Method and system for performing data independent acquisition mass spectrometry

Abstract

In one aspect, a method of operating an analysis device for measuring at least one analyte within a sample is disclosed, the method comprising receiving, with a digital data processor, a sample collection rate for introducing the sample into the analysis device, and calculating one or more optimal operating parameters of the analysis device based on the sample collection rate by optimizing a figure of merit associated with the measurement of the analyte, where the operating parameters include a duration of the measurement period and / or a selection associated with the measurement. The analysis device may be operated at the optimal operating parameters while receiving the sample at the sample collection rate to generate sample measurement data corresponding to the analyte. The sample measurement data may be processed to obtain information about the analyte.

Description

[0001] Related applications

[0002] This application claims priority to U.S. Provisional Application No. 63 / 538,907, filed September 18, 2023, the contents of which are incorporated herein by reference in their entirety. Technical Field

[0003] This disclosure generally relates to systems and methods for performing mass spectrometry, and more specifically to systems and methods for performing data-independent acquisition (DIA) mass spectrometry. Background Technology

[0004] This disclosure generally provides systems and methods for operating a mass spectrometer in DIA operating mode.

[0005] Mass spectrometry (MS) is an analytical technique used to determine the structure of chemical substances being tested, with both qualitative and quantitative applications. MS can be used to identify unknown compounds, determine the elemental composition of molecules, determine the structure of compounds by observing fragments, and quantify the amount of a specific chemical compound in a mixed sample. Mass spectrometers detect chemical entities in ionic form, necessitating the conversion of the analyte into charged ions.

[0006] DIA (Distributed Interference Aspect) mass spectrometry is a technique in which the mass range of interest is divided into multiple mass windows, each characterized by an m / z range, and MS / MS analysis is performed on all compounds (typically peptides) within each window. Therefore, DIA enables the acquisition of mass data for all compounds (e.g., peptides) within a target mass range without prior knowledge of one or more specific target compounds for the desired mass analysis. For example, in some mass spectrometers, the m / z range of each window can be set using a bandpass window of a mass filter, and the bandpass window can be scanned to cover the entire m / z range of interest. The m / z width and m / z step size of the bandpass window determine the sensitivity and selectivity of the MS / MS analysis. Summary of the Invention

[0007] In one aspect, a method is disclosed for operating an analytical apparatus for measuring at least one analyte within a sample. The method includes receiving one or more input parameters using a digital data processor, and calculating one or more optimal operating parameters for one or more components of the analytical apparatus based on one or more input parameters (including a sample acquisition rate), by optimizing a quality factor (also referred to herein as an optimization criterion) associated with the measurement of the analyte. The one or more input parameters include a sampling period, for example, a sampling period associated with the sample acquisition rate used to introduce the sample into the analytical apparatus. By way of example, the operating parameters may include the duration of the measurement period and / or a selectivity associated with the measurement. The analytical apparatus can be operated with optimal operating parameters while receiving the sample at the sample acquisition rate to generate sample measurement data corresponding to the analyte. The sample measurement data can be processed to obtain information about the analyte.

[0008] By way of example rather than limitation, the information obtained can indicate the presence of an analyte in the sample, such as whether the sample contains an analyte at a concentration above the detection limit (LOD) of the analytical device. As another example, the information obtained can provide the concentration of the analyte in the sample. In some cases, this information can indicate whether two or more target analytes of interest are present in the sample simultaneously.

[0009] The quality factor can be defined in a variety of different ways, for example, based on the type of analytical apparatus, the target analyte of interest, and / or the specific application utilizing the analytical apparatus. By way of example, and not limitation, the quality factor can be based at least on the target resolution desired by the measurement data. In various implementations, the target resolution can be defined based on a specific measurement mode and the instrument used. By way of example, and not limitation, in some mass spectrometry applications, the target resolution can be defined as the minimum separation of ions along the m / z dimension that allows them to be distinguished for identification.

[0010] As another example, the quality factor (also referred to herein as an optimization criterion or performance metric) can be defined at least in part based on a target minimum signal-to-noise ratio for the measured data. In some cases, the quality factor can be defined at least in part based on target selectivity. In some implementations, the quality factor can be defined as a combination of two or more criteria discussed herein. For example, the quality factor can be defined based on a combination of target resolution and target sensitivity.

[0011] The methods described above can be applied to a variety of analytical devices. By way of example and not limitation, the analytical device can be a mass spectrometry system, such as a liquid chromatography-mass spectrometry (LC) system, or a mass spectrometry system employing any of the flow injection, acoustic energy, and laser radiation methods to introduce the sample into the ion source of the mass spectrometer. As another example, the mass spectrometry system can utilize ion mobility spectrometry, such as differential mobility mass spectrometry (DMS) or field asymmetric ion mobility spectrometry (FAIMS), to separate ions based on ion migration before introducing ions with target migrations into the downstream mass spectrometer.

[0012] In a related aspect, an analytical apparatus for measuring at least one analyte in a sample is disclosed. The apparatus includes: an analyte measurement module for receiving the sample and generating analyte measurement data; and a digital data processor configured to receive one or more input parameters and to calculate optimal values ​​for one or more operating parameters of one or more components of the analytical apparatus, at least in part based on the input parameters, by optimizing a quality factor associated with the measurement of the analyte. The one or more input parameters include a sampling period, for example, a sampling period associated with a sample acquisition rate for introducing the sample into the analytical apparatus. By way of example, the operating parameters may include the duration of the measurement period and the bandwidth of a filter and / or the rate at which the filter output can be changed. The analytical apparatus may also include a controller for receiving the optimal operating parameters and configuring an operating mode of one or more components of the analytical apparatus (e.g., the analyte measurement module) based on the optimal operating parameters. A data processing module may receive measurement data generated by one or more components operating in this operating mode and process the measurement data to generate information about at least one analyte.

[0013] In some embodiments of the analytical apparatus described above, the quality factor may be defined in a manner suitable for the analytical apparatus (including its intended use, such as those discussed above).

[0014] By way of example, in some implementations, the analytical apparatus may be a mass spectrometry system, such as an LC-MS system. In some such implementations, the mass spectrometry system may be configured to operate in DIA mode.

[0015] In some embodiments, a mass spectrometry system may include: an ion source for receiving a sample, such as eluent exiting an LC column, and ionizing one or more analytes in the sample, such as the eluent, to generate a plurality of precursor ions; and a mass filter, located downstream of the ion source, for receiving the plurality of precursor ions and allowing those precursor ions having m / z ratios within the bandpass window of the mass filter to pass through. The system may also include: an ion dissociation device for receiving ions passing through the mass filter and dissociating at least a portion of the ions to generate a plurality of product ions; and a mass analyzer, such as a time-of-flight (ToF) mass analyzer, located downstream of the ion dissociation device to receive the plurality of product ions and having an ion detector for detecting at least a portion of the received product ions to generate ion detection data associated with the product ions. By way of example, operating parameters may include the m / z width of the bandpass window of the mass filter and the rate at which the bandpass window of the mass filter is scanned during data acquisition (e.g., by moving the lower and upper m / z limits of the bandpass window). The digital data processor is configured to calculate optimal values ​​for operating parameters based on the sampling period, the m / z range associated with the precursor ion of interest, and the data acquisition rate of the mass analyzer. The sampling period refers to the time during which the sample is available for mass analysis. The data acquisition rate refers to the rate at which the mass spectrometer collects data points during a measurement period. It is typically measured as the number of mass spectra acquired per second. In embodiments where the mass analyzer is a time-of-flight (TOF) mass analyzer, the data acquisition rate is related to a pulse frequency associated with a voltage pulse applied to the deflection electrodes of the TOF mass analyzer. By way of example, in various embodiments, the mass analyzer can have a data acquisition rate ranging from approximately 1000 spectra per second to approximately 10000 spectra per second.

[0016] In a related aspect, a mass spectrometry system is disclosed, comprising: a separation device, such as an LC column, for receiving a sample and separating various components of the sample to generate at least one eluent, for example, exiting the LC column during at least one elution period; and an ion source for receiving the sample, such as at least one eluent, and ionizing one or more analytes therein to generate a plurality of precursor ions. A mass filter, located downstream of the ion source, is used to receive the plurality of precursor ions and allow those precursor ions having an m / z ratio within the bandpass window of the mass filter to pass through. The mass spectrometry system may further include an ion dissociation device for receiving the precursor ions passing through the mass filter and dissociating at least a portion of them to generate a plurality of product ions. A mass analyzer, such as a time-of-flight (ToF) mass analyzer, located downstream of the ion dissociation device, can receive the plurality of product ions and provide mass detection data associated with the product ions. The mass spectrometry system also includes a digital data processor configured to receive multiple input parameters and calculate the m / z width of the bandpass window of the mass filter and the scan rate of the bandpass window in the m / z dimension. These input parameters include the sampling period, the m / z range associated with the precursor ion of interest, and the data acquisition rate associated with the mass analyzer. As noted above, the sampling period refers to the time period during which the sample is available for analysis (also referred to herein as a time interval). By way of example and not limitation, the sampling period may coincide with: i) LC peaks, ii) sample injection from a reservoir or matrix (e.g., via acoustic or laser energy), and iii) the time period corresponding to the analysis of the sample introduced into the mass spectrometer via sample infusion. For example, the delivery of eluent leaving the LC column can be predicted based on the operating settings of the LC column. In other sample delivery systems such as acoustic jetting or infusion, the sample delivery device can provide timing information about the delivery time of the sample of interest to the mass spectrometer.

[0017] The controller, communicating with the digital data processor and the quality filter, can receive calculated operating parameters, namely, the m / z width of the bandpass window of the quality filter and the scan rate of the bandpass window in the m / z dimension. The controller can then configure the quality filter to operate according to the calculated operating parameters. For example, the controller can send a control signal to the power supply to adjust the voltage applied to the quality filter, thereby configuring the quality filter to operate according to the calculated operating parameters.

[0018] In some implementations, the digital data processor can be configured to calculate the scan rate of the bandpass window of the quality filter in the m / z dimension according to the following relationship:

[0019] Equation (1)

[0020] in,

[0021] This indicates the scan rate of the bandpass window, expressed in Daltons per second.

[0022] This represents the maximum m / z ratio within the m / z range associated with the precursor ion.

[0023] The minimum m / z ratio representing the m / z range associated with the precursor ion, and

[0024] Indicates the LC sampling time.

[0025] Furthermore, the digital data processor can be configured to calculate based on the following relationship :

[0026] Equation (2)

[0027] in,

[0028] This represents the time width corresponding to half the maximum value of the LC peak, and

[0029] N is an integer, for example, an integer equal to or greater than 2, such as an integer in the range of 2 to 20.

[0030] The digital data processor can also be configured to calculate the m / z width of the bandpass window of the quality filter according to the following relationship:

[0031] Equation (3)

[0032] Equation (4)

[0033] in,

[0034] This represents the m / z width of the bandpass window, expressed in Daltons.

[0035] This indicates the rate of the scan bandpass window, expressed in Daltons per TOF pulse.

[0036] This indicates the rate of the scan bandpass window, measured in Daltons per second.

[0037] This indicates the number of TOF pulses per measurement cycle for the minimum ion rate per cycle.

[0038] The digital data processor can also be configured to calculate based on the following relationship :

[0039] Equation (5)

[0040] in,

[0041] This represents the minimum rate at which ions are incident on the TOF detector.

[0042] The digital data processor can also be configured to calculate based on the following relationship :

[0043] Equation (6).

[0044] In a related aspect, a method is disclosed for operating an MS system having a mass filter and a mass analyzer such as a time-of-flight (TOF) mass analyzer to perform mass spectrometry. This method includes processing multiple input parameters using a digital data processor to calculate multiple operating parameters of the mass filter. By way of example, the input parameters may include a sampling period, such as the time width associated with an LC peak of the eluent leaving the LC column of the LC-MS system (e.g., characterized by the full width at half maximum (FWHM) of the LC peak), and a data acquisition rate, such as the pulse frequency associated with the operation of the TOF mass analyzer, i.e., the frequency at which a voltage pulse is applied to the deflection electrode of the TOF mass analyzer. In various embodiments, the operating parameters may include the m / z width of the bandpass window of the mass filter (ion having an m / z ratio within the m / z width can pass through the mass filter) and the scan rate of the bandpass window of the mass filter during data acquisition. A controller is employed to control the operation of the mass filter according to the calculated operating parameters during data acquisition.

[0045] The above method may further include introducing a sample into an analyte separation device, such as an LC column, and guiding the sample exiting the analyte separation device, such as the eluent exiting the LC column, to an ion source in an MS system to ionize one or more analytes in the sample to generate multiple precursor ions. The precursor ions may be introduced into a mass filter of the MS system. Precursor ions having an m / z ratio within the bandpass window of the mass filter pass through the mass filter and are introduced into a downstream ion dissociation device, such as a collision chamber, wherein at least a portion of the precursor ions undergoes dissociation to generate multiple product ions. The multiple product ions are received by a mass analyzer, such as a TOF mass analyzer, which generates ion detection data associated with the product ions. A data processing unit may receive and process the ion detection data to generate a mass spectrum of the product ions.

[0046] A further understanding of the various aspects of this teaching can be obtained by referring to the following detailed description in conjunction with the associated accompanying drawings, which are briefly described below. Attached Figure Description

[0047] Figure 1 It is a flowchart depicting the various steps of implementing the method according to this teaching.

[0048] Figure 2 This is a schematic diagram of an analysis apparatus according to an embodiment of this teaching.

[0049] Figure 3 This is a flowchart depicting the various steps of an implementation of the method for performing LC-MS mass spectrometry according to this teaching.

[0050] Figure 4 This is an example of an implementation of an LC-MS system based on the embodiments of this teaching.

[0051] Figure 5 This is a schematic representation of DIA data acquisition by scanning the bandpass window of a quadrupole quality filter.

[0052] Figure 6 Examples of implementations of digital data processors and / or controllers utilized in various embodiments of this teaching are illustrated schematically, and

[0053] Figure 7 A graph showing the number of ToF pulses corresponding to the 95% confidence interval, which is a function of the numerical value of the ion rate per cycle. Detailed Implementation

[0054] It will be understood that, for clarity, the following discussion will set forth various aspects of the implementation of the applicant's teachings, while omitting certain specific details where convenient or appropriate. For example, the discussion of similar or analogous features in alternative implementations will be slightly shortened. For brevity, well-known ideas or concepts will also not be discussed in detail. Those skilled in the art will recognize that some implementations of the applicant's teachings may not require certain details specifically described in each implementation, which are set forth herein only to provide a thorough understanding of the implementations. Similarly, it will be apparent that the described implementations can be readily modified or varied based on common general knowledge without departing from the scope of this disclosure. The following detailed description of the implementations should not in any way be considered as limiting the scope of the applicant's teachings.

[0055] As used herein, the terms “about” and “substantially equal to” refer to variations in numerical quantities that may occur, for example, through real-world measurement or processing procedures, through unintentional errors in such procedures, or through differences in the manufacture, origin, or purity of the composition or reagent. Generally, as used herein, the terms “about” and “substantially” mean 10% greater or less than the stated value or range of values, or the complete conditions or states. For example, a concentration value of about 30% or substantially equal to 30% may mean a concentration between 27% and 33%. These terms also refer to variations that would be considered equivalent by those skilled in the art, provided that such variations do not cover values ​​known from prior art practice.

[0056] 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 “ / ”.

[0057] As used herein in the context of analytical apparatus, the term "resolution" refers to the apparatus's ability to distinguish individual components within a sample that provide closely spaced analytical signals. Resolution can be defined in several ways depending on the specific analytical apparatus and the type of measurement performed. For example, for an analytical apparatus employing spectroscopic methods for the analytical analysis of a sample, resolution can refer to the apparatus's ability to distinguish two closely spaced spectral features (e.g., peaks) in a chromatogram. Chromatographic resolution can refer to the degree of separation between two adjacent peaks in a chromatogram. In mass spectrometry systems such as LC-MS, the term resolution can refer to the system's ability to distinguish (identify) ions with very close m / z ratios. For example, resolution can refer to the system's ability to identify precursor ions with very close m / z ratios. By way of example, in some cases where two or more analytes cannot be adequately separated by a separation device located upstream of the mass spectrometer, resolution can refer to the mass spectrometer's ability to distinguish ions associated with such analytes. For example, when two or more analytes are co-eluted from an LC column, resolution can refer to the ability to identify precursor ions associated with the co-eluted analytes.

[0058] As used in the context of analytical apparatus in this paper, the term “selectivity” refers to the ability of an apparatus to accurately and selectively identify (and optionally quantify) a specific analyte in a sample in the presence of other substances and / or potential interfering factors.

[0059] In the context of analytical devices, including mass spectrometers, the term "sensitivity" refers to the ability of a device to detect minute changes or variations in the amount or concentration of an analyte in the sample being analyzed. For example, sensitivity can be defined as the ratio of a change in the device's response (e.g., the detection signal generated by the device) to a corresponding change in the amount or concentration of the analyte being measured. In other words, sensitivity can be determined by the detection limit (LoD) of the analytical device, which is based on the minimum amount of analyte that the device can detect (identify).

[0060] In the context of analytical apparatus, the term "measurement cycle" refers to a series of steps or processes that the apparatus follows to generate analytical data for a sample (or sample portion) introduced into the apparatus. In the context of an LC-MS system, a measurement cycle may include introducing eluent leaving an LC column into an ion source to generate precursor ions, passing the precursor ions through a mass filter to select the precursor ion of interest, dissociating the selected precursor ions to generate product ions, and using a mass analyzer (e.g., a TOF mass analyzer) to generate an ion detection signal corresponding to the product ions. "Measurement cycle time" refers to the time required for the apparatus to perform a measurement cycle.

[0061] The "bandpass window scan rate" in the terminology of a quality filter refers to the rate at which the range of m / z values ​​covered by the bandpass window changes. Such changes can be achieved incrementally, for example, by shifting the lower and upper limits of the bandpass window by a certain step size (i.e., shifting by a certain m / z value). For instance, scanning the bandpass window can be achieved by selecting an m / z step size smaller than the m / z bandwidth of the bandpass window.

[0062] Mass spectrometers operating in DIA mode typically include a mass filter, such as a quadrupole mass filter, which can be configured to allow ions with m / z ratios within the target range to pass through. Ions passing through the mass filter can be dissociated (e.g., fragmented) via a downstream ion dissociation device, such as a collision chamber, to generate product ions. The product ions can be received by a time-of-flight (TOF) mass analyzer that generates an ion detection signal, which is processed to generate a mass spectrum of the product ions. In such a system, the measurement dynamic range can be controlled by the data accumulation time, such as the time corresponding to the number of ToF pulses used when the precursor ions pass through the mass filter, and the ability to measure multiple simultaneous ion collisions on the ion detector of the ToF mass analyzer. Compared to binary ion detection systems, ion detection systems capable of measuring multiple simultaneous ion arrivals can have an extended detection upper limit. However, the lower limit for ion detection and the associated uncertainty range are defined by the number of available opportunities to measure ions in both multi-component and binary ion detection systems.

[0063] A wider passband window for the quality filter enables precursor filtering of a larger number of TOF pulses, resulting in a longer data accumulation time (measurement time). However, measurement selectivity can be increased by narrowing the passband window of the quality filter. In some cases, the measurement selectivity is proportional to the m / z range of the passband window in some scans of the quality filter. When scanning the DIA, the m / z step size used to scan the quality filter is much smaller than the m / z width of the passband window. In such cases, the step size determines the upper limit of selectivity, where the passband window size (the width of the passband window in m / z) is the convolution kernel.

[0064] In various embodiments of this teaching, the operating parameters of an analytical apparatus, such as a mass spectrometer, can be optimized to provide a balance between sensitivity (which may be related to data acquisition time) and selectivity (which may be related to, for example, the m / z width of the mass filter and the precursor sampling step size in an MS / MS instrument). More generally, the operating parameters can be adjusted to optimize the quality factor associated with the measurement (e.g., involving the detection and, optionally, quantification of the analyte in the sample under study).

[0065] As discussed in more detail below, in various embodiments, by way of example, a digital data processor is employed to calculate multiple operating parameters for operating the analytical apparatus, such as a mass spectrometer, based on multiple input parameters that can be input by the user. The determination of output parameters can be performed before sample analysis is initiated or after sample analysis has been initiated. By way of example, this teaching can be applied to any mass spectrometer having a mass filter located upstream of the mass analyzer, wherein the mass filter can be scanned at a rate slower than the rate at which the mass analyzer can collect data. In various embodiments, this teaching allows for rapid data acquisition while ensuring data resolution is within acceptable limits, as discussed in more detail below. In some embodiments, the mass analyzer can generate spectral data at a rate of approximately 1000 to approximately 10000 spectra per second.

[0066] about Figure 1The flowchart illustrates a method for operating an analytical device for measuring at least one analyte in a sample, comprising using a digital data processor to receive one or more input parameters (including a sampling period, e.g., a sampling period associated with a sample acquisition rate) for introducing a sample into the analytical device, and calculating multiple optimal operating parameters for operating the analytical device based on the sample acquisition rate by optimizing a quality factor associated with the measurement of the analyte. The analytical device can then be operated with the optimal operating parameters while receiving the sample during the sampling period to generate sample measurement data corresponding to the analyte. This measurement data can be processed to obtain information about the analyte. By way of example, the obtained information may indicate the presence of an analyte in the sample, e.g., the presence of an analyte above a detection limit associated with the analytical device. In some embodiments, the obtained information may provide information about the presence of one or more analytes in the sample and the quantification of those analytes.

[0067] The quality factor can be defined in a variety of different ways, such as based on the specific application of the analytical apparatus. By way of example, and not limitation, the quality factor can be defined as the expected minimum signal-to-noise ratio associated with the measurement data. Furthermore, instead of the above, or in addition to the above, the quality factor can be based on the selectivity and / or resolution and / or sensitivity associated with the measurement data.

[0068] Figure 2 An analytical apparatus 200 according to an embodiment is schematically depicted. The analytical apparatus 200 includes an analyte measurement module 202, which can receive a sample and generate analyte measurement data corresponding to one or more analytes in the sample. In this embodiment, the analytical apparatus 200 receives a sample from a sample delivery component 204, which may be, for example, a storage container in which the sample is stored. In some embodiments, the analytical apparatus may include one or more components located upstream of the analyte measurement module 202 to provide sample processing. By way of example and not limitation, such components may include a sample processing module 203, for example, a filtration device, an ion source, etc.

[0069] The analytical apparatus 200 may also include a digital data processor 206, which may receive one or more input parameters and be configured to calculate one or more operating parameters for operating the analytical apparatus. By way of example, and not limitation, the input parameters may include sampling period (the period during which the sample is available for analysis), target selectivity, target sensitivity, all of which are by way of example. The digital data processor may calculate one or more operating parameters for the operation of one or more components of the analytical apparatus, for example, operating parameters for the operation of the analyte measurement module, based at least in part on the input parameters. In various embodiments, the digital data processor calculates the operating parameters by optimizing a quality factor associated with the measurement of one or more target analytes of interest. By way of example, the operating parameters may include, for example, the rate at which the filters associated with the analytical apparatus are scanned.

[0070] Continue to refer to Figure 2 The analytical apparatus may also include a controller 208 that can receive operating parameters and control the operation of the analyte measurement module with respect to the calculated operating parameters. In some embodiments, the analyte measurement module 202 may include multiple components, each of which can provide a specific function. For example, in some cases where the analyte apparatus is a mass spectrometer, the measurement module may include a mass filter, an ion dissociation device, and a mass analyzer. Operating parameters may be used to operate one or more of such components. For example, in an LC-MS system, operating parameters may be applied to the mass filter of the LC-MS system, as discussed in more detail below.

[0071] The data processing module 210 can receive measurement data generated by the analyte measurement module and process the measurement data to generate information about at least one target analyte of interest. For example, the data processing module 210 can process the measurement data to quantify the concentration of one or more analytes of interest in the sample.

[0072] The analytical apparatus can be of various types. Some examples include, but are not limited to, mass spectrometry systems such as LC-MS systems, which employ flow injection, acoustic energy, and laser radiation to introduce the sample into the ion source of the mass spectrometer. Other examples include mass spectrometry systems that employ separation devices such as ion mobility spectrometers before introducing the sample into the ion source.

[0073] In some implementations, this teaching can be used to perform LC-MS measurements, for example, LC coupled with tandem mass spectrometry. This is illustrated by way of example and reference. Figure 3The flowchart, in one embodiment, discloses a method for performing LC-MS, wherein a digital data processor is used to process one or more input parameters to calculate one or more operating parameters of the mass filter of the MS system. The one or more input parameters include the time width associated with the LC peak of the eluent leaving the LC column of the LC-MS system and the pulse frequency associated with the time-of-flight mass analyzer operating the MS system. The one or more operating parameters include the m / z width of the bandpass window of the mass filter (i.e., the m / z range of ions allowed to pass through the mass filter) and the rate at which the bandpass window is scanned in the m / z dimension (e.g., the time rate at which the lower and upper limits of the m / z of the mass filter's bandpass window change).

[0074] The controller is configured to control the operation of the quality filter based on calculated operating parameters. For example, a digital data processor may communicate with the controller to transmit calculated operating parameters associated with the quality filter to the controller, and the controller may generate control signals for controlling the operation of the quality filter with the calculated operating parameters. While in some embodiments the digital data processor and the controller may be implemented as two separate units, in other embodiments the controller may include a digital data processor for processing input parameters and may also include circuitry for generating control parameters for controlling the operation of the quality filter.

[0075] Continue to refer to Figure 3 The flowchart describes introducing a sample into an LC column and directing the eluent exiting the column to an ion source that ionizes one or more analytes in the sample to generate multiple precursor ions. These precursor ions are then introduced into a mass filter downstream of the ion source, configured to allow target precursor ions with m / z ratios within the filter's bandpass window to pass through. Ions passing through the mass filter are then introduced into an ion dissociation device, where they undergo dissociation to generate multiple product ions. These product ions are subsequently introduced into a time-of-flight (TOF) mass analyzer, which generates ion detection data associated with the product ions.

[0076] By way of example, in some implementations, the digital data processor can calculate the m / z width of the bandpass window of the quality filter and the scan rate of the bandpass window in the m / z dimension based on the following relationship that extends the above equations (1) to (6).

[0077] Ion detection typically follows a Poisson process. Considering the Poisson process and a 95% confidence interval, the upper limit of the minimum value of ions incident on the ion detector is (…). It can be obtained through the following relationship:

[0078] Equation (7)

[0079] parameter and It is defined above.

[0080] By way of example, in various implementations, the upper limit of the ion rate estimate can be selected as 20%, such that the following relationship is obtained using the above equations (1) to (7).

[0081] Equation (8)

[0082] Equation (9)

[0083] Equation (10)

[0084] The m / z width of the bandpass window of the quadrupole mass filter can be calculated using the above relationships (9) and (10) for a target 95% confidence limit for the ion detection rate. The scan rate of the bandpass window of the mass filter can be determined using the above equation (3).

[0085] This teaching can be applied to various mass spectrometers, including those configured to operate in DIA mode. It is presented by way of example rather than limitation. Figure 4 An LC-MS spectroscopic system 400 is schematically depicted, comprising a liquid chromatography (LC) column 401 capable of receiving a sample and an ion source 403 connected to the LC column 401 to receive the eluent exiting the LC column. The ion source can ionize one or more analytes in the received eluent to generate multiple ions, which can be received via an ion director, such as a QJet ion director, through a mass spectrometer aperture 402. The QJet ion director includes a set of rods 401 arranged in a quadrupole configuration, two of which, 401a / 401b, are visible in the figure, and employs a combination of gas dynamics and a radio frequency field to focus the ions. Ions exiting the QJet ion director are received by ion director Q0, which includes a set of quadrupoles 404, two of which, 404a / 404b, are visible in the figure. An RF voltage can be applied to this set of quadrupoles to induce radial confinement of the ions and generate an ion beam, which is then received by the ion mass filter Q1. Ion directors QJet and Q0, and mass filter Q1 are arranged in a differential pumping chamber with gradually decreasing pressure.

[0086] The ion lens IQ0 focuses ions exiting the ion guide Q0 into the mass filter Q1. The mass filter Q1 includes a short, thick lens 406 comprising a set of quadrupoles (two of which, 406a / 406b, are visible in the figure), to which an RF field can be applied to focus the ions. The mass filter Q1 also includes a set of quadrupoles 410, two of which, 410a / 410b, are visible in the figure, to which a combination of RF and DC voltages can be applied to enable the selection of one or more precursor ions having an m / z ratio within the target m / z range, such as all precursor ions of interest, when the mass spectrometer is operating in DIA mode, for transmission via the ion lens IQ2 to the downstream ion dissociation device Q2, such as the collision chamber in this example.

[0087] In this embodiment, the collision chamber Q2 includes a set of rods 417, two of which, 417a / 417b, are visible in the figure. The set of rods is arranged in a quadrupole configuration and pressurized by the introduction of nitrogen to allow for the collisional fragmentation of ions received by the collision chamber Q2.

[0088] Ions exiting chamber Q2 are focused by a set of ion-focusing optics 415 into a time-of-flight (ToF) mass analyzer 418, which provides mass analysis of those ions. More specifically, the ToF mass analyzer 418 may include a deflection electrode 419 to which a pulsed voltage can be applied to guide the received ions into a field-free ion drift region, through which the ions are incident on the ion detector 420 of the mass analyzer. The ion detection signal generated by the ion detector can be processed by a data processing module 425 to generate a mass spectrum of the product ions.

[0089] Continue to refer to Figure 4 The DC voltage source 426 and RF voltage source 428, operating under the control of the controller 430, can apply RF voltage and DC voltage to the quality filter Q1 in a manner known in the art and as informed by this teaching to configure the bandpass window of the quality filter. By way of example and not limitation, the RF voltage applied to the rod of the quality filter Q1 can have a frequency in the range of about 200 kHz to about 1 MHz and a peak-to-peak amplitude (V) in the range of about 100 volts to about 10 kilovolts (kV). pp In various implementations, the applied DC resolution voltage can be adjusted to change the m / z width of the bandpass window of the quality filter.

[0090] More specifically, in this embodiment, the digital data processor 425, which communicates with the controller 430, can receive multiple input parameters, such as those discussed above, and can process the input parameters to generate multiple operating parameters, including the m / z width of the bandpass window of the quality filter and the rate used to scan the bandpass window. The digital data processor 425 can transmit the operating parameters to the controller, which can then send control signals to an RF voltage source and a DC voltage source to control the operation of the quality filter according to the calculated operating parameters.

[0091] When operating in DIA mode, the controller can be programmed according to this teaching to set the bandpass window of the Q1 mass filter to allow ions in the target m / z range to pass through, for example, according to equation (3) above. Additionally, the controller can send control signals to the RF voltage source and the DC voltage source to cause the bandpass window of the Q1 mass filter to be scanned at a desired rate, for example, according to equation (1) above, during DIA.

[0092] Through further illustration, Figure 5 This is a schematic representation of data acquisition in DIA mode, which is achieved by scanning the bandpass window of a quadrupole mass filter (e.g., the Q1 quadrupole mass filter discussed above) within a single measurement cycle and with a single collision energy (CE) while maintaining a constant m / z width of the mass filter. For simplicity, the quadrupole mass filter is referred to herein as the Q1 filter. Ion measurements are depicted in a three-dimensional space with the following dimensions: (ToF pulse precursor mass, measured ion m / z, and intensity).

[0093] exist Figure 5 In the diagram, the quadrupole mass filter is represented by a horizontal line of finite length, indicating the m / z width of the bandpass window of the mass filter. A continuous scan of the bandpass window of the quadrupole mass filter is represented by a horizontal line moving diagonally from the upper left corner (low precursor m / z, first TOF pulse) to the lower right corner (high precursor m / z, last TOF pulse). The ions measured at different m / z values ​​in each ToF pulse correspond to the product ions and any residual precursor ions that arrive at the ToF analyzer when the pulse is applied. To simplify the diagram, only a few ToF pulses are plotted between the first and last opportunity to observe ion fragments generated via the dissociation of precursor ions. For each annotated pulse, a single ToF pulse spectrum is represented by a diagonal line, which, when added together, forms a measurement period spectrum represented by a diagonal axis labeled as fragment m / z.

[0094] The TOF pulse exponent and the Q1 filter start / stop m / z are related. For this illustrative example, it is assumed that the filter m / z width is constant and that the Q1 start / stop m / z depends linearly on the TOF pulse.

[0095] Typically, the composition of the precursor mixture (and corresponding ion fragments) changes continuously along the TOF pulse dimension, although most precursor ions are identical between consecutive TOF pulses. For simplicity, in this example, it is assumed that a single precursor P exists in the sample, which in turn generates two ion fragments, where the less abundant ion fragment is depicted as a solid circle and the more abundant ion fragment as a hollow circle. Starting with a TOF pulse p and ending with a TOF pulse q, the precursor ion P is transported through a Q1 mass filter with a bandpass window of width Q. Ion fragments are generated according to a probability density function and transported through the TOF path. For each detected ion, the ion drift time from the corresponding ToF pulse corresponds to m / z and is recorded as an MS2 single ToF pulse spectrum, represented in this case as a diagonal mz line, i.e., MS2 m / z.

[0096] Typically, precursor ions are transported through a Q1 mass filter over multiple consecutive ToF pulses. If the ion m / z intensity is plotted across the ToF pulses, the m / z values ​​of the precursor ion and all its fragments will resemble a rectangular pulsed trace (QIT), where the pulsed shape is associated with the off-on-off precursor ion transport probability defined by the Q1 start / stop mass. In the simple case where only one precursor ion exists at a given LC period, non-zero ion detection intensity is possible from the ToF pulse at which the Q1 mass filter first allows the precursor ion to pass (in this illustrative example, the upper limit of the Q1 mass filter is equal to the m / z of the precursor ion of interest; in other words, the Q1 line terminates at the precursor ion m / z) until the ToF pulse at which the lower limit of the Q1 filter is equal to the m / z of the precursor ion of interest (i.e., the precursor ion's last chance to pass through the Q1 filter; in other words, the Q1 line begins at the precursor ion m / z).

[0097] This figure shows that more abundant ions (i.e., ions represented as hollow circles) are generated and recorded in each ToF pulse, while less abundant ions (i.e., ions represented as solid circles) are recorded only in a few ToF pulses corresponding to the “visible” time window of precursor P. Despite the counting noise associated with the Poisson process of ion detection, the QIT corresponding to the more abundant ions resembles the expected rectangular QIT pulse. The MS spectrum for one measurement period is the sum of all the individual ToF pulse spectra and is annotated as a bottom diagonal axis with two schematic peak shapes.

[0098] The various digital data processors and controllers used in the practice of this teaching (such as those discussed above) can be implemented using software, firmware, and hardware in ways known in the art and as instructed by this teaching. By way of example, Figure 6 An example of an implementation 600 of the aforementioned digital data processor 432, having a digital processing unit 602, is schematically depicted. This digital processing unit 602 can communicate with a random access memory (RAM) module 604 and a permanent memory module 605 via one or more communication buses 603. By way of example, various instructions for processing input parameters to calculate operating parameters for operating the quality filter can be stored in the permanent memory module 605 and can be transferred by the processing unit 602 to the RAM module 604 for execution during operation. By way of example, the instructions stored on the digital data processor can be based on the relationship between the m / z width of the bandpass window of the quality filter in the LC-MS system and its scan rate, as discussed above. However, as noted above, this teaching is not limited to LC-MS systems and can be applied to the operation of other analysis devices.

[0099] The following examples are provided to further illustrate various aspects of this teaching and are not intended to necessarily indicate the best way to practice this teaching and / or the best results that can be obtained.

[0100] Example

[0101] Figure 7 This shows the minimum ion rate incident on the ion detector of the ToF mass analyzer for each measurement cycle. An example of the number of ToF pulses corresponding to a 95% confidence interval, which is a function of the logarithm of the precursor. In other words, the Y-axis indicates the minimum number of ToF pulses during the m / z "visible" period of the precursor per cycle to achieve a 95% confidence level when estimating the ion rate (ion rate on the X-axis).

[0102] Assuming the LC peak associated with the eluent leaving the LC column of the LC-MS system has a duration characterized by PWHH = ~3 seconds, the measurement cycle duration can be chosen to be approximately 1 second to ensure a sufficient number of sampling points across the LC peak (typically at least 3 points). Based on the assumption that the precursor ions of interest have an m / z ratio in the range of 400 Da to 900 Da and a pulse frequency of 10 kHz (i.e., the frequency of the voltage pulse applied to the deflection electrode of the ToF mass analyzer), and that the desired minimum ion rate incident on the ion detector per measurement cycle is 0.1 ions (or 10 cps for a given pulse frequency), using Equation (5) above, the minimum number of ToF pulses (i.e., the voltage pulse applied to the deflection electrode of the mass analyzer) per cycle for 0.1 ions can be calculated as 960. Substituting the calculated minimum number of ToF pulses into Equations (10) and (3), the m / z width of the bandpass window of the Q1 mass filter for the 95% confidence interval can be calculated as:

[0103]

[0104] Furthermore, the scan rate (i.e., Q1 velocity) of the bandpass window of the Q1 quality filter can be calculated as:

[0105]

[0106] Although some aspects have been described in the context of a system and / or apparatus, it is clear that these aspects also represent descriptions of the corresponding methods, where blocks or devices correspond to method steps or features of method steps. Similarly, aspects described in the context of method steps also represent descriptions of corresponding blocks or items or features of the corresponding devices. Some or all of the method steps can be performed by (or using) hardware devices such as processors, microprocessors, programmable computers, or electronic circuits. In some embodiments, some or more of the most important method steps can be performed by such devices.

[0107] Depending on the specific implementation requirements, embodiments of the present invention can be implemented in hardware and / or software. Implementations can be performed using a non-transitory storage medium, such as a digital storage medium like a floppy disk, DVD, Blu-ray, CD, ROM, PROM, EPROM, EEPROM, or flash memory, on which electronically readable control signals are stored. This digital storage medium cooperates with (or is capable of cooperating with) a programmable computer system to execute the corresponding method. Therefore, the digital storage medium can be computer-readable.

[0108] Those skilled in the art will understand that various changes can be made to the above embodiments without departing from the scope of this teaching.

Claims

1. A method of operating an analytical apparatus for measuring at least one analyte in a sample, comprising: Using digital data processors: Receive the sample acquisition rate for introducing the sample into the analytical apparatus, and Multiple optimal operating parameters of the analytical device are calculated based on the sample acquisition rate by optimizing the quality factor associated with the measurement of the analyte, wherein the operating parameters include the duration of the measurement cycle and the selectivity associated with the measurement; While receiving the sample at the stated sample acquisition rate, the analytical apparatus is operated with the stated optimal operating parameters to generate sample measurement data corresponding to the analyte; and The sample measurement data are processed to obtain information about the analyte.

2. The method according to claim 1, wherein, The information about the analyte indicates whether the analyte is present in the sample.

3. The method according to any one of claims 1 and 2, wherein, The information regarding the analyte provides the concentration of the analyte in the sample.

4. The method according to claim 1, wherein, The quality factor is defined at least in part based on at least one of the target resolution, the minimum signal-to-noise ratio of the target associated with the measurement data, and the target selectivity.

5. The method according to claim 1, wherein, The analytical apparatus includes a mass spectrometry system.

6. The method according to claim 5, wherein, The mass spectrometry system is configured to operate in data-independent acquisition (DIA) mode.

7. An analytical apparatus for measuring at least one analyte in a sample, comprising: The analyte measurement module is used to receive the sample and generate analyte measurement data. A digital data processor is configured to receive a sample acquisition rate for introducing the sample into the analytical apparatus, and to calculate optimal values ​​for a plurality of operating parameters of the analytical apparatus, at least in part based on the sample acquisition rate, by optimizing a quality factor associated with the measurement of the analyte, wherein the operating parameters include the duration of the measurement cycle and a selectivity associated with the measurement. A controller is configured to receive the optimal operating parameters and configure the operating mode of the analyte measurement module based on the optimal operating parameters. A data processing module is configured to receive measurement data generated by the analyte measurement module operating in the said operating mode, and process the measurement data to generate information about the at least one analyte.

8. The analytical apparatus according to claim 7, wherein, The quality factor is defined at least in part based on at least one of the target resolution, the minimum signal-to-noise ratio of the target associated with the measurement data, and the target selectivity.

9. The analytical apparatus according to any one of claims 7 and 8, wherein, The analytical apparatus includes a mass spectrometry system, and optionally, the mass spectrometer includes an LC-MS system.

10. The analytical apparatus according to claim 9, wherein, The mass spectrometry system is configured to operate in data-independent acquisition (DIA) mode.

11. The analytical apparatus according to claim 9, wherein, The mass spectrometry system includes: An ion source for receiving a sample and ionizing at least one analyte in the sample to generate a plurality of ions; A mass filter, located downstream of the ion source, is used to receive the plurality of ions and allow ions having an m / z ratio within the bandpass window of the mass filter to pass through; An ion dissociation device for receiving ions passing through the mass filter and dissociating at least a portion of the ions to generate a plurality of product ions; and A quality analyzer, located downstream of the ion dissociation device, receives the plurality of product ions and has an ion detector for detecting at least a portion of the received product ions to generate quality detection data associated with the product ions. The operating parameters include the m / z width of the bandpass window of the quality filter and the rate at which the bandpass window is scanned during data acquisition. The digital data processor is configured to calculate the optimal values ​​of the operating parameters based on the data acquisition rate and the m / z range associated with the precursor ion of interest.

12. The analytical apparatus according to claim 11, wherein, The quality analyzer includes a time-of-flight (TOF) quality analyzer.

13. The analytical apparatus according to claim 12, wherein, The data acquisition rate of the TOF mass analyzer is determined based on the pulse frequency associated with the voltage applied to the reflector electrodes of the TOF mass analyzer.

14. A mass spectrometry system, comprising: An ion source is used to receive a sample and ionize one or more analytes in the sample to generate multiple ions. A mass filter, located downstream of the ion source, is used to receive the plurality of ions and allow ions having an m / z ratio within the bandpass window of the mass filter to pass through; An ion dissociation device is used to receive ions passing through the mass filter and dissociate at least a portion of the ions to generate a plurality of product ions; A quality analyzer, located downstream of the ion dissociation device, receives the plurality of product ions and provides quality detection data associated with the product ions; A digital data processor configured to receive one or more input parameters and compute one or more operating parameters, the one or more input parameters including a sampling period, an m / z range associated with the precursor ion of interest, and a data acquisition rate associated with the mass analyzer, the one or more operating parameters including a bandpass window of the mass filter and a scan rate of the bandpass window in the m / z dimension; as well as A controller that communicates with the digital data processor is configured to receive the operating parameters and configure the quality filter to operate based on the calculated operating parameters.

15. The mass spectrometry system according to claim 14, wherein, The digital data processor is configured to calculate the scan rate of the bandpass window in the m / z dimension according to the following relationship: in, This represents the scan rate of the bandpass window, expressed in Daltons per second. This represents the maximum m / z ratio within the m / z range associated with the precursor ion. The minimum m / z ratio representing the m / z range associated with the precursor ion, and Indicates the LC sampling time.

16. The mass spectrometry system according to claim 15, wherein, Defined according to the following relationship: in, This represents the time width corresponding to half the maximum value of the LC peak, and N is an integer.

17. The mass spectrometry system according to claim 16, wherein, The digital data processor is configured to calculate the m / z width of the bandpass window of the quality filter according to the following relationship: in, This represents the m / z width of the bandpass window, expressed in Daltons. This indicates the rate at which the bandpass window is scanned, measured in Daltons per TOF pulse. This indicates the rate at which the bandpass window is scanned, measured in Daltons per second. This indicates the number of TOF pulses per measurement cycle for the minimum ion rate per cycle.

18. The mass spectrometry system according to claim 16, wherein, Defined according to the following relationship: in, This represents the minimum rate at which ions are incident on the TOF detector.

19. The mass spectrometry system according to claim 18, wherein, Defined according to the following relationship: 。 20. The mass spectrometry system according to any one of claims 14 to 19, wherein, It also includes a separation device located upstream of the ion source, wherein the separation device may optionally include either an LC column or an ion mobility spectrometer.

21. The mass spectrometry system according to claim 20, wherein, The sampling period is at least a portion of the elution time of the sample from the LC column.

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