Threshold-based IDA Exclusion List

Abstract

First, an MS scan of the mass range of a control sample containing no metabolites is performed (601) to generate background peak m / z and intensity values ​​for background precursor ions (602). The background peaks are selected for an exclusion list, where an m / z value and an intensity value are included for each background peak (604). Next, an MS scan of the mass range of an experimental sample containing metabolites is performed (610) to generate peak m / z and intensity values ​​for precursor ions (612). Peaks are selected for a peak list, where an m / z value and an intensity value are included for each peak (614). Finally, each peak in the peak list that has both an m / z value and an intensity value corresponding to the m / z value and the intensity value of a background peak in the exclusion list is excluded from the peak list (616).

Description

Technical Field

[0001] (Cross - Reference to Related Applications) This application claims the benefit of U.S. Provisional Patent Application No. 62 / 916,759, filed October 17, 2019, the content of which is hereby incorporated by reference in its entirety.

Background Art

[0002] Introduction The teachings herein relate to a mass spectrometer for detecting metabolites of a sample in an information - dependent acquisition (IDA) mass spectrometry experiment. More specifically, the mass spectrometer is operated to distinguish metabolite ions from background ions having similar mass - to - charge ratios (m / z) by including intensity and retention time parameters in an IDA exclusion list.

[0003] The apparatus and methods disclosed herein are also implemented in conjunction with a computer system such as a processor, a controller, a microcontroller, or the computer system of FIG. 1. Background Art of Mass Spectrometry

[0004] Mass spectrometry (MS) is an analytical technique for the detection and quantification of chemical compounds based on the analysis of the m / z values of ions formed from the chemical compounds. MS involves the ionization of one or more target compounds from a sample to produce precursor ions, and the mass spectrometry of the precursor ions.

[0005] Tandem mass spectrometry or mass spectrometry / mass spectrometry (MS / MS) involves the ionization of one or more target compounds from a sample, the selection of one or more precursor ions of one or more compounds, the fragmentation of one or more precursor ions into product ions, and the mass spectrometry of the product ions.

[0006] Mass spectrometers are often coupled with chromatography or other separation systems to identify and characterize target compounds eluting from a sample. In such coupled systems, compounds in the eluting solvent are ionized, and a series of mass spectra are acquired at defined time intervals. These times can range, for example, from 1 second to 100 minutes or more. Intensity values derived from the series of mass spectra form a chromatogram. For example, the sum of all intensities generates a total ion chromatogram (TIC), and the intensity of one mass value generates an extracted ion chromatogram (XIC).

[0007] The peaks found in the chromatogram are used to identify or characterize known peptides or compounds in the sample because they elute at known times called retention times. More specifically, the retention time of the peak and / or the area of the peak are used to identify or characterize (quantify) known peptides or compounds in the sample.

[0008] In conventional separation-coupled mass spectrometry systems, precursor ions of known compounds are selected for analysis. MS / MS scans are then performed at each separation interval over the mass range containing the precursor ions. 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, as an XIC.

[0009] Both MS and MS / MS can provide qualitative and quantitative information. The measured precursor or product ion spectra can be used to identify the molecule of interest. The intensities of the precursor ions and product ions can also be used to quantify the amount of compound present in the sample.

[0010] A number of different types of experimental acquisition methods or workflows can be implemented 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).

[0011] In targeted acquisition methods, one or more transitions of precursor ions to product ions are predefined or known with respect to the compound of interest. As the sample is introduced into the tandem mass spectrometer, one or more transitions are monitored during each of multiple periods or cycles. In other words, the mass spectrometer selects and fragments the precursor ions of each transition and performs targeted mass spectrometry on the product ions of the transition. As a result, intensities (product ion intensities) are generated for each transition. Targeted acquisition methods include, but are not limited to, multiple reaction monitoring (MRM) and selected reaction monitoring (SRM).

[0012] In IDA methods, the user can define criteria for performing untargeted mass spectrometry of product ions while the sample is being introduced into the tandem mass spectrometer. For example, in IDA methods, precursor ions or mass spectrometry (MS) survey scans are performed to generate a precursor ion peak list. The user can select criteria for filtering the peak list with respect to a subset of the precursor ions on the peak list. MS / MS is then performed on each of the precursor ions in the subset of precursor ions. Product ion spectra are generated for each precursor ion. MS survey scans followed by multiple MS / MS scans can be repeatedly (iteratively) performed on the precursor ions in the subset of precursor ions as the 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 and the term "DDA" is a trademark of Waters.

[0013] The measurement of complex (e.g., biological) samples by different omics techniques such as proteomics and metabolomics leads to different types, large numbers, and a wide dynamic range of compounds. In proteomics and many other sample types, the complexity and dynamic range of the compounds are very large. This poses challenges for conventional targeting and IDA methods and requires ultra-fast MS / MS acquisition to thoroughly interrogate the sample in order to perform both the identification and quantification of a wide range of analytes.

[0014] As a result, DIA methods, a third broad category of tandem mass spectrometry, have been developed. These DIA methods have been used to increase the reproducibility and comprehensiveness of data collection from complex samples. DIA methods can also be referred to as non-specific fragmentation methods. In conventional DIA methods, the operation of the tandem mass spectrometer is not varied during the MS / MS scan based on data obtained in previous precursor or product ion scans. Instead, a precursor ion mass range is selected. A precursor ion mass selection window is then advanced across the precursor ion mass range. All precursor ions within the precursor ion mass selection window are fragmented, and all product ions of all precursor ions within the precursor ion mass selection window are mass analyzed. Problem of endogenous background peaks

[0015] When conducting drug metabolite identification studies, IDA is generally performed on samples from dosed subjects. The resulting MS / MS spectra are used to confirm that the putative metabolites are actually related to the starting drug and to localize the sites of metabolic transformation.

[0016] Figure 2 is an exemplary schematic diagram 200 showing a method by which a tandem mass spectrometer operated to identify drug metabolites in a simple sample using the IDA method can generate an IDA list containing endogenous background precursor ions in addition to metabolite precursor ions. In the IDA method of Figure 2, the tandem mass spectrometer first performs a full MS scan 210 of 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 figure, these devices are shown as quadrupoles, but can also be other types of devices. The mass analyzer generates intensity measurements for the precursor ions, as shown in the precursor mass spectrum 212.

[0017] The tandem mass spectrometer then selects all precursor ions having an intensity above a certain threshold 213. All precursor ions having an intensity above the threshold 213 are added to the threshold list 214. If the number of ions on the threshold list 214 is sufficiently small to be analyzed by MS / MS within a defined cycle time as shown in Figure 2, the threshold list 214 becomes the IDA list 216. Note that only the IDA list 214 contains the m / z of each precursor ion. Also note that precursor ions having an intensity above the threshold 213 are added to the threshold list 214 according to their m / z values. However, as discussed below, there are also other methods for selecting the order of precursor ions on the threshold list 214.

[0018] For each precursor ion on the IDA list 216, the tandem mass spectrometer performs an MS / MS scan. For example, in the MS / MS scan 221, a precursor ion with an 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 the MS / MS scans 222 and 223, 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.

[0019] The product ion spectra of the MS / MS scans 221, 222, and 223 are compared with the known product ion spectra for known drugs to determine whether they are likely to correspond to metabolites. Note that precursor ions with m / z values of 114 and 153 are endogenous background ion peaks. As a result, the endogenous background ion peaks can also be compared with the known metabolite peaks in the IDA method. For simple samples, this is not a problem.

[0020] However, for more complex samples, this can prevent the IDA method from being triggered for one or all of the metabolite peaks because much of the available cycle time is used to obtain MS / MS spectra of endogenous background peaks that are not needed. As a result, drug metabolites may not be identified.

[0021] FIG. 3 is an exemplary schematic diagram 300 showing how a tandem mass spectrometer operated to identify drug metabolites in a complex sample using the IDA method can generate an IDA list that does not include metabolite precursor ions. In the IDA method of FIG. 3, the tandem mass spectrometer first performs a full MS scan 310 of the complex sample. In the MS scan 310, all precursor ions of the sample are selected in a mass filter, passed through a dissociation device, and mass analyzed in a mass analyzer. In this figure, these devices are shown as quadrupoles, but they can also be other types of devices. The mass analyzer generates intensity measurements for the precursor ions, as shown in the precursor mass spectrum 312.

[0022] The tandem mass spectrometer then selects all precursor ions having an intensity above a certain threshold 313. All precursor ions having an intensity above the threshold 313 are added to the threshold list 314.

[0023] Since the complex sample is scanned, the precursor mass spectrum 312 includes six endogenous background precursor ion peaks in addition to metabolite peaks, which have an m / z value of 215. If the defined cycle time provides only enough time for the MS / MS scans to be performed on five precursor ion peaks, the threshold list 314 is compiled into the IDA list 316.

[0024] For each precursor ion on the IDA list 316, the tandem mass spectrometer performs an MS / MS scan. Since there are five precursor ion peaks on the IDA list 316, five MS / MS scans 321 - 325 are performed, generating five product ion spectra.

[0025] The product ion spectra of the MS / MS scans 321 - 325 are then compared with known product ion spectra for known drugs to determine whether they are likely to correspond to metabolites. The metabolites may not themselves be "known". Note that in the precursor ion spectrum 312, the metabolite precursor ion with m / z 215 is preceded by six endogenous background precursor ions. Since the IDA list 316 is limited to only five precursor ion peaks, the metabolite precursor ion with m / z 215 was not added to the list. As a result, the product ion spectra of the MS / MS scans 321 - 325 provide only the product ions of the endogenous background precursor ions. As a result, no known drug metabolites are found in this case.

[0026] Performing the analysis via IDA acquisition is one of the most widely used methods for generating MS / MS information in an automated fashion. Over the years, several filters for filtering threshold peak lists for subsets of precursor ions to be dissociated have been developed to optimize the automated selection of ions of interest in specific applications.

[0027] In metabolite research, control samples can be obtained and analyzed. Control samples are similar to metabolite samples but represent the conditions before drug administration. Naturally, the more similar the control sample is to the experimental sample, the better. For example, the control sample can be pre-dose but from the same subject as the corresponding dosed sample. Putative metabolites are found by searching for peaks that appear in the dosed sample but not in the control sample.

[0028] It is possible to analyze the control sample by finding all the peaks before the acquisition of the dosed sample. It has been previously shown that this list of peaks can be used as an IDA exclusion list when obtaining data on the dosed sample. This prevents IDA from being triggered on background peaks and thus increases the likelihood that MS / MS will be obtained for actual drug metabolites of interest.

[0029] Figure 4 is an exemplary schematic diagram 400 showing how a tandem mass spectrometer is operated to first perform an MS scan on a control sample to generate an exclusion list and then use the exclusion list in an IDA method applied to a complex sample to identify drug metabolites in the complex sample. In the IDA method of Figure 4, the tandem mass spectrometer first performs a full MS scan 401 of the control sample. The control sample is known to contain no metabolites of interest. In MS scan 401, all precursor ions of the control sample are selected in a mass filter, transmitted through a dissociation device, and mass analyzed in a mass analyzer. In this figure, these devices are shown as quadrupoles, but can also be other types of devices. The mass analyzer generates intensity measurements for the precursor ions, as shown in precursor mass spectrum 402.

[0030] The tandem mass spectrometer then selects all precursor ions having an intensity above a certain threshold of 403. All precursor ions having an intensity above the threshold of 403 are added to the exclusion list 404. Since the control sample does not contain the metabolite of interest, all precursor ions on the exclusion list 404 are endogenous background ions.

[0031] The tandem mass spectrometer then performs a full MS scan 410 of the experimental sample known to contain the metabolite 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 figure, these devices are shown as quadrupoles, but can also be other types of devices. The mass analyzer generates intensity measurements for the precursor ions, as shown in the precursor mass spectrum 412.

[0032] The tandem mass spectrometer then selects all precursor ions having an intensity above a certain threshold of 413. All precursor ions having an intensity above the threshold of 413 are added to the threshold list 414. Since the experimental sample contains the metabolite of interest, the threshold list 414 includes metabolite precursor ions with m / z 215 in addition to all endogenous background ions.

[0033] The tandem mass spectrometer removes the precursor ion peaks on the exclusion list 404 from the threshold list 414. This generates the IDA list 416. The IDA list 416 here contains only the metabolite precursor ions with m / z 215.

[0034] For each precursor ion on the IDA list 416, the tandem mass spectrometer performs an MS / MS scan. Since there is only one precursor ion peak on the IDA list 416, only the MS / MS scan 421 is performed, generating one product ion spectrum.

[0035] The generated ion spectrum of the MS / MS scan 421 is then compared with known generated ion spectra for known drugs to determine whether they are likely to correspond to metabolites. Note that by using the exclusion list 404, the MS / MS scan is not performed on endogenous background precursor ion peaks. This ensures that the MS / MS scan 421 is performed on metabolite precursor ions with m / z 215.

[0036] One problem associated with using an exclusion list derived from a control sample is that MS / MS will not be triggered for peaks related to drug metabolites having m / z similar to the background peak, even if the peak intensity is considerably greater for drug metabolites being compared to the background peak.

[0037] Figure 5 is an exemplary schematic diagram 500 showing how an exclusion list from an MS scan performed on a control sample can also remove metabolite peaks in an IDA method when metabolite and background peaks have similar m / z values. In the IDA method of Figure 5, the tandem mass spectrometer first performs a full MS scan 501 of the control sample. The control sample is known to not contain the metabolite of interest. In the MS scan 501, all precursor ions of the control sample are selected in a mass filter, passed through a dissociation device, and mass analyzed in a mass analyzer. In this figure, these devices are shown as quadrupoles, but can also be other types of devices. The mass analyzer generates intensity measurements for the precursor ions, as shown in the precursor mass spectrum 502.

[0038] The tandem mass spectrometer then selects all precursor ions having an intensity above a certain threshold 503. All precursor ions having an intensity above the threshold 503 are added to the exclusion list 504.

[0039] The tandem mass spectrometer then performs a full MS scan 510 of an experimental sample known to contain the metabolite of interest. In the 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 figure, these devices are shown as quadrupoles, but they can also be other types of devices. The mass analyzer generates intensity measurements for the precursor ions, as shown in the precursor mass spectrum 512.

[0040] The tandem mass spectrometer then selects all precursor ions having an intensity above a certain threshold 513. All precursor ions having an intensity above the threshold 513 are added to the threshold list 514. Since the experimental sample contains the metabolite of interest, the threshold list 514 includes the metabolite precursor ion 518 with m / z 190. However, background ions 517 with m / z 190 are also present. As a result, the threshold list 514 contains two ion peaks with m / z 190.

[0041] Next, the tandem mass spectrometer removes the precursor ion peaks that are on the exclusion list 504 from the threshold list 514. Since the metabolite precursor ion 518 and the background ion 517 have the same m / z value of 190, they are both excluded. As a result, the IDA list 516 here contains no ion peaks and no MS / MS scans are performed. As a result, when the metabolite and the background peak have similar m / z values, the MS / MS scan is not triggered for the drug metabolite even when the control sample and the exclusion list are used.

[0042] As a result, an additional system method for operating the tandem mass spectrometer in the IDA method is required to distinguish between background and metabolite ions having similar m / z values. Summary of the Invention Means for Solving the Problems

[0043] A system, method, and computer program product are disclosed for excluding endogenous background ions having the same mass / 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.

[0044] The tandem mass spectrometer receives an ion beam from the ion source device generated by ionizing a control sample that does not contain metabolite compounds. The tandem mass spectrometer performs an MS scan of a certain mass range on the ion beam and generates background peak m / z and intensity values for the background precursor ions. The tandem mass spectrometer selects one or more of the background peaks of the background precursor ions with respect to the exclusion list and includes the m / z value and intensity value for each of the selected one or more background peaks in the exclusion list.

[0045] The tandem mass spectrometer then creates a peak list for the IDA method by analyzing the experimental sample. The tandem mass spectrometer receives an ion beam from the ion source device generated by ionizing an experimental sample that contains metabolite compounds. The tandem mass spectrometer performs an MS scan of that mass range on the ion beam and generates peak m / z and intensity values for the precursor ions. The tandem mass spectrometer selects one or more of the peaks of the precursor ions with respect to the peak list and includes the m / z value and intensity value for each of the selected one or more peaks in the peak list.

[0046] Finally, the tandem mass spectrometer excludes from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peaks in the exclusion list.

[0047] These and other features of the applicant's teachings are described herein. This specification also provides, for example, the following items. (Item 1) A system for excluding endogenous background ions having the same mass / charge ratio (m / z) as metabolite ions from a peak list in an information-dependent acquisition (IDA) mass spectrometry experiment, an ion source device, and a tandem mass spectrometer, wherein the tandem mass spectrometer (a) receives an ion beam from the ion source device generated by ionizing a control sample not containing a metabolite compound, performs a mass spectrometry (MS) scan of a certain mass range on the ion beam, generates background peak m / z and intensity values for background precursor ions, selects one or more of the background peaks of the background precursor ions with respect to an exclusion list, and includes the m / z value and intensity value for each background peak of the one or more selected background peaks in the exclusion list to create the exclusion list; (b) receives an ion beam from the ion source device generated by ionizing an experimental sample containing the metabolite compound, performs an MS scan of the mass range on the ion beam, generates peak m / z and intensity values for precursor ions, selects one or more of the peaks of the precursor ions with respect to a peak list, and includes the m / z value and intensity value for each peak of the one or more selected peaks in the peak list to create the peak list; (c) excludes each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peak in the exclusion list from the peak list and a tandem mass spectrometer that comprises a system. (Item 2) The system according to Item 1, wherein the m / z value and intensity value of the peak in the peak list correspond to the m / z value and intensity value of the background peak in the exclusion list when the m / z value matches within an m / z tolerance factor and the intensity value matches within an intensity tolerance factor. (Item 3) The system according to Item 1, wherein the tandem mass spectrometer further scales the peak list or the exclusion list before comparing the peaks in step (c). (Item 4) The tandem mass spectrometer further selects one known background peak on the peak list and the exclusion list; Calculating a ratio of the intensity value of the one known background peak on the peak list and the intensity value of the one known background peak on the exclusion list; Multiplying each intensity value on the peak list or the exclusion list by the ratio; The system according to item 4, wherein the intensity of the peak list or the exclusion list is scaled by: (Item 5) The tandem mass spectrometer further comprises: Selecting two or more known background peaks on the peak list and the exclusion list; Calculating a ratio of a combination of intensity values of the two or more known background peaks on the peak list and a combination of intensity values of the two or more known background peaks on the exclusion list; Multiplying each intensity value on the peak list or the exclusion list by the ratio; The system according to item 4, wherein the intensity of the peak list or the exclusion list is scaled by: (Item 6) The tandem mass spectrometer further includes a sample introduction device, and the tandem mass spectrometer further comprises: In step (a), receiving an ion beam from the ion source device that receives one or more compounds from the control sample over time from the sample introduction device, performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam, generating background peak m / z and intensity values for background precursor ions over time, selecting, at each time step, one or more of the background peaks of the background precursor ions with respect to the exclusion list, and including, in the exclusion list, the m / z value, intensity value, and dwell time value for each of the selected one or more of the background peaks; In step (b), receiving an ion beam from the ion source device that receives one or more compounds from the experimental sample over time from the sample introduction device, performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam, generating peak m / z and intensity values for precursor ions over time, selecting, at each time step, one or more of the peaks of the precursor ions with respect to the peak list, and including, within the peak list, the m / z value, intensity value, and dwell time value for each peak of the selected one or more peaks. In step (c), excluding from the peak list each peak having an m / z value, intensity value, and dwell time corresponding to the m / z value, intensity value, and dwell time of the background peaks of the exclusion list. The system according to item 1. (Item 7) The m / z value, intensity value, and dwell time of the peaks in the peak list are corresponding to the m / z value, intensity value, and dwell time of the background peaks of the exclusion list when the m / z value matches within the m / z tolerance factor, the intensity value matches within the intensity tolerance factor, and the dwell time value matches within the dwell time tolerance factor. The system according to item 1. (Item 8) A method for excluding endogenous background ions having the same mass / charge ratio (m / z) as metabolite ions from a peak list in an information-dependent acquisition (IDA) mass spectrometry experiment, receiving an ion beam from an ion source device generated by ionizing a control sample not containing a metabolite compound using a tandem mass spectrometer; performing a mass spectrometry (MS) scan of a certain mass range on the ion beam using the tandem mass spectrometer to generate background peak m / z and intensity values for background precursor ions; selecting, using the tandem mass spectrometer, one or more of the background peaks of the background precursor ions with respect to the exclusion list and including, within the exclusion list, the m / z value and intensity value for each background peak of the selected one or more background peaks; receiving an ion beam from the ion source device generated by ionizing the experimental sample containing the metabolite compound using the tandem mass spectrometer. Using the tandem mass spectrometer, performing an MS scan of the mass range on the ion beam to generate peak m / z and intensity values for precursor ions; Using the tandem mass spectrometer, selecting one or more than one of the peaks of the precursor ions with respect to the peak list, and including the m / z value and intensity value for each peak of the selected one or more than one peak in the peak list; Using the tandem mass spectrometer, excluding from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peak in the exclusion list; A method comprising. (Item 9) The method according to item 8, wherein the m / z value and intensity value of the peak in the peak list correspond to the m / z value and intensity value of the background peak in the exclusion list when the m / z value matches within the m / z tolerance factor and the intensity value matches within the intensity tolerance factor. (Item 10) The method according to item 8, further comprising scaling the peak list or the exclusion list before excluding from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peak in the exclusion list. (Item 11) The step of scaling the peak list or the exclusion list comprises: Selecting one known background peak on the peak list and the exclusion list; Calculating the 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; Multiplying each intensity value on the peak list or the exclusion list by the ratio. The method according to item 10, comprising. (Item 12) The step of scaling the peak list or the exclusion list comprises: Selecting two or more known background peaks on the peak list and the exclusion list; Calculating the ratio of the combination of the intensity values of the two or more known background peaks on the peak list to the combination of the intensity values of the two or more known background peaks on the exclusion list; Multiplying each intensity value on the peak list or the exclusion list by the ratio. The method according to item 10, comprising. (Item 13) Receiving an ion beam from the ion source device that receives, over time, one or more compounds from the control sample from the sample introduction device; Performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam to generate background peak m / z and intensity values for background precursor ions over time; At each time step, selecting one or more of the background peaks of the background precursor ions with respect to the exclusion list and including, within the exclusion list, the m / z value, intensity value, and dwell time value for each background peak that is one or more of the selected background peaks; Receiving an ion beam from the ion source device that receives, over time, one or more compounds from the experimental sample from the sample introduction device; Performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam to generate peak m / z and intensity values for precursor ions over time; At each time step, selecting one or more of the peaks of the precursor ions with respect to the peak list and including, within the peak list, the m / z value, intensity value, and dwell time value for each peak that is one or more of the selected peaks; Excluding from the peak list each peak having an m / z value, intensity value, and dwell time value corresponding to the m / z value, intensity value, and dwell time value of the background peaks of the exclusion list; The method according to item 8, further comprising: (Item 14) The m / z value, intensity value, and dwell time of the peaks in the peak list are those corresponding to the m / z value, intensity value, and dwell time of the background peaks in the exclusion list when the m / z value matches within the m / z tolerance factor, the intensity value matches within the intensity tolerance factor, and the dwell time value matches within the dwell time tolerance factor, according to the method described in item 13. (Item 15) A computer program product comprising a non-transitory and tangible computer-readable storage medium, the content of the non-transitory and tangible computer-readable storage medium including a program with instructions executable on a processor to implement a method for excluding endogenous background ions having the same mass / charge ratio (m / z) as metabolite ions from a peak list in an information-dependent acquisition (IDA) mass spectrometry experiment, the method comprising: Providing a system, the system comprising one or more distinct software modules, the distinct software modules comprising a control module and an analysis module; Instructing a tandem mass spectrometer to receive an ion beam from an ion source device generated by ionizing a control sample not containing a metabolite compound using the control module; Instructing the tandem mass spectrometer to perform a mass spectrometry (MS) scan of a mass range on the ion beam using the control module to generate background peak m / z and intensity values for background precursor ions; Using the analysis module to select one or more of the background peaks of the background precursor ions with respect to an exclusion list and including the m / z value and intensity value for each of the selected one or more background peaks in the exclusion list; Instructing the tandem mass spectrometer to receive an ion beam from the ion source device generated by ionizing an experimental sample containing the metabolite compound using the control module; Instructing the tandem mass spectrometer to perform an MS scan of the mass range on the ion beam using the control module to generate peak m / z and intensity values for precursor ions; Using the analysis module to select one or more of the peaks of the precursor ions with respect to a peak list and including the m / z value and intensity value for each of the selected one or more peaks in the peak list; Using the analysis module, excluding from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and the intensity value of the background peak of the exclusion list A computer program product including the above.

Brief Description of the Drawings

[0048] Those skilled in the art will understand that the drawings described below are for illustrative purposes only. The drawings are not intended to limit the scope of the present teachings in any way.

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[0058] Before one or more embodiments of the present teachings are described in detail, those skilled in the art will understand that the present teachings are not limited to the details of the structures, arrangements of components, and arrangements of steps described or illustrated in the figures in the form for carrying out the following inventions in their applications. It should also be understood that the expressions and technical terms used herein are for the purpose of description and should not be regarded as limiting.

Embodiments for Carrying Out the Invention

[0059] Description of Various Embodiments Computer-Implemented System

[0060] FIG. 1 is a block diagram illustrating a computer system 100 in which an embodiment of the present teachings may be implemented. The computer system 100 includes a bus 102 or other communication mechanism for communicating information, and a processor 104 coupled to the bus 102 for processing information. The computer system 100 also includes a memory 106, which may be a random access memory (RAM) or other dynamic storage device coupled to the bus 102 for storing instructions to be executed by the processor 104. The memory 106 may also be used to store temporary variables or other intermediate information during execution of instructions by the processor 104. The computer system 100 further includes a read-only memory (ROM) 108 or other static storage device coupled to the bus 102 for storing static information and instructions for the processor 104. A storage device 110, such as a magnetic disk or optical disk, is provided for storing information and instructions and is coupled to the bus 102.

[0061] Computer system 100 can be coupled via bus 102 to a display 112, such as a cathode ray tube (CRT) or a 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 a cursor control 116, such as a mouse, trackball, or cursor direction keys, for communicating direction information and command selections to processor 104 and controlling cursor movement on display 112. This input device typically has two degrees of freedom in two axes, i.e., a first axis (i.e., x) and a second axis (i.e., y), which enable the device to specify a position in a plane.

[0062] Computer system 100 can implement the present teachings. According to certain implementations of the present teachings, results are provided by computer system 100 in response to processor 104 executing one or more sequences of one or more instructions contained within memory 106. Such instructions can be read into memory 106 from another computer-readable medium, such as storage device 110. Execution of the sequence of instructions contained in memory 106 causes processor 104 to perform the processes described herein. Alternatively, wired circuitry can be used in place of, or in combination with, software instructions for implementing the present teachings. Accordingly, implementations of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0063] In various embodiments, computer system 100 can be connected across a network to one or more other computer systems such as 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 serve other computer systems. One or more computer systems that store and serve data can be referred to as servers or clouds in a cloud computing scenario. One or more computer systems can include, for example, one or more web servers. Other computer systems that send and receive data to and from the server or cloud can be referred to as clients or cloud devices, for example.

[0064] As used herein, the term "computer-readable medium" refers to any medium that participates in providing instructions to 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 includes, for example, optical or magnetic disks such as storage device 110. Volatile media includes dynamic memory such as memory 106. Transmission media includes coaxial cables, copper wire, and fiber optics, including the wiring that comprises bus 102.

[0065] A general form of a computer-readable medium or a computer program product can include, for example, a floppy (registered trademark) disk, a flexible disk, a hard disk, a magnetic tape, or any other magnetic medium, a CD-ROM, a digital video disk (DVD), a Blu-ray disk, any other optical medium, a thumb drive, a memory card, RAM, PROM, and EPROM, flash-EPROM, any other memory chip or cartridge, or any other tangible medium that can be read by a computer.

[0066] Various forms of computer-readable media may be involved in carrying one or more sequences of one or more instructions to the processor 104 for execution. For example, the instructions may initially be carried on the magnetic disk of a remote computer. The remote computer can load the instructions into its dynamic memory and use a modem to send the instructions via a telephone line. A modem local to the computer system 100 can receive the data on the telephone line and use an infrared transmitter to convert the data into an infrared signal. An infrared detector coupled to the bus 102 can receive the data carried by the infrared signal and place the data on the bus 102. The bus 102 carries the data to the memory 106, from where the processor 104 reads and executes the instructions. The instructions received by the memory 106 may optionally be stored on the storage device 110 either before or after execution by the processor 104.

[0067] According to various embodiments, instructions configured to be executed by a processor to implement 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 well known in the art for storing software. The computer-readable medium is accessed by a suitable processor for executing the instructions configured to be executed.

[0068] The following description of various implementations of the present teachings is presented for purposes of illustration and description. It is not intended to be exhaustive or to limit the present teachings to the precise forms disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practice of the present teachings. Additionally, the implementations described include 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 by both object-oriented and non-object-oriented programming systems. IDA exclusion list with intensity and retention time

[0069] As described above, when performing metabolite identification studies, IDA is generally performed on samples from dosed subjects. The resulting MS / MS spectra are used to confirm that the putative metabolites are in fact related to the starting drug and to locate the sites of metabolic transformation. For simple samples, conventional IDA functions well. However, for more complex samples, endogenous background ions can prevent the IDA method from being triggered for one or all of the metabolite peaks because much of the available cycle time is used to obtain MS / MS spectra of the endogenous background peaks that are not needed. As a result, drug metabolites may not be identified.

[0070] One solution to this problem is to first analyze a similar control sample that does not contain metabolites to generate a background ion peak list. This list can then be used as an IDA exclusion list when obtaining data on the dosed sample. This prevents the IDA from being triggered on the background peaks and thus increases the likelihood that MS / MS will be obtained for the actual drug metabolites of interest.

[0071] One problem associated with using an exclusion list derived from a control sample is that MS / MS will not be triggered for peaks related to drug metabolites that have m / z values similar to the background peaks. As a result, additional system methods for operating the tandem mass spectrometer in the IDA method are needed to distinguish between background and metabolite ions with similar m / z values.

[0072] In various embodiments, the tandem mass spectrometer includes the intensity of each background peak in the IDA exclusion list. The IDA method then triggers an MS / MS scan for the dosed sample if either there are no corresponding peaks for the control sample or the peaks in the control sample have the same retention time and are smaller in intensity. An acceptance factor can be used when comparing peak intensities. For example, the IDA method triggers an MS / MS scan only if the intensity is 1.5 times or greater than that of the background peak. This modification of the IDA method reduces the likelihood that an MS / MS scan will not be triggered for drug metabolites when using the exclusion list.

[0073] As described above, mass spectrometers are often coupled with chromatography or other separation systems to identify and characterize the compounds of interest eluting from a sample. In such coupled systems, the compounds in the eluting solvent are ionized and a series of mass spectra are acquired at defined time intervals. The time it takes for an analyte or metabolite to elute from injection to detection is referred to as the retention time (RT). As a result, metabolite ions can also be distinguished from endogenous background ions based on their retention times.

[0074] In various embodiments, therefore, the tandem mass spectrometer includes the intensity and retention time of each background peak in the IDA exclusion list. The IDA method then triggers an MS / MS scan for the dosed sample if either there are no corresponding peaks for the control sample or the peaks in the control sample have the same retention time and are smaller in intensity.

[0075] Figure 6 is an exemplary schematic diagram 600 showing a method by which adding intensity and retention time to an exclusion list from an MS scan performed on a control sample according to various embodiments can prevent metabolite peaks from being removed in the IDA method when metabolite peaks and background peaks have similar m / z values. In the IDA method of Figure 6, the tandem mass spectrometer first performs several full MS scans of the control sample as the control sample is eluted using a separation device. The three-dimensional chromatogram 602 shows mass peaks generated for every four endogenous background ions. The control sample is known to not contain the metabolite of interest. In each MS scan 601 performed at different time steps, all precursor ions of the control sample are selected in a mass filter, passed through a dissociation device, mass analyzed in a mass analyzer, and a precursor ion spectrum is generated for each time step. In this figure, these devices are shown as quadrupoles, but can also be other types of devices.

[0076] At each time step, the tandem mass spectrometer then selects all peaks having an intensity above a certain threshold 603. All precursor ion peaks having an intensity above the threshold 603 are added to an exclusion list 604. In addition, the intensity and retention time of each peak are also added to the exclusion list 604, where three columns are generated in the exclusion list 604.

[0077] The tandem mass spectrometer then performs several full MS scans 610 of an experimental sample known to contain the metabolite of interest. In each MS scan 610 performed at different time steps, all precursor ions of the experimental sample are selected in a mass filter, passed through a dissociation device, mass analyzed in a mass analyzer, and a precursor ion spectrum is generated for each time step. The three-dimensional chromatogram 612 shows the generated mass peaks.

[0078] The tandem mass spectrometer then selects all peaks having an intensity above a certain threshold 613. All precursor ion peaks having an intensity 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, where three columns are generated in the threshold list 614. Since the experimental sample contains the metabolite of interest, the threshold list 614 includes a 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. As a result, the threshold list 614 includes two ion peaks with m / z 190.

[0079] Next, the tandem mass spectrometer removes the precursor ion peaks that are on the exclusion list 604 from the threshold list 614. Previously, the metabolite precursor ion peak 618 and the background ion peak 617 of the threshold list 614 had the same m / z value of 190 as the background ion peak of the exclusion list 604, so both of them were excluded.

[0080] However, here, the retention time and intensity of the precursor ion peak 618 and the background ion peak 617 of the threshold list 614 are also compared with the retention time and intensity of the background ion peak of the exclusion list 604. From this comparison, it is found that the background ion peak 617 of the threshold list 614 matches the background ion peak of the exclusion 604 and is excluded. However, even if the m / z and retention time of the metabolite precursor ion peak 618 of the threshold list 614 match the m / z and retention time of the background ion peak of the exclusion 604, the intensities do not match. As a result, the metabolite precursor ion peak 618 of the threshold list 614 is not excluded and is therefore added to the IDA list 616. Note that all other peaks of the threshold list 614 match the peaks of the exclusion list 604 and are excluded.

[0081] Also, although the IDA list 616 is shown as a separate list, it should be noted that the IDA list 616 can simply be the threshold list 614 after peaks have been excluded. Further, note that the threshold list 614 is constantly updated and excluded in real time as peaks are obtained during separation, and thus the IDA list 616 also constantly changes during separation.

[0082] During separation, for each precursor ion peak on the IDA list 616, the tandem mass spectrometer performs an MS / MS scan while the precursor ion peak is on the IDA list 616. In this case, since there is only one precursor ion peak on the IDA list 616, as long as the metabolite precursor ion peak 618 is on the IDA list 616, only the MS / MS scan 621 is performed, generating an ion spectrum for each MS / MS scan.

[0083] The ion spectra generated by the MS / MS scan 621 are then compared with known ion spectra for known drugs to determine whether they are likely to correspond to metabolites. Note that by using the exclusion list 604 with additional intensity and retention time parameter values, the MS / MS scan is not performed for both endogenous background precursor ion peaks and metabolite ion peaks that have similar m / z values but different intensities or different retention times. In other words, metabolite ion peaks are no longer erroneously excluded.

[0084] In various embodiments, different tolerance factors for matching the values of each parameter are used when comparing m / z, retention time, and intensity between the threshold list and the exclusion list. For example, the tolerance factor for intensity can be, but is not limited to, a factor of 1.5. This means that if m / z and retention also match, the MS / MS scan is triggered for a peak on the threshold list 614 only if the intensity is 1.5 times the intensity of the peak on the exclusion list 604.

[0085] Note that the concentrations of the control sample and the experimental sample can be different. As a result, in various embodiments, the intensities of the threshold list 614 or the exclusion list 604 are scaled before the two lists are compared. For example, the control and experimental urine samples can have different volumes. Urine is known to naturally contain certain compounds such as creatinine. As a result, the ratio of the intensities for creatinine in the threshold list and the exclusion list can be used to scale all the intensities in the threshold list or the exclusion list. System for excluding background peaks from a peak list

[0086] FIG. 7 is a schematic diagram 700 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. The system of FIG. 7 includes an ion source device 710 and a tandem mass spectrometer 701.

[0087] The ion source device 710 can be, but is not limited to, a chemical ionization (CI) source device such as an electrospray ionization source (ESI) device, 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.

[0088] The tandem mass spectrometer 701 includes, for example, a mass filter device 720, a dissociation device 730, and a mass analyzer 740. In the system of FIG. 7, the mass filter device 720, the dissociation device 730, and the mass analyzer 740 are shown as quadrupole devices. Those skilled in the art will understand that any of these stages can include other types of mass spectrometry devices including, but not limited to, an ion trap, an orbitrap, an ion mobility device, a time-of-flight (TOF) device, an electron-based dissociation (ExD) collision cell, or a Fourier transform ion cyclotron resonance (FT-ICR) device.

[0089] The tandem mass spectrometer 701 first creates an exclusion list by analyzing a control sample. The tandem mass spectrometer 701 receives an ion beam from an ion source device 710 generated by ionizing a control sample that does not contain metabolite compounds. Note that in FIG. 7, 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.

[0090] The tandem mass spectrometer 701 performs an MS scan of a certain mass range on the ion beam and generates 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 with respect to the exclusion list and includes the m / z value and intensity value for each background peak of the selected one or more background peaks in the exclusion list.

[0091] The tandem mass spectrometer 701 then creates a peak list for the IDA method by analyzing an experimental sample. The tandem mass spectrometer 701 receives an ion beam from an ion source device generated by ionizing an experimental sample that contains metabolite compounds. The tandem mass spectrometer 701 performs an MS scan of that mass range on the ion beam and generates peak m / z and intensity values for precursor ions. The tandem mass spectrometer 701 selects one or more of the peaks of the precursor ions with respect to the peak list and includes the m / z value and intensity value for each peak of the selected one or more peaks in the peak list.

[0092] Finally, the tandem mass spectrometer 701 excludes each peak in the peak list that has both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peak in the exclusion list.

[0093] In various embodiments, the tandem mass spectrometer 701 further performs an MS / MS scan of each precursor ion peak on the peak list to identify metabolite compounds.

[0094] In various embodiments, the tandem mass spectrometer 701 selects one or more than one of the peaks of the precursor ions with respect to the peak list by selecting the first N peaks measured above a certain threshold intensity level. In another embodiment, the tandem mass spectrometer 701 selects one or more than one of the peaks of the precursor ions with respect to the peak list by selecting the N peaks with the highest intensities.

[0095] In various embodiments, 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 if the m / z value matches within the m / z tolerance factor and the intensity value matches within the intensity tolerance factor. As explained above, the intensity tolerance factor can be, for example, 1.5 times the intensity of the background peaks in the exclusion list.

[0096] In various embodiments, the tandem mass spectrometer 701 further compares the peaks in the two lists and scales the peak list or the exclusion list before matching. As explained 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 the ratio of the intensity value of one known background peak on the peak list and the intensity value of 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 that ratio.

[0097] In various embodiments, two or more background ions can be used to scale the peak list or the exclusion list. For example, the tandem mass spectrometer 701 selects two or more known background peaks on the peak list and the exclusion list. The tandem mass spectrometer 701 calculates the ratio of the combination of intensity values of two or more known background peaks on the peak list and the combination of intensity values of two or more known background peaks on the exclusion list. The combination of intensity values of two or more known background peaks can be, but is not limited to, an average value, a median value, or a weighted intensity average. The tandem mass spectrometer 701 then multiplies each intensity value on the peak list or the exclusion list by that ratio.

[0098] In various embodiments, the tandem mass spectrometer 701 further includes a sample introduction device 760. The sample introduction device 760 introduces one or more target compounds from the sample into the ion source device 710 over time. The sample introduction device 760 can perform techniques including, but not limited to, injection, liquid chromatography, gas chromatography, capillary electrophoresis, or ion mobility.

[0099] When using the sample introduction device 760, the tandem mass spectrometer 701 receives an ion beam from the ion source device 710 that receives one or more compounds from a control sample over time from the sample introduction device 760. The tandem mass spectrometer 701 then performs a plurality of MS scans of a mass range at a plurality of different time steps on the ion beam, generating background peak m / z and intensity values for background precursor ions over time. At each time step, the tandem mass spectrometer 701 selects one or more of the background peaks of the background precursor ions with respect to the exclusion list and includes the m / z value, intensity value, and dwell time value for each of the selected one or more of the background peaks in the exclusion list.

[0100] Next, the tandem mass spectrometer 701 receives an ion beam from an ion source device 710 that receives one or more compounds from the experimental sample over time from a sample introduction device 760. The tandem mass spectrometer 701 performs a plurality of MS scans of its mass range at a plurality of different time steps on the ion beam, generating peak m / z and intensity values for precursor ions over time. For each time step, the tandem mass spectrometer 701 selects one or more of the peaks of the precursor ions with respect to the peak list and includes in the peak list the m / z value, intensity value, and dwell time value for each peak of the one or more selected peaks.

[0101] Finally, the tandem mass spectrometer 701 excludes from the peak list each peak having an m / z value, intensity value, and dwell time corresponding to the m / z value, intensity value, and dwell time of the background peaks in the exclusion list.

[0102] In various embodiments, the m / z value, intensity value, and dwell time of the peaks in the peak list correspond to the m / z value, intensity value, and dwell time of the background peaks in the exclusion list when the m / z value matches within the m / z tolerance factor, the intensity value matches within the intensity tolerance factor, and the dwell time value matches within the dwell time tolerance factor.

[0103] 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 independently perform one or more than one of the steps described above. The processor 750 controls or provides instructions, for example, by 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, the computer system of FIG. 1, or the tandem mass spectrometer, and any device capable of transmitting and receiving control signals and data thereto and therefrom and processing data. The processor 750 communicates with the tandem mass spectrometer 701. Although shown as a separate device, the processor 750 can also be a processor or controller of the tandem mass spectrometer 701 or another device. Method for excluding background peaks from a peak list

[0104] FIG. 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.

[0105] In step 810 of method 800, an ion beam generated by ionizing a control sample that does not contain a metabolite compound is received from an ion source device using a tandem mass spectrometer.

[0106] In step 820, a mass spectrometry (MS) scan of a certain mass range is performed on the ion beam using a tandem mass spectrometer to generate background peak m / z and intensity values for background precursor ions.

[0107] In step 830, using a tandem mass spectrometer, one or more of the background peaks of the background precursor ions are selected with respect to an exclusion list, and in the exclusion list, the m / z value and the intensity value are included for each of the background peaks of the one or more selected background peaks.

[0108] In step 840, using a tandem mass spectrometer, an ion beam generated by ionizing an experimental sample containing metabolite compounds is received from an ion source device.

[0109] In step 850, using a tandem mass spectrometer, an MS scan of its mass range is performed on the ion beam to generate peak m / z and intensity values for the precursor ions.

[0110] In step 860, using a tandem mass spectrometer, one or more of the peaks of the precursor ions are selected with respect to a peak list, and in the peak list, the m / z value and the intensity value are included for each of the peaks of the one or more selected peaks.

[0111] In step 870, using a tandem mass spectrometer, each peak in the peak list having both an m / z value and an intensity value corresponding to the m / z value and the intensity value of the background peaks in the exclusion list is excluded. Computer program product for excluding background peaks from a peak list

[0112] In various embodiments, the computer program product includes a program with instructions that are executed on a processor such that the content thereof implements 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. The method is implemented by a system that includes one or more distinct software modules.

[0113] FIG. 9 is a schematic diagram of a system 900 that implements 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, including one or more distinct software modules. The system 900 includes a control module 910 and an analysis module 920.

[0114] The control module 910 instructs the tandem mass spectrometer to receive an ion beam from an ion source device generated by ionizing a control sample that does not contain metabolite compounds. The control module 910 performs an MS scan of a certain mass range on the ion beam and instructs the tandem mass spectrometer to generate background peak m / z and intensity values for background precursor ions. The analysis module 920 selects one or more of the background peaks of the background precursor ions with respect to the exclusion list and includes the m / z value and intensity value for each of the selected one or more background peaks in the exclusion list.

[0115] The control module 910 instructs the tandem mass spectrometer to receive an ion beam from an ion source device generated by ionizing an experimental sample that contains metabolite compounds. The control module 910 performs an MS scan of that mass range on the ion beam and instructs the tandem mass spectrometer to generate peak m / z and intensity values for precursor ions. The analysis module 920 selects one or more of the peaks of the precursor ions with respect to the peak list and includes the m / z value and intensity value for each of the selected one or more peaks in the peak list. Finally, the analysis module 920 excludes each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peaks in the exclusion list from the peak list.

[0116] Furthermore, in the description of various embodiments, this specification may present methods and / or processes as a particular sequence of steps. However, to the extent that a method or process does not depend on a particular order of the steps described herein, the method or process should not be limited to the particular sequence of steps described. As will be understood by those skilled in the art, other sequences of steps may be possible. Accordingly, the particular order of steps described herein should not be construed as a limitation with respect to the claims. Additionally, claims directed to methods and / or processes should not be limited to performing those steps in the written order, and those skilled in the art can readily understand that the sequence can be varied and still remain within the spirit and scope of the various embodiments.

Claims

1. A system for excluding endogenous background ions having the same mass / charge ratio (m / z) as metabolite ions from a peak list in an information-dependent acquisition (IDA) mass spectrometry experiment, comprising: an ion source device; a tandem mass spectrometer, wherein the tandem mass spectrometer: (a) receives an ion beam from the ion source device generated by ionizing a control sample not containing a metabolite compound, performs a mass spectrometry (MS) scan of a certain mass range on the ion beam, generates background peak m / z and intensity values for background precursor ions, selects one or more of the background peaks of the background precursor ions with respect to an exclusion list, and includes the m / z value and intensity value for each background peak of the selected one or more background peaks in the exclusion list to create the exclusion list; (b) receives an ion beam from the ion source device generated by ionizing an experimental sample containing the metabolite compound, performs an MS scan of the mass range on the ion beam, generates peak m / z and intensity values for precursor ions, selects one or more of the peaks of the precursor ions with respect to a peak list, and includes the m / z value and intensity value for each peak of the selected one or more peaks in the peak list to create the peak list; (c) excluding from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of a background peak in the exclusion list; and a tandem mass spectrometer for performing the above steps; A system comprising the above components.

2. The system according to claim 1, wherein the m / z value and intensity value of a peak in the peak list correspond to the m / z value and intensity value of a background peak in the exclusion list when the m / z value is within an m / z tolerance factor and the intensity value is within an intensity tolerance factor.

3. The system according to claim 1, wherein the tandem mass spectrometer further scales the peak list or the exclusion list before comparing peaks in step (c).

4. The tandem mass spectrometer further comprises: selecting one known background peak on the peak list and the exclusion list; Calculating the ratio of the intensity value of the one known background peak on the peak list and the intensity value of the one known background peak on the exclusion list; Multiplying each intensity value on the peak list or the exclusion list by the ratio; The system according to claim 3, wherein the peak list or the exclusion list is scaled by the above steps.

5. The tandem mass spectrometer further comprises: Selecting two or more known background peaks on the peak list and the exclusion list; Calculating the ratio of the combination of the intensity values of the two or more known background peaks on the peak list and the combination of the intensity values of the two or more known background peaks on the exclusion list; Multiplying each intensity value on the peak list or the exclusion list by the ratio; The system according to claim 3, wherein the peak list or the exclusion list is scaled by the above steps.

6. The tandem mass spectrometer further includes a sample introduction device, and the tandem mass spectrometer further comprises: In step (a), receiving an ion beam from the ion source device that receives one or more compounds from the control sample over time from the sample introduction device, performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam, generating background peak m / z and intensity values for background precursor ions over time, selecting one or more of the background peaks of the background precursor ions with respect to the exclusion list at each time step, and including the m / z value, intensity value, and residence time value for each of the selected one or more of the background peaks in the exclusion list; In step (b), receiving an ion beam from the ion source device that receives one or more compounds from the experimental sample over time from the sample introduction device, performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam, generating peak m / z and intensity values for precursor ions over time, and at each time step, selecting one or more of the peaks of the precursor ions with respect to the peak list, and including the m / z value, intensity value, and dwell time value for each peak of the selected one or more peaks in the peak list, In step (c), excluding from the peak list each peak having an m / z value, intensity value, and dwell time value corresponding to the m / z value, intensity value, and dwell time value of the background peak in the exclusion list, The system according to claim 1.

7. The m / z value, intensity value, and dwell time value of the peak in the peak list are corresponding to the m / z value, intensity value, and dwell time value of the background peak in the exclusion list when the m / z value matches within the m / z tolerance factor, the intensity value matches within the intensity tolerance factor, and the dwell time value matches within the dwell time tolerance factor. The system according to claim 1.

8. A method for excluding endogenous background ions having the same mass / charge ratio (m / z) as metabolite ions from a peak list in an information-dependent acquisition (IDA) mass spectrometry experiment, Receiving an ion beam from an ion source device generated by ionizing a control sample not containing a metabolite compound using a tandem mass spectrometer; Performing a mass spectrometry (MS) scan of a certain mass range on the ion beam using the tandem mass spectrometer to generate background peak m / z and intensity values for background precursor ions; Using the tandem mass spectrometer to select one or more of the background peaks of the background precursor ions with respect to the exclusion list and including the m / z value and intensity value for each background peak of the selected one or more background peaks in the exclusion list; Receiving an ion beam from the ion source device generated by ionizing the experimental sample containing the metabolite compound using the tandem mass spectrometer, Performing an MS scan of the mass range on the ion beam using the tandem mass spectrometer to generate peak m / z and intensity values for precursor ions; Using the tandem mass spectrometer to select one or more than one of the peaks of the precursor ions with respect to the peak list, and including the m / z value and intensity value for each peak of the selected one or more than one peak in the peak list; Using the tandem mass spectrometer to exclude from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peak in the exclusion list; A method comprising. **Claim 9** The method according to claim 8, wherein the m / z value and intensity value of the peak in the peak list correspond to the m / z value and intensity value of the background peak in the exclusion list when the m / z value matches within the m / z tolerance factor and the intensity value matches within the intensity tolerance factor. **Claim 10** The method according to claim 8, further comprising scaling the peak list or the exclusion list before excluding from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and intensity value of the background peak in the exclusion list. **Claim 11** The step of scaling the peak list or the exclusion list comprises selecting one known background peak on the peak list and the exclusion list; calculating the 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; multiplying each intensity value on the peak list or the exclusion list by the ratio. The method according to claim 10, comprising. **Claim 12** The step of scaling the peak list or the exclusion list comprises selecting two or more known background peaks on the peak list and the exclusion list; calculating the ratio of the combination of the intensity values of the two or more known background peaks on the peak list to the combination of the intensity values of the two or more known background peaks on the exclusion list; multiplying each intensity value on the peak list or the exclusion list by the ratio. The method according to claim 10, comprising. **Claim 13** Receiving an ion beam from the ion source device that receives one or more compounds from the control sample over time from the sample introduction device; Performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam to generate background peak m / z and intensity values for background precursor ions over time; At each time step, selecting one or more of the background peaks of the background precursor ions with respect to the exclusion list, and including the m / z value, intensity value, and residence time value for each background peak of one or more of the selected background peaks within the exclusion list; Receiving an ion beam from the ion source device that receives one or more compounds from the experimental sample over time from the sample introduction device; Performing a plurality of MS scans of the mass range at a plurality of different time steps on the ion beam to generate peak m / z and intensity values for precursor ions over time; At each time step, selecting one or more of the peaks of the precursor ions with respect to the peak list, and including the m / z value, intensity value, and residence time value for each peak of one or more of the selected peaks within the peak list; Excluding from the peak list each peak having an m / z value, intensity value, and residence time value corresponding to the m / z value, intensity value, and residence time value of the background peak in the exclusion list; The method according to claim 8, further comprising.

14. The m / z value, intensity value, and residence time value of the peaks in the peak list are such that when the m / z value matches within the m / z tolerance factor, when the intensity value matches within the intensity tolerance factor, and when the residence time value matches within the residence time tolerance factor, corresponding to the m / z value, intensity value, and residence time value of the background peak in the exclusion list, the method according to claim 8.

15. A computer program product comprising a non-transitory and tangible computer-readable storage medium, wherein the content of the non-transitory and tangible computer-readable storage medium includes a program with instructions to be executed on a processor to implement a method for excluding endogenous background ions having the same mass / charge ratio (m / z) as metabolite ions from a peak list in an information-dependent acquisition (IDA) mass spectrometry experiment, the method comprising: Providing a system, the system comprising one or more distinct software modules, the distinct software modules comprising a control module and an analysis module; Instructing a tandem mass spectrometer to receive an ion beam from an ion source device generated by ionizing a control sample not containing a metabolite compound using the control module; Instructing the tandem mass spectrometer to perform a mass spectrometry (MS) scan of a certain mass range on the ion beam using the control module to generate background peak m / z and intensity values for background precursor ions; Using the analysis module to select one or more of the background peaks of the background precursor ions with respect to an exclusion list and include the m / z value and intensity value for each of the selected one or more background peaks in the exclusion list; Instructing the tandem mass spectrometer to receive an ion beam from the ion source device generated by ionizing an experimental sample containing the metabolite compound using the control module; Instructing the tandem mass spectrometer to perform an MS scan of the mass range on the ion beam using the control module to generate peak m / z and intensity values for precursor ions; Using the analysis module to select one or more of the peaks of the precursor ions with respect to a peak list and include the m / z value and intensity value for each of the selected one or more peaks in the peak list; Using the analysis module, excluding from the peak list each peak having both an m / z value and an intensity value corresponding to the m / z value and the intensity value of the background peak of the exclusion list A computer program product comprising

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