External ion source spatial positioning analysis

Abstract

A computer-implemented method for spatial positioning including collecting mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample, calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions, and determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source.

Description

EXTERNAL ION SOURCE SPATIAL POSITIONING ANALYSISRELATED APPLICATIONS

[0001] The present patent application claims the priority benefit of U.S. Provisional Patent Application Ser. No. 63 / 615,680 , filed December 28, 2023, the content of which is hereby incorporated by reference in its entirety into this disclosure.FIELD

[0002] The present disclosure relates generally to sample analysis, and more particularly, to improving sample analysis through positioning of an ion source using mass spectrometry data.BACKGROUND

[0003] Mass spectrometry (MS) data may provide valuable and distinctive insight into the composition and properties of analytes (e.g., information about the identity of analytes, the presence or absence of certain impurities and their identities, and / or relative quantification). However, several factors may influence the quality of the MS data obtained. For example, the positioning of the ion source (e.g., relative to the mass spectrometer's inlet) can influence the quality of the MS data obtained.

[0004] In conventional methods, some ion sources may be manually positioned by a user (e.g., because ion sources might not necessarily be pre-positioned relative to the MS inlet), which introduces user error and variability of MS data. Furthermore, positioning of ion source may be a time-consuming process; it can also lead to incorrect and inconsistent placement by users. Additionally, the quality of the MS data obtained may depend on the type of the source and / or its operation parameters (e.g., the applied voltage and gaspressure for a gas-assisted electrospray ionization source). Thus, a position for one type of source and / or operation parameters might not work optimally for another type of source and / or operation parameters. Further, the quality of the MS data might depend on the analyte characteristics (e.g., structure, ionization characteristics, and / or quantity). For example, at certain positions of ion sources, higher quality MS data might be obtained for analytes present in higher quantities in a sample as compared to analytes present in lower quantities. Yet, in some situations, the analytes present in the lower quantities might be of a particular interest (e.g., for impurity analysis) and, thus, a higher quality of MS data might be desirable for them. Further, in certain cases, ion sources might be subject to certain degrees of freedom with respect to movement and, thus, periodic adjustments might be necessary.

[0005] Methods, devices, systems, and software for providing spatial positioning analysis and improving the positioning of ion sources relative to the MS orifice are described, as are methods, devices, systems, and software for achieving more qualitative mass spectrometry data that may be used for spatial positioning of an ion source.SUMMARY

[0006] One aspect of the disclosure is a computer-implemented method for spatial positioning including collecting mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample, calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or morespatial positions, and determining a target spatial position of the ion source using the calculated value for each of the one or more spatial positions of the ion source.

[0007] In an aspect, the intensity of the first and / or second ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more mass to charge (m / z) values. In some aspects, the intensity of the first ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values for an analyte peak, wherein the sample comprises the analyte. In some aspects, the intensity of the second ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values for a valley between one or more analyte peaks.

[0008] One aspect of the disclosure is a computer-implemented method for spatial positioning comprising: collecting mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample, calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions, and determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source. In an aspect, the intensity of the ion signal of interest comprises a base peak intensity.

[0009] In some aspects, the calculated value is based on a product of an absolute value of the base peak intensity and the ratio of an absolute or normalized value of the base peak intensity and the absolute or normalized TIC. In an aspect, the intensity of the ionsignal of interest comprises an extracted ion signal intensity ora sum of extracted ion signal intensities for one or more m / z values. In some aspects, the calculated values are based on the product of an absolute value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the ratio of an absolute or normalized value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the absolute or normalized TIC.

[0010] In some aspects, the computer-implemented method includes positioning the ion source at predetermined spatial positions as a function of time. In an aspect, positioning the ion source is performed using an automated script. In an aspect, the computer- implemented method includes tracking the spatial positions of the ion source, wherein the tracking and / or the collecting of the MS data is initiated by a movement of the ion source.

[0011] In an aspect, the computer-implemented method includes generating one or more plots using the collected MS data of the sample and the spatial positions and / or the predetermined spatial positions of the ion source. In some aspects, the one or more plots comprise the calculated values as a function of time, a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source. In an aspect, the one or more plots further comprise an absolute or normalized value of a base peak intensity divided by the absolute or normalized TIC, the absolute or normalized value of the extracted ion signal intensity divided by the absolute or normalized TIC, the absolute or normalized sum of extracted ion signal intensities divided by the absolute or normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time. In some aspects, the computer-implemented method includes positioning the ion source based on thedetermined target spatial position.

[0012] One aspect of the disclosure is a computer program with program code for performing the computer-implemented method disclosed.

[0013] One aspect of the disclosure is computer-implemented method for spatial positioning including receiving mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample, calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions, and displaying a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface.

[0014] One aspect of the disclosure is a computer-implemented method for spatial positioning including receiving mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample, calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions, and displaying a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface.

[0015] In some aspects, the computer-implemented method for spatial positioning includes determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source.

[0016] One aspect of the disclosure is one or more non-transitory computer-readable storage media comprising instructions, which when executed by one or more computing devices, cause the one or more computing devices to: collect mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample, calculate a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions, and determine a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source.

[0017] One aspect of the disclosure is one or more non-transitory computer-readable storage media comprising instructions, which when executed by one or more computing devices, cause the one or more computing devices to: collect mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample, calculate a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions, and determine a target spatial position of the ionsource using the calculated values for each of the one or more spatial positions of the ion source.

[0018] In some aspects, the one or more non-transitory computer-readable storage media includes instructions, which when executed by one or more computing devices, cause the one or more computing devices to display a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface.

[0019] These and other advantages, aspects, and novel features of the present disclosure, as well as details of illustrated embodiments thereof, will be more fully understood from the following description and drawings.BRIEF DESCRIPTION OF THE FIGURES

[0020] Various aspects and embodiments of the present disclosure are shown in the drawings and described therein and elsewhere throughout the disclosure. In the drawings, like references indicate like parts.

[0021] FIG. 1 provides a schematic illustration of a system hardware block diagram for an embodiment of the disclosed methods, devices, and systems.

[0022] FIG. 2 provides a schematic block diagram of software components for an embodiment of the disclosed systems.

[0023] FIG. 3 provides example plots of processed MS data as an example ion source is moved between various spatial positions as a function of time.

[0024] FIG. 4A provides an example plot of Base Peak Intensity (BPI) as an example ion source is moved between various spatial positions and an ion signal is plotted as a function of time.- 1-

[0025] FIG. 4B provides an example plot of Total Ion Current (TIC) as an example ion source is moved between various spatial positions and ion current is plotted as a function of time.

[0026] FIG. 4C provides an example trace of an example ratio of a normalized BPI and a normalized TIC.

[0027] FIG. 4D provides an example trace of an example product of the absolute BPI and a ratio of normalized BPI and normalized TIC.

[0028] FIG. 5A provides an example deconvoluted MS data at an example position of an ion source corresponding to a highest BPI.

[0029] FIG. 5B provides an example deconvoluted MS data at an example position of an ion source corresponding to the highest TIC.

[0030] FIG. 5C provides an example deconvoluted MS data at an example position of an ion source corresponding to a highest product of the absolute BPI and a ratio of normalized BPI and normalized TIC.

[0031] FIG. 6 provides an example illustration of changes in spatial position of an ion source as a function of time.

[0032] FIG. 7 provides an example user interface depicting spatial positions of the ion source (in X, Y, and Z) and certain MS data.

[0033] FIG. 8 provides an example of a 2-dimensional map of a slice of motion with one static axis as the ion source moves through the various spatial positions.

[0034] FIG. 9 provides an example representation of signal levels associated with predetermined spatial positions of the ion source.DETAILED DESCRIPTION

[0035] In various aspects and embodiments of the present disclosure, systems,components, devices, methods, software, and / or combinations thereof are provided for positioning an ion source, improving the positioning of ion sources (e.g., relative to an inlet of a mass spectrometer), and / or displaying certain plots to assist with spatial positioning to determine a target spatial position of an ion source.

[0036] In conventional methods, ion sources (e.g., devices used to ionize samples for an MS analysis) may be manually positioned by a user because they are not necessarily prepositioned as part of the design of an interface with a mass spectrometer. Such manual positioning might yield suboptimal quality and variability of MS data. Additionally, a spatial position that works for one type of an ion source, operation parameters, and / or sample might not work for another type of source, operation parameters, and / or sample. Further, ion sources might change their spatial position as time passes (e.g., due to environmental factors such as vibrations, or removal and reattachment). Thus, adjustments and / or changes to a spatial position of an ion source might be needed.

[0037] Optimizing a placement of the ion source aids in obtaining higher quality MS data. However, optimization can be a long and cumbersome process. For example, optimization may involve performing multiple infusions, logging results, processing data, and repeating this process until a satisfactory result (e.g., good quality MS data) is achieved. Further, even after a lengthy and cumbersome process (e.g., manual process), optimal quality data might still not be achieved. And, because spatial positioning of the ion source is cumbersome, MS experiments might then be run suboptimally, which leads to inferior data (e.g., additional noise, insufficient sensitivity, positioning in a way as to foul the mass spectrometer, missing data, etc.).

[0038] Further, MS analysis might be coupled to an upstream separation technique, like liquid chromatography, capillary electrophoresis, isoelectric focusing, etc. In someexamples, the separation may terminate with a pulled glass capillary which must be positioned relative to an atmospheric pressure inlet. In other examples, an upstream separation and ionization of a sample for MS analysis may be performed on a microfluidic chip with integrated electrospray ionization. For example, isoelectric focusing (e.g., imaged isoelectric focusing (icIEF)) might be used for the upstream separation. Examples of systems and methods for such analysis include published PCT Patent Application Publication Nos. WO 2017 / 095813, WO 2019 / 148198, WO 2019 / 232397, WO 2021 / 030353, and WO 2021 / 222171 , which are hereby incorporated by reference for all purposes.

[0039] In some examples, MS data obtained via such icIEF-MS analysis may include a complicated assortment of mass-to-charge ratios (or masses) and background ions that make it difficult to correlate icIEF data with MS data. Thus, it is crucial to position an electrospray from an ion source (e.g., a microfluidic chip) in a location where good quality MS data can be collected.

[0040] In some embodiments, a solution is provided, by, e.g., systems, components, devices, methods, software, and / or combinations thereof for spatial positioning (e.g., optimization of spatial positioning).

[0041] As utilized herein, circuitry or module is “operable” to perform a function whenever the circuitry or module comprises the necessary hardware and code (if any is necessary) to perform the function, regardless of whether performance of the function is disabled or not enabled (e.g., by a user-configurable setting, factory trim, etc.).

[0042] As utilized herein, “and / or” means any one or more of the items in the list joined by “and / or.” As an example, “x and / or y” means any element of the three-element set {(x), (y), (x. y)}- lnother words, “x and / or y” means “one or both of x and y.” As anotherexample, “x, y, and / or z” means any element of the seven-element set {(x), (y), (z), (x, y), (x, z), (y, z), (x, y, z)}. In other words, “x, y and / or z” means “one or more of x, y, and z.” As utilized herein, the term “exemplary” means serving as a non-limiting example, instance, or illustration. Further, as utilized herein, the terms “for example” and “e.g.,” set off lists of one or more non-limiting examples, instances, or illustrations.

[0043] The terminology used herein is for the purpose of describing particular examples only and is not intended to be limiting of the disclosure. As used herein, the singular forms are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises,” “includes,” “comprising,” “including,” “has,” “have,” “having,” and the like when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and / or groups thereof.

[0044] It will be understood that, although the terms first, second, etc. may be used herein to describe various elements, these elements should not be limited by these terms. These terms are only used to distinguish one element from another element. Thus, for example, a first element, a first component, or a first section discussed below could be termed a second element, a second component, or a second section without departing from the teachings of the present disclosure. Similarly, various spatial terms, such as “upper,” “lower,” “side,” and the like, may be used in distinguishing one element from another element in a relative manner. It should be understood, however, that components may be oriented in different manners, for example, a device may be turned sideways so that its “top” surface is facing horizontally and its “side” surface is facing vertically, without departingfrom the teachings of the present disclosure.

[0045] In some embodiments, a computer-implemented method for spatial positioning is provided. In some embodiments, the method includes collecting mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions. In some embodiments, the MS data includes an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample. In some embodiments, the method further includes calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions. In some embodiments, the method further includes determining a target spatial position of the ion source using the calculated value for each of the one or more spatial positions of the ion source. In some embodiments, the calculated value is based on a product of the absolute intensity of the first ion signal of interest and a ratio of the absolute intensity of the first ion signal of interest and the absolute intensity of the second ion signal of interest. In some embodiments, the calculated value is based on a product of the absolute intensity of the first ion signal of interest and a ratio of the normalized intensity of the first ion signal of interest and the normalized intensity of the second ion signal of interest. In some embodiments, the intensity of the first and / or second ion signal of interest includes an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more mass to charge (m / z) values. In some embodiments, the intensity of the first ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values for an analyte peak, wherein the sample comprises the analyte. In some embodiments, the intensity of the firstion signal of interest comprises an extracted ion signal intensity or a sum of different extracted ion signal intensities at one or more m / z values and one or more different times for an analyte peak, wherein the sample comprises the analyte. In some embodiments, one or more m / z values may correspond to one or more impurities in the sample. In some embodiments, the intensity of the second ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values for a valley between one or more analyte peaks.

[0046] In some embodiments, a computer-implemented method for spatial positioning includes collecting mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample. In some embodiments, the MS data comprises an intensity of an ion signal of interest and a total ion current (TIC) corresponding to the sum of all ion signal introduced to the MS.

[0047] In some embodiments, the method further includes calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC (nTIC) at each of the one or more spatial positions. In some embodiments, the method further includes determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source. In some embodiments, the calculated value is based on a product of the absolute intensity of the ion signal of interest and a ratio of the absolute intensity of the ion signal of interest and the absolute TIC. In some embodiments, the calculated value is based on a product of the absolute intensity of the ion signal of interest and a ratio of the normalized intensity of the ion signal of interestand the normalized TIC. In some embodiments, the intensity of the ion signal of interest comprises a base peak intensity (BPI). In some embodiments, the intensity of the ion signal of interest comprises a base peak intensity (BPI) where the ion intensity will correspond to the most abundant ion in a given spectrum at a given time and position. In some embodiments, the base peak is the peak with the greatest intensity in an MS data (e.g., it may be a different ion at different times or positions). In some embodiments, the BPI is normalized (to produce normalized BPI (nBPI)) relative to the overall highest BPI in the MS data collected for one or more positions of the ion source. In some embodiments, the TIC is normalized (to produce normalized TIC (nTIC)) relative to the overall highest TIC in the MS data collected for one or more positions of the ion source. In some embodiments, the calculated value is based on a product of an absolute value of the base peak intensity (AbsBPI) and the ratio of an absolute or normalized value of the base peak intensity (AbsBPI or nBPI, respectively) and the absolute or normalized TIC (AbsTIC or nTIC, respectively). In some embodiments, the calculated value is based on or is AbsBPI*(nBPI / nTIC). In some embodiments, the calculated value is based on or is AbsBPI*(AbsBPI / AbsTIC). In some embodiments, the intensity of the ion signal of interest includes an extracted ion signal intensity (XIC) or a sum of extracted ion signal intensities for one or more m / z values. In some embodiments, the one or more m / z values correspond to one or more analytes in the sample. In some embodiments, the one or more m / z values correspond to one or more impurities in the sample. In some embodiments, the calculated values are based on the product of an absolute value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the ratio of an absolute or normalized value of the extracted ion signal intensity or the sum of extracted ion signal intensities (AbsXIC or nXIC, respectively) and the absolute or normalized TIC (AbsTIC or nTIC,respectively). In some embodiments, the calculated values are based on the product of the absolute value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the ratio of the absolute value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the absolute TIC. In some embodiments, the calculated values are based on the product of the absolute value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the ratio of the normalized value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the normalized TIC.

[0048] In some embodiments, the spatial position of the ion source is a position relative to a mass spectrometer (e.g., a mass spectrometer inlet). In some embodiments, the spatial position of the ion source is a position relative to a certain starting point (e.g., an initial position of the ion source). In some embodiments, the spatial position may be expressed with one or more of X, Y, and Z coordinates. In some embodiments, a target spatial position of the ion source may be a position at which an MS data of the desired quality (e.g., a signal to noise ratio of deconvoluted MS data,) is obtained, a position at which an MS data of a better quality (as compared to one or more of other positions) is obtained, or a position at which an MS data of the best quality (as compared to all other positions) is obtained for, e.g., one or more of analytes (e.g., analytes in the sample) and / or under particular operating conditions. In some embodiments, the target spatial position of the ion source may be a position at which a deconvoluted MS data of the desired quality is obtained, a position at which a deconvoluted MS data of a better quality (as compared to one or more of other positions) is obtained, or a position at which a deconvoluted MS data of the best quality (as compared to all other positions) is obtained for, e.g., one or more of analytes (e.g., analytes in the sample) and / or under particular operating conditionsIn some embodiments, such target position may be determined without deconvoluting MS data at one or more position of the ion source to determine such position.

[0049] In some examples, an MS data is collected under one or more operational parameters. In some embodiments, the MS data may be collected under the same conditions (e.g., without varying any of the operational parameters). In some embodiments, MS data is collected under two or more operational parameters. In some embodiments, MS data is collected under two or more operational parameters applied as part of mass spectrometric detection and / or to the ionization source. For example, the MS data may be collected using different ion source voltage (e.g., electrospray voltage applied to solution in conductance with the tip of a microfluidic chip or sprayer used for ionization), nebulization gas pressure, flow rate of the sample, etc.

[0050] In some embodiments, methods further include positioning the ion source at predetermined spatial positions a function of time. In some embodiments, the ion source might be placed in an initial position (e.g., a position designated as (0, 0, 0) in an X, Y, Z coordinate system) and then move along one or more of X, Y, Z axis at a certain time. In some embodiments, the ion source might move at a certain time into predetermined positions (105, 0, 0), (110, 0, 0), (115, 0, 0), (105, 0, 0.25), (110, 0, 0.25), (115, 0, 0.25), etc. In some embodiments, the ion source may be placed on a stage, platform, or other device that is able to move the source into certain positions and / or certain directions (e.g., in X, Y, and Z coordinates). In some examples, the ion source may be moved to various spatial positions and MS data may be gathered at each of the spatial positions as the ion source is moved.

[0051] In some embodiments, the positioning of the ion source is performed using an automated script. For example, an automated script might move the ion source into aposition with a particular X, Y, and Z coordinates at a particular time without user input. In some embodiments, the MS data may be collected and / or presented in a way to provide a user with quick visualization to facilitate finding a target spatial position for the ion source. In some embodiments, the spatial positions may be predefined by the user, by the program, or may be pre-selected by a user via the user interface.

[0052] In some embodiments, methods further include tracking the spatial positions of the ion source, wherein the tracking and / or the collecting of the MS data is initiated by a movement of the ion source. In some embodiments, the ion source moves in random directions, and such positions are tracked and linked to the MS data collected at such positions. In some embodiments, the ion source moves between predetermined positions. In some embodiments, the tracking is used to confirm that the source in fact moved into the predetermined positions.

[0053] Various samples may be used with the systems, components, devices, methods, software, and / or combinations thereof for spatial positioning (e.g., optimization of spatial positioning). For example, quality MS data might be desired for one or more substances of interest. In some embodiments, a sample comprising one or more substances of interest might be used with the systems, components, devices, methods, software, and / or combinations thereof for spatial positioning (e.g., optimization of spatial positioning). For example, MS data of a sample (comprising one or more substances of interest) may be collected as a function of a spatial position of an ion source for one or more spatial positions. In some embodiments, spatial positioning is optimized for one or more substances of interest (using a sample comprising one or more substances of interest). In some embodiments, while quality MS data might be desired for one or more substances of interest, such one or more substances of interest might be available in limited quantities,might be costly, or it might be otherwise undesirable to use one or more substances of interest for spatial positioning. In such embodiments, a sample that does not comprise one or more substances of interest might be used for spatial positioning. In some examples, a sample comprising one or more substances analogous to the one or more substances of interest might be used. For example, if one or more substances of interest are certain antibodies, similar antibodies might be used in a sample for spatial optimization. In some examples, one or more substances analogous to the one or more substances of interest might have similar impurity profile, weight, ionization qualities to the one or more substances of interest.

[0054] In some embodiments, the substances of interest are separated using electrophoretic techniques prior to MS analysis. In certain embodiments, the substance of interest may be combined with ampholyte(s) and / or anodic and / or cathodic spacer(s) and may be subjected to isoelectric focusing in a separation channel by applying an electric field across the separation channel. Ampholytes are amphoteric molecules that contain both acidic and basic groups and that exist mostly as zwitterions within a certain range of pH. The electric field across a fluid channel used in isoelectric focusing may be generated by the use of electrodes and electrolyte solutions. The portion of the electrolyte solution on the anode side of the fluid channel is known as an "anolyte". That portion of the electrolyte solution on the cathode side of the fluid channel is known as a "catholyte". A variety of electrolytes may be used in the disclosed methods and devices including, but not limited to, phosphoric acid, sodium hydroxide, ammonium hydroxide, glutamic acid, lysine, formic acid, dimethylamine, triethylamine, acetic acid, piperidine, diethylamine, and / or any combination thereof. The electrolytes may be used at any suitable concentration in aqueous and / or organic solutions, such as 0.0001 %, 0.001 %, 0.01%, 0.1 %, 1%, 10%,20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, etc. The concentration of the electrolytes may be at least 0.0001 %, 0.001 %, 0.01 %, 0.1 %, 1 %, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%. The concentration of the electrolytes may be at most 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 1 %, 0.1 %, 0.01 %, 0.001 %, 0.0001 %.

[0055] The disclosed methods, devices, systems, and software may be used for separation and characterization of analytes obtained from any of a variety of biological or non-biological samples. Examples include, but are not limited to, tissue samples, cell culture samples, whole blood samples (e.g., venous blood, arterial blood, or capillary blood samples), plasma, serum, saliva, interstitial fluid, urine, sweat, tears, protein samples derived from industrial enzyme or biologic drug development or manufacturing processes, environmental samples (e.g., air samples, water samples, soil samples, surface swipe samples), and the like. In some embodiments, the samples may be processed using any of a variety of techniques known to those of skill in the art prior to analysis using the disclosed methods and devices for integrated chemical separation and mass spectrometric characterization. For example, in some embodiments the samples may be processed to extract proteins or nucleic acids. Samples may be collected from any of a variety of sources or subjects, e.g., inorganic sources or organic sources like bacteria, virus, plants, animals, or humans.

[0056] Various systems and / or devices might be used for introduction of a sample into a mass spectrometer (e.g., with the systems, components, devices, methods, software, and / or combinations thereof for spatial positioning (e.g., optimization of spatial positioning)). In some embodiments, such systems and / or devices include a source of ions directed towards a mass spectrometer. In some embodiments, such systems and / or devices include a capillary. In some embodiments, such systems and / or devices include amicrofluidic chip. In some embodiments, such systems and / or devices further include a pump. In some embodiments, such systems and / or devices further include a movable stage. In some embodiments, a capillary is positioned on a movable stage. In some embodiments, a microfluidic chip is positioned on a movable stage. In some embodiments a pump is positioned on a movable stage. In some embodiments, such systems and / or devices include a separation system.

[0057] Various methods may be used (e.g., with the systems, components, devices, methods, software, and / or combinations thereof for spatial positioning (e.g., optimization of spatial positioning)) for delivery of a sample into a mass spectrometer to collect mass spectrometry data. In some embodiments, a sample might be introduced continuously. In some embodiments, a sample might be introduced by a continuous infusion. In some embodiments, a sample having a consistent concentration (e.g., the same concentration over time) may be introduced. In some embodiments, a sample with the same concentration is introduced by a continuous infusion. In some embodiments, a sample is introduced in such a way (e.g., with the same concentration via continuous infusion) that the only changing parameter for the acquisition of the MS data is a spatial position of the ion source (that is used to obtain MS data). In some embodiments, a sample is introduced into mass spectrometer after a separation using a separation system (e.g., a sample is introduced into a separation system, separated, and then further introduced into a mass spectrometer). Other methods for delivery of a sample into a mass spectrometer might be used.

[0058] Various methods may be used for ionization of a sample (e.g., with the systems, components, devices, methods, software, and / or combinations thereof for spatial positioning (e.g., optimization of spatial positioning)). In some embodiments, a samplemight be ionized via a chemical ionization to collect MS data. In some embodiments, a sample might be ionized via electrospray ionization (ESI) to collect MS data. In some embodiments, a sample might be ionized on a microfluidic chip with integrated ESI interface. Other methods of ionization might also be used.

[0059] In some embodiments, one or more plots are generated using the collected MS data of the sample and the spatial positions and / or the predetermined spatial positions of the ion source. In some embodiments, the one or more plots comprise the calculated values as a function of time, a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source. In some embodiments, the one or more plots comprise the calculated values as a function of time, a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source, and / or a function of the applied operational parameters. In some embodiments, the one or more plots further comprise the absolute or normalized value of the base peak intensity divided by the absolute or normalized TIC, the absolute or normalized value of the extracted ion signal intensity divided by the absolute or normalized TIC, the absolute or normalized sum of extracted ion signal intensities divided by the absolute or normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time. In some embodiments, the one or more plots further comprise the normalized value of the base peak intensity divided by the normalized TIC, the normalized value of the extracted ion signal intensity divided by the normalized TIC, the normalized sum of extracted ion signal intensities divided by the normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predeterminedspatial position of the ion source, and / or time. In some embodiments, the one or more plots further comprise the absolute value of the base peak intensity divided by the absolute TIC, the absolute value of the extracted ion signal intensity divided by the absolute TIC, the absolute sum of extracted ion signal intensities divided by the absolute TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time. In some embodiments, the one or more plots include 2D plots. In some embodiments, the one or more plots include 3D plots. In some embodiments, the one or more plots include heat maps. In some embodiments, other forms of plots may also be used. In some embodiments, the one or more plots include a combination of two or more different types of plots (e.g., a 2D plot and a heat map). In some embodiments, the plots may be displayed side by side. In some embodiments, the plots may be displayed side by side in space or time. In some embodiments, the plots are overlaid. In some embodiments, the one or more plots depict information related to the determination of a target spatial position of the ion source. For example, raw or processed MS data may be displayed for one or more of the spatial positions of the ion source and the target position highlighted or signified by other means. In some embodiments, the one or more plots visualize information to help user determine a target spatial position of the ion source (e.g., using the calculated value for each of the one or more spatial positions of the ion source).

[0060] In some embodiments, methods further include positioning the ion source based on the determined target spatial position. In some embodiments, a user may position the ion source based on the determined target spatial position. In some embodiments, the positioning of the ion source is performed automatically based on the determined targetspatial position. In some embodiments, the positioning might be done using a stage, platform, or other device (e.g., that the ion source may be placed on) that is able to move the source into certain positions and / or certain directions (e.g., in X, Y, and Z coordinates). In some embodiments, a user interface may present several target positions to be used (e.g., based on one or more calculated values).

[0061] In some embodiments, methods may be performed by a computer program with program code for performing the computer-implemented methods. In some embodiments, a computer-implemented method for spatial positioning is provided. In some embodiments, the method includes receiving mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample. In some embodiments, the method further includes calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions. In some embodiments, the method further includes displaying a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface. In some embodiments, the method includes calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute intensity of the ion signal of interest and an absolute TIC at each of the one or more spatial positions. In some embodiments, the method includes calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of a normalized intensity of the ion signal of interest and a normalized TIC ateach of the one or more spatial positions.

[0062] In some embodiments, a computer-implemented method for spatial positioning includes receiving mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample. In some embodiments, the method further comprises calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions. In some embodiments, the method further includes displaying a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface. In some embodiments, the method comprises calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute intensity of the first ion signal of interest and an absolute intensity of the second ion signal of interest at each of the one or more spatial positions. In some embodiments, the method comprises calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of a normalized intensity of the first ion signal of interest and a normalized intensity of the second ion signal of interest at each of the one or more spatial positions.

[0063] In some embodiments, MS data may be acquired on a mass spectrometer using one computer and then received using another computer (e.g., another computer used for calculating a value). In some embodiments, MS data may be synchronously acquired on a mass spectrometer using one computer and received using another computer (e.g.,another computer used for calculating a value). In some embodiments acquisition and further processing is done using the same computer.

[0064] In some embodiments, the computer-implemented method for spatial positioning further comprising determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source. In some embodiments, one or more non-transitory computer-readable storage media is provided including instructions, which when executed by one or more computing devices, cause the one or more computing devices to: collect mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of as ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample; calculate a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions; and determine a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source. In some embodiments, the value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute intensity of the ion signal of interest and an absolute TIC at each of the one or more spatial positions. In some embodiments, the value is based on a product of an absolute intensity of the ion signal of interest and a ratio of a normalized intensity of the ion signal of interest and a normalized TIC at each of the one or more spatial positions. In some embodiments, one or more non-transitory computer- readable storage media is provided including instructions, which when executed by one or more computing devices, cause the one or more computing devices to collect mass spectrometry (MS) data of a sample as a function of spatial position of an ion source forone or more spatial positions, the MS data comprising an intensity of one or more ion signals of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample; and the data used to calculate a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions; and the calculated values for each of the one or more spatial positions of the ion source used to determine a target spatial position of the ion source. In some embodiments, the value is based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute intensity of the ion signal of interest and an absolute TIC at each of the one or more spatial positions. In some embodiments, the value is based on a product of an absolute intensity of the ion signal of interest and a ratio of a normalized intensity of the ion signal of interest and a normalized TIC at each of the one or more spatial positions. In some embodiments, one or more non-transitory computer- readable storage media is provided including instructions, which when executed by one or more computing devices, cause the one or more computing devices to collect mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample; calculate a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions; and determine a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source. In some embodiments, the value based on aproduct of an absolute intensity of the first ion signal of interest and a ratio of an absolute intensity of the first ion signal of interest and an absolute intensity of the second ion signal of interest at each of the one or more spatial positions. In some embodiments, the value based on a product of an absolute intensity of the first ion signal of interest and a ratio of a normalized intensity of the first ion signal of interest and a normalized intensity of the second ion signal of interest at each of the one or more spatial positions.

[0065] In some embodiments, the one or more non-transitory computer-readable storage media further includes instructions, which when executed by one or more computing devices, cause the one or more computing devices to display a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface.

[0066] FIG. 1 provides a schematic illustration of a system hardware block diagram 100 for one embodiment of the disclosed methods, devices, and systems. As illustrated, a system of the present disclosure may comprise one or more of the following hardware components: (i) a chemical separation system (e.g., a capillary or microfluidic device designed to perform an analyte separation, e.g., an isoelectric focusing-based separation, and one or more high-voltage power supplies), (ii) an electrospray ionization (ESI) interface for a mass spectrometer that, in some cases, may be directly integrated with the separation system (as indicated by the dashed line), (iii) a mass spectrometer, (iv) an imaging device or system, (v) a processor or computer, and (vi) a computer memory device, or any combination thereof. In some embodiments, a system may comprise a system (or a device) for introduction of a sample into a mass spectrometer. In some embodiments, a system may comprise a system (or a device) for introduction of a sample into a mass spectrometer. The chemical separation system, ESI interface, and / or imagingsystem might be absent. In some embodiments, a system (or device) for introduction of a sample into a mass spectrometer might be present instead of a chemical separation system and / or ESI interface. In some embodiments, a system (or device) for introduction of a sample into a mass spectrometer might be coupled to an ionization device. In some embodiments, a system (or device) for introduction of a sample into a mass spectrometer might have an integrated ionization device. In some embodiments, a system (or device) for introduction of a sample into a mass spectrometer might be coupled to or have an integrated ion source. In some embodiments, an ion source might be an electrospray ionization (ESI) source. In some embodiments, an ionization device or an integrated ionization device

[0067] In some embodiments, the system may further comprise one or more capillary or microfluidic device flow controllers (e.g., programmable syringe pumps, peristaltic pumps, high performance liquid chromatography (HPLC) pumps, etc.), temperature controllers configured to maintain a specified temperature for all or a portion of a capillary or microfluidic device, additional photo sensors or image sensors (e.g., photodiodes, avalanche photodiodes, CMOS image sensors and cameras, CCD image sensors and cameras, etc.), light sources (e.g., light emitting diodes (LEDs), diode lasers, fiber lasers, gas lasers, halogen lamps, arc lamps, etc.), other types of sensors (e.g., temperature sensors, flow sensors, pH sensors, conductivity sensors, etc.), computer memory devices, computer display devices (e.g., comprising a graphical user interface), digital communication devices (e.g., intranet, internet, Wi-Fi, Bluetooth®, or other hardwired or wireless communication hardware), and the like.

[0068] In some embodiments, the system may comprise an integrated system in which a selection of functional hardware components are packaged in a fixed configuration. Insome embodiments, the system may comprise a modular system in which the selection of functional hardware components may be changed in order to reconfigure the system for new applications. In some embodiments, some of these functional system components, e.g., capillaries or microfluidic devices are replaceable or disposable components.

[0069] A variety of different mass spectrometers may be utilized in different embodiments of the disclosed systems and / or methods including, but not limited to, time-of-flight mass spectrometers, quadrupole mass spectrometers, ion trap or orbitrap mass spectrometers, distance-of-flight mass spectrometers, Fourier transform ion cyclotron resonance spectrometers, resonance mass measurement spectrometers, and nanomechanical mass spectrometers.

[0070] FIG. 2 provides a schematic block diagram 200 of the software components for an embodiment of the disclosed systems. As illustrated in FIG. 2, a system of the present disclosure may comprise a plurality of software modules. For example, a system may comprise a system control software module, a data acquisition software module, a data processing software module, or any combination thereof. In general, these software modules will be configured to operate within an operating system or environment hosted by a computer processor and may communicate and share data with each other and / or the operating system to allow synchronized data acquisition.

[0071] In some embodiments, a system control software module may comprise software for one or more of the following: (i) coordinating of a stage, platform, or other device that is able to move an ion source to various positions and / or in certain directions (e.g., X, Y, and Z coordinates) relative to a mass spectrometer, (ii) coordinating the operation of an ion source and / or its operation parameters (e.g., nebulizer gas pressures, ion source voltages, and / or sample infusion rates), (iii) coordinating the collection of MS data, (iv)providing feedback control of one or more operation parameters of an ion source and / or mass spectrometer based on data derived reoptimization parameters (e.g., MS data, data from imaging of a separation channel and / or a Taylor cone), (v) controlling data acquisition by the mass spectrometer while moving the ion source to various positions, (vi) monitoring voltage at an ESI tip and adjusting circuit voltages, (vii) monitoring gas pressure and / or adjusting gas pressure between the ion source and the mass spectrometer (e.g., at the inlet), and / or (vii) controlling the stage, platform, or other device that is able to move the ion source to various positions based on user input, preconfigured settings, or any combination thereof.

[0072] In some embodiments, a data acquisition module may comprise software for: controlling motion data or image acquisition by one or more sensors or systems, storing or transferring (e.g. exporting or importing) said motion or image data, and providing a software interface with system control and / or data processing software modules, controlling data acquisition by one or more mass spectrometer systems, storing or transferring said mass spectrometer data (or other downstream analytical instrument data), and providing a software interface with system control and / or data processing software, or any combination thereof.

[0073] In some embodiments, a data processing module may comprise software for: processing data or images. In some embodiments, a data processing module may comprise software for one or more of the following: (i) processing MS data; (ii) processing data for a spatial position of an ion source; (iii) calculating a value based on an MS data (e.g., calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of theone or more spatial positions (e.g., wherein the MS data comprises an intensity of a first ion signal of interest and an intensity of a second ion signal of interest)), calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions (e.g., wherein the MS data comprises an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample)); (iv) determining a target spatial position of the ion source (e.g., using the calculated values for each of the one or more spatial positions of the ion source); (v) determining the position(s) of one or more pl standards or analyte peaks in a separation channel while the separation is being performed, after the separation is complete, or after mobilization of the pl standards and analyte peaks towards a separation channel outlet or electrospray tip, (vi) processing images and determining a velocity, an exit time, and / or an electrospray emission time for one or more pl standard or analyte peaks, (vii) processing of images of a Taylor cone to monitor electrospray performance, and / or (viii) processing images of a Taylor cone, determining a shape, density, or other characteristic of the Taylor cone, and calculating an adjustment to be made to one or more operating parameters comprising the position (i.e. , alignment and / or separation distance) of the electrospray tip or orifice relative to the mass spectrometer inlet, the fluid flow rate through the electrospray tip or orifice, the voltage between the electrospray tip or orifice and the mass spectrometer, etc., or any combination thereof, to affect a change in a quality of the mass spectrometer data; or any combination thereof.

[0074] The disclosed system and application software may be implemented using any of a variety or programming languages and environments known to those of skill in the art.Examples include, but are not limited to, C, C++, C#, PL / I, PL / S, PL / 8, PL-6, SYMPL, Python, Java, LabView, Visual Basic, .NET and the like.

[0075] In some embodiments, as noted above, the data processing module may comprise image processing software for characterizing the shape, density, or other visual indicator of Taylor cone function, processing of motion and / or MS data, etc. Any of a variety of image processing algorithms known to those of skill in the art may be utilized for image preprocessing or image processing in implementing the disclosed methods and systems. Examples include, but are not limited to: Canny edge detection methods, Canny-Deriche edge detection methods, first-order gradient edge detection methods (e.g., the Sobel operator), second order differential edge detection methods, phase congruency (phase coherence) edge detection methods, other image segmentation algorithms (e.g., intensity thresholding, intensity clustering methods, intensity histogram-based methods, etc.), feature and pattern recognition algorithms (e.g., the generalized Hough transform for detecting arbitrary shapes, the circular Hough transform, etc.), and mathematical analysis algorithms (e.g., Fourier transform, fast Fourier transform, wavelet analysis, autocorrelation, Savitzky-Golay smoothing, Eigen analysis, etc.), or any combination thereof.

[0076] One or more processors or computers may be employed to implement the methods disclosed herein. The one or more processors may comprise a hardware processor such as a central processing unit (CPU), a graphic processing unit (GPU), a general-purpose processing unit, or computing platform. The one or more processors may be comprised of any of a variety of suitable integrated circuits (e.g., application specific integrated circuits (ASICs) designed specifically for implementing deep learning network architectures, or field-programmable gate arrays (FPGAs) to accelerate compute time, etc., and / or to facilitate deployment), microprocessors, emerging next-generationmicroprocessor designs (e.g., memristor-based processors), logic devices and the like.Although the disclosure is described with reference to a processor, other types of integrated circuits and logic devices may also be applicable. The processor may have any suitable data operation capability. For example, the processor may perform 512 bit, 256 bit, 128 bit, 64 bit, 32 bit, or 16 bit data operations. The one or more processors may be single core or multi core processors, or a plurality of processors configured for parallel processing.

[0077] The one or more processors or computers used to implement the disclosed methods may be part of a larger computer system and / or may be operatively coupled to a computer network (a “network”) with the aid of a communication interface to facilitate transmission of and sharing of data. The network may be a local area network, an intranet and / or extranet, an intranet and / or extranet that is in communication with the Internet, or the Internet. The network in some cases is a telecommunication and / or data network. The network may include one or more computer servers, which in some cases enables distributed computing, such as cloud computing . The network, in some cases with the aid of the computer system, may implement a peer-to-peer network, which may enable devices coupled to the computer system to behave as a client or a server.

[0078] The computer system may also include memory or memory locations (e.g., random-access memory, read-only memory, flash memory, Intel® Optane™ technology), electronic storage units (e.g., hard disks), communication interfaces (e.g., network adapters) for communicating with one or more other systems, and peripheral devices, such as cache, other memory, data storage and / or electronic display adapters. The memory, storage units, interfaces and peripheral devices may be in communication with the one or more processors, e.g., a CPU, through a communication bus, e.g., as is found on amotherboard. The storage unit(s) may be data storage unit(s) (or data repositories) for storing data.

[0079] The one or more processors, e.g., a CPU, execute a sequence of machine- readable instructions, which are embodied in a program (or software). The instructions are stored in a memory location. The instructions are directed to the CPU, which subsequently program or otherwise configure the CPU to implement the methods of the present disclosure. Examples of operations performed by the CPU include fetch, decode, execute, and write back. The CPU may be part of a circuit, such as an integrated circuit. One or more other components of the system may be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

[0080] The storage unit stores files, such as drivers, libraries, and saved programs. The storage unit stores user data, e g., user-specified preferences and user-specified programs. The computer system in some cases may include one or more additional data storage units that are external to the computer system, such as located on a remote server that is in communication with the computer system through an intranet or the Internet.

[0081] Some aspects of the methods and systems provided herein are implemented by way of machine (e.g., processor) executable code stored in an electronic storage location of the computer system, such as, for example, in the memory or electronic storage unit. The machine executable or machine readable code is provided in the form of software. During use, the code is executed by the one or more processors. In some cases, the code is retrieved from the storage unit and stored in the memory for ready access by the one or more processors. In some situations, the electronic storage unit is precluded, and machine-executable instructions are stored in memory. The code may be pre-compiled and configured for use with a machine having one or more processors adapted to executethe code or may be compiled at run time. The code may be supplied in a programming language that is selected to enable the code to execute in a pre-compiled or as-compiled fashion. The code may be or refer to or include a script to run predetermined steps and / or methods. The code may be run based on one or more triggers either internally or between systems for synchronization of data sets, such as a user request or by inputting information at a user interface. The code may be run automatically based on one or more triggers or at a preset time, or as part of an installation process, along with other software and / or code.

[0082] Various aspects of the disclosed methods and devices may be thought of as “products” or “articles of manufacture”, e.g., “computer program or software products”, typically in the form of machine (or processor) executable code and / or associated data that is stored in a type of machine readable medium, where the executable code comprises a plurality of instructions for controlling a computer or computer system in performing one or more of the methods disclosed herein. Machine-executable code may be stored in an optical storage unit comprising an optically readable medium such as an optical disc, CD- ROM, DVD, or Blu-Ray disc. Machine-executable code may be stored in an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or on a hard disk. “Storage” type media include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memory chips, optical drives, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software that encodes the methods and algorithms disclosed herein.

[0083] All or a portion of the software code may at times be communicated via the Internet or various other telecommunication networks. Such communications, for example, enableloading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server.Thus, other types of media that are used to convey the software encoded instructions include optical, electrical and electromagnetic waves, such as those used across physical interfaces between local devices, through wired and optical landline networks, and over various atmospheric links. The physical elements that carry such waves, such as wired or wireless links, optical links, or the like, are also considered media that convey the software encoded instructions for performing the methods disclosed herein. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

[0084] The computer system typically includes, or may be in communication with, an electronic display for providing, for example, images captured by a machine vision system. The display is typically also capable of providing a user interface (Ul). Examples of Ill’s include but are not limited to graphical user interfaces (GUIs), web-based user interfaces, and the like.

[0085] As noted above, the disclosed methods, devices, systems, and software have potential application in a variety of fields including, but not limited to, proteomics research, drug discovery and development, and clinical diagnostics. For example, the improved information content and data quality that may be achieved for separation-based electrospray ionization mass spectrometry (ESI-MS) analysis of analyte samples using the disclosed methods may be of great benefit for the characterization of biologic and biosimilar pharmaceuticals during development and / or manufacturing. Other applications may include, but are not limited to, analysis of environmental pollutants, pesticides, smallmolecules, metabolites, peptides, post-translational modifications, glycoforms, antibodydrug conjugates, fusion proteins, viruses, allergens, single cell organisms, and other applications.

[0086] The disclosed methods, devices, systems, and software may utilize any of a variety of upstream analyte separation techniques known to those of skill in the art. For example, in some embodiments, the imaged separation may be an electrophoretic separation, such as, isoelectric focusing (e.g., icIEF), capillary gel electrophoresis, capillary zone electrophoresis, isotachophoresis, capillary electrokinetic chromatography, micellar electrokinetic chromatography, flow counterbalanced capillary electrophoresis, electric field gradient focusing, dynamic field gradient focusing, and the like, that produces one or more separated analyte fractions from an analyte mixture.

[0087] FIG. 3 provides an example plot 300 of MS data of a sample as a function of a spatial position of an ion source for one or more spatial positions. In this example, the spatial position of the ion source is changing as a function of time. In this example, the MS data is based on an extracted intensity of a first ion signal of interest and an extracted intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample. For example, FIG. 3 provides an example of the MS data including peak-to-hump ratio (p / h). FIG. 3 further provides an example for an MS data including signal to noise ratio (divided by 10, s / n / 10) for an extracted ion current (XIC) signal.

[0088] FIG. 3. further provides an example of an MS data including a signal intensity to noise (divided by 10000, ss / 10000n) for a different selected XIC signal. FIG. 3 also provides an example of a signal intensity (divided by 100, s / 100). As can be seen in FIG. 3, a position that corresponds to the highest signal intensity (s / 100) might not be the sameposition as corresponding to the highest p / h, s / n / 10, and / or ss / 10000n. However, these spatial positions corresponding to the highest p / h, s / n / 10, and / or ss / 10000n might correspond to better quality of the MS data (e g., deconvoluted MS data) as compared to the spatial position with the highest total signal intensity. The example plots may be presented to the user and / or monitored (e.g., for maxima, local maxima, minima, local minima, etc.) in order to aid in determining possible target positions for the ion source. In some examples, certain segments and / or spatial positions may be bypassed and / or picked. In some embodiments, the example plots may be used to automatically select a target spatial position or to present to a user for manual selection. For example, the plots and / or graphs may be provided to the user with an identification of the MS data, spatial position, and / or time (e.g., to aid in determining a target spatial position of the ion source). In some examples, the spatial position, time point, or other sections of the plots and / or graphs may be highlighted (e.g., to further aid in determining the target spatial position).

[0089] FIGs. 4A-4D provide examples of an MS data of a sample collected as a function of a spatial position of an ion source (for one or more spatial positions). FIG. 4A provides an example of MS data comprising base peak intensity (BPI). In this example, the electrospray ion source is moved between various spatial positions (e.g., as a function of time) and is used to ionize the sample for spray into the MS inlet and the MS data is collected for each position of the ion source (e.g., as a function of time). As illustrated, a first maker 1 in FIG. 4A designates a position of the ion source (e.g., as function of time) with the highest BPI.

[0090] FIG. 4B provides another example of an MS data of a sample collected as a function of a spatial position of an ion source (for one or more spatial positions). FIG. 4B provides an example of an MS data comprising Total Ion Current (TIC). In this example,the ion source is also moved between various spatial positions (e.g., as a function of time) and is used to ionize the sample (e.g., via electrospray ionization (ESI)); the sample is sprayed into the MS inlet and the total ion current from the MS data is collected for each position of the ion source and plotted as a function of time. In FIG. 4B, the second marker 2 designates a position of the ion source (e.g., as a function of time) with the highest TIC.

[0091] FIG. 4C provides an example of a ratio of a normalized BPI (nBPI) and a normalized TIC (nTIC) (e.g., nBPI / nTIC) as the ion source is moved between various spatial positions (e.g., as a function of time). In some examples, a normalized BPI may be calculated by normalizing a BPI as a fraction relative to the overall highest BPI in the MS data collected. A normalized TIC may be calculated by normalizing a TIC as a fraction relative to the highest overall TIC in the MS data collected. In FIG. 4C, third marker 3 designates a position of the ion source (e.g., as a function of time) with the highest nBPI / nTIC ratio. Although FIG. 4C depicts an example ratio of normalized BPI and normalized TIC, the absolute BPI and absolute TIC may be used, and / or any combination thereof.

[0092] FIG. 4D provides an example of a calculated value based on a product of an absolute intensity of the ion signal of interest and a ratio of a normalized intensity of the ion signal of interest and a normalized TIC at one or more spatial positions of the ion source. In particular, FIG. 4D provides an example of a product of the absolute BPI (AbsBPI; e.g., such as the BPI provided in FIG. 4A) and the ratio of normalized BPI (nBPI) and normalized TIC (nTIC) as the ion source is moved between various positions (e.g., as a function of time). In FIG. 4D, fourth marker 4 designates a position of the ion source (e.g., as a function of time) with the highest AbsBPI*(nBPI / nTIC) value. In some examples, this position might be a target spatial position of the ion source (that is determined using theAbsBPr(nBPIZnTIC) value). Similar to FIG 4D, in some embodiments, a product of the absolute BPI (AbsBPI; e.g., such as the BPI provided in FIG. 4A) and the ratio of absolute BPI and absolute TIC (AbsTIC) as the ion source is moved between various positions (e.g., as a function of time) may be calculated. And, similar to FIG 4D, a marker may designate a position of the ion source (e.g., as a function of time) with the highest AbsBPI*(AbsBPI / AbsTIC) value. In some embodiments, this position may be a target spatial position of the ion source (that is determined using the AbsBPI*(AbsBPI / AbsTIC) value). Although FIG. 4D depicts examples using the product of the highest absolute BPI and the ratio of the normalized BPI to normalized TIC, other values may be used, such as the ratio of absolute BPI to absolute TIC, ratio of BPI to TIC, etc.

[0093] FIGs. 5A-5C provide examples of deconvoluted MS data obtained with the ion source at the spatial positions 1 , 2, and 4, respectively, as described above for FIGs. 4A, 4B, and 4D. FIG. 5C provides an example of a deconvoluted MS data (e.g., better quality MS data) obtained by determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source (e.g., AbsBPI*(nBPI / nTIC) value) as compared to the ion source positions selected using BPI or TIC values (e.g., in FIGs. 5A and 5B, respectively). Moreover, in this example, the target spatial position of the ion source (which resulted in a better quality deconvoluted MS data) was determined without time-consuming deconvolution of the MS data nor prior knowledge of molecular masses (nor mass to charge ratio values) of interest, but rather by using AbsBPI*(nBPI / nTIC) value, which provides a more efficient determination of the target spatial position of the ion source.

[0094] FIG. 6 provides a visualization of positioning the ion source as a function of time at spatial positions — e.g., a time-resolved log of spatial positions of the ion source (whichis moved in X and Z coordinates in this example, although additional coordinates may be used) as described in FIGs 4A-4D. In some examples, ion source is positioned at spatial positions as a function of time — e.g., the ion source may be positioned at the specific positions shown in FIG. 6 (or other positions) as a function of time. In some examples, the predetermined spatial positions may be spatial positions that are configured and / or selected by a user in advance, spatial positions that are provided by an automated script, and / or default spatial positions that are pre-programmed. In some examples, the spatial positions may be determined and / or modified in real-time based on measurements obtained from the spatial positions. In FIG. 6, positioning of the ion source is performed using an automated script; the automated script positions the ion source at specific X and Z coordinates at specific times (e.g., in a stepwise manner). In some examples, a user may provide a number of spatial positions that should be used prior to running an automated script. FIG. 6 also includes the first, second, third, and fourth markers from FIGs. 4A, 4B, 4C, and 4D, respectively. In some examples, the fourth marker 4 may be selected as the target spatial position as described above.

[0095] FIG. 7 provides an example visual representation of one or more plots generated using the raw data and calculated values in a graphical user interface. In the plot in FIG.7, the AbsBPr(nBPI / nTIC) value is displayed (designated as M-factor) for each of the spatial positions of the ion source in a graphical user interface. In some embodiments, similar to the plot in FIG. 7, the AbsBPI*(AbsBPI / AbsTIC) value might be displayed for each of the spatial positions of the ion source in a graphical user interface. In the example in FIG. 7, plots of TIC and certain XIC are further overlaid. In the example of FIG. 7, three arrows show the spatial positions of the ion source corresponding to the highest AbsBPI*(nBPI / nTIC) value, the highest TIC and certain XIC values. In some examples, atarget spatial position may be determined to be the position of the ion source with the highest AbsBPr(nBPI / nTIC) value (e.g., shown with a solid black arrow). In some examples, a target spatial position may be determined to be the position of the ion source with the highest AbsBPI*(AbsBPI / AbsTIC) value. In some examples, the visual representation (e.g., such as provided in the example in FIG. 7) may be presented to the user so that the user may review the spatial positioning analysis. In some examples, such representation may provide the target spatial position. In some examples, the user may review the data to modify the target spatial position provided, and / or may elect to proceed with the target position provided.

[0096] FIG. 7 also provides an example of a user interface depicting the spatial positions (e.g., X and YZ positions) for the ion source as a function of time. In some examples, the ion source may be moved in predetermined positions. In some examples, tracking of the spatial positions of the ion source may be performed, wherein the tracking and / or the collecting of the MS data is triggered for synchronous acquisition or by a movement of the ion source. For example, tracking of the ion source X, Y, Z coordinates may be tracked and displayed in a plot (e.g., such as depicted in FIG. 7).

[0097] In some embodiments, a user may utilize a pull-down menu or other similar menu to view one or more plots comprising calculated values as a function of time, a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source. In some embodiments, the plots might comprise the AbsBPr(nBPI / nTIC). In some embodiments, the plots may comprise the AbsBPI*(AbsBPI / AbsTIC). In some embodiments, the plots may comprise the absolute or normalized value of the base peak intensity divided by the absolute or normalized TIC, the absolute or normalized value of the extracted ion signal intensity divided by the absolute or normalized TIC, the absoluteor normalized sum of extracted ion signal intensities divided by the absolute or normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time. In some embodiments, the plots may comprise the absolute value of the base peak intensity divided by the absolute TIC, the absolute value of the extracted ion signal intensity divided by the absolute TIC, the absolute sum of extracted ion signal intensities divided by the absolute TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time. In some embodiments, the plots may comprise the normalized value of the base peak intensity divided by the normalized TIC, the normalized value of the extracted ion signal intensity divided by the normalized TIC, the normalized sum of extracted ion signal intensities divided by the normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time. For example, a user may utilize a pull-down menu and select the TIC, XIC, and / or BPI traces to display them as a function of the spatial position of the ion source, the predetermined spatial position of the ion source, and / or time. Such plots may comprise the plots provided in FIG. 7 in the top portion 702 (e.g., as single or overlaid plots). For example, FIG. 7 provides sample plots of the normalized value of the base peak intensity (nBPI 70), the normalized TIC (nTIC 80), and the normalized value of the extracted ion signal intensity (nXIC 90) in the time domain. In some embodiments, a user may further select plots or portions of the plots in order to determine a target spatial position for the ion source. For example, a bottom portion 704 of FIG. 7 shows the spatialpositions of the ion source for X and YZ over time. Although the bottom portion 704 depicts spatial positions as X v. YZ, other similar plots may be shown.

[0098] FIG. 8 provides another example of user interface depicting one or more plots comprising the calculated values as a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source. For example, the ion source might move along two axes (e.g., X and Z) and the calculated value (e.g., AbsBPI*(nBPI / nTIC) value or AbsBPI*(AbsBPI / AbsTIC) value) might be depicted as a heat map 800 shown in FIG. 8. In some embodiments, plots of the absolute or normalized value of the base peak intensity divided by the absolute or normalized TIC, the absolute or normalized value of the extracted ion signal intensity divided by the absolute or normalized TIC, the absolute or normalized sum of extracted ion signal intensities divided by the absolute or normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time (and / or other parameters) might be also provided as heat maps (e.g., as additional heat maps displayed side by side with the heat map for the calculated values as a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source). In some embodiments, plots of the normalized value of the base peak intensity divided by the normalized TIC, the normalized value of the extracted ion signal intensity divided by the normalized TIC, the normalized sum of extracted ion signal intensities divided by the normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time (and / or other parameters) might be also provided as heat maps (e.g., as additional heat maps displayed side by side with the heatmap for the calculated values as a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source).

[0099] In some embodiments, plots of the absolute value of the base peak intensity divided by the absolute TIC, the absolute value of the extracted ion signal intensity divided by the absolute TIC, the absolute sum of extracted ion signal intensities divided by the absolute TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time (and / or other parameters) might be also provided as heat maps (e.g., as additional heat maps displayed side by side with the heat map for the calculated values as a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source). The heat map(s) may be used to determine a target spatial position of the ion source (e.g., using the calculated values for each of the one or more spatial positions of the ion source), and / or may be used in conjunction with other plots, such as those depicted in FIGs. 3-9, for, example.[000100] FIG. 9 provides another example of a graphical user interface 900 that can display a visual representation of one on more plots 310 generated using the calculated values. MS data may be collected using one or more operational parameters. In some examples, a graphical user interface may display two or more of the operational parameters (e.g., when MS data is collected for different nebulizer gas pressures, ion source voltages, sample infusion rate). FIG. 9 also provides an example of an interface 900 that displays spatial positions of the ion source using a specific number (e.g., predetermined spatial positions 1 through 16, although more or fewer spatial positions may be utilized). In some examples, a triggered scripted motion may be used to establish acorrelation between a point in time, a spatial position, and a signal of the ion source using the ion source received at the MS. The MS data may be compiled in a way to provide a user with quick visualization to facilitate determination of a target spatial position for the ion source. In some examples, the spatial positions may be predefined by the user, by the program, or may be pre-selected by a user via the user interface. In some embodiments, the spatial positions may be selected based on MS data received from the ion source, or may be determined in real-time based on the MS data. In the example of FIG. 9, sixteen example spatial positions are shown, although fewer or more spatial positions may be utilized and / or programmed. For example, the ion source may be moved through more or fewer spatial positions in order to determine a target spatial position (e g., to provide quality MS data).[000101] In some examples, a portion of the data 320 displayed may be selected and displayed to the user as corresponding to a target spatial position (e.g., the portion corresponding to the highest calculated values). In some other examples, the user may highlight the portion of the data 320. In some examples, certain MS data (e.g., the absolute or normalized value of the base peak intensity divided by the absolute or normalized TIC, the absolute or normalized value of the extracted ion signal intensity divided by the absolute or normalized TIC, the absolute or normalized sum of extracted ion signal intensities divided by the absolute or normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities) may be shown for the selected portion. In some examples, certain MS data (e.g., the normalized value of the base peak intensity divided by the normalized TIC, the normalized value of the extracted ion signal intensity divided by the normalized TIC, the normalized sum of extracted ion signal intensities divided by the normalized TIC, the base peak intensity, theTIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities) may be shown for the selected portion. In some examples, the spatial position the ion source, the predetermined spatial position of the ion source, and / or time may be shown for the highlighted portion.[000102] Although some aspects have been described in the context of an apparatus, it is clear that these aspects also represent a description of the corresponding method, where a block or device corresponds to a method step or a feature of a method step. Analogously, aspects described in the context of a method step also represent a description of a corresponding block or item or feature of a corresponding apparatus. Some or all of the method steps may be executed by (or using) a hardware apparatus, like for example, a processor, a microprocessor, a programmable computer or an electronic circuit. In some embodiments, some one or more of the most important method steps may be executed by such an apparatus.[000103] Generally, embodiments of the present disclosure may be implemented through the use of computer program products embodied on computer-readable medium. Such computer program products may include instructions executable by processors and / or computing devices such as processor and / or computing device. While particular embodiments of the various aspects of the present disclosure have been illustrated and described, it would be apparent to those skilled in the art that various other changes and modifications can be made and are intended to fall within the spirit and scope of the present disclosure. Furthermore, although the present disclosure has been described herein in the context of particular implementations in particular environments for particular purposes, those of ordinary skill in the relevant arts will recognize that its usefulness is not limited thereto and that the present disclosure may be beneficially implemented in any number ofenvironments for any number of purposes. Accordingly, the claims set forth below should be construed in view of the full breadth and spirit of the present disclosure as described herein.

Claims

WHAT IS CLAIMED IS:

1. A computer-implemented method for spatial positioning comprising: collecting mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample; calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions; and determining a target spatial position of the ion source using the calculated value for each of the one or more spatial positions of the ion source.

2. The computer-implemented method of claim 1 , wherein the intensity of the first and / or second ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more mass to charge (m / z) values.

3. The computer-implemented method of claim 1 or 2, wherein the intensity of the first ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values for an analyte peak, wherein the sample comprises the analyte.

4. The computer-implemented method of claim 1 or 2, wherein the intensity of the second ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values for a valley between one or more analyte peaks.

5. A computer-implemented method for spatial positioning comprising: collecting mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample;calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions; and determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source.

6. The computer-implemented method of claim 5, wherein the intensity of the ion signal of interest comprises a base peak intensity.

7. The computer-implemented method of claim 6, wherein the calculated value is based on a product of an absolute value of the base peak intensity and the ratio of an absolute or normalized value of the base peak intensity and the absolute or normalized TIC.

8. The computer-implemented method of claim 5, wherein the intensity of the ion signal of interest comprises an extracted ion signal intensity or a sum of extracted ion signal intensities for one or more m / z values.

9. The computer-implemented method of claim 8, wherein the calculated values are based on the product of an absolute value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the ratio of an absolute or normalized value of the extracted ion signal intensity or the sum of extracted ion signal intensities and the absolute or normalized TIC.

10. The computer-implemented method of any one of claims 1 , 2, or 5-9, further comprising positioning the ion source at predetermined spatial positions as a function of time.11 . The computer-implemented method of any one of claims 1 , 2, or 5-9, wherein positioning the ion source is performed using an automated script.

12. The computer-implemented method of any one of claims 1 , 2, or 5-9, further comprising tracking the spatial positions of the ion source, wherein the tracking and / or thecollecting of the MS data is initiated by a movement of the ion source.

13. The computer-implemented method of any one of claims 1 , 2, or 5-9, further comprising positioning the ion source at predetermined spatial positions as a function of time and generating one or more plots using the collected MS data of the sample and the spatial positions and / or the predetermined spatial positions of the ion source.

14. The computer-implemented method of any one of claims 1 , 2, or 5-9, further comprising positioning the ion source at predetermined spatial positions as a function of time and generating one or more plots using the collected MS data of the sample and the spatial positions and / or the predetermined spatial positions of the ion source, wherein the one or more plots comprise the calculated values as a function of time, a function of the spatial positions, and / or a function of the predetermined spatial positions of the ion source.

15. The computer-implemented method of any one of claims 1 , 2, or 5-9, further comprising positioning the ion source at predetermined spatial positions as a function of time and generating one or more plots using the collected MS data of the sample and the spatial positions and / or the predetermined spatial positions of the ion source, wherein the one or more plots further comprise an absolute or normalized value of a base peak intensity divided by the absolute or normalized TIC, the absolute or normalized value of the extracted ion signal intensity divided by the absolute or normalized TIC, the absolute or normalized sum of extracted ion signal intensities divided by the absolute or normalized TIC, the base peak intensity, the TIC, the extracted ion signal intensity, and / or the sum of extracted ion signal intensities as a function of the spatial position the ion source, the predetermined spatial position of the ion source, and / or time.

16. The computer-implemented method of any one of claims 1 , 2, or 5-9, further comprising positioning the ion source based on the determined target spatial position.

17. A computer program with program code for performing the computer- implemented method according to any one of claims 1 , 2, or 5-9.

18. A computer-implemented method for spatial positioning comprising: receiving mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample; calculating a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions; displaying a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface.

19. A computer-implemented method for spatial positioning comprising: receiving mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample; calculating a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions; displaying a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source on a graphical user interface.

20. The computer-implemented method for spatial positioning of claims 18 or 19 further comprising determining a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source.

21. One or more non-transitory computer-readable storage media comprising instructions, which when executed by one or more computing devices, cause the one or more computing devices to:collect mass spectrometry (MS) data of a sample as a function of spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of an ion signal of interest and a total ion current (TIC), wherein the MS data is obtained using the ion source to ionize the sample; calculate a value based on a product of an absolute intensity of the ion signal of interest and a ratio of an absolute or normalized intensity of the ion signal of interest and an absolute or normalized TIC at each of the one or more spatial positions; and determine a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source.

22. One or more non-transitory computer-readable storage media comprising instructions, which when executed by one or more computing devices, cause the one or more computing devices to: collect mass spectrometry (MS) data of a sample as a function of a spatial position of an ion source for one or more spatial positions, the MS data comprising an intensity of a first ion signal of interest and an intensity of a second ion signal of interest, wherein the MS data is obtained using the ion source to ionize the sample; calculate a value based on a product of an absolute intensity of the first ion signal of interest and a ratio of an absolute or normalized intensity of the first ion signal of interest and an absolute or normalized intensity of the second ion signal of interest at each of the one or more spatial positions; and determine a target spatial position of the ion source using the calculated values for each of the one or more spatial positions of the ion source. display a visual representation of one or more plots generated using the calculated values for each of the one or more spatial positions of the ion source.

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