Threshold-based ida exclusion list

Abstract

First, MS scans of a quality range of a control sample that does not include metabolites are performed (601), resulting in background peak m / z and intensity values of background precursor ions (602). Background peaks are selected for an exclusion list and the m / z and intensity values of each background peak are included in the exclusion list (604). Next, MS scans of a quality range of an experimental sample that includes metabolites are performed (610), resulting in peak m / z and intensity values of precursor ions (612). Peaks are selected for a peak list and the m / z and intensity values of each peak are included in the peak list (614). Finally, each peak in the peak list having m / z and intensity values corresponding to the m / z and intensity values of the background peaks of the exclusion list are excluded from the peak list (616).

Description

[0001] Related Applications

[0002] This application claims the benefit of U.S. Provisional Patent Application Serial No. 62 / 916,759, filed on October 17, 2019, the contents of which are incorporated herein by reference in their entirety. Technical Field

[0003] This article teaches a mass spectrometry apparatus for detecting metabolites in samples during information-related acquisition (IDA) mass spectrometry experiments. More specifically, the mass spectrometer distinguishes metabolite ions from background ions with similar mass-to-charge ratios (m / z) by including intensity and retention time parameters in the IDA exclusion list.

[0004] The apparatus and methods disclosed herein are also applicable to processors, controllers, microcontrollers, or computer systems (such as...) Figure 1 (The computer system) is combined for execution. Background Technology

[0005] Mass spectrometry background

[0006] Mass spectrometry (MS) is an analytical technique that detects and quantifies compounds by analyzing the m / z values ​​of ions formed from chemical compounds. MS involves ionizing one or more compounds of interest from a sample, generating precursor ions, and performing mass analysis on these precursor ions.

[0007] Tandem mass spectrometry, or mass spectrometry / mass spectrometry (MS / MS), involves ionizing one or more compounds of interest from a sample, selecting one or more precursor ions of one or more compounds, splitting one or more precursor ions into product ions, and performing mass analysis on the product ions.

[0008] Mass spectrometers are often coupled with chromatographic or other separation systems to identify and characterize compounds of interest eluted from a sample. In such coupled systems, the compound in the eluent is ionized, and a series of mass spectra are acquired at specified time intervals. These time ranges, for example, from 1 second to 100 minutes or longer. The intensity values ​​derived from the series of mass spectra form chromatograms. For example, the sum of all intensities generates a total ion chromatogram (TIC), and the intensity of a single mass value generates an extracted ion chromatogram (XIC).

[0009] Peaks found in a chromatogram are used to identify or characterize known peptides or compounds in a sample because they elute at a known time known as the retention time. More specifically, the retention time and / or area of ​​a peak are used to identify or characterize (quantify) known peptides or compounds in a sample.

[0010] In a traditional, separate coupled mass spectrometry system, a precursor ion of a known compound is selected for analysis. Then, MS / MS scans are performed on each separation interval on a mass range that includes the precursor ion. The intensities of the product ions found in each MS / MS scan are collected over time and analyzed as a collection of spectra or, for example, an XIC.

[0011] Both MS and MS / MS can provide qualitative and quantitative information. The measured precursor or product ion spectra can be used to identify molecules of interest. The intensities of the precursor and product ions can also be used to quantify the amount of a compound present in a sample.

[0012] A number of different types of experiment acquisition methods or workflows can be performed using a tandem mass spectrometer. Three broad categories of these workflows are targeted acquisition, information-dependent acquisition (IDA) or data-dependent acquisition (DDA), and data-independent acquisition (DIA).

[0013] In a targeted acquisition method, one or more transitions from a precursor ion to a product ion for a compound of interest are predefined or known. When a sample is introduced into the tandem mass spectrometer, the one or more transitions are monitored during each of a number of time periods or cycles. In other words, the mass spectrometer selects and fragments the precursor ion for each transition and performs targeted mass analysis on the product ion of the transition. Thus, an intensity (product ion intensity) is produced for each transition. Targeted acquisition methods include, but are not limited to, multiple reaction monitoring (MRM) and selected reaction monitoring (SRM).

[0014] In an IDA method, when a sample is introduced into the tandem mass spectrometer, the user can specify criteria for performing non-targeted mass analysis of product ions. For example, in an IDA method, a precursor ion or mass spectrometry (MS) survey scan is performed to generate a list of precursor ion peaks. The user can select criteria to filter the list of peaks to find a subset of the precursor ions on the list of peaks. Then, MS / MS is performed on each precursor ion of the subset of precursor ions. A product ion spectrum is produced for each precursor ion. The MS survey scan followed by multiple MS / MS scans can be performed (iteratively) on the precursor ions of the subset of precursor ions when a sample is introduced into the tandem mass spectrometer. IDA can also be referred to as data-dependent analysis (Thermo Fisher) or data-directed analysis (Waters). For example, the term“data-dependent” is a trademark of Thermo Fisher, while the term“DDA” is a trademark of Waters.

[0015] Measuring complex (e.g., biological) samples by different omics techniques, such as proteomics, metabolomics, etc., results in different types, large amounts, and wide dynamic ranges of compounds. In proteomics and many other sample types, the complexity and dynamic range of compounds is very large. This poses a challenge to traditional targeted and IDA methods, requiring very high speed MS / MS acquisition to deeply interrogate the sample in order to both identify and quantify a wide range of analytes.

[0016] Accordingly, DIA methods, the third major class of tandem mass spectrometry, have been developed. These DIA methods have been used to improve the reproducibility and comprehensiveness of data collection from complex samples. DIA methods can also be referred to as non-specific fragmentation methods. In traditional DIA methods, the action of the tandem mass spectrometer does not change between MS / MS scans based on data acquired in previous precursor ion or product ion scans. Rather, a precursor ion mass range is selected. The precursor ion mass selection window is then stepped across the precursor ion mass range. All precursor ions in the precursor ion mass selection window are fragmented, and all product ions of all precursor ions in the precursor ion mass selection window are mass analyzed.

[0017] Endogenous background peak problems

[0018] When performing drug metabolite identification studies, it is common to perform IDA on samples from dosed subjects. The resulting MS / MS spectra are used to confirm that putative metabolites are in fact related to the starting drug and to locate the site of metabolic transformation.

[0019] Figure 2 is an exemplary diagram 200 illustrating how a tandem mass spectrometer operated to identify drug metabolites in a simple sample using an IDA method produces an IDA list that includes endogenous background precursor ions in addition to the metabolite precursor ions. In this example, the simple sample includes three metabolite precursor ions, M1, M2, and M3, and two endogenous background precursor ions, B1 and B2. Figure 2 In the IDA method of, the tandem mass spectrometer first performs a full MS scan 210 on the simple sample. In the MS scan 210, all precursor ions of the sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, these devices are shown as four groups, but other types of devices are possible. The mass analyzer produces an intensity measurement of the precursor ions, as shown in the precursor mass spectrum 212.

[0020] The tandem mass spectrometer then selects all precursor ions with an intensity above a certain threshold 213. All precursor ions with an intensity above the threshold 213 are added to a threshold list 214. If the number of ions on the threshold list 214 is small enough to be interrogated in a single MS / MS scan, then the MS / MS scan is performed 215. The MS / MS scan 215 produces a product ion spectrum 216. The product ion spectrum 216 is then compared to a library of product ion spectra 217 to identify the metabolite precursor ions. The product ion spectrum 216 is also compared to a library of product ion spectra 218 to identify the endogenous background precursor ions. Figure 2The threshold list 214 is then converted to an IDA list 216 by MS / MS analysis of the specified cycle time shown in the middle. Note that the IDA list 214 includes only the m / z of each precursor ion. Also, note that the precursor ions with intensities above the threshold 213 are added to the threshold list 214 according to m / z value. However, as discussed below, there are other methods for selecting the order of the precursor ions on the threshold list 214.

[0021] For each precursor ion on the IDA list 216, the tandem mass spectrometer performs an MS / MS scan. For example, in MS / MS scan 221, the precursor ion with m / z value of 114 is selected in the mass filter, dissociated into product ions in the dissociation device, and the product ions are mass analyzed in the mass analyzer. Similarly, in MS / MS scans 222 and 223, the precursor ions with m / z values of 153 and 215 from the IDA list 216 are selected and dissociated, respectively, and their product ions are mass analyzed.

[0022] The product ion spectra of MS / MS scans 221, 222, and 223 are compared to known product ion spectra of known drugs to determine if they can correspond to metabolites. Note that the precursor ions with m / z values of 114 and 153 are endogenous background ion peaks. Thus, it is also possible to compare the endogenous background ion peaks to the known metabolite peaks in the IDA method. For simple samples, this is not a problem.

[0023] However, for more complex samples, this prevents the IDA method from triggering on one or all of the metabolite peaks because most of the available cycle time is used to acquire unwanted MS / MS spectra of the endogenous background peaks. Thus, the drug metabolites can not be identified.

[0024] Figure 3 is an example diagram 300 showing how a tandem mass spectrometer operated to identify drug metabolites in a complex sample using the IDA method can produce an IDA list that does not include the metabolite precursor ions. In this example, the sample is a mixture of a drug and its metabolites. The drug has a precursor ion with m / z value of 114 and the metabolite has a precursor ion with m / z value of 153. The sample is analyzed using the IDA method. Figure 3 In the IDA method of, the tandem mass spectrometer first performs a full MS scan 310 of the complex sample. In MS scan 310, all of the precursor ions of the sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, the devices are shown as four groups, but other types of devices are possible. The mass analyzer produces an intensity measurement of the precursor ions, as shown by precursor mass spectrum 312.

[0025] The tandem mass spectrometer then selects all of the precursor ions with intensities above a certain threshold 313. All of the precursor ions with intensities above the threshold 313 are added to a threshold list 314.

[0026] Because complex samples are scanned, precursor mass spectrum 312 includes six endogenous background precursor ion peaks in addition to the metabolite peak with m / z value of 215. If the specified cycle time only provides enough time to perform MS / MS scans on five precursor ion peaks, then threshold list 314 is truncated to IDA list 316.

[0027] For each precursor ion on IDA list 316, the tandem mass spectrometer performs an MS / MS scan. Since there are five precursor ion peaks on IDA list 316, five MS / MS scans 321-325 are performed, resulting in five product ion spectra.

[0028] The product ion spectra of MS / MS scans 321-325 are then compared to known product ion spectra of known drugs to determine if they can correspond to metabolites. The metabolites themselves can not be "known." Note that in precursor ion spectrum 312, the metabolite precursor ion with m / z of 215 is preceded by six endogenous background precursor ions. Since IDA list 316 is limited to only five precursor ion peaks, the metabolite precursor ion with m / z 215 is not added to the list. Thus, the product ion spectra of MS / MS scans 321-325 only provide product ions of endogenous background precursor ions. Thus, no known drug metabolites are found in this case.

[0029] Acquisition via IDA is one of the most widely used methods to generate MS / MS information in an automated fashion. Over the years, several filters have been developed to filter the threshold peak list of a subset of precursor ions to be dissociated to optimize the automatic selection of ions of interest in specific applications.

[0030] In metabolite studies, a control sample can be acquired and analyzed. The control sample is similar to the metabolite sample, but represents the condition before the drug was administered. Of course, the more similar the control sample is to the experimental sample, the better. For example, the control sample can come from the same subject as the corresponding dosed sample, but before dosing. By searching for peaks that are present in the dosed but not the control sample, putative metabolites are found.

[0031] It is possible to analyze the control sample by finding all peaks before acquiring the dosed sample. It has been shown previously that this peak list can be used as an IDA exclusion list when acquiring data for the dosed sample. This prevents IDA from triggering on background peaks and thus increases the chance that MS / MS will be acquired for actual drug metabolites of interest.

[0032] Figure 4is an example diagram 400 showing how a tandem mass spectrometer is operated to first perform a MS scan on a control sample to produce an exclusion list and then operated to identify drug metabolites in a complex sample by using the exclusion list in an IDA method applied to the complex sample. In Figure 4 In the IDA method of, the tandem mass spectrometer first performs a full MS scan 401 on a control sample. The control sample is known to not include any metabolites of interest. In the MS scan 401, all precursor ions of the control sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, these devices are shown as four groups, but can be other types of devices. The mass analyzer produces intensity measurements for the precursor ions, as shown in the precursor mass spectrum 402.

[0033] The tandem mass spectrometer then selects all precursor ions with intensities above a certain threshold 403. All precursor ions with intensities above the threshold 403 are added to an exclusion list 404. Since the control sample does not include metabolites of interest, all precursor ions on the exclusion list 404 are endogenous background ions.

[0034] The tandem mass spectrometer then performs a full MS scan 410 on an experimental sample known to include metabolites of interest. In the MS scan 410, all precursor ions of the experimental sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, these devices are shown as four groups, but can be other types of devices. The mass analyzer produces intensity measurements for the precursor ions, as shown in the precursor mass spectrum 412.

[0035] The tandem mass spectrometer then selects all precursor ions with intensities above a certain threshold 413. All precursor ions with intensities above the threshold 413 are added to a threshold list 414. Since the experimental sample includes metabolites of interest, the threshold list 414 includes the metabolite precursor ion with m / z 215 in addition to all endogenous background ions.

[0036] The tandem mass spectrometer removes the precursor ion peaks on the exclusion list 404 from the threshold list 414. This produces an IDA list 416. The IDA list 416 now only includes the metabolite precursor ion with m / z 215.

[0037] For each precursor ion on the IDA list 416, the tandem mass spectrometer performs a MS / MS scan. Since there is only one precursor ion peak on the IDA list 416, only MS / MS scan 421 is performed, resulting in one product ion spectrum.

[0038] The product ion spectrum of MS / MS scan 421 is then compared to known product ion spectra of known drugs to determine if they can correspond to metabolites. Note that by using the exclusion list 404, MS / MS scans are not performed on endogenous background precursor ion peaks. This ensures that MS / MS scan 421 is performed on the metabolite precursor ion of m / z 215.

[0039] One problem with using an exclusion list derived from a control sample is that for peaks of a drug metabolite with a similar m / z to a background peak, MS / MS will not be triggered, even if the peak intensity of the drug metabolite is relatively greater compared to the background peak.

[0040] Figure 5 is an example diagram 500 showing how an exclusion list from MS scans performed on a control sample can also remove metabolite peaks in an IDA method if the metabolite peak and the background peak have similar m / z values. In this example, the control sample does not include the metabolite of interest. The control sample is analyzed in MS scan 501. In MS scan 501, all precursor ions of the control sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, these devices are shown as four groups, but can be other types of devices. The mass analyzer produces an intensity measurement of the precursor ions, as shown in precursor mass spectrum 502. Figure 5 In the IDA method of, the tandem mass spectrometer first performs a full MS scan 501 on a control sample. The control sample is known to not include the metabolite of interest. In MS scan 501, all precursor ions of the control sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, these devices are shown as four groups, but can be other types of devices. The mass analyzer produces an intensity measurement of the precursor ions, as shown in precursor mass spectrum 502.

[0041] The tandem mass spectrometer then selects all precursor ions with an intensity above a certain threshold 503. All precursor ions with an intensity above threshold 503 are added to an exclusion list 504.

[0042] The tandem mass spectrometer then performs a full MS scan 510 on an experimental sample known to include the metabolite of interest. In MS scan 510, all precursor ions of the experimental sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer. In this diagram, these devices are shown as four groups, but can be other types of devices. The mass analyzer produces an intensity measurement of the precursor ions, as shown in precursor mass spectrum 512.

[0043] The tandem mass spectrometer then selects all precursor ions with an intensity above a certain threshold 513. All precursor ions with an intensity above threshold 513 are added to a threshold list 514. Since the experimental sample includes the metabolite of interest, threshold list 514 includes the metabolite precursor ion 518 with m / z 190. However, there is also a background ion 517 with m / z 190. Thus, threshold list 514 includes two ion peaks with m / z 190.

[0044] Next, the tandem mass spectrometer removes from the threshold list 514 the precursor ion peaks on the exclusion list 504. Because the metabolite precursor ion 518 and the background ion 517 have the same m / z value 190, they are both excluded. Thus, the IDA list 516 now does not include the ion peak and does not perform a MS / MS scan. Thus, when a metabolite and background peak have similar m / z values, even with a control sample and exclusion list, MS / MS scans of drug metabolites are not triggered.

[0045] Thus, additional system methods for operating a tandem mass spectrometer in an IDA method are needed to distinguish between background and metabolite ions having similar m / z values. SUMMARY

[0046] Disclosed are systems, methods, and computer program products for excluding endogenous background ions having the same mass-to-charge ratio (m / z) as metabolite ions from a peak list in an information dependent acquisition (IDA) mass spectrometry experiment. The system includes an ion source device and a tandem mass spectrometer.

[0047] The tandem mass spectrometer receives an ion beam from the ion source device, which is produced by ionizing a control sample that does not include a metabolite compound. The tandem mass spectrometer performs a MS scan of a mass range on the ion beam, producing background peak m / z and intensity values for background precursor ions. The tandem mass spectrometer selects one or more of the background peaks of the background precursor ions for an exclusion list and includes in the exclusion list the m / z value and intensity value of each of the selected one or more background peaks.

[0048] The tandem mass spectrometer next creates a peak list for the IDA method by analyzing an experimental sample. The tandem mass spectrometer receives an ion beam from the ion source device, which is produced by ionizing an experimental sample that includes a metabolite compound. The tandem mass spectrometer performs a MS scan of a mass range on the ion beam, producing peak m / z and intensity values for precursor ions. The tandem mass spectrometer selects one or more of the peaks of the precursor ions for the peak list and includes in the peak list the m / z value and intensity value of each of the selected one or more peaks.

[0049] Finally, the tandem mass spectrometer excludes from the peak list each peak having an m / z value and intensity value corresponding to an m / z value and intensity value of a background peak of the exclusion list.

[0050] These and other features of the Applicant's teachings are set forth with particularity. BRIEF DESCRIPTION OF DRAWINGS

[0051] Those skilled in the art will appreciate that the figures described below are for illustration purposes only. The figures are not intended to limit the scope of the present teachings in any way.

[0052] Figure 1is a block diagram illustrating a computer system on which embodiments of the present teachings can be implemented.

[0053] Figure 2 is an exemplary diagram showing how a tandem mass spectrometer operated to identify drug metabolites in a simple sample using an information dependent acquisition (IDA) method can produce an IDA list that includes endogenous background precursor ions in addition to metabolite precursor ions.

[0054] Figure 3 is an exemplary diagram showing how a tandem mass spectrometer operated to identify drug metabolites in a complex sample using an IDA method can produce an IDA list that does not include metabolite precursor ions.

[0055] Figure 4 is an exemplary diagram showing how a tandem mass spectrometer is operated to first perform a mass spectrometry (MS) scan on a control sample to produce an exclusion list and then operated to identify drug metabolites in a complex sample by using the exclusion list in an IDA method applied to the complex sample.

[0056] Figure 5 is an exemplary diagram showing how an exclusion list from a MS scan performed on a control sample can remove a metabolite peak in an IDA method if the metabolite peak has a similar m / z value to a background peak.

[0057] Figure 6 is an exemplary diagram showing how adding intensity and retention time to an exclusion list from a MS scan performed on a control sample in an IDA method prevents a metabolite peak from being removed if the metabolite peak has a similar m / z value to a background peak, according to various embodiments.

[0058] Figure 7 is a schematic diagram of an apparatus for excluding endogenous background ions having the same m / z as metabolite ions from a peak list in an IDA mass spectrometry experiment, according to various embodiments.

[0059] Figure 8 is a flowchart showing a method 800 for excluding endogenous background ions having the same m / z as metabolite ions from a peak list in an IDA mass spectrometry experiment, according to various embodiments.

[0060] Figure 9 is a schematic diagram of a system including one or more different software modules that perform a method for excluding endogenous background ions having the same m / z as metabolite ions from a peak list in an IDA mass spectrometry experiment, according to various embodiments.

[0061] Before one or more embodiments of the teaching are described, it is to be understood that the teaching is not limited in its application to the details of construction, the arrangements of components, and the arrangement of steps set forth in the following detailed description or illustrated in the drawings. Also, it is to be understood that the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. DETAILED DESCRIPTION

[0062] Computer-implemented system

[0063] Figure 1 is a block diagram that illustrates a computer system 100 upon which an embodiment of the teaching can be implemented. Computer system 100 includes a bus 102 or other communication mechanism for communicating information, and a processor 104 coupled with bus 102 for processing information. Computer system 100 also includes a memory 106, which can be a random access memory (RAM) or other dynamic storage device, coupled to bus 102 for storing information and instructions to be executed by processor 104. Memory 106 also can be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor 104. Computer system 100 further includes a read only memory (ROM) 108 or other static storage device coupled to bus 102 for storing static information and instructions for processor 104. A storage device 110, such as a magnetic disk or optical disk, is provided and coupled to bus 102 for storing information and instructions.

[0064] Computer system 100 can be coupled via bus 102 to a display 112, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 114, including alphanumeric and other keys, is coupled to bus 102 for communicating information and command selections to processor 104. Another type of user input device is cursor control 116, such as a mouse, trackball, or cursor direction keys for communicating direction information and command selections to processor 104 and for

[0065] The computer system 100 can perform the present teachings. Consistent with certain implementations of the present teachings, results are provided by the computer system 100 in response to the processor 104 executing one or more sequences of one or more instructions contained in the memory 106. Such instructions can be read into the memory 106 from another computer-readable medium, such as the storage device 110. Execution of the sequences of instructions contained in the memory 106 causes the processor 104 to perform the process described herein. Alternatively, hard-wired circuitry can be used in place of software instructions to implement the present teachings. Thus, implementations of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0066] In various embodiments, the computer system 100 can be connected to one or more other computer systems across a network, such as the computer system 100, to form a networked system. The network can include a private network or a public network, such as the Internet. In a networked system, one or more computer systems can store data and provide it to other computer systems. In a cloud-computing scenario, the one or more computer systems that store and provide data can be referred to as a server or a cloud. For example, the one or more computer systems can include one or more web servers. For example, other computer systems that send and receive data to and from the server or cloud can be referred to as clients or cloud devices.

[0067] As used herein, the term "computer-readable medium" refers to any medium that participates in providing instructions to the processor 104 for execution. Such a medium can 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 the storage device 110. Volatile media include dynamic memory, such as the memory 106. Transmission media include coaxial cables, copper wire, and fiber optics, including the wires that comprise the bus 102.

[0068] Common forms of computer-readable media or computer program products include, for example, a floppy disk, a flexible disk, a hard disk, magnetic tape, or any other magnetic medium, a CD-ROM, digital video disk (DVD), a Blu-ray disk, any other optical medium, a thumb drive, a memory card, 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.

[0069] Various forms of computer readable media can be involved in carrying one or more sequences of one or more instructions to the processor 104 for execution. For example, the instructions can initially be carried on a magnetic disk of a remote computer. The remote computer can load the instructions into its dynamic memory and send the instructions over a telephone line using a modem. A modem local to the computer system 100 can receive the data on the telephone line and use an infra-red transmitter to convert the data to an infra-red signal. An infra-red detector coupled to the bus 102 can receive the data carried in the infra-red signal and place the data on the bus 102. The bus 102 carries the data to the memory 106, from which the processor 104 retrieves and executes the instructions. The instructions received by the memory 106 can optionally be stored on a storage device 110 either before or after execution by the processor 104.

[0070] According to various embodiments, instructions configured to be executed by a processor to perform a method are stored on a computer readable medium. The computer readable medium can be a device that stores digital information. For example, the computer readable medium includes a compact disc read-only memory (CD-ROM) as is known in the art for storing software. The computer readable medium is accessed by a processor adapted to execute the instructions configured to be executed.

[0071] The following description of various implementations of the present teachings has been presented for the purpose 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 can be acquired from practice of the present teachings. Additionally, the described implementation includes software but the present teachings can be implemented as a combination of hardware and software or

[0072] IDA exclusion list with intensity and retention time

[0073] As described above, when performing drug metabolite identification studies, IDA is typically performed on samples from dosed subjects. The resulting MS / MS spectra are used to confirm that putative metabolites are in fact related to the starting drug and to locate the site of metabolic transformation. For simple samples, routine IDA works well. However, for more complex samples, endogenous background ions can prevent the IDA method from triggering on one or all of the metabolite peaks, as much of the available cycle time is used to acquire unwanted MS / MS spectra of endogenous background peaks. As a result, drug metabolites can not be identified.

[0074] One solution to this problem is to first analyze a similar control sample that does not contain metabolites in order to generate a list of background ion peaks. This list can then be used as an IDA exclusion list when acquiring data for the dosed sample. This prevents IDA from triggering on background peaks, thereby increasing the chance that MS / MS will be acquired for actual drug metabolites of interest.

[0075] One problem with using the exclusion list from the control sample is that peaks for drug metabolites with m / z values similar to the background peaks will not trigger MS / MS. Therefore, additional system methods for operating the tandem mass spectrometer are needed in the IDA method in order to distinguish between background and metabolite ions with similar m / z values.

[0076] In various embodiments, the tandem mass spectrometer includes the intensity of each background peak in the IDA exclusion list. The IDA method then triggers MS / MS scans of the dosed sample if there is no corresponding peak in the control sample or the peak in the control sample is less intense. A tolerance factor can be used to compare the peak intensities. For example, the IDA method only triggers MS / MS scans if the intensity is 1.5 times or more the intensity of the background peak. This change to the IDA method reduces the chance that MS / MS scans will not be triggered for drug metabolites when using the exclusion list.

[0077] As described above, mass spectrometers are often coupled with chromatography or other separation systems in order to identify and characterize compounds of interest that elute from a sample. In such coupled systems, the compounds in the elution solvent are ionized and a series of mass spectra are acquired at specified time intervals. The elution time from injection to detection of an analyte or metabolite is referred to as the retention time (RT). Therefore, metabolite ions can also be distinguished from endogenous background ions based on their retention times.

[0078] Therefore, in various embodiments, the tandem mass spectrometer includes the intensity and the retention time of each background peak in the IDA exclusion list. The IDA method then triggers MS / MS scans of the dosed sample if there is no corresponding peak in the control sample or the peak in the control sample has the same retention time and is less intense.

[0079] Figure 6 is an exemplary graph 600 illustrating how adding intensity and retention time to the exclusion list from MS scans performed on a control sample in the IDA method prevents metabolite peaks from being removed if the metabolite peaks have similar m / z values to the background peaks, according to various embodiments. In this example, the control sample does not contain the metabolite of interest. The control sample does contain a background peak with a similar m / z value to the metabolite of interest. The retention time of the background peak is also similar to the metabolite of interest. The exclusion list from the control sample contains the m / z value and the retention time of the background peak. The IDA method then triggers MS / MS scans of the dosed sample. The dosed sample contains the metabolite of interest. The metabolite of interest has a similar m / z value to the background peak and a similar retention time to the background peak. The IDA method does not trigger MS / MS scans of the metabolite of interest because the m / z value and the retention time of the metabolite of interest are in the exclusion list from the control sample. Figure 6In the IDA method, when eluting a control sample using a separation device, the tandem mass spectrometer first performs multiple full MS scans on the control sample. The three-dimensional chromatogram 602 shows the mass peaks produced for each of the four endogenous background ions. The control sample is known to not include the metabolite of interest. In each MS scan 601 performed at a step of different time, all precursor ions of the control sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer, producing a precursor ion spectrum at each time step. In this figure, the devices are shown as four groups, but can be other types of devices as well.

[0080] At each time step, the tandem mass spectrometer then selects all peaks with intensities above a certain threshold 603. All precursor ion peaks with intensities above the threshold 603 are added to the exclusion list 604. In addition, the intensity and retention time of each peak are also added to the exclusion list 604, now producing three columns in the exclusion list 604.

[0081] The tandem mass spectrometer then performs multiple full MS scans 610 on an experimental sample known to include the metabolite of interest. In each MS scan 610 performed at a step of different time, all precursor ions of the experimental sample are selected in the mass filter, transmitted through the dissociation device, and mass analyzed in the mass analyzer, producing a precursor ion spectrum at each time step. The three-dimensional chromatogram 612 shows the mass peaks produced.

[0082] The tandem mass spectrometer then selects all peaks with intensities above a certain threshold 613. All precursor ion peaks with intensities above the threshold 613 are added to the threshold list 614. In addition, the intensity and retention time of each peak are also added to the threshold list 614, now producing three columns in the threshold list 614. Since the experimental sample includes the metabolite of interest, the threshold list 614 includes the metabolite precursor ion peak 618 with m / z 190, intensity 1500, and retention time 41 minutes. However, there is also a background ion peak 617 with m / z 190, intensity 1000, and retention time 41 minutes. Thus, the threshold list 614 includes two ion peaks with m / z 190.

[0083] Next, the tandem mass spectrometer removes from the threshold list 614 the precursor ion peaks that are on the exclusion list 604. Previously, because the metabolite precursor ion peak 618 and the background ion peak 617 of the threshold list 614 had the same m / z value 190 as the background ion peaks of the exclusion list 604, they were both excluded.

[0084] However, now the retention times and intensities of precursor ion peak 618 and background ion peak 617 of threshold list 614 are additionally compared to the retention times and intensities of background ion peaks of exclusion list 604. From this comparison, it is found that background ion peak 617 of threshold list 614 matches a background ion peak of exclusion list 604 and is excluded. However, although the m / z and retention time of metabolite precursor ion peak 618 of threshold list 614 match the m / z and retention time of a background ion peak of exclusion list 604, the intensities do not match. Thus, metabolite precursor ion peak 618 of threshold list 614 is not excluded and is therefore added to IDA list 616. Note that all other peaks of threshold list 614 match peaks of exclusion list 604 and are excluded.

[0085] It is also noted that although IDA list 616 is shown as a separate list, IDA list 616 can simply be threshold list 614 after the exclusion of peaks. It is further noted that as peaks are acquired during the separation, threshold list 614 is constantly updated and excluded in real time, and thus IDA list 616 is also constantly changing during the separation.

[0086] During the separation, for each precursor ion peak on IDA list 616, the tandem mass spectrometer performs an MS / MS scan on the precursor ion peak on IDA list 616. Since in this case there is only one precursor ion peak on IDA list 616, as long as metabolite precursor ion peak 618 is on IDA list 616, only MS / MS scan 621 is performed, resulting in a product ion spectrum for each MS / MS scan.

[0087] The product ion spectrum of MS / MS scan 621 is then compared to known product ion spectra of known drugs to determine if they can possibly correspond to metabolites. Note that by using exclusion list 604 with additional intensity and retention time parameter values, MS / MS scans are not performed on both endogenous background precursor ion peaks and metabolite ion peaks that have similar m / z values but different intensities or retention times. In other words, metabolite ion peaks are no longer incorrectly excluded.

[0088] In various embodiments, when comparing m / z, retention time, and intensity between threshold list and exclusion list, different tolerance factors for matching the values of each parameter are used. For example, the tolerance factor for intensity can be, but is not limited to, a factor of 1.5. This means that if the m / z and retention also match, then MS / MS scans are only triggered for peaks of threshold list 614 if the intensity is 1.5 times the intensity of the peak on exclusion list 604.

[0089] Note that the concentrations of the control sample and the experiment can be different. Thus, in various embodiments, the intensities of the threshold list 614 or the exclusion list 604 are scaled before comparing the two lists. For example, the control and experiment urine samples can have different volumes. It is known that urine naturally contains certain compounds, such as creatinine. Thus, the ratio of the creatinine intensities in the threshold list and the exclusion list can be used to scale all of the intensities in the threshold list or the exclusion list.

[0090] System for excluding background peaks from a peak list

[0091] Figure 7 is a schematic diagram 700 of an apparatus for excluding endogenous background ions having the same m / z as a metabolite ion from a list of peaks in an IDA mass spectrometry experiment, according to various embodiments. Figure 7 The system of includes an ion source device 710 and a tandem mass spectrometer 701.

[0092] The ion source device 710 can be, but is not limited to, an electrospray ion source (ESI) device, a chemical ionization (CI) source device (such as an atmospheric pressure chemical ionization source (APCI) device), an atmospheric pressure photoionization (APPI) source device, or a matrix assisted laser desorption source (MALDI) device. In an exemplary embodiment, the ion source device 710 is an ESI device.

[0093] The tandem mass spectrometer 701 includes, for example, a mass filter device 720, a dissociation device 730, and a mass analyzer 740. In an exemplary embodiment, the mass filter device 720 is a quadrupole device, the dissociation device 730 is a collision cell device, and the mass analyzer 740 is a quadrupole device. Figure 7 In the system of, the mass filter device 720, the dissociation device 730, and the mass analyzer 740 are shown as quadrupole devices. Those of ordinary skill in the art will recognize that any of these stages can include other types of mass spectrometry devices, including but not limited to ion traps, orbitrap, ion mobility devices, time-of-flight (TOF) devices, electron-based dissociation (ExD) collision cells, or Fourier transform ion cyclotron resonance (FT-ICR) devices.

[0094] The tandem mass spectrometer 701 first creates an exclusion list by analyzing a control sample. The tandem mass spectrometer 701 receives a beam of ions from the ion source device 710, which is produced by ionizing a control sample that does not include the metabolite compound. Note that in Figure 7 In, the ion source device 710 is shown as part of the tandem mass spectrometer 701. However, the ion source device 710 can also be a separate device.

[0095] The tandem mass spectrometer 701 performs MS scans of a mass range on the ion beam, resulting in background peak m / z and intensity values for background precursor ions. The tandem mass spectrometer 701 selects one or more of the background peaks of the background precursor ions for the exclusion list and includes the m / z value and intensity value of each of the selected one or more background peaks in the exclusion list.

[0096] The tandem mass spectrometer 701 next creates a peak list for the IDA method by analyzing the experimental sample. The tandem mass spectrometer 701 receives an ion beam from the ion source device that is produced by ionizing the experimental sample including the metabolite compounds. The tandem mass spectrometer 701 performs MS scans of a mass range on the ion beam, resulting in peak m / z and intensity values for precursor ions. The tandem mass spectrometer 701 selects one or more peaks of the precursor ions for the peak list and includes the m / z value and intensity value of each of the selected one or more peaks in the peak list.

[0097] Finally, the tandem mass spectrometer 701 excludes each peak of the peak list that has a m / z value and intensity value that corresponds to a m / z value and intensity value of a background peak of the exclusion list.

[0098] In various embodiments, the tandem mass spectrometer 701 also performs MS / MS scans on each precursor ion peak on the peak list in order to identify metabolite compounds.

[0099] In various embodiments, the tandem mass spectrometer 701 selects the one or more peaks of the precursor ions of the peak list by selecting the top N peaks measured above a certain threshold intensity level. In another embodiment, the tandem mass spectrometer 701 selects the one or more peaks of the precursor ions of the peak list by selecting the N peaks with the highest intensities.

[0100] In various embodiments, the m / z value and intensity value of a peak of the peak list corresponds to the m / z value and intensity value of a background peak of the exclusion list if the m / z values match within an m / z tolerance factor and if the intensity values match within an intensity tolerance factor. As described above, the intensity tolerance factor can be, for example, 1.5 times the intensity of the background peaks of the exclusion list.

[0101] In various embodiments, the tandem mass spectrometer 701 further scales the peak list or the exclusion list prior to comparing and matching the peaks in the two lists. As described above, a single known background peak can be used to scale the peak list or the exclusion list. For example, the tandem mass spectrometer 701 selects one known background peak on the peak list and the exclusion list. The tandem mass spectrometer 701 calculates a ratio of the intensity value of the one known background peak on the peak list to the intensity value of the one known background peak on the exclusion list. The tandem mass spectrometer 701 then multiplies each intensity value on the peak list or the exclusion list by the ratio.

[0102] In various embodiments, two or more background ions can be used to scale the peak list or the exclusion list. For example, tandem mass spectrometer 701 selects two or more known background peaks on the peak list and the exclusion list. Tandem mass spectrometer 701 calculates a ratio of a combination of intensity values of the two or more known background peaks on the peak list to a combination of intensity values of the two or more known background peaks on the exclusion list. The combination of intensity values of the two or more known background peaks can be, but is not limited to, an average, a median, or an intensity-weighted average. Tandem mass spectrometer 701 then multiplies each intensity value on the peak list or the exclusion list by the ratio.

[0103] In various embodiments, tandem mass spectrometer 701 further includes a sample introduction device 760. For example, sample introduction device 760 introduces one or more compounds of interest from a sample over time to ion source device 710. Sample introduction device 760 can perform techniques including, but not limited to, injection, liquid chromatography, gas chromatography, capillary electrophoresis, or ion migration.

[0104] When using sample introduction device 760, tandem mass spectrometer 701 receives an ion beam from ion source device 710 that receives one or more compounds from a control sample from sample introduction device 760 over time. Tandem mass spectrometer 701 then performs a plurality of MS scans of a mass range on the ion beam at a plurality of different time steps, producing background peak m / z and intensity values of background precursor ions over time. At each time step, tandem mass spectrometer 701 selects one or more background peaks of background precursor ions for the exclusion list and includes in the exclusion list an m / z value, an intensity value, and a retention time value of each of the selected one or more background peaks.

[0105] Next, tandem mass spectrometer 701 receives an ion beam from ion source device 710 that receives one or more compounds from an experimental sample from sample introduction device 760 over time. Tandem mass spectrometer 701 performs a plurality of MS scans of a mass range on the ion beam at a plurality of different time steps, producing peak m / z and intensity values of precursor ions. For each time step, tandem mass spectrometer 701 selects one or more precursor ion peaks for the peak list and includes in the peak list an m / z value, an intensity value, and a retention time value of each of the selected one or more peaks.

[0106] Finally, tandem mass spectrometer 701 excludes from the peak list each peak having an m / z value, an intensity value, and a retention time corresponding to an m / z value, an intensity value, and a retention time of a background peak of the exclusion list.

[0107] In various embodiments, the m / z value, intensity value, and retention time of a peak of the peak list correspond to the m / z value, intensity value, and retention time of a background peak of the exclusion list if the m / z values match within an m / z tolerance factor, if the intensity values match within an intensity tolerance factor, and if the retention time values match within a retention time tolerance factor.

[0108] In various embodiments, the processor 750 can be used to control or instruct the tandem mass spectrometer 701 to perform any of the steps described above or to perform one or more of the steps described above independently. The processor 750 controls or provides instructions by, for example, controlling one or more voltage, current, or pressure sources (not shown). The processor 750 can be, but is not limited to, a computer, a microprocessor, Figure 1 a computer system of the present disclosure or any device capable of sending and receiving control signals and data from the tandem mass spectrometer and processing the data. The processor 750 is in communication with the tandem mass spectrometer 701. The processor 750 is shown as a separate device, but can be a processor or controller of the tandem mass spectrometer 701 or another device.

[0109] Method for excluding background peaks from a peak list

[0110] Figure 8 is a flowchart showing a method 800 for excluding endogenous background ions having the same m / z as a metabolite ion from a peak list in an IDA mass spectrometry experiment, according to various embodiments.

[0111] In step 810 of the method 800, an ion beam is received from an ion source device, the ion beam being produced by ionizing a control sample that does not include a metabolite compound using a tandem mass spectrometer.

[0112] In step 820, a mass spectrometry (MS) scan of a mass range is performed on the ion beam using the tandem mass spectrometer, resulting in background peak m / z and intensity values of background precursor ions.

[0113] In step 830, one or more of the background peaks of background precursor ions are selected for the exclusion list using the tandem mass spectrometer and the m / z value and intensity value of each of the selected one or more background peaks are included in the exclusion list.

[0114] In step 840, an ion beam is received from an ion source device using the tandem mass spectrometer, the ion beam being produced by ionizing an experimental sample that includes a metabolite compound.

[0115] In step 850, a MS scan of a mass range is performed on the ion beam using the tandem mass spectrometer, resulting in peak m / z and intensity values of precursor ions.

[0116] In step 860, the tandem mass spectrometer is used to select one or more peaks of the peak list for a precursor ion and include in the peak list the m / z value and intensity value of each of the selected one or more peaks.

[0117] In step 870, the tandem mass spectrometer is used to exclude from the peak list each peak having an m / z value and intensity value corresponding to an m / z value and intensity value of a background peak of the exclusion list.

[0118] Computer program product for excluding background peaks from a peak list

[0119] In various embodiments, a computer program product comprises a tangible computer-readable storage medium whose contents include a program with instructions executable by a processor to perform a method for excluding from a peak list in an IDA mass spectrometry experiment endogenous background ions having the same m / z as a metabolite ion. The method is performed by a system comprising one or more different software modules.

[0120] Figure 9 is a schematic diagram of a system 900 comprising one or more different software modules that perform a method for excluding from a peak list in an IDA mass spectrometry experiment endogenous background ions having the same m / z as a metabolite ion according to various embodiments. The system 900 comprises a control module 910 and an analysis module 920.

[0121] The control module 910 instructs the tandem mass spectrometer to receive an ion beam from an ion source device that is produced by ionizing a control sample that does not include a metabolite compound. The control module 910 instructs the tandem mass spectrometer to perform a MS scan of a mass range on the ion beam, thereby producing background peak m / z and intensity values for background precursor ions. The analysis module 920 selects one or more background peaks of the background precursor ions for an exclusion list and includes in the exclusion list the m / z value and intensity value of each of the selected one or more background peaks.

[0122] The control module 910 instructs the tandem mass spectrometer to receive an ion beam from an ion source device that is produced by ionizing an experimental sample that includes a metabolite compound. The control module 910 instructs the tandem mass spectrometer to perform a MS scan of a mass range on the ion beam, thereby producing peak m / z and intensity values for precursor ions. The analysis module 920 selects one or more peaks of the peak list for a precursor ion and includes in the peak list the m / z value and intensity value of each of the selected one or more peaks. Finally, the analysis module 920 excludes from the peak list each peak having an m / z value and intensity value corresponding to an m / z value and intensity value of a background peak of the exclusion list.

[0123] Also, in the description, where various embodiments have been described as a process, it is understood that the steps of the processes can be carried out in any order as the process is essentially provided for convenience and the reciting of the steps in any particular order does not necessarily outline the overall discovery. With regard to the various functions performed by the elements and components (including mechanical, electrical, and / or other components) described herein, the functions can be combined or separated into other functions as desired in various embodiments. In some embodiments, various functions described herein can be implemented as one or more software programs or components. Each of the software programs or components can be implemented in a high-level procedural and / or object-oriented programming and / or scripting language, and / or in assembly or machine language, and stored in a computer-readable medium. The software programs and components can be executed by a computer, a network element, a network, and / or other computing device.

Claims

1. A system for excluding endogenous background ions with the same mass-to-charge ratio m / z as metabolite ions from a peak list in an information correlation acquisition (IDA) mass spectrometry experiment, comprising: Ion source equipment; as well as Tandem mass spectrometer, the tandem mass spectrometer: a. An exclusion list is created by receiving an ion beam generated by ionizing a control sample excluding metabolite compounds from an ion source device, performing a mass range mass spectrometry (MS) scan on the ion beam to generate background peak m / z and intensity values ​​of background precursor ions, selecting one or more background peaks from the background peaks of background precursor ions for an exclusion list, and including the m / z and intensity values ​​of each of the selected one or more background peaks in the exclusion list. b. A peak list is created by receiving an ion beam generated by ionizing an experimental sample containing the metabolite compound from an ion source device, performing an MS scan of the ion beam within the mass range to generate peak m / z and intensity values ​​of the precursor ions, selecting one or more peaks from the precursor ion peaks for a peak list, and including the m / z and intensity values ​​of each of the selected one or more peaks in the peak list. c. Scaling or scaling the intensity of the peak list or exclusion list using the following methods: Select a known background peak from the peak list and the exclusion list. Calculate the ratio of the intensity value of a known background peak in the peak list to the intensity value of a known background peak in the exclusion list, and multiply each intensity value in the peak list or exclusion list by that ratio. d. Remove each peak from the peak list that has both an m / z value and an intensity value corresponding to the background peak in the exclusion list.

2. The system of claim 1, wherein if the m / z value matches within the m / z tolerance factor and if the intensity value matches within the intensity tolerance factor, then the m / z value and intensity value of the peaks in the peak list correspond to the m / z value and intensity value of the background peaks in the exclusion list.

3. The system of claim 1, wherein the tandem mass spectrometer further scales the peak list or exclusion list before comparing peaks in step d.

4. The system of claim 1, wherein the tandem mass spectrometer further scales the intensity of the peak list or exclusion list by: Select two or more known background peaks from the peak list and exclusion list. Calculate the ratio of the intensity values ​​of a combination of two or more known background peaks from the peak list to the intensity values ​​of a combination of two or more known background peaks from the exclusion list, and Multiply each intensity value in the peak list or exclusion list by this ratio.

5. The system of claim 1, wherein the tandem mass spectrometer further comprises a sample introduction device, wherein the tandem mass spectrometer also... In step a, an ion beam is received from an ion source device that receives one or more compounds from a control sample over time from a sample introduction device. Multiple MS scans of the ion beam within the stated mass range are performed at multiple different time steps to generate background peak m / z and intensity values ​​of background precursor ions over time. At each time step, one or more background peaks from an exclusion list of background precursor ions are selected, and the exclusion list includes the m / z value, intensity value, and retention time value of each of the selected one or more background peaks. In step b, an ion beam is received from an ion source device that receives one or more compounds from an experimental sample over time from a sample introduction device. Multiple MS scans of the ion beam within the stated mass range are performed at multiple different time steps to generate peak m / z and intensity values ​​of precursor ions over time. At each time step, one or more peaks from a peak list of precursor ions are selected, and the peak list includes the m / z value, intensity value, and retention time value of each of the selected peaks. In step d, each peak that has an m / z value, intensity value, and retention time corresponding to the background peak in the exclusion list is excluded from the peak list.

6. The system of claim 1, wherein if the m / z value matches within the m / z tolerance factor, if the intensity value matches within the intensity tolerance factor, and if the retention time value matches within the retention time tolerance factor, then the m / z value, intensity value, and retention time of the peaks in the peak list correspond to the m / z value, intensity value, and retention time of the background peaks in the exclusion list.

7. A method for excluding endogenous background ions with the same mass-to-charge ratio m / z as metabolite ions from a peak list in an information correlation acquisition (IDA) mass spectrometry experiment, comprising: The ion beam generated by ionizing a control sample that does not contain metabolite compounds is received from the ion source device using a tandem mass spectrometer. Mass spectrometry (MS) scans of the ion beam within a mass range were performed using a tandem mass spectrometer to generate background peak m / z and intensity values ​​for background precursor ions. Use a tandem mass spectrometer to select one or more background peaks from the background peaks of the background precursor ions for the exclusion list, and include the m / z value and intensity value of each of the selected one or more background peaks in the exclusion list; A tandem mass spectrometer is used to receive an ion beam generated by ionizing an experimental sample containing the metabolite compounds from an ion source device. MS scans of the ion beam within the stated mass range were performed using a tandem mass spectrometer to generate peak m / z and intensity values ​​for the precursor ions. Use a tandem mass spectrometer to select one or more peaks from the precursor ions for the peak list, and include the m / z value and intensity value of each of the selected one or more peaks in the peak list; Scaling or excluding the peak list can be done using the following methods: Select a known background peak from the peak list and the exclusion list. Calculate the ratio of the intensity value of a known background peak in the peak list to the intensity value of a known background peak in the exclusion list, and Multiply each intensity value on the peak list or exclusion list by that ratio; and After scaling the peak list or exclusion list, use a tandem mass spectrometer to exclude each peak from the peak list that has both an m / z value and an intensity value corresponding to the background peak in the exclusion list.

8. The method of claim 7, wherein if the m / z value matches within the m / z tolerance factor and if the intensity value matches within the intensity tolerance factor, then the m / z value and intensity value of the peaks in the peak list correspond to the m / z value and intensity value of the background peaks in the exclusion list.

9. The method of claim 7, wherein the scaling peak list or exclusion list comprises: Select two or more known background peaks from the peak list and exclusion list. Calculate the ratio of the intensity values ​​of a combination of two or more known background peaks from the peak list to the intensity values ​​of a combination of two or more known background peaks from the exclusion list, and Multiply each intensity value in the peak list or exclusion list by this ratio.

10. The method of claim 7, further comprising: An ion source device receives an ion beam from one or more compounds introduced from a control sample over time. Multiple MS scans of the mass range were performed on the ion beam at multiple different time steps to generate background peak m / z and intensity values ​​of background precursor ions over time. At each time step, select one or more background peaks from the background precursor ions in the exclusion list, and include the m / z value, intensity value, and retention time value of each of the selected one or more background peaks in the exclusion list. An ion source device receives an ion beam from one or more compounds introduced from an experimental sample over time. Multiple MS scans of the mass range were performed on the ion beam at multiple different time steps to generate the peak m / z and intensity values ​​of the precursor ions over time. At each time step, select one or more peaks from the precursor ion peaks in the peak list, and include in the peak list the m / z value, intensity value, and retention time value of each of the selected peaks, as well as... Exclude from the peak list any peak whose m / z value, intensity value, and retention time value correspond to the background peak in the exclusion list.

11. The method of claim 10, wherein if the m / z value matches within the m / z tolerance factor, if the intensity value matches within the intensity tolerance factor, and if the retention time value matches within the retention time tolerance factor, then the m / z value, intensity value, and retention time of the peaks in the peak list correspond to the m / z value, intensity value, and retention time of the background peaks in the exclusion list.

12. A computer program product comprising a non-transitory and tangible computer-readable storage medium containing instructions executable on a processor for performing a method for excluding endogenous background ions having the same mass-to-charge ratio m / z as metabolite ions from a peak list in an information correlation acquisition (IDA) mass spectrometry experiment, the method comprising: A system is provided, wherein the system includes one or more different software modules, and wherein the different software modules include a control module and an analysis module; The control module instructs the tandem mass spectrometer to receive the ion beam generated by ionizing a control sample that does not contain metabolite compounds from the ion source device; The control module is used to instruct the tandem mass spectrometer to perform mass range mass spectrometry (MS) scans on the ion beam, thereby generating background peak m / z and intensity values ​​for background precursor ions; Use the analysis module to select one or more background peaks from the background peaks of the background precursor ions for the exclusion list and include the m / z value and intensity value of each of the selected one or more background peaks in the exclusion list; The control module is used to instruct the tandem mass spectrometer to receive an ion beam generated by ionizing an experimental sample containing the metabolite compounds from the ion source device; The control module is used to instruct the tandem mass spectrometer to perform an MS scan of the ion beam within the mass range, thereby generating the peak m / z and intensity values ​​of the precursor ions. Use the analysis module to select one or more peaks from the precursor ion peaks for the peak list, and include the m / z value and intensity value of each of the selected one or more peaks in the peak list; Scaling or excluding the peak list can be done using the following methods: Select a known background peak from the peak list and the exclusion list. Calculate the ratio of the intensity value of a known background peak in the peak list to the intensity value of a known background peak in the exclusion list, and Multiply each intensity value in the peak list or exclusion list by that ratio; as well as After scaling the peak list or exclusion list, use the analysis module to exclude each peak from the peak list that has both the m / z value and intensity value corresponding to the background peak in the exclusion list.

Images