System and method of processing mass spectrometric data

Abstract

In one aspect, a method of processing mass spectrometric data is disclosed, which includes using a multi-channel ion detection system comprising n multiple independent channels to receive ions, wherein each of the channels generates an independent output signal associated with an ion detection period, identifying an ion detection event as corresponding to a single ion detection based on a predefined pattern of the output signals associated with the ion detection period, where the output signals are generated substantially concurrently.

Description

Attorney Ref. No. 4277-0426WO01SYSTEM AND METHOD OF PROCESSING MASS SPECTROMETRIC DATA RELATED APPLICATIONS

[0001] This application claims priority to, and the benefit of, U.S. Provisional Application No. 63 / 737,865 filed on December 23, 2024 and U.S. Provisional Application No. 63 / 806,312 filed on May 15, 2025, the contents of both of which are incorporated herein by reference in their entireties.TECHNICAL FIELD

[0002] The present disclosure relates generally to (A) mass spectrometry, and in particular to (B) methods and / or (C) systems for processing mass spectrometric data, and much more in particular to ion events generated by an ion detector, e.g., an ion detector employed in a time-of-flight (TOF) mass spectrometer.BACKGROUND

[0003] Mass spectrometry (MS) is an analytical technique for determining the structure of 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, so a conversion of the analytes to charged ions must occur.

[0004] In a mass spectrometer, an ion detector is utilized to detect ions and to generate ion detection signals in response to such ion detections. By way of example, in a time-of-flight (TOF) mass spectrometer, ions received by a TOF mass analyzer are (A) directed via application of a voltage to a pusher electrode of the mass analyzer to a drift region of the mass spectrometer and (B) detected by an ion detector after passage through the drift region.14922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01

[0005] For a given ion detection event (ion detection signal), there is typically a need to determine the number of ions associated with that ion detection event, e.g., to quantify a target analyte of interest in a sample under analysis.SUMMARY

[0006] In one aspect, a computer-processing method of directing a computer system to process mass spectrometric data is disclosed, where the computer-processing method includes receiving n multiple, independent output signals associated with an ion detection period and generated by a multi-channel ion detection system associated with a mass analyzer of a mass spectrometer. The multi-channel ion detection system includes n multiple, independent channels configured to receive and detect ions, wherein each of the n multiple independent channels is configured to generate an independent ion detection signal in response to incidence of one or more ions received by each of the n multiple, independent channels. The method further includes processing the received output signals to identify an ion detection signal corresponding to a single ion detection event based on a predefined pattern of the received independent output signals.

[0007] In various embodiments, the multiple, independent ion detection signals are generated substantially concurrently.

[0008] In various embodiments, an output signal indicates an ion detection event in the case where its amplitude exceeds a predefined threshold. Other criteria for classifying an output signal as an ion detection event may also be utilized. By way of example, an output signal extending over a temporal period can be integrated and the integrated value can be compared with a predefined threshold to determine whether or not the output signal indicates an ion detection event, e.g., if the integrated value exceeds a predefined threshold, it can be considered as corresponding to an ion detection event.

[0009] In various embodiments, an ion detection event is identified as a single ion detection event for the case where only one of the received independent output signals indicates an ion detection event.

[0010] In various embodiments, an estimated error associated with identification of the ion detection event corresponding to a single ion detection event can be computed. By way of 24922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01example, the estimated error can be computed via the application of Poisson statistics to the ion detection event.

[0011] By way of example, and without limitation, the number of n multiple independent ion detection channels can be two (2), four (4), or any number of independent channels that can be provided by an ion detector of a mass analyzer.

[0012] In various embodiments, the n multiple independent ion detection channels correspond to ion detection channels of an ion detector of any one of a TOF mass analyzer and an electrostatic trap analyzer.

[0013] In a related aspect, a computer-processing method of directing a computer system to process ion-detector data is disclosed, which includes reading said ion-detector data generated by an ion detector associated with a mass analyzer of a mass spectrometer, said ion detector including a single ion detection channel configured to receive and detect ions associated with a plurality of ion pulses, and processing said ion-detector data to identify an ion detection event contained in said ion-detection data, said ion detection event being associated with an ion pulse of a plurality of temporally consecutive ion pulses, as corresponding to a single ion detection event for the case where no ion detection event is generated by remaining pulses of said plurality of temporally consecutive ion pulses.

[0014] In various embodiments of the above computer-processing method, the ion detector can be incorporated with any one of a TOF mass analyzer and an electrostatic trap mass analyzer.

[0015] In various embodiments of the above computer-processing method, the plurality of temporally consecutive ion pulses is generated via application of a plurality of temporally consecutive voltage pulses to a pusher electrode of a TOF mass analyzer.

[0016] In various embodiments of the above computer-processing method, an estimated error associated with the identification of the ion detection event as a single ion detection event can be computed. By way of example, and without limitation, a subset (a number) of the plurality of consecutive ion pulses and Poisson statistics can be utilized to compute the estimated error.34922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01

[0017] In a related aspect, a method of performing mass spectrometry is disclosed, which includes introducing, into a mass analyzer of a mass spectrometer, one or more ions or fragment ions thereof corresponding to one or more target analytes, said ions being generated in response to ionization of a sample, generating, by using an ion detector associated with said mass analyzer, a plurality of output signals by a multi-channel ion detection system of the ion detector, and transmitting, to a computer system including a processor, the output signals generated by said multi-channel ion detection system of said ion detector. The computer processing system is configured to process the output signals to identify an ion detection event corresponding to a target ion as a single ion detection event for the case where: one of said output signals generated by one channel of said multi-channel ion detection system provides indication of an ion detection event, and remaining channels of said multi-channel ion detection system provide indication of no ion detection event.

[0018] In various embodiments of the above method, the mass analyzer can include any one of a TOF mass analyzer and an electrostatic trap mass analyzer.

[0019] In various embodiments of the above method, the one or more output signals are generated using a data independent acquisition method, such as a SWATH acquisition method.

[0020] In various embodiments of the above method, the plurality of output signals is generated substantially concurrently by the ion detection channels of the multi-channel ion detection system.

[0021] In a related aspect, a mass spectrometer is disclosed, which includes a mass filter configured to be in communication with an ion source, said ion source being configured to receive a sample and ionize one or more analytes in the sample to generate sample ions and fragment ions thereof. The mass filter is positionable downstream of the ion source, and the mass filter is also configured to receive the sample ions and configured to allow passage of at least a portion of the sample ions and the fragment ions thereof having m / z ratios in a desired range. The mass spectrometer further includes an ion dissociation device being positioned downstream of the mass filter, the ion dissociation device configured to receive the sample ions and the fragment ions thereof passing through the mass filter and also configured to cause dissociation thereof to generate a plurality of product ions. The mass spectrometer further includes a mass analyzer with an ion detector configured to generate ion detection signals in 44922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01response to detection of the plurality of product ions that were generated by said ion dissociation device. The mass analyzer is configured to transmit, either directly or indirectly, to an analysis module, which is configured to be either directly or indirectly in communication with the mass analyzer, the ion detection signals that were generated, and the analysis module is configured to determine whether any of the ion detection signals corresponds to a single ion detection event.

[0022] In various embodiments of the above mass spectrometer, the ion detector includes n multiple, independent ion detection channels, where each of the channels of such n multiple, independent ion detection channels is configured to generate an independent output signal during a common ion detection period.

[0023] In various embodiments, the analysis module can be configured to identify an ion detection event as corresponding to a single ion detection event based on a predefined pattern of independent output signals generated substantially concurrently by the n multiple independent ion detection channels.

[0024] In various embodiments of the above mass spectrometer, the ion detector can include a single ion detection channel and the analysis module can be configured to identify an ion detection event associated with one of a plurality of temporally consecutive ion pulses as a single ion detection event when no ion detection event is generated by other pulses of the plurality of temporally consecutive ion pulses.

[0025] In a related aspect, a mass spectrum formed by a mass spectrometer according to various embodiments of the present teachings, such as those described herein, is disclosed.

[0026] In yet another related aspect, a unit of chemical designed and manufactured in accordance with information obtained from a mass spectrum formed by a mass spectrometer according to various embodiments of the present teachings is disclosed. The mass spectrum, obtained through mass spectrometry, is configured to provide information used to identify and design a chemical. While the obtained mass spectrum does not directly make a chemical, it provides vital information that helps chemists create or analyze compounds. The information contained in or provided by the mass spectrum may be used as follows: (A) Molecular Composition: the mass spectrum reveals the molecular weight of a compound and its individual fragments. This helps chemists verify the composition of the chemical they are trying to make or54922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01identify unknown substances. (B) Structural Information: by analyzing the fragmentation pattern in the mass spectrum, chemists can infer how atoms are arranged within a molecule. This insight is essential for understanding and designing the structure of a chemical. (C) Purity Assessment: mass spectrometry detects impurities in a chemical sample. Before making a compound, chemists ensure the precursors are pure using this method. (D) Reaction Monitoring: during synthesis, the mass spectrum can be used to track intermediates and confirm that reactions are proceeding as planned. (E) Quantification: by comparing the intensity of signals in the spectrum, chemists can quantify the amount of a compound in a sample, ensuring they use the correct proportions during chemical synthesis.

[0027] In one aspect, a method of processing mass spectrometric data is disclosed, which includes using a multi-channel ion detection system comprising n multiple, independent channels to receive ions, wherein each of the channels generates an independent ion detection signal in response to incidence of one or more ions thereon, and identifying an ion detection event as corresponding to a single ion detection event based on a predefined pattern of ion detection signals generated substantially concurrently by said multiple, independent channels in response to an ion detection event.

[0028] In various embodiments, the ion detection event is identified as a single ion detection event for the case where one of said n ion detection channels indicates an ion detection event and the other ion detection channels indicate no ion detection event. By way of example, the n multiple channels can include more than two (2) channels, such as four (4) channels.

[0029] In various embodiments, an ion signal associated with an ion detection channel can be considered as corresponding to an ion detection event for the case where the ion signal intensity (e.g., the signal level generated by an ADC) is greater than a predefined threshold.

[0030] In various embodiments, an error associated with the determination that an ion detection event is a single ion detection event can be computed. By way of example, and without limitation, in various embodiments, Poisson statistics may be employed for computing the error.

[0031] In various embodiments, the present teachings can be utilized at a variety of ion count rates, i.e., ion count per unit time. In particular, in various embodiments, the present teachings64922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01can provide distinct advantages for the case where the ion count rate is less than about 30 events in accumulation period (scan) which can be made up of, e.g., more than 100 pulses or chances for observation. At such low ion count rates, all ion arrivals are likely single ion events and the total number of events is not enough to average out the analog-to-digital noise which could yield ion intensity measurements with poor intensity accuracy and make it more difficult to discriminate the signal from the noise in the final spectrum.

[0032] In various embodiments, the multiple, independent channels correspond to ion detection channels of an ion detector of a TOF mass analyzer.

[0033] In various embodiments, the ion detection signals can be generated via acquisition of the mass spectrometric data in a data independent acquisition (DIA) mode, such as a SWATH (Sequential Windowed Acquisition of all Theoretical Mass Spectra) data acquisition mode.

[0034] In other embodiments, the ion detection signals can be generated via trapping a plurality of ions in an ion trap positioned upstream of a TOF mass analyzer and releasing the ions, e.g., in a mass-dependent manner, for detection via the TOF mass analyzer. In yet other embodiments, the ion detection signals can be generated in a multiple reaction monitoring (MRM) data acquisition mode.

[0035] The methods for processing mass spectrometric data according to the present teachings can be performed at runtime (e.g., during data acquisition) or subsequent to the acquisition of the mass spectrometric data.

[0036] In a related aspect, a method of processing mass spectrometric data is disclosed, which includes using an ion detector including a single ion detection channel to receive ions associated with a plurality of ion pulses, and identifying an ion detection event corresponding to a target ion and associated with an ion pulse of a plurality of temporally consecutive ion pulses as corresponding to a single ion detection event corresponding to that target ion for the case where no ion detection event corresponding to that target ion is generated by any of the other pulses of said plurality of temporally consecutive ion pulses.

[0037] In various embodiments, the ion detector can be an ion detector of any of a TOF mass analyzer or an electrostatic trap analyzer. By way of example, the ion pulses can be generated via application of a plurality of voltage pulses applied to a pusher electrode of a time-of-flight 74922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01mass analyzer to direct at least a portion of ions received by the mass analyzer toward an ion detector thereof. In some such embodiments, a trigger signal can be applied to the ion detector in response to the application of a voltage pulse to the pusher electrode to initiate collection of ion signal data by the ion detector during a given time interval. In some such embodiments, an ion signal event detected by the ion detector during one of a plurality of such time intervals can be classified as a single ion detection event for the case where no ion events are detected in the other time intervals of said plurality of time intervals.

[0038] In a related aspect, a method of performing mass spectrometry is disclosed, which includes ionizing a sample to generate one or more ions corresponding to one or more target analytes, using an ion detector of a mass analyzer to detect one or more ion detection events corresponding to said ions or fragment ions thereof, said mass analyzer including a multi-channel ion detection system, a processor receiving ion detection signals generated by said channel of the multi-channel ion detection system and identifying an ion detection event detected by said multiple channels as a single ion detection event for the case where one of said channels indicates an ion detection event and the other channels indicate no ion detection event.

[0039] In a related aspect, a mass spectrometer is disclosed, which includes an ion source configured to receive a sample and ionize one or more analytes in the sample to generate sample ions. A mass filter can receive the sample ions and can be configured to allow passage of sample ions having desired m / z ratios while inhibiting the passage of other sample ions. In some embodiments, an ion dissociation device can receive the sample ions passing through the mass filter and can cause the dissociation of those sample ions to generate a set of product ions. The mass spectrometer can further include a mass analyzer, e.g., a TOF mass analyzer, that can receive the product ions and generate ion detection signals. An analysis module in communication with the mass analyzer can receive the ion detection signals and process those signals in accordance with the present teachings to identify single ion events.

[0040] In a related aspect, a computer-readable medium is disclosed, which stores instructions for executing a method for processing mass spectrometric data for identifying single ion detection events in accordance with various embodiments of the present teachings.

[0041] In yet another related aspect, a computer system is disclosed that includes computer-usable memory tangibly storing computer-executable code configured to execute a method for 84922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01processing mass spectrometric data according to various embodiments of the present teachings, such as those discussed herein.

[0042] Further understanding of various aspects of the present teachings can be obtained by reference to the following detailed description in conjunction with the associated drawings, which are described briefly below.BRIEF DESCRIPTION OF THE DRAWINGS

[0043] FIG. 1 is a flow chart depicting various steps in a method according to an embodiment of the present teachings;

[0044] FIG. 2 is a flow chart depicting various steps for performing a method according to an embodiment of the present teachings;

[0045] FIG. 3 is a flow chart depicting various steps for performing a method according to an embodiment of the present teachings;

[0046] FIG. 4 is a flow chart depicting various steps for performing a method according to another embodiment;

[0047] FIG. 5 schematically depicts a mass spectrometer according to an embodiment of the present teachings;

[0048] FIG. 6 schematically depicts an example of an implementation of an analysis module employed in the mass spectrometer shown in FIG. 5;

[0049] FIG. 7 shows examples of plots corresponding to the probability of detecting no ion signals on 3 channels of a 4-channel ion detection system;

[0050] FIG. 8 shows an example of lost ion counts as a function of ion rate; and

[0051] FIG. 9 shows an example of lost ion counts as a function of ion rate on inner channels and the outer channels of a 4-channel ion detection system.DETAILED DESCRIPTION

[0052] 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 details94922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01wherever 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.

[0053] 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 mean 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.

[0054] 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

[0055] As noted above, in mass spectrometry, it is generally desired to determine the number of ions associated with an ion detector event (signal). It is, however, challenging to discriminate between single-ion and multiple-ion detection events. In particular, ion detector pulses generated in response to the detection of single-ion events can exhibit a wide range of pulse height distributions. In cases in which a large number of ions is detected, the errors caused by such variations can be averaged out. For example, the ion detector signals associated with a large number of TOF (Time-of-Flight) pushes can be averaged to reduce such errors.

[0056] However, for low intensity signals, such approaches are not generally suitable.104922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01

[0057] The detection of ions includes discrete time events, that is, only an integer number of ions can strike an ion detector to generate an ion detection event. Single ion strikes can produce a range of ion detection signal amplitudes realized from the amplification stage of an ion detector (e.g., a multi-channel photomultiplier (MPC)). The distribution of single ion amplitudes can be affected by a variety of factors, such as the depth to which the ion penetrates the photomultiplier tube. In particular, the deeper the ion travels down the photomultiplier tube before striking its surface, the smaller will be the avalanche cascade. Another factor is the geometry and charge of the molecule, which can affect the probability of generating a second electron initiating the cascade. Further, multiple ion strikes can produce a range of signal amplitudes that can overlap those generated by single ion strikes or other multiple ion strikes.

[0058] In TOF mass spectrometers, for the case where the TOF pulse rate is high, most ion detection events correspond to single ion strikes. In such a regime, a time digital converter (TDC) can function accurately. Analog digital converters (ADC) can, however, be noisy at low ion count rates (ions counts per unit time), and hence can render the discrimination between single or low multiple ion events (e.g., double ion events) difficult or impractical.

[0059] For intense ion count rates e.g., an ion count rate of at least l / 3rfof the frequency of pulses applied to a pusher electrode of the TOF mass analyzer, there is a higher probability that ion detection events would correspond to multiple ion strikes for a given TOF push. In such a high ion count regime, ion detection statistics can lead to a confusion between single ion and multiple ion detection events. By way of example, and without limitation, about 4% of the ion detection events can correspond to double ion strikes. In such a regime, TDC can be nonlinear (e.g., the output can be 0 or 1). ADC can function accurately as noise averages out for higher ion count rates.

[0060] Preferably, intensity values corresponding to stored ion detection data provide an accurate number of ions for each ion detection event, which can frequently be a single ion of interest. This can advantageously lead to a high compression, fast spectral assembly, and ease of interpretation. By way of example, the application of Poisson statistics to ion detection events can be used to determine the probability of single ion detection events. By way of example, and without limitation, one ion detection event out of 10 chances to observe can have a very high probability of being a single ion detection event.114922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01

[0061] With reference to the flow chart of FIG. 1, in various embodiments, multiple ion detection channels (n) can be used to independently monitor an ion detection event associated with an ion type in step 102 and signals associated with such channels can be compared across the channels in step 104 to determine whether the ion detection event can be classified as a single ion detection event. For example, a pattern of presence and absence of ion detection signals across the channels can be used to classify an ion detection event monitored concurrently by multiple ion detection channels as a single ion detection event.

[0062] By way of example, and without limitation, the presence of an ion detection signal in one ion detection channel together with the absence of ion detection signals in the other ion detection channels can be used to classify the ion detection event monitored concurrently by the multiple ion detection channels as a single ion detection event. In various embodiments, an error associated with such classification of the ion detection event can be estimated based on the number of ion detection channels that are employed and modeling the probability of ion detection by each ion detection channel based on Poisson statistics.

[0063] By way of example, and without limitation, and with reference to the flow chart of FIG. 2, in an embodiment, at data acquisition time, the output signals, generated by an ADC for a single TOF pulse, are stored in a buffer independently for each of a plurality of multiple ion detection channels in steps 202 and 204. By way of illustration, and without any loss of generality, the number of independent ion detection channels is assumed to be four (4) in the following discussion. The ADC data output can be processed into (time, intensity) pairs, where the intensity may be an estimate of the number of ion strikes (i.e., an estimate of ion count).

[0064] In various embodiments, in step 206, the total ion counts for each ion type for each ion detection channel are tracked. For example, the total ion counts for a given time of flight (e.g., in the three (3) ns range) can be tracked. For a given time of flight, the ion counts associated with the various multiple channels can be compared with predefined criteria to determine whether the respective ion detection event corresponds to a single ion detection event.

[0065] By way of example, for the case where four (4) independent ion detection channels are utilized, the presence of an ion detection signal in one channel and the absence of an ion detection signal in the other channels can indicate that the ion detection signal corresponds to a single ion detection event in step 206. By way of example, the presence or absence of an ion 124922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01detection signal in each channel can be determined based on a comparison of the output of the ADC associated with that channel with one or more predefined thresholds.

[0066] Further, in various embodiments, Poisson statistics can be used to estimate an error associated with such a single ion detection determination. For example, for the case where four (4) independent ion detection channels are utilized, the probability of detecting two ions in one channel and no ions in the other channels of a set of multiple independent ion detection channels can be calculated as less than 0.5% based on Poisson statistics.

[0067] Such an approach can be utilized post-acquisition of ion detection data or at runtime.

[0068] In particular, such an approach can be applied for each TOF pulse, leading to deeper analog noise removal.

[0069] In various embodiments, a minor error (typically less than 1%) that can arise from the use of such a method for classification of ion detection events can be recovered for the case where assembling multi-pulse scan since loss becomes deterministic. Assuming the signal during the record period for an entire scan was reasonably constant, the error incurred by assigning 1 to all events which occurred on only one channel can be calculated since counts per second and the number of pulses of the scan can be used to arrive at an ion rate. Since the error estimate for the noise reduction method is a known function of the ion rate, the introduced error can be calculated.

[0070] The above method for classification of ion detection events is not restricted to the use of 4 multiple independent ion detection channels. For example, lower number of channels, such as 3, or a higher number of channels, such as 6, 8, 16, etc., can be employed. In general, as the number of independent multiple channels increases, the error associated with classification of an ion detection event based on the detection of an ion signal in only one channel decreases.

[0071] The above approach for classification of ion detection events can be utilized for processing ion detection data in a variety of different mass spectrometers. By way of example, such data processing methods can be used for processing of data generated by a TOF mass analyzer. In particular, such methods can be useful in mass spectrometers in which ions are trapped in an ion trap positioned upstream of a TOF mass analyzer, with ions being released134922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01intermittently from the trap to reach the TOF mass analyzer, e.g., due to a low rate of TOF pulses.

[0072] In a related aspect, with reference to FIG.3, a method of processing ion detection events generated by a single ion detection channel, rather than multiple ion detection channels, is disclosed in which a plurality of temporally consecutive ion monitoring intervals can be treated as separate ion detection channels. By way of example, and without any loss of generality, for a given ion type (i.e., for a given time of flight), the outputs of a single ion detection channel for a plurality of temporally consecutive TOF pulses can be considered as corresponding to the outputs of multiple independent channels for a single TOF pulse and can be stored in a buffer in steps 302 and 304. The pattern of such temporally adjacent outputs generated by the single ion detection channel can then be utilized to classify certain ion detection events as corresponding to a single ion detection, in step 306.

[0073] With reference to the flow chart of FIG. 4, in one such embodiment, an ion detector having a single ion detection channel can be utilized to receive ions associated with a plurality of ion pulses in step 402, and, in step 404, an ion detection event corresponding to a target ion (e.g., an ion having a target m / z value) and associated with an ion pulse of the plurality of temporally consecutive ion pulses can be identified as corresponding to a single ion detection event for the case where no ion detection event associated with that target ion is generated by any of the other ion pulses of the plurality of temporally consecutive ion pulses. In various embodiments, a signal generated by the ion detector can be identified as an ion detection event for the case where its intensity (e.g., as characterized by the output level of an ADC digitizing the ion signal) exceeds a threshold.

[0074] By way of example, and without loss of generality, for four (4) temporally consecutive TOF pulses, if only one of the pulses leads to an ion detection signal by the single ion detection channel, the ion detection event can be classified as a single ion detection event. Again, the number of consecutive TOF pulses that can be employed is not restricted to four (4), but a lower or a higher number of consecutive TOF pulses (e.g., 3, 8, 16, etc.) can be utilized.

[0075] By way of further illustration, in some such embodiments, at data acquisition time, all data generated by the single ion detection channel can be stored in a buffer. The output signal (e.g., estimated as total ion counts) for each ion (i.e., for a given time-of-flight, such as three (3)144922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01ns) and each pulse can be tracked. For a given ion and for n (e.g., four (4)) TOF pulses, if an ion detection event is detected for one of those pulses (e.g., no ion signal is detected for three (3) pulses and an ion signal is detected for one pulse), a single ion detection event is indicated.

[0076] Similar to the previous multi-channel approach, the error associated with such a single channel approach can be estimated based on the number of temporally consecutive TOF pluses that are employed and modeling ion detection events using Poisson statistics. For example, for the case where utilizing four (4) temporally consecutive TOF pulses, the probability of detecting two (2) ions in one pulse and no ions in the other pulses can be estimated, based on Poisson statistics. The probability is a function of real ion rate. The function has a maximum at an ion rate of 0.55, where the probability is 2.031%. The average error across all ion rates is -0.896%.

[0077] Such an approach can be applied to each pulse by considering several adjacent pulses, leading to a deeper analog noise removal. Further, similar to the previous multi-channel approach, a minor error associated with this approach can be recovered for the case where assembling multi-pulse scan since loss becomes deterministic.

[0078] Such a single channel approach can be applied during runtime or in post-processing. The postprocessing case assumes all raw data was stored.

[0079] As noted above, various embodiments of the present teachings can be used in connection with processing of data generated by a variety of mass analyzers, and in particular accurate mass analyzers, such as TOF, and electrostatic trap analyzers.

[0080] The mass correction methods and systems according to the present teachings can be incorporated into a variety of mass spectrometers. By way of example, FIG. 5 schematically depicts a mass spectrometric system 500 (herein also referred to as a mass spectrometer) according to an embodiment that includes an LC column 502 that can receive a sample and separate a plurality of analytes in the sample based on their elution times from the LC column. The mass spectrometric system 500 further includes an ion source 504 that receives an eluate exiting the LC column and ionizes one or more analytes contained in the eluate to generate a plurality of sample ions (herein also referred to as precursor ions).4922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01

[0081] In many implementations, one or more ion guides 506 receive the precursor ions and provide focusing of the ions to generate an ion beam received by a mass filter 508. By way of example, the ion guide(s) can include a plurality of rods arranged in a quadrupole configuration to which RF and DC voltages generated by a RF / DC voltage sources 510 / 512 can be applied in a manner known in the art to provide radial confinement of the received ions.

[0082] In other embodiments, an ion mobility spectrometer (IMS), such as a differential mobility spectrometer (DMS), can be utilized as a separation device to separate ions based on their mobility with the ions exiting the IMS being received by the one or more ion guides 506.

[0083] The mass filter 508 provides an ion transmission window that allows transmission of ions having m / z values within an m / z range through the mass filter. By way of example, the mass filter 508 can include a plurality of rods arranged in a quadrupole configuration to which RF voltages as well as a discriminating DC voltage can be applied via the RF / DC voltage sources 510 / 512, respectively, to generate an ion transmission window. The RF and DC voltage sources are controlled by a controller 518. In this implementation, the ions passing through the mass filter 508 are received by an ion fragmentation device 514 that causes fragmentation of the precursor ions to generate a plurality of product ions.

[0084] The product ions are received by a time-of-flight (TOF) mass analyzer 520 that detects the ions and generates ion detection signals in response to the detection of the ions. A mass analysis module 522 receives the ion detection signals from the TOF mass analyzer and processes those signals to generate a mass spectrum. Further, in various embodiments, the analysis module can be configured to perform a mass correction of the measured mass peaks in accordance with the present teachings. By way of example, the analysis module can perform such mass correction during data acquisition or post data acquisition.

[0085] In various embodiments, the data analysis module 522 according to the present teachings can be implemented in software, firmware, and / or hardware and combinations thereof. By way of example, a digital data processing system including a digital data processor, one or more random access memory modules and one or more communications buses that allow communication between various components of the system can be configured (programmed) to process ion detection data received from a multi-channel or a single-channel ion detection164922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01system and to operate on the received data in accordance with various embodiments to identify single-ion detection events (within a margin of error).

[0086] By way of example, FIG.6 is a block diagram that illustrates an example of an implementation of the analysis module as a computer system 600, which includes a bus 602 or other communication mechanism for communicating information, and a processor 604 coupled with bus 602 for processing information. Computer system 600 also includes a memory 606, which can be a random-access memory (RAM) or other dynamic storage device, coupled to bus 602 for determining base calls, and instructions to be executed by processor 604.

[0087] Memory 606 may also be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor 604. Computer system 600 can further include a read-only memory (ROM) 608 or other static storage device coupled to bus 602 for storing static information and instructions for processor 604. A storage device 610, such as a magnetic disk or an optical disk, can be provided and may be coupled to bus 602 for storing information (data) and / or computer executable instructions.

[0088] Computer system 600 may be coupled via bus 602 to a display 612, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 614, including alphanumeric and other keys, is coupled to bus 602 for communicating information and command selections to processor 604. Another type of user input device is cursor control 616, such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor 604 and for controlling cursor movement on display 612. The computer system 600 further includes a communication module 618 that allows the computer system to communicate with other devices and systems, and in particular, with a database 620.

[0089] Computer system 600 can perform the present teachings. Consistent with certain implementations of the present teachings, results are provided by computer system 600 in response to processor 604 executing one or more sequences of one or more instructions contained in memory 606. Such instructions may be read into memory 606 from another computer-readable medium, such as storage device 610. Execution of the sequences of instructions contained in memory 606 causes processor 604 to perform the process described herein. Alternatively, hard-wired circuitry may be used in place of or in combination with 174922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01software instructions to implement the present teachings. Thus, implementations of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0090] By way of example, in various embodiments, the computer system 600 can perform a method according to the present teachings. By way of example, the instructions for performing the method can be stored in the ROM 608 and can be transferred to the RAM 606 during runtime by the processor for execution.

[0091] The term “computer-readable medium” as used herein refers to any media that can participate in providing instructions to processor 604 for execution. Such a medium may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media include, for example, optical or magnetic disks, such as storage device 610. Volatile media can include dynamic memory, such as memory 606. Transmission media can include coaxial cables, copper wire, and fiber optics, including the wires that comprise bus 602.

[0092] Common forms of computer-readable media include, for example, a flexible disk, hard disk, magnetic tape, or any other magnetic medium, a CD-ROM, any other optical medium, or any other physical medium with patterns of holes, a RAM, PROM, and EPROM, a FLASH-EPROM, any other memory chip or cartridge, or any other tangible medium from which a computer can read.

[0093] Various forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to processor 604 for execution.

[0094] In accordance with various embodiments, instructions configured to be executed by a processor to perform a method according to various embodiments of the present teachings are stored on a computer-readable medium. The computer-readable medium can be a device that stores digital information. For example, a computer-readable medium may include a compact disc read-only memory (CD-ROM) as is known in the art for storing software. The computer-readable medium may be accessed by a processor suitable for executing instructions configured to be executed.184922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01

[0095] The following examples are provided for further elucidation of various aspects of the present teachings and are not provided necessarily to indicate the optimal ways of practicing the present teachings or optimal results that may be obtained.

[0096] Examples

[0097] Example 1

[0098] FIG. 7 shows plots corresponding to the probability of detecting no ion signals on three (3) channels of a 4-channel ion detection system (Plot 1), the probability of detecting an ion signal on only one channel of the 4-channel ion detection system (Plot 2), and the probability of detecting more than one ion count on a channel of the 4-channel ion detection system (Plot 3) as a function of the rate of ions incident on the ion detection system. The data was calculated from the range of ion rates and the Poisson distribution.

[0099] Example 2

[0100] As noted above, in various embodiments, a spectrum can be assembled post data acquisition from detector events and the counts for a summed peak and the ion rate can be calculated. Further, the incurred loss can be corrected based on the calculated ion rate, which is the total counts per second or area of the peak from the assembled spectra divided by the pulser frequency. Once the ion rate is known, the error loss function calculated given the number of channels, or pulses used, can be applied to correct for loss in intensity due to noise filtering. This assumes constant ion rate during the period in which the spectra were assembled.

[0101] Moreover, such a correction can also be applied to spectra assembled at run-time post scan, but prior to writing the data to a storage device (e.g., a disk).

[0102] By way of example, FIG. 8 shows lost ion counts as a function of ion rate. All of the plots were calculated at the given ion rates.

[0103] Example 3

[0104] In various embodiments in which a multi-channel ion detection system (e.g., a 4-channel ion detection system) is employed, it can be assumed that the distribution of ions incident on the different channels is substantially uniform. By way of example, in various N194922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01TOF systems in which one or more ion mirrors are employed in the ion pathway between a pusher electrode and an ion detector, such an assumption may be safe.

[0105] In other systems, the distribution of the ions on different channels of a multi-channel ion detection system may not be uniform. For example, in some cases in which an ion trap (e.g., a Zeno™ trap) is employed, a non-uniform distribution of ions across various channels may be observed.

[0106] By way of illustration, FIG.9 shows lost ion counts as a function of ion rate on inner channels (Plot labeled as Inner), the outer channels (Plot labeled as Outer) of a 4-channel ion detection system used to receive ions from a Zeno™ ion trap as well as a plot labeled Average obtained by averaging the lost counts associated with the inner and the outer channels.

[0107] The above descriptions of various implementations of the present teachings have been presented for purposes of illustration and description. It is not exhaustive and does not limit the present teachings to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from the practice of the present teachings.Additionally, the described implementation includes software but the present teachings may be implemented as a combination of hardware and software or in hardware alone. The present teachings may be implemented with both object-oriented and non-object-oriented programming systems.

[0108] Depending on certain implementation requirements, embodiments of the present teachings, the controller can be implemented in hardware, firmware and / or in software.

[0109] In some embodiments, the instructions for operating the optical system can be stored using a non-transitory storage medium such as a digital storage medium, for example 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.

[0110] While various embodiments have been illustrated and described in detail in the drawings and foregoing description, such illustration and description are to be considered illustrative or exemplary and not restrictive; embodiments of the present disclosure are not 204922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01limited to the disclosed embodiments. Other variations to the disclosed embodiments can be understood and effected by those skilled in the art in practicing embodiments of the present disclosure, from a study of the drawings, the disclosure, and the appended claims.

[0111] In the claims, the word “comprising” does not exclude other elements or steps, and the indefinite article “a” or “an” does not exclude a plurality. A single processor or other processing unit may fulfill the functions of several items recited in the claims. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measured cannot be used to advantage. Any reference signs in the claims should not be construed as limiting the scope.

[0112] 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.214922-6174-6564, v. 1

Claims

Attorney Ref. No. 4277-0426WO01Claims:

1. A computer-processing method of directing a computer system to process mass spectrometric data, said computer-processing method comprising:receiving n multiple independent output signals associated with an ion detection period and generated by a multi-channel ion detection system associated with a mass analyzer, said multi-channel ion detection system comprising n multiple independent channels configured to receive and detect ions, wherein each of the n multiple independent channels is configured to generate an independent ion detection signal in response to incidence of one or more ions received by said each of the n multiple independent channels, andprocessing said n multiple independent output signals, which were received, to identify an ion detection signal as corresponding to a single ion detection event based on a predefined pattern of said n multiple independent output signals, which were received.

2. The computer-processing method of Claim 1, wherein said single ion detection event is identified as said single ion detection event for the case where only one of said n multiple independent output signals, which were received, indicates an ion detection event.

3. The computer-processing method of Claim 2, wherein any of said n multiple independent output signals indicates said ion detection event in the case where an amplitude of a signal of said n multiple independent output signals exceeds a predefined threshold.

4. The computer-processing method of any one of Claims 2 to 3, further comprising computing an estimated error associated with identification of the ion detection event as corresponding to said single ion detection event.

5. The computer-processing method of Claim 4, wherein said step of computing the estimated error comprises applying Poisson statistics to the ion detection event.

6. The computer-processing method of any one of Claims 1 to 3, wherein said n multiple independent channels include more than two channels.

7. The computer-processing method of Claim 6, wherein said n multiple independent channels include four channels.224922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO018. The computer-processing method of any one of Claims 1 to 3, wherein said n multiple independent channels respectively correspond to ion detection channels of an ion detector of any one of a TOF mass analyzer and an electrostatic trap analyzer.

9. The computer-processing method of any one of Claims 1 to 3, wherein said n multiple independent output signals are generated substantially concurrently.

10. A method of performing mass spectrometry, comprising:introducing, into a mass analyzer of a mass spectrometer, one or more ions or fragment ions thereof corresponding to one or more target analytes, said one or more ions being generated in response to ionization of a sample,generating, by using an ion detector associated with said mass analyzer, a plurality of output signals by a multi-channel ion detection system of the ion detector, andtransmitting, to a computer system including a processor, the plurality of output signals generated by said multi-channel ion detection system of said ion detector, andwherein the computer system is configured to process said plurality of output signals to identify an ion detection event corresponding to a target ion as a single ion detection event for the case where:one of said plurality of output signals generated by one channel of said multi-channel ion detection system provides indication of said ion detection event, and remaining channels of said multi-channel ion detection system provide indication of no ion detection event.

11. The method of Claim 10, wherein said mass analyzer comprises any of a TOF mass analyzer and an electrostatic trap mass analyzer.

12. The method of Claim 10, wherein said plurality of output signals are generated using a data independent acquisition method.

13. The method of any one of Claims 10- 12, wherein said plurality of output signals is generated substantially concurrently.

14. A mass spectrometer, comprising:234922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01a mass filter configured to be in communication with an ion source, said ion source being configured to receive a sample and ionize one or more analytes in the sample to generate sample ions and fragment ions thereof,said mass filter being positionable downstream of the ion source, and said mass filter also configured to receive said sample ions and configured to allow passage of at least a portion of said sample ions and said fragment ions thereof having m / z ratios in a desired range,an ion dissociation device being positioned downstream of the mass filter, the ion dissociation device configured to receive the sample ions and said fragment ions thereof passing through the mass filter, and also configured to cause dissociation thereof to generate a plurality of product ions, anda mass analyzer having a detector configured to generate ion detection signals in response to detection of said plurality of product ions that were generated by said ion dissociation device, andwherein said mass analyzer is configured to transmit either directly or indirectly to an analysis module, which is configured to be either directly or indirectly in communication with said mass analyzer, said ion detection signals that were generated, andwherein said analysis module is configured to determine whether any one of said ion detection signals corresponds to a single ion detection event.

15. The mass spectrometer of Claim 14, wherein said detector includes n multiple independent ion detection channels, wherein each channel of said n multiple independent ion detection channels is configured to generate an independent output signal during a common ion detection period.

16. The mass spectrometer of Claim 15, wherein said analysis module is configured to identify an ion detection event as corresponding to said single ion detection event based on a predefined pattern of independent output signals generated substantially concurrently by said n multiple independent ion detection channels.

17. The mass spectrometer of Claim 14, wherein said detector includes a single ion detection channel, and said analysis module is configured to identify an ion detection event associated with one of a plurality of temporally consecutive ion pulses as said single ion detection event when no244922-6174-6564, v. 1Attorney Ref. No. 4277-0426WO01ion detection event is generated by other pulses of said plurality of temporally consecutive ion pulses.

18. A mass spectrum formed by the mass spectrometer of any one of Claims 14 to 17.

19. A unit of chemical designed and manufactured in accordance with information obtained from a mass spectrum formed by the mass spectrometer of Claim 14.4922-6174-6564, v. 1

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