Method of scheduling ions for analysis

Abstract

A method of scheduling ions for analysis in a mass-to-charge ratio (m / z) range of interest is provided. The method includes obtaining a list of ion intensities and associated m / z of ions to be analyzed; obtaining a plurality of target m / z or a plurality of target m / z ranges to be analyzed; assigning each target m / z or target m / z range to a first group or a second group based on the list of ion intensities and associated m / z of the ions and an intensity threshold, wherein the target m / z or target m / z range in the first group is associated with higher intensity ions than the target m / z or target m / z range in the second group; sequentially selecting and outputting ions having target m / z or target m / z range assigned to the first group for analysis using an ion selection device; and sequentially selecting and outputting ions having target m / z or target m / z range assigned to the second group for analysis using an ion selection device.

Description

Technical Field

[0001] This disclosure relates to mass spectrometry. Specifically, this disclosure relates to an ion dispatching method. Background Technology

[0002] US-A-2939952 discloses a tandem mass spectrometer that employs a quadrupole mass filter to isolate target ions before fragmentation and further downstream mass analysis. A characteristic of the quadrupole mass filter is that unselected ions bombard the quadrupole of the filter, resulting in the loss of valuable analyte ions and simultaneously contaminating and ultimately degrading the electrodes. Depending on the isolation window employed, the theoretical sensitivity loss can easily exceed 99%.

[0003] One solution is to accumulate and separate ions upstream of the quadrupole so that the m / z of the ions delivered to the device roughly matches the range of the isolation window, and thus minimize ion loss to achieve pre-separation accuracy. Residual loss then becomes a factor affecting the resolution of pre-separation and the alignment quality with the quadrupole isolation window.

[0004] This method was initially described by Hoyes in GB-A-2442638, in which ions are first loaded into an ion trap. An RF pseudobarrier prevents the release of higher m / z ions unless overcome by a DC or traveling wave, pushing them toward the outlet, where they are then released for quadrupole selection / fragmentation, etc. Giles in US-B-6914241B and Bateman in US-B-6838662 further describe methods using reverse traveling waves and nonlinear DC gradients to separate ions within a guide. These ions reach equilibrium positions and can be released in a time-dependent manner via a quadrupole by adjusting the DC or traveling wave amplitude, thus significantly improving its efficiency. Figure 1 This illustrates ion separation under the action of these two opposing forces, while Figure 2 A schematic diagram of an ion dispatching method using an ion dispatching device and a quadrupole is shown.

[0005] Several techniques are available to implement this "ion dispatching" process. Typical methods involve separating ions under the influence of two different forces, such as DC potential, RF pseudopotential (or traveling wave), or collision resistance with a buffer gas. An ion dispatching method involving parallel ion acquisition followed by serial fragmentation is disclosed in US-B-10665441. A parallel accumulation-serial fragmentation method based on a Trapped Ion Mobility Device is also disclosed in Meier, F. et al. ParallelAccumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed ​​and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device. Journal of Proteome Research 2015, 12, 5378-5387, US-B9891194 and US-B-10794861. Other specific implementations include accumulation in multiple traps orthogonally via RF pseudopotential (US-B-10199208) or via ion mobility (US-B-9607817).

[0006] It is also known to use traveling waves to propel ions through ion guides. US-B-7375344 discloses a series of applications of out-of-phase RF potentials, while Giles et al, Applications of a traveling wave-based radio-frequency-only stacked ring ion guide, Rapid Commun. Mass Spectrom. 2004;18:2401–2414 discloses applying a switching DC pulse to a continuous axial segment of an ion guide to generate a potential front that moves downward at the center of the guide over time, thereby dragging ions along with it.

[0007] Mass spectrometers control ion loading in the trapping device by varying the ion accumulation time, a process known as automatic gain control (AGC). Ion scheduling devices, by converting a continuous ion beam into time-varying pulses of concentrated ions with similar m / z, inevitably disrupt this process. This problem is believed to be solvable by downstream beam attenuation devices, and most promisingly by altering the duty cycle of fast pulsed ion optics gating elements. US-B-7960690 has demonstrated this effect with a 1kHz switch, where ion packets with pulse widths <2ms are expected.

[0008] Tandem mass spectrometry involves the isolation and fragmentation of the eluted analyte, followed by the generation of fragment mass spectra and mass analysis to return structural and quantitative information. These MS / MS or MS2 spectra are typically supplemented by a large-scale investigation of unfragmented precursor ions (referred to as MS1, MS, or full MS analysis), which provides accurate m / z and intensity information. This analysis is optional for data-independent acquisition (DIA) methods, but for data-dependent acquisition (DDA) methods, a list of precursor targets for MS2 analysis is required. The dynamic range of MS1 spectra poses a substantial problem. Digested peptide concentrations can vary by up to 10 orders of magnitude, but the dynamic range of a single mass spectra (e.g., orbital trap mass analyzer) is limited to 4. Furthermore, the number of ions that can be injected into an orbital trap mass analyzer is limited by the capacity of the accumulating C-trap, approximately 10⁵, so low-intensity peptide precursor signals can easily be masked, and potential targets available for fragmentation may be missed or poorly quantified.

[0009] One important approach to improving the dynamic range of MS1 spectra is the High Dynamic Range (HDR) method, or Boxcar method. This method involves subdividing the wide m / z range of interest for analysis into many narrower isolation windows, each separately injected into a C-trap with different fill times set according to the ion current (Meier et al, Nature Methods, 2018, 15, 440-448). The total ion population is then analyzed together, for example, in an orbital trap mass analyzer. This method attenuates densely packed regions while amplifying sparsely packed mass regions, enhancing many relatively weak peaks and significantly improving the effective dynamic range of the scan. The trade-off is a substantial increase in the time required for multiple fills to accumulate ions. Due to the long fill times of the low-level windows and the milliseconds required to switch the quadrupole and ion source voltages, HDR analysis rapidly impacts the achievable MS2 scan rate.

[0010] In this context, this disclosure provides an improved, or at least commercially relevant, alternative method for scheduling ions for analysis. Summary of the Invention

[0011] According to the first aspect, a method is provided for scheduling ions for analysis within a range of mass-to-charge ratios (m / z) of interest. The method includes: Obtain a list of ionic intensities and associated m / z for the ions to be analyzed; Obtain the m / z ratio of multiple targets or the m / z range of multiple targets to be analyzed; Based on the ionic strength of the ions and a list of associated m / z values, as well as an intensity threshold, each target m / z or target m / z range is assigned to either a first group or a second group, wherein the target m / z or target m / z range in the first group is associated with ions of higher intensity compared to the target m / z or target m / z range in the second group. The ion selector sequentially selects and outputs ions with the target m / z or target m / z range assigned to the first group for analysis; and The ion selector is used to sequentially select and output ions with the target m / z or target m / z range assigned to the second group for analysis.

[0012] The interplay between ion scheduling and rapid (200–400 Hz) spectral acquisition, fast switching between MS1 ​​and MS2 analyses, and control of ion swarms in space-charge-constrained downstream trap regions (e.g., via automatic gain control) has presented significant technical challenges. The first aspect of the approach provides methods for scheduling ions for analysis (e.g., mass spectrometry or ion mobility analysis) that offer improved control over the ion swarm to enhance the dynamic range of mass analyses using the scheduled ions.

[0013] To schedule ions for analysis, the first aspect of the method obtains a list of targets to be analyzed. The target list may include a target m / z or a target m / z range (e.g., for the DDA method) corresponding to a specific ion species (e.g., a specific precursor ion for the DDA method).

[0014] The first aspect of the method also obtains a list of ionic intensities and associated m / z values ​​for the ions to be analyzed. The list of ionic intensities can be obtained using prior survey analyses performed by a mass spectrometry system, or it can be a prediction of expected ions based, for example, on previous experiments or measurements of the mass spectrometry system. The first aspect of the method utilizes knowledge of ionic intensities and associated m / z values ​​to group targets with similar intensities (target m / z or target m / z ranges). After grouping, the targets are scheduled for analysis sequentially (e.g., by m / z or ion mobility order, or any other specified order). The sequential separation of the target ions is performed using an ion selection device, which in some embodiments may include an ion scheduling device.

[0015] Grouping analyses based on the intensity of target m / z ions (or the expected intensity of ions within each target m / z range) can improve the dynamic range of subsequent analyses.

[0016] Furthermore, by sequentially outputting ions within each group of targets, the overall speed of the output targets can be increased by reducing the time required for the ion selection device to stabilize between consecutive outputs.

[0017] In some embodiments, the ion selection device may have an associated fill time for receiving ions, wherein the fill time for selecting and outputting ions of a second set of target m / z or a target m / z range is longer than the fill time for selecting and outputting ions of a first set of target m / z or a target m / z range. Therefore, by analyzing relatively high-intensity targets in the first set, the fill time for the first set can be relatively short. This, in turn, allows for the expenditure of additional time to acquire ions of the second set of targets (i.e., a longer fill time), where the ion intensity is lower. Thus, an improved dynamic range can be achieved for ions falling within the second set of targets.

[0018] While the first aspect of the method covers dividing the target m / z or target m / z range into two groups, it should be understood that in some embodiments, three or more groups of target m / z or target m / z ranges may be provided, each group having an associated ion intensity range. Based on the ion intensity and a list of associated m / z values, each target m / z value or target m / z range can be assigned to one of the three or more groups. Therefore, a target m / z or target m / z range can be grouped with other targets having similar intensities. The fill time associated with each group of targets can be adjusted based on the ion intensity within that group.

[0019] The number of targets in each group can be selected based on the type of experiment being performed. The number of targets in each group can also depend on the characteristics of the ion selection device and the distribution and intensity of the ion population to be analyzed. For example, in some embodiments, the number of targets in the first group (the ions with the highest intensity) may depend on the number of relatively high-intensity ion species present. In some embodiments, the number of targets in the first group may not exceed: 20, 15, or 10. Subsequent groups may have a similar number of targets, or the second group (and the third group, and so on) may have a larger number of targets, such as approximately 50 targets per group.

[0020] In some embodiments, the ion selection device may sequentially select and output ions with a target m / z or target m / z range assigned to the first group for analysis before selecting and outputting ions assigned to the second group of ions. Therefore, in some embodiments, the ion species with the highest intensity may be scheduled for analysis first, followed by ions with lower intensities.

[0021] In some embodiments, the ion selection device may sequentially select and output ions with a target m / z or target m / z range assigned to a second group for analysis before selecting and outputting ions assigned to a first group. Therefore, in some embodiments, relatively low-intensity ion species may be prioritized for analysis first. Compared to methods that analyze ion species in intensity order, ion scheduling methods can improve the detection of lower-intensity species by prioritizing lower-intensity species.

[0022] In some embodiments where ions are assigned to three or more groups, the ion groups can be analyzed in any order. Specifically, the groups can be analyzed in ascending or descending order of intensity.

[0023] In some embodiments, the ion selection device can select and output ions assigned to each group in a corresponding ion selection cycle. Thus, in a first ion selection cycle, the ion selection device can fill with ions, then select and output ions having a target m / z value or target m / z range assigned to the first (or second) group. In a second ion selection cycle, the ion selection device can fill with ions, then select and output ions having a target m / z value or target m / z range assigned to the next group, and so on. If ions are assigned to three or more groups, an associated number of ion selection cycles can be performed.

[0024] In some embodiments, the ion selection device may include an ion scheduling device configured to separate ions into multiple ion packets based on their m / z or ion mobility, and to sequentially output the ion packets in order of their m / z or ion mobility. According to this disclosure, the ion scheduling device is understood as a means of separating a number of ions into ion packets, which are separated sequentially according to the ion's m / z or ion mobility. When the ion selection device includes an ion scheduling device, the ion selection cycle may correspond to a cycle of the ion scheduling device (i.e., filling and subsequent emptying of the ion scheduling device).

[0025] In some embodiments, the ion selection device may further include a mass filtering device configured to receive each ion packet. For each ion packet, the mass filtering device may select a subset of ions based on multiple target m / z values ​​or multiple target m / z ranges. Therefore, the subset of ions output by the mass filtering device may correspond to a target m / z or target m / z range to be scheduled for analysis. Thus, the ion scheduling device and the mass filtering device can operate in coordination to schedule ions with different target m / z or target m / z ranges for analysis in a sequential manner, which improves the dynamic range of the ions to be analyzed.

[0026] In some embodiments, for each target m / z or target m / z range of the first group, ions can be transferred to a mass filtration device without undergoing separation in an ion dispatching device. The mass filtration device can be used to select a subset of ions with each target m / z or target m / z range. Therefore, for relatively strong ions requiring a limited fill time, it is preferable not to use an ion separation device to separate the ions. Instead, strong ions can be directly selected (filtered) using a mass filtration device. Ions with lower strength forming part of a second group (or a third group, and so on) can still be separated using an ion dispatching device to separate the lower-strength ions from the higher-strength ions targeted in the first group.

[0027] In some embodiments, the ion scheduling device may perform multiple ion scheduling cycles. For example, each ion scheduling cycle may include the ion scheduling device receiving ions, wherein the ion scheduling device divides the ions into multiple ion packets based on the ion's m / z or ion mobility, and sequentially outputs multiple groups. Ions having a target m / z or target m / z range assigned to a first group may be output during one or more first ion scheduling cycles. Ions having a target m / z or target m / z range assigned to a second group may be output during one or more second ion scheduling cycles. If the target m / z or target m / z range is assigned to three or more groups, three or more ion scheduling cycles may be performed accordingly. By scheduling ions for analysis within multiple ion scheduling cycles, targets of similar intensity can be scheduled for analysis within the same ion scheduling cycle, thereby improving the dynamic range of the ion output for analysis.

[0028] In some embodiments, each ion packet output by the ion scheduling device may have an associated m / z range or ion mobility range, wherein if two or more target m / z values ​​or target m / z ranges of the first group are within the m / z range or ion mobility range of the ion packet, multiple first ion scheduling cycles are performed such that no more than one subset of ions is selected from each ion packet. If multiple first ion scheduling cycles (or multiple ion scheduling cycles of any other group) are to be performed, the target m / z values ​​or target m / z ranges may be scheduled in intensity order, wherein the target with the highest intensity is scheduled first. Thus, within the first group, the initial first ion scheduling cycle can select ions with relatively higher intensity compared to subsequent first ion scheduling cycles. The fill time of each first ion scheduling cycle can be adjusted to reflect the different intensities of the target ions in each first ion scheduling cycle. Similarly, the fill time of each second ion scheduling cycle can be adjusted, and so on.

[0029] In some embodiments that perform multiple ion scheduling cycles (e.g., multiple first ion scheduling cycles, or any other group of ion scheduling cycles), the fill time of the ion scheduling device can be adjusted for each ion scheduling cycle. For example, the fill time can be adjusted based on the average intensity of ions within a target m / z or target m / z range selected in the ion scheduling cycle. The ion scheduling cycle can be repeated until all target m / z or target m / z ranges for a group have been completed.

[0030] In some embodiments, the target m / z or target m / z range can be upgraded from a second group to a first group to increase the utilization of the ion packets output by the ion dispatcher. Similarly, if three or more groups are used, the target m / z or target m / z range can be upgraded from one group to another group associated with a higher ion intensity range (e.g., the target m / z can be upgraded from a fourth group to a third group with a higher ion intensity range). Therefore, ions can be dispatched for analysis in a manner that effectively utilizes the ion packets output by the ion dispatcher.

[0031] In some embodiments, a target m / z value or target m / z range can be downgraded from a first group to a second group to increase the utilization of the ion packets output by the ion dispatcher. Similarly, if three or more groups are used, a target m / z value or target m / z range can be downgraded from one group to another group associated with a lower ion intensity range (e.g., a target m / z value can be downgraded from a second group to a third group with an even lower ion intensity range). By downgrading the ions, particularly those assigned to the first group (i.e., the highest intensity ion species), the first group can include a limited number of relatively high-intensity ion species. Therefore, the filling time of the ion dispatcher for, for example, the first group of ions can be reduced, thereby reducing the cycle time of the ion dispatcher.

[0032] In some embodiments, the ion dispatching device may output ion packets having an m / z range or ion mobility range but lacking a target m / z or target m / z range. In such cases, the ions may be discarded. The mass spectrometry system can still utilize these ion packets if the ions have further uses. For example, a "spare" ion packet in a set can be used to measure undisturbed precursor ions, for additional MS2 measurements, or even for a separate full MS measurement performed from a bypass, to avoid wasting ions or time.

[0033] In some embodiments, the allocation of target m / z or target m / z range to the first and second groups can be optimized to reduce the occurrence of ion scheduling cycles where output ion packets do not have associated target m / z or target m / z ranges. For example, the target m / z or target m / z range can be upgraded to an upper group to utilize available ion packets in earlier ion scheduling cycles. Upgrading the target m / z or target m / z range can follow the maximum intensity difference to avoid the upgrade substantially affecting the dynamic range of ions with the upgraded target m / z or target m / z range.

[0034] In some embodiments, the method of the first aspect may be provided as part of a data-independent acquisition (DIA) mass spectrometry method. For the DIA method, the m / z range of interest is divided into multiple target m / z ranges (i.e., DIA windows) for analysis. Typically, the width of each DIA window may not exceed 20Th, 10Th, 5Th, 3Th, or 2Th. Wherein, for ions in each target m / z range output by the ion selection device, the DIA method further includes fragmenting the ions in each target m / z range and performing mass analysis on the ions. By incorporating the ion scheduling method of the first aspect into the DIA mass spectrometry method, the ion output within each DIA window can have an improved dynamic range.

[0035] In some embodiments, the method of the first aspect may be provided as part of a data-dependent acquisition (DDA) mass spectrometry method. For the DDA method, multiple target m / z values ​​of interest can be obtained. For example, the target m / z value of interest can be identified based on the highest intensity of a class from a list of obtained m / z values ​​and associated intensities. The target m / z values ​​can be assigned to two or more groups based on intensity, and then output by an ion selection device. The DDA method may further include fragmenting ions within each target m / z range and performing mass analysis on the fragment ions. By incorporating the ion scheduling method of the first aspect into the DDA mass spectrometry method, the ion output within each DDA window can have an improved dynamic range.

[0036] In some embodiments, the ion selection device may include a first ion scheduling device and a second ion scheduling device. The first ion scheduling device may be configured to separate ions into multiple first ion packets based on their m / z or ion mobility, and sequentially output the first ion packets to the second ion scheduling device in order of their m / z or ion mobility. The second ion scheduling device may be configured to separate each ion packet into multiple second ion packets based on their m / z or ion mobility, and sequentially output the second ion packets in order of their m / z or ion mobility. In some embodiments, the first ion scheduling device may have a larger ion capacity than the second ion scheduling device. Therefore, the first ion scheduling device may accumulate a relatively large number of ions and then release them in approximately m / z order. The second ion scheduling device may then further subdivide these narrower m / z ranges into ion packets with finer resolution, as discussed above. The fill time of the second ion scheduling device may be controlled for each m / z range of ions received from the first ion scheduling device to improve the dynamic range of the scheduled ions.

[0037] In some embodiments, the fill time of the second ion scheduling device can be adjusted for each received first ion packet based on a list of the ionic strengths and associated m / z values ​​of the ions to be analyzed. Therefore, the dynamic range of the ions scheduled for analysis can be improved.

[0038] In some embodiments, for the second group of ions, a pre-filter or mass filter disposed upstream of the ion selection device can selectively attenuate the ions supplied to the ion selection device based on a target m / z or target m / z range for the first group. For example, the pre-filter can be used as a notch filter or a bandpass filter. That is, the pre-filter can selectively remove ions of a target m / z or m / z range assigned to the first group. Therefore, the ions to be separated as part of the second group can have a further improved dynamic range because ions from the first group can be filtered out before entering the ion selection device.

[0039] In some embodiments, the ion dispatching device may include a linear ion director within which ions are separated. In other embodiments, the ion dispatching device may include multiple ion traps (multi-trap ion dispatching device). Each ion trap may have an associated m / z receiving window or an associated ion mobility receiving window. In some embodiments, the multiple ion traps may sequentially output ion packets, such that the ion dispatching device outputs ion packets based on the m / z or ion mobility of the ions. Thus, the multi-trap ion dispatching device may accumulate ions in each ion trap in parallel and then output ion packets sequentially from the ion traps. In some embodiments, for one or more target m / z or target m / z ranges, the ion dispatching device may simultaneously output ions from two or more ion traps to form ion packets.

[0040] In some embodiments, the method of the first aspect may be provided as part of a high dynamic range (HDR) mass spectrometry method. In such embodiments, the HDR method may further include: Accumulates ions in the ion trap that are associated with one or more target m / z values ​​or target m / z ranges from the first group output by the ion selector; and Mass analysis of the accumulated ions is performed in the MS1 domain to generate one or more mass spectra of ions assigned to the first group. Accumulates ions in the ion trap that are associated with one or more target m / z values ​​or target m / z ranges from the second group output by the ion selector; and Mass analysis of the accumulated ions is performed in the MS1 domain to generate one or more mass spectra for ions assigned to the second group; and HDR mass spectra are assembled based on the mass spectra of ions assigned to the first and second groups. By incorporating the ion scheduling method of the first aspect into HDR mass spectrometry, the time spent accumulating ions for the HDR method can be significantly reduced. This, in turn, allows HDR analysis to be more easily integrated into DDA or DIA workflows.

[0041] In some embodiments, the target m / z or the target m / z range assigned to the first group does not exceed: 10, 7, 5, or 3. By limiting the number of targets in the first group, some ion packets output by the ion scheduling device can be skipped (i.e., one or more ion packets may not have associated targets). This, in turn, allows for minimizing the fill time of the first ion scheduling cycle, thereby allowing for rapid completion of the first ion scheduling cycle. This, in turn, can improve the overall cycle speed of the method or increase the time for ion accumulation in subsequent groups.

[0042] In some embodiments, ions to be analyzed can be scheduled for different types of analysis (e.g., MS1, MS2, MS3, or MSn). In embodiments requiring, for example, MS3 analysis, the AGC target for MS3 analysis may be significantly higher than, for example, the AGC target for MS1 or MS2 analysis, to allow for sufficient viable ions after the second-stage fragmentation. Therefore, in some embodiments, the grouping of targets can be reallocated to account for this situation. Thus, in some embodiments, the step of obtaining multiple target m / z or multiple target m / z ranges to be analyzed may include obtaining the target ion current of one or more target m / z or target m / z ranges. The target ion current may also be taken into account when each target m / z or target m / z range is assigned to a first group or a second group based on the ion strength and a list of associated m / z values ​​and an intensity threshold. The target m / z or target m / z range assigned to the first group may be reallocated to the second group based on, for example, the target ion current of the target m / z or target m / z range.

[0043] While in some embodiments the ion selection device may include an ion scheduling device, it should be understood that the method of the first aspect is not limited to ion scheduling methods. Therefore, in some embodiments, the ion selection device may be a mass filtering device that filters ions and outputs a subset of ions based on having a target m / z value or target m / z range for each of the first and second groups of target m / z values ​​or target m / z ranges.

[0044] According to a second aspect of this disclosure, a mass spectrometry system is provided for analyzing ions in a range of interest (m / z). The mass spectrometry system includes an ion selection device and a mass analyzer. The mass spectrometry system is configured to perform the method of the first aspect.

[0045] Therefore, the mass spectrometry system of the second aspect can be used to perform the ion scheduling method according to the first aspect of this disclosure. It should therefore be understood that the mass spectrometry system of the second aspect can incorporate any optional features and associated advantages of the first aspect. In some embodiments, the mass spectrometry system may include a controller configured to cause the mass spectrometry system to perform the method of the first aspect.

[0046] According to a third aspect of this disclosure, a computer program is provided that includes instructions for causing a mass spectrometry system of the second aspect to perform the steps of the method of the first aspect. Therefore, it should be understood that the computer program of the third aspect may incorporate any optional features and associated advantages of the first or second aspect discussed above.

[0047] According to a fourth aspect of this disclosure, a computer-readable medium is provided having a computer program of the third aspect stored thereon. Therefore, it should be understood that the computer-readable medium of the fourth aspect may incorporate any optional features and associated advantages of the first, second, or third aspects discussed above. Attached Figure Description

[0048] Embodiments of this disclosure will now be described with reference to the following non-limiting drawings, in which: - Figure 1 This is a schematic diagram illustrating the separation of ions with different m / z along an ion guide by using a variable DC force to counteract the axial pseudopotential (T-wave) force; - Figure 2 This is a schematic diagram of an ion dispatching method, which accumulates and releases ions with three different m / z values ​​according to an analytical quadrupole isolation window. - Figure 3A A schematic diagram of an ion dispatching device including a single ion trap ion dispatching device according to the present disclosure is shown; - Figure 3B A schematic diagram of an ion dispatching device including a bypass according to the present disclosure is shown; - Figure 3C A schematic diagram of a multi-ion trap ion dispatching device according to the present disclosure is shown; - Figure 4 This is a schematic diagram of a mass spectrometry system including an ion control device according to an embodiment of the present disclosure; - Figure 5 A flowchart of a method according to an embodiment of the present disclosure is shown; - Figure 6 The mass spectra are shown, including the m / z peaks assigned to different groups; - Figure 7 A schematic diagram of the ion dispatching device and the attenuation ion gate is shown; - Figure 8A This is a diagram illustrating the analytical sequence used in the ion scheduling method; - Figure 8B It is shown Figure 8A The graph shows the m / z deviation of the ion pack in the m / z range for each ion scheduling cycle analyzed. - Figure 9 A flowchart of another method according to an embodiment of the present disclosure is shown; - Figure 10A The graph is obtained by classifying 42 DIA windows (10Th, 350-760 throughout the cycle) into optimization groups based on the intensity of ions in the same cycle and sufficient m / z dispersion > 50Th.

[0049] - Figure 10B It shows Figure 10A The m / z target pair analysis of the group; and

[0050] - Figure 11 A schematic diagram of a pre-filter placed upstream of an ion dispatching device is shown, which is used to limit the incident mass range and remove excess ions. Detailed Implementation

[0051] In this disclosure, the term "intensity," when used to refer to an ion aggregate, means the quantity or flux of a particular type of ions generated from a common sample and detected by a mass spectrometer operating under controlled conditions (e.g., but not limited to, within a common measurement time period). In practice, ion intensity refers to the amplitude of a signal corresponding to the quantity or flux of a particular ion type detected. In many cases, the phrase "specific type," as used above, can refer to ions containing a specific mass-to-charge (m / z) ratio or a specific range of restricted m / z ratios. In many cases, the measured m / z ratio can be associated with or indicate the presence of a particular ion composition (i.e., ion species).

[0052] According to embodiments of this disclosure, a spectrometer system is provided. For example, Figure 4 A schematic diagram of a spectrometer system according to an embodiment of the present disclosure is shown. The spectrometer system is a mass spectrometry system 1. The ion scheduling (ion scheduling) method according to an embodiment of the present disclosure can be performed by the mass spectrometry system 1. In other embodiments, the spectrometer system may include an ion mobility analyzer (ion mobility spectrometer system).

[0053] Mass spectrometry system 1 can be used to analyze data from chromatographic devices such as liquid chromatography (LC) columns. Figure 4 (Not shown in the image) The sample is supplied. One such example of an LC column is the ProSwift (RTM) monolithic column from Thermo Fisher Scientific, Inc., which provides high-performance liquid chromatography (HPLC) by forcing a sample carried in the mobile phase through a stationary phase that consists of irregular or spherical particles under high pressure. In an HPLC column, sample molecules elute at different rates depending on their degree of interaction with the stationary phase. In other embodiments, sample molecules may be supplied by any other suitable means, such as gas chromatography columns or other sample delivery methods known to those skilled in the art.

[0054] An ion source can be used to ionize sample molecules to generate precursor ions. Figure 4 In the embodiments, the ion source is an electrospray ionization source (ESI source) 20 under atmospheric pressure.

[0055] The precursor ions generated by the ESI source 20 can then enter the vacuum chamber of the mass spectrometry system 1 and be guided by the capillary 25 into the ion funnel 30. The precursor ions are focused by the ion funnel 30 into the injection filter 40, which injects the precursor ions into the ion dispatching device 50. In some embodiments, it can be used as a mass filter to selectively attenuate ions.

[0056] Figure 4 The illustrated ion scheduling device 50 includes an ion separation path 52 (along which ions are separated according to their m / z ratio) and a bypass path 54 (along which ions are not separated according to their m / z ratio). The ion scheduling device also includes a path selection region 56, which selects whether ions travel along the ion separation path 52 or along the bypass path 54. Therefore, Figure 4 The ion control device 50 shown is an ion control device including a bypass, such as... Figure 3B As further shown. It should be understood that, Figure 3A )and Figure 3C The ion dispatching device of the mass spectrometry system 1 can also be used as the ion dispatching device 50 of the mass spectrometry system 1, as further described below. Further details of the ion dispatching device 50 according to this disclosure are discussed in more detail below.

[0057] Ion attenuation device 60 may be located at the distal end of ion dispatching device 50. Ion attenuation device 60 may be configured to control the passage of precursor ions from ion dispatching device 50 into a downstream mass selector in the form of a quadrupole mass filter 70. Alternatively, ion attenuation device 60 may be composed of a static lens ( Figure 4 Instead of (not shown in the image), the static lens can be configured to guide ions from the ion dispatching device 50 to the quadrupole mass filter 70 without any intentional attenuation of the ions. In some embodiments, the ion attenuation device 60 may also be located after (i.e., downstream of) the quadrupole mass filter 70.

[0058] The quadrupole mass filter 70 is typically, but not necessarily, segmented and functions as a bandpass filter, allowing selected m / z or a limited range of m / z to pass through while excluding precursor ions of other m / z. Therefore, the quadrupole mass filter 70 can be an ion selection device according to this disclosure. That is, the quadrupole mass filter 70 can be configured to select a subset of ions from a given quantity of ions received by the quadrupole mass filter 70. In some embodiments, the quadrupole mass filter 70 can be operated to sequentially select and output ions in order of their m / z (e.g., increasing or decreasing m / z). For example, the quadrupole mass filter 70 can be gradually moved along its passband or m / z window to change the m / z of the ions output by the quadrupole mass filter 70. The quadrupole mass filter 70 can also operate in RF-only mode, in which it is not m / z selective, i.e., it essentially transmits all m / z precursor ions.

[0059] although Figure 4 A quadrupole mass filter 70 is shown, but it should be understood that any suitable ion selection device that can filter ions based on the m / z or ion mobility of ions can be used as an ion selection device. Figure 4 In some embodiments, the quadrupole mass filter 70 is downstream of the ion dispatching device 50. In some embodiments, the quadrupole mass filter 70 may be used in conjunction with the ion dispatching device 50 to form an ion selection device.

[0060] Furthermore, in some embodiments, more than one ion selection device 50 may be provided. For example, an additional mass selection device may be provided downstream of the ion routing multipole 120. In this way, MS3 or MSn scans may be performed if necessary (typically using a time-of-flight (TOF) mass analyzer 150 for mass analysis).

[0061] Mass spectrometry system 1 can operate in various modes for the analysis of precursor ions in the MS1 and / or MS2 domains. In the first operating mode, a first mass analyzer (e.g., Figure 4 The orbital trap mass analyzer 110 analyzes precursor ions in the MS1 domain. Therefore, according to this disclosure, in the first operating mode of the mass spectrometry system 1, MS1 analysis can be performed using the orbital trap mass analyzer 110.

[0062] In the first operating mode, precursor ions can exit the quadrupole mass filter 70 through the ion gate 80 and the transfer multipole 90 and enter the first ion trap 100 (bent trap or C-trap). The first ion trap 100 has a longitudinally extending electrode supplied with an RF voltage and an end cap supplied with a DC voltage. The result is a potential well extending along the longitudinal axis of the first ion trap 100. In the first operating mode, ions can be trapped and cooled in the first ion trap 100, or transferred to the ion routing multipole 120, where the ions are cooled. The movement of ions can be controlled by applying a DC end cap voltage to the first ion trap 100. The implantation time (IT) of ions implanted into the first ion trap 100 (or the ion routing multipole 120) determines the number of precursor ions (ion swarms) available for subsequent analysis. Depending on the analysis to be performed, precursor ions can be directed from the first ion trap 100 or from the ion routing multipole 120 to different parts of the mass spectrometry system 1.

[0063] If the precursor ions are to be analyzed by the orbital trap mass analyzer 110, and if the ions are cooled in the ion routing multipole 120, they can then be transferred back to the first ion trap 100 for analysis by the orbital trap mass analyzer 110. The precursor ions can then be orthogonally ejected from the first ion trap 100 toward the orbital trap mass analyzer 110. Figure 4 As shown, the orbital capture quality analyzer 110 can be an Orbitrap sold by Thermo Fisher Scientific, Inc. TM Mass Analyzer. The orbit trap mass analyzer 110 has an eccentric injection port through which precursor ions are coherently injected into the orbit trap mass analyzer 110. The precursor ions are then trapped within the orbit trap mass analyzer 110 by a superlog electric field and perform reciprocating motion in the longitudinal direction while orbiting around the internal electrodes.

[0064] The axial component (more or less) of the motion of the ion packet in the orbital trap mass analyzer 110 is defined as simple harmonic motion, where the angular frequency in the z-direction is related to the square root of the mass-to-charge ratio of a given ion species. Therefore, as time progresses, the precursor ions separate according to their mass-to-charge ratio.

[0065] Precursor ions in the orbital trapping mass analyzer 110 are detected using an image current detector (not shown), which generates a "transient" in the time domain containing information about all ion species as they pass through the detector. This transient is then subjected to a Fast Fourier Transform (FFT), producing a series of peaks in the frequency domain. Based on these peaks, a mass spectrum representing the abundance / ion intensity relative to m / z can be generated.

[0066] In the above configuration, precursor ions within the mass range of interest (selected by the quadrupole mass filter 70) are analyzed by the orbital trap mass analyzer 110 without fragmentation. The resulting mass spectrum is represented as MS1.

[0067] although Figure 4 The orbital trapping mass analyzer 110 is shown, but it should be understood that other mass analyzers may be used as the first mass analyzer according to embodiments of this disclosure. For example, a Fourier transform ion cyclotron resonance (FTICR) mass analyzer may be used to analyze precursor ions in the MS1 domain. Mass analyzers such as the orbital trapping mass analyzer 110 and the ion cyclotron resonance mass analyzer may also be used in this invention even when other types of signal processing, different from Fourier transform, are used to obtain mass spectrometry information from transient signals (see, for example, WO-A-2013 / 171313, ThermoFisher Scientific). In some embodiments, a TOF mass analyzer may also be used instead of the orbital trapping mass analyzer 110 to analyze precursor ions in the MS1 domain.

[0068] In the second operating mode of the mass spectrometry system 1, precursor ions can be analyzed by the TOF mass analyzer 150 (the second mass analyzer) in the MS1 domain (the MS1 scan performed by the TOF mass analyzer 150). The precursor ions to be analyzed by the second mass analyzer can be mass filtered by the quadrupole mass filter 70. Therefore, precursor ions can be filtered to include precursor ions from the m / z range of interest or from a sub-m / z range of interest.

[0069] To enable the TOF mass analyzer 150 to analyze precursor ions, the precursor ions can enter the first ion trap 100 from the quadrupole exit lens / tangent lens arrangement 80 and the first transfer multipole 90, and continue their path through the first ion trap 100 into the ion routing multipole 120. Therefore, the first ion trap 100 can also be effectively operated as an ion guide in the second operating mode. Alternatively, the precursor ions can be cooled in the first ion trap 100 and subsequently ejected axially from the first ion trap 100 into the ion routing multipole 120. The precursor ions can then continue through the ion routing multipole 120 and be ejected from the ion routing multipole 120 at the opposite axial end of the first ion trap 100. Therefore, the ion routing multipole 120 can also be effectively operated as an ion guide in the second operating mode.

[0070] The ejected precursor ions enter ion director 130. Ion director 130 can be configured to guide the precursor ions from ion routing multipole 120 to ion processor 140. Ion processor 140 can be configured to process the ions into ion packets suitable for injection into TOF mass analyzer 150. Ion processor 140 may include an RF voltage-controlled third ion trap containing a buffer gas. For example, a suitable buffer gas is one with a pressure range of 5 x 10⁻⁶. -4 mbar to 2x10 -2 Nitrogen gas is contained within mbar. An ion processor can optionally be used to induce ion fragmentation for analysis in the MS2 domain. For analysis in the MS1 domain, ion fragmentation is not intended, and ions can therefore be transferred from the fragmentation chamber 141 of the ion processor to the extraction trap 142 of the ion processor without undergoing any intentional fragmentation. The ion processor 140 is capable of rapidly cutting off the applied RF voltage and applying a DC voltage to extract the captured precursor ions. Suitable flat extraction traps, also known as rectangular ion traps, are further described in US9,548,195(B2).

[0071] although Figure 4 The embodiments shown depict ion processor 140 (ion trap), but it should be understood that other methods may also be provided to form ion packets of precursor ions. For example, the relatively slow transfer of ions through a multipole can be used to influence ion focusing, which can then be ejected as a single packet into TOF mass analyzer 150. Alternatively, orthogonal displacement of precursor ions can be used to form ion packets. Further details of these alternatives can be found in US-A-20030001088, which describes a traveling-wave ion focusing method, the contents of which are incorporated herein by reference.

[0072] exist Figure 4 The TOF mass analyzer 150 shown is a multiple reflection time-of-flight mass analyzer (MR-TOF). The TOF mass analyzer 150 is constructed around two opposing ion mirrors 160, 162 that extend in the drift direction. The mirrors are opposite each other in a direction orthogonal to the drift direction. Ion processor 140 injects ions into the first mirror 160, and the ions then oscillate between the two mirrors 160, 162. The ejection angle of the ions from the extraction trap 140 and the additional deflectors 170, 172 allows control over the ion energy in the drift direction, guiding the ions along the length of the mirrors 160, 162 during oscillation, thus producing a Z-shaped trajectory. The mirrors 160, 162 are tilted relative to each other, creating a potential gradient that delays the ion drift velocity and causes the ions to be reflected back in the drift dimension and focused onto detector 180.

[0073] The precursor ions accumulated in the ion processor 140 are injected as ion packets into the TOF mass analyzer 150 (the second mass analyzer). The time taken for the precursor ions to reach the detector 180 is recorded by the TOF mass analyzer 150 and used to generate an MS1 ​​mass spectrum of the precursor ions.

[0074] In the third operating mode of mass spectrometry system 1, TOF mass analyzer 150 (second mass analyzer) can be used to analyze precursor ions in the MS2 domain (MS2 scan).

[0075] To analyze precursor ions in the MS2 domain, some precursor ions can be transferred from the quadrupole mass filter 70 to the ion routing multipole 120 in a manner similar to the second operating mode described above. The precursor ions to be transferred can be ion packets already output from the ion dispatching device 50, or precursor ion packets that have not yet been dispatched. The output ions (i.e., ion packets) can be further mass-selected by the quadrupole mass filter 70. For example, the output ions can be further mass-selected to include target precursor ion species, or further mass filtering can be performed using the m / z isolation window (target m / z range) of the quadrupole mass filter 70 (e.g., as part of the DIA method), as described in more detail below.

[0076] The ions can then be transferred to the fragmentation chamber 141 of the ion processor 140. The fragmentation chamber 141 is in... Figure 4 The mass spectrometry system 1 contains a high-energy collisional dissociation (HCD) device. A buffer gas can be supplied to the fragmentation chamber 141. When the precursor ions are to be fragmented, the kinetic energy of the precursor ions may increase, causing the precursor ions that reach the fragmentation chamber 141 and collide with the buffer gas molecules to fragment into fragment ions.

[0077] Despite Figure 4 The ion processor 140 shows an HCD fragmentation chamber 141, but alternatively other fragmentation devices employing methods such as collision-induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), photodissociation, etc., may be used.

[0078] Fragmented ions can be injected from fragmentation chamber 141 into extraction trap 142 of the ion processor. The ejected fragmented ions can accumulate in extraction trap 142 to form ion packs. The fragmented ions can then be injected into TOF mass analyzer 150 as described above.

[0079] It should be understood that in some embodiments, the first mass analyzer (orbit trap mass analyzer 110) and the second mass analyzer (TOF mass analyzer 150) can operate simultaneously. That is, the mass spectrometry system 1 can operate in the first operating mode simultaneously with a second or third operating mode. According to this disclosure, the ion dispatching device 50 can be operated to output ion bundles (and / or subsets of ions from the quadrupole mass filter 70) such that the orbit trap mass analyzer 110 and the TOF mass analyzer 150 can operate efficiently and also have improved dynamic range.

[0080] Mass spectrometry system 1 can be located in the controller ( Figure 4 Under the control of (not shown), the controller is configured, for example, to control the timing of the ejection of the trapping assembly, control one or more power supplies (not shown) to set appropriate potentials on electrodes such as quadrupoles for focusing and filtering ions, capture mass spectrometry data from the orbital trapping device 110, capture mass spectrometry data from the orbital trapping mass analyzer 110 and the TOF mass analyzer 150, control the sequence of MS1 and MS2 scans, etc. It should be understood that the controller may include a computer operable according to a computer program containing instructions to cause the mass spectrometry system 1 to perform the steps according to the method described herein.

[0081] Next, a method for ion scheduling using the ion scheduling device 50 will be described. Figure 1 This is an illustrative diagram showing a general principle of ion dispatching using traveling waves. It should be understood that... Figure 1 The diagram shown is only one possible mechanism for ion dispatching using the ion dispatching device 50, and other methods of ion dispatching can also be applied to the methods of this disclosure. Figure 1 In this process, nonlinear DC potential (opposite potential gradient) and traveling wave (time-varying potential) cause ion separation over a certain length. Figure 1 This shows a traveling wave at a certain moment; in practice, the traveling wave is made to travel in the first direction ( Figure 1 (From left to right) Proceeding continuously. The relative DC force and pseudoforce cause ions with different m / z to stabilize at different positions.

[0082] In order to achieve Figure 1m / z-dependent separation (or ion mobility-dependent separation) can be achieved by opposing a potential gradient (e.g., a static field) with a pseudo-force generated by a dynamic (time-varying) potential. In some ion dispatching devices 50 of this disclosure, an axial pseudo-potential generated by a traveling wave (T-wave) is opposed to a rising DC gradient. Such a T-wave can be a multiphase (e.g., 3-phase or higher) traveling wave. The pseudo-force propels ions until they reach a region where the DC force is equal to or greater than the pseudo-force, at which point the ions are captured (or, if the DC gradient is insufficient, the ions are expelled from the device). Since the pseudo-force depends on m / z, the capture location of the ions also depends on their m / z. Therefore, ions can be captured at various different locations in the separation (first) direction.

[0083] Separated ions (or separated ion packets) can be released from the ion dispatching device 50 in an m / z-dependent manner by applying a DC potential or traveling wave amplitude / frequency (or duty cycle / pulse velocity of a digital waveform) through scanning / stepping. Alternatively, many other methods of ion extraction from the guide can be applied: DC gradients and T-waves can be removed, and ions are released over time based on their spatial separation / drift time, or a very slow traveling wave can be applied to drive out ions in a slow beam, and so on. The accumulated ions can then be released to, for example, a quadrupole mass filter 70 matched to its m / z, and thus losses at the quadrupole can be mitigated.

[0084] Specifically, it should be understood that in some embodiments, the ion scheduling device 50 may be configured to separate ions based on ion mobility. Therefore, the ion scheduling device 50 may divide ions into multiple ion packets (ion packs), each ion pack having a different range of ion mobility. The ion scheduling device 50 may then output the ion packs sequentially based on ion mobility (e.g., outputting ion packs in ascending order of ion mobility, or outputting ion groups in descending order of ion mobility). For example, various scheduling devices (or portions thereof) described herein may be configured to separate ions based on ion mobility by: (1) stopping the generation of traveling wave voltage AC voltage oscillations (see...) Figure 1 (2) Maintaining a constant potential gradient (i.e., a linear change in DC potential, rather than a linear change in DC potential) over the entire length of the corresponding device or section. Figure 1 (The nonlinear changes shown at the top) while maintaining controlled gas pressure within the device or section.

[0085] Because ions can be separated from each other based on their ion mobilities, data can be obtained from a specific set of target ion species, which are the targets of analysis based on their specific individual ion mobilities. Such methods may include: Obtain a list of ionic strength and associated ionic mobility values ​​for the ions to be analyzed; Obtain the mobility range of multiple target ions to be analyzed; Based on a list of ion strengths, the associated mobility of the ions, and an intensity threshold, each target ion mobility range is assigned to a first group or a second group, wherein the target mobility range in the first group is associated with a higher ion strength compared to the target ion mobility range in the second group. The ion selector is used to sequentially select and output ions with the target ion mobility range assigned to the first group for analysis. The ion selector sequentially selects and outputs ions with the target ion mobility range assigned to the second group for analysis; and Mass analysis was performed on the first and second groups of accumulated ions output separately.

[0086] Since the application of traveling wave potential typically requires axial segmentation of the electrode, it can be achieved using, for example, stacked ring ion directors and / or related structures. Figure 1 The ion scheduling arrangement is shown. Figure 3A An example of a linear ion dispatching device 200 is shown, which is a device for separating ions, in which the following can be implemented? Figure 1 The method. The linear ion dispatching device 200 includes a separator region 201, a pre-accumulation region 202, a funnel / initial capture region 203, and an ion outlet 204.

[0087] In this particular example, the linear ion dispatching device 200 has a stacked ring structure and also includes an optional segment for ion trapping from the inlet capillary and a pre-accumulation region 202 to maximize the duty cycle. Apart from the separation region 201 in which T-waves and DC gradients are applied, the single ion trap ion dispatching device 200 is shown to include a similar pre-accumulation region 202 for pre-accumulating ions during the operation of the separator 201.

[0088] The linear ion dispatching device 200 includes an ion funnel 203, which can be opened from an inlet capillary or, for example, Figure 4 The illustrated ion gate receives ions, and a small funnel-shaped region compresses the extracted ions as they leave the device into a higher vacuum (lower pressure) region. The funnel-shaped region 203 and the pre-accumulation region 202 may have their own applied DC offset and gradient, and a controllable (i.e., variable) DC barrier may be provided between the accumulator 202 and the separator 201. A potential (e.g., from an auxiliary electrode, not shown) may be applied within the guide to cause ions to move laterally (i.e., perpendicular to the axis of the ion guide) to allow a large amount of charge to be distributed over a wider region to reduce space charge effects.

[0089] After the ions have passed through the separation region 201 of the linear ion dispatching device 200, they exit the device through the ion outlet 204, for example, to reach an ion guide at a higher vacuum (lower pressure). Therefore, broadly speaking, the separation region and / or accumulation region described herein can be a vacuum region. The separation region 201 and / or accumulation region 202 can be at a lower pressure than the upstream region of the device (i.e., the region upstream of the separation region 201 and / or accumulation region 202) and / or at a higher pressure than the downstream region of the device (i.e., the region downstream of the separation region and / or accumulation region). Various hermetically sealed housings and pumping methods can be provided to ensure the formation of a vacuum.

[0090] The characteristics of the traveling wave can preferably be configured such that ions pass through the wave, experiencing a pseudo-force rather than being completely entrained within it. This can be achieved, for example, by varying the frequency and / or voltage amplitude of the traveling wave. In principle, a sufficiently high traveling wave potential will only carry away ions and no separation will occur unless the opposite DC is set high enough to balance the effect. Therefore, the opposite potential and the time-varying potential can be fine-tuned to optimize separation performance.

[0091] Linear ion scheduling device 200 can be operated to output ions (or ion packets) separated according to their m / z. First, ions can be transferred from the implantation flat electrode 40 to a pre-accumulation region 202 via an ion funnel 203. Ions (e.g., ions with mixed m / z values, such as ions spanning the m / z range of interest) can accumulate in the pre-accumulation region 202. The time allowed for ions to accumulate in the pre-accumulation region 202 (i.e., the fill time) determines the total number of ions to be separated in a single ion scheduling cycle. Therefore, by varying the fill time of the ion scheduling device, the number of ions available to the ion scheduling device can be controlled. As discussed further below, the fill time of the ion scheduling device 50 can be controlled to improve the dynamic range of the mass spectrometry system.

[0092] Ions can then be transferred from the pre-accumulation region 202 to the separation region 201, which can be achieved by applying a DC gradient / offset or a traveling wave to propel the ions along the path of the pre-accumulation region 203. Once the pre-accumulation region 203 has been emptied of ions, further transfer of ions from the pre-accumulation region 203 to the separation region 201 is prevented (e.g., by activating an ion gate). Figure 3A(Not shown in the diagram), and as ions enter, the pre-accumulation region 203 begins to accumulate more ions. Simultaneously, the separation process begins in the separation region 201. The amplitude of the DC gradient (which is preferably curved) is reduced (or alternatively, an increase in the traveling wave amplitude, or both) to the level required for the first lowest m / z ion to leave. After a short delay (typically approximately 0.25 ms to 5 ms), a first ion packet is extracted from the separation region 201. The first ion packet has an m / z value falling within a first m / z extraction window, which may be the lowest of a plurality of m / z extraction windows to be used in the ion scheduling loop. The controller may select the m / z range for each m / z extraction window based on the target m / z or target m / z range to be output, according to the ion scheduling method.

[0093] For example, mass spectrometry system 1 may be conducting an experiment in the m / z range of interest, from 300 m / z to 900 m / z. Within this range of interest, each ion packet output by ion dispatcher 50 may span an m / z extraction window of approximately the same size (although in some embodiments, the m / z extraction window may have different sizes). For example, the width of each m / z extraction window may be at least: 10Th, 20Th, 30Th, 50Th, 70Th, 100Th, 150Th, or 200Th. The m / z extraction window width achievable by ion dispatcher 50 depends on the resolution of ion dispatcher 50 and the operating frequency of ion dispatcher 50 (i.e., the duration of the ion dispatch cycle). Ions may be separated into m / z-dependent (or ion mobility-dependent) packets within separation region 201, where the ion packet closest to the outlet has the lowest (average) m / z. The next ion pack further inside the separation region 201 will have a higher (average) m / z, and so on, with the innermost ion packs having even higher (average) m / z. Therefore, each ion pack can span a different m / z range. In some embodiments, the m / z range of each ion pack separated in the separation region 201 may overlap with that of other ion packs. That is, ions with a given m / z (or ion mobility) can be distributed among two or more ion packs (depending on the m / z range of the ion packs).

[0094] Therefore, ion packets can be output sequentially from the ion dispatching device 200 in m / z order. For example, for the m / z range of interest from 300 m / z to 900 m / z and an m / z extraction window width of approximately 100 Th, the first ion packet (lowest m / z) can have a range of 300 m / z to 400 m / z. The second ion packet can have a range of 400 m / z to 500 m / z, the third packet has a range of 500 m / z to 600 m / z, and so on.

[0095] The extracted ion packets can exit the ion dispatching device 50 and proceed to the downstream quadrupole mass filter 70 (or other ion selection device) for further ion selection. The DC gradient applied to the ion dispatching device 50 can then be further reduced to the next m / z extraction window in the sequence, and so on, until the range of interest in m / z has been traversed (i.e., ions in m / z extraction windows spanning the range of interest in m / z have been cleared). At this point, the accumulation region 202 can be cleared again, and the cycle repeats.

[0096] Therefore, in each cycle of the linear ion scheduling device 200, ions can be output from the linear ion scheduling device 200 according to their m / z. That is, ions can be output from the linear ion scheduling device 200 in the form of a packet sequence, with the m / z of each consecutive ion packet typically increasing. Specifically, ions can be extracted from the linear ion scheduling device 200 using an m / z extraction window sequence. It should be understood that the general techniques for ion scheduling described with respect to the linear ion scheduling device 200 can also be applied to... Figure 3B Bypass ion regulation device 300 and Figure 3C 400 multi-ion trap ion dispatching device.

[0097] like Figure 3A As shown, ions can be output from the linear ion dispatcher 200 in approximately m / z order of ion packets, where they are further separated by a quadrupole mass filter 70. The fill time (cumulative time, or injection time) of the quadrupole mass filter 70 can be controlled by a controller. Specifically, the fill time can be controlled based on known characteristics of the ion groups injected from the ion dispatcher 50 into the quadrupole mass filter 70 in an attempt to improve the dynamic range of the spectrometer system, as further described below.

[0098] Next, we will refer to Figure 5 The flowchart describes a method 500 for scheduling ions for analysis within the m / z range of interest. Method 500 can be derived from... Figure 4 The mass spectrometry system 1 is used for this purpose.

[0099] In step 501, mass spectrometry system 1 acquires data indicating the m / z and associated intensity of the ions within the m / z range of interest. For example, mass spectrometry system 1 can acquire this data by performing mass analysis on ions generated by ESI source 20. The mass analysis can be a mass analysis performed in the MS1 domain within the m / z range of interest (i.e., a survey analysis of the analyte). This mass analysis can be performed, for example, by an orbital trap mass analyzer or a TOF mass analyzer 150. In some embodiments, data obtained from other mass analyses performed by mass spectrometry system 1 can be used to acquire data indicating the m / z and associated intensity of the ions within the m / z range of interest. For example, automatic gain control (AGC) can be used to measure the generated data. In some embodiments, mass analysis can be performed to provide an impression of the distribution of ion species within the m / z range of interest. Therefore, the survey analysis performed can be performed at a relatively lower resolution and / or with a relatively short associated fill time and / or for a relatively short duration compared to other mass analyses performed by mass spectrometry system 1.

[0100] Figure 6 Typical mass spectra that might be obtained as a result of investigational analysis are shown. For example... Figure 6 As shown, the peaks corresponding to the ion species are distributed within the range of m / z of interest (10 m / z to 2000 m / z).

[0101] As part of step 501, the method also obtains multiple target m / z values ​​or multiple target m / z ranges to be analyzed. Ions with target m / z values ​​or multiple target m / z ranges can be scheduled according to the ion scheduling method 500 of this disclosure. Depending on the type of analysis to be performed (e.g., DIA, DDA, HDR), the target can be a target m / z value (i.e., for a single ion species) or a target m / z range (i.e., for ions falling within an m / z window). The number of targets may depend on the analysis to be performed. For example, for DDA analysis, the top 10, 20, 30, or 40 ion species with the highest intensities can be used as targets. For DIA analysis, the m / z range of interest can be divided into, for example, at least 50 target m / z ranges to be analyzed.

[0102] In step 502, the method assigns each target m / z or target m / z range to one of a plurality of groups (e.g., a first group or a second group). Each target is assigned based on the ion intensity associated with the target m / z or target m / z range. For the target m / z range, the intensity considered when assigning a group can be, for example, the average intensity within the target m / z range. Each group to which a target is assigned has an associated intensity range (or intensity threshold). For example, a first group with the highest intensity of targets can be defined by a first intensity threshold. Target m / z ranges (or target m / z ranges with average intensity) with associated intensities greater than the first intensity threshold can be assigned to the first group. A second group can be defined by a first intensity threshold and a second intensity threshold. Thus, targets with associated intensities no greater than the first intensity threshold but greater than the second intensity threshold can be assigned to the second group. A third group can be defined by a second intensity threshold and a third intensity threshold, and so on. Therefore, it should be understood that each group can span an intensity range.

[0103] In some embodiments, intensity thresholds can be specified by absolute ionic intensity. In some embodiments, intensity thresholds can be normalized to ionic intensities obtained from survey analyses. That is, a first intensity threshold, a second intensity threshold, and a third intensity threshold can be specified as a percentage of the intensity of the most intense ion species (i.e., the relative abundance of each ion species). For example, the first intensity threshold could be about 10% of the intensity of the most intense ion species. The second intensity threshold could be about 1% of the intensity of the most intense ion species. The third intensity threshold could be about 0.1% of the intensity of the most intense ion species. In some embodiments, such as for DDA analysis, targets falling below the lowest intensity threshold may not be distinguishable from noise (e.g., ions below about 0.1% of the intensity of the most intense ion species) and therefore cannot be assigned to a group.

[0104] Figure 6 The diagram also shows an example of grouping targets. Figure 6 In this process, each peak corresponding to an ion species is assigned to a group based on the relative intensity (or relative abundance) of each ion peak. Each ion peak or target m / z with a relative abundance greater than 10% is assigned to the first group. Each target m / z with a relative abundance of at least 1% and no greater than 10% is assigned to the second group. Each target m / z with a relative abundance of at least 0.1% and no greater than 1% is assigned to the third group. It should be understood that... Figure 6 The number of groups and the ion intensity distribution between groups shown are only one possible example, and other intensity distributions and / or number of groups can be used.

[0105] In step 503, the target m / z or target m / z range within the first group can be analyzed. In an embodiment of method 500, for each target m / z or target m / z range of the first group, ions can be transferred to the mass filter device 70 without undergoing separation in the ion dispatching device. Therefore, a subset of ions for each target m / z or target m / z range of the first group can be selected from the entire ion population using the quadrupole mass filter 70. Since the target m / z values ​​or target m / z ranges of the first group are associated with relatively high-intensity ions, the relatively short fill time of the quadrupole mass filter 70 can be used to obtain an appropriate number of ions for each ion subset to be output. Furthermore, since all targets are relatively high-intensity species, the effect of one high-intensity ion species suppressing another is limited, thus limiting the advantage of further separating the targets of the first group using the ion dispatching device 50. Instead, the cycle time of the method can be improved by not operating the ion dispatching device 50 on the first group.

[0106] The ion subset output from the quadrupole mass filter 70 can then be transferred to the orbital trap mass analyzer 110 or the TOF mass analyzer 150 for mass analysis in, for example, the MS1 or MS2 domain as described above. If MS2 analysis (or MS3, or MSn) is required, the ions used for each target analysis can be fragmented before analysis. The specific mass analysis to be performed will depend on the type of mass spectrometry experiment being performed (e.g., DIA, DDA, HDR, etc.).

[0107] For the ion scheduling device 50, the cycle time of each ion scheduling cycle may be related to the speed of the ion scheduling device 50, the desired signal amplification, any need to limit ion accumulation time to prevent overload, and the number of individual ion packets to be output in the cycle. For relatively low-intensity ion swarms (e.g., targets in the second group), it is generally desirable to maximize the fill time and the number of target windows. This may result in relatively slow cycles, but can improve signal amplification. In some embodiments, particularly for the first group of targets, when the target window is small, the ion scheduling device 50 can be operated faster, for example, by adjusting the voltage to skip unmeasured areas or reducing the resolution. This is particularly advantageous when measuring a small number of high-intensity species, which requires lower amplification, shorter ion accumulation time, and fewer target windows. Thus, in some embodiments, the number of target m / z or target m / z ranges allocated to the first group may not exceed: 10, 7, 5, or 3. Therefore, the first ion scheduling cycle can be optimized to be performed within a finite time, thereby freeing up additional analysis time for lower-intensity targets.

[0108] In steps 504, 505, and 506, additional groups of target m / z values ​​or target m / z ranges are scheduled for analysis. For the second and subsequent groups, ion scheduling device 50 can be used to separate ions into packets based on their m / z or ion mobility. For each group, the fill time of ion scheduling device 50 can be set based on the intensity associated with the ions in that group. Therefore, the fill time for selecting and outputting ions for the second group of target m / z values ​​or target m / z ranges can be longer than the fill time for selecting and outputting ions for the first group of target m / z values ​​or target m / z ranges. Therefore, the ion packets output by ion scheduling device 50 may include larger ion clusters for the target in the second group than are available in other cases.

[0109] For a target m / z or target m / z range of a second group (or virtually any other group), multiple ion scheduling cycles can be performed to analyze all target m / z or target m / z ranges of that group. Each ion scheduling cycle may include an ion scheduling device 50 receiving ions, wherein the ion scheduling device 50 divides the ions into multiple ion packets based on the ion's m / z or ion mobility, and outputs multiple groups sequentially. Each ion packet output by the ion scheduling device 50 has an associated m / z range or ion mobility range. For each ion packet output by the ion scheduling device 50, a quadrupole mass filter 70 may select a subset of ions based on the target m / z or target m / z range. If two or more target m / z or target m / z ranges of a group (e.g., the second group) fall within the m / z range or ion mobility range of the ion packet, multiple ion scheduling cycles (e.g., multiple second ion scheduling cycles) are performed such that no more than one subset of ions is selected from each ion packet. By separating ions into packets based on m / z or ion mobility before selecting ion subsets for each target m / z or target m / z range, the influence of relatively strong precursors on the dynamic range can be reduced or eliminated. Therefore, each ion subset output for the second (and subsequent) groups may have an increased number of ions due to increased fill time, thus improving the dynamic range of subsequent mass analyses.

[0110] As shown in step 505, a subset of ions for each target m / z or target m / z range in the second group (or subsequent group) is output from the ion dispatching device 50 and the mass filter 70 and mass analysis is performed in MS1 ​​or MS2 (as the case may be).

[0111] In some embodiments, ions to be analyzed can be scheduled for different types of analysis (e.g., MS1, MS2, MS3, or MSn). In embodiments requiring, for example, MS3 analysis, the AGC target for MS3 analysis can be significantly higher than, for example, the AGC target for MS1 or MS2 analysis, to allow for sufficient viable ions after the second-stage fragmentation. In this case, the grouping of scans should consider not only the peak intensity but also the number of different ions required by the method. Therefore, in some embodiments, obtaining multiple target m / z or multiple target m / z ranges to be analyzed includes obtaining the target ion current of one or more target m / z or target m / z ranges. Thus, each target m / z or target m / z range can be assigned to a first group or a second group based on the ion intensity and a list of associated m / z, the target ion current, and an intensity threshold, wherein the target m / z or target m / z range assigned to the first group can be reassigned to the second group based on the target ion current. For example, if a relatively strong target m / z is scheduled for MS3 analysis, the relatively strong ion species can be grouped with the lower-intensity ion species scheduled for MS2 analysis, since the cumulative time of the two analyses in the ion scheduling device 50 may be similar.

[0112] As shown in step 506, once all target m / z values ​​or target m / z ranges of, for example, the second group have been acquired, the method can acquire ions of the next group of target m / z values ​​or target m / z ranges until all desired groups have been acquired (e.g., Figure 6 (The example shows three groups). Once all targets in all groups have been collected, one cycle of ion scheduling method 500 is complete. Figure 5 As shown, ion dispatching method 500 can then be repeated. For example, the cycle of method 500 can be performed multiple times as the sample elutes from the column to accurately characterize the sample.

[0113] Essentially, the method of this disclosure recognizes that multiple cycles of the ion scheduling device 50 can typically be performed to analyze all target m / z or target m / z ranges. Therefore, the fill level of the ion scheduling device 50 can vary between the ion scheduling cycles. Relatively strong ion species can be output on one or more first ion scheduling cycles with relatively short fill times, where they will correspondingly (relatively) decay. Relatively weaker precursors can be output on one or more second ion scheduling cycles with longer fill times until the finite ion capacity of the ion scheduling device 50 is reached, in order to improve the dynamic range of ion species output by method 500.

[0114] According to the ion scheduling method of this disclosure, the number of target m / z values ​​or target m / z ranges to be assigned to each group or each ion scheduling cycle within each group can be specified. The number of target m / z values ​​or target m / z ranges in each ion scheduling cycle of the ion scheduling device 50 can depend on the separation resolution of the ion scheduling device and the ion capacity of the ion scheduling device 50. For example, if the ion scheduling device 50 separates ions into ion packets, each ion packet covering not less than, for example, 10% of the m / z range of interest, then it can be concluded that no more than 10 target m / z values ​​or target m / z ranges can be analyzed in each ion scheduling cycle.

[0115] For example, in a method for scheduling ions for a DIA method, it may be necessary to analyze ions in the m / z range of 100 m / z to 1000 m / z. Therefore, the ion scheduling device 50 can be configured to output ion packets, each spanning an m / z range of approximately 100 Th (e.g., packets spanning 100 m / z to 200 m / z, 200 m / z to 300 m / z…900 m / z to 1000 m / z). A quadrupole mass filter can then select a subset of ions with a 10 Th isolation window. It should be understood that the quadrupole cannot select the target m / z range in a regular sequence 100-110, 110-120, etc., but instead can instead perform a single emission from each extracted range in each cycle: 100-110, 200-210…900-910, then the next cycle 110-120, 210-220,…, 910-920, and so on, until all DIA windows are measured. If each ion scheduling cycle can be completed in about 100 ms, then a complete DIA cycle will take about one second.

[0116] To further improve the ion transport efficiency of the ion scheduling method, a subset of ions can be selected from the center range of each ion packet. That is, the center range of each ion packet can coincide with the target m / z or target m / z range to be output for the ion scheduling cycle. The ion species at the edges of each ion packet in the ion scheduling device 50 may suffer transport losses from the ion scheduling device 50.

[0117] To allow analysis of all (e.g., all) DIA target m / z ranges while selecting from the central region of each ion group, the DIA method may further include offsetting the m / z range of each ion packet separated by the ion scheduling device 50 for different ion scheduling cycles. That is, the central m / z of each ion packet output by the ion scheduling device can be offset such that the central m / z coincides with the central m / z of the DIA window to be extracted in the ion scheduling cycle. Therefore, for each of multiple ion scheduling cycles, the bias of the ion scheduling device is varied so that multiple ion groups span different m / z ranges or ion mobility ranges.

[0118] As a simplified explanation of this concept, Figure 8A A series of simplified analyses to be performed as part of the 60-window DIA method are shown, covering the m / z range of interest from 300 m / z to 900 m / z, as well as the 10Th broad target m / z range of the ion to be analyzed. Figure 8B The m / z deviation between the center of the approximately 100Th extraction window of the ion dispatching device 50 and the center of the quadrupole isolation window is shown. Figure 8A In the example, the target m / z ranges to be analyzed in the first ion scheduling cycle are 300-310, 400-410, 500-510, 600-610, 700-710, and 800-810. In practice, the target m / z range for each ion scheduling cycle can be non-uniformly distributed within the m / z range of interest, allowing the ion scheduling device to align the m / z range of each ion packet with the target m / z range. However, the ion scheduling device 50 can optimize its bias for each ion scheduling cycle so that the center m / z of each ion packet is as close as possible to the corresponding target m / z or target m / z range. For example, the m / z range of each ion packet can be varied to minimize the average difference between the center m / z of each ion packet and the center m / z of the corresponding target m / z or target m / z range.

[0119] The bias of the ion dispatching device 50, which is used to change the m / z range of each ion packet output by the ion dispatching device 50, can be achieved by changing the timing or amplitude of the AC or DC voltage ramp used for ion separation. For example, for such... Figure 3A The linear ion dispatching device 200 shown can achieve bias by changing the timing of the application of the AC or DC voltage ramp. For devices that continuously fill the trap array, such as... Figure 3C The multi-trap ion scheduling device 400 shown has an ion scheduling device 50 whose deviation can vary over several ion scheduling cycles to account for the parallel filling of ion traps 402.

[0120] As can be understood from the simplified example, when grouping targets by m / z or m / z range, the ion intensities between different targets can vary significantly. Generally, the method of this disclosure provides multiple ion scheduling cycles, each serving targets with similar intensities. Furthermore, since targets with similar intensities are typically not uniformly distributed within the m / z range of interest, the ion scheduling device 50 may also need to ensure sufficient m / z (or ion mobility) spacing between targets within the same cycle of the ion scheduling device 50 to avoid losses from overlapping extraction windows (which can adversely affect the dynamic range). Moreover, preferably, the maximum number of targets is scheduled in each ion scheduling cycle to efficiently operate the mass spectrometry system 1.

[0121] Essentially, assigning the target m / z value or target m / z range to different groups and different ion scheduling cycles within each group is an optimization problem. Figure 9 A flowchart of an iterative method 600 for allocating targets according to an embodiment of the present disclosure is shown. Figure 9 Method 600 can be derived from Figure 4 The mass spectrometry system 1 is used for this purpose.

[0122] In step 601, a list of candidate precursors with ionic strength and associated m / z is obtained. This list can be generated by a method such as a full MS1 analysis or survey analysis of the m / z range of interest as described above. The list of candidate precursors may include multiple ion species within a target m / z value or a relatively narrow target m / z range.

[0123] In step 602, targets can be sorted by intensity, and in step 603, targets can be assigned to groups based on one or more intensity thresholds. Each intensity threshold (or intensity range) can be specific to a particular group. The intensity thresholds can be fixed; for example, a first intensity threshold for a first group might require targets to have ion currents >1 x 10⁷ ions / second. In some embodiments, the intensity thresholds can be dynamic based on the number of groups and ion intensity ranges specified for the method. The purpose of assigning targets to different groups is to prevent targets with low-intensity ions from being assigned to the same group with very high-intensity ions (and thus having the same ion scheduling cycle).

[0124] In step 604, method 600 proceeds to begin with target scheduling ions from the first group. The first ion scheduling loop can be filled downwards from the target with the highest intensity. As shown in step 605, if each subsequent target satisfies a specified set of conditions, it can be added (step 606) to the pending ion scheduling loop. The specified conditions for the ion scheduling loop may include a minimum interval (minimum m / z interval or minimum ion mobility interval) with other targets added to the pending ion scheduling loop. If a target m / z or target m / z range is too close to another target m / z or target m / z range already added to the pending ion scheduling loop, that target m / z can be discarded (step 607). The method can then proceed to step 608, in which it is checked whether there are any other target m / z values ​​or target m / z ranges within the group that have not yet been considered for scheduling as part of the pending ion scheduling loop (and have been scheduled or discarded). If other targets are available for consideration, the method can repeat steps 605 through 608 to consider other targets. In step 608, the method can also determine that the ion scheduling cycle has scheduled the maximum number of permissible targets. For example, if the ion scheduling device 50 is configured to separate ions into no more than 10 ion packets, the maximum number of targets scheduled can be 10.

[0125] Once the pending ion scheduling cycle is full (i.e., the maximum number of targets has been scheduled), or no other targets are available for consideration, method 600 proceeds to step 609, where the ion scheduling device 50 and the quadrupole mass filter 70 proceed to separate ions into packets and select ion subsets based on the scheduled target m / z value or target m / z range. One or more fill times, such as those of the ion scheduling device 50 and the quadrupole mass filter 70, can be adjusted based on the ion intensity within the group / ion scheduling cycle. The scheduled ions are then output for analysis by the orbital trapping mass analyzer 110 or the TOF mass analyzer 150.

[0126] Once the ion scheduling device 50 outputs ions for one ion scheduling cycle, the next ion scheduling cycle can be filled. For the next ion scheduling cycle, previously rejected targets can be reconsidered, starting with the target with the highest intensity (steps 610, 603, 604). The ion scheduling cycle can be filled before moving to the next group of targets, until all targets in a group are used up. After analyzing all groups, the candidate precursor list can be refreshed, and allocation can begin again.

[0127] Figure 10A and 10B It shows Figure 9An example of the method is provided, which classifies 42 DIA windows (10Th, total m / z range of interest 350–760) into optimized groups based on intensity and ions in the same group having Δm / z > 50, according to a random intensity distribution. Figure 10a shows a plot of intensity versus number of scans (analyses), illustrating groupings of similar intensities and the order in which targets are scheduled for analysis. Figure 10b shows the number of analyses scheduled for m / z targets. In this example, the mass distance rule (Δm / z > 50) is allowed to be ignored for group 1 because these ions represent targets that are too strong for the ion scheduling device 50 and can be better measured by conventional MS / MS procedures, preferably using the bypass region 54 in the ion scheduling device 50. Without a bypass, these targets can preferably be scheduled near a conventional full MS or AGC survey scan when no conventional ion scheduling operation is performed.

[0128] Figure 9 , Figure 10A and Figure 10B Method 600 illustrates the processing of target groups by mass spectrometry system 1 in order of intensity from highest to lowest (i.e., group 1, then group 2, then group 3, etc.). In some embodiments, it may be preferred to first analyze the lower-intensity, higher-numbered groups by mass spectrometry system 1, because otherwise these ion species may no longer be detectably eluted by the time the instrument reaches them. It should also be understood that the intensity of some ion species identified in the survey analysis may increase over time (i.e., species detected at the start of elution rather than at the tail of elution) and may further intensify with delays in processing. Such cases can be identified based on their performance in previous cycles / survey analyses. Peak detection algorithms are also known to predict the peak shape when ion species are detected in previous analyses or survey analyses, which can be used to update the intensity list of the obtained ion species.

[0129] Therefore, the method and mass spectrometry system 1 according to this disclosure aim to improve the dynamic range of the instrument incorporated into the ion dispatching device 50 by classifying ions into the ion dispatching device 50 approximately based on intensity distribution. This reduces or eliminates overload of the ion dispatching device 50 due to relatively strong targets and underfilling of the ion dispatching device due to relatively sparse targets. Furthermore, the method according to this disclosure can also accelerate target acquisition by reducing the ion accumulation time of many relatively strong ion species.

[0130] When processing low-intensity precursors, overload of the ion dispatching device 50 may be prevented through pre-filtration or separation-dependent attenuation within the device. Therefore, the ion dispatching method according to this disclosure can be combined with or complemented by any other precursor ion sorting and filtering method, such as dynamic exclusion, exclusion based on other parameters (such as resolution), and the use of an inclusion list that includes the target (e.g., integrating high-sensitivity measurements of standards and known biomarkers into the DDA / DIA method).

[0131] When very high-intensity ions are mixed with low-intensity ions, the ion dispatching method may have a reduced dynamic range. In such cases, the very high-intensity ion species overfill the ion dispatching device 50 and may prevent the acquisition of increased signal strength from the low-intensity ion species using a longer accumulation time.

[0132] To address this issue, in some embodiments, the ion selection device 50 may include a first ion dispatching device and a second ion dispatching device. Figure 4 (Not shown in the diagram). Therefore, the first ion dispatching device can be configured to separate ions into multiple first ion packets based on their m / z or ion mobility, and sequentially output the first ion packets to the second ion dispatching device in order of their m / z or ion mobility. The second ion dispatching device can then be configured to separate each ion packet into multiple second ion packets based on their m / z or ion mobility, and sequentially output the second ion packets in order of their m / z or ion mobility. In such embodiments, the first upstream ion dispatching device may have a larger ion capacity than the second ion dispatching device. Therefore, the first ion dispatching device can accumulate a relatively large number of ions and then release them in approximately m / z order. The second ion dispatching device can then further subdivide these narrower m / z ranges into ion packets with finer resolution, as discussed above. The fill time of the second ion dispatching device can be controlled for each m / z range of ions received from the first ion dispatching device to improve the dynamic range of the dispatched ions.

[0133] Another solution to the problem of mixing very strong and low-strength ions is to use, for example, Figure 3CThe multi-well ion dispatching device 400 is shown. The multi-well ion dispatching device 400 is relatively resistant to this type of mixing because only one ion trap 402 can be filled by a single high-intensity ion species, while the rest remain empty. Therefore, the multi-well ion dispatching device 400 can also be used to perform ion dispatching methods. In the multi-well ion dispatching device 400, ions of different m / z (or ion mobilities) can be separated orthogonally (i.e., orthogonally to the overall linear direction of the ion dispatching device) by multiple RF electrodes 406 of the multi-well ion dispatching device 400. The RF electrodes 406 orthogonally separate ions in a manner similar to the RF electrodes 206 of other ion dispatching devices by a combination of T-wave and DC potential. Ions are also guided along the axial length of the ion dispatching device 400 such that when ions pass through the ion separation region 401 of the multi-well ion dispatching device 400, each ion is guided to one of the multiple ion traps 402. Ions of different m / z take different paths through the ion separation region 401 and are therefore guided to different ion traps 402. Ions are restricted in the lateral direction (lateral to the axial direction of ion travel) by RF electrode 406 and DC protection electrodes 410, 412 located on opposite sides of the multi-trap ion control device 400.

[0134] Generally, each ion trap 402 may define an outlet to allow ions trapped within the ion trap 402 to leave the ion separation region 401. Two, three, four, or more ion traps 402 may be present, each ion trap serving to allow ions within a corresponding m / z extraction window to leave the ion separation region 401. Each m / z extraction window may span an m / z range, thereby allowing the output of an ion packet according to the method described above. Multiple m / z extraction windows provided by multiple ion traps 402 may span the m / z range of interest. For example, for an m / z range of interest from 300 m / z to 900 m / z, five ion traps 402 may have m / z acceptance windows of 300 m / z to 420 m / z, 420 m / z to 540 m / z, 540 m / z to 660 m / z, 660 m / z to 780 m / z, and 780 m / z to 900 m / z.

[0135] The m / z range of ions passing through each ion trap 402 can be adjusted or regulated, for example, by appropriately selecting the voltage applied by the electrode arrangement and / or by adjusting the gas flow within the separation region. Thus, ions with a given m / z can be directed to a specific ion trap 402 among the multiple ion traps 402 under specific conditions, but to different ion traps 402 under other conditions. Therefore, the voltage applied to the ion traps may vary in each ion scheduling cycle to ensure that the subset of ions selected from each ion pack as described above is located at the center of the pack.

[0136] The multiple ion traps 402 are preferably spaced apart in a direction transverse to the axial length of the multi-trap ion dispatching device 400. Therefore, ions separated in the transverse direction are divided into ion packets corresponding to the m / z extraction windows of the ion traps 402 of the multi-trap ion dispatching device 400.

[0137] Additional potential (e.g., DC force) can be applied to the multi-ion trap ion dispatching device 400 along the axial length of the device 400 (i.e., Figure 3C The horizontal direction (in the middle) pulls the ions towards the outlet. For example, a DC gradient can be applied to only the DC top plate PCB ( Figure 3C (not shown) or a shaped counter electrode (if it is an RF blanket type) or an additional DC electrode mounted between the RF electrodes 406, or by shaping the RF electrodes 406. Figure 3C In this embodiment, each RF electrode 406 may extend along the axial length of the multi-trap ion dispatching device 400, i.e., the electrode may extend toward the outlet of the ion trap 402, or orthogonal to the direction in which the multiple ion traps are spaced apart. Therefore, a traveling wave / reverse DC can be directly applied to the RF electrodes 406 to divide ions into ion dispatching groups. Further configurations of the multi-trap ion dispatching device 400 are described in GB 2312733.5, the contents of which are incorporated herein by reference.

[0138] In some embodiments incorporating a multi-well ion dispatching device 400, ions can be proportionally split among more than one ion well due to the separation resolution of the multi-well ion dispatching device 400. In such cases, for one or more target m / z or target m / z ranges, the ion dispatching device simultaneously outputs ions from two or more ion wells 402 to form an ion packet. This can be particularly advantageous for relatively low-intensity ion species or to improve quantitative accuracy. A signal correction function can be provided to describe how the ion signal is split among the multiple ion wells 402; this function can be a calibrated function.

[0139] Another method to further reduce high-intensity precursor mixing is to provide an upstream mass filtration device 45, such as a small analytical quadrupole pre-filter upstream of the ion dispatching device 50. For example, Figure 11 A schematic diagram of an ion control device 50, a quadrupole mass filter 70, and an upstream mass filter 45 is shown. The quadrupole mass filter 70 and the ion control device 50 can be configured as described above regarding... Figure 4 The arrangement is as described herein. Ion dispatching device 50 can be any ion dispatching device described herein, such as linear ion dispatching device 200. Upstream mass filtration device 45 can be another quadrupole mass filter, commonly referred to as an injection filter or pre-filter.

[0140] An upstream mass filtration device can exclude one or more relatively high-intensity precursors from one or more cycles of the ion dispatching device 50. Therefore, method 500 (e.g., as part of step 502) can identify target m / z or target m / z ranges to be selectively removed when analyzing a second set of targets. Targets to be selectively removed can be selected based on very high intensity (e.g., intensity above a predetermined threshold).

[0141] In practice, high-intensity ions can be excluded from the ions input to the ion separation path 52 using a notch quality filter. Such a device can reject or attenuate a relatively narrow m / z range within the range of interest provided to the ion separation device for, for example, a second ion scheduling cycle. Therefore, a notch quality filter can be configured to remove "notches" from the ion pack's m / z range. One such notch quality filter includes an additional RF oscillator, which can be applied to a quadrupole ion director or... Figure 11 The upstream mass filter device 45 resonates with the oscillation of the target m / z ions. Such notch mass filters are further described at least in Miller, PE, & Denton, MB (1990), “A notchrejection quadrupole mass filter”, International journal of mass spectrometry and ion processes, 96(1), 17-26). In some embodiments, multiple notches can be applied by applying multiple additional sine waves to remove two or more relatively strong classes from the m / z range of interest. Such waveforms can be used to induce resonant jets of multiple high-intensity types without significantly impairing the target species over a wide mass range, as further described in Belov, ME, Nikolaev, EN, Anderson, GA, Auberry, KJ, Harkewicz, R., & Smith, RD (2001), “Electrospray ionization-Fourier transform ion cyclotronmass spectrometry using ion preselection and external accumulation for ultrahigh sensitivity” Journal of the American Society for Mass Spectrometry, 12(1), 38-48.

[0142] Therefore, the upstream mass filtration unit 45 can supply a reduced m / z range to the ion dispatching unit 50, removing some or all of the relatively strong precursors (e.g., all targets from the first group). Such filtration may compress the measured m / z space and thus limit the number of individual packets that can be output per cycle. However, this technique may be advantageous for separating lower-intensity ion species for analysis within an improved dynamic range.

[0143] Although Figure 11 An upstream mass filter 45 operating as a band-resistance m / z filter is shown, but it should also be understood that some ion dispatching devices 50 can themselves operate as band-resistance filters. For example, if the m / z of the ions is too high, Figure 3A and Figure 3B The DC gradient of the ion dispatching devices 200 and 300 may reject ions, while low m / z ions may be propelled forward by the T wave across the DC barrier. Typically, the ion dispatching device 50 is set to place the desired limit of the m / z range of interest at the limit of the ion dispatching device 50, but this can be changed if necessary to exclude some ion species.

[0144] The ion scheduling method according to this disclosure can also be applied to high dynamic range (HDR) mass spectrometry. Generally, HDR or Boxcar scanning methods break down the entire m / z range of interest into a series of individual quadrupole isolation windows, which are pre-programmed or dynamically generated based on the position of strong peaks. These quadrupole isolation windows are then accumulated separately into C-trap 100 and injected together into orbital trap mass analyzer 110. These individual windows are lossy, similar to the lossy nature of conventional MS2 signal acquisition. Therefore, the ion scheduling method according to this disclosure can be applied to HDR methods to reduce ion loss and improve dynamic range and / or cycle time.

[0145] Therefore, it can be used, for example, as Figure 5 The ion scheduling method shown is used to schedule the target m / z or target m / z range in HDR mass spectrometry. Therefore, as Figure 5 As shown, a series of target m / z ranges can be obtained based on survey analysis and listed in order of intensity. The peaks with the highest intensity (target m / z) can be assigned to the first group and scheduled for analysis. These target m / z can be accumulated in C trap 100 and analyzed together in a single mass analysis, for example using an orbital trap mass analyzer 110, to produce mass spectra associated with the first group.

[0146] The remaining target m / z ranges can be grouped based on m / z region and intensity classification, for example, regarding Figure 7As described, because the target m / z range can be relatively wide, with the range of interest split into, for example, no more than 20, 15, 12, or 10 target m / z ranges, rather than the approximately 100 used for typical DIA analysis, the HDR method may require fewer cycles of the ion scheduling apparatus. Ions from a second group can be accumulated in the MS1 domain and subjected to mass analysis to generate one or more mass spectra assigned to the ions from the second group. HDR mass spectra can then be assembled based on the mass spectra assigned to the first and second groups of ions.

[0147] The HDR method described above accumulates subsets of ions and performs a single MS1 analysis for each target group. Such techniques may be particularly suitable for mass analyzers with relatively long cycle times, such as orbital trap mass analyzer 110, where the analysis duration is at least similar to the time taken to accumulate all ions before HDR MS1 analysis (e.g., exceeding 100 ms). For relatively fast mass analyzers, such as TOF mass analyzer 150 which can obtain mass spectra in approximately 5 ms, performing multiple MS1 analyses as ions accumulate for each target m / z range may be advantageous. For example, one or more subsets of ions can be accumulated in C trap 100 and then sent for MS1 analysis at TOF mass analyzer 150. Thus, for each ion scheduling cycle, one or more subsets of ions accumulated in the ion trap can be analyzed in the MS1 domain to generate a partial HDR mass spectrum. A full HDR mass spectrum can then be assembled from multiple partial mass spectra accumulated covering different target m / z and target m / z ranges. Advantageously, by breaking down a complete MS1 analysis into multiple partial MS1 analyses, the target of the MS1 analysis can be scheduled using an ion scheduling method that can be interleaved with other targets for different purposes (e.g., MS2 analysis).

[0148] In some embodiments, particularly for HDR methods, an attenuation ion gate 80 may be positioned downstream of the ion selection device. For example, Figure 7 A decaying ion gate 80 is shown, which can be set to... Figure 4Between the quadrupole mass filter 70 and the C-trap 100 in the mass spectrometry system 1. An attenuating ion gate 80 selectively attenuates ions identified as relatively strong, so as to selectively remove such ions from the subset of ions output from the quadrupole mass filter 70. Ions of relatively low strength may not be attenuated by the attenuating ion gate 80. The attenuating ion gate can be similar to HDR or Boxcar scanning methods, but provides an improved dynamic range of ions output for analysis in a more efficient or continuous manner using available ions. Since the ion scheduling device 50 outputs ions in order of m / z or associated mobility, the downstream attenuating ion gate 80 can operate sequentially on the released ions. For example, in some embodiments, the attenuating ion gate 80 can be an attenuating dual ion gate, such as that described in US 8,026,475 B2. Such attenuating dual ion gates can achieve linear timing control down to 10 μs, thereby enabling precise ion attenuation.

[0149] As described above, the quadrupole mass filter 70 can also be used as an ion selection device according to this disclosure (i.e., there is no ion dispatching device 50). The ion dispatching method according to this disclosure is also applicable to such mass spectrometry systems because sorting the mass analysis by m / z order is effective. The ion dispatching technique of this disclosure improves upon simply sorting the targets to be analyzed by m / z order by assigning ions into groups based on intensity and prioritizing groups with higher intensity.

[0150] For example, a quadrupole mass filter 70 can be used as an ion selection device in DDA mass spectrometry incorporating an ion scheduling method according to the present disclosure. Therefore, based on intensity thresholds, the list of m / z targets for DDA analysis can be classified into multiple groups (e.g., 4 groups). Each group can have, for example, about 25 targets. The ion clusters of each group can then be sorted by m / z. In this way, relatively high-priority strong peaks can be measured without automatically skipping lower-intensity peaks. In some embodiments, classifying target m / z into groups can also take into account the distance of the target m / z to its neighboring target m / z.

[0151] Therefore, according to this disclosure, a method is provided for scheduling ions for analysis using a mass spectrometry system 1, wherein ions are grouped based on their m / z and relative intensity and scheduled accordingly for analysis.

Claims

1. A method for scheduling ions for analysis within a range of mass-to-charge ratios of interest, the method comprising: Obtain a list of the ionic strengths and associated mass-to-charge ratios of the ions to be analyzed; Obtain multiple target mass-to-charge ratios or multiple target mass-to-charge ratio ranges to be analyzed; Based on the list of ionic strengths and associated mass-to-charge ratios of the ions and intensity thresholds, each target mass-to-charge ratio or target mass-to-charge ratio range is assigned to a first group or a second group, wherein the target mass-to-charge ratio or target mass-to-charge ratio range in the first group is associated with ions of higher strength compared to the target mass-to-charge ratio or target mass-to-charge ratio range in the second group; The ion selection device is used to sequentially select and output ions with the target mass-to-charge ratio or target mass-to-charge ratio range assigned to the first group for analysis. as well as The ion selection device is used to sequentially select and output ions with the target mass-to-charge ratio or target mass-to-charge ratio range assigned to the second group for analysis.

2. The method according to claim 1, characterized in that, The ion selection device has an associated fill time for receiving ions, wherein the fill time for selecting and outputting ions of the second set of target mass-to-charge ratios or target mass-to-charge ratio ranges is longer than the fill time for selecting and outputting ions of the first set of target mass-to-charge ratios or target mass-to-charge ratio ranges.

3. The method according to claim 1, characterized in that, Provide three or more sets of target mass-to-charge ratios or target mass-to-charge ratio ranges, each with an associated ion strength range. Each target mass-to-charge ratio or target mass-to-charge ratio range is assigned to one of the three or more groups based on a list of the ionic strengths and associated mass-to-charge ratios of the ions.

4. The method according to claim 1, characterized in that, The ion selection device includes an ion scheduling device configured to separate the ions into multiple ion packets based on the ion's mass-to-charge ratio or ion mobility, and to output the ion packets sequentially in order of their mass-to-charge ratio or ion mobility.

5. The method according to claim 4, characterized in that, The ion selection device further includes a mass filtration device configured to receive each ion packet; and For each ion pack, the mass filtration device selects the ion subset based on the plurality of target mass-to-charge ratio values ​​or the plurality of target mass-to-charge ratio ranges.

6. The method according to claim 5, characterized in that, For each target mass-to-charge ratio or target mass-to-charge ratio range in the first group, ions are transferred to the mass filtration device without undergoing separation in the ion dispatching device; and The mass filtration device is used to select a subset of ions having each target mass-to-charge ratio or target mass-to-charge ratio range.

7. The method according to claim 5, characterized in that, The ion scheduling device executes multiple ion scheduling cycles, wherein each ion scheduling cycle includes: The ion dispatching device receives ions, wherein the ion dispatching device separates the ions into multiple ion packets according to the ion mass-to-charge ratio or ion mobility, and outputs multiple such groups sequentially. During one or more first ion scheduling cycles, ions with a target mass-to-charge ratio or a target mass-to-charge ratio range assigned to the first group are output, and During one or more second ion scheduling cycles, ions with a target mass-to-charge ratio or a target mass-to-charge ratio range assigned to the second group are output.

8. The method according to claim 7, characterized in that, Each ion packet output by the ion dispatching device has an associated mass-to-charge ratio range or ion mobility range. If two or more target mass-to-charge ratios or target mass-to-charge ratio ranges of the first group fall within the mass-to-charge ratio range or ion mobility range of the ion pack, then multiple first ion scheduling loops are executed such that no more than one subset of ions is selected from each ion pack.

9. The method according to claim 8, characterized in that, Upgrade the target mass-to-charge ratio or target mass-to-charge ratio range from the second group to the first group in order to increase the utilization rate of the ion packets output by the ion dispatching device.

10. A method for scheduling ions for analysis according to claim 1, said method being provided as part of a data-independent acquisition mass spectrometry method, wherein the mass-to-charge ratio range of interest is divided into multiple target mass-to-charge ratio ranges to be analyzed. For each target mass-to-charge ratio range of ions output by the ion selection device, the method further includes: Fragment the ions within each target mass-to-charge ratio range; as well as Mass analysis was performed on the ions.

11. The method according to claim 1, characterized in that, The ion selection device includes a first ion dispatching device and a second ion dispatching device. The first ion dispatching device is configured to separate the ions into a plurality of first ion packets based on the ion's mass-to-charge ratio or ion mobility, and to output the first ion packets to the second ion dispatching device in order of their mass-to-charge ratio or ion mobility. The second ion dispatching device is configured to separate each first ion packet into multiple second ion packets based on the mass-to-charge ratio or ion mobility of the ions, and to output the second ion packets sequentially in order of their mass-to-charge ratio or ion mobility.

12. The method according to claim 11, characterized in that, The ion capacity of the first ion dispatching device is greater than that of the second ion dispatching device.

13. The method according to claim 1, characterized in that, For the second group of ions, a pre-filter disposed upstream of the ion selection device selectively attenuates the ions supplied to the ion selection device based on the target mass-to-charge ratio or target mass-to-charge ratio range of the first group.

14. The method according to claim 5, characterized in that, The ion dispatching device includes multiple ion traps, each ion trap having an associated mass-to-charge ratio accepting window or an associated ion mobility accepting window, and The plurality of ion traps output ion packets in sequence, such that the ion scheduling device outputs the ion packets according to the mass-to-charge ratio or ion mobility of the ions.

15. The method according to claim 14, characterized in that, For one or more target mass-to-charge ratios or target mass-to-charge ratio ranges, the ion dispatching device simultaneously outputs ions from two or more ion traps to form an ion pack.

16. The method of claim 1, wherein when the method is provided as part of a high dynamic range mass spectrometry method, the method further comprises: Ions associated with one or more target mass-to-charge ratios or target mass-to-charge ratio ranges of the first group output by the ion selection device are accumulated in the ion trap; as well as Mass analysis of the accumulated ions is performed in the MS1 domain to generate one or more mass spectra of the ions assigned to the first group. Ions associated with one or more target mass-to-charge ratios or target mass-to-charge ratio ranges of the second group output by the ion selection device are accumulated in the ion trap; as well as Mass analysis of the accumulated ions is performed in the MS1 domain to generate one or more mass spectra for the ions assigned to the second group; and Assemble a high dynamic range mass spectrometer based on the mass spectra of the ions assigned to the first group and the second group.

17. The method according to claim 1, characterized in that, The target mass-to-charge ratio or the range of target mass-to-charge ratios assigned to the first group shall not exceed: 10, 7, 5 or 3.

18. The method according to claim 1, characterized in that, Obtaining multiple target mass-to-charge ratios or multiple target mass-to-charge ratio ranges to be analyzed includes obtaining target ion currents for one or more of the target mass-to-charge ratios or target mass-to-charge ratio ranges, and Each target mass-to-charge ratio or target mass-to-charge ratio range is assigned to a first group or a second group based on the list of ionic strengths and associated mass-to-charge ratios of the ions, the target ionic current, and the strength threshold. The target mass-to-charge ratio or target mass-to-charge ratio range assigned to the first group may be reassigned to the second group based on the target ionic current of the target mass-to-charge ratio or target mass-to-charge ratio range.

19. The method according to claim 1, characterized in that, The ion selection device is a mass filtration device that filters the ions and outputs a subset of ions based on the target mass-to-charge ratio or target mass-to-charge ratio range for each of the target mass-to-charge ratio values ​​or target mass-to-charge ratio ranges in the first group and the second group.

20. A mass spectrometry system for analyzing ions within a range of mass-to-charge ratios of interest, the mass spectrometry system comprising: Ion selector; and Quality analyzer The mass spectrometry system is configured to perform the method according to claim 1.

21. A method, the method comprising: Obtain a list of ionic strength and associated ionic mobility values ​​for the ions to be analyzed; Obtain the mobility range of multiple target ions to be analyzed; Based on a list of ion strengths, the associated mobility of the ions, and an intensity threshold, each target ion mobility range is assigned to a first group or a second group, wherein the target ion mobility range in the first group is associated with a higher ion strength compared to the target ion mobility range in the second group. The ion selection device is used to sequentially select and output ions with the target ion mobility range assigned to the first group for analysis. The ion selection device is used to sequentially select and output ions with the target ion mobility range assigned to the second group for analysis. as well as Mass analysis was performed on the first and second groups of accumulated ions output separately.

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