Peak integration correction without parameter adjustment

Abstract

A separation device is instructed to separate compounds from a sample over a period of time. A mass spectrometer is instructed to measure a plurality of intensities of at least one ion of the separated compounds over a period of time and generate a chromatogram. At least one peak of the at least one ion is identified from the chromatogram using a peak-finding algorithm. Two or more different peak integrated areas are calculated for the at least one peak by applying the peak-finding algorithm with two or more different values ​​for at least one peak-finding parameter. Two or more plots of the at least one peak, each graphically illustrating a different peak integrated area, are simultaneously displayed on a display device. In response, data indicating a user selection of one of the two or more plots is received from a user selection device.

Description

[Technical field]

[0001] (Related Applications) This application claims the benefit of U.S. Provisional Patent Application No. 62 / 860,310, filed June 12, 2019, the contents of which are incorporated by reference in their entirety herein.

[0002] The teachings herein relate to an apparatus and method for peak integration in chromatographic systems, including but not limited to liquid chromatographs (LC) and gas chromatographs (GC). More specifically, the integration areas for two or more chromatographic peaks are displayed simultaneously to a user, and the user is allowed to select a preferred integration area. The method reduces the time it takes to review and select a suitable integration area for a chromatographic peak. The method is independent of the detection system used (mass spectrometry (MS), ultraviolet (UV), etc.). [Background technology]

[0003] The apparatus and methods disclosed herein may be implemented in conjunction with a processor, controller, microcontroller, or computer system, such as the computer system of FIG.

[0004] (Mass spectrometry background) 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 the ions formed from those compounds. MS involves ionization of one or more compounds of interest from a sample, generation of precursor ions, and mass analysis of the precursor ions.

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

[0006] Mass spectrometers are often coupled to a chromatograph or other separation system to identify and characterize compounds of interest eluting from a sample. In such coupled systems, compounds in the elution 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. The intensity values ​​derived from the series of mass spectra form a chromatograph. For example, the sum of all the intensities generates a total ion chromatograph (TIC) and the intensity of one mass value generates an extracted ion chromatograph (XIC).

[0007] The peaks found in the chromatograph elute at known times, called retention times, and are therefore used to identify or characterize known peptides or compounds in the sample. More specifically, the retention times of the peaks and / or the areas of the peaks are used to identify or characterize (quantify) known peptides or compounds in the sample.

[0008] In a conventional separation-coupled mass spectrometry system, a precursor ion of a known compound is selected for analysis. An MS / MS scan is then performed at each interval of separation across 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, for example, as a collection of spectra or XICs.

[0009] 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.

[0010] (Isolated device background) As explained above, mass spectrometers are often coupled with separation systems or devices to identify and characterize compounds of interest eluted from a sample. Such separation devices can include, but are not limited to, liquid chromatography (LC) devices, gas chromatography devices, capillary electrophoresis devices, or ion mobility devices. LC devices are generally interfaced with mass spectrometers to quantify the amount of compounds of interest in a sample.

[0011] 2 is an exemplary schematic diagram of an LC device 200 for a mass spectrometer. The LC device 200 includes two separate devices: a high performance liquid chromatograph (HPLC) device 210 and a direct dosing or injection device 220.

[0012] In the HPLC device 210, one of two solvents 211 or 212 is selected using a valve 215. The solvent 211 or 212 is moved to the valve 215 using pumps 213 and 214, respectively. A sample 216 is mixed with the selected solvent using a mixer 217, and the resulting mixture is sent through a liquid chromatograph (LC) column 218. The sample 216 is selected using, for example, an autosampler 219.

[0013] In a direct input or injection device 220, the sample is already mixed with a solvent in a fluid pump 221. The fluid pump 221 is shown as a syringe pump, but can be any type of pump.

[0014] The use of the HPLC device 210 or the direct input or injection device 220 is selected using valve 230. The selected mixture or mobile phase composition is transmitted sequentially from valve 230 to an ion source (not shown) of a mass spectrometer (not shown).

[0015] (Chromatography peak integration problem) As explained above, the result of a separation-coupled mass spectrometry experiment is generally a TIC or XIC. These chromatographs are essentially a collection of intensities that are a function of time. Chromatographs are often used to determine the amount of a particular compound present in a sample. To quantify or quantitate a compound, either the precursor ion or product ion peaks in the chromatograph are integrated. Peak integration generally refers to finding the area under a peak in the chromatograph.

[0016] For all quantitative work involving chromatographic peak integration, accuracy of peak finding in the chromatograph is important. For many application areas (pharmaceutical, clinical, etc.), this is particularly true, where users traditionally manually inspect every chromatograph and correct any that are not integrated well enough. Peaks are routinely reintegrated even when the total peak area difference may not seem particularly large to someone unfamiliar with the art.

[0017] In all existing separation-coupled mass spectrometry software, the review process consists of visually inspecting the chromatographic ensemble and the corresponding default peak integrations (with default peak-finding parameters). When the default integrations are not satisfactory, the user adjusts the peak-finding parameters, applies the new values, and visually observes the results. This process is repeated until the user is satisfied. In some cases, the user essentially gives up, either at the beginning of the parameter-changing step or after several failed attempts, and manually draws the peak baseline. However, some laboratories do not allow such fully manual integration (considered to be too subjective), and the user must continue to adjust the parameters. The peak baseline is essentially the boundary of the area at the base of the peak.

[0018] 3 is an exemplary interactive table 300 showing peak finding parameters that are displayed to the user by the peak finding algorithm and used by the peak finding algorithm to integrate peaks. Table 300 is generated, for example, by one of SCIEX's peak finding algorithms. Note that table 300 allows the user to change parameters and reintegrate a particular peak.

[0019] FIG. 4 is an exemplary plot 400 of a chromatographic peak displayed to a user by a peak finding algorithm and showing the correct integration of the chromatographic peak according to the parameters of FIG. 3. Using the parameters of FIG. 3, the peak finding algorithm applies a peak baseline 411 to integrate or find the area under the peak 410. Note that the peak baseline 411 has vertical and horizontal components. The vertical component of the peak baseline 411 separates the area of ​​the peak 410 from the interfering peak 420. Also note that the peak baseline 411 is shown as a vertical and horizontal line. In some embodiments, for some algorithms, the baseline may be a curve. For example, the baseline may be a curve that follows the peak 420 and more accurately subtracts its contribution.

[0020] FIG. 5 is an exemplary plot 500 of a chromatographic peak displayed to a user by a peak finding algorithm and showing an incorrect integration of the chromatographic peak according to the parameters of FIG. 3. Using the parameters of FIG. 3, the peak finding algorithm applies a peak baseline 511 and integrates or finds the area under the peak 510. In FIG. 5, the peak 510 is incorrectly integrated because the integration includes a contribution from an interfering peak 520. In other words, the applied peak baseline 511 does not exclude the contribution from the interfering peak 520. To correct this integration, a skilled reviewer would change one or more parameters of FIG. 3 and reintegrate the peak 520 of FIG. 5. Unfortunately, this is an iterative and manual process according to the procedures used by current peak finding algorithms.

[0021] As a result, a fundamental problem with the procedures used by current peak finding algorithms is that it takes too long to reintegrate incorrect peaks. More specifically, iterative adjustment of peak finding parameters for incorrectly integrated peaks takes too long. This is especially true because in many cases it is not immediately clear which peak finding parameters should be adjusted and by how much.

[0022] Also, while a well-trained and experienced analyst can usually perform the corrections with reasonable efficiency, this is far from the case for a novice. Indeed, beyond the actual time required, an even greater problem is probably user frustration from struggling to find a set of parameters that will integrate in the desired way.

[0023] As a result, additional systems and methods are needed to review and select suitable integrations for chromatographic peaks without specialized knowledge of the peak-finding parameters of one or more peak-finding algorithms, and to reduce the time required to select a suitable integration. Summary of the Invention [Means for solving the problem]

[0024] A system, method, and computer program product for selecting an integrated area for a chromatographic peak is disclosed. The apparatus includes a separation device, a mass spectrometer, a display device, a user selection device, and a processor.

[0025] The processor instructs the separation device to separate the compound from the sample over a period of time. The processor instructs the mass spectrometer to measure a plurality of intensities of at least one ion of the separated compound over the period of time and generate a chromatogram. The processor identifies at least one peak of the at least one ion from the chromatogram using a peak finding algorithm. The processor also calculates two or more different peak integral areas for the at least one peak using the peak finding algorithm by applying the peak finding algorithm with two or more different values ​​for the at least one peak finding parameter. The processor simultaneously displays on the display device two or more plots of the at least one peak, each plot graphically illustrating a different peak integral area of ​​the two or more different peak integral areas. In response, the processor receives data from the user selection device indicating a user selection of one of the two or more plots.

[0026] These and other features of the applicants' teachings are set forth herein. The present specification also provides, for example, the following items: (Item 1) 1. A system for selecting an integrated area for a chromatographic peak, comprising: A separation device; A mass spectrometer; A processor, the processor comprising: instructing the separation device to separate compounds from the sample for a period of time; instructing the mass spectrometer to measure a plurality of intensities of at least one ion of the separated compounds over the period of time to generate a chromatogram; identifying at least one peak of said at least one ion from said chromatograph using a peak finding algorithm, and calculating two or more different peak integral areas for said at least one peak by applying said peak finding algorithm with two or more different values ​​for at least one peak finding parameter without manual and iterative adjustment of said two or more different values ​​by a user; The processor and A system comprising: (Item 2) The system further comprises a display device and a user selection device, the processor further comprising: displaying, on said display device, two or more plots of said at least one peak simultaneously, each plot graphically illustrating a different peak integral area of ​​said two or more different peak integral areas; receiving data from the user selection device indicative of a user selection of one of the two or more plots; The system according to item 1, (Item 3) 2. The system of claim 1, wherein the two or more different values ​​for the at least one peak finding parameter are predetermined and received by the processor. (Item 4) 2. The system of claim 1, wherein the two or more different values ​​for the at least one peak finding parameter are generated by the processor. (Item 5) 5. The system of claim 4, wherein the two or more different values ​​for the at least one peak finding parameter generated represent all different possible values ​​within a selected range for the at least one peak finding parameter. (Item 6) 5. The system of claim 4, wherein the two or more different values ​​for the at least one peak finding parameter generated represent a subset of all different possible values ​​within a selected range for the at least one peak finding parameter. (Item 7) 7. The system of claim 6, wherein the subset is found by calculating how the peak integral area changes as a function of the value of the at least one peak finding parameter, selecting a peak integral area change threshold, and including only values ​​of the at least one peak finding parameter in the subset for which the peak integral area changes by more than the peak integral area change threshold. (Item 8) 3. The system of claim 2, wherein the processor further calculates a numerical area value for each of the two or more different peak integrated areas, and the processor displays the calculated numerical area value together with each of the two or more plots. (Item 9) 3. The system of claim 2, wherein each plot of the two or more plots graphically illustrates a different peak integrated area by shading a different peak integrated area and by displaying a different peak baseline. (Item 10) 3. The system of claim 2, wherein the processor further determines a selected peak integration area of ​​the two or more distinct peak integration areas from a selection of one of the two or more plots, calculates a numerical area value for the selected peak integration area, and calculates an amount of the compound in the sample from the numerical area value. (Item 11) 3. The system of claim 2, wherein the processor further displays, on the display device, the at least one peak finding parameter and a value used for the at least one peak finding parameter together with each of the two or more plots. (Item 12) 1. A method for selecting an integrated area for a chromatographic peak, comprising: instructing the separation device, using a processor, to separate the compound from the sample over a period of time; instructing the mass spectrometer to measure, using said processor, a plurality of intensities of at least one ion of said separated compounds over said time period to generate a chromatogram; using said processor to identify at least one peak of said at least one ion from said chromatograph using a peak finding algorithm and calculating two or more different peak integral areas for said at least one peak by applying said peak finding algorithm with two or more different values ​​for at least one peak finding parameter without manual and iterative adjustment of said two or more different values ​​by a user; A method comprising: (Item 13) using said processor to simultaneously display on a display device two or more plots of said at least one peak, each plot graphically illustrating a different peak integral area of ​​said two or more different peak integral areas; receiving, using the processor, data from a user selection device indicative of a user selection of one of the two or more plots; Item 13. The method of item 12, further comprising: (Item 14) 1. A computer program product comprising a non-transitory and tangible computer readable storage medium, the contents of which include a program with instructions that execute on a processor to perform a method for selecting an integrated area for a chromatographic peak, the method comprising: providing a system comprising one or more distinct software modules, the distinct software modules comprising a control module and an analysis module; instructing a separation device to separate compounds from a sample over a period of time using said control module; commanding the mass spectrometer to measure a plurality of intensities of at least one ion of the separated compounds over the period of time using the control module to generate a chromatogram; using the analysis module to identify at least one peak of the at least one ion from the chromatograph using a peak finding algorithm and calculating two or more different peak integral areas for the at least one peak by applying the peak finding algorithm with two or more different values ​​for at least one peak finding parameter without manual and iterative adjustment of the two or more different values ​​by a user; displaying, using the display module, on a display device, two or more plots of the at least one peak, each plot graphically illustrating a different peak integral area of ​​the two or more different peak integral areas; receiving data from a user selection device, using the user selection module, indicative of a user selection of one of the two or more plots; 2. A computer program product comprising: (Item 15) The distinct software modules further comprise a display module and a user selection module, and the method further comprises: displaying, using the display module, on a display device, two or more plots of the at least one peak, each plot graphically illustrating a different peak integral area of ​​the two or more different peak integral areas; receiving data from a user selection device, using the user selection module, indicative of a user selection of one of the two or more plots; Item 15. The computer program product of item 14, comprising: [Brief description of the drawings]

[0027] Those skilled in the art will understand that the drawings, described below, are for illustration purposes only and are not intended to limit the scope of the present teachings in any way.

[0028] [Figure 1] FIG. 1 is a block diagram illustrating a computer system on which embodiments of the present teachings may be implemented.

[0029] [Diagram 2] FIG. 2 is an exemplary schematic diagram of an LC device for a mass spectrometer.

[0030] [Diagram 3] FIG. 3 is an exemplary interactive table showing the peak finding parameters displayed to the user by the peak finding algorithm and used by the peak finding algorithm to integrate the peaks.

[0031] [Figure 4] FIG. 4 is an exemplary plot of a chromatographic peak displayed to the user by the peak finding algorithm, showing the correct integration of the chromatographic peak according to the parameters of FIG.

[0032] [Diagram 5]FIG. 5 is an exemplary plot of a chromatographic peak displayed to a user by the peak finding algorithm, showing the incorrect integration of the chromatographic peak according to the parameters of FIG.

[0033] [Figure 6] FIG. 6 is an exemplary display of three different possible integrals of the same peak shown in FIG. 5, allowing a user to simultaneously review multiple integrals and select a particular integral without requiring expert knowledge of the peak-finding parameters of a particular peak-finding algorithm, in accordance with various embodiments.

[0034] [Figure 7] FIG. 7 is a plot of the percentage change in peak area as a function of the peak splitting factor parameter, according to various embodiments.

[0035] [Figure 8] FIG. 8 is a schematic diagram of a system for selecting an integrated area for a chromatographic peak, according to various embodiments.

[0036] [Figure 9] FIG. 9 is a flow chart illustrating a method for selecting an integrated area for a chromatographic peak according to various embodiments.

[0037] [Figure 10] FIG. 10 is a schematic diagram of a system including one or more distinct software modules that implements a method for selecting an integrated area for a chromatographic peak, according to various embodiments.

[0038] 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 in their application to the details of construction, the arrangement 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 OF THE PREFERRED EMBODIMENTS

[0039] (Computer Implemented Systems) 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 with 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 executed by the processor 104. The memory 106 may also be used to store temporary variables or other intermediate information during execution of instructions executed 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 and coupled to the bus 102 for storing information and instructions.

[0040] The computer system 100 may 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 the processor 104. Another type of user input device is a cursor control 116, such as a mouse, trackball, or cursor direction keys, for communicating directional information and command selections to the processor 104 and for controlling cursor movement on the display 112. This input device typically has two degrees of freedom in two axes, a first axis (i.e., x) and a second axis (i.e., y), that allow the device to specify a position in a plane.

[0041] The computer system 100 is capable of implementing the present teachings. According to one implementation 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 may 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 processes described herein. Alternatively, hard-wired circuitry may be used in place of or in combination with software instructions to implement the present teachings. Thus, implementation of the present teachings is not limited to any specific combination of hardware circuitry and software.

[0042] In various embodiments, computer system 100 can be connected to one or more other computer systems, such as computer system 100, across a network 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 and pass data to other computer systems. The one or more computer systems that store and pass data may be referred to as servers or clouds in a cloud computing scenario. The one or more computer systems may include, for example, one or more web servers. The other computer systems that send and receive data to and from the server or cloud may be referred to as clients or cloud devices, for example.

[0043] The term "computer-readable medium" as used herein refers to any medium that participates in providing instructions to processor 104 for execution. Such media may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media include, for example, optical or magnetic disks, such as storage device 110. Volatile media include dynamic memory, such as memory 106. Transmission media include coaxial cables, copper wire and fiber optics, including the wires that comprise bus 102.

[0044] Common forms of computer readable media or computer program products include, for example, a floppy 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 from which a computer can read.

[0045] 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 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 infrared transmitter to convert the data to an infrared signal. An infrared detector coupled to the bus 102 can receive the data carried in the infrared signal and place the data on the bus 102. The bus 102 carries the data to memory 106, from which the processor 104 reads and executes the instructions. The instructions received by memory 106 may optionally be stored on a storage device 110 either before or after execution by the processor 104.

[0046] According to various embodiments, the instructions configured to be executed by the processor to perform the 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 disk 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 to execute the instructions configured to be executed.

[0047] 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 form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practice of the present teachings. In addition, while the described implementations include software, the present teachings may be implemented as a combination of hardware and software or in hardware alone. The present teachings may be implemented with both object-oriented and non-object-oriented programming systems.

[0048] (Display of multiple chromatographic peak integrations) As explained above, the fundamental problem with the procedure used by current peak finding algorithms is that it takes too long to reintegrate incorrectly integrated peaks. More specifically, manual and iterative adjustment of peak finding parameters for incorrectly integrated peaks takes too long. And while a well-trained and experienced analyst can usually perform the corrections with reasonable efficiency, this is far from the case for a novice.

[0049] As a result, additional systems and methods are needed to review and select suitable integrations for chromatographic peaks without specialized knowledge of the peak-finding parameters of one or more peak-finding algorithms, and to reduce the time required to select a suitable integration.

[0050] In various embodiments, multiple different possible peak integrals are displayed to the user simultaneously and the user is allowed to select the preferred one. By reducing the number of iterations, the method reduces the time it takes to review and select a suitable integral for a chromatographic peak. In essence, many different integrals are generated in only one iteration.

[0051] The method also allows for the selection of an appropriate integral without requiring expert knowledge of the peak finding parameters of a specific peak finding algorithm. The peak finding parameter values ​​are still adjusted between multiple different possible peak integrals. However, they are adjusted automatically. The user only needs to visually inspect the areas of multiple displayed peaks, select the best plotted integral graph, and select the correct peak finding parameters for the peak.

[0052] Figure 6 is an example display 600 of three different possible integrations of the same peak shown in Figure 5 that allows a user to simultaneously review multiple integrations and select a particular integration without requiring expert knowledge of the peak-finding parameters of a specific peak-finding algorithm, according to various embodiments. Plots 610, 620, and 630 graphically depict three different integrations of the same chromatographic peak. Each plot includes area integral shading and peak baselines.

[0053] From plots 610, 620, and 630, the user can more quickly select the correct integral. There are no iterations. The user simply visually inspects and compares the integrals (areas) of plots 610, 620, and 630. Also, there is no need to adjust any peak finding parameter values. This is done automatically. To select the correct integral and peak finding parameter values, the user simply clicks on one of the plots 610, 620, and 630.

[0054] For example, a comparison of plots 610, 620, and 630 shows that in plot 620, the peak baseline 621 excludes the small interference peak 520 at the start of the peak 510, but does not exclude the shoulder at the end of the peak 510. As a result, plot 620 is more likely to be selected by a user. In contrast, in plot 610, the peak baseline 611 excludes the small interference peak 520 at the start of the peak 510, as well as the shoulder at the end of the peak 510. As in FIG. 5, in plot 630, the peak baseline 631 does not exclude the small interference peak 520 at the start of the peak 510.

[0055] Conventionally, for example, a user is presented with a table of peak-finding parameter values, such as table 300 of Figure 3, and a single plot of the integrated peak, such as plot 500 of Figure 5. The user can then iteratively change the peak-finding parameter values ​​in the table and a single updated plot of the reintegrated peak is viewed.

[0056] In contrast, in various embodiments described herein, the user is presented with a single display of multiple plots of different integrals, such as the display shown in Figure 6. The user can then click on an integral plot and select that value for that integral and peak finding parameters.

[0057] In various embodiments, when a user performs an "adjust integration mode," multiple different possible peak integrals are provided, and in various embodiments, the multiple different possible peak integrals are determined in different ways.

[0058] In one embodiment, an administrator defines initial distinct peak finding parameter values. As a result, two or more sets of initial distinct peak finding parameter values ​​are created by the administrator. This requires additional up-front administrator time, but is acceptable for assays that are expected to be used over long periods of time or by less trained operators.

[0059] In another embodiment, the values ​​of one or more parameters are varied over their useful ranges and a representative value for each parameter is selected for each significantly different result. One exemplary peak finding parameter is the peak splitting factor.

[0060] 7 is a plot 700 of the percentage change in peak area as a function of the peak splitting factor parameter, according to various embodiments. Plot 700 shows that there are only three different peak splitting factor values ​​that affect the percentage change in peak area. Note that within the range of parameters investigated, there are only three different peak splitting factor values ​​that affect the percentage change in peak area. However, the parameters were varied over what was believed to be the most useful range.

[0061] All peak splitting factor values ​​greater than 2 provide the same percentage change in peak area as 2. For most peak finding algorithms, there is not a particularly large number of different possible values ​​for the parameters, at least not a large number for a computer to programmatically search. However, the number can be "large" for manual searches.

[0062] As a result, it is possible to explore the parameter space almost completely. In various alternative embodiments, a "design for experiment" approach can be used to explore the space more efficiently. Under a design for experiment approach, a subset of all possible parameter values ​​is found and used. The subset can be chosen randomly or based on something known about the experiment.

[0063] In various embodiments, a combination of two or more peak finding algorithms is used to find the different integrals. For example, it is possible to combine what are essentially different peak finding algorithms (such as MQ4 and AutoPeak from SCIEX) and vary the individual parameters for each.

[0064] In various embodiments, the number of different (but still reasonable) peak integrals is kept small. Also, in various embodiments, even laboratories that do not allow completely manual integration (i.e., baseline drawing) can let the user draw a manual baseline and then automatically select the set of parameters that most closely approximates that integral (or allow the user to choose from a subset of the most similar integrals). Or, the selection can be iterative, i.e., the user can select a "close" integral in a first step and then fine-tune it in a second step.

[0065] In various embodiments, in systems aimed at least in part at experienced users, the value of the peak finding parameter may still be displayed. When the user selects one of the possible integrals displayed, the value of the parameter changes to reflect the selection. The display of the parameter's value may still be interactive, allowing the user to further manually adjust the parameter.

[0066] In various alternative embodiments, the peak finding parameters and their values ​​are not displayed, at least during routine peak review. This is desirable, especially in cloud systems that involve data review in a web browser, since a simpler user interface (UI) is generally required compared to desktop systems.

[0067] Generally, the calculation of some of the possible peak integrals does not require a large amount of computer processing time, however, in various embodiments, if the calculation of the possible peak integrals does consume a large amount of computer processing time, the integrals can be pre-calculated and stored during the initial generation of results, or can be done on the fly when the user selects to change a particular integral.

[0068] In various embodiments, a high quality integration algorithm is used first to minimize the number of peaks that need to be corrected. For example, AutoPeak has a "smarter" shoulder detection than MQ4 and has a higher first-pass correct rate, and therefore can be used first.

[0069] It should be noted that no peak finding algorithm is or ever will be perfect, and therefore some manual correction is always required. Currently, once even a few peaks need to be corrected, the user must understand the meaning of the different available parameters and the extent to which they are likely to change the integral. As noted above, the various embodiments described herein can eliminate the need to present the parameters to the user, thus enabling less experienced users to obtain good results.

[0070] Most simply, the embodiments described herein reduce the time required for peak integration correction. If the integration parameters can be largely removed from the peak review user interface, this means that the user does not need to understand their meaning or use. This not only results in obvious cost savings for the customer, but also directly reduces user frustration with parameter adjustments. Also, as noted above, the embodiments described herein reduce the time required for manual peak reintegration.

[0071] (Chromatography Peak Integration System) 8 is a schematic diagram 800 of a system for selecting an integrated area for a chromatographic peak, according to various embodiments. The system of FIG. 8 includes a separation device 810, a mass spectrometer 820, a display device 831, a user selection device 832, and a processor 830.

[0072] Processor 830 is used to control separation device 810 and mass spectrometer 820 or provide them with instructions to analyze data collected from mass spectrometer 820. Processor 830 provides instructions, for example, by controlling or controlling one or more voltage, current, or pressure sources (not shown). Processor 830 can be a separate device, as shown in Figure 8, or can be a processor or controller of separation device 810 or mass spectrometer 820. Processor 830 can be, without limitation, a controller, computer, microprocessor, the computer system of Figure 1, or any device capable of sending and receiving control signals and data therefrom and capable of processing data.

[0073] The processor 830 instructs the separation device 810 to separate the compounds from the sample over a period of time. The separation device 810 can be an HPLC system, as shown in Figure 8. In various alternative embodiments, the separation device 810 can be any type of separation device for a mass spectrometer, including, but not limited to, a liquid chromatography (LC) device, a gas chromatography device, a capillary electrophoresis device, or an ion mobility device.

[0074] The processor 830 instructs the mass spectrometer 820 to measure a plurality of intensities of at least one ion of the separated compounds over the period of time and generate a chromatograph. The mass spectrometer 820 can be a quadrupole mass spectrometer, as shown in Figure 8. In various alternative embodiments, the mass spectrometer 820 can be any type of mass spectrometer, including, but not limited to, a quadrupole or triple quadrupole (QqQ), ion trap, orbitrap, time-of-flight (TOF) mass spectrometer, or a Fourier transform (FT) mass spectrometer.

[0075] The processor 830 uses a peak finding algorithm to identify at least one peak of the at least one ion from the chromatograph. The processor 830 also uses the peak finding algorithm to calculate two or more different peak integral areas for the at least one peak by applying the peak finding algorithm with two or more different values ​​for the at least one peak finding parameter without manual and iterative adjustment of the two or more different values.

[0076] In various embodiments, processor 830 simultaneously displays two or more plots of at least one peak, each plot graphically illustrating different peak integrated areas of two or more different peak integrated areas, on display device 831. Display device 831 can be a display of processor 830, as shown in Figure 8. In various alternative embodiments, display device 831 can be a display of another processor or computer (not shown), including, but not limited to, a display of a processor or computer of separation device 810 or mass spectrometer 820.

[0077] In various embodiments, processor 830 receives data indicative of a user selection of one of the two or more plots from a user selection device 832. User selection device 832 can be a keyboard of processor 830, as shown in Figure 8. In various alternative embodiments, user selection device 832 can be a touch screen of display device 831, a mouse, a keypad, or any other type of input device of processor 830 or another processor or computer (not shown), including, but not limited to, a display of a processor or computer of separation device 810 or mass spectrometer 820.

[0078] In various embodiments, the two or more different values ​​for at least one peak finding parameter used to calculate the two or more different peak integrated areas are predetermined and received by the processor 830. The two or more different values ​​are determined by a system administrator and entered into the processor 830 by the administrator.

[0079] In various alternative embodiments, two or more different values ​​are generated by the processor 830. For example, two or more different values ​​for at least one peak finding parameter are generated to represent all different possible values ​​within a selected range for the at least one peak finding parameter.

[0080] Alternatively, two or more different values ​​for the at least one peak finding parameter are generated to represent a subset of all different possible values ​​within a selected range for the at least one peak finding parameter. In various embodiments, the subset is found by calculating how the peak integral area changes as a function of the value of the at least one peak finding parameter, selecting a peak integral area change threshold, and including only values ​​of the at least one peak finding parameter in the subset at which the peak integral area changes above the peak integral area change threshold. FIG. 7, for example, shows results from calculating how the peak integral area changes as a function of the value of the peak splitting factor parameter. FIG. 7 shows that only three values ​​of the peak splitting factor parameter significantly change the peak integral area. As explained above, there are only three values ​​over the range analyzed (assumed to be the useful range).

[0081] In various embodiments, in addition to selecting a peak integrated area change threshold, some other output from the peak finder can also be used, for example the start or end of the peak can be used.

[0082] In various embodiments, the peak finding algorithm used can be a combination of two or more peak finding algorithms.

[0083] In various embodiments, the processor 830 further calculates a numerical area value for each of the two or more distinct peak integrated areas. The processor 830 then displays the calculated numerical area values ​​along with each of the two or more plots.

[0084] In various embodiments, each plot of the two or more plots graphically illustrates a different peak integrated area by shading a different peak integrated area and by displaying a different peak baseline.

[0085] In various embodiments, the processor 830 further determines selected peak integration areas of two or more different peak integration areas from a selection of one of the two or more plots. The processor 830 calculates a numerical area value for the selected peak integration areas. Finally, the processor 830 calculates the amount of the compound in the sample from the numerical area value.

[0086] In various embodiments, the processor 830 further displays the at least one peak finding parameter and the value used for the at least one peak finding parameter along with each of the two or more plots on the display device 831. The value used for the at least one peak finding parameter may, for example, be editable.

[0087] In various alternative embodiments, the peak finding parameters and peak finding parameter values ​​are not displayed with more than one plot.

[0088] (Chromatographic peak integration method) FIG. 9 is a flow chart illustrating a method 900 for selecting an integrated area for a chromatographic peak, according to various embodiments.

[0089] In step 910 of method 900, the separation device is instructed, using a processor, to separate compounds from the sample over a period of time.

[0090] In step 920, the mass spectrometer is instructed, using the processor, to measure a plurality of intensities of at least one ion of the separated compounds over the period of time to generate a chromatogram.

[0091] In step 930, at least one peak of at least one ion is identified from the chromatograph using a peak finding algorithm, and two or more different peak integrated areas are calculated for the at least one peak by applying the peak finding algorithm with two or more different values ​​for at least one peak finding parameter without manual and iterative adjustment of the two or more different values ​​using a processor.

[0092] In various embodiments, two or more plots of at least one peak, each graphically illustrating a different peak integrated area of ​​two or more different peak integrated areas, are displayed simultaneously on a display device using a processor.

[0093] In various embodiments, using a processor, data indicative of a user selection of one of the two or more plots is received from a user selection device.

[0094] (Chromatographic Peak Integration Computer Program Product) In various embodiments, a computer program product includes a tangible computer-readable storage medium, the contents of which include a program with instructions for execution on a processor to perform a method for selecting an integrated area for a chromatographic peak, the method being performed by a system including one or more distinct software modules.

[0095] 10 is a schematic diagram of a system 1000 that includes one or more distinct software modules that implement a method for selecting an integrated area for a chromatographic peak, according to various embodiments. The system 1000 includes a control module 1010 and an analysis module 1020.

[0096] The control module 1010 instructs the separation device to separate compounds from the sample over a period of time. The control module 1010 instructs the mass spectrometer to measure a plurality of intensities of at least one ion of the separated compounds over the period of time and generate a chromatogram.

[0097] The analysis module 1020 uses a peak finding algorithm to identify at least one peak of at least one ion from the chromatograph. The analysis module 1020 calculates two or more different peak integral areas for the at least one peak by applying the peak finding algorithm with two or more different values ​​for at least one peak finding parameter without manual and iterative adjustment of the two or more different values.

[0098] In various embodiments, the system 1000 further includes a display module 1030 and a user selection module 1040. The display module 1030 simultaneously displays, on a display device, two or more plots of at least one peak, each plot graphically illustrating different peak integral areas of the two or more different peak integral areas. The user selection module 1040 receives data from a user selection device indicating a user selection of one of the two or more plots.

[0099] While the present teachings are described in conjunction with various embodiments, it is not intended that the present teachings be limited to such embodiments. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents, as will be appreciated by those skilled in the art.

[0100] Furthermore, in describing various embodiments, the present specification may present the method and / or process as a particular sequence of steps. However, to the extent that the method or process does not rely on the particular order of steps described herein, the method or process should not be limited to the particular sequence of steps described. As one of ordinary skill in the art would understand, other sequences of steps may be possible. Thus, the particular order of steps described herein should not be construed as a limitation on the claims. In addition, claims directed to methods and / or processes should not be limited to the execution of those steps in the order written, and one of ordinary skill in the art can readily understand that the sequence may be varied and still remain within the spirit and scope of the various embodiments.

Claims

1. 1. A system for selecting an integrated area for a chromatographic peak, comprising: A separation device; A mass spectrometer; A processor, the processor comprising: instructing the separation device to separate compounds from the sample for a period of time; instructing the mass spectrometer to measure a plurality of intensities of at least one ion of the separated compounds over the period of time to generate a chromatogram; applying the peak finding algorithm with two or more different values ​​for at least one peak finding parameter of a peak finding algorithm, thereby identifying from the chromatogram two or more different boundaries of at least one peak of the at least one ion using the peak finding algorithm without manual and iterative adjustment of the two or more different values ​​by a user; calculating, for the at least one peak, two or more different peak integrated areas based on the two or more different boundaries; The processor and A system comprising:

2. The system further comprises a display device and a user selection device, the processor further comprising: displaying, on said display device, two or more plots of said at least one peak simultaneously, each plot graphically illustrating a different peak integral area of ​​said two or more different peak integral areas; receiving data from the user selection device indicative of a user selection of one of the two or more plots; The system of claim 1 , further comprising:

3. The system of claim 1 , wherein the two or more different values ​​for the at least one peak finding parameter are predetermined and received by the processor.

4. The system of claim 1 , wherein the two or more different values ​​for the at least one peak finding parameter are generated by the processor.

5. 5. The system of claim 4, wherein the two or more different values ​​for the at least one peak finding parameter generated represent all different possible values ​​within a selected range for the at least one peak finding parameter.

6. 5. The system of claim 4, wherein the two or more different values ​​for the at least one peak finding parameter generated represent a subset of all different possible values ​​within a selected range for the at least one peak finding parameter.

7. 7. The system of claim 6, wherein the subset is found by calculating how the peak integral area changes as a function of the value of the at least one peak finding parameter, selecting a peak integral area change threshold, and including only values ​​of the at least one peak finding parameter in the subset for which the peak integral area changes by more than the peak integral area change threshold.

8. 3. The system of claim 2, wherein the processor is further configured to calculate a numerical area value for each of the two or more different peak integrated areas, and wherein the processor displays the calculated numerical area value along with each of the two or more plots.

9. 3. The system of claim 2, wherein each plot of the two or more plots graphically illustrates a different peak integrated area by shading a different peak integrated area and by displaying a different peak baseline.

10. 3. The system of claim 2, wherein the processor further determines selected peak integral areas of the two or more distinct peak integral areas from a selection of one of the two or more plots, calculates a numerical area value for the selected peak integral areas, and calculates an amount of the compound in the sample from the numerical area value.

11. 3. The system of claim 2, wherein the processor further displays, on the display device, the at least one peak finding parameter and a value used for the at least one peak finding parameter along with each of the two or more plots.

12. 1. A method for selecting an integrated area for a chromatographic peak, comprising: instructing the separation device, using a processor, to separate the compound from the sample over a period of time; instructing the mass spectrometer to measure, using said processor, a plurality of intensities of at least one ion of said separated compounds over said time period to generate a chromatogram; applying the peak finding algorithm using the processor with two or more different values ​​for at least one peak finding parameter of a peak finding algorithm, thereby identifying from the chromatogram two or more different boundaries of at least one peak of the at least one ion using the peak finding algorithm without manual and iterative adjustment of the two or more different values ​​by a user; calculating, for the at least one peak, two or more different peak integrated areas based on the two or more different boundaries; A method comprising:

13. using said processor to simultaneously display on a display device two or more plots of said at least one peak, each plot graphically illustrating a different peak integral area of ​​said two or more different peak integral areas; receiving, using the processor, data from a user selection device indicative of a user selection of one of the two or more plots; The method of claim 12 further comprising:

14. 1. A computer program product comprising a non-transitory and tangible computer readable storage medium, the contents of which include a program with instructions that execute on a processor to perform a method for selecting an integrated area for a chromatographic peak, the method comprising: providing a system comprising one or more distinct software modules, the distinct software modules comprising a control module and an analysis module; instructing a separation device to separate compounds from a sample over a period of time using said control module; commanding the mass spectrometer to measure a plurality of intensities of at least one ion of the separated compounds over the period of time using the control module to generate a chromatogram; applying the peak finding algorithm using the analysis module with two or more different values ​​for at least one peak finding parameter of a peak finding algorithm, thereby identifying from the chromatogram two or more different boundaries of at least one peak of the at least one ion using the peak finding algorithm without manual and iterative adjustment of the two or more different values ​​by a user; calculating, for the at least one peak, two or more different peak integrated areas based on the two or more different boundaries; using a display device to simultaneously display on said display device two or more plots of said at least one peak, each plot graphically illustrating a different peak integral area of ​​said two or more different peak integral areas; receiving data from a user selection device, using the user selection device, indicative of a user selection of one of the two or more plots; 2. A computer program product comprising:

15. The distinct software modules further comprise a display module and a user selection module, and the method further comprises: using the display module to simultaneously display on a display device two or more plots of the at least one peak, each plot graphically illustrating a different peak integral area of ​​the two or more different peak integral areas; receiving data from a user selection device, using the user selection module, indicative of a user selection of one of the two or more plots; 15. The computer program product of claim 14, comprising:

Images