A method for performing MS / MS of intense ion beams using a bandpass filtering collision cell to enhance the robustness of mass spectrometry

Abstract

The mass spectrometer comprises a first mass filter having a transmission bandwidth configured to receive a plurality of ions and allow transmission of ions having m / z ratios within a desired range, and a second mass filter positioned downstream of the first mass filter to select ions having target m / z values ​​within its transmission window for mass analysis, the transmission bandwidth of the first mass filter encompassing at least two m / z ratios of interest such that one of the m / z ratios corresponds to the target m / z value within the transmission window of the second mass filter.

Description

[Technical Field]

[0001] (Related Applications) This application claims priority to U.S. Provisional Application No. 63 / 166,162, filed March 25, 2021, entitled "Method of Performing MS / MS of High Intensity Ion Beams Using A Bandpass Filtering Collision Cell To Enhance Mass Spectrometry Robustness," and U.S. Provisional Application No. 63 / 115,702, filed November 19, 2020, entitled "An Approach To Synchronize An Ion Guide With SWATH Acquisition," which are incorporated herein by reference in their entireties.

[0002] (background) The present teachings relate to mass filters that may be utilized in a variety of mass spectrometers and mass spectrometers in which such mass filters may be incorporated. [Background technology]

[0003] Mass spectrometry (MS) is an analytical technique for determining the structure of test chemicals, in both qualitative and quantitative applications. MS can be useful for identifying unknown compounds, determining the composition of atomic elements in molecules, determining the structure of compounds by observing their fragmentation, and quantifying the amount of specific chemical compounds in mixed samples. Mass spectrometers detect chemical components as ions; therefore, conversion of analytes to charged ions must occur during the sampling process.

[0004] Some mass spectrometer systems use a mass analyzer to monitor multiple reaction monitoring (MRM) transitions associated with analytes in the sample under study by selecting precursor ions having a target mass / charge (m / z) ratio and generating multiple product ions that can be followed by fragmentation of the selected precursor ions and then mass analyzed.

[0005] In conventional systems, ions with different masses are present in an ion guide positioned upstream of the mass analyzer, and the masses may extend upward in mass from the low mass cutoff of the ion guide. For example, as shown diagrammatically in FIG. 1, in such conventional systems, ions with different masses may be present in an ion guide positioned upstream of the mass analyzer, and the masses may extend upward in mass from the low mass cutoff of the ion guide. 10 Ions with masses m can exist in parallel in the upstream ion guide when the low mass cutoff of the ion guide is lower than m. However, in some cases, such a configuration can lead to contamination of the downstream mass analyzer with unwanted ions.

[0006] A mass filter can be positioned upstream of the mass analyzer, where the mass filter provides a bandpass window that can limit the range of ions that are transmitted to the downstream mass analyzer, thereby reducing contamination of the mass analyzer and other downstream components with unwanted ions (i.e., ions whose analysis is not desired). While the use of such a mass filter can reduce contamination, it can also reduce the speed at which MRM measurements can be made.

[0007] In particular, when the mass analyzer is transitioned to select the next precursor ion, the bandpass window of the upstream mass filter must be adjusted to allow transmission of the new precursor ion, followed by refilling of the mass filter. Thus, there is a need for enhanced methods of performing mass analysis, and in particular for enhanced mass analysis methods that can be employed for MRM transition monitoring. Summary of the Invention [Means for solving the problem]

[0008] The present teachings relate to methods and systems for performing mass analysis in which the ion transmission bandwidths of ion guides, individually and / or in combination with the ion transmission windows of a downstream mass analyzer, are configured to perform tandem mass analysis while reducing, and preferably eliminating, contamination of the high vacuum components of the mass analyzer.

[0009] For example, in one aspect, the present teachings relate to performing data-independent acquisition (DIA) tandem mass analysis methods using a multipole ion guide in an ion guide chamber as a mass filter or pre-filter, For example, the multipole ion guide can be configured to provide a wider ion mass selection window relative to the ion selection window provided by a downstream mass filter utilized to perform DIA mass analysis. Ion path component contamination issues

[0010] Contamination of ion path components can affect the performance of tandem mass spectrometers. Contamination tests on various experimental sample matrices (e.g., lipid, pulverized plasma, tea / arugula matrix) show that the degree of debris accumulation leading to performance degradation varies for various ion path components. In general, contamination on tandem mass spectrometer-related areas, such as on the IQ1 lens or Q1 quadrupole rods, is likely to cause further performance degradation. Such performance degradation can be characterized, for example, by sensitivity loss or peak width changes due to charging.

[0011] Similar amounts of debris were found in the QJet (R) A significantly lesser effect on performance degradation is observed when unwanted species accumulate on ion guide regions such as the Q0 quadrupole or Q1 quadrupole. Therefore, it is desirable to filter out unwanted species prior to the high vacuum (low pressure) region of the mass analyzer to prevent contamination on these critical tandem mass analyzer regions.

[0012] As explained below, SWATH (R) Acquisition is a DIA method in which all precursor ions within a defined or selected Q1 precursor ion mass selection window are transferred to a fragmentation device (e.g., a collision cell) to generate a single MS / MS spectrum. Alternatively, the Q1 precursor ion mass selection window is sequentially stepped across the entire precursor ion mass range of the analysis (traditional SWATH). (R) in), or scanned (SWATH(R) (In the current SWATH (R) In acquisition, during Q1 scanning over a selected Q1 precursor ion mass selection window, unwanted ions outside the selected Q1 precursor ion mass selection window are filtered out and deposited onto the Q1 rod.

[0013] Some tandem mass spectrometers use SWATH (R) In MS / MS acquisition, a 100% fixed ion transmission control (ITC) is applied, passing all ions into Q1 for precursor selection. This means that all ion current outside the precursor ion mass or m / z range is diverted to the Q1 rod. This increases the contamination rate, which in turn affects system performance. For example, the increased contamination rate adversely affects the sensitivity and shape of the Q1 transmission window. In particular, if the Q1 precursor ion mass selection window becomes less square due to contamination, the transmission efficiency and coverage of the mass range of interest are reduced, which affects the accuracy of ion extraction and quantification.

[0014] As a result, additional systems and methods are needed to reduce contamination of tandem mass spectrometers when operating in DIA mass analysis mode in order to maintain instrument sensitivity, precursor ion transmission efficiency, and coverage of the precursor ion mass range of interest. Tandem mass spectrometry and SWATH (R)

[0015] In general, tandem mass spectrometry, or MS / MS, is a well-known technique for analyzing compounds. Tandem mass spectrometry involves ionizing one or more compounds from a sample, selecting one or more precursor ions of the one or more compounds, fragmenting the one or more precursor ions into product ions, and mass analyzing the product ions.

[0016] Tandem mass spectrometry can provide both qualitative and quantitative information. The product ion spectrum can be used to identify a molecule of interest. The intensity of one or more product ions can be used to quantify the amount of a compound present in a sample.

[0017] Many different types of experimental methods or workflows can be performed using tandem mass spectrometers. Three broad categories of these workflows are targeted acquisition, information-dependent acquisition (IDA) or data-dependent acquisition (DDA), and data-independent acquisition (DIA).

[0018] In targeted acquisition method, one or more transitions of precursor ions to product ions are predefined for the compound of interest.As sample is introduced into tandem mass spectrometer, one or more transitions are measured during each period or cycle of multiple periods or cycles.In other words, the tandem mass spectrometer selects and fragments the precursor ions of each transition, and performs targeted mass analysis on the product ions of the transition.As a result, a mass spectrum is generated for each transition.Targeted acquisition method includes, but is not limited to, multiple reaction monitoring (MRM) and selected reaction monitoring (SRM).

[0019] In the IDA method, a user can define criteria for performing targeted or non-targeted mass analysis of product ions while a sample is being introduced into a tandem mass spectrometer. For example, in the IDA method, a precursor ion or mass spectrometry (MS) survey scan is performed to generate a precursor ion peak list. The user can select criteria for filtering the peak list for a subset of precursor ions on the peak list. MS / MS is then performed on each precursor ion of the subset of precursor ions. A product ion spectrum is generated for each precursor ion. MS / MS is repeatedly performed on precursor ions of the subset of precursor ions as the sample is introduced into the tandem mass spectrometer.

[0020] However, in proteomics and many other sample types, the complexity and dynamic range of compounds is enormous. This poses challenges to traditional targeted and IDA methods, requiring ultrafast MS / MS acquisition to exhaustively interrogate samples to both identify and quantify a wide range of analytes. IDA methods are limited by their inherent stochastic sampling, which leads to missing data points and a lack of confidence in quantification. SRM assays have inherent limitations on the number of compounds that can be reliably quantified, and method development time is expensive.

[0021] As a result, a third broad category of tandem mass spectrometry, DIA methods, has been developed. These DIA methods are being used to increase the reproducibility and comprehensiveness of data collection from complex samples. DIA methods may also be referred to as nonspecific fragmentation methods. (SWATH (R) In conventional DIA methods (such as MS / MS acquisition), the operation of the tandem mass analyzer is not varied between MS / MS scans based on data acquired in previous precursor or product ion scans. Instead, a precursor ion mass range is selected. The precursor ion mass selection window is then stepped across the precursor ion mass range. All precursor ions within the precursor ion mass selection window are fragmented, and all product ions of all precursor ions within the precursor ion mass selection window are mass analyzed.

[0022] The precursor ion mass selection window used to analyze the entire mass range can be varied depending on the mass range being analyzed, the MS / MS accumulation time, and the required acquisition speed (cycle time). The time it takes to analyze the entire mass range once is referred to as the cycle time. Generally, for LC, the cycle time is defined by the width of the chromatographic peak. Enough points (intensity as a function of elution time) must be acquired across the LC peak to determine its shape. When cycle time is defined by LC, the number of experiments or mass spectrometry acquisitions that can be performed within one cycle defines the length (accumulation time) that each experiment or acquisition can accumulate ion observations.

[0023] Applying a narrow precursor ion mass selection window across a wide precursor ion mass range during each cycle requires a short MS / MS accumulation time per precursor window. Applying a wide precursor ion mass selection window allows for the use of increased MS / MS accumulation times for the same cycle time. Generally, better selectivity can be achieved with a narrow precursor window, while better sensitivity can be achieved with a wide window using a longer accumulation.

[0024] Optimized Swath (R) The approach considers both the effect on selectivity and the effect on sensitivity. (R) In acquisition, the precursor ion mass selection window, which is stepped across the precursor mass range in each cycle, can typically have a width of 3 to 100 amu. (R) In , all precursor ions within each precursor ion mass range are fragmented and all product ions of all precursor ions within each mass selection window are mass analyzed.

[0025] U.S. Pat. No. 8,809,770 (incorporated herein by reference in its entirety) describes a SWATH (R)This paper describes a method in which the obtained data can be used to provide quantitative and qualitative information about precursor ions of a compound of interest. In particular, product ions found from fragmenting precursor ions within a precursor ion mass selection window are compared to a database of known product ions of the compound of interest. In addition, ion traces or extracted ion chromatograms (XICs) of product ions found from fragmenting precursor ions within the precursor ion mass selection window are analyzed to provide quantitative and qualitative information.

[0026] However, for example, SWATH (R) Identifying compounds of interest in samples analyzed using NMR can be difficult because either no precursor ion information exists within the precursor ion mass selection window to help determine the precursor ions that make up each product ion, or the precursor ion information provided is derived from mass spectrometry (MS) observations with low sensitivity. In addition, because there is little or no specific precursor ion information within the precursor ion mass selection window, it is also difficult to determine whether a product ion is convoluted with or includes contributions from multiple precursor ions within the precursor ion mass selection window.

[0027] As a result, scanning SWATH (R) It's called SWATH (R) A method was developed to scan a precursor ion mass selection window in acquisition. Essentially, a scanning SWATH (R) In , a precursor ion mass selection window is scanned across the mass range such that successive windows have large overlapping areas and small non-overlapping areas. This scanning makes the resulting product ions a function of the precursor ion mass selection window being scanned. This additional information can then be used to identify one or more precursor ions responsible for each product ion.

[0028] Scanning SWATH (R)is described in International Publication No. WO 2013 / 171459 A2 (hereinafter "the '459 Application"). In the '459 Application, a precursor ion mass selection window is scanned over time such that the range of the precursor ion mass selection window varies over time. The timing at which product ions are detected is then correlated with the timing of the precursor ion mass selection window through which those precursor ions were transmitted.

[0029] The correlation can be performed by first plotting the mass-to-charge ratio (m / z) of each detected product ion as a function of the precursor ion m / z value transmitted by the quadrupole mass filter. Because the precursor ion mass selection window is scanned over time, the precursor ion m / z value transmitted by the quadrupole mass filter can also be thought of as time. The start and end times at which a particular product ion is detected are correlated to the start and end times at which that precursor ion is transmitted from the quadrupole. As a result, the start and end times of the product ion signals are used to determine the start and end times of their corresponding precursor ions.

[0030] In one aspect, a system, method, and computer program product are disclosed for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter. The system includes an ion source device, a tandem mass analyzer, and a processor. The ion source device ionizes one or more compounds of a sample to generate an ion beam. The tandem mass analyzer includes an ion guide chamber and a multipole ion guide disposed within the ion guide chamber. The ion guide chamber includes an entrance orifice for receiving ions generated by the ion source device and at least one exit opening for transmitting ions from the ion guide chamber into a vacuum chamber housing at least one fragmentation device.

[0031] The processor receives a plurality of different precursor ion mass selection windows spanning a precursor ion mass range selected for the DIA method, and calculates, from the plurality of different precursor ion mass selection windows, two or more different multipole ion guide precursor ion mass selection windows for transmission during the same time cycle of the tandem mass analyzer.

[0032] During each cycle time of a plurality of time cycles of the tandem mass analyzer, for each selection window of a plurality of different precursor ion mass selection windows, the processor instructs the multipole ion guide to transmit precursor ions from the ion beam within the multipole ion guide precursor ion mass selection window of two or more different multipole ion guide precursor ion mass selection windows, the multipole ion guide precursor ion mass selection windows having a width equal to or greater than the width of the selection window of a downstream mass filter configured to perform DIA mass analysis.

[0033] In a related aspect, a mass spectrometer is disclosed that includes a first mass filter having a transmission bandwidth configured to receive a plurality of precursor ions and allow transmission of ions having m / z ratios within a desired range, and a second mass filter positioned downstream of the first mass filter to select ions having target m / z ratios within its transmission window for mass analysis. A controller is operably coupled to the first mass filter to set the transmission bandwidth of the first mass filter to encompass at least two m / z ratios, at least one of which is within the transmission window of the second mass filter. The controller is configured to vary the transmission bandwidth of the first mass filter over time so that any two consecutive transmission bandwidths of the first mass filter have at least one m / z ratio in common. The controller can be coupled to the second mass filter to move the transmission window of the second mass filter to select different target m / z ratios.

[0034] In some embodiments the controller may be configured to correlate the variation in transmission bandwidth of the first mass filter with the variation in transmission window of the second mass filter over time so as to enable mass analysis by the second mass filter of ions having different m / z ratios transmitted through the first mass filter as the transmission bandwidth of the first mass filter is shifted over time.

[0035] In some embodiments, the controller may be configured to set the ion transmission bandwidth of the first mass filter to the initial ion transmission bandwidth, and to set the ion transmission window of the second mass filter to allow passage of ions having an m / z ratio encompassed by the initial bandwidth of the first mass filter.

[0036] In some embodiments, the controller may be configured to adjust the transmission window of the second mass filter to capture the next m / z ratio of interest and shift the ion transmission bandwidth of the first mass filter to cover the next m / z ratio of interest and other m / z ratios of interest.

[0037] In some embodiments, the controller may be further configured to adjust the transmission window of the second mass filter to shift the transmission bandwidth of the first mass filter substantially in parallel.

[0038] In some embodiments, the controller may be further configured to shift the ion transmission window of the second mass filter prior to adjusting the ion transmission bandwidth of the first mass filter.

[0039] In some embodiments the controller may be configured to shift the ion transmission bandwidth of the first mass filter while the second mass filter monitors ions having an m / z ratio that was covered by the transmission bandwidth of the first mass filter prior to the shift.

[0040] In some embodiments, the controller may be configured to set the transmission bandwidth of the first mass filter to allow transmission of ions having an m / z ratio of three or more.

[0041] In some embodiments, either the transmission bandwidth of the first mass filter or the transmission window of the second mass filter may be less than about 2,000 Da, for example, in the range of about 0.1 Da to about 1,500 Da, or in the range of about 1 Da to about 1,000 Da, or in the range of about 10 Da to about 500 Da, or in the range of about 100 Da to about 300 Da.

[0042] In some embodiments, an ion source can be positioned upstream of the first mass filter to generate a plurality of precursor ions. The ion source can receive a sample and ionize at least a portion of the sample to generate ions. A variety of ion sources can be employed in practicing the present teachings.

[0043] In some embodiments, either of the first and second mass filters comprises at least one set of rods arranged in a multipole configuration to provide radial confinement of ions to at least one of them, to which one or more RF voltages can be applied to filter ions having a certain m / z ratio, for example low m / z ions, and to which a DC resolving voltage can be applied to at least one of them to generate its transmission bandwidth. In some such embodiments, the multipole configuration can be a quadrupole configuration, although other configurations such as a hexapole can also be employed.

[0044] In some embodiments, at least one set of rods includes multiple sets of rods positioned in tandem, each rod set comprising multiple rods arranged in a multipole configuration, and optionally, a DC voltage offset is applied between at least two of the rod sets to generate an electric field for accelerating ions passing through the first mass filter. By way of example and not limitation, the DC voltage offset can be in the range of about 0 volts to about 200 volts.

[0045] In some embodiments, the transmission bandwidth of the first mass filter has an m / z width that exceeds the m / z width of the transmission window of the second mass filter.

[0046] In a related aspect, a system for performing a data-independent acquisition (DIA) method for mass analysis is disclosed, comprising: a first mass filter for receiving a plurality of precursor ions; a second mass filter positioned downstream of the first mass filter for receiving ions exiting the first mass filter; and a controller operatively coupled to the first mass filter and the second mass filter for configuring the second mass filter to provide a plurality of ion selection windows over a DIA mass analysis cycle, such that the mass selection windows collectively span a precursor ion mass range associated with the DIA analysis. The controller may configure the first mass filter to provide a plurality of ion transmission bandwidths, each configured to pre-filter precursor ions with respect to at least one respective one of the ion selection windows of the second mass filter, such that the ion transmission bandwidths of the first mass filter each have an m / z width that exceeds the m / z width of a respective ion selection window of the second mass filter.

[0047] In some embodiments, at least one of the ion transmission bandwidths of the first mass filter has a lower low m / z cutoff and a higher high m / z cutoff than the individual low m / z cutoff and high m / z cutoff of said at least one individual ion selection window of the second mass filter, hi some such embodiments, the at least one individual ion selection window of the second mass filter comprises at least two consecutive ion selection windows.

[0048] In some embodiments, at least two of the ion transmission bandwidths of the first mass filter may have at least one m / z ratio in common.

[0049] In some embodiments, at least two of the plurality of ion transmission bandwidths of the first mass filter have different m / z widths.

[0050] In some embodiments, the system may further include a fragmentation device positioned downstream of the second mass filter to receive precursor ions exiting the second mass filter and cause fragmentation of at least some of them to generate a plurality of product ions. Further, a mass analyzer may be positioned downstream of the fragmentation device to receive the product ions and generate a mass spectrum thereof.

[0051] In some embodiments, the first and second mass filters can each be positioned within an exhaust chamber, and the second exhaust chamber can be maintained at a lower pressure than the pressure at which the first exhaust chamber is maintained.

[0052] In some embodiments, the mass filters may each be implemented via a multipole rod set positioned within a separate exhaust chamber. In some such embodiments, RF and DC voltage sources may be employed to apply RF voltages to the rods to provide radial confinement of ions, and a DC resolving voltage may be applied across at least two of the rods of the multipole rod set to generate a desired ion transmission bandwidth / window in a manner known in the art. A controller may be operably coupled to the RF and DC voltage sources to adjust the RF and DC voltages to generate the desired transmission bandwidth / window of the first and second mass filters.

[0053] In some embodiments, the first multipole rod set can include multiple rod sections, each spaced apart from an adjacent rod section and extending along a central longitudinal axis of the multipole rod set. In some embodiments, the multiple rod sections include a first rod section, a second rod section positioned downstream of the first rod section, and a third rod section positioned downstream of the second rod section. In some such embodiments, the first rod section is configured to receive ions from an upstream ion source and cause cooling of the received ions, and the second rod section is configured to filter the cooled ions received from the first rod section. Furthermore, the third rod section is configured to transmit ions received through the second rod section out of the mass filter.

[0054] The mass filter may further include a plurality of auxiliary electrodes positioned between the rods of the plurality of rod sets, wherein an RF voltage applied to the rods of the multipole rod set provides a low m / z cutoff and a DC voltage difference applied between the multipole rod set and the auxiliary electrodes provides a high m / z cutoff.

[0055] In a related aspect, a mass filter for receiving a plurality of precursor ions, the mass filter being in a low vacuum (about 5e -5At pressures above 10 Torr, for example, -3 Torr ~ approx. 10 -2 A system for performing data-independent acquisition (DIA) mass analysis in a tandem mass spectrometer is disclosed, including a mass filter positioned in a region of the mass analyzer maintained at a pressure in the range of 1000 torr. A controller is operably coupled to the mass filter and configured to control the mass filter to provide a plurality of ion selection windows over a DIA mass analysis cycle, the ion selection windows collectively spanning a precursor ion mass range associated with the DIA mass analysis. An ion fragmentation device is positioned downstream of the mass filter to receive precursor ions transmitted through the mass filter and cause fragmentation of at least some of the received precursor ions to generate a plurality of product ions. No other mass filter functionality is provided between the mass filter and the ion fragmentation device. For example, in some embodiments, no other mass filter is positioned between the mass filter and the ion fragmentation device. In other embodiments, one or more additional mass filters may be positioned between the mass filter and the ion fragmentation device, but such mass filters are not maintained in a functional mode during operation of the system.

[0056] In some embodiments, at least two of the ion selection windows can overlap. Further, in some embodiments, at least two of the ion selection windows can have different m / z widths. Also, in some embodiments, at least two of the ion selection windows can overlap and have different m / z widths.

[0057] In some embodiments, the mass filter can include a multipole rod set configured for application of RF and / or DC voltages thereto to generate an ion selection window. By way of example, the multipole rod set can include a quadrupole rod set, a hexapole rod set, among others. At least one RF voltage source and at least one DC voltage source can be utilized to generate the RF and / or DC voltages for application to the multipole rod set. A controller can be operably coupled to the RF and DC voltage sources to control them to adjust the RF and / or DC voltages to generate the ion selection window.

[0058] In some embodiments, the mass filter and fragmentation device may be positioned in two different evacuated chambers, the chamber in which the fragmentation device is positioned being maintained at a different pressure than the chamber in which the mass filter is positioned.

[0059] In a related aspect, a mass spectrometer is disclosed that includes a first mass filter having a transmission bandwidth (bandpass window) configured to receive a plurality of ions and allow transmission of ions having m / z ratios within a desired range, and a second mass filter (which may be configured as a mass analyzer) positioned downstream of the first mass filter to select ions having target m / z values ​​within the transmission window for mass analysis, wherein the bandpass window of the first mass filter covers at least two m / z ratios of interest, such that one of the m / z ratios corresponds to a target m / z value within the transmission window of the second mass filter.

[0060] In some embodiments, a controller is coupled to the first mass filter for shifting its bandpass window over time to include different m / z ratios of interest. The controller is coupled to the second mass filter (in many embodiments configured as a mass analyzer) for moving the transmission window of the mass filter to select different target m / z values. The controller may be configured to correlate the time variation of the bandpass window of the first mass filter with the time variation of the transmission window of the second mass filter so as to enable mass analysis by the second mass filter (mass analyzer) of ions having different m / z ratios transmitted through the first mass filter as the bandpass window of the first mass filter is shifted over time.

[0061] As an example, the controller may be configured to set the bandpass window of a first mass filter to an initial value, and to set the transmission window of a second mass filter (mass analyzer) to allow passage of one of the ions covered by the initial bandpass window of the first mass filter. The controller may also be configured to adjust the transmission window of the second mass filter (mass analyzer) to cover a next m / z ratio of interest, and shift the bandpass window of the first mass filter to cover the next m / z ratio of interest and at least another m / z ratio of interest. In some embodiments, the controller may select the m / z ratio of interest from a list of m / z ratios previously provided to the controller.

[0062] In some embodiments, the controller may be configured to shift the bandpass window of the first mass filter and that of the second filter (mass analyzer) substantially in parallel, for example in some such embodiments the controller may be configured to shift the bandpass window of the first mass filter while the second mass filter is monitoring ions with an m / z ratio that is covered by the bandpass window of the first mass filter prior to the shifting.

[0063] In general, the bandpass window of the first mass filter can be selected to allow passage of multiple m / z ratios while ensuring that it continues to block the passage of unwanted ions. By way of example, in some embodiments, the bandpass window of the first mass filter can be in the range of about 30 Da to about 200 Da. Further, in some such embodiments, the bandpass window of the second mass filter (mass analyzer) can be selected to allow passage of m / z ratios of interest while blocking the passage of unwanted ions. By way of example, in some embodiments, the bandpass window of the second mass filter (mass analyzer) can be in the range of about 0.3 Da to about 100 Da, e.g., in the range of about 10 Da to about 50 Da.

[0064] In some embodiments, the first mass filter can include a set of rods arranged in a quadrupole configuration to which RF and DC voltages can be applied to provide radial confinement of ions and a desired bandpass window for ion transmission. In some such embodiments, the first mass filter can include multiple rod sections, each arranged in a quadrupole configuration. In some such embodiments, RF voltages are applied to some of the rod sets, for example, rod sets positioned proximate the entrance and exit of the first mass filter, while RF and DC resolving voltages are applied to at least one of the rod sets positioned between the rod sets to which the RF voltages are applied. Furthermore, in some such embodiments, at least one DC offset voltage can be applied between at least two consecutive rod sets to provide an axial electric field that can promote the passage of ions through the mass filter. In some such embodiments, the DC offset voltage is selected to ensure that ions continue to travel through the mass filter while maintaining low axial kinetic energy as they exit the mass filter. By way of example, in some embodiments, the DC offset voltage can be in the range of about 0 V to about 20 V. In some embodiments where collisional fragmentation of ions within the first mass filter may be desired, a higher DC offset voltage may be employed, for example as high as 200V.

[0065] In some embodiments, a collision cell can be positioned downstream of the second mass filter to receive ions passing through the second mass filter and cause fragmentation of at least some of those ions to generate a plurality of product ions. A mass analyzer can be positioned downstream of the collision cell to receive at least some of the product ions and provide a mass analysis thereof. An ion detector can be positioned downstream of such mass analyzer to detect ions passing through the mass analyzer and generate a detection signal in response to detection of the ions. An analyzer in communication with the ion detector can receive the detection signals generated by the detector and process the detection signals to generate a mass spectrum of the product ions.

[0066] In some embodiments, the mass spectrometer can be a time-of-flight (ToF) mass spectrometer. Further, in some embodiments, the mass spectrometer can be a SWATH mass spectrometer. (R) The MS is configured to operate in a data-independent acquisition (DIA) mode, such as in a data acquisition mode. In some embodiments, the mass spectrometer can be a tandem mass spectrometer (such as a triple quadrupole mass spectrometer) or any other MS system known in the art. For some experiments, the MS is operated in MRM mode to monitor successive parent ions in Q1 and corresponding daughter ions in Q3.

[0067] In some embodiments, the system further includes an ion source positioned upstream of the first mass filter for ionizing the sample under investigation and generating a plurality of ions. A variety of ion sources, such as those listed below, can be employed in the practice of the present teachings.

[0068] A further understanding of various aspects of the present teachings can be obtained by reference to the following detailed description and the associated drawings briefly described below. [Brief explanation of the drawings]

[0069] [Figure 1] FIG. 1 is a schematic example of a bandpass window of a conventional mass filter, providing multiple bandpass windows, each of which encompasses a certain m / z ratio.

[0070] [Figure 2] FIG. 2 is a flow chart depicting various steps in an embodiment of a method according to the present teachings for performing mass spectrometry.

[0071] [Figure 3] FIG. 3 illustrates a schematic of a mass filter in accordance with the present teachings.

[0072] [Figure 4A] FIG. 4A shows a schematic example of a bandpass window of a mass filter in accordance with the present teachings, where the bandpass window covers two or three m / z ratios at a time for transmission.

[0073] [Figure 4B] FIG. 4B shows a schematic example of a bandpass window of a mass filter in accordance with the present teachings, where the bandpass window covers two m / z ratios at a time for transmission.

[0074] [Figure 5] FIG. 5 shows a schematic of the quadrupole rod set, viewed axially.

[0075] [Figure 6] FIG. 6 schematically depicts a cross-sectional view of a multipole ion guide that can be configured as a mass filter for use in some embodiments of the present teachings.

[0076] [Figure 7] FIG. 7 depicts another schematic diagram of the multipole ion guide shown in FIG.

[0077] [Figure 8] FIG. 8 illustrates a schematic of a mass spectrometer in accordance with an embodiment of the present teachings.

[0078] [Figure 9A] Figures 9A, 9B, and 9C show examples of bandpass windows obtained for a four-section mass filter such as that depicted diagrammatically in Figure 3 through application of suitable RF and resolved DC voltages to the various rods of the mass filter. [Figure 9B] Figures 9A, 9B, and 9C show examples of bandpass windows obtained for a four-section mass filter such as that depicted diagrammatically in Figure 3 through application of suitable RF and resolved DC voltages to the various rods of the mass filter. [Figure 9C] Figures 9A, 9B, and 9C show examples of bandpass windows obtained for a four-section mass filter such as that depicted diagrammatically in Figure 3 through application of suitable RF and resolved DC voltages to the various rods of the mass filter.

[0079] [Figure 10A] FIG. 10A shows the transit time from lens IQ0 to the detector as a function of ion mass for the following DC settings of the QJet® ion guide and for various sections of the ion guide Q0:

[0080] [Figure 10B] FIG. 10B shows a time section of the data presented in FIG. 10A extending from t=0 to t=3 ms.

[0081] [Figure 11] FIG. 11 diagrammatically illustrates an example of a controller that may be implemented in a mass spectrometer in accordance with the present teachings.

[0082] [Figure 12] FIG. 12 shows a timing diagram illustrating one example of operating a mass filter and a downstream mass analyzer in accordance with an embodiment of the present teachings.

[0083] [Figure 13]FIG. 13 shows another timing diagram for operating a mass filter and a downstream mass analyzer in accordance with an embodiment of the present teachings.

[0084] [Figure 14] FIG. 14 is an exemplary diagram illustrating how different precursor ion mass selection windows spanning a mass range are scanned in a conventional DIA method, in which various embodiments may be implemented.

[0085] [Figure 15] FIG. 15 is an exemplary diagram showing how a multipole Q0 ion guide may perform mass filtering by using different Q0 precursor ion mass selection windows, according to various embodiments.

[0086] [Figure 16] FIG. 16 is an exemplary diagram showing how a Q0 ion guide can perform mass pre-filtering by using a Q0 precursor ion mass selection window and pre-filter a Q1 precursor ion mass selection window, according to various embodiments.

[0087] [Figure 17] FIG. 17 is an exemplary diagram showing how a Q0 ion guide can perform mass pre-filtering using one Q0 precursor ion mass selection window and pre-filter two different Q1 precursor ion mass selection windows, according to various embodiments.

[0088] [Figure 18] FIG. 18 is an exemplary schematic diagram of a Q0 multipole ion guide with segmented rods that may be used for mass filtering or pre-filtering, according to various embodiments.

[0089] [Figure 19]FIG. 19 is an exemplary schematic diagram showing the Q0 multipole ion guide of U.S. Published Application No. 2018 / 0096832 (hereinafter "the '832 application") and International Publication No. WO 2020 / 039371 (hereinafter "the '371 application") in which various embodiments may be implemented.

[0090] [Figure 20] FIG. 20 is an exemplary perspective view of an auxiliary electrode of the '832 and '371 applications in which various embodiments may be implemented.

[0091] [Figure 21] FIG. 21 is an exemplary cross-sectional view of a Q0 multipole ion guide of the '371 application in which various embodiments may be implemented.

[0092] [Figure 22] FIG. 22 is an exemplary plot showing how different RF voltages applied to the quadrupole rods produce different precursor ion mass selection window widths and different DC voltages applied to T-bar electrodes interposed between the quadrupole rods of a Q0 multipole ion guide, in accordance with various embodiments.

[0093] [Figure 23] FIG. 23 is an exemplary plot of the same data shown in FIG. 23 showing different central mass locations and widths that can be produced using a Q0 multipole ion guide including quadrupole rods and T-bars interposed therebetween, according to various embodiments.

[0094] [Figure 24] FIG. 24 is an exemplary table showing different RF quadrupole rod voltages and DC T-bar voltages applied to the quadrupole rods and T-bars, respectively, of a Q0 multipole ion guide to generate a Q0 precursor ion mass selection window of 150 Da, according to various embodiments.

[0095] [Figure 25]FIG. 25 is an exemplary plot showing how the DC voltage applied to the auxiliary electrodes of a Q0 multipole ion guide varies with the RF voltage applied to the multipole rod sets of the Q0 multipole ion guide to maintain a constant Q0 precursor ion mass selection window width, according to various embodiments.

[0096] [Figure 26-1] FIG. 26 is an exemplary flowchart showing a method for synchronizing a Q0 precursor ion mass selection window with a Q1 precursor ion mass selection window according to various embodiments. [Figure 26-2] FIG. 26 is an exemplary flowchart showing a method for synchronizing a Q0 precursor ion mass selection window with a Q1 precursor ion mass selection window according to various embodiments.

[0097] [Figure 27] FIG. 27 is a schematic diagram showing a system for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, according to various embodiments.

[0098] [Figure 28] FIG. 28 is a flow chart illustrating a method for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, according to various embodiments.

[0099] [Figure 29] FIG. 29 is a block diagram illustrating a computer system on which embodiments of the present teachings may be implemented.

[0100] [Figure 30] FIG. 30 is a schematic diagram of a system including one or more distinct software modules that implements a method for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, according to various embodiments. DETAILED DESCRIPTION OF THE INVENTION

[0101] Detailed Description It should be understood that, for clarity, the following discussion will detail various aspects of embodiments of the present disclosure, omitting certain specific details whenever convenient or appropriate. For example, discussion of like or similar features in alternative embodiments may be somewhat abbreviated. Well-known concepts or ideas may also be discussed in less detail for the sake of brevity. Those skilled in the art will recognize that some embodiments of the present disclosure may not require some of the details specifically described in every implementation, and this is described herein only to provide a thorough understanding of the embodiments. Likewise, it will be apparent that the described embodiments may be susceptible to modification or alteration in accordance with common general knowledge without departing from the scope of the present disclosure. The following detailed description of embodiments is not intended to limit the scope of the applicant's teachings in any way.

[0102] As used herein, the terms "about" and "substantially equal" refer to variations in numerical quantities that may occur, for example, through real-world measurement or handling procedures, through unintentional errors in these procedures, through differences in the manufacture, source, or purity of compositions or reagents, and the like. Typically, the terms "about" and "substantially" as used herein mean 10% above or below the stated value or range of values ​​or perfect condition or state. For example, a concentration value of about 30% or substantially equal to 30% may refer to a concentration of 27% to 33%. The terms also refer to variations that would be recognized as equivalent by those of ordinary skill in the art, unless such variations encompass known values ​​practiced by the prior art.

[0103] As used herein, the term "and / or" includes any and all combinations of one or more of the associated listed items and may be abbreviated as " / ".

[0104] The present teachings relate to systems and methods for performing mass analysis, and in particular to such methods and systems employing at least one mass filter positioned upstream of a mass analyzer, the mass filter configured to have a bandpass window encompassing a plurality of m / z ratios, at least one of which corresponds to an m / z ratio within the bandpass window of the downstream mass analyzer. Without loss of generality, to illustrate various aspects of the present teachings, the embodiments described below include a mass filter and a downstream mass analyzer placed in tandem. However, it should be understood that the present teachings are not limited to mass analysis systems having only a mass filter and a downstream mass analyzer.

[0105] Unlike conventional systems, in systems according to the present teachings, the upstream mass filter can have a bandpass window in the mass-to-charge (m / z) ratio domain that covers multiple m / z ratios that are transferred to the downstream mass analyzer. In many embodiments, the bandpass window of the downstream mass analyzer is configured to allow passage of one m / z ratio at a time. In other embodiments, the downstream mass analyzer has a bandpass window that covers multiple m / z ratios. As discussed in more detail below, by configuring the bandpass window of the upstream mass filter to allow ions across multiple m / z ratios to be transmitted, more rapid analysis of multiple ions with different m / z ratios can be achieved. In the following discussion, in some cases, the first mass filter will be referred to as the first mass analyzer and the second mass filter will be referred to as the second mass analyzer.

[0106] Various terms are used herein in accordance with their ordinary meaning in the art. The terms "bandpass window," "transmission bandwidth," "transmission window," and "bandwidth" are used interchangeably herein to refer to the range of m / z ratios that may be transmitted through a mass filter or mass analyzer, while the passage of ions with m / z ratios outside that range is substantially reduced, or preferably prevented.

[0107] The term "Q0" refers to the component of a tandem mass analyzer that initially receives ions from the ion beam in the collisional cooling region. Note also that the term "Q1" refers to the component of a tandem mass analyzer that initially receives ions from the Q0 component and is located in a vacuum chamber having a lower pressure than the vacuum chamber containing the Q0 component. Depending on its functionality and / or configuration, "Q0" may be referred to as a mass filter, first mass filter, pre-filter, ion guide, multipole ion guide, or quadrupole ion guide. Depending on its functionality and / or configuration, "Q1" may be referred to as a mass analyzer, mass filter, mass filter device, second mass filter, quadrupole, or quadrupole rod.

[0108] The "low pressure region of the mass spectrometer" is approximately 5 × 10 -5 "Intermediate-pressure region" of a mass spectrometer refers to a region (e.g., various evacuated chambers) of the mass spectrometer (e.g., the chamber in which the Q1 mass analyzer is located) that is maintained at a pressure below 200 psi. An "intermediate-pressure region" of a mass spectrometer refers to a region (e.g., the chamber in which the Q0 mass analyzer is located) that is maintained at a pressure about 10-50 times higher than the pressure of the low-pressure region. In some cases, a mass spectrometer can include a high-pressure region, e.g., a region maintained at a pressure of about 2-10 Torr.

[0109] While example embodiments described herein may include multiple modules for implementing aspects of the present teachings, it should be understood that various aspects of example processes according to the present teachings may also be performed by one or more modules. In addition, it should be understood that the term controller / control unit refers to a module that may be implemented in hardware / firmware / software or a combination thereof. In some embodiments, the controller may include a processor, memory, and one or more communication buses for providing communication between its various components. For example, instructions for performing various methods disclosed herein, such as analyzing ion detection signals to generate mass spectra, may be stored in one or more memory modules and used during runtime by the processor to implement the methods.

[0110] 2, a method according to an embodiment of the present teachings for performing mass analysis includes introducing a plurality of ions into a mass filter having a bandpass window that allows transmission of at least two ions of interest having different m / z ratios. This is followed by introducing ions transmitted through the mass filter into a downstream mass analyzer that is configured to allow passage of ions having one of the m / z ratios within the bandpass window of the upstream mass filter. In some embodiments, the downstream mass analyzer allows passage of ions with multiple m / z ratios.

[0111] Subsequently, the bandpass window of the mass filter can be adjusted so that it will encompass at least one of the m / z ratios previously within its bandwidth for transmission and selected by the downstream mass analyzer, as well as at least the new m / z ratio.

[0112] The ions are then transmitted through the mass filter with the updated bandpass window to a downstream mass analyzer, which in turn is adjusted to select ions having m / z ratios common between the previous and adjusted bandwidths of the mass filter (i.e., ions that can be transmitted through the mass filter in its original and updated configurations). (R) When operating in acquisition mode, the downstream mass analyzer is adjusted to select a range of ions with different m / z ratios. As an example, in some TOF MS / MS systems, the downstream mass analyzer can be operated in low resolution mode so that an isotopic cluster of ions or a range of m / z values ​​is transmitted through the mass analyzer.

[0113] Again, in some embodiments, at least some of the ions selected by the mass analyzer can be fragmented to generate multiple product ions, which can, in turn, undergo mass analysis. As discussed in more detail below, adjustment of the bandpass window of the mass filter and that of the downstream mass analyzer can occur substantially in parallel. Alternatively, the bandpass window of the mass filter can be shifted (updated) prior to updating the bandpass window of the downstream mass analyzer. Furthermore, as discussed in more detail below, in some embodiments, ion fragmentation can occur in one or more sections of the mass filter that are located upstream of a section configured with a bandpass window configured in accordance with the present teachings to encompass two or more m / z ratios associated with the fragment ions.

[0114] The above method can be utilized to perform multiple reaction monitoring mass spectrometry (MRM). For example, referring to FIG. 3, in one example of implementation of such an embodiment, the ion guide QJet (R) can receive ions from an upstream ion source (not shown in FIG. 3) and focus the received ions into an ion beam that is transmitted into a mass filter Q0. (R)The ion guide QJet includes four rods 10 (two of which are visible in FIG. 3) arranged according to a quadrupole configuration. An RF source 12 applies RF voltage to the four rods 10 in a manner known in the art, causing the ion guide QJet (R) Ion lens IQ0 provides radial focusing of ions passing through the ion guide QJet (R) and the mass filter Q0, and the QJet (R) and Q0 chambers to provide enhanced transmission and focusing of ions.

[0115] In this embodiment, mass filter Q0 includes four sets of rods Q0A, Q0B, Q0C and Q0D that are positioned in series with respect to each other in a quadrupole configuration to provide a passageway through which ions received via mass filter Q0's entrance 14 may propagate to its exit 16 where they exit mass filter Q0. In this embodiment, RF voltage source 12 (or separate RF voltage sources) and DC voltage source 20a apply RF and DC voltages to the rods of mass filter Q0 to provide radial focusing of ions and to establish a bandpass window (i.e. transmission window) for the passage of ions through mass filter Q0.

[0116] In other words, ions having m / z ratios that fall within the bandpass window of mass filter Q0 are allowed to pass through mass filter Q0, while transmission of ions having m / z ratios that fall outside the bandpass window is substantially reduced, preferably prevented. As discussed in more detail below, in this embodiment, RF voltages (signals) are applied to first, second, and fourth sets of rods Q0A, Q0B, and Q0D, while RF voltages and resolving DC voltages (to set the bandpass window of mass filter Q0) are applied to third set of rods Q0C, as discussed in more detail below. Furthermore, in this embodiment, the rods of the Q0A and Q0B rod sets are tilted with respect to the longitudinal axis of mass filter Q0 to provide an upstream effective potential that exceeds the downstream effective potential, thereby generating an off-axis axial gradient that points downstream along the length of the rods of the Q0A and Q0B rod sets. Additionally, in this embodiment, rod sets Q0A and Q0B have a smaller field radius than the Q0C rod set. Furthermore, in this embodiment, because the RF voltages applied to the Q0A and Q0B rod sets are obtained via capacitive coupling from an RF voltage supply that applies an RF voltage to the Q0C rod set, the RF voltages applied to the Q0A and Q0B rod sets have a lower amplitude than the amplitude of the RF voltage applied to the Q0C rod set. As a result, ions at the exit of the Q0B rod set exhibit a higher value for the Mathieu q parameter than at the entrance to the Q0C section. The higher q value at the exit of the Q0B rod set results in a higher effective potential at the exit of the Q0B rod set than at the entrance of the Q0C rod set, thereby reducing ion reflection at the Q0B / Q0C boundary.

[0117] In some such embodiments, the bandpass window of mass filter Q0 (e.g., a quadrupole mass filter) can be configured to include the mass of the next precursor ion to be monitored in addition to the mass of the precursor ion of interest. This is shown diagrammatically in Figures 4A and 4B. In this example, mass filter Q0 is initially configured to have a bandpass window (BP1) that allows transmission of ions with m / z ratios of m1 and m2, and mass analyzer Q1 is configured to allow transmission of ions with an m / z ratio of m1. When the transmission window of mass analyzer Q1 is shifted to the next mass of interest, i.e., ions with an m / z ratio of m2, the bandpass window of mass filter Q0 is adjusted to allow transmission of ions with an m / z ratio of m2 and ions with an m / z ratio of m3 (this adjusted bandpass window is designated herein as BP2).

[0118] In many embodiments, such adjustment of the bandpass window of mass filter Q0 can be accomplished by first adjusting at least one operating parameter (e.g., RF voltage or DC resolving voltage) to create a wider bandpass window, and then adjusting at least another operating parameter to narrow the bandpass window of the mass filter to the desired width. For example, the DC resolving voltage and the amplitude of the applied RF voltage can be used to adjust the bandpass window of the mass filter.

[0119] In some embodiments, the order in which the RF voltage and DC resolving voltage are changed may depend on the required RF and DC resolving voltages for the subsequent bandpass window. For example, if the subsequent bandpass window is to remain the same size but be shifted toward a lower mass, the resolving DC voltage will need to be decreased before the RF amplitude is decreased (see, e.g., the transition from BP5 to BP6 in Table 1 below). If the desired width of the subsequent bandpass window is less than the current bandpass window, the RF voltage may first be increased to create a wider bandpass window before increasing the DC resolving voltage to narrow the bandpass window to the desired width (see, e.g., the transition from BP3 to BP4 in Table 1 below). If the bandpass were moving toward a lower mass pair, such as transitioning from BP4 to BP3, the width of the bandpass window is narrowed by decreasing the RF voltage amplitude, followed by a decrease in the DC resolving voltage.

[0120] By way of further illustration, Table 1 below provides examples of RF voltages and DC resolving voltages for adjusting the bandpass of a mass filter in accordance with the present teachings. This example shows that if the width of the bandpass window is increased, the bandpass resolving DC voltage can be decreased even though the bandpass window is moved to higher masses. An example of achieving such a change in bandpass window can be seen in Table 1 below by comparing row BP3 with row BP4 of the table. In this example, a bandpass window of 265 to 295 requires a resolving DC voltage of 52.4 V, while a bandpass window of 275 to 385 requires a lower resolving DC voltage of 46.8 V. [Table 1]

[0121] As an example, and referring to Figure 4B, first the bandpass window of mass filter Q0 can be increased to cover both m2 and m3 without perturbing the flow of m2 ions into downstream mass analyzer Q1. Following the change in mass filter Q0's RF voltage, the DC resolving voltage applied to mass filter Q0 is adjusted to adjust its bandpass window to the desired width. In many such embodiments, mass analyzer Q1 is operated to select ions with an m / z ratio of m3 while the DC resolving voltage applied to mass filter Q0 is adjusted. Continuing with reference to Figure 4A, the bandpass window of mass filter Q0 can be adjusted to cover the m / z ratios of m3 and m4 (i.e., the bandpass window designated as BP3). In this example, this is followed by adjusting the bandpass window of mass filter Q0 to cover m4 and m5 (see the bandpass window designated as BP4).

[0122] In this embodiment, the RF and DC voltage sources 12, 20a, and 20b are operated under the control of a controller 22 to control the application of RF and DC voltages to the mass filter Q0 and mass analyzer Q1 to set and adjust the bandpass window of the mass filter Q0 and the transmission window of the mass analyzer Q1. More specifically, the controller 22 can be programmed to control the RF and DC voltage sources so that the RF and DC voltages applied to the rods of the mass filter Q0 and mass analyzer Q1 provide the desired bandpass window for the mass filter Q0 and also enable transmission of ions having the desired m / z ratio through the downstream mass analyzer Q1. Furthermore, the controller 22 can update the bandpass window of the mass filter Q0 to the next bandpass window and also adjust the RF and / or DC voltages applied to the mass analyzer Q1 to switch the transmission of ions through the mass analyzer Q1 from one m / z ratio to another.

[0123] For example, at the start of a measurement cycle, the controller 22 may set the bandpass window of mass filter Q0 and the transmission window of mass analyzer Q1 such that the bandpass window of mass filter Q0 will cover a number of m / z ratios of interest and the transmission window of mass analyzer Q1 will cover one of those m / z ratios. After a preset period of time (e.g. the time required for mass analyzer Q1 to process ions having the m / z ratio of interest), the controller 22 switches the transmission window of mass analyzer Q1 to the next m / z ratio of interest that is already within the bandwidth window of mass filter Q0, and shifts the bandwidth window of mass filter Q0 to cover the new m / z ratio of interest in addition to the m / z ratios being processed by mass analyzer Q1, for example based on a predetermined list of m / z ratios of interest previously provided to the controller.

[0124] In some embodiments, the controller 22 may be configured to shift the transmission bandwidth of mass filter Q0 and the transmission window of mass analyzer Q1 substantially in parallel. In other embodiments, the controller 22 may be configured to shift the transmission bandwidth of mass filter Q0 before shifting the transmission window of mass analyzer Q1 to the next m / z of interest. For example, referring again to Figure 4B, while mass analyzer Q1 is monitoring ions with an m / z of m2, the controller 22 may shift the transmission bandwidth of mass filter Q0 to cover ions with m / z ratios of m2 and m3 (i.e. from BP1 to BP2). The controller 22 may then shift the transmission window of mass analyzer Q1 to cover the m / z ratio of m3 while ions with an m / z ratio of m3 are equilibrating in mass filter Q0, for example via collisional cooling.

[0125] 12 shows a timing diagram illustrating one example of operating mass filter Q0 and mass analyzer Q1 in accordance with an embodiment of the present teachings. In this example, the Q1 mass analyzer is configured to measure m1, while the RF voltage and DC resolving voltage applied to mass filter Q0 are set so that the bandpass window of mass filter Q0 will encompass masses m1 and m2. At time t1', the bandpass window of mass analyzer Q1 is adjusted to monitor m2, and at time t1, the RF voltage is increased, followed by an increase in the DC resolving voltage at a subsequent time t2, so that the bandpass window of mass filter Q0 covers masses m2 and m3 while mass analyzer Q1 continues to monitor m2. At time t2', mass analyzer Q1 is switched to monitor m3, while the bandpass window of the Q0 mass filter continues to cover masses m2 and m3. At time t3, the RF voltage is increased to change the bandpass window of mass filter QO, followed by an increase in the DC resolving voltage at a subsequent time t4 to cover m3 and m4 while mass analyzer Q1 continues to monitor m3. Mass analyzer Q1 is then switched to monitor m4. In this example, the controller changes the RF voltage of mass filter QO before changing the DC resolving voltage of mass filter QO, represented by the timing for the bandpass window changing from BP1 to BP2 to BP3 (see Table 1 above).

[0126] 13 shows another timing diagram for operating mass filter Q0 and mass analyser Q1. Mass analyser Q1 is set to monitor m1 while its bandpass window encompasses m1 and m2. At time t1', mass analyser Q1 switches to m2 while its bandpass window still encompasses m1 and m2 and mass analyser Q1 continues to monitor m2. At time t1, the DC resolving voltage applied to mass filter Q0 is reduced to change the bandpass window of mass filter Q0 to encompass m2 and m3, and at time t2, the RF voltage applied to mass filter Q0 is increased to narrow the bandpass window while mass analyser Q1 is still monitoring m2. Subsequently, at time t2', mass analyzer Q1 switches to monitoring m3, and subsequently, at time t3, the RF voltage applied to mass filter Q0 is increased to change the bandpass window of mass filter Q0 to include m3 and m4, followed by an increase in the DC resolving voltage applied to mass filter Q0 at time t4. Subsequently, at time t3', mass analyzer Q1 switches to monitoring m4. In this example, the DC resolving voltage applied to mass filter Q0 is changed prior to the application of RF voltage to mass filter Q0, and this is represented by the timing for the bandpass window changing from BP3 to BP4 to BP5 (see Table 1).

[0127] Note that all ions with masses above the low mass cutoff of the mass filter Q0 sections located upstream of the section in which the bandpass window is created are present in those upstream sections.

[0128] In some embodiments, the controller 22 shifts the bandpass window of the mass filter Q0 and the bandpass window of the mass analyzer Q1 in a direction that increases the m / z ratio, while in other embodiments the controller 22 can be configured to shift the bandpass window of the mass filter Q0 and the bandpass window of the mass analyzer Q1 in a direction that decreases the m / z ratio.

[0129] In some cases, the bandpass window of mass filter Q0 can encompass more than two m / z ratios. For example, as shown in Figure 4A, bandpass window BP5, which follows bandpass window BP4, encompasses three m / z ratios: m5, m6, and m7.

[0130] Furthermore, the bandpass window of mass filter Q0 can be configured to allow the passage of ions having any desired m / z ratio. In some embodiments, the selection of the bandpass window of mass filter Q0 can be informed by the number of unwanted ions that may be contained within the bandpass window that may lead to contamination. Unwanted ions are those that mass analyzer Q1 would not select for transmission to downstream components, for example as precursor ions for subsequent fragmentation in a collision cell to monitor MRM transitions.

[0131] As described above and shown in Figure 3, in this embodiment, mass filter Q0 includes four sets of rods Q0A, Q0B, Q0C, and Q0D that are arranged in series with one another. In this embodiment, each of the four sets Q0A, Q0B, Q0C, and Q0D includes four rods arranged in a quadrupole configuration. The sections of mass filter Q0 that are configured to provide a bandpass window in accordance with the present teachings are implemented as quadrupoles; however, other sections of mass filter Q0 can be implemented using other multipole configurations, such as hexapoles, octopoles, etc.

[0132] Referring to Figure 5, for each of the four rod sets Q0A, Q0B, Q0C, and Q0D, the rods marked with an "A" are electrically connected and are referred to as the A poles. The rods marked with a "B" are electrically connected and are referred to as the B poles.

[0133] An RF signal is applied to the first and fourth sets of rods Q0A and Q0D. Additionally, in this embodiment, an RF signal is similarly applied to the second set of rods Q0B. The RF signals applied to the first and second sets of rods Q0A and Q0B provide radial focusing of the received ions through the process of collisional cooling, which in turn results in a smaller radial divergence of the ion beam than at the entrance of the first set of rods Q0A. One advantage of using two sets of rods Q0A and Q0B rather than a single rod set having the same length as the combination of the two rod sets is that a DC voltage offset applied between the two sets of rods Q0A and Q0B can help ions continue to move without losing so much axial kinetic energy that they would stop within the section. Furthermore, the DC voltage offset applied to the rod sets Q0C and Q0D is selected to ensure that the axial kinetic energy of ions will be lower as they exit the mass filter Q0 region, pass through lens IQ1, and reach the mass analyzer Q1. This in turn can aid in timing the filling of mass filter Q0 and the transmission of ions received by mass filter Q0 to the downstream mass analyser Q1.

[0134] For the third set of rods, Q0C, in addition to the RF signal being applied to provide radial confinement, a DC resolving voltage is also applied across the rods of the third set, Q0C, to define the bandwidth window of the mass filter, Q0. As described above, no resolving DC voltage is applied to the rods of the first, second, and fourth sets, Q0A, Q0B, and Q0D.

[0135] For each rod set (or rod section), the phase of the RF signal applied to the A pole is shifted by 180° relative to the phase of the RF signal applied to the B pole. Furthermore, for the third set of rods Q0C, the resolved DC voltages applied to the A and B poles have opposite polarities. By way of example, in some embodiments, the applied RF voltage can have a frequency in the range of about 500 kHz to about 2 MHz and a zero-to-peak voltage in the range of about 500 V to about 10 kV, although other frequencies and / or voltages can also be employed based, for example, on the specific application.

[0136] The selection of the RF drive frequency may depend on the desired mass range, the available voltage range of the power supply, and the field radius of the quadrupole mass filter. The Mathieu equation, reproduced below, can be used to determine the RF drive frequency based on the Mathieu a and q parameters. [ka] [ka] where e represents the ion charge, U represents the DC resolving voltage, V represents the RF drive amplitude, r represents the field radius (i.e., the radius of the ion path provided by the quadrupole rods), Ω represents the angular drive frequency, and m represents the ion mass. Table 2 below provides some examples of the above parameters. [Table 2]

[0137] At very low RF drive frequencies, scattering losses for low-mass ions increase. At very high RF drive frequencies, the cost of implementing the required high RF voltages, such as the cost of voltage feedthroughs and cables to radially confine a maximum mass of 2,000 Da at a 1 MHz RF drive frequency, becomes excessively high. The field radius can also be reduced to allow higher frequencies to be used with lower RF and DC amplitudes while still providing a mass range of 2,000 Da. Reducing the field radius can allow the use of lower RF and DC voltages, but this can lead to an overall reduction in the number of transmitted ions, especially with intense ion beams and their associated space charge effects.

[0138] In this embodiment, an RF voltage source applies an RF signal, for example with a frequency and voltage within the aforementioned ranges, to the Q0C section, and the RF voltages for application to the Q0A, Q0B, and Q0D sections are derived from the Q0C voltage via capacitive coupling. In this embodiment, the peak-to-zero amplitudes of the RF voltages applied to the Q0A, Q0B, and Q0D sections are approximately 90% of the individual RF voltage amplitudes applied to the Q0C section. The RF voltages generate electric fields for radial confinement of ions as they pass through the various sections of the mass filter Q0. Furthermore, in this embodiment, a DC voltage source 20a applies the required DC offset voltage depicted in FIG. 3 to the ion guide QJet (R) and applied to various sections of mass filter Q0 to generate an axial DC electric field for promoting axial movement of ions through mass filter Q0.

[0139] The DC potential drops between the various compartments can range, for example, from 0 V, where the ions are not aided in their axial movement, to optimized potentials shown in FIG. 3 to move ions so that they will not stop in any of the compartments, e.g., a 10 V voltage drop between Q0A and Q0B, a 6 V drop between Q0B and Q0C, and a 4 V drop between Q0C and Q0D.

[0140] In some embodiments, at least some of the ions received by mass filter Q0 may be fragmented in its upstream section (e.g., in this embodiment, Q0B) before arriving at Q0C. As an example, the voltage drop between Q0A and Q0B may be up to 200V when used to fragment ions prior to entering Q0C, for the case of flow through MS3. In such an embodiment, a bandpass window is applied to Q0C around the fragment ions to be selected by the downstream mass analyzer Q1. A potential drop of up to 200V may also be applied to Q0C around the fragment ions to be selected by the QJet (R) QJet for the purpose of fragmenting ions as they transition between IQ0 and IQ0A and / or between IQ0 and Q0A. (R) / IQ0 and IQ0 / Q0A.

[0141] In other embodiments, other voltages are applied to the ion guide QJet to generate electric fields to promote axial movement of ions through the mass filter Q0. (R) and can be applied to a section of the mass filter Q0.

[0142] A mass analyzer Q1, positioned downstream of mass filter Q0, receives ions transmitted through mass filter Q0 and selects from the received ions those having the desired m / z ratio for transmission to downstream components of the mass analyzer, as discussed in more detail below.

[0143] In other embodiments, the mass filter described in U.S. Pat. No. 10,741,378 (the "'378 patent"), entitled "RF / DC Filter to Enhance Mass Spectrometer Robustness," (which is incorporated herein by reference in its entirety), may be employed. Briefly, Figures 2 and 3 of the '378 patent, reproduced herein as Figures 6 and 7, describe an ion guide 120 including a set of four rods 130 a and 130 b extending from a proximal entrance end positioned adjacent an entrance orifice to a distal exit end positioned adjacent an exit aperture. The rods 130 a and 130 b are arranged to form a quadrupole rod set 130 that encloses a space through which ions may travel from the entrance end to the exit end according to a quadrupole configuration. As with the previous embodiment, the rods 130 can each be electrically coupled to an RF power supply (not shown in FIGS. 6 and 7) such that the rods on opposite sides of the central axis together form a rod pair to which substantially the same RF signal is applied, the phase of the RF signal applied to one rod set being opposite the respective phase of the RF signal applied to the other rod set. A DC offset voltage can also be applied to the rods of the quadrupole rod sets.

[0144] 6 and 7, the ion guide 120 additionally includes a plurality of auxiliary electrodes 140 interposed between the rods of the quadrupole rod set 130. The auxiliary electrodes 140 can each be coupled to a DC power supply to provide an auxiliary electrical signal thereto so as to control the transmission of ions through the ion guide 120. For example, in some embodiments, a DC voltage can be applied to the auxiliary electrodes that is equal to a DC offset voltage applied to the rods of the quadrupole rod set.

[0145] Another mass filter suitable for use in the practice of the present teachings is described in the '371 application, entitled "RF / DC cutoff to reduce contamination and enhance robustness of mass spectrometry," which is incorporated herein by reference in its entirety. Briefly, this publication discloses a system and method utilizing a multipole ion guide that can receive ions from an ion source for transmission to a downstream mass analyzer. The system can include auxiliary electrodes interposed within the quadrupole rod set to which RF and / or DC signals can be applied to control or manipulate the transmission of ions from the multipole ion guide. For example, one pair of the auxiliary electrodes can be maintained at a positive potential and another pair of the auxiliary electrodes can be maintained at a negative potential.

[0146] The present teachings can be incorporated into a variety of different mass spectrometers. As an example, FIG. 8 diagrammatically depicts a mass spectrometer 100 including an ion source 102 for generating a plurality of ions. A variety of ion sources can be employed in practicing the present teachings. Some examples of suitable ion sources include, but are not limited to, electrospray ionization devices, nebulizer-assisted electrospray devices, chemical ionization devices, nebulizer-assisted atomization devices, chemical ionization devices, matrix-assisted laser desorption / ionization (MALDI) ion sources, photoionization devices, laser ionization devices, thermospray ionization devices, inductively coupled plasma (ICP) ion sources, sonic spray ionization devices, glow discharge ion sources, and electron impact ion sources, among others.

[0147] The generated ions pass through an orifice 104a in the curtain plate 104 and an orifice 106a in an orifice plate 106, which is positioned downstream of the curtain plate 104 and separated from the curtain plate 104 such that a gas curtain chamber is formed between the orifice plate 106 and the curtain plate 104. A curtain gas supply (not shown) provides a curtain gas flow (e.g., of nitrogen) between the curtain plate 104 and the orifice plate 106 to help keep the downstream section of the mass spectrometer clean by de-clustering and evacuating neutral particles. The curtain chamber can be maintained at an elevated pressure (e.g., above atmospheric pressure), while the downstream section of the mass spectrometer can be maintained at one or more selected pressures via evacuation through one or more vacuum pumps (not shown).

[0148] In this embodiment, ions passing through the orifices 104a and 106a of the curtain plate 104 and the orifice plate 106 are guided by the ion guide QJet (R) , which comprises four rods 108 (two of which are visible in this view) arranged in a quadrupole configuration to form an ion beam for transmission to downstream components of the mass spectrometer 100. In use, the ion guide QJet (R) can be employed to trap and focus ions received through the openings in the orifice plate 106 using a combination of gas dynamics and radio frequency fields.

[0149] The ion beam is guided by the QJet ion guide. (R) and is focused via lens IQ0 into first mass filter Q0, which is implemented in the manner discussed above. In some embodiments, the pressure in first mass filter Q0 can be maintained within a range of, for example, about 3 mTorr to about 10 mTorr.

[0150] The first mass filter Q0 delivers ions downstream to the second mass filter Q1 via an ion lens IQ1 and a stub lens ST1, which functions as a Brubaker lens, and is implemented in the manner discussed above.

[0151] More specifically, in this embodiment, the quadrupole rod set 110 of the second mass filter Q1 can be operated as a transmission RF / DC quadrupole mass filter to select ions having an m / z value of interest. By way of example, the quadrupole rod set 110 of the second mass filter Q1 can be provided with RF / DC voltages suitable for operation in a mass-resolved mode. For example, the parameters of the applied RF and DC voltages can be selected so that the second mass filter Q1 establishes a transmission window for selected m / z ratios, such that these ions can traverse the second mass filter Q1 largely undisturbed. However, ions with m / z ratios that fall outside the window will not achieve a stable trajectory within the quadrupole and may be prevented from traversing the quadrupole rod set of the second mass filter Q1. It should be understood that this mode of operation is merely one possible mode of operation for the second mass filter Q1.

[0152] In this embodiment, ions selected by the second mass filter Q1 are focused into the collision cell Q2 via a stub lens ST2 and an ion lens IQ2. In this embodiment, the collision cell Q2 includes a pressurized compartment that can be maintained at a pressure, for example, in the range of about 1 mTorr to about 10 mTorr, although other pressures can also be used for this or other purposes. A suitable collision gas (e.g., nitrogen, argon, helium, etc.) can be provided using a gas inlet (not shown) to fragment at least a portion of the ions received by the collision cell Q2.

[0153] In this embodiment, collision cell Q2 includes four rods arranged in a quadrupole configuration, to which an RF voltage can be applied to provide radial confinement of ions received by collision cell Q2.

[0154] Product ions generated by collision cell Q2 are received by downstream quadrupole mass analyzer Q3 via ion lens IQ3 and stub lens ST3, which function to focus the product ions into quadrupole mass analyzer Q3. Quadrupole mass analyzer Q3 includes four rods 114 arranged relative to one another in a quadrupole configuration, to which RF and DC voltages can be applied in a manner known in the art to provide mass analysis of the product ions. Ions passing through mass analyzer Q3 are detected by downstream detector 122, which generates an ion detection signal in response to the incident ions. A pair of lenses 116 and 118 helps to focus the ions onto the detector. In this embodiment, lens 116 is implemented as a 90% transmission mesh that defines the edge of the trapping region when Q3 is used as a linear ion trap. Lens 118, in turn, provides shielding for the trapping region, reducing electric field penetration from floating potentials applied to the detector (e.g., −6 kV in positive ion mode and +4 kV in negative ion mode for a 4822D Channeltron detection system, or from the −15 kV and +5.5 kV detector floating potentials applied to HEDs used in high dynamic range detection systems such as those described in U.S. Pat. Nos. 10,074,529 and 9,991,104, which are incorporated herein by reference in their entireties).

[0155] An analyzer 124, in communication with the detector 122, receives the ion detection signal, processes the ion detection signal, and generates a mass spectrum of the product ions, thereby enabling monitoring of MRM transitions corresponding to the precursor ions. As is known in the art, the analyzer 124 can be implemented in hardware / firmware and / or software using techniques known in the art as informed by the present teachings. For example, the analyzer 124 can include a processor, one or more random access memory (RAM) modules, one or more permanent memory modules, and at least one communication bus to enable communication between these and other components.

[0156] In a related aspect, the present teachings provide methods and systems that aid in reducing contamination of high-vacuum components of a mass spectrometer, such as the quadrupole rods of the second mass filter Q1. Contamination of ion path components can adversely affect the performance of a tandem mass spectrometer. In general, contamination of high-vacuum components can degrade mass spectrometer performance more than contamination of components used before the high-vacuum components, such as the quadrupole rods of the first mass filter Q0 or auxiliary electrodes such as those described in the '371 application and the '378 patent. For example, SWATH (R) In DIA modes of operation such as (also referred to herein as DIA methods), unwanted precursor ions having m / z ratios outside the ion selection window of the second mass filter Q1 may be filtered out and deposited on the quadrupole rods of the second mass filter Q1. Such contamination may adversely affect the sensitivity and shape of the ion selection window of the second mass filter Q1, which in turn may reduce precursor ion transmission efficiency and effective coverage for the mass range of interest. The reduced coverage of the mass range of interest may in turn reduce the SWATH (R) This affects the accuracy of ion extraction and quantification in the analysis.

[0157] Accordingly, some embodiments of methods and systems according to the present teachings are directed to reducing contamination of the low-pressure mass analyzer of a mass spectrometer operating in DIA mode, thereby maintaining instrument sensitivity, precursor ion transmission efficiency, and coverage of the precursor ion mass range of interest.

[0158] By way of example, some embodiments of the present teachings may employ a SWATH filter in which only the rod set of the first mass filter Q0 is employed for precursor ion selection, or the ion transmission bandwidth of the first mass filter Q0 configured to pre-filter precursor ions is selected to be larger than the ion transmission window provided by the downstream second mass filter Q1. (R) Such embodiments therefore provide a method and system for performing mass spectrometry in a SWATH mode. (R) When operated in this mode, contamination of the second mass filter Q1 can be reduced.

[0159] In various embodiments, contamination of a tandem mass spectrometer operating in DIA mode is reduced by performing mass filtering in a multipole ion guide Q0, for example a quadrupole ion guide. The ion guide Q0 may perform the mass filtering typically performed by a mass filter device Q1 (e.g. a mass filter device formed by using a set of multipole rods such as quadrupole rods), or the ion guide Q0 may perform pre-filtering to improve the mass filtering performed by the mass filter Q1. In other words, the mass-filtering ion guide Q0 may be used to replace the mass filter Q1 in the DIA method, or it may be used to pre-filter precursor ions for the mass filter Q1 in the DIA mode of operation.

[0160] In any DIA method, different precursor ion mass selection windows spanning the precursor ion m / z or mass range of interest are selected for the experiment. These different precursor ion mass selection windows are selected by the user or method developer of the DIA method. During each time cycle of the tandem mass spectrometer, these different precursor ion mass selection windows are each used to transmit precursor ions to the fragmentation device. Note that the terms "mass" and "m / z" are used interchangeably herein. Generally, mass spectrometry measurements are made at m / z and converted to mass by multiplying by charge.

[0161] FIG. 14 is an exemplary diagram 200 illustrating how different precursor ion mass selection windows spanning a mass range are scanned in a conventional DIA method, in which various embodiments can be implemented. In this example, five different precursor ion mass selection windows 210 are selected for the DIA method, spanning precursor ion mass ranges M1 through M6. In FIG. 14, the different precursor ion mass selection windows 210 are shown as non-overlapping windows, meaning the ion mass selection windows have the same length or width. However, these ion selection windows can also be overlapping windows and / or have variable lengths.

[0162] In the DIA method, precursor ions in each of the different precursor ion mass selection windows 210 are transmitted and fragmented, and the resulting product ions are mass analyzed in each time cycle of the tandem mass analyzer. As a result, five MS / MS spectra are generated per time cycle of the tandem mass analyzer. Each MS / MS spectrum can be obtained at a single collision energy or averaged over a range of collision energies during fragmentation.

[0163] 14, each of the different precursor ion mass selection windows 210 is selected and transmitted using a mass filter device in the high vacuum region of the tandem mass spectrometer, which may be, for example, a quadrupole Q1.

[0164] In other embodiments, the multipole ion guide Q0 can perform mass filtering or pre-filtering by using different Q0 precursor ion mass selection bandwidths. With respect to mass filtering, each of the different Q0 precursor ion mass selection windows is substantially equivalent to or wider than each of the different precursor ion mass selection windows selected for the DIA method. In other words, with respect to mass filtering, each of the different Q0 precursor ion mass selection windows is equivalent to or wider than the different precursor ion mass selection windows selected for the DIA method.

[0165] Figure 15 is an exemplary schematic diagram 300 showing how a multipole ion guide Q0 can perform mass filtering by using different Q0 precursor ion mass selection windows, according to various embodiments. In Figure 15, five different Q0 precursor ion mass selection windows 310 have been selected for the DIA method, spanning the precursor ion mass range of M1 through M6. Again, in Figure 15, the different Q0 precursor ion mass selection windows 310 are shown as non-overlapping windows, all having the same length or width. However, these windows can also be overlapping windows and can have variable lengths.

[0166] In the DIA method, different precursor ion mass selection windows 310 are each selected and transmitted using a multipole ion guide (e.g., a quadrupole) as the mass filter Q0 prior to the low-pressure region. In addition, no other mass filter devices, such as a quadrupole mass filter Q1 or a second mass filter, are used. Ions transmitted by mass filter Q0 are sent to a fragmentation device, and the resulting product ions are mass analyzed in each time cycle of the tandem mass analyzer. Again, five MS / MS spectra are generated per time cycle of the tandem mass analyzer. Each MS / MS spectrum can be obtained at a single collision energy or averaged over a range of collision energies during fragmentation.

[0167] In such an embodiment, eliminating the need for a second mass filter device, such as quadrupole Q1, significantly reduces contamination problems in the low-pressure region of the tandem mass spectrometer. This also reduces the complexity of the instrument. Generally, a second mass filter device can provide higher mass resolution than using a single ion guide mass filter. However, because a wide precursor ion mass selection window is used in DIA experiments, the reduced mass resolution of ion guide mass filter Q0 does not pose any problems.

[0168] However, in various embodiments, the multipole ion guide mass filter Q0 can also be used as a pre-filter for the second mass filter Q1. In mass pre-filtering, each of the plurality of precursor ion mass selection windows for the first mass filter Q0 is used to pre-filter ions with respect to a corresponding window of a plurality of different precursor ion mass selection windows for the second mass filter Q1 employed to implement the DIA method. As a result, the precursor ion mass selection window of the first mass filter Q0 is configured to have a larger mass or m / z width than its corresponding precursor ion mass selection window of the second mass filter Q1.

[0169] Figure 16 is an exemplary schematic diagram 400 showing how an ion guide may perform mass pre-filtering by using precursor ion mass selection windows of a first mass filter Q0 and pre-filter the precursor ion mass selection windows of a second mass filter Q1, according to various embodiments. In Figure 16, five different precursor ion mass selection windows 410 of the second mass filter Q1 are selected for the DIA method, spanning the precursor ion mass range M1 to M6. In addition, each of the five different precursor ion mass selection windows 420 of the first mass filter Q0 is calculated to pre-filter a window of the five different precursor ion mass selection windows 410 of the second mass filter Q1.

[0170] 16, each of the different precursor ion mass selection windows 420 in the first mass filter Q0 has a larger bandwidth than its corresponding window in the different precursor ion mass selection window 410 in the second mass filter Q1. In this example, each window 420 in the first mass filter Q0 has a lower low m / z cutoff and a higher high m / z cutoff than its corresponding ion selection window 410 in the second mass filter Q1. This reduces both low mass contamination and the much more problematic high mass contamination.

[0171] However, pre-filtering ions is not without cost. As explained below, there is a cost in the time required to refill at least the first mass filter Q0. As a result, in various embodiments, one window of the first mass filter Q0 can be used to pre-filter two or more windows of the second mass filter Q1. In some such embodiments, the window of the first mass filter Q0 spans a range of m / z ratios that exceeds the combined range of m / z ratios associated with two consecutive ion selection windows of the second mass filter Q1.

[0172] As an example, Figure 17 is a schematic diagram 500 illustrating how an ion guide Q0 can perform mass pre-filtering using one precursor ion mass selection window and pre-filter two different precursor ion mass selection windows for a second mass filter Q1, according to various embodiments. In Figure 17, four different precursor ion mass selection windows 510 for the second mass filter Q1 are selected for the DIA method, spanning the precursor ion mass range M1 to M5. In addition, each of the two different precursor ion mass selection windows 520 for the first mass filter Q0 is calculated to pre-filter two of the four different precursor ion mass selection windows 510 for the second mass filter Q1. While this example shows the bandpass windows of the first mass filter Q0 covering two different precursor ion mass selection windows of the second mass filter Q1, it is also possible for the bandpass windows of the first mass filter Q0 to cover more than two different selection windows for the second mass filter Q1, for example, three, four, five, etc.

[0173] In various embodiments, mass filtering or pre-filtering by the first mass filter Q0 can be performed by applying tailored waveforms to the ion guide rods, for example using multiple segmented ion guide rods or using auxiliary electrodes placed between the ion guide rods. As an example, in some embodiments, tailored waveforms can be applied by applying combs of different frequencies to the rods of the multipole ion guide (i.e., the first mass filter Q0). The combs of different frequencies define the masses that are not transmitted. In other words, the precursor ion mass selection window of the first mass filter Q0 is formed by excluding masses outside the window by applying RF signals with corresponding frequencies to the rods of the multipole ion guide. Compartmentalized multipole ion guide rods

[0174] 18 is an exemplary schematic diagram 600 of a multipole ion guide 610 that may be used as a mass filter Q0, with segmented rods that may be used for mass filtering or pre-filtering, according to various embodiments. The multipole ion guide 610 includes a segmented rod set 620. Each rod of the segmented rod set 620 is spaced apart from and extends alongside a central longitudinal axis 630. Each rod of the segmented rod set 620 is also segmented into three different longitudinal sections. These sections are a first section 621, a middle section 622, and a final section 623. The first section 621 is used to receive and cool ions entering the multipole ion guide 610 from the ion source 601. The final section 623 is used to transmit ions from the multipole ion guide 610. The middle section 622 is used to filter or pre-filter ions.

[0175] As in a conventional quadrupole mass filter Ql, an RF voltage 641 of an RF electrical signal and a DC voltage 642 of a DC electrical signal are applied to the rod sections of the intermediate section 622. A processor or controller 640 applies or controls these electrical signals. The RF voltage 641 defines the low m / z cutoff of the precursor ion mass selection window for the multipole ion guide 610 (i.e., mass filter QO), and the DC voltage 642 defines the high m / z cutoff of the precursor ion mass selection window for the multipole ion guide 610 (i.e., mass filter QO). It will be apparent to those skilled in the art that the segmented mass filter QO may comprise any number of sections, and any section may be used to filter or pre-filter ions. Auxiliary electrodes between multipole ion guide rods

[0176] The above-referenced '832 and '371 applications describe systems and methods utilizing a multipole ion guide Q0 that receives ions from an ion source for transmission to downstream mass analyzer components but may prevent contaminating ions from being transmitted into the low-pressure chamber of the mass analyzer. The '832 and '371 applications are incorporated herein by reference in their entireties. A DC signal is provided to auxiliary electrodes interposed within the multipole rod set to control or manipulate the transmission of ions from the multipole ion guide Q0.

[0177] Figure 19 is an exemplary schematic diagram 700 showing a multipole ion guide 720 (i.e., Q0) of the '832 and '371 applications in which various embodiments may be implemented. In Figure 19, ions generated by an ion source device 701 can be extracted into a coherent ion beam by passing successively through openings in an orifice plate 702 and a skimmer 703. The ions form a narrow, highly focused ion beam that enters the ion guide chamber 710 through a skimmer opening 711.

[0178] The multipole ion guide 720 is housed within the ion guide chamber 710. The rods of the multipole rod set 730 surround and extend along the central axis of the multipole ion guide 720, thereby defining a space through which ions of a highly focused ion beam are transmitted. The multipole ion guide 720 also includes auxiliary electrodes 740 that extend along a portion of the multipole ion guide 720 and are interposed between the rods of the multipole rod set 730.

[0179] The multipole ion guide 720 uses a multipole rod set 730 and an auxiliary electrode 740 to bandpass filter ions of a highly focused ion beam. An RF voltage and a DC offset voltage are applied to the rods of the multipole rod set 730. The RF voltage defines the low m / z cutoff of the bandpass filter. A DC voltage 751 is applied to the auxiliary electrode 740. The DC voltage 751 is applied using, for example, a processor or controller 750. The relative difference between the DC voltage 751 and the DC offset voltage applied to the rods of the multipole rod set 730 defines the high m / z cutoff for the bandpass filter. In other words, the DC voltage 751 of the auxiliary electrode 740 is used to define the high m / z cutoff for the bandpass filter.

[0180] Ions filtered by the multipole rod set 730 and auxiliary electrode 740 of the multipole ion guide 720 are transmitted to the low-pressure chamber 760. Ions are transmitted from the ion guide chamber 710 to the low-pressure chamber 760, for example, through the IQ1 lens 761. It will be apparent to those skilled in the art that a mass analyzer may include additional vacuum stages, which may include additional ion guides. In some of the above embodiments, the present teachings can be implemented by configuring the ion guides and mass filters employed in SCIEX brand mass analyzers. Ion guide Q0 typically operates in a vacuum stage having a pressure range of approximately 1 to 12 millitorr, although other pressures may also be employed. Other ion guides, including ion guides operating in various other pressure regimes, may also be used to create the bandpass filter.

[0181] FIG. 20 is an exemplary perspective view 800 of the auxiliary electrode of the '832 and '371 applications, various embodiments of which may be implemented based on the present teachings. As shown in FIG. 20 , the auxiliary electrode 740 may include four T-shaped electrodes 840 having a base portion 850 and a stem portion 860 extending therefrom. The electrodes 840 may be 10 mm in length, and the stems 860 may be approximately 6 mm in length. The electrodes 840 may be coupled to a mounting ring 842, which may be mounted at a desired location in the multipole ion guide. In other embodiments, the electrodes 840 may have different lengths, and the stems 860 may have different lengths. The electrode dimensions may be optimized for different workflows or ion guide rod geometries.

[0182] The exemplary mounting ring 842 may include notches (e.g., like rod 720a, shown in phantom) for securely engaging rods of a multipole ion guide. As shown, a single electrical conductor 844 may be coupled to a DC power supply (not shown) and may also be electrically coupled to one or more of the electrodes 840. The same DC voltage may be applied to all of the electrodes 840, or different DC voltages may be applied to different electrodes 840. In some embodiments, opposing electrodes may have a positive DC potential and adjacent pairs may have a negative DC potential. In additional embodiments, the potentials applied to the two pairs of electrodes may be offset or symmetrically arranged around the DC offset potential of the Q0 rod.

[0183] Figure 21 is an exemplary cross-sectional view 900 of the multipole ion guide Q0 of the '371 application in which various embodiments may be implemented. In Figure 21, the multipole ion guide 720 is depicted as a quadrupole including a set of four rods 930a and 930b. The rods 930a and 930b surround and extend along the central axis of the multipole ion guide 720, thereby defining a space through which ions are transmitted.

[0184] The multipole ion guide 720 further includes a plurality of auxiliary electrodes 940 interposed between the quadrupole rods 930a and 930b of the multipole ion guide 720 that also extend along the central axis (shown in phantom). Each auxiliary electrode 940 can be separated from another auxiliary electrode 940 by a rod of the quadrupole rods 930a and 930b. Furthermore, the auxiliary electrodes 940 can be disposed adjacent to and between a first pair of rods 930a and a second pair of rods 930b, respectively.

[0185] While the quadrupole rods 930a and 930b are maintained at a DC offset voltage, where a first RF voltage at a first frequency and a first phase is applied to a first group of rods 930a and a second RF voltage at the opposite phase (e.g., of the same amplitude (V p-p) as the first RF voltage) is applied to a second group of rods 930b, various auxiliary electrical signals can be applied to the auxiliary electrodes 940. As shown in FIG. 21 , each auxiliary electrode 940 has a DC voltage 910 of the same amplitude. In other words, all T-shaped electrodes 940 with their base portions 950 and stem portions 960, respectively, are biased at the same DC voltage 910. However, as explained above, in some embodiments, one pair of electrodes can be biased at a positive potential relative to the DC offset voltage of the rods, and the other pair of electrodes can be biased at a negative potential relative to the DC offset potential of the rods. In some embodiments, the positive and negative potential biases can have the same magnitude.

[0186] Each auxiliary electrode 940 has a DC voltage that is different from the DC offset voltage 910 applied to quadrupole rods 930a and 930b. As a result, a mass window generating device for a multipole ion guide is created, as described in the '371 application.

[0187] Although the '832 and '371 applications indicate that auxiliary electrodes can be applied to a multipole ion guide Q0 to filter ions in tandem mass analysis, it has not previously been thought possible to do this in a DIA method. In other words, it has not been thought possible to use a multipole ion guide Q0 with auxiliary electrodes, or even with a multipole ion guide Q0 at all, to create two or more different precursor ion mass selection windows within the same cycle of a tandem mass analyzer.

[0188] The DIA method requires a consistent and reproducible bandpass window for a given RF voltage and auxiliary electrode DC voltage to the multipole ion guide Q0 as the precursor ion window is moved in a step size or scanning manner. In addition, the DIA method requires that the bandpass or precursor ion mass selection window of the multipole ion guide Q0 be changed as quickly as the precursor ion mass selection window of the mass filter Q1 without limiting the cycle time of the tandem mass analyzer.

[0189] The following examples are provided to further illustrate various aspects of the present teachings and do not necessarily represent the best way to practice the present teachings or the best results that may be obtained. Hereinafter, when "Q0" modifies another term, the modified term will be understood to be associated with a multipole ion guide, mass filter, first mass filter, pre-filter, or equivalent, implemented with a structure comprising multiple sets of rods positioned in series as Q0 shown in Figures 3 and 8. When "Q1" modifies another term, the modified term will be understood to be associated with a mass analyzer, mass filter, second mass filter, or equivalent, implemented with a structure shown as Q1 in Figures 3 and 8. [Example]

[0190] Example 1 Figures 9A, 9B, and 9C show examples of bandpass windows obtained for a four-section mass filter Q0, such as that depicted diagrammatically in Figure 3, via application of suitable RF and resolved DC voltages to the various rods of the mass filter Q0 in the manner discussed above.

[0191] More specifically, Figure 9A shows a bandpass window spanning approximately 400 to approximately 500 Da. This bandpass window was achieved by applying an RF signal with a frequency of 1.0 MHz and a zero-to-peak voltage amplitude of 421.5 volts to Q0C, and by capacitively coupling Q0A, Q0B, and Q0D to Q0C such that the voltages applied to Q0A, Q0B, and Q0D are approximately 90% of the voltage applied to Q0C. The resolving DC voltage on the A pole is +73.4 V, and the resolving DC voltage on the B pole is -73.4 V, which, combined with an offset voltage of -6 V, results in a total voltage of +67.4 V on the A pole and -79.4 V on the B pole. The bandpass window is determined solely by the resolving DC voltage; the offset DC voltage determines the axial kinetic energy of the ions, helping them continue their axial motion.

[0192] FIG. 9B shows a bandpass window spanning from about 700 Da to about 800 Da achieved by applying an RF signal with a frequency of 1.0 MHz and a zero-to-peak pole-to-ground amplitude of 899.6 volts and a resolving DC voltage having a pole-to-ground amplitude of 136.1 volts.

[0193] Figure 9C shows a bandpass window spanning from about 800 to about 1,000 Da achieved by applying an RF signal with a frequency of 1.0 MHz and a zero-to-peak pole-to-ground amplitude of 1,009.0 volts and a resolving DC voltage with a pole-to-ground amplitude of 146.8 volts. Example 2

[0194] A mass spectrometer such as that shown in Figure 3 was employed to acquire the data discussed in this section. In particular, the measurements presented in Figures 10A and 10B were performed using the mass filter Q0 depicted in Figure 3, with a 45° ST1 to block ion trapping in the ST1 region and a 37° ST3 to prevent ion trapping in ST3. The presented data were collected with CAD=0. A higher CAD setting would have the effect of further slowing down ion transit times due to collisions in the collision cell Q2.

[0195] More specifically, Figure 10A shows the QJet (R) The following DC settings of the various sections of the ion guide and mass filter Q0, i.e., QJet (R) Figure 10B shows the transit time from lens IQ1 to detector 122 as a function of ion mass for / IQ1 / Q0A = +10V, Q0B = 0V, Q0C = -6V, and Q0D = -10V. Figure 10B shows a time section of the data presented in Figure 10A extending from t = 0 to t = 3 ms. Additionally, the vertical dashed lines represent the calculated transit time for the associated mass from ion lens IQ1 to exit lens 118. The time from the exit lens to the output of the digital pulse is negligible due to the high magnetic field present in the detector region. A Tektronix DPO 7254C high-speed oscilloscope was used to monitor the digital pulse created when an ion was detected. The oscilloscope was triggered by the pulse used to switch lens IQ1 from non-transmission mode to transmission mode. In this example, 200 acquisitions were used to construct the histograms presented in Figures 10A and 10B.

[0196] These measurements show that in the depicted example, if the time for mass analyzer Q1 to perform a measurement is approximately 3 milliseconds, when mass analyzer Q1 switches to the next m / z ratio, the intensity of the next m / z ion (e.g., m2 in the above description) will be at the 60% level if the next ion was contained within the bandpass window of mass filter Q0. In such a case, mass analyzer Q1 measurement can begin as soon as mass analyzer Q1 switches to the next ion, without waiting for the bandpass of mass filter Q0 to switch.

[0197] The techniques described above also involve two or more SWATH (R) The precursor window is contained within the bandpass window of the first mass filter Q0. (R) This can be expanded to include other acquisition methods. (R) Acquisition is a data-independent acquisition (DIA) method in which all precursor ions within a defined or selected precursor ion mass selection window of the second mass filter Q1 are transferred to a fragmentation device or collision cell to generate one MS / MS spectrum. (R) The acquisition mode is typically performed on a TOF MS instrument. In such cases, the ion optics after the collision cell Q2 may be TOF ion optics. (R) In the second mass filter, Q1, the precursor ion mass selection window is sequentially stepped across the entire precursor ion mass range of the analysis. The time it takes to analyze the entire mass range once is referred to as the cycle time. The cycle time is limited by the chromatographic peak resolution; sufficient points must be acquired across an LC peak to determine its shape. To keep the cycle time constant during an analysis, adjustments are required between the MS / MS accumulation time, the entire precursor mass range, and the precursor mass selection window width.

[0198] The MS / MS accumulation time is the time spent on each precursor ion window to collect MS / MS information. Generally, better selectivity can be achieved with narrow precursor windows, while better sensitivity can be achieved with wider windows using longer MS / MS accumulations.

[0199] For example, in nanoflow proteomics analysis involving peptide masses ranging from 400 Da to 1,250 Da, MS / MS accumulation times can range from 50 ms to 100 ms, and the precursor window of the second mass filter Q1 can range from 10 Da to 100 Da. In some cases, when a narrow precursor window (e.g., 3 Da) is applied throughout the entire mass range, MS / MS accumulation can be reduced to as short as 20 ms to maintain cycle time. One or more narrow precursor windows may require applying short MS / MS accumulations. (R) In such cases, two or more precursor windows may be selected in a manner or condition such that the bandpass window of the second mass filter Q1 is SWATH. (R) As it shifts with the precursor window, it can be contained within one bandpass window of the first mass filter Q0.

[0200] As described above, a controller employed to practice various aspects of the present teachings as discussed above can be implemented in hardware / firmware / software, or a combination thereof. As an example, FIG. 11 diagrammatically depicts an example implementation of a controller 1100 including a processor 1102, a random access memory (RAM) module 1104, a permanent memory module 1106, and a communication bus 1108 that allows the processor 1102 to communicate with other components of the controller 1100. In some embodiments, various instructions for performing different functions of the controller 1100, such as activating and deactivating an electrostatic deflector and / or analyzing a detection signal generated by an ion detector, can be stored in the permanent memory module 1106 and transferred during runtime by the processor 1102 to the RAM module 1104, which can execute those instructions to perform the respective functions. Example 3

[0201] To determine whether a multipole ion guide Q0 with auxiliary electrodes could be used for the DIA method, several experiments were performed. These experiments investigated the Q0 bandpass performance. These experiments were performed using a separate Q0 RF power supply on a modified tandem mass spectrometry system. The multipole ion guide Q0 used was a Q0 quadrupole, with four T-shaped auxiliary electrodes (T-bars) interposed between the rods of the quadrupole. Both the auxiliary electrode DC potential (QTB, the potential difference between two pairs of T-bar electrodes) and the Q0 RF voltage (Q0A, Vp-p) were adjustable using modified firmware / software to allow these two parameters to be varied.

[0202] These experiments were performed to determine (1) whether varying the voltage applied to the T-bars and rods of the quadrupole Q0 could generate a wide selection of Q0 precursor ion mass selection window widths and locations, (2) whether the Q0 precursor ion mass selection window was reproducible, (3) whether the Q0 precursor ion mass selection window was consistent for a range of different compounds, (4) whether the Q0 precursor ion mass selection window was independent of the magnitude of the transmitted ion current, and (5) whether the Q0 quadrupole refill time substantially affected the cycle time of the tandem mass spectrometer. (1) Window location and width as a function of quadrupole and T-bar voltages

[0203] 22 is an exemplary plot 1000 showing how different RF voltages applied to the quadrupole rods produce different precursor ion mass selection window widths when different DC voltages are applied to T-bar electrodes interposed between the quadrupole rods of multipole ion guide Q0, according to various embodiments. In plot 1000, different lines connecting data points represent increasing RF voltages (Vp-p, 19 voltages from 200 to 2,000 V in 100 V increments) applied to the quadrupole rods. For example, line 1001 connects values ​​measured when an RF voltage of 200 V is applied to the quadrupole rods of multipole ion guide Q0. Similarly, line 1019 connects values ​​measured when an RF voltage of 2,000 V is applied to the quadrupole rods of multipole ion guide Q0.

[0204] Plot 1000 shows that varying the voltages applied to the T-bars and rods of the quadrupole Q0 can produce a wide selection of Q0 precursor ion mass selection window widths and locations. As explained above, the RF voltage applied to the quadrupole rods defines the low m / z cutoff, which defines the location of the Q0 precursor ion mass selection window. The DC voltage applied to the T-bars defines the width of the Q0 precursor ion mass selection window, which in turn provides the high m / z cutoff.

[0205] Plot 1000 shows that for a given location within the precursor ion mass range (defined by a particular RF quadrupole voltage), the width of the Q0 precursor ion mass selection window (defined by a particular DC T-bar voltage) can be varied over a wide range (e.g., 100-1,000 Da). Plot 1000 also shows that this is possible over a wide range of locations (defined by the overall range of RF quadrupole voltages that can be used). The window over which the highest masses are obtained is defined by the maximum RF that can be delivered to the Q0 rod.

[0206] This large matrix of possible Q0 precursor ion mass selection window locations and widths means that it is possible to use the rods and T-bars of the Q0 multipole ion guide Q0 to create the different windows required for DIA methods. In DIA methods, the Q0 precursor ion mass selection window is moved or stepped across a mass range. As a result, the location of the window, as defined by the RF quadrupole voltages, is constantly changing. For example, line 1020 shows that different DC T-bar voltage values ​​are available to move (by increasing the RF quadrupole voltage) a fixed 150 Da wide Q0 precursor ion mass selection window across a mass range.

[0207] In the DIA method, the precursor ion mass selection window width can increase as the window is moved across a mass range. For example, line 1030 shows that different DC T-bar voltage values ​​are available to move a Q0 precursor ion mass selection window that increases in width from 100 Da to 250 Da as the window is moved across a mass range.

[0208] Finally, in the DIA method, the precursor ion mass selection window can have different widths at different mass locations. For example, curve 1040 shows that different DC T-bar voltage values ​​can be used to move a Q0 precursor ion mass selection window having a width that starts at 450 Da at the beginning of a mass range, decreases to 150 Da in the middle of the mass range, and increases back to 450 Da at the end of the mass range.

[0209] Figure 23 is an exemplary plot 1100 of the same data shown in Figure 22, showing different central mass locations and widths that can be produced using a multipole ion guide Q0 that includes quadrupole rods and T-bars interposed between them, according to various embodiments. Plot 1100 shows that varying the voltages applied to the T-bars and rods of quadrupole Q0 can produce a wide selection of Q0 precursor ion mass selection window widths and central mass locations.

[0210] In plot 1100, the different lines connecting the data points represent increasing RF voltages (Vp-p, 19 voltages from 200 to 2,000 V in 100 V increasing increments) applied to the quadrupole rods. For example, line 1101 connects the values ​​measured when an RF voltage of 200 V is applied to the quadrupole rods of Q0 multipole ion guide Q0. Similarly, line 1119 connects the values ​​measured when an RF voltage of 2,000 V is applied to the quadrupole rods of multipole ion guide Q0.

[0211] The points connected by RF voltage lines in plot 1100 represent different DC T-bar voltages. Within each RF voltage line, the DC T-bar voltage increases from the right to the left of the plot.

[0212] Like Figure 22, plot 1100 in Figure 23 shows a large matrix of possible Q precursor ion mass selection window locations and widths. This again shows that it is possible to use the rods and T-bars of the multipole ion guide Q to create the different windows required for the DIA method. Line 1120, line 1130, and curve 1140 show that different DC T-bar voltage values ​​can be used to move the Q precursor ion mass selection window (with increasing RF quadrupole voltage) with fixed, increasing, and variable widths, respectively. (2) Window reproducibility

[0213] 24 is an exemplary table 1200 showing different RF quadrupole rod voltages and DC T-bar voltages applied to the quadrupole rods and T-bars, respectively, of multipole ion guide Q0 to generate a 150 Da Q0 precursor ion mass selection window at different mass locations, according to various embodiments. Table 1200 shows that the window widths are reproducible for all 11 different central mass locations. (3) Consistency across a range of different compounds

[0214] Reserpine samples, a mixture of 211 known compounds, and a bovine serum albumin (BSA) digest were analyzed using a multipole ion guide Q0, which contains quadrupole rods and a T-bar spaced between them. p-p RF quadrupole rod voltages were applied to the quadrupole rods, and a 640 V DC T-bar voltage was applied to the T-bar. These voltages produced Q precursor ion mass selection window widths of 151 Da, 157 Da, and 145 Da for the reserpine sample, the mixture of 211 known compounds, and the BSA digest, respectively. These results demonstrate that the multipole ion guide Q, including the quadrupole rods and T-bar, can produce consistent Q precursor ion mass selection window widths across a range of different compounds with different charge states. (4) Ion current magnitude independent

[0215] A mixture of 211 known compounds prepared at five different dilutions (2x, 10x, 100x, 1,000x, and 10,000x) was analyzed using a multipole ion guide Q0, which includes quadrupole rods and a T-bar interposed between them. The Q0 precursor ion mass selection window used did not shift between different concentrations of the mixture used, even though these concentrations varied across several orders of magnitude. As a result, the Q0 precursor ion mass selection window was found to be independent of ion current intensity. (5) Q0 refill time

[0216] In a multipole ion guide Q0, which includes quadrupole rods and a T-bar interposed between them, the region between the Q0 / T-bar and the next mass analyzer component contains only ions within a selected specific window. When that window changes, time is required to reintroduce new ions into the region downstream of the T-bar. From preliminary tests, a Q0 refill time of <5 ms (accounting for a 3 ms cycle time) was estimated.

[0217] In a typical DIA method, the accumulation time per precursor ion mass selection window is in the range of 50 ms to 100 ms. As a result, a multipole ion guide Q0, including quadrupole rods and T-bars, can be used without substantially affecting Q1 scan rates and cycle times.

[0218] In preliminary tests, the RF quadrupole rod voltage was fixed, and only the DC T-bar voltage was varied to generate two Q0 precursor ion mass selection windows. MRM was performed with a 2 ms dwell time and a 1 ms pause time. The Q0 refill time was estimated from the rise time of the second window ion intensity. Note that the DC T-bar voltage can be rapidly varied, with rise and fall times of approximately 180 μs and 50 μs, respectively, for a full DC swing from -750 Vdc to +750 Vdc at the output of the lens module, using, for example, a commercial lens amplifier (750 V lens). Q1 synchronous pre-filter

[0219] In various embodiments, the Q0 precursor ion mass selection window can be coupled to the Q1 precursor ion mass selection window to simultaneously filter out unwanted ions outside the Q1 precursor m / z range. To accomplish this, a Q0 multipole ion guide with a multipole rod set and auxiliary electrodes is operated as shown in Figure 16.

[0220] In conventional DIA methods, the Q1 precursor ion mass selection window is calibrated based on the Q1 RF voltage and DC resolution offset voltage, where the RF voltage defines the low m / z cutoff and the DC voltage defines the window width. (R) In, for example, the precursor Q1 window is controlled by a scanning Q1 RF voltage with a fixed DC resolution offset voltage.

[0221] 25 is an exemplary plot 1300 showing how the DC voltage applied to the auxiliary electrodes of the multipole ion guide Q0 varies with the RF voltage applied to the multipole rod set of the multipole ion guide Q0 to maintain a constant Q0 precursor ion mass selection window width, according to various embodiments. A Q0 precursor ion mass selection window width of 150 Da is maintained as the RF voltage applied to the multipole rod set of the Q0 multipole ion guide is increased. Plot 1300 shows the DC voltage (QTB) applied to the auxiliary electrodes of the multipole ion guide Q0 to maintain a window width of 150 Da as the RF voltage is increased.

[0222] It will be apparent to those skilled in the art that narrower Q0 precursor ion mass selection window widths can be selected using alternative ion guide bandpass approaches, such as a segmented Q0 with RF and DC potentials applied to it.

[0223] Plot 1300 shows that in a multipole ion guide Q0 with a multipole rod set and auxiliary electrodes, the DC voltage applied to the auxiliary electrodes (QTB) for the high m / z cutoff of a given mass window scales linearly with the RF voltage applied to the multipole rod set. For a given RF voltage, various window widths can be achieved by adjusting the Tbar DC voltage, which determines the high m / z cutoff. Thus, it is possible to achieve a Q0 precursor ion mass selection window with a width and mass location that is synchronized with the Q1 precursor ion mass selection window, as shown in FIG. 16.

[0224] Both the low-mass side and the high-mass side of the Q0 precursor ion mass selection window can be synchronized with the Q1 precursor ion mass selection window. The low-mass cutoff is coupled through synchronizing the RF voltages on the Q1 and Q0 rods. This can be achieved either using one RF generator, as in a standard instrument, or by using separate RF generators. In a standard instrument, one RF power supply is used, and the Q0 RF signal is capacitively coupled to the Q1 RF signal. As a result, the RF voltage changes on Q0 and Q1 are synchronized; for example, on a standard instrument, the Q0 RF signal amplitude is approximately two-thirds of the Q1 RF signal amplitude.

[0225] This difference allows the ion guide Q0 to transmit ions from lower masses compared to the mass filter Q1 (the difference, in this case, can be approximately 100-200 Da). When the ion guide Q0 is controlled by a separate power supply, the Q0 RF voltage can be coupled to the Q1 RF voltage based on the power supply frequency and the window setting (low mass side) from the DIA method. The Q0 RF voltage can be set to create a low mass cutoff slightly lower than the low mass end of the Q1 window (e.g., by lowering the Q0 RF amplitude by an offset).

[0226] The Q0 precursor ion mass selection window on the high mass side can be linked to the Q1 precursor ion mass selection window by controlling the DC voltage of the auxiliary electrodes. As shown in Figures 22 and 23, the dependence of the DC voltage of the auxiliary electrodes on mass location and window width when using the ion guide Q0 as a bandpass filter has been mapped, so that it is possible to set the DC voltage of the auxiliary electrodes to achieve the desired bandpass window based on the mass window setting in the DIA method.

[0227] The DC voltage can be adjusted to bandpass ions with m / z slightly higher than the high-mass end of the Q1 window. As the precursor window is stepped from low to high mass, the DC voltage increases with increasing RF voltage. The voltage value can be automatically set based on the window settings in the DIA method, allowing synchronization of the Q0 bandpass window to the Q1 precursor window in the DIA cycle. The width of the bandpass window will depend on the Q0 bandpass approach used.

[0228] 26 is an exemplary flowchart showing a method 1400 for synchronizing a Q0 precursor ion mass selection window with a Q1 precursor ion mass selection window, according to various embodiments. In step 1410 of method 1400, a DIA method is created and the start and end masses for each Q1 precursor ion mass selection window that will be used to span the entire mass range of the analysis are defined.

[0229] If the standard method of RF control is used, step 1410 moves to step 1420. In step 1420, a low m / z cutoff is calculated based on the Q1 RF voltage, and a high m / z cutoff for the Q0 precursor ion mass selection window is defined for each Q1 precursor ion mass selection window that traverses the entire mass range of the analysis.

[0230] In step 1430, the DC voltage of the auxiliary electrode is defined for each Q1 precursor ion mass selection window across the entire mass range of the analysis (a pre-filter method is created). In step 1440, a method table is constructed by combining and synchronizing the DIA method and the DC voltage control method.

[0231] If separate RF control is used, step 1410 moves to step 1450. In step 1450, both the width and low and high m / z cutoffs of the Q0 precursor ion mass selection window are defined for each Q1 precursor ion mass selection window that traverses the entire mass range of the analysis.

[0232] In step 1460, the Q0 RF voltages applied to the multipole rod set and the DC voltages applied to the auxiliary electrodes are defined for each Q1 precursor ion mass selection window that spans the entire mass range of the analysis (a pre-filter method is created).

[0233] The separate RF control of method 1400 allows for more flexibility in controlling the Q0 precursor ion mass selection window on the low-mass side and the extent to which these windows are wider than the Q1 precursor ion mass selection window. Conventional DIA methods apply a Q1 window in the range of 5 to 50 Da. In various embodiments, the Q0 window is given a width of 150 Da, and the Q1 window is centered within this 150 Da window for best performance. When a single RF generator is used to apply RF voltages to both Q0 and Q1, the low-mass cutoff difference between Q0 and Q1 is not adjustable (approximately 100 to 200 Da), but the DC potential can be set to transfer a wider Q0 window, such as 300 Da, to ensure that the Q1 window is covered.

[0234] Scanning SWATH (R)In this mode of operation, the Q1 RF voltage is scanned with a fixed resolution offset, producing a progressively larger window as the scan moves from low mass to high mass. In various embodiments, the Q0 RF voltage is scanned simultaneously with the Q1 RF voltage, and the DC voltage applied to the Q0 auxiliary electrode varies with the Q0 RF voltage to increase the width of the Q0 window as the window is moved. Examples of windows with increasing window widths as they are moved are shown in Figures 22 and 23.

[0235] One advantage of various embodiments is flexible control over the high m / z cutoff of the Q0 precursor ion mass selection window. As shown in Figures 22 and 23, the window width can be controlled to a fixed value across the entire mass range, varied in an increasing / decreasing order, or customized to a variable window based on DIA methods. For example, many applications use a variable precursor ion mass selection window optimized to transmit high-intensity m / z ranges using a small window and low-intensity m / z ranges using a large window as an approach to balancing sensitivity and selectivity. The exemplary flowchart in Figure 26 specifically refers to an embodiment in which a Q0 T bar is used to create a bandpass. It will be clear to those skilled in the art that the present teachings apply to any method of creating a bandpass in a higher-pressure region or regions upstream of the first mass analyzer. The specific steps in the flowchart in Figure 26 will vary for different bandpass approaches. System for mass filtering precursor ions in DIA methods

[0236] 27 is a schematic diagram 1500 illustrating a system for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, according to various embodiments. The system of FIG. 27 includes an ion source device 1510, a tandem mass analyzer 1520, and a processor 1550.

[0237] The ion source device 1510 ionizes one or more compounds of a sample and produces an ion beam. The ion source device 1510 is shown as a separate device from the tandem mass spectrometer 1520. In various alternative embodiments, the ion source device 1510 is a component of the tandem mass spectrometer 1520. The ion source device 1510 can be any ion source known in the art, including, but not limited to, a chemical ionization (CI) source device, such as an electrospray ion source (ESI) device or an atmospheric pressure chemical ionization (APCI) device or an atmospheric pressure photoionization (APPI) source device.

[0238] The tandem mass spectrometer 1520 includes an ion guide chamber 1530 and a multipole ion guide 1531 disposed within the ion guide chamber 1530. The ion guide chamber 1530 includes an entrance orifice 1532 for receiving ions generated by the ion source device 1510 and at least one exit aperture 1533 for transmitting ions from the ion guide chamber 1530 into a vacuum chamber 1540 that houses at least one fragmentation device 1541.

[0239] 27, the tandem mass analyzer 1520 also includes a time-of-flight (TOF) mass analyzer 1542 positioned within the vacuum chamber 1540. Those skilled in the art will appreciate that any component of the tandem mass analyzer 1520 may include other types of mass analysis devices, including, but not limited to, an ion trap, an orbitrap, a quadrupole device, an ion mobility device, or a Fourier transform ion cyclotron resonance (FT-ICR) device, which may also include additional pumping stages and ion guides.

[0240] The processor 1550 receives a plurality of different precursor ion mass selection windows spanning the precursor ion mass range selected for the DIA method, and from the plurality of different precursor ion mass selection windows, the processor 1550 calculates two or more different multipole ion guide precursor ion mass selection windows for transmission during the same time cycle of the tandem mass analyzer 1520.

[0241] During each cycle time of the plurality of time cycles of the tandem mass spectrometer 1520, for each selection window of the plurality of different precursor ion mass selection windows, the processor 1550 instructs the multipole ion guide 1531 to transmit precursor ions from the ion beam within the multipole ion guide precursor ion mass selection window of two or more different multipole ion guide precursor ion mass selection windows, the multipole ion guide precursor ion mass selection window having a width greater than or equal to the width of the selection window and including the mass range of the selection window.

[0242] In various embodiments, the multipole ion guide 1531 is the only mass filter of the tandem mass analyzer 1520. The two or more different multipole ion guide precursor ion mass selection windows calculated for transmission during each cycle time are a plurality of different precursor ion mass selection windows. The multipole ion guide 1531 transmits precursor ions from the ion beam directly to at least one fragmentation device 1541 of the tandem mass analyzer 1520. As shown in FIG. 15 , during each cycle time of a plurality of time cycles of the tandem mass analyzer, for each selection window of the plurality of different precursor ion mass selection windows, the processor 1550 further instructs the multipole ion guide 1531 to transmit precursor ions from the ion beam within the multipole ion guide precursor ion mass selection window of two or more different multipole ion guide precursor ion mass selection windows having widths equal to the width of the selection window.

[0243] In various embodiments, the processor 1550 instructs the multipole ion guide 1531 to transmit precursor ions by applying an RF voltage to define a low m / z cutoff of the multipole ion guide precursor ion mass selection window and applying a DC voltage to define a high m / z cutoff of the multipole ion guide precursor ion mass selection window.

[0244] In various embodiments, the multipole ion guide 1531 includes a rod set and a plurality of auxiliary electrodes, such as the multipole ion guide of FIG. 19. The rod set includes a first group of rods and a second group of rods. Each rod is spaced apart from and extends alongside the central longitudinal axis. A plurality of auxiliary electrodes are also spaced apart from and extend alongside the central longitudinal axis along at least a portion of the rods of the rod set. At least one auxiliary electrode of the plurality of auxiliary electrodes is interposed between each of the rods of the rod set such that an auxiliary electrode is adjacent to each of a single rod of the first group of rods and a single rod of the second group of rods.

[0245] The processor 1550 also applies voltages of the RF electrical signal to the rod set to define a low m / z cutoff of the multipole ion guide precursor ion mass selection window, and applies DC voltages to the plurality of auxiliary electrodes to define a high m / z cutoff of the multipole ion guide precursor ion mass selection window.

[0246] In various embodiments, the multipole ion guide 1531 includes a segmented rod set, such as the multipole ion guide of Figure 18. Each rod of the segmented rod set is spaced apart from and extends alongside a central longitudinal axis. Each rod of the segmented rod set is also segmented into three or more identical, distinct longitudinal sections. These distinct longitudinal sections include at least a first section for receiving ions entering the multipole ion guide, a final section for transmitting ions from the multipole ion guide, and an intermediate section located between the first and final sections.

[0247] The processor 1550 further applies voltages of the RF electrical signal to the rod sections of the bandpass section to define a low m / z cutoff of the multipole ion guide precursor ion mass selection window, and the processor 1550 applies RF voltages to the rod sections of the intermediate section to define a high m / z cutoff of the multipole ion guide precursor ion mass selection window.

[0248] In various embodiments, the multipole ion guide 1531 is a non-segmented rod set and does not include auxiliary electrodes. However, non-segmented ion guides with only RF / DC are generally not effective in bandpass at currently used pressures. Ions can have a wide range of radial amplitudes at the entrance to the ion guide. Therefore, a single RF / DC combination filters ions based on their radial position value. As a result, there is likely to be a dramatic loss of ion intensity with increasing resolving DC values. This is different for collisionally cooled ions such as those produced in segmented ion guides.

[0249] In various embodiments, the multipole ion guide 1531 can be configured as a pre-filter for a mass filter device (not shown) of the tandem mass spectrometer 1520. For example, the tandem mass spectrometer 1520 can further include a mass filter device positioned between the multipole ion guide 1531 and the fragmentation device 1541. The mass filter can be located, for example, within the vacuum chamber 1540. The multipole ion guide 1531 also transmits precursor ions from the ion beam directly to the mass filter device.

[0250] During each cycle time of the plurality of time cycles of the tandem mass spectrometer, for each selection window of the plurality of different precursor ion mass selection windows, the processor 1550 further instructs the multipole ion guide 1531 to transmit precursor ions from the ion beam within multipole ion guide precursor ion mass selection windows of two or more different multipole ion guide precursor ion mass selection windows having widths greater than the width of each selection window. The processor 1550 instructs the mass filter device to transmit precursor ions received from the multipole ion guide 1531 within each selection window.

[0251] In various embodiments, the RF electrical signal received by the multipole ion guide 1531 is capacitively coupled to the RF electrical signal received by the mass filter device. Specifically, the processor 1550 can apply an RF voltage to the multipole ion guide that is capacitively coupled to the RF signal received by the mass filter device for each selection window. This is done so that the voltage of the RF electrical signal received by the multipole ion guide 1531 defines a low m / z cutoff for each selection window that is the same as, or a fraction of, the voltage of the RF signal received by the mass filter device for each selection window.

[0252] In various embodiments, the RF voltage received by the multipole ion guide 1531 is a fraction of the RF voltage received by the mass filter device. Specifically, the RF voltage applied to the multipole ion guide 1531 for each selection window is capacitively coupled to the RF signal received by the mass filter device for each selection window. This is done so that the RF voltage received by the multipole ion guide defines a low m / z cutoff for each selection window that is a fraction of the voltage of the RF signal received by the mass filter device for each selection window. Additionally, the low m / z cutoff for each selection window in the multipole ion guide 1531 has a lower m / z value than the low m / z cutoff for each selection window in the mass filter device.

[0253] In various embodiments, the multipole ion guide 1531 and the mass filter device have different RF signal sources. Specifically, the processor 1550 energizes the multipole ion guide 1531 with an RF electrical signal that is from a different signal source than the RF signal received by the mass filter device for each selection window.

[0254] In various embodiments, one multipole ion guide precursor ion mass selection window can be used for two or more different precursor ion mass selection windows as shown in Figure 17. Specifically, processor 1550 instructs multipole ion guide 1531 to transmit precursor ions using the same multipole ion guide precursor ion mass selection window of the two or more different multipole ion guide precursor ion mass selection windows for at least two different selection windows of the plurality of different precursor ion mass selection windows.

[0255] In various embodiments, the processor 1550 calculates two or more different multipole ion guide precursor ion mass selection windows using a lookup table derived from experimental data, such as the data shown in Figures 22 and 23.

[0256] 29, or any device capable of sending and receiving control signals and data to and from a tandem mass spectrometer and processing data. The processor 1550 communicates with the ion source device 1510 and the tandem mass spectrometer 1520. Although shown as a separate device, the processor 1550 may be a processor or controller for the tandem mass spectrometer 1520 or another device. The processor 1550 controls or commands the tandem mass spectrometer 1520 or its components, for example, by controlling one or more voltage sources, one or more valves, or one or more pumps (not shown) of the tandem mass spectrometer 1520. Method for mass filtering precursor ions in DIA methods - Patent Application 20070122997

[0257] 28 is a flowchart showing a method 1600 for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, according to various embodiments. In step 1610 of method 1600, a plurality of different precursor ion mass selection windows spanning a precursor ion mass range selected for the DIA method are received using a processor. In step 1620, two or more different multipole ion guide precursor ion mass selection windows are calculated for transmission during the same time cycle of a tandem mass analyzer from the plurality of different precursor ion mass selection windows using a processor. The tandem mass analyzer includes an ion guide chamber and a multipole ion guide disposed within the ion guide chamber. The ion guide chamber includes an entrance orifice for receiving ions generated by an ion source device and at least one exit aperture for transmitting ions from the ion guide chamber into a vacuum chamber housing at least one fragmentation device. In step 1630, during each of a plurality of time cycles of the tandem mass analyzer, for each selection window of a plurality of different precursor ion mass selection windows, the multipole ion guide of the tandem mass analyzer is instructed using the processor to transmit precursor ions from the ion beam within the multipole ion guide precursor ion mass selection window of two or more different multipole ion guide precursor ion mass selection windows, the multipole ion guide precursor ion mass selection windows having widths greater than or equal to the widths of each selection window and including the mass range of each selection window. Computer Implementation System

[0258] 29 is a block diagram illustrating a computer system 1800 in which embodiments of the present teachings may be implemented. The computer system 1800 includes a bus 1802 or other communication mechanism for communicating information and a processor 1804 coupled with the bus 1802 for processing information. The computer system 1800 also includes memory 1806, which may be a random access memory (RAM) or other dynamic storage device, coupled to the bus 1802 for storing instructions to be executed by the processor 1804. The memory 1806 may also be used for storing temporary variables or other intermediate information during execution of instructions to be executed by the processor 1804. The computer system 1800 further includes a read-only memory (ROM) 1808 or other static storage device coupled to the bus 1802 for storing static information and instructions for the processor 1804. A storage device 1810, such as a magnetic disk or optical disk, is provided and coupled to the bus 1802 for storing information and instructions.

[0259] Computer system 1800 may be coupled via bus 1802 to a display 1812, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 1814, including alphanumeric and other keys, is coupled to bus 1802 for communicating information and command selections to processor 1804. Another type of user input device is a cursor control 1816, such as a mouse, trackball, or cursor direction keys, for communicating directional information and command selections to processor 1804 and for controlling cursor movement on display 1812. The input device typically has two degrees of freedom in two axes, a first axis (i.e., x) and a second axis (i.e., y), that allow the device to define a position in a plane.

[0260] In some embodiments, computer system 1800 can be employed to implement the present teachings. Consistent with an implementation of the present teachings, results are provided by computer system 1800 in response to processor 1804 executing one or more sequences of one or more instructions contained in memory 1806. Such instructions may be read into memory 1806 from another computer-readable medium, such as storage device 1810. Execution of the sequences of instructions contained in memory 1806 causes processor 1804 to perform the processes described herein. Alternatively, hardwired circuitry may be used in place of or in combination with software instructions to implement the present teachings. Thus, implementation of the present teachings is not limited to any specific combination of hardware circuitry and software.

[0261] In various embodiments, computer system 1800 can be connected to one or more other computer systems, such as computer system 1800, across a network to form a networked system. The network can include a private network or a public network such as the Internet. In a networked system, one or more computer systems can store data and provide services to other computer systems. The one or more computer systems that store and provide services may be referred to as servers or clouds in a cloud computing scenario. The one or more computer systems may include, for example, one or more web servers. Other computer systems that send and receive data to and from the servers or clouds may be referred to as, for example, clients or cloud devices.

[0262] The term "computer-readable medium" as used herein refers to any medium that participates in providing instructions to processor 1804 for execution. Such media may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media include, for example, optical or magnetic disks, such as storage device(s) 1810. Volatile media include dynamic memory, such as memory 1806. Transmission media include coaxial cables, copper wire and fiber optics, including the wires that comprise bus 1802.

[0263] Common forms of computer-readable media or computer program products include, for example, a floppy disk, flexible disk, hard disk, magnetic tape or any other magnetic medium, CD-ROM, digital video disk (DVD), Blu-ray® disc, any other optical medium, thumb drive, memory card, RAM, PROM, and EPROM, FLASH-EPROM, any other memory chip or cartridge, or any other tangible medium from which a computer can read.

[0264] Various forms of computer-readable media may be involved in carrying one or more sequences of one or more instructions to processor 1804 for execution. For example, the instructions may initially be carried on a magnetic disk of a remote computer. The remote computer can load the instructions into its dynamic memory and send the instructions over a telephone line using a modem. A modem local to computer system 1800 can receive the data on the telephone line and use an infrared transmitter to convert the data to an infrared signal. An infrared detector coupled to bus 1802 can receive the data carried in the infrared signal and place the data on bus 1802. Bus 1802 carries the data to memory 1806, from which processor 1804 retrieves and executes the instructions. The instructions received by memory 1806 may optionally be stored on storage device 1810 either before or after execution by processor 1804.

[0265] According to various embodiments, instructions configured to be executed by a processor to implement the method are stored on a computer-readable medium. The computer-readable medium may be a device that stores digital information. For example, the computer-readable medium may include a compact disc read-only memory (CD-ROM), as known in the art, for storing software. The computer-readable medium is accessible by a suitable processor to execute the instructions that the computer-readable medium is configured to execute.

[0266] The description of various implementations of the present teachings has been presented for purposes of illustration and description. It is not exhaustive and does not limit the present teachings to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practice of the present teachings. In addition, while the described implementations include software, the present teachings can be implemented as a combination of hardware and software, or in hardware alone. The present teachings can be implemented using both object-oriented and non-object-oriented programming systems. Computer program product for filtering precursor ions in DIA methods - Patent Application 20070122997

[0267] In various embodiments, a computer program product includes a tangible computer-readable storage medium, the contents of which include a program with instructions for execution on a processor to perform a method for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, the method being performed by a system including one or more distinct software modules.

[0268] 30 is a schematic diagram of a system 1700 including one or more distinct software modules that implement a method for mass filtering precursor ions in a DIA method using a multipole ion guide mass filter, according to various embodiments. The system 1700 includes an input module 1710, an analysis module 1720, and a control module 1730.

[0269] The input module 1710 receives a plurality of different precursor ion mass selection windows spanning a precursor ion mass range selected for the DIA method. The analysis module 1720 calculates two or more different multipole ion guide precursor ion mass selection windows from the plurality of different precursor ion mass selection windows for transmission during the same time cycle of the tandem mass analyzer. The tandem mass analyzer includes an ion guide chamber and a multipole ion guide disposed within the ion guide chamber. The ion guide chamber includes an entrance orifice for receiving ions generated by the ion source device and at least one exit opening for transmitting ions from the ion guide chamber into a vacuum chamber housing at least one fragmentation device.

[0270] The control module 1730 instructs the multipole ion guide of the tandem mass analyzer to transmit precursor ions from the ion beam within the multipole ion guide precursor ion mass selection windows of two or more different multipole ion guide precursor ion mass selection windows, each having a width greater than or equal to the width of each selection window and including the mass range of each selection window, for each selection window of a plurality of different precursor ion mass selection windows, during each of a plurality of time cycles of the tandem mass analyzer.

[0271] While the present teachings will be described in conjunction with various embodiments, it is not intended that the present teachings be limited to such embodiments. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents, as will be appreciated by those skilled in the art.

[0272] Furthermore, in describing various embodiments, the specification may present the method and / or process as a particular sequence of steps. However, to the extent the method or process does not rely on the particular order of steps described herein, the method or process should not be limited to the particular sequence of steps described. As one of ordinary skill in the art would understand, other sequences of steps are possible. Thus, the particular order of steps described herein should not be construed as a limitation on the claims. In addition, claims directed to the method and / or process should not be limited to performing those steps in the order described; one of ordinary skill in the art can readily understand that the sequence can be varied and still remain within the spirit and scope of various embodiments.

[0273] Those skilled in the art will appreciate that various modifications can be made to the above-described embodiments without departing from the scope of the present invention.

Claims

1. 1. A mass spectrometer comprising: a first mass filter for receiving a plurality of precursor ions and having a transmission bandwidth configured to allow transmission of ions having m / z ratios within a desired range; a second mass filter positioned downstream of the first mass filter to select ions having a target m / z ratio within its transmission window for mass analysis; a controller coupled to the first mass filter for setting a transmission bandwidth of the first mass filter to encompass at least two m / z ratios, at least one of which is within a transmission window of the second mass filter; Equipped with wherein the controller is configured to vary the transmission bandwidth of the first mass filter over time such that any two consecutive transmission bandwidths of the first mass filter have at least one m / z ratio in common.

2. 10. The mass spectrometer of claim 1, wherein the controller is coupled to the second mass filter for moving the transmission window of the second mass filter to select different target m / z ratios.

3. 3. A mass spectrometer as claimed in claim 2, wherein the controller is configured to correlate the variation in transmission bandwidth of the first mass filter with the variation in transmission window of the second mass filter over time, so as to enable mass analysis by the second mass filter of ions having different m / z ratios transmitted through the first mass filter as the transmission bandwidth of the first mass filter is shifted over time.

4. 4. The mass spectrometer of claim 3, wherein the controller is configured to set the ion transmission bandwidth of the first mass filter to an initial ion transmission bandwidth, and to set the ion transmission window of the second mass filter to allow passage of ions having an m / z ratio encompassed by the initial bandwidth of the first mass filter.

5. 10. A mass spectrometer as claimed in any preceding claim, wherein the controller is configured to adjust a transmission window of the second mass filter to capture a next m / z ratio of interest and to shift the ion transmission bandwidth of the first mass filter to cover the next m / z ratio of interest and another m / z ratio of interest.

6. A mass spectrometer according to any one of claims 2 to 5, wherein the controller is further configured to adjust the transmission window of the second mass filter to shift the transmission bandwidth of the first mass filter substantially in parallel.

7. 6. A mass spectrometer according to any one of claims 2 to 5, wherein the controller is configured to shift the ion transmission window of the second mass filter prior to adjusting the ion transmission bandwidth of the first mass filter.

8. 6. A mass spectrometer according to any one of claims 2 to 5, wherein the controller is configured to shift the ion transmission bandwidth of the first mass filter whilst the second mass filter monitors ions having an m / z ratio that was covered by the transmission bandwidth of the first mass filter prior to the shift.

9. 10. A mass spectrometer according to any one of the preceding claims, wherein the controller is configured to set the transmission bandwidth of the first mass filter to allow transmission of ions having an m / z ratio of three or more.

10. 10. A mass spectrometer according to any one of the preceding claims, wherein the transmission bandwidth of either the first mass filter or the second mass filter is less than about 2,000 Da.

11. 10. A mass spectrometer according to any one of the preceding claims, further comprising an ion source positioned upstream of said first mass filter for generating said plurality of precursor ions.

12. 10. A mass spectrometer as claimed in any preceding claim, wherein either the first mass filter or the second mass filter comprises at least one set of rods arranged in a multipole configuration, at least one of which can have one or more RF voltages applied to provide radial confinement of the ions, and at least one of which can have a DC resolving voltage applied to generate the transmission bandwidth thereof, the multipole configuration optionally comprising a quadrupole configuration.

13. 13. The mass spectrometer of claim 12, wherein the at least one set of rods comprises multiple sets of rods positioned in series, each rod set comprising multiple rods arranged in a multipole configuration, and optionally a DC voltage offset is applied between at least two of the rod sets to generate an electric field for accelerating ions passing through the first mass filter, and optionally the DC voltage offset is in the range of about 0 volts to about 200 volts.

14. 10. A mass spectrometer according to any one of the preceding claims, wherein the transmission bandwidth of the first mass filter has an m / z width that exceeds the m / z width of the transmission bandwidth of the second mass filter.

15. 10. A mass spectrometer according to any one of the preceding claims, wherein the first mass filter and the second mass filter are located in separate differentially pumped vacuum chambers.

16. 16. The mass spectrometer of claim 15, wherein the pressure difference between the two separate differentially pumped vacuum chambers is in the range of about 10 to about 50 times.

17. 17. A mass spectrometer as claimed in claim 16, wherein the second mass filter is positioned downstream of the first mass filter and maintained in a chamber at a lower pressure.

18. 1. A system for implementing a data independent acquisition (DIA) method for mass spectrometry, comprising: a first mass filter for receiving a plurality of precursor ions; a second mass filter positioned downstream of said first mass filter to receive ions exiting said first mass filter; a controller operably coupled to the first mass filter and the second mass filter for configuring the second mass filter to provide a plurality of ion selection windows over a DIA mass analysis cycle such that the mass selection windows collectively span a precursor ion mass range associated with DIA analysis; Equipped with the controller further configures the first mass filter to provide a plurality of ion transmission bandwidths, each configured to pre-filter the precursor ions with respect to at least one respective one of the ion selection windows of the second mass filter, such that each ion transmission bandwidth of the first mass filter has an m / z width that exceeds the m / z width of the one respective ion selection window of the second mass filter.

19. 20. The system of claim 18, wherein at least one of the ion transmission bandwidths of the first mass filter has a lower low m / z cutoff and a higher high m / z cutoff than the respective low m / z cutoff and high m / z cutoff of the at least one respective ion selection window of the second mass filter.

20. 20. The system of claim 18, wherein the at least one individual ion selective window of the second mass filter comprises at least two consecutive ion selective windows.

21. A system according to any one of claims 18 to 20, wherein at least two of the transmission bandwidths of the first mass filter have at least one m / z ratio in common.

22. 22. The system of claim 21, wherein any two consecutive transmission windows of the first mass filter have at least one m / z ratio in common.

23. 23. A system according to any one of claims 18 to 22, wherein at least two of the plurality of ion transmission bandwidths of the first mass filter have different m / z widths.

24. 23. A system according to any one of claims 18 to 22, further comprising a fragmentation device positioned downstream of the second mass filter to receive the precursor ions exiting the second mass filter and cause fragmentation of at least some of the precursor ions to generate a plurality of product ions.

25. 25. The system of claim 24, further comprising a mass analyzer positioned downstream of the fragmentation device to receive the product ions and generate a mass spectrum of the product ions.

26. A system according to any one of claims 18 to 25, further comprising a first exhaust chamber and a second exhaust chamber in which the first mass filter and the second mass filter are disposed, respectively.

27. 27. The system of claim 26, wherein the second exhaust chamber is maintained at a pressure lower than the pressure at which the first exhaust chamber is maintained.

28. 28. The system of any one of claims 24-27, further comprising a first multipole rod set positioned within the first chamber and a second multipole rod set positioned within the second chamber, each of the plurality of rod sets configured for application of an RF voltage and / or a DC voltage thereto to generate any of the ion transmission bandwidth and the ion transmission window.

29. 30. The system of claim 28, comprising at least one RF voltage source and at least one DC voltage source, the at least one RF voltage source and the at least one DC voltage source for generating the RF voltage and the DC voltage, respectively.

30. 30. The system of claim 29, wherein the controller is operatively coupled to the RF voltage source and the DC voltage source to adjust the RF voltage and the DC voltage to generate the ion transmission bandwidth of the first mass filter and the ion transmission window of the second mass filter.

31. 31. The system of claim 30, wherein the first multipolar rod set comprises a plurality of rod segments, each rod segment spaced apart from an adjacent rod segment and extending along a central longitudinal axis of the multipolar rod set.

32. 32. The system of claim 31 , wherein the plurality of rod sections comprises a first rod section, a second rod section positioned downstream of the first section, and a third rod section positioned downstream of the second rod section.

33. 33. The system of claim 32, wherein the first rod section is configured to receive ions from an upstream ion source and cause cooling of the received ions.

34. 34. The system of claim 33, wherein the second rod section is configured to filter the cooled ions received from the first rod section, and the third rod section is configured to transmit ions received through the second rod section out of the mass filter.

35. 35. The system of any one of claims 28-34, wherein the mass filter further comprises a plurality of auxiliary electrodes disposed between rods of the plurality of rod sets, wherein an RF voltage applied to the rods of the multipole rod set provides a low m / z cutoff, and a DC voltage difference applied between the multipole rod set and the auxiliary electrodes provides a high m / z cutoff.

36. 1. A system for performing data-independent acquisition (DIA) mass analysis in a tandem mass spectrometer, comprising: a mass filter for receiving a plurality of precursor ions, said mass filter having a mass of about 5e －５ a mass filter positioned in a low pressure region of the mass spectrometer maintained at a pressure above Torr; a controller operably coupled to the mass filter and configured to control the mass filter such that the mass filter provides a plurality of ion selection windows over a DIA mass analysis cycle, the ion selection windows collectively spanning a precursor ion mass range associated with the DIA mass analysis; and an ion fragmentation device positioned downstream of the mass filter to receive precursor ions transmitted through the mass filter and cause fragmentation of at least some of the received precursor ions to generate a plurality of product ions; Equipped with A system wherein no other mass filter functionality is located between said mass filter and said ion fragmentation device.

37. 37. The system of claim 36, wherein at least two of the ion-selective windows overlap.

38. 38. The system of any one of claims 36 and 37, wherein at least two of the ion selection windows have different m / z widths.

39. 39. A system according to any one of claims 36 to 38, wherein the mass filter comprises a multipole rod set configured for application of RF and / or DC voltages thereto to generate the ion selection window, the multipole rod set optionally comprising a quadrupole rod set.

40. 40. The system of claim 39, further comprising at least one RF voltage source and at least one DC voltage source for generating the RF voltage and / or the DC voltage.

41. 41. The system of claim 40, wherein the controller is operably coupled to the RF voltage source and the DC voltage source to control the RF voltage source and the DC voltage source to adjust the RF voltage and / or the DC voltage to generate the ion selection window.

42. 42. The system of any one of claims 36-41, further comprising a first exhaust chamber in which the mass filter is positioned and a second exhaust chamber in which the fragmentation device is positioned, the second exhaust chamber being maintained at a pressure below that at which the first exhaust chamber is maintained.

Images