trapping amplitude is reduced to the second RF trapping amplitude (V2) and before ions in the second mass range (MR2) are trapped in the ion trap 100. Fig.11 As shown in , the RF capture amplitude is reduced from a first RF capture amplitude (V1) to a second RF capture amplitude (V2) discontinuously, i.e., as a step change. Alternatively, the RF capture amplitude reduction may occur over a longer period of time, so that the RF amplitude reduction occurs as a gradient change rather than a step change.

[0133] Fig.10 and Fig.11Embodiments of the invention may be particularly useful for addressing the challenges faced when performing mass analysis under high ion load conditions. High load conditions are common when measuring particularly challenging samples. In known arrangements for high ion load conditions, particularly in proteomics applications based on liquid chromatography-mass spectrometry, deposition of untransmitted or untrapped ions with relatively high m / z may occur when ions are trapped in the ion trap / fragmentation cell. Deposition occurs when ions collide with the rods and lenses of the ion trap / fragmentation cell due to space charge effects or unstable trajectories and leave residues thereon. Deposition leads to charging effects that may degrade system performance. In fact, if the deposit forms an insulating layer, the deposit may be charged by particles that subsequently collide. This will produce field disturbances, thereby changing the ion trajectory and causing ions to be lost from the ion capture component.

[0134] exist Fig.10 and Fig.11 In an embodiment of the present invention, ions are separated into ions in a first mass range (MR1) (ions with relatively high m / z) and ions in a second mass range (MR2) (ions with relatively low m / z) upstream of the ion trap 100 and the fragmentation device 120. The ion separation makes it possible to optimize the trapping conditions and the transmission conditions for the ions with relatively high m / z (ions in the first mass range) and the ions with relatively low m / z (ions in the second mass range).

[0135] Ions in the first mass range (MR1) are trapped in a longer trapping volume because the ions in the first mass range (MR1) are passed through the ion trap 100 to the fragmentation cell 120 and are trapped inside the fragmentation cell 120. By passing the ions through the ion trap into the fragmentation cell, the RF potential and DC potential applied to the lens upstream of the ion trap can focus the ions and accelerate them into the ion trap, thereby reducing the deposition of large mass ions on the corresponding lenses. The lens upstream of the ion trap is, for example, the S-lens 30 and the TK lens 50 or the entrance lens of the ion trap itself. In fact, if the ions are instead trapped in a relatively short volume of the ion trap alone, the DC potential applied to the entrance lens of the trap will need to decelerate the ions passing therethrough. The ions are also trapped at a higher pressure because the fragmentation cell 120 operates at a higher pressure than the C-trap 100. Providing a longer, higher pressure trapping volume for ions with relatively high m / z improves the cooling of ions with relatively high m / z and thus reduces the deposition of ions with relatively high m / z during trapping. Longer, higher pressure trapping volumes are particularly preferred for intact proteins, for example, which have relatively long stopping paths. Indeed, due to the high momentum of intact proteins, the number of collisions required to cool the ions is higher, which, assuming a fixed pressure, requires a longer trapping path / distance than for smaller species. Thus, Fig.10 and Fig.11The embodiment enables mass analysis over a large mass range and reduces deposition of ions with relatively high m / z under high load conditions. The lower pressure of the ion trap 100 compared to the fragmentation cell 120 may be advantageous because the co-trapped ions of the first and second mass ranges (MR1 and MR2) are subsequently accelerated out of the ion trap 100 to the mass analyzer 110.

[0136] exist Fig.10 and Fig.11 In an embodiment of the present invention, ions in the first mass range (MR1) are transferred from the fragmentation cell 120 to the ion trap 100 for subsequent mass analysis. The transfer of the captured ions to the ion trap 100 requires the addition of additional energy to the captured ions. Therefore, before the ions are transferred from the fragmentation cell 120 to the ion trap 100, the captured ions in the first mass range (MR1) are cooled (step 1004). The captured ions are cooled for a period of time sufficient for the captured ions to reduce their kinetic energy so that they remain inside the ion capture assembly during the transfer of the ions to the ion trap 100. The ions in the second mass range (MR2) are not transferred along with the ions in the first mass range (MR1). In fact, after the ions in the first mass range (MR1) have been transferred to the ion trap 100, captured therein, and cooled, the ions in the second mass range (MR2) are directly injected into the ion trap 100. By transferring the ions in the first mass range (MR1) while not transferring the ions in the second mass range (MR2), ion losses during transfer are prevented. In practice, ions in the first mass range (MR1) are transmitted while applying a first RF trapping amplitude to the ion trap 100 and the fragmentation cell 120. The first RF trapping amplitude (V1) generates a potential well having a barrier sufficient to prevent ions in the first mass range (MR1) from escaping.

[0137] If ions in the second mass range (MR2) are also simultaneously transmitted to the ion trap 100 when the first RF trapping amplitude (V1) is applied, ions in the second mass range (MR2) will be lost. In fact, ions below the low mass cutoff of the ion trap 100 / fragmentation cell 120 when the first RF trapping amplitude is applied will be lost. If ions in the first mass range (MR1) are transmitted to the ion trap 100 at the second RF trapping amplitude (V2) along with ions in the second mass range (MR2) while cooled, some ions in the first mass range (MR1) will be lost. The potential well generated by the second RF trapping amplitude (V2) has a lower potential barrier (energy required for ions to escape the potential well) than the potential well generated by the first RF trapping amplitude (V1). Therefore, ions in the first mass range (MR1) with the additional energy imparted during transmission will have sufficient energy to escape the potential well generated by the second RF trapping amplitude (V2). Therefore, some ion losses in the first mass range (MR1) may occur during transmission.

[0138] Comparison of Figures 12(a) and 12(b) demonstrates the trade-off between maximizing mass range and providing a longer, higher pressure trapping volume for relatively more massive ions. Figure 3 and Figure 4 12( b ) shows the mass spectrum obtained when performing ion trapping in the fragmentation cell 120 and transferring ions in the first and second mass ranges to the ion trap 100 together while applying a second RF trapping amplitude (V2). Fig.10 and Fig.11 The mass spectrum obtained when the method is used. Using the calibration sample Calmix discussed above, the mass spectra of Figures 12(a) and 12(b) were obtained. When comparing Figures 12(a) and 12(b), it can be seen in Figure 12(a) that only ions with m / z up to 622 are analyzed. In fact, ions with m / z greater than 622 have been lost during the transmission of ions to the ion trap 100. In Figure 12(b), ions with m / z of 42 to at least 1422 have been trapped in the same trapping component and analyzed at the same time. Therefore, Figure 12(b) shows that Fig.10 and Fig.11 The embodiment makes it possible to capture relatively large mass ions in a longer, higher pressure trapping volume while also maximizing the mass range analyzed. Thus, the conditions for capturing relatively high mass ions (ions in the first mass range) (MR1) and relatively smaller mass ions (ions in the second mass range) (MR2) are optimized, making it possible to analyze large mass and small mass ions together.

[0139] Although FIG. 12(a) and FIG. 12(b) illustrate the adjacent Figure 2The ion cooling device of the fragmentation cell 120 and the ion trap as its ion trap 100, but the present invention may be equally used with other combinations of adjacent ion trapping / cooling devices. The ion cooling device may be an ion trap, such as a C-trap. The ion trap may be a first ion trap and the ion cooling device may be a second ion trap.

[0140] Although it has been compared with Fig.10 and Fig.11 The ion trap described in the embodiment is described as a C-trap 100, but the ion trap may be an ion trap that is also configured to perform mass analysis. Therefore, the mass analysis described in step 1012 may be performed in the ion trap, so there is no need to eject the trapped ions for mass analysis.

[0141] like Figure 2 As shown in FIG. 1 , the ion cooler (fragmentation cell 120) is downstream of the ion trap 100. However, the present invention may equally be used with an ion trap downstream of the ion cooler.

[0142] Fig.10 and Fig.11The introduction and capture of ions within the second mass range (MR2) in the ion trap 100 is described. Alternatively, the ions within the second mass range (MR2) can be introduced and captured in an ion cooling device (fragmentation cell 120) and then transferred to the ion trap 100 (similar to steps 1002-1005). In this embodiment, once the ions within the first mass range (MR1) have been cooled in the ion trap 100 (step 1007), the RF capture amplitude applied to the fragmentation cell 120 is reduced to a corresponding second RF capture amplitude. The low mass cutoff value of the fragmentation cell 120 when the corresponding second RF capture amplitude is applied to the fragmentation cell 120 is the same as the low mass cutoff value of the ion trap 100 when the second RF capture amplitude is applied to the ion trap 100. The ions within the second mass range (MR2) are selected upstream of the fragmentation cell 120 and the ion trap 100 (step 1009). Ions in the second mass range (MR2) are then introduced into the fragmentation cell 120 and trapped in the fragmentation cell 120 by applying a corresponding second RF trapping amplitude to the fragmentation cell 120. The ions in the second mass range (MR2) are then cooled and subsequently transferred to the ion trap 100 while applying a corresponding second RF trapping amplitude to the fragmentation cell 120 and applying a second RF trapping amplitude (V2) to the ion trap 100. The ions in the second mass range (MR2) are then trapped in the ion trap 100 by the second RF trapping amplitude (V2). Once trapped, the trapped ions in the first and second mass ranges are cooled together. The ions in the first mass range (MR1) and the ions in the second mass range (MR2) can be ejected from the ion trap 100 to the mass analyzer 110 together. This method can be performed using three, four, five or more different mass ranges. In fact, the method can include applying n additional RF trapping amplitudes to the fragmentation cell 120, n being one or more. Each of these RF trapping amplitudes can be between the first and second RF trapping amplitudes. Each of the ions introduced into the fragmentation cell 120 and having a corresponding nth mass range (m / z ratio range) is trapped by applying n additional trapping amplitudes to the fragmentation cell 120. The controller 130 maintains the current RF trapping amplitude applied to the fragmentation cell 120 and to the ion trap 100 for a period of time sufficient for the ions inside the fragmentation cell 120 to cool, be transported to and trapped in the ion trap 100, and cool inside the ion trap 100 before reducing the RF trapping amplitude to a relatively lower trapping amplitude. Once transported to the trap 100, the ions cool therein for a period of time sufficient for the trapped ions to reduce their kinetic energy so that they remain trapped when the RF trapping amplitude is reduced.

[0143] Each of the n additional RF capture amplitudes may be an intermediate RF capture amplitude, i.e., those between the first and second RF capture amplitudes (V1, V2). In this arrangement, instead of dropping the RF capture amplitude directly from the first capture amplitude to the second capture amplitude, the RF capture amplitude is stepped down through the intermediate RF capture amplitudes. Thus, the RF capture amplitude varies less each time it is performed.

[0144] Alternatively, with Fig.10 and Fig.11 Compared to the method of , n additional RF trapping amplitudes can be used to increase the mass range of ions ultimately trapped within the ion trap assembly. For example, one or more of the n additional RF trapping amplitudes may not be between the first and second RF trapping amplitudes. One or more of the n additional RF trapping amplitudes may be greater than the first RF trapping amplitude (V1). Therefore, before reducing the RF trapping amplitude to the first RF trapping amplitude (V1), by applying this larger RF trapping amplitude, it will be possible to capture ions with a larger mass than the upper mass limit of the first mass range (MR1). Alternatively or additionally, one or more of the n additional RF trapping amplitudes may be less than the second RF trapping amplitude (V2). By applying this lower RF trapping amplitude, the low mass cutoff of the ion trap assembly will be reduced. Therefore, by reducing the RF trapping amplitude to this lower RF trapping amplitude after applying the second RF trapping voltage (V2), it will be possible to trap ions having a lower mass than the low mass cutoff of the ion trap assembly when applying the second RF trapping amplitude (V2).

[0145] The RF trapping amplitude applied to the ion cooler and ion trap may be varied synchronously, for example where both devices are connected to the same RF power supply. Alternatively, the RF trapping amplitude applied to the ion cooler may be controlled independently of the RF trapping amplitude applied to the ion trap.

[0146] It should be understood that in reference to Figure 2 , Fig.10 and Fig.11 In the described embodiment, ions are introduced into the ion cooler (fragmentation cell 120) in one direction and then transported from the ion cooler to the ion trap 100 in the opposite direction, ie, the ions change direction.

[0147] In some other embodiments, ions do not need to change direction when transported between devices within the ion trap assembly. Fig.13 Schematic of the Orbitrap from Thermo Fisher Scientific TM FusionLumos mass spectrometer 15, which Figure 2Components common to the apparatus are given similar reference numerals, and the ion cooling apparatus / ion trap may be equipped with a dual-pressure linear ion trap 1140. In this case, the high-pressure ion trap 1120 may be the ion cooling apparatus and the low-pressure ion trap 1110 may be the ion trap. In this embodiment, the ions do not need to change direction. For example, referring to Fig.10 and Fig.11 , the first and second RF trapping amplitudes are applied to the ion cooler (high pressure ion trap 1120) and the ion trap (low pressure ion trap 1110) in the manner described above. The difference is that the ions are introduced from the ion source 20 into the ion cooler (high pressure ion trap 1120) in one direction and then transported from the ion cooler 1120 to the ion trap (low pressure ion trap 1110) in the same direction, i.e., the ions do not change direction. It will be appreciated that Figure 2 The description of the mass spectrometer components shown in FIG. 1 applies equally to Fig.13 Components of the mass spectrometer shown in FIG. 1 have like reference numerals.

[0148] In some embodiments, the method includes ejecting the trapped ions from the ion trap assembly and optionally transmitting the ejected ions to a mass analyzer. In a variation of any of the above embodiments, the ion trap and the mass analyzer can be the same device, i.e., so that there is no ejection from the ion trap to the mass analyzer. For example, in Fig.13 In the embodiment shown, the low pressure ion trap 1110 is a mass analyzing ion trap having a detector 1115 .

[0149] In some embodiments, the ion cooling device (which may also be configured to fragment the ions) may be a fragmentation cell 105 upstream of the ion trap, such as Fig.13 Orbitrap shown TM The fragmentation cell 105 may be an ion cooler, the high pressure ion trap 1120 may be an ion trap that receives ions transmitted from the ion cooler (fragmentation cell 105), and the low pressure ion trap 1110 may be a mass analyzer that receives trapped ions ejected from the high pressure ion trap 1120. In this case, the ions do not need to be trapped in the ion cooler (fragmentation cell 105) and the ion cooler (fragmentation cell 105) may be operated in a transmission mode. For example, referring to Fig.10 and Fig.11 , the first and second RF trapping amplitudes are separately applied to the ion cooler and the ion trap in the manner described above.

[0150] In all of the described embodiments in which the RF trapping amplitude is decreased from a first trapping amplitude to a second trapping amplitude, it will be appreciated that the RF trapping frequency may alternatively (or additionally) be increased from the first trapping frequency to the second trapping frequency.

[0151] It will be appreciated that the ion trapping assembly may include one or more further electrode assemblies. At least one of the further electrode assemblies may be configured to fragment ions.

[0152] It should be understood that Figure 2 The controller 130 can be configured to control ion capture and fragmentation according to the methods described herein. For example, the controller 130 can be configured to control the RF capture amplitude / frequency applied to the electrode assembly of the ion trap and / or the electrode assembly of the fragmentation cell according to the methods described herein. The controller 130 can be configured to apply the RF capture amplitude to one or more additional electrode assemblies to transfer product ions and / or precursor ions from the electrode assembly configured to fragment ions to one or more additional electrode assemblies before or after reducing the RF capture amplitude applied to the electrode assembly configured to fragment ions.

[0153] It will be appreciated that the controller 130 may be configured to cause the ion trap assembly to eject trapped ions from the ion trap assembly. The mass spectrometer may further include a mass analyzer configured to receive ions ejected from the ion trap assembly and to mass analyze the ejected ions.

[0154] It should be understood that Figure 2 The specific arrangement of components shown in is not essential to the method described subsequently. In fact, other arrangements for implementing the ion trapping method of embodiments of the present invention are suitable.

[0155] Although relative to Q Hybrid Quadrupole The present invention is discussed in the context of a C-trap for a mass spectrometer, and it will be appreciated that the present invention is equally applicable to other ion traps used with or without a mass analyser. For example, the ion capture assembly may comprise a C-trap, an ion guide, a fragmentation cell, a linear ion trap, a 3D ion trap, a magnetic trap or an electrostatic trap. The present invention may be used in a linear ion trap (e.g., with curved electrodes or straight elongated electrodes) or even in a 3D (Paul type) ion trap. The ion trap may operate as an ion storage device without mass analysis of the ions, or it may operate in the context of mass analysis of the trapped ions, wherein the ion trap itself is a mass analyser. The ion trap is preferably an RF multipole ion trap, preferably a quadrupole, or a hexapole, or an octopole ion trap. In addition, in embodiments in which the ion trap is configured to eject stored ions into a mass analyzer for mass analysis of the ions, the mass analyzer need not be of the orbital capture type, but may be another type of mass analyzer, such as a time-of-flight (ToF) mass analyzer or an FT-ICR mass analyzer, or another type of ion trap mass analyzer, including an electrostatic ion trap mass analyzer.

[0156] The method steps of cooling the trapped ions have been described and shown in the accompanying drawings as a separate, manually programmed time period dedicated to cooling. Cooling may instead occur during the time period required to change the electronics to adjust the RF trapping amplitude / frequency. This may be the case if the time required to change the electronics to adjust the RF trapping amplitude / frequency is greater than the time required to reduce the energy of the trapped ions so that the trapped ions remain trapped while the RF trapping amplitude / frequency is changed. If so, the RF trapping amplitude / frequency may not be held constant while cooling the trapped ions. In fact, the RF trapping amplitude may be reduced immediately after the ions are trapped at a relatively high RF trapping amplitude. Cooling will then occur during the adjustment of the electronics to reduce the RF trapping amplitude. Similarly, the RF trapping frequency may be increased after the ions are trapped at a relatively low RF trapping frequency. Cooling will then occur during the adjustment of the electronics to increase the RF trapping frequency. Typical cooling times may be on the order of at least 1-10 milliseconds, or at least 1-5 milliseconds, such as at least 1 millisecond, at least 2 milliseconds, or at least 3 milliseconds, or at least 4 milliseconds, or at least 5 milliseconds. In 1x10 -3 At a background pressure of mbar, typical cooling times for eg peptides and singly charged ions in the range 400-1000 Th will be a few milliseconds.

[0157] The method of the present invention can be started in any order or applied simultaneously with step 405 and step 406. For example, when the RF capture amplitude is reduced from a relatively high capture amplitude to a relatively low capture amplitude, the RF amplitude applied to other components of the mass spectrometer upstream of the ion trap can also be reduced at the same time. The same applies to Figure 5 and Figure 6 Methods and Fig.10 and Fig.11 For example, step 605 and step 606 may be started in any order or performed simultaneously. Similarly, step 1008 and step 1009 may be started in any order or performed simultaneously.

[0158] exist Figure 3 , Figure 5 and Fig.10 In the method, ions can be introduced as a continuous ion stream to the ion trap assembly while the other steps of the method are performed. Of course, only those ions in the relevant mass range will be selected by the upstream ion device when the relevant RF amplitude is applied. Similarly, only those ions in the relevant mass range will be trapped in the ion trap assembly when the relevant RF trapping amplitude is applied. By way of example, refer to Figure 3In the method, ions can be continuously introduced into the ion trap assembly while steps 402 to 408 are performed. Similarly, ions can be continuously introduced into the ion trap assembly while steps 602 to 620 are performed. Alternatively, the introduction of ions into the ion trap assembly can be performed intermittently. For example, while the RF trapping amplitude is reduced and / or cooling is performed, ions can be introduced into the ion trap assembly only when the relevant RF trapping amplitude is applied and stopped. By way of example, referring to Figure 3 In the method, the first ion introduction can be performed while performing step 402 and step 403. The ion introduction can be stopped while performing step 404 and step 405. The second ion introduction can be performed while performing step 406 and step 407. The ion introduction can be stopped while performing step 408 and step 409. Generally, the time of introducing ions into the ion capture assembly is controlled so as not to overfill the ion capture assembly, that is, to avoid the above relative Figure 8 The time of introducing ions into the ion trap assembly will generally therefore depend on the ion current.

[0159] Each mass range (MR) may or may not overlap with each other. By way of example, the first and second mass ranges (MR1, MR2) may overlap with each other. The intensity of ions inside the overlapping region may not be proportional to the intensity of ions outside the overlapping region. The controller 130 may be configured to compensate for this situation, thereby ensuring that the relative abundance in the resulting mass spectrum is not distorted by double counting of ions in the overlapping region.

[0160] Figure 4 , Figure 69 show that the RF trapping amplitude reduction occurs discontinuously. Alternatively, the RF trapping amplitude reduction may occur continuously. By continuously reducing the RF trapping amplitude, the LMCO of the ion trapping assembly is continuously reduced from the LMCO of a first RF trapping amplitude (V1) to the LMCO of a lower second RF trapping amplitude (V2). The lower mass limit value of the selected mass range transmitted by the upstream ion device may also be continuously reduced. For example, if the upstream ion device is one or more of the RF components upstream of the ion trapping assembly, such as the S-lens 30, the lower mass limit value of the selected mass range is continuously reduced by continuously reducing the RF amplitude applied to the RF components upstream of the ion trapping assembly. The RF trapping amplitude applied to the ion trapping assembly may be continuously reduced in synchronization with the reduction of the lower mass limit value of the selected mass range. Therefore, ions with decreasing m / z ratios pass through the transmission multipole 90, the S-lens 30, the injection flat rods 40, the bent flat rods 50, the quadrupole mass filter 70, the quadrupole exit lens / splitter lens arrangement 80, and are introduced and captured in the ion trap assembly. The rate at which the RF capture amplitude is reduced is selected by the controller 130 so that the ions with larger masses inside the ion trap assembly have sufficient time to reduce their kinetic energy, thereby reducing the RF capture amplitude to introduce ions with smaller mass ratios while they remain trapped in the ion trap assembly. Ions can be introduced into the ion trap assembly while reducing the RF capture amplitude. Ions can be continuously introduced into the ion trap assembly while applying the RF capture amplitude. Alternatively, ions can be intermittently introduced into the ion trap assembly as a series of multiple injections to avoid overfilling the ion trap assembly. Generally, the time at which ions are introduced into the ion trap assembly is controlled so as not to overfill the ion trap assembly, that is, to avoid overfilling the ion trap assembly relative to the above. Figure 8 The space charge effect discussed. The time for introducing ions into the ion trapping assembly will generally therefore depend on the ion current. In embodiments where the RF trapping amplitude is continuously reduced, the rate of this reduction process may be constant. Alternatively, the rate of reducing the RF trapping amplitude may not be constant. For example, the rate of reducing the RF trapping amplitude may decrease as the RF trapping amplitude decreases. Alternatively, the rate of reducing the RF trapping amplitude may increase as the RF trapping amplitude decreases. Optionally, the first RF trapping amplitude (V1) may be constantly applied for a period of time before the RF trapping amplitude is continuously reduced to a second RF trapping amplitude (V2). The second RF trapping amplitude (V2) may then be constantly applied for a period of time.

[0161] Figure 4 , Figure 69 shows that each RF trapping amplitude is applied for the same duration. As discussed above, this is desirable to avoid distortions in the resulting mass spectrum. Instead, the RF trapping amplitudes can be applied for different durations. Alternatively, some RF trapping amplitudes can be applied for the same duration and some RF trapping amplitudes can be applied for different durations. Applying different RF trapping amplitudes for different durations can result in distortions in the intensity of the ions. The controller 130 can be further configured to compensate for such distortions so that the peaks of the mass spectrum are proportional.

[0162] Figure 6 The third, fourth and fifth RF capture amplitudes (V3, V4, V5) are shown as each equally spaced between the first and second RF capture amplitudes (V1, V2). However, the third, fourth and fifth RF capture amplitudes (V3, V4, V5) may not be equally spaced between the first and second RF capture amplitudes (V1, V2).

[0163] Embodiments of the present invention discuss selecting ions within a certain mass range by an upstream ion device upstream of an ion capture assembly. Any ion device with adjustable mass transmission characteristics (i.e., variable upper mass limit values ​​and / or lower mass limit values) can be used to implement this selection. For example, the mass filter 70 can be set to a desired mass range by the controller 130 so that the mass filter 70 filters sample ions according to the desired mass range. For a wide "full MS" scan, this option is less desirable because selecting a mass range by using the mass filter 70 generally provides a mass range that is too narrow. Embodiments of the present invention discuss adjusting the upstream ion device to change the lower mass limit value of the selected mass range of ions transmitted by the upstream ion device. Alternatively or additionally, the upstream ion device can be adjusted to change the upper mass limit value of the selected mass range of ions transmitted by the upstream ion device.

[0164] In some embodiments, ions can be selected by an upstream ion device (upstream of the ion trap), preferably by a mass selector such as a mass filter 70, thereby selecting a first and a second m / z ratio range (and optionally n additional m / z ratio ranges) that are preferably non-overlapping. This can make it possible to increase the dynamic range of the analysis and make it possible to make better quantification. Therefore, in some embodiments, ions can be selected in a first m / z ratio range and introduced into an ion capture assembly while applying a first RF capture amplitude to the ion trap, thereby capturing introduced ions with m / z ratios within the first m / z ratio range and cooling the captured ions. The RF capture amplitude is then reduced from the first RF capture amplitude to a lower second RF capture amplitude, thereby reducing the low mass cutoff of the ion capture assembly, and ions can be selected in a second m / z ratio range (non-overlapping with the first range) and introduced into the ion capture assembly while applying a lower second RF capture amplitude to the ion capture assembly, thereby capturing introduced ions with m / z ratios within the second m / z ratio range. In this case, the upper limit of the second mass range is clearly defined by the mass filter, while the lower limit may preferably be defined by the same mass filter or by a low mass cutoff corresponding to the second RF amplitude. The m / z ratios of the second m / z ratio range are preferably lower than the m / z ratios of the first range. In such embodiments, the lower mass limit of the second m / z ratio range is lower than, and in some cases, the upper mass limit is lower than, the low mass cutoff of the ion trapping assembly when the first RF trapping amplitude is applied.

[0165] Selecting ions according to a mass range upstream of the ion trap assembly is optional. For example, the ion trap assembly may receive all sample ions generated by the ion source 20, and the RF trapping amplitude applied to the ion trap assembly will control the ion trapping of ions to trap only those ions in the desired mass range.

[0166] Prior to injection into the mass analyzer 110, ions within the first mass range (MR1) and / or ions within the second mass range (MR2) may be fragmented in the fragmentation cell 120. The fragments may be accumulated in the C-trap 100 as a single pulse prior to injection into the mass analyzer for acquisition as a single spectrum. Alternatively, in the case where the mass analyzer 110 is a TOF mass analyzer, the fragment ions in the fragmentation cell 120 may continuously leak from the fragmentation cell 120.

[0167] Embodiments of the present invention may be applicable to capturing product ions / fragment ions generated from precursor ions. An ion capture assembly, which may be an ion trap, may be configured to fragment ions or include means for fragmenting ions. Precursor ions may be introduced into the ion capture assembly and fragmented to generate product ions. A first RF capture amplitude applied to the ion capture assembly may be varied to capture product ions within a certain m / z ratio range. For example, product ions having m / z ratios within a first m / z ratio range may be captured in the ion trap assembly by applying a first RF capture amplitude. Those captured product ions may be cooled to reduce their energy so that when the RF capture amplitude is reduced, the captured product ions remain trapped in the ion trap assembly. The RF capture amplitude may be reduced to a relatively lower second RF capture amplitude, thereby reducing the low mass cutoff of the ion trap. Product ions having m / z ratios within a second m / z ratio range may be captured at the second RF capture amplitude. The lower mass limit of the second m / z ratio range is lower than a low mass cutoff of the ion trap assembly when the first RF trapping amplitude is applied.

[0168] Precursor ions may be introduced into an ion capture assembly and / or continuously fragmented in an ion trap assembly. For example, step (a) of embodiment 20 may be performed continuously while steps (b) to (f) are performed. Alternatively, the introduction and fragmentation of precursor ions may occur intermittently to avoid overfilling the ion capture assembly. For example, the introduction and fragmentation of ions may occur only for a period of time while a first RF capture amplitude is applied to capture a desired number of product ions. The introduction and fragmentation of ions may be stopped while the captured product ions are cooled in step (d) of embodiment 20. The introduction and fragmentation of ions may occur again for a period of time while a second RF capture amplitude is applied to capture a desired number of product ions. The product ions captured by the first RF capture amplitude may be generated from precursor ions that are the same as the product ions captured by the second RF capture amplitude. Alternatively, the product ions captured by the first RF capture amplitude may be generated from different precursor ions than the product ions captured by the second RF capture amplitude. Product ions trapped by the first RF trapping amplitude may be generated at the same or different collision energies than product ions trapped by the second RF trapping amplitude.Product ions trapped by the first RF trapping amplitude and product ions trapped by the second RF trapping amplitude may be co-ejected into a mass analyzer.

[0169] A method of trapping ions in an ion trapping assembly configured to fragment ions may include applying n additional RF trapping amplitudes to the ion trap, each of which is an intermediate trapping amplitude between a first and a second RF trapping amplitude, wherein n≥1, and each of the n additional RF trapping amplitudes causes the capture of product ions having a corresponding nth m / z ratio range, each of which has a lower mass limit; the method also includes cooling the product ions trapped at a relatively high RF trapping amplitude before reducing the RF trapping amplitude to a relatively lower trapping amplitude.

[0170] In some embodiments, the method of capturing product ions in an ion trap configured to fragment ions can be applied to the fragmentation cell 120 of the mass spectrometer shown. In some embodiments, the fragmentation cell 120 includes an RF capture device, such as an RF multipole, so that the fragmentation cell 120 can be operated according to the present invention. The fragmentation cell 120 operates at a higher pressure than the ion trap 100 and can be operated in a high fragmentation mode and a low fragmentation mode (low fragmentation includes a mode without fragmentation), for example, by applying a suitable bias voltage between the ion trap 100 and the fragmentation cell 120. In some operating methods, after capturing product ions / fragment ions generated from precursor ions in the fragmentation cell 120 according to the present invention, the product ions / fragment ions can be transferred from the fragmentation cell 120 to the ion trap 100 while applying a lower second RF capture amplitude. Thus, in some embodiments, trapped product ions / fragment ions having m / z ratios within a first and second m / z ratio range (MR1, MR2) are transferred from an ion trap configured to fragment the ions to a further ion trap having a different pressure than the ion trap configured to fragment the ions, and the ions are transferred while applying a lower second RF trapping amplitude (V2). Typically, the further ion trap is maintained at a lower pressure than the ion trap configured to fragment the ions, e.g., a pressure at least 1 or at least 2 orders of magnitude lower. More typically, the pressure in the ion trap configured to fragment the ions multiplied by the length of the ion trap configured to fragment the ions is significantly higher than the pressure in the further ion trap multiplied by the length of the further ion trap. This ensures efficient capture and transfer of high-m / z ions, such as intact proteins or protein complexes.

[0171] The above embodiments involving fragmenting ions in an ion trap may also apply, mutatis mutandis, to an ion capture assembly comprising a plurality of electrode assemblies, at least one of which is configured to fragment ions. For example, the above embodiments involving fragmenting ions in an ion trap may also apply, mutatis mutandis, to reference Fig.10 and Fig.11The described embodiment, wherein the ion trapping assembly to which the RF trapping amplitude is applied comprises an ion cooling device (fragmentation cell 120) and an ion trap (ion trap 100). For example, when the first and second RF trapping amplitudes are applied, the fragmentation step can be applied to the ions introduced into the fragmentation cell 120. In this way, product ions having m / z ratios within the first m / z ratio range (MR1) can be trapped along with product ions having m / z ratios within the second m / z ratio range (MR2). The lower mass limit of the second m / z ratio range (MR2) can be lower than the low mass cutoff of the ion trapping assembly when the first RF trapping amplitude (V1) is applied.

[0172] For example, precursor ions may be introduced into an ion cooling device (fragmentation cell 120) of an ion trapping assembly. The precursor ions may then be fragmented in the ion cooling device to generate product ions. Product ions having an m / z ratio within a first m / z ratio range may be captured and cooled in the ion cooling device while applying a first RF capture amplitude (V1) to the ion cooling device. The product ions may then be transferred from the ion cooling device to an ion trap (ion trap 100) with minimal additional energy while applying a corresponding first RF capture amplitude to the ion trap and applying the first RF capture amplitude (V1) to the ion cooling device. Thus, during the transfer, the low mass cutoff of the ion trap is the same as the low mass cutoff of the ion cooling device. The product ions may then be captured and cooled in the ion trap while applying a corresponding first RF capture amplitude. Once cooled, the RF capture amplitude applied to the ion cooling device is reduced to a corresponding second RF capture amplitude. Optionally, the RF capture amplitude applied to the ion trap is reduced to a second RF capture amplitude (V2) so that the low mass cutoff of the ion trap is the same as the low mass cutoff of the ion cooling device. Further fragmentation of the precursor ions may optionally occur in an ion cooler. Product ions having m / z ratios within a second m / z ratio range may then be trapped in the ion cooler by applying a corresponding second RF trapping amplitude to the ion cooler. The product ions may be cooled in the ion cooler while applying a corresponding second RF trapping amplitude to the ion cooler. The product ions may then be transferred from the ion cooler to an ion trap (ion trap 100) with minimal additional energy while applying a corresponding second RF trapping amplitude to the ion cooler and applying a second RF trapping amplitude (V2) to the ion trap. The product ions may then be trapped in the ion trap by applying a second RF trapping amplitude (V2) to the ion trap. In such embodiments, the ion cooler is preferably located upstream of the ion trap. Product ions having m / z ratios within the first and second m / z ratio ranges (MR1, MR2) may then be transferred from an ion trap configured to fragment the ions to another ion trap having a pressure different from that of the ion trap of the ion trapping assembly while applying a second RF trapping amplitude (V2). The controller 130 may be configured to control the trapping and fragmentation of ions according to this method.

[0173] Optionally, the further ion trap may have a lower pressure than the ion trap and ion cooling device of the ion trap assembly.The pressure of the further ion trap multiplied by the length of the further ion trap may be less than the pressure of the ion trap of the ion trap assembly multiplied by the length of the ion trap of the ion trap assembly.

[0174] Product ions within the second mass range (MR2) may not be captured in the ion cooler and may not be transferred to the ion trap. In practice, product ions within the second mass range (MR2) may pass through the ion cooler to the ion trap while applying a second RF capture amplitude to the ion cooler and to the ion trap. Once the product ions within the first mass range (MR1) are cooled, the product ions within the second mass range (MR2) may be captured in the ion trap by applying a second RF capture amplitude (V2) to the ion trap. In an alternative embodiment, fragmentation may be performed in the ion trap of the ion trap assembly rather than in the ion cooler ion trap. The product ions may then be transferred to the ion cooler and captured therein. By yet another alternative, the ion trap and the ion cooler may both fragment the precursor ions to generate product ions. A first RF capture amplitude (V1) may be applied to the ion trap to capture product ions within the first mass range. A second RF capture amplitude (V2) may be applied to the ion cooler to capture product ions within the second mass range. The trapped ions may be cooled before being transferred to a further ion trap.

[0175] The present invention has been described with respect to lowering the low mass cutoff of an ion trap assembly by reducing the RF trapping amplitude. However, the low mass cutoff of an ion trap assembly may also be lowered by increasing the RF trapping frequency applied to the ion trap assembly. In addition, both the RF trapping amplitude and the RF trapping frequency may be varied such that the net effect is to lower the low mass cutoff of the ion trap assembly.

[0176] In fact, the method can be regarded as a method of trapping ions in an ion trap assembly, which includes introducing ions into the ion trap assembly; applying a first RF trapping waveform to the ion trap assembly to trap the introduced ions having an m / z ratio within a first m / z ratio range; cooling the trapped ions; changing the RF trapping waveform from the first RF trapping waveform to a second RF trapping waveform to reduce a low mass cutoff value of the ion trap assembly; and at the second RF trapping waveform, trapping the introduced ions having an m / z ratio within a second m / z ratio range, wherein the mass lower limit value of the second m / z ratio range is lower than the low mass cutoff value of the ion trap assembly when the first RF trapping waveform is applied.

[0177] The first RF capture waveform may include a first RF capture amplitude and the second RF capture waveform includes a second RF capture amplitude, wherein the first RF capture amplitude is greater than the second RF capture amplitude.

[0178] The first RF capture waveform may include a first RF capture frequency and the second RF capture waveform includes a second RF capture frequency, wherein the first RF capture frequency is less than the second RF capture frequency.

Claims

1. A method for trapping ions in an ion trap assembly, the method comprising: (a) introducing ions into the ion trap assembly, (b) applying a first RF trapping amplitude to the ion trap assembly to thereby trap incoming ions having m / z ratios within a first m / z ratio range; (c) cooling the trapped ions; (d) reducing the RF trapping amplitude from the first RF trapping amplitude to a lower second RF trapping amplitude, thereby reducing a low mass cutoff of the ion trapping assembly; and (e) trapping incoming ions having m / z ratios within a second m / z ratio range at said second lower RF trapping amplitude; wherein the mass lower limit of the second m / z ratio range is lower than the low mass cutoff of the ion trapping assembly when the first RF trapping amplitude is applied, wherein the total number of trapped ions in the ion trapping assembly is maintained below a threshold value determined as a function of the first and second RF trapping amplitudes, wherein the ion trapping assembly comprises an ion trap and an ion cooler, wherein in step (b) the first RF trapping amplitude is applied to the ion cooler such that ions having m / z ratios within the first m / z ratio range are trapped in the ion cooler; wherein in step (c), the captured ions are cooled in the ion cooling device; Wherein, after step (c) and before step (d), the method comprises step (c)(i), which comprises transferring trapped ions from the ion cooling device to the ion trap while applying the first RF trapping amplitude to the ion cooling device and simultaneously applying the corresponding first RF trapping amplitude to the ion trap, whereby the ion trap and the ion cooling device have the same low mass cutoff during the ion transfer in step (c)(i), and the transferred ions in the ion trap are trapped at the corresponding RF trapping amplitude; wherein, in step (d), the RF trapping amplitude applied to the ion trap is reduced to the lower second RF trapping amplitude, thereby reducing the low mass cutoff value of the ion trap, and wherein, in step (d), the RF trapping amplitude applied to the ion cooling device is reduced to the corresponding second RF trapping amplitude, so that the ion trap and the ion cooling device have the same low mass cutoff value during step (d).

2. The method according to claim 1, further comprising: applying n additional RF trapping amplitudes to the ion trapping assembly, each of which is an intermediate trapping amplitude between the first and second RF trapping amplitudes, wherein n≥1, each of the n additional RF trapping amplitudes causing trapping of incoming ions having a corresponding nth m / z ratio range, each of the nth m / z ratio ranges having a lower mass limit; The method also includes cooling the incoming ions trapped at the relatively high RF trapping amplitude before reducing the RF trapping amplitude to the relatively lower trapping amplitude.

3. The method of claim 2, wherein the first RF capture amplitude, the second RF capture amplitude, and / or each of the n additional intermediate RF capture amplitudes are applied for the same duration or wherein at least some of the first RF capture amplitude, the second RF capture amplitude, and / or each of the n additional intermediate RF capture amplitudes are applied for different times.

4. The method of claim 2 or 3, wherein the RF trapping amplitude is continuously reduced from the first RF trapping amplitude to the second RF trapping amplitude, thereby continuously reducing the low mass cutoff value of the ion trapping assembly.

5. The method of claim 4, wherein the method comprises continuously cooling the trapped ions while continuously reducing the RF trapping amplitude.

6. The method of claim 1 , wherein ions within a selected m / z ratio range are introduced into the ion trap assembly from an upstream ion device, wherein the upstream ion device transmits ions within the selected m / z ratio range, the method further comprising: adjusting the upstream ion device to reduce the lower mass limit of the selected m / z ratio range; and The RF trapping amplitude is reduced from the first RF trapping amplitude to the second lower RF trapping amplitude, and the lower mass limit of the selected m / z ratio range of the upstream ion device is reduced.

7. The method according to claim 1, in, In step (e), ions within the m / z ratio range are trapped in the ion cooler by a corresponding second RF trapping amplitude applied to the ion cooler; The method further comprises step (e)(i), comprising transmitting trapped ions within the second m / z ratio range from the ion cooling device to the ion trap, while applying a corresponding second RF trapping amplitude to the ion cooling device and applying a second RF trapping amplitude to the ion trap, and at the second RF trapping amplitude, trapping the transmitted ions having m / z ratios within the second m / z ratio range in the ion trap.

8. The method of claim 7 , wherein the method comprises applying n additional RF trapping amplitudes to the ion cooling device, each being an intermediate trapping amplitude between the first RF trapping amplitude and the corresponding second RF trapping amplitude, wherein n≥1, the n additional RF trapping amplitudes each causing incoming ions having a corresponding nth m / z ratio range to be trapped in the ion cooling device, the nth m / z ratio ranges each having a lower mass limit; the method further comprises cooling the incoming ions trapped in the ion cooling device at a relatively high RF trapping amplitude; transmitting the trapped ions to the ion trap while applying the relatively high RF trapping amplitude; trapping the transmitted ions in the ion trap by applying the relatively high RF trapping amplitude, and cooling the trapped ions in the ion trap before reducing the RF trapping amplitude to a relatively low trapping amplitude.

9. The method according to claim 1, wherein the introduced ions of step (a) are introduced into the ion cooling device.

10. The method of claim 9, wherein the introduced ions of step (a) are introduced into the ion cooling device and transferred from the ion trap to the ion cooling device.

11. The method of claim 1, wherein step (e) comprises introducing ions into the ion trap assembly, wherein the introduced ions of step (e) are introduced into the ion trap.

12. The method of claim 1, wherein step (e) comprises introducing ions into the ion trap assembly, wherein the introduced ions of step (e) are introduced into the ion cooling device.

13. The method of claim 1, wherein the ion cooling device is a fragmentation cell.

14. The method of claim 1, wherein the corresponding first RF capture amplitude is the same as the first RF capture amplitude.

15. The method of claim 1, wherein the corresponding second RF capture amplitude is the same as the second RF capture amplitude.

16. A method of trapping ions in an ion trap assembly, the method comprising: (a) introducing ions into the ion capture assembly; (b) applying a first RF trapping frequency to the ion trap assembly to thereby trap incoming ions having m / z ratios within a first m / z ratio range; (c) cooling the trapped ions; (d) increasing the RF trapping frequency from the first RF trapping frequency to a second RF trapping frequency, thereby reducing a low mass cutoff of the ion trapping assembly; and (e) trapping incoming ions having m / z ratios within a second m / z ratio range at the second RF trapping frequency; wherein the mass lower limit of the second m / z ratio range is lower than a low mass cutoff of the ion trap assembly when the first RF trapping frequency is applied, wherein the total number of trapped ions in the ion trapping assembly is maintained below a threshold value determined as a function of the first and second RF trapping frequencies, wherein the ion trapping assembly comprises an ion trap and an ion cooler, wherein in step (b), the first RF trapping frequency is applied to the ion cooler so that ions having m / z ratios within the first m / z ratio range are trapped in the ion cooler; wherein in step (c), the captured ions are cooled in the ion cooling device; Wherein, after step (c) and before step (d), the method comprises step (c)(i), which comprises transferring trapped ions from the ion cooling device to the ion trap while applying the first RF trapping frequency to the ion cooling device and simultaneously applying the first corresponding RF trapping frequency to the ion trap, whereby the ion trap and the ion cooling device have the same low mass cutoff during the ion transfer in step (c)(i), and the transferred ions in the ion trap are trapped at the corresponding RF trapping frequency; wherein in step (d), the RF trapping frequency applied to the ion trap is increased by the second higher RF trapping frequency, thereby reducing the low mass cutoff value of the ion trap, Wherein, in step (d), the RF trapping frequency applied to the ion cooling device is increased to a corresponding second RF trapping frequency, so that the ion trap and the ion cooling device have the same low mass cutoff value during step (d).

17. A method of trapping ions in an ion trap assembly, wherein the ion trap assembly is configured to fragment the ions, the method comprising: (a) introducing precursor ions into the ion trap assembly, (b) fragmenting the introduced precursor ions to generate product ions; (c) applying a first RF trapping amplitude to the ion trapping assembly to thereby trap product ions having m / z ratios within a first m / z ratio range; (d) cooling the trapped product ions; (e) reducing the RF trapping amplitude from the first RF trapping amplitude to a second lower RF trapping amplitude, thereby reducing a low mass cutoff of the ion trapping assembly; and (f) trapping product ions having m / z ratios within a second m / z ratio range at the second lower RF trapping amplitude; wherein the mass lower limit of the second m / z ratio range is lower than a low mass cutoff of the ion trapping assembly when the first RF trapping amplitude is applied, wherein the total number of trapped ions in the ion trapping assembly is maintained below a threshold value determined as a function of the first and second RF trapping frequencies, wherein the ion trapping assembly comprises an ion trap and an ion cooling arrangement, wherein the ion trap and / or the ion cooling arrangement are arranged to fragment the ions, wherein in step (c), the first RF trapping amplitude is applied to the ion cooling device, so that product ions having m / z ratios within a first m / z ratio range are trapped in the ion cooling device; wherein in step (d), the captured ions are cooled in the ion cooling device; wherein, after step (d) and before step (e), the method comprises a step (d)(i) comprising transferring trapped ions from the ion cooling device to the ion trap while applying the first RF trapping amplitude to the ion cooling device and simultaneously applying a corresponding first RF trapping amplitude to the ion trap, so that the ion trap and the ion cooling device have the same low mass cutoff during the ion transfer in step (d)(i), and at the corresponding first RF trapping amplitude, the transferred ions in the ion trap are trapped; Wherein, in step (e), the RF trapping amplitude applied to the ion trap is reduced to the second lower RF trapping amplitude, thereby reducing the low mass cutoff value of the ion trap.

18. The method according to claim 17, in, In step (f), ions within the m / z ratio range are trapped in the ion cooler by a corresponding second RF trapping amplitude applied to the ion cooler; The method further comprises step (f)(i), comprising transmitting trapped ions within the second m / z ratio range from the ion cooling device to the ion trap, while applying a corresponding second RF trapping amplitude to the ion cooling device and applying the second RF trapping amplitude to the ion trap, and at the second RF trapping amplitude, trapping the transmitted ions having m / z ratios within the second m / z ratio range in the ion trap.

19. The method of claim 18, wherein the method comprises applying n additional RF trapping amplitudes to the ion cooling device, each being an intermediate trapping amplitude between a first RF corresponding second RF trapping amplitude, wherein n≥1, the n additional RF trapping amplitudes each causing incoming ions having a corresponding nth m / z ratio range to be trapped in the ion cooling device, the nth m / z ratio ranges each having a lower mass limit; the method further comprises cooling the incoming ions trapped in the ion cooling device at a relatively high RF trapping amplitude; transmitting the trapped ions to the ion trap while applying a relatively high RF trapping amplitude; trapping the transmitted ions in the ion trap by applying a relatively high RF trapping amplitude, and cooling the trapped ions in the ion trap before reducing the RF trapping amplitude to a relatively low trapping amplitude.

20. The method of claim 1 or 17, wherein the ion cooling device has a different pressure than the ion trap.

21. The method of claim 1 or 17, wherein the lower mass limit value of the second m / z ratio range is less than the lower mass limit value of the first m / z ratio range.

22. The method of claim 1 or 17, wherein a lower mass limit value of the first m / z ratio range is greater than an upper mass limit value of the second m / z ratio range, such that the first m / z ratio range and the second m / z ratio range do not overlap.

23. A controller for controlling ion capture in an ion capture assembly, the ion capture assembly having an electrode assembly, the controller being configured to: causing ions to be introduced into the ion trap assembly; applying a first RF trapping amplitude to the electrode assembly for a duration sufficient to allow cooling of the ion-trapped incoming ions, thereby trapping incoming ions having m / z ratios within a first m / z ratio range; reducing the RF trapping amplitude applied to the electrode assembly from the first RF trapping amplitude to the second lower RF trapping amplitude that traps incoming ions having m / z ratios within a second m / z ratio range, wherein the mass lower limit of the second m / z ratio range is lower than a low mass cutoff of the ion trapping assembly when the first RF trapping amplitude is applied, wherein the controller is configured to determine a threshold value for the total number of trapped ions within the ion trapping assembly as a function of the first and second RF trapping amplitudes, further wherein the controller is configured to control application of the first and second RF trapping amplitudes so as to maintain a total number of trapped ions in the ion trapping assembly below a threshold, The ion trap assembly includes an ion trap and an ion cooling device, each of the ion trap and the ion cooling device has an electrode assembly, and the controller is configured to: applying a first RF trapping amplitude to the electrode assembly of the ion cooling device to trap incoming ions having m / z ratios within a first m / z ratio range, transferring trapped ions from the ion cooler to the ion trap while applying the first RF trapping amplitude to the electrode arrangement of the ion cooler and the ion trap, applying a respective first RF trapping amplitude to the electrode arrangement of the ion trap sufficient to allow the ion trap and the ion cooling device to have the same low mass cutoff during ion transport; applying a respective first RF trapping amplitude to the electrode arrangement of the ion trap for a duration sufficient to allow cooling of trapped ions; reducing an RF trapping amplitude applied to an electrode arrangement of the ion trap from the first RF trapping amplitude to the second lower RF trapping amplitude; and An RF trapping amplitude applied to an electrode arrangement of the ion cooling device is reduced from a first RF trapping amplitude to a corresponding second RF trapping amplitude such that the ion trap and the ion cooling device have the same low low mass cutoff value.

24. A controller according to claim 23, wherein the controller is further configured to: apply n additional RF trapping amplitudes to the ion trapping assembly, each of which is an intermediate trapping amplitude between the first and second RF trapping amplitudes, wherein n≥1, the n additional RF trapping amplitudes each cause the trapping of incoming ions having a corresponding nth m / z ratio range, and each of the n additional RF trapping amplitudes is applied for a duration sufficient to allow cooling of ions trapped at this nth RF trapping amplitude.

25. The controller according to claim 23, wherein the controller is configured to: causing ions to be introduced into the ion trap of the ion trap assembly from an upstream ion device that transmits ions within a selected m / z ratio range, causing ions having m / z ratios within the first m / z ratio range to be introduced into the ion cooling device, and or by applying a corresponding second RF trapping amplitude to an electrode arrangement of the ion cooling device, so that ions having m / z ratios within a second m / z ratio range are introduced and trapped in the ion cooling device; Alternatively, by applying the lower second RF trapping amplitude to the electrode arrangement of the ion trap, ions having m / z ratios within a second m / z ratio range are introduced and trapped in the ion trap.

26. A controller according to claim 25, wherein if the controller is configured to cause ions with m / z ratios within a second m / z ratio range to be introduced and trapped in the ion cooling device by applying a corresponding second RF trapping amplitude to the electrode arrangement of the ion cooling device, the controller is further configured to cause ions with m / z ratios within the second m / z ratio range to be transferred from the ion cooling device to the ion trap while applying a second RF trapping amplitude to the ion trap and applying a corresponding second RF trapping amplitude to the ion cooling device.

27. A controller according to any one of claims 23-24, wherein the controller is further configured to continuously reduce the RF trapping amplitude applied to the electrode assembly while continuously cooling the trapped ions.

28. A controller for controlling ion capture in an ion capture assembly, the ion capture assembly having an electrode assembly, the controller being configured to: allowing ions to be introduced into an ion trap assembly; applying a first RF trapping frequency to the electrode assembly for a duration sufficient to allow cooling of the trapped incoming ions, thereby trapping incoming ions having m / z ratios within a first m / z ratio range; increasing the RF trapping frequency applied to the electrode assembly from a first RF trapping frequency to a second higher RF trapping frequency that traps incoming ions having m / z ratios within a second m / z ratio range, wherein the mass lower limit of the second mass range is lower than the low mass cutoff value of the ion trap assembly when the first RF trapping frequency is applied, wherein the controller is configured to determine a threshold value for the total number of trapped ions within the ion trapping assembly as a function of the first and second RF trapping frequencies, further wherein the controller is configured to control the application of the first and second RF trapping frequencies so as to maintain a total number of trapped ions in the ion trapping assembly below a threshold, wherein the ion trapping assembly comprises an ion trap and an ion cooling arrangement, wherein the ion trap and / or the ion cooling arrangement are configured to fragment the ions, applying the first RF trapping frequency to an electrode arrangement of the ion cooler so that product ions having m / z ratios within a first m / z ratio range are trapped in the ion cooler; transferring trapped ions from the ion cooler to the ion trap while applying the first RF trapping frequency to an electrode arrangement of the ion cooler and simultaneously applying a corresponding first RF trapping frequency to an electrode arrangement of the ion trap, such that the ion trap and the ion cooler have the same low mass cutoff during ion transfer; applying a first RF trapping frequency to the electrode arrangement of the ion trap for a duration sufficient to allow cooling of trapped ions; increasing an RF trapping frequency applied to an electrode arrangement of the ion trap from a corresponding first RF trapping frequency to a higher second RF trapping frequency; An RF trapping frequency applied to an electrode arrangement of the ion cooler is increased from a first RF trapping frequency to a corresponding second RF trapping frequency such that the ion trap and the ion cooler have the same low mass cutoff.

29. A controller for controlling ion fragmentation and trapping in an ion trap assembly, wherein the ion trap assembly comprises an electrode assembly and is arranged to fragment ions, the controller being arranged to: causing precursor ions to be introduced into the ion trap assembly; causing the introduced precursor ions to fragment to generate product ions; applying a first RF trapping amplitude to the electrode assembly for a duration sufficient to allow cooling of the trapped product ions, thereby trapping product ions having m / z ratios within a first m / z ratio range; reducing an RF trapping amplitude applied to the electrode assembly from a first RF trapping amplitude to a second, lower RF trapping amplitude that traps product ions having m / z ratios within a second m / z ratio range, wherein the mass lower limit of the second m / z ratio range is lower than a low mass cutoff of the ion trap assembly when the first RF trapping amplitude is applied, wherein the controller is configured to determine a threshold value for the total number of trapped ions within the ion trapping assembly as a function of the first and second RF trapping frequencies, Further wherein the controller is configured to control the application of the first and second RF trapping frequencies so as to maintain a total number of trapped ions in the ion trapping assembly below a threshold, wherein the ion trapping assembly comprises an ion trap and an ion cooling arrangement, wherein the ion trap and / or the ion cooling arrangement are configured to fragment ions, the ion trap and the ion cooling arrangement each having an electrode assembly, the controller being configured to: applying the first RF trapping amplitude to an electrode arrangement of the ion cooler so that product ions having m / z ratios within a first m / z ratio range are trapped in the ion cooler; transferring trapped ions from the ion cooler to the ion trap while applying the first RF trapping amplitude to the electrode arrangement of the ion cooler and simultaneously applying a corresponding first RF trapping amplitude to the ion trap, such that the ion trap and the ion cooler have the same low mass cutoff during ion transfer; applying a first RF trapping amplitude to an electrode arrangement of the ion trap for a duration sufficient to allow cooling of trapped ions; reducing an RF trapping amplitude applied to an electrode arrangement of the ion trap from a corresponding first RF trapping amplitude to a lower second RF trapping amplitude; An RF trapping amplitude applied to an electrode arrangement of the ion cooler is reduced from a first RF trapping amplitude to a corresponding second RF trapping amplitude such that the ion trap and the ion cooler have the same low mass cutoff value.

30. An ion trapping assembly comprising: Electrode assembly; and A controller according to any one of claims 23 to 29.

31. A mass spectrometer comprising: an ion source configured to generate ions; an ion trap assembly configured to receive ions generated by the ion source; and A controller according to any one of claims 23 to 29.

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