Methods and systems for performing data independent acquistion mass spectrometry

Abstract

In one aspect, a method of operating an analytical device for measuring at least one analyte within a sample is disclosed, which includes utilizing a digital data processor to receive a sample acquisition rate for introduction of the sample into the analytical device, and to compute one or more optimal operating parameters of the analytical device based on the sample acquisition rate by optimizing a figure-of-merit associated with measurement of the analyte, where the operating parameters include a temporal duration of a measurement cycle and / or selectivity associated with the measurement. The analytical device can be operated at the 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 derive information about the analyte.

Description

METHODS AND SYSTEMS FOR PERFORMING DATA INDEPENDENT ACQUISITION MASS SPECTROMETRYRelated Applications

[0001] This application claims priority to U.S. Provisional Application No. 63 / 538,907 filed on September 18, 2023, the contents of which are incorporated herein by reference in their entirety.Technical Field

[0002] The present disclosure relates generally to systems and methods for performing mass spectrometry, and in particular to systems and methods for performing data independent acquisition (DIA) mass spectrometry.Background

[0003] The present disclosure generally provides systems and methods for operating a mass spectrometer in a DIA operational mode.

[0004] Mass spectrometry (MS) is an analytical technique for determining the structure of test chemical substances with both qualitative and quantitative applications. MS can be useful for identifying unknown compounds, determining the composition of atomic elements in a molecule, determining the structure of a compound by observing its fragmentation, and quantifying the amount of a particular chemical compound in a mixed sample. Mass spectrometers detect chemical entities as ions such that a conversion of the analytes to charged ions must occur.

[0005] DIA mass spectrometry is a technique in which a mass range of interest is divided into a plurality of mass windows, each characterized by an m / z range, and MS / MS analysis for all compounds (typically peptides) within each window is performed. As such, DIA allows mass data acquisition for all compounds (e.g., peptides) within a target mass range without a priori knowledge regarding one or more specific target compounds for which mass analysis is desired. For example, in some mass spectrometers, the bandpass window of a mass filter can be employed to set the m / z range of each window and the bandpass window can be scanned tocover the entire m / z range of interest. The m / z width of the bandpass window and the m / z step size can determine the sensitivity and selectivity of the MS / MS analysis.Summary

[0006] In one aspect, a method of operating an analytical device for measuring at least one analyte within a sample is disclosed, which includes utilizing 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 introduction of the sample into the analytical device, and to compute one or more optimal operating parameters of one or more components of the analytical device based on the one or more input parameters, including the sample acquisition rate, by optimizing a figure-of-merit (herein also referred to as the optimization criteria) associated with measurement of the analyte. By way of example, the operating parameters can include a temporal duration of a measurement cycle and / or a selectivity associated with the measurement. The analytical device can be operated at the 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 derive information about the analyte.

[0007] By way of example, and without limitation, the derived information can indicate whether the analyte is present in the sample, e.g., at a concentration greater than a limit-of- detection (LOD) of the analytical device. As another example, the derived information can provide a concentration of the analyte in the sample. In some cases, the information can indicate whether two or more target analytes of interest are concurrently present in the sample.

[0008] The figure-of-merit can be defined in a variety of different ways, e.g., based on the type of the analytical device, the target analyte of interest and / or a particular application for which the analytical device is utilized. By way of example, and without limitation, the figure-of- merit can be at least based on a target resolution desired for the measurement data. In various embodiments, the target resolution can be defined based on a particular measurement modality and the instrumentation that is employed. By way of example, and without limitation, the target resolution in some mass spectrometry applications may be defined as a minimum separation of ions along the m / z dimension that can be distinguished so as to lead to identification of those ions.

[0009] As another example, the figure-of-merit (herein also referred to as optimization criteria or performance metric) can be defined at least partially based on a target minimum signal-to-noise ratio for the measurement data. In some cases, the figure-of-merit can be defined at least partially based on a target selectivity. In some embodiments, the figure-of-merit can be defined as a combination of two of more of the criteria discussed herein. For example, a figure- of-merit can be defined based on a combination of a target resolution and a target sensitivity.

[0010] The above method can be applied to a variety of analytical devices. By way of example, and without limitation, the analytical device can be a mass spectrometry system, such as a liquid chromatography (LC)- mass spectrometry (MS) system, mass spectrometry systems that employ any of flow injection, acoustic energy, and laser radiation for introduction of a sample into an ion source of a mass spectrometer. As another example, the mass spectrometry system may utilize an ion mobility spectrometer, such as a differential mobility spectrometer (DMS) or a field asymmetric ion mobility spectrometer (FAIMS), to separate ions based on their mobility before introducing ions with a target mobility into a downstream mass spectrometer.

[0011] In a related aspect, an analytical device for measuring at least one analyte in a sample is disclosed, which includes an analyte measurement module for receiving the sample and generating analyte measurement data, and a digital data processor that is configured to receive one or more input parameters, including a sampling period, e.g., a sampling period associated with a sample acquisition rate for introduction of the sample into the analytical device, and to compute optimal values of one or more operating parameters of one or more components of the analytical device based at least in part on the input parameter(s) by optimizing a figure-of-merit associated with measurement of the analyte. By way of example, the operating parameters can include a temporal duration of a measurement cycle and a bandwidth of a filter and / or the rate at which the filter’s output can be varied. The analytical device can further include a controller for receiving the optimal operating parameters and to configure an operational mode of one or more components of the analytical device (such as an analyte measurement module of the analytical device) based on the optimal operating parameters. A data processing module can receive the measurement data generated by the one or more components operating in that operational mode and process the measurement data to generate information regarding the at least one analyte.

[0012] In some implementations of the above analytical device, the figure-of-merit can be defined in a manner suitable for that analytical device including the intended use of the device, such as those discussed above.

[0013] By way of example, in some embodiments, the analytical device can be a mass spectrometry system, such as an LC-MS system. In some such embodiments, the mass spectrometry system can be configured to operate in a DIA mode.

[0014] In some embodiments, the mass spectrometry system can include an ion source for receiving a sample, e.g., an eluate exiting an LC column, and ionizing one or more analytes in the sample, e.g., the eluate, to generate a plurality of precursor ions, and a mass filter positioned downstream from said ion source for receiving the plurality of precursor ions and allowing passage of those precursor ions that have m / z ratios within its bandpass window. The system can further include an ion dissociation device for receiving the ions passing through the mass filter and causing dissociation of at least a portion thereof to generate a plurality of product ions, and a mass analyzer, e.g., a time-of-flight (ToF) mass analyzer, positioned 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, the operating parameters can include an m / z width of a bandpass window of the mass filter and a rate for scanning the bandpass window of the mass filter (e.g., by moving the low m / z and high m / z bounds of the bandpass window) during data acquisition. The digital data processor is configured to compute the optimal values of the operating parameters based on a sampling period, an m / z range associated with precursor ions of interest, and a data acquisition rate of the mass analyzer. The sampling period refers to a time period in which a sample is available for mass analysis. The data acquisition rate refers to the speed at which the mass spectrometer collects data points in a measurement cycle. It is typically measured as the number of mass spectra acquired per second. In embodiments in which the mass analyzer is a time-of-flight (ToF) mass analyzer, the data acquisition rate is related to a pulse frequency associated with voltage pulses applied to a deflector electrode of the TOF mass analyzer. By way of example, in various embodiments, the mass analyzer can have a data acquisition rate in a range of about 1000 spectra per second to about 10,000 spectra per second.

[0015] In a related aspect, a mass spectrometry system is disclosed, which includes a separation device, e.g., an LC column, for receiving a specimen and separating various components of the specimen to generate a sample, e.g., at least one eluate exiting the LC column during at least one elution period, and an ion source for receiving the sample, e.g., the at least one eluate, and ionizing one or more analytes therein to generate a plurality of precursor ions. A mass filter is positioned downstream from the ion source for receiving the plurality of precursor ions and allowing passage of those precursor ions that have m / z ratios within its bandpass window. The mass spectrometry system can further include an ion dissociation device for receiving the precursor ions passing through the mass filter and causing dissociation of at least a portion thereof to generate a plurality of product ions. A mass analyzer, e.g., a time-of-flight (ToF) mass analyzer, positioned 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 further includes a digital data processor that is configured to receive a plurality of input parameters comprising a sampling period, an m / z range associated with precursor ions of interest, and a data acquisition rate associated with the mass analyzer and computes an m / z width of the bandpass window of the mass filter and a rate for scanning of the bandpass window in the m / z dimension. As noted above, the sampling period refers to a time period (herein also referred to as a time interval) in which a sample is available for analysis. By way of example, and without limitation, the sampling period may coincide with: i) an LC peak, ii) sample injection from a reservoir or a matrix (e.g., via acoustic or laser energy), and iii) a time period corresponding to the analysis of a sample introduced into a mass spectrometer via sample infusion. For example, delivery of an eluate exiting an LC column may be predicted based on the operational setting of the LC column. In other sample delivery systems, e.g., acoustic ejection or infusion, the sample delivery device may provide timing information regarding the delivery time of a sample of interest to the mass spectrometer.

[0016] A controller in communication with the digital data processor and the mass filter can receive the computed operating parameters, namely, the m / z width of the bandpass window of the mass filter, and a rate for scanning the bandpass window in the m / z dimension. The controller can in turn cause the mass filter to operate at the computed operating parameters. Forexample, the controller can send control signals to power supplies to adjust voltages applied to the mass filter so as to configure the mass filter to operate at the computed operating parameters.

[0017] In some embodiments, the digital data processor can be configured to compute the scanning rate of the bandpass window of the mass filter in m / z dimension according to the following relation:where, denotes the scanning rate of the bandpass window in units of Dalton persecond, maxPrecursor _mz denotes maximum m / z ratio of the m / z range associated with the precursor ions, minPrecursorjnz denotes minimum m / z ratio of the m / z range associated with the precursor ions, andTcycle denotes LC sampling time.

[0018] Further, the digital data processor can be configured to compute Tcycie in accordance with the following relation:where,PWHH denotes a temporal width corresponding to half maximum of the LC peak, andN is an integer, e.g., an integer that is equal to or greater than 2, e.g., in a range of 2 to 20.

[0019] The digital data processor can also be configured to compute an m / z width of the bandpass window of the mass filter according to the following relations:where,Qlwidth(Da) denotes the m / z width of the bandpass window in units of Dalton,Qlspeedpulsedenotes the rate at which the bandpass window is scanned in units of Dalton per TOF pulse, denotes the rate at which the bandpass window is scanned in units ofDalton per second,N QlpulsesminionRateperCyciedenotes the number of TOF pulses per measurement cycle for a minimum ion rate per cycle.

[0020] The digital data processor can be further configured to compute N QlpulsesminionRateperCycieaccording to the following relation:where, minlonRatePerCycle denotes a minimum rate at which ions are incident on the TOF detector.

[0021] The digital data processor can also be configured to compute minlonRatePerCycle according to the following relation: mini onRateP erCycle > -Tcycle- Eq. (6). pulsefrequency

[0022] In a related aspect, a method of operating an MS system having a mass filter and a mass analyzer, e.g., a time-of-flight (TOF) mass analyzer, to perform mass spectrometry is disclosed, which includes utilizing a digital data processor to process a plurality of input parameters to compute a plurality of operating parameters of the mass filter. By way of example, the input parameters can include a sampling period, e.g., a temporal width associated with an LC peak of an eluate exiting an LC column of the LC-MS system (e.g., characterized by full width at half maximum (FWHM) of the LC peak), and a data acquisition rate, e.g., a pulse frequency associated with operation of a TOF mass analyzer, i.e., a frequency at which voltage pulses are applied to a deflector electrode of the TOF mass analyzer. In various embodiments, the operating parameters can include an m / z width of a bandpass window of the mass filter (ions having m / z ratios within the m / z width can pass through the mass filter) and a rate for scanning the bandpass window of the mass filter during data acquisition. A controller is employed to effect operationof the mass filter in accordance with the computed operating parameter(s) during data acquisition.

[0023] The above method can further include introducing a specimen into an analyte separation device, e.g., an LC column, directing a sample exiting the analyte separation device, e.g., an eluate exiting the LC column, to an ion source of the MS system so as to ionize one or more analytes in the sample to generate a plurality of precursor ions. The precursor ions can be introduced into the mass filter of the MS system. The precursor ions having m / z ratios within the bandpass window of the mass filter pass through the mass filter and are introduced into a downstream ion dissociation device, e.g., a collision cell, in which at least a portion of the precursor ions undergo dissociation to generate a plurality of product ions. The plurality of the product ions is received by the mass analyzer, e.g., TOF mass analyzer, which generates ion detection data associated with the product ions. A data processing unit can receive the ion detection data and process the ion detection data to generate a mass spectrum of the product ions.

[0024] Further understanding of various aspects of the present teachings can be obtained with reference to the following detailed description in conjunction with the associated drawings, which are described briefly below.Brief Description of the Drawings

[0025] FIG. 1 is a flow chart depicting various steps of an embodiment of a method according to the present teachings,

[0026] FIG. 2 is a schematic view of an analytical device according to an embodiment of the present teachings,

[0027] FIG. 3 is a flow chart depicting various steps of an embodiment of a method according to the present teachings for performing LC-MS mass spectrometry,

[0028] FIG. 4 is an example of an embodiment of an LC-MS system according to an embodiment of the present teachings,

[0029] FIG. 5 is a schematic representation of acquisition of DIA data by scanning the bandpass window of a quadrupole mass filter,

[0030] FIG. 6 schematically depicts an example of an implementation of a digital data processor and / or a controller utilized in various embodiments of the present teachings, and

[0031] FIG. 7 illustrates a graph indicating the number of ToF pulses corresponding to 95% confidence interval as a function of logarithm of number of ion rate per cycle.Detailed Description

[0032] It will be appreciated that for clarity, the following discussion will explicate various aspects of embodiments of the applicant’s teachings, while omitting certain specific details wherever convenient or appropriate to do so. For example, discussion of like or analogous features in alternative embodiments may be somewhat abbreviated. Well-known ideas or concepts may also for brevity not be discussed in any great detail. The skilled person will recognize that some embodiments of the applicant’s teachings may not require certain of the specifically described details in every implementation, which are set forth herein only to provide a thorough understanding of the embodiments. Similarly, it will be apparent that the described embodiments may be susceptible to alteration or variation according to common general knowledge without departing from the scope of the disclosure. The following detailed description of embodiments is not to be regarded as limiting the scope of the applicant’s teachings in any manner.

[0033] As used herein, the terms “about” and “substantially equal” refer to variations in a numerical quantity that can occur, for example, through measuring or handling procedures in the real world; through inadvertent error 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 means 10% greater or less than the value or range of values stated or the complete condition or state. For instance, a concentration value of about 30% or substantially equal to 30% can mean a concentration between 27% and 33%. The terms also refer to variations that would be recognized by one skilled in the art as being equivalent so long as such variations do not encompass known values practiced by the prior art.

[0034] 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

[0035] The term “resolution,” as used herein in the context of an analytical device, refers to the ability of the device to distinguish between separate components within a sample that may provide closely-spaced analytical signals. Resolution can be defined in several ways depending on the particular analytical device and the type of measurements that are performed. For example, for analytical devices that employ spectroscopy for analytical analysis of a sample, resolution can refer to the ability of the device to distinguish between two closely-spaced spectral features (e.g., spectral peaks) in a spectrum. Chromatographic resolution can refer to the degree of separation between two adjacent peaks on a chromatogram. In a mass spectrometry system, e.g., LC-MS, the term resolution can refer to the ability of the system to distinguish (identify) ions having very close m / z ratios. For example, the resolution may refer to the ability of the system to identify precursor ions having very close m / z ratios. By way of example, in some cases where two or more analytes cannot be sufficiently separated by a separation device positioned upstream of a mass spectrometer, the resolution can refer to the ability of the mass spectrometer to distinguish ions associated with such analytes. For example, when two or more analytes are coeluting from an LC column, the resolution can refer to the ability to identify precursor ions associated with the co-eluting analytes.

[0036] The term “selectivity,” as used herein in the context of an analytical device refers to the ability of the device to accurately and selectively identify (and optionally quantify) a specific analyte in a sample in the presence of other substances and / or potential interferents.

[0037] The term “sensitivity” in the context of an analytical device, including a mass spectrometer, refers to the ability of the device to detect small changes or variations in the quantity or concentration of an analyte in a sample under analysis. For example, sensitivity can be defined as the ratio of the change in the device’s response (e.g., a detection signal generated by the device) to a corresponding change in the quantity or concentration of the analyte being measured. In other words, the sensitivity can be determined by the limit-of-detection (LoD) of the analytical device, which is based on the minimum amount of an analyte that is detectable (identifiable) by the device.

[0038] The term “measurement cycle” in the context of an analytical device, refers to a series of steps or processes that the device follows to generate analytical data for a sample (or sample portion) introduced into the device. In the context of an LC-MS system, a measurement cycle can include the introduction of an eluate exiting the LC column to an ion source to generate precursor ions, the passage of the precursor ions through a mass filter to select precursor ion(s) of interest, the dissociation of the selected precursor ions to generate product ions and using a mass analyzer (e.g., a TOF mass analyzer) to generate ion detection signals corresponding to the product ions. The “measurement cycle time” refers to the time required for the device to perform a measurement cycle.

[0039] The term “rate of scanning of the bandpass window” of a mass filter refers to how quickly the range of m / z values that the bandpass window covers is changed. Such a change can be achieved in a step- wise fashion, e.g., by moving the lower and the upper bounds of the bandpass window by a certain step size (i.e., by a certain m / z value). For example, the scanning of the bandpass window can be achieved by choosing an m / z step size that is less than the m / z bandwidth of the bandpass window.

[0040] Mass spectrometers operating in a DIA mode typically include a mass filter, e.g., a quadrupole mass filter, that can be configured to allow passage of ions having m / z ratios within a target range. The ions passing through the mass filter can be dissociated (e.g., fragmented) via a downstream ion dissociation device, e.g., a collision cell, to generate product ions. The product ions can be received by a time-of-flight (TOF) mass analyzer that generates ion detection signals, which are processed to generate a mass spectrum of the product ions. In such systems, measurement dynamic range can be governed by data accumulation time, e.g., a time corresponding to the number of ToF pulses utilized while the precursor ions are transmitted through the mass filter, and the ability to measure multiple simultaneous ion hits on the ion detector of the ToF mass analyzer. Ion detection systems that are capable of measuring multiple simultaneous ion arrivals can have an extended detection upper bound compared to binary ion detection systems. However, a lower bound for ion detection and the associated uncertainty interval is defined by the number of available opportunities to measure an ion, in both multiple and binary ion detection systems.

[0041] A wider bandpass window of the mass filter enables precursor filtering for a larger number of TOF pulses, thus leading to a longer data accumulation time (measurement time). However, measurement selectivity can be increased by narrowing the bandpass window of the mass filter. In some cases in which the m / z step size for scanning the mass filter is equal to the m / z range associated with the bandpass window of the mass filter, the measurement selectivity is proportional to the m / z range of the bandpass window. In scanning DIA, the m / z step size for scanning the mass filter is much smaller than the m / z width of the mass filter’s bandpass window. In such cases, the step size can determine the upper selectivity limit with the bandpass window size (the width of the bandpass window in m / z) being the convolution kernel.

[0042] In various embodiments of the present teachings, the operating parameters of an analytical device, such as a mass spectrometer, can be optimized to provide a balance between sensitivity, which can relate to data acquisition time, and selectivity, which can relate to, e.g., the m / z width of the mass filter and precursor sampling step in an MS / MS instrument. More generally, the operating parameters can be adjusted so as to optimize a figure-of-merit associated with a measurement, e.g., a measurement directed to detection and optionally quantification of an analyte in a sample under investigation.

[0043] As discussed in more detail below, in various embodiments, a digital data processor is employed to compute a plurality of operating parameters for operating an analytical device, e.g., a mass spectrometer, based on a plurality of input parameters, which can be inputted by a user, by way of example. The determination of the output parameters can be done prior to the initiation of sample analysis or after sample analysis has been initiated. By way of example, the present teachings can be utilized in any mass spectrometer having a mass filter positioned upstream of a mass analyzer, where the mass filter can be scanned more slowly than the rate at which the mass analyzer can collect data. In various embodiments, the present teachings allow providing fast data acquisition while ensuring that the data resolution is within an acceptable range, as discussed in more detail below. In some embodiments, the mass analyzer can generate spectral data at a rate of about 1000 to about 10,000 spectra per second.

[0044] With respect to the flow chart of FIG. 1, a method of operating an analytical device for measuring at least one analyte within a sample includes utilizing a digital data processor toreceive one or more input parameters, including a sampling period, e.g., one associated with a sample acquisition rate for introduction of the sample into the analytical device, and to compute a plurality of optimal operating parameters for operating the analytical device based on the sample acquisition rate by optimizing a figure-of-merit associated with the measurement of the analyte. The analytical device can then be operated at the optimal operating parameters while receiving the sample during the sampling period to generate sample measurement data corresponding to the analyte. The measurement data can be processed to derive information about the analyte. By way of example, the derived information can indicate whether the analyte is present in the sample, e.g., above a limit-of-detection associated with the analytical device. In some embodiments, the derived information can provide information about one or more analytes present in the sample and also quantification of those analytes.

[0045] The figure-of-merit can be defined in a variety of different ways, e.g., based on a particular application of the analytical device. By way of example, and without limitation, the figure-of-merit can be defined as a desired minimum signal-to-noise ratio associated with the measurement data. Further, instead of, or in addition to, the figure-of-merit can be based on the selectivity and / or resolution and / or sensitivity associated with the measurement data.

[0046] FIG. 2 schematically depicts an analytical device 200 according to an embodiment, which includes an analyte measurement module 202 that can receive a sample and generate analyte measurement data corresponding to one or more analytes in the sample. In this embodiment, the analytical device 200 receives the sample from a sample-delivery component 204, which can be, for example, a reservoir in which the sample is stored. In some embodiments, the analytical device can include one or more components positioned upstream of the analyte measurement module 202 to provide processing of the sample. By way of example, and without limitation, such components may include a sample-processing module 203, such as a filtering device, an ion source, among others.

[0047] The analytical device 200 can further include a digital data processor 206 that can receive one or more input parameters and is configured to compute one or more operating parameters for operating the analytical device. By way of example, and without limitation, the input parameter(s) can include a sampling period (a period during which a sample is available foranalysis), a target selectivity, a target sensitivity, all by way of example. The digital data processor can compute at least in part based on the input parameter(s) one or more operating parameters for the operation of one or more components of the analytical device, e.g., the operating parameters for the operation of the analyte measurement module. In various embodiments, the digital data processor computes the operating parameters via optimizing a figure-of-merit associated with the measurement of one or more target analytes of interest. By way of example, the operating parameter(s) can include, e.g., a rate at which a filter associated with the analytical device is scanned.

[0048] With continued reference to FIG. 2, the analytical device can further include a controller 208 that can receive the operating parameters and can effect the operation of the analyte measurement module at the computed operating parameters. In some embodiments, the analyte measurement module 202 can include multiple components, each of which can provide certain functionality. For example, in some cases in which the analyte device is a mass spectrometer, the measurement module may include a mass filter, an ion dissociation device and a mass analyzer. The operating parameters can be utilized to operate one or more of such components. For example, as discussed in more detail below, in an LC-MS system, the operating parameters can be applied to a mass filter of an LC-MS system.

[0049] A data processing module 210 can receive measurement data generated by the analyte measurement module and process the measurement data to generate information regarding 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.

[0050] The analytical device can be a variety of analytical devices. Some examples include, without limitation, a mass spectrometry system, e.g., an LC-MS system, mass spectrometry systems that employ any of flow injection, acoustic energy, and laser radiation for introduction of a sample into an ion source of a mass spectrometer. Other examples include mass spectrometry systems that employ separation devices such as an ion mobility spectrometer, before introducing a sample into an ion source.

[0051] In some embodiments, the present teachings can be employed for performing LC-MS measurements, e.g., LC coupled to tandem mass spectrometry. By way of example and withreference to the flow chart of FIG. 3, in one embodiment, a method for performing LC-MS is disclosed in which a digital data processor is utilized to process one or more input parameters, including a temporal width associated with an LC peak of an eluate exiting an LC column of an LC-MS system and a pulse frequency associated with operating a time-of-flight mass analyzer of the MS system, to compute one or more operating parameters of a mass filter of the MS system, including an m / z width of a bandpass window of the mass filter (i.e., the m / z range of ions that are allowed to pass through the mass filter) and a rate for scanning the bandpass window in the m / z dimension (e.g., a temporal rate at which the lower and the upper m / z bounds of the bandpass window of the mass filter are varied) during data acquisition, e.g., during data acquisition when the LC-MS system is being operated in a DIA mode.

[0052] A controller is configured to effect the operation of the mass filter based on the computed operating parameter(s). For example, the digital data processor can be in communication with the controller to transmit the computed operating parameters associated with the mass filter to the controller and the controller can generate control signals for effecting the operation of the mass filter at the computed operating parameters. While in some embodiments the digital data processor and the controller can be implemented as two separate units, in other embodiments the controller can incorporate the digital data processor for processing the input parameters and can further include circuitry for generating control parameters for controlling the operation of the mass filter.

[0053] With continued reference to the flow chart of FIG. 3, a sample is introduced into the LC column and the eluate exiting the LC column is directed to an ion source, which ionizes one or more analytes in the sample to generate a plurality of precursor ions. The precursor ions are introduced into the mass filter, which is positioned downstream of the ion source, where the mass filter is configured to allow passage of target precursor ions having m / z ratios within a bandpass window of the mass filter. The ions passing through the mass filter are introduced into an ion dissociation device in which they undergo dissociation to generate a plurality of product ions. The product ions are in turn introduced into a time-of-flight (TOF) mass analyzer, which generates ion detection data associated with the product ions.

[0054] By way of example, in some embodiments, the digital data processor can compute the m / z width of the bandpass window of the mass filter and the scanning rate of the bandpass window in m / z dimension according to the following the relations, which extend the above Eqs. (l) - (6).

[0055] The ion detection can generally follow a Poisson process. Considering Poisson process and 95% confidence interval, the upper bound of the minimum at which ions are incident on the ion detector minlonRateUpperBound) can be obtained via the following relation: mini onRateUpper Bound = minlonRatePerCycle + 1.96

[0056] The parameters minlonRatePerCycle andNQlpulsesminIonRatePerCycieare defined above.

[0057] By way of example, in various embodiments, the upper bound of the ion rate estimate can be selected to be 20%, which results in the following relations using the above Eqs. ( 1 )-(7): 0.2 Eq. (8)96.04 minlonRatePerCycle , minlonRatePerCycle Eq. (9)

[0058] The above relations Eq. (9) and Eq. (10) can be utilized to compute the m / z width of the bandpass window of a quadrupole mass filter for a target 95% confidence limit for the rate of ion detection. The rate of scanning the bandpass window of the mass filter can be determined using the above Eq. (3).

[0059] The present teachings can be incorporated in a variety of mass spectrometers, including those mass spectrometers that are configured to be operated in a DIA mode. By way of example, and without limitation, FIG. 4 schematically depicts an LC-MS spectrometry system 400 that includes a liquid chromatography (LC) column 401 that can receive a specimen and anion source 403 that is in communication with the LC column 401 to receive an eluate exiting the LC column. The ion source can ionize one or more analytes within the received eluate to generate a plurality of ions that can be received by an ion guide, for example a Q Jet ion guide, via an orifice 402 of the mass spectrometer, where the QJet ion guide 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 radio frequency fields to cause focusing of the ions. The ions exiting the QJet ion guide are received by an ion guide Q0 that includes a set of quadrupole rods 404, two of which 404a / 404b are visible in the figure, to which RF voltages can be applied for causing radial confinement of the ions and generate an ion beam that is in turn received by an ion mass filter QI. The ion guides QJet, Q0, and the mass filter QI are disposed in differentially-pumped chambers that are maintained at progressively lower pressures.

[0060] An ion lens IQ0 focuses the ions exiting the Q0 ion guide into the mass filter QI. The mass filter QI includes a stubby lens 406 that includes a set of quadrupole rods (two of which 406a / 406b are visible in the figure) to which an RF field can be applied to cause focusing of the ions. The mass filter QI further includes a set of quadrupole rods 410, two of which 410a / 410b are visible in the figure, to which a combination of RF and DC voltages can be applied to allow the selection of one or more precursor ions, e.g., all precursor ions of interest when the mass spectrometer is operating in a DIA mode, having m / z ratios within a target m / z range for transmission to a downstream ion dissociation device Q2, e.g., a collision cell in this example via an ion lens IQ2.

[0061] In this embodiment, the collision cell Q2 includes a set of rods 417, two of which 417a / 417b are visible in the figure, that are arranged in a quadrupole configuration and is pressurized via introduction of nitrogen gas to allow collisional fragmentation of the ions received by the collision cell Q2.

[0062] The ions exiting the cell Q2 are focused by a set of ion focusing optics 415 into a time-of-flight (ToF) mass analyzer 418, which can provide mass analysis of those ions. More specifically, the ToF mass analyzer 418 can include a deflection electrode 419 to which pulsed voltages can be applied to direct the received ions into a field-free ion drift region through which the ions pass to be incident on an ion detector 420 of the mass analyzer. The ion detectionY1signals generated by the ion detector can be processed using a data processing module 425 to generate the mass spectrum of the product ions.

[0063] With continued reference to FIG. 4, a DC voltage source 426 and an RF voltage source 428 operating under control of a controller 430 can apply RF and DC voltages to the mass filter QI in a manner known in the art and as informed by the present teachings to configure the bandpass window of the mass filter. By way of example, and without limitation, the RF voltage applied to the rods of the QI mass filter can have a frequency in a range of about 200 kHz to about 1 MHz and a peak-to-peak amplitude (Vpp) in a range of about 100 volts to about 10 kilovolts (kV). In various embodiments, an applied DC resolving voltage can be adjusted to change the m / z width of the bandpass window of the mass filter.

[0064] More specifically, in this embodiment, a digital data processor 425, which is in communication with the controller 430, can receive a plurality of input parameters, such as those discussed above, and can process the input parameters to generate a plurality of operating parameters, which include an m / z width of the bandpass window of the mass filter and a rate for scanning the bandpass window. The digital data processor 425 can transmit the operating parameters to the controller, which can in turn send control signals to the RF and DC voltage sources so as to effect the operation of the mass filter in accordance with the computed operating parameters.

[0065] When operating in a DIA mode, the controller can be programmed in accordance with the present teachings to set the bandpass window of QI mass filter to allow passage of ions within a target m / z range, e.g., in accordance with Eq. (3) above. Also, the controller can send control signals to the RF and the DC voltage sources to cause a scan of the bandpass window of the QI mass filter at a desired rate, e.g., in accordance with Eq. (1) above, e.g., during DIA.

[0066] By way of further illustration, FIG. 5 is a schematic representation of acquisition of data in a DIA mode by scanning the bandpass window of a quadrupole mass filter (e.g., the QI quadrupole mass filter discussed above) within a single measurement cycle, and at a single collision energy (CE), while maintaining the m / z width of the mass filter constant. For simplicity, the quadrupole mass filter is referred to herein as the QI filter. The ion measurementis depicted in a 3-dimensional space with the following dimensions: (ToF pulse precursor mass, measured ion m / z, and intensity).

[0067] In FIG. 5, the quadrupole mass filter is represented by finite-length horizontal lines, which indicate the m / z width of the mass filter’s bandpass window. The continuous scanning of the bandpass window of the quadrupole mass filter is represented by the horizontal lines moving diagonally from top left corner (low precursor m / z, first TOF pulse) to the bottom right corner (high precursor m / z, last ToF pulse). The measured ions at different m / z values in each ToF pulse will correspond to the product ions and any residual precursor ions arriving at the ToF analyzer when the pulse is applied. To simplify the graph, only a few ToF pulses are drawn between the first and the last opportunity to observe an ion fragment generated via dissociation of a precursor ion. For each annotated pulse, single ToF pulse spectrum is represented by diagonal lines, which sum up to a measurement cycle spectrum that is represented by the diagonal axis labeled as Fragment m / z.

[0068] TOF pulse index and the QI filter start / stop m / z are correlated. For this illustrative example, it is assumed that the filter’s m / z width is constant and the dependence of QI start / stop m / z on ToF pulse is linear.

[0069] In general, the composition of a precursor mixture (and corresponding ion fragments) changes continuously along the TOF-pulse dimension, although most precursor ions are the same between consecutive TOF pulses. For simplicity, in this example, it is assumed that a single precursor P is present in the sample, which in turn generates two ion fragments, where the less abundant ion fragment is depicted as solid circles and the more abundant ion fragment is depicted as open circles. Starting from TOF pulse p and concluding with ToF pulse q, the precursor ion P is transmitted by the QI mass filter having a bandpass window with an m / z width of Q. Ion fragments are generated according to a probability density function and are passed through the TOF path. Ion drift time from a corresponding ToF pulse is equivalent to m / z for each detected ion and is recorded as MS2 single-ToF pulse spectrum, represented as diagonal mz-lines - MS2 m / z in this case.

[0070] In general, a precursor ion will be transmitted through the QI mass filter for a number of consecutive ToF pulses. If an ion m / z intensity is plotted across the ToF pulses, the m / zvalues of the precursor ion and all its fragments will resemble the rectangular-pulse-like trace (QIT), where the pulse-like shape is associated with off-on-off precursor ion transmission probability as defined by QI start / stop mass. In a simple case in which only one precursor ion is present at a given LC cycle, non-zero ion detection intensity is possible for the first time at a ToF pulse at which QI mass filter allows the passage of the precursor ion for the first time (in this illustrative example, the QI mass filter’s upper bound is equal to m / z of the precursor ion of interest; in other words, Ql-line terminates at the precursor ion m / z) up to a ToF pulse where the QI filter’s lower bound is equal to the m / z of the precursor ion of interest (i.e., the last chance for the precursor ion to pass through the QI filter; in other words, the QI line begins at the m / z of the precursor ion).

[0071] The diagram shows that the more abundant ions (i.e., ions represented as open circles) are generated and recorded in every ToF pulse while the less abundant ions (i.e., ions represented as solid circles) are recorded in only a few of the ToF pulses corresponding to precursor P “visible” time window. Despite the counting noise associated with Poisson process of ion detection, the QIT corresponding to more abundant ion resembles an expected rectangular QIT pulse. MS spectrum for one measurement cycle is a sum of all individual ToF pulse spectra and is annotated as the bottom diagonal axes with two schematic peak shapes.

[0072] Various digital data processors and controllers utilized in the practice of the present teachings, such as those discussed above, can be implemented using software, firmware, and hardware in a manner known in the art and as informed by the present teachings. By way of example, FIG. 6 schematically depicts an example of implementation 600 of the above digital data processor 432 having a digital processing unit 602 that can communicate via one or more communications buses 603 with a random-access memory (RAM) module 604 and a permanent memory module 605. By way of example, various instructions for processing the input parameters to compute the operating parameter(s) for operating the mass filter can be stored in the permanent memory 605 module and can be transferred to the RAM module 604 by the processing unit 602 during runtime for execution. By way of example, the instructions stored on the digital data processor can be based on the relations discussed above for computing the m / z width of a bandpass window of a mass filter of an LC-MS system and a scanning rate thereof.However, as noted above, the present teachings are not restricted to LC-MS systems and can be applied to the operation of other analytical devices.

[0073] The following example is provided for further elucidation of various aspects of the present teachings and is not intended to be necessarily indicative of optimal ways of practicing the present teachings and / or optimal results that can be obtained.

[0074] Example

[0075] FIG. 7 shows an example of the number of ToF pulses corresponding to 95% confidence interval as a function of logarithm of the minimum ion rate incident on the ion detector of the ToF mass analyzer per measurement cycle (minlonRatePerCycle). In other words, the Y-axis indicates the minimum number of ToF pulses during which precursor m / z is “visible” per cycle to enable 95% confidence in estimating the ion rate (ion rate on X-axis).

[0076] Assume that an LC peak associated with an eluate exiting an LC column of an LC- MS system has a temporal duration characterized by PWHH = ~ 3 seconds. In order to have a sufficient number of sample points across the LC peak (typically a minimum of 3 points), the duration of a measurement cycle can be selected to be about 1 second. Based on the assumption that the precursor ions of interest have m / z ratios in a range of 400 to 900 Da and a pulse frequency of 10 kHz (i.e., the frequency of voltage pulses applied to the deflector 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 the given pulse frequency), using the above Eq. (5) the minimum number of ToF pulses (i.e., voltage pulses applied to the deflector electrode of the mass analyzer) can be calculated to be 960 for 0.1 ions per cycle. Substituting the calculated minimum number of ToF pulses in Eqs. (10) and (3), the m / z width of the bandpass window of the QI mass filter for 95% confidence interval can be calculated to be: 960 = ~53 Da

[0077] Further, the rate of scanning of the bandpass window of the QI mass filter (i.e., QI speed) can be calculated as:Qlfspee ) = 553 0.553 Da per ToF pulse

[0078] Although some aspects have been described in the context of a system and / or an apparatus, it is clear that these aspects also represent a description of the corresponding method, where a block or device corresponds to a method step or a feature of a method step.Analogously, aspects described in the context of a method step also represent a description of a corresponding block or item or feature of a corresponding apparatus. Some or all of the method steps may be executed by (or using) a hardware apparatus, like for example, a processor, a microprocessor, a programmable computer or an electronic circuit. In some embodiments, some one or more of the most important method steps may be executed by such an apparatus.

[0079] Depending on certain implementation requirements, embodiments of the invention can be implemented in hardware and / or in software. The implementation can be performed using a non-transitory storage medium such as a digital storage medium, for example a floppy disc, a DVD, a Blu-Ray, a CD, a ROM, a PROM, and EPROM, an EEPROM or a FLASH memory, having electronically readable control signals stored thereon, which cooperate (or are capable of cooperating) with a programmable computer system such that the respective method is performed. Therefore, the digital storage medium may be computer readable.

[0080] Those having ordinary skill in the art will appreciate that various changes can be made to the above embodiments without departing from the scope of the present teachings.

Claims

What is claimed is:

1. A method of operating an analytical device for measuring at least one analyte within a sample, comprising: utilizing a digital data processor to: receive a sample acquisition rate for introduction of the sample into the analytical device, and compute a plurality of optimal operating parameters of the analytical device based on the sample acquisition rate by optimizing a figure-of-merit associated with measurement of the analyte, wherein the operating parameters include a temporal duration of a measurement cycle and selectivity associated with the measurement; operating the analytical device at the optimal operating parameters while receiving the sample at the sample acquisition rate to generate sample measurement data corresponding to the analyte; and processing the sample measurement data to derive information about the analyte.

2. The method of Claim 1 , wherein the information about the analyte indicates whether the analyte is present in the sample.

3. The method of any one of Claims 1 and 2, wherein the information about the analyte provides a concentration of the analyte in the sample.

4. The method of Claim 1 , wherein the figure-of-merit is defined at least partially based on at least one of a target resolution, a target minimum signal-to-noise ratio associated with the measurement data, and a target selectivity.

5. The method of Claim 1, wherein the analytical device comprises a mass spectrometry system.

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

7. An analytical device for measuring at least one analyte in a sample, comprising: an analyte measurement module for receiving the sample and generating analyte measurement data, a digital data processor configured to receive a sample acquisition rate for introduction of the sample into the analytical device and to compute optimal values of a plurality of operating parameters of the analytical device based at least in part on the sample acquisition rate by optimizing a figure-of-merit associated with measurement of the analyte, wherein the operating parameters include a temporal duration of a measurement cycle and selectivity associated with the measurement, a controller for receiving the optimal operating parameters and to configure an operational mode of the analyte measurement module based on the optimal operating parameters, and a data processing module for receiving the measurement data generated by the analyte measurement module operating in said operational mode and processing the measurement data to generate information regarding the at least one analyte.

8. The analytical device of Claim 7, wherein the figure-of-merit is defined at least partially based on at least one of a target resolution, a target minimum signal-to-noise ratio associated with the measurement data, and a target selectivity.

9. The analytical device of any one of Claims 7 and 8, wherein said analytical device comprises a mass spectrometry system, and wherein optionally said mass spectrometer comprises an LC-MS system.

10. The analytical device of Claim 9, wherein said mass spectrometry system is configured to operate in a data independent acquisition (DIA) mode.

11. The analytical device of Claim 9, wherein said mass spectrometry system comprises: 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 positioned downstream from said ion source for receiving the plurality of ions and allowing passage of ions having m / z ratios within its bandpass window; an ion dissociation device for receiving the ions passing through the mass filter and causing dissociation of at least a portion thereof to generate a plurality of product ions; and a mass analyzer positioned 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 mass detection data associated with the product ions, wherein said operating parameters comprise an m / z width of a bandpass window of the mass filter and at rate at which the bandpass window is scanned during data acquisition, and wherein the digital data processor is configured to compute the optimal values of the operating parameters based on said data acquisition rate, an m / z range associate with precursor ions of interest.

12. The analytical device of Claim 11, wherein said mass analyzer includes a time of flight (TOF) mass analyzer.

13. The analytical device of Claim 12, wherein the data acquisition rate of the TOF mass analyzer is determined based on a pulse frequency associated with voltages applied to a reflector electrode of the TOF mass analyzer.

14. A mass spectrometry system, comprising: an ion source for receiving a sample and ionizing one or more analytes therein to generate a plurality of ions; a mass filter positioned downstream from said ion source for receiving the plurality of ions and allowing passage of ions having m / z ratios within its bandpass window; an ion dissociation device for receiving the ions passing through the mass filter and causing dissociation of at least a portion thereof to generate a plurality of product ions; a mass analyzer positioned downstream of the ion dissociation device to receive the plurality of product ions and provide mass detection data associated with the product ions; a digital data processor configured to receive one or more input parameters including a sampling period, an m / z range associated with precursor ions of interest, and a data acquisition rate associated with the mass analyzer and computing one or more operating parameters including a bandpass window of the mass filter and a rate of scanning of the bandpass window in m / z dimension; and a controller in communication with said digital data processor for receiving the operating parameters and configuring the mass filter to operate based on said computed operating parameters.

15. The mass spectrometry system of Claim 14, wherein the digital data processor is configured to compute the scanning rate of the bandpass window in m / z dimension according to the following relation:wherein, denotes the scanning rate of the bandpass window in unitsof Dalton per second, maxPrecursor _mz denotes maximum m / z ratio of the m / z range associated with the precursor ions, minPrecursor jnz denotes minimum m / z ratio of the m / z range associated with the precursor ions, andTcyde denotes LC sampling time.

16. The mass spectrometry system of Claim 15, wherein Tcycie is defined in accordance with the following relation:PWHH (second) Tcycie = - - - wherein,PWHH denotes a temporal width corresponding to half maximum of the LC peak, andN is an integer.

17. The mass spectrometry system of Claim 16, wherein the digital data processor is configured to compute an m / z width of the bandpass window of the mass filter according to the following relation:wherein,Qlwidth(Da) denotes the m / z width of the bandpass window in units of Dalton, denotes the rate at which the bandpass window is scanned inunits of Dalton per TOF pulse, denotes the rate at which the bandpass window is scanned in unitsof Dalton per second,NQlpulsesminionRateperCyCiedenotes the number of TOF pulses per measurement cycle for a minimum ion rate per cycle.

18. The mass spectrometry system of Claim 16, wherein N QlpulsesminionRateperCycieis defined according to the following relation:wherein minlonRatePerCycle denotes a minimum rate at which ions are incident on the TOF detector.

19. The mass spectrometry system of Claim 18, wherein minlonRatePerCycle is defined according to the following relations: minlonRatePerCycle > -Tcycle- pulse frequency20. The mass spectrometry system of any one of Claims 14 - 19, wherein further comprising a separation device positioned upstream of said ion source, wherein the separation device optionally comprises any of an LC column, an ion mobility spectrometer, .

21. The mass spectrometry system of Claim 20, wherein said sampling period is at least a fraction of an elution time of the sample from the LC column.

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