Mass spectrometer signal correction systems

Abstract

Disclosed herein are scientific instrument support systems, as well as related methods, computing devices, and computer-readable media. A scientific instrument support apparatus is disclosed comprising generating logic to generate mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, determining logic to determine, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to a first non-deuterated tag and a second reporter ion peak intensity corresponding to a first deuterated tag, and normalizing logic to normalize reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

Description

MASS SPECTROMETER SIGNAL CORRECTION SYSTEMSCross-Reference to Related Applications

[0001] This application claims priority to U.S. Provisional Application Serial No. 63 / 654,308 titled "MASS SPECTROMETER SIGNAL CORRECTION SYSTEMS” filed on May 31, 2024, the entire disclosure of which is incorporated by reference herein in its entirety.Background

[0002] Signal correction in mass spectrometry aims to compensate for signal variation to ensure accurate and reliable quantification.Brief Description of the Drawings

[0003] Embodiments will be readily understood by the following detailed description in conjunction with the accompanying drawings. To facilitate this description, like reference numerals designate like structural elements. Embodiments are illustrated by way of example, not by way of limitation, in the figures of the accompanying drawings.

[0004] FIG. 1 is a block diagram of an example scientific instrument support module for performing support operations, in accordance with various embodiments.

[0005] FIG. 2 is a flow diagram of an example method of performing support operations, in accordance with various embodiments.

[0006] FIG. 3 is a block diagram of an example scientific instrument support module for performing support operations, in accordance with various embodiments.

[0007] FIG. 4 is a flow diagram of an example method of performing support operations, in accordance with various embodiments.

[0008] FIG. 5 is an example of a graphical user interface that may be used in the performance of some or all of the support methods disclosed herein, in accordance with various embodiments.

[0009] FIG. 6 is a block diagram of an example computing device that may perform some or all of the scientific instrument support methods disclosed herein, in accordance with various embodiments.

[0010] FIG. 7 is a block diagram of an example scientific instrument support system in which some or all of the scientific instrument support methods disclosed herein may be performed, in accordance with various embodiments.

[0011] FIG. 8 is a graph illustrating retention time shifts of peptide coupled product.Detailed Description

[0012] Disclosed herein are scientific instrument support systems, as well as related methods, computing devices, and computer-readable media. For example, in some embodiments, methods and systems for correcting signals in mass spectrometry are disclosed. In some embodiments, a scientific instrument support apparatus is disclosed comprising generating logic to generate mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, wherein the plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags, wherein the plurality of non-deuterated channels comprises anon-deuterated control channel corresponding to a first non-deuterated tag and the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag, determining logic to determine, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag, and normalizing logic to normalize reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

[0013] One goal in proteomics is the quantification of proteins and / or peptides in samples. Labeling technology, such as Tandem Mass Tags™ (TMT®) technology, for example, facilitates multiplexed quantitative analysis of multiple samples allowing researchers to compare protein and / or peptide abundances across many samples simultaneously. In a tandem mass tag (TMT) experiment, samples are first prepared before being analyzed by an LC-MS instrument, for example. During sample preparation, proteins are first extracted from samples. This typically involves cell lysis and protein solubilization using buffers and detergents. The extracted proteins are then enzymatically digested into smaller peptides. Trypsin is commonly used for protein digestion. After protein digestion, each sample is tagged, or labeled, with a TMT reagent. TMT reagents are available in sets with different reporter ions, each having a unique mass-to-charge (m / z) ratio. The TMT reagents are designed to react with primary amines in peptides. Each tag includes a reporter region, a balance region, and a reactive group. All of the tags in a TMT reagent set have the same overall mass. However, each tag has a different reporter region mass. After the samples are tagged, all the samples are combined, or pooled, into a single combined sample which is then provided to a separation device (separated using liquid chromatography or gas chromatography, for example). The combined sample contains peptides from all the original samples, each peptide of each sample tagged with a unique tag. For example, peptides from a first sample are tagged with a first tag and peptides from a second sample are tagged with a second tag unique from the first tag, continuing with as many unique tags available in the set of tags provided.

[0014] The combined sample is subjected to chromatography to separate the peptides based on their hydrophobicity and other properties. Because all the tags generally have consistent chemical properties, including mass and hydrophobicity, the tags affect each sample equivalently during the separation stage. Any shifts in retention time (the amount of time it takes for a peptide to elute), for example, due to the tags will affect all peptides equivalently. Thus, a specific peptide present in multiple samples will elute at the same time allowing for the relative quantification (using mass spectrometry, for example) of that specific peptide across the multiple samples containing that specific peptide using the tags, discussed in greater detail below. The separated peptides enter a mass spectrometer and are ionized to achieve a full MS1 scan. A window of m / z and / or precursor ions are then selected to perform an MS2 scan producing fragment ions which include reporter ions from the TMT tags. The fragment ions are then analyzed in a mass analyzer where reporter ions of the tags, as well as the fragment ions of the peptide, are analyzed.

[0015] The resulting spectrum shows an abundance of each reporter ion corresponding to each tag for that specific peptide in addition to an abundance, or intensity, of the fragment ions of the tagged peptide. The relative reporter ion abundance, or intensity, directly represents the relative quantity of that specific peptide (combination of peptide fragment ions measured in the mass spectrometer along with the reporter ions) for each sample that was pooled into the combined sample.

[0016] Providing as many unique tags (providing unique reporter masses) within a tag reagent kit with the same overall mass therefore allows for increased sample size allowing users to simultaneously analyze more samples increasing throughput and efficiency. A new tag reagent kit was recently developed to increase the tag count of existing reagent kits. To achieve this, a single Hydrogen of each tag of an existing set of tags was replaced by deuterium to double the available number of unique tags in the set. This development increased the amount of available unique mass tags in a tag reagent kit. However, this modification of the existing tags, the addition of deuterium, resulted in the additional tags being slightly more hydrophilic (and thus, ultimately coupled peptides). This decrease in hydrophobicity of the tags containing deuterium introduced a challenge in traditional TMT labeling experiments.

[0017] The relative difference in hydrophobicity between the non-deuterated tags of the TMT kit and the deuterated tags of the TMT kit resulted in a TMT kit having a set of tags (with the deuterium) with a slight difference in retention time in the corresponding peptide coupled products relative to the counterpart set of tags without the deuterium. In other words, peptides labeled with a deuterated tag elute slightly before the same peptides labeled with a non-deuterated tag. This slight shift causes reporter ion intensities in the resulting MS2 spectrum which cannot be compared directly without intervention.

[0018] Embodiments disclosed herein provide a way to account for the aforementioned shift in retention time thereby allowing for the resulting MS2 spectrum to be used for more accurate quantification of the peptide coupled product(s). Embodiments disclosed herein normalize the resulting intensities of the reporter ions of the non-deuterated tags and the deuterated tags relative to each other. After normalization, the intensities of the reporter ions across the entire set of reagent tags can then be used to accurately quantify the peptides. In at least one instance, embodiments disclosed herein can be thought of as aligning peaks experiencing this relative shift in retention time so that the resulting reporter ion intensities can be directly compared.

[0019] Embodiments disclosed allow a user to define control channels. A channel may be defined as one of the samples tagged with a unique tag, for example. In at least one instance, two control channels are used. In at least one instance, more than two control channels are used. The two control channels comprise a first channel from a deuterated tag set and a second channel corresponding to a non-deuterated tag set. The ratio of the reporter ion intensity of the first channel and the reporter ion intensity of the second channel is determined and is defined as a normalization, or correction, ratio. The correction ratio is then applied to the other channels to ensure that the reporter ion intensities of the non-control deuterated tag channels and the non-control non-deuterated tag channels are corrected to account for the retention time shift-caused differences between the two tag sets. Quantification of the tagged peptides can then be performed asnormal after all of the deuterated tags are normalized with respect to the non-deuterated tags or after all of the non-deuterated tags are normalized with respect to the deuterated tags.

[0020] Because all of the deuterated tags elute at the same time and all of the non-deuterated tags elute at the same time (which is slightly different than the time of elution of the deuterated tags), the only requirement for the selection of control channels is that one of the control channels corresponds to a deuterated tag and the other control channel corresponds to a non-deuterated tag. The control channels need not contain reporter ions with the same nominal mass. In at least one instance, the channels chosen for control channels include a channel with a sample tagged with a deuterated tag and a channel with a sample tagged with a non-deuterated tag. In at least one instance, the deuterated tags and the non- deuterated tags chosen for the control channels comprise different reporter masses. As long as one of the control channels is tagged with a deuterated tag and the other control channel is tagged with a non- deuterated tag, the resulting correction ratio can still be used to normalize all deuterated channels and non- deuterated channels relative to each other. This is because the retention time shift is the same across all deuterated channels relative to non-deuterated channels regardless of reporter mass. In at least one instance, embodiments disclosed herein require a user to make a selection of two control channels as outlined above and an error is generated unless a channel from each set of tags is identified as a control channel.

[0021] In at least one instance, more than one control channel of the same tag type is defined and an average of the control channel reporter ion intensities is calculated before determining the correction ratio. In other words, a user may define two control channels corresponding to two different deuterated tags and one or more control channels corresponding to different non-deuterated tags. In such an instance, embodiments disclosed herein are to average the reporter ion intensities before determining the correction ratio. If a user defines more than one control channel corresponding to different non-deuterated tags, an average of the reporter ion intensities corresponding to the non-deuterated tags of the non-deuterated control channels is calculated before determining the correction ratio.

[0022] Regarding the application of the normalization, or correction, ratio to either set of tags (deuterated or non-deuterated), in at least one instance, the determined correction ratio is applied such that the set of channels reading with lower reporter ion intensity (either the non-deuterated channels or the deuterated channels) are raised according to the determined correction ratio. In at least one instance, the determined correction ratio is applied such that the set of channels reading with greater reporter ion intensity (either the non-deuterated channels or the deuterated channels) is lowered, or dampened, according to the determined correction ratio. Deuterated channels will show greater reporter ion intensity than non-deuterated channels if the MS2 is triggered before the apex of the chromatographic peak, and deuterated channels will show lesser reporter ion intensity than non-deuterated channels if the MS2 is triggered after the apex of the chromatographic peak. Reporter ion intensity of both channels will be the same if the MS2 is triggered directly between the chromatographic peak apex of the deuterated channels and the chromatographic peakapex of the non-deuterated channels. Regardless, a correction, or normalization, ratio can be determined at any point during the peak using two control channels as described herein.

[0023] In at least one instance, the control channels contain the same quantity of the same sample to ensure that each one of the control channels contains the same quantity of peptides tagged with a nondeuterated tag and a deuterated tag. This would result in a 1:1 normalization meaning that the channels would be adjusted at the determined correction ratio without any additional adjustment (to the determined correction ratio, e.g.). If a first control channel contains a first amount of the sample and a second control channel contains a second amount of the sample, where the second amount is 50% of the first amount, for example, then the determined normalization ratio would be adjusted by 50% to reflect the difference in the control channels. Specifically, if the reporter ion intensity of the first control channel is 100 and the reporter ion intensity of the second control channel is 75, the normalization ratio would be determined as 4:3 before adjusting for the sample quantity difference between the control channels. Thus, embodiments disclosed herein would adjust the quantity of the reporter ion intensity of the second control channel by increasing it 100% to mitigate the difference in control channel sample quantity (the second control channel containing 50% of the sample quantity contained in the first control channel) before defining the normalization ratio. The actual normalization ratio in this instance would be 100:150, 4:6, or 2:3. In at least one instance, a user defines a relative amount of sample tagged for each control channel by way of percentages, for example, and the embodiments disclosed herein adjust the determined normalization ratio according to the relative sample amount defined by the user.

[0024] In at least one instance, mass tag reagents labelled with Deuterium force the labelled peptides to be held up leading to slightly different retention times than their non-deuterated, mass tag-labeled counterparts. Using them together in one experiment requires a correction for that retention time difference.

[0025] The methods and systems disclosed herein may provide an algorithmic scheme that calculates the ratio between designated control channels, one of which is labelled with deuterium, the other of which with Hydrogen according to the design of the isobaric mass tag under consideration. The ratio between the control channels is then used to correct the abundances of all deuterated channels against the abundances of the non-deuterated channels.

[0026] The scientific instrument support embodiments disclosed herein may achieve improved performance relative to conventional approaches. The precision of quantitation experiments using isobaric mass tags can be retained, even if deuterated mass tags are involved using the methods and systems disclosed herein. The methods and systems disclosed herein allow for correction of the deuterium shift in reporter-labeled peptides, open the isotope labeling to an arbitrary number of H / D substitutions in the reporter modification, and increase the chemical space for synthesizing labels for reporter ion quantification. The methods and systems disclosed herein allow for retention time correction of deuterated isobaric mass tags that rely solely on two control channels.

[0027] The embodiments disclosed herein thus provide improvements to scientific instrument technology (e.g., improvements in the computer technology supporting such scientific instruments, among otherimprovements). In at least one instance, the embodiments disclosed herein enable the expansion of tag sets by providing signal correction after the data is acquired to be able to directly compare signal intensities across the entire expanded tagged channels. The embodiments disclosed herein further provide a robust signal correction method by enabling a user to use multiple control channels in a tag set.

[0028] In the following detailed description, reference is made to the accompanying drawings that form a part hereof wherein like numerals designate like parts throughout, and in which is shown, by way of illustration, embodiments that may be practiced. It is to be understood that other embodiments may be utilized, and structural or logical changes may be made, without departing from the scope of the present disclosure. Therefore, the following detailed description is not to be taken in a limiting sense.

[0029] Various operations may be described as multiple discrete actions or operations in turn, in a manner that is most helpful in understanding the subject matter disclosed herein. However, the order of description should not be construed as to imply that these operations are necessarily order dependent. In particular, these operations may not be performed in the order of presentation. Operations described may be performed in a different order from the described embodiment. Various additional operations may be performed, and / or described operations may be omitted in additional embodiments.

[0030] For the purposes of the present disclosure, the phrases "A and / or B" and "A or B" mean (A), (B), or (A and B). For the purposes of the present disclosure, the phrases "A, B, and / or C" and "A, B, or C" mean (A), (B), (C), (A and B), (A and C), (B and C), or (A, B, and C). Although some elements may be referred to in the singular (e.g., "a processing device”), any appropriate elements may be represented by multiple instances of that element, and vice versa. For example, a set of operations described as performed by a processing device may be implemented with different ones of the operations performed by different processing devices. As used herein, the phrase "based on” should be understood to mean "based at least in part on,” unless otherwise specified.

[0031] The description uses the phrases "an embodiment," "various embodiments,” and "some embodiments," each of which may refer to one or more of the same or different embodiments. Furthermore, the terms "comprising," "including," "having," and the like, as used with respect to embodiments of the present disclosure, are synonymous. When used to describe a range of dimensions, the phrase "between X and Y" represents a range that includes X and Y. As used herein, an "apparatus” may refer to any individual device, collection of devices, part of a device, or collections of parts of devices. The drawings are not necessarily to scale.

[0032] FIG. 1 is a block diagram of a scientific instrument support module 1000 for performing support operations, in accordance with various embodiments. The scientific instrument support module 1000 may be implemented by circuitry (e.g., including electrical and / or optical components), such as a programmed computing device. The logic of the scientific instrument support module 1000 may be included in a single computing device, or may be distributed across multiple computing devices that are in communication with each other as appropriate. Examples of computing devices that may, singly or in combination, implement the scientific instrument support module 1000 are discussed herein with reference to the computing device4000 of FIG. 6, and examples of systems of interconnected computing devices, in which the scientific instrument support module 1000 may be implemented across one or more of the computing devices, is discussed herein with reference to the scientific instrument support system 5000 of FIG. 7.

[0033] Deuterated TMTpro Tags (TMTproD) replace a single H with deuterium, which results in a more hydrophilic target reagent and a slight shift in the retention time of the peptide-coupled product. As a result, TMTproD reporters are shifted to their nondeuterated counterparts, and a comprehensive quantitative analysis (e.g., between deuterated and non-deuterated reporters) of the entire >30 mass tags set may not be possible. A retention time (RT) shift-dependent correction of the reporter intensity is needed.

[0034] The slight RT shift is shown in FIG. 8. The difference in the measured quantification value (e.g., the intensity of the reporter peak) depends on the position of the MS2 trigger on the elution peak of the tagged peptide. If the peptide is triggered directly at the apex, no shift is observed. In cases of triggers before the elution profile reaches the apex, the deuterated labels show an increased intensity; if the trigger is behind the apex, the non-deuterated labels show an increased intensity.

[0035] Referring to FIG. 8, a graphic 6000 shows chromatogram data 6001 and individual graphs 6010, 6011, 6012, and 6013 of peptide coupled products tagged with various tags. The chromatographic peaks shown in graph 6010 illustrate a first peak corresponding to a non-deuterated tag (127c) and a second peak corresponding to a deuterated tag (127d). As can be seen in the graph 6010, the peak corresponding to the deuterated tag (127d) eluted slightly before the peak corresponding to the non-deuterated tag (127c). The chromatographic peaks shown in graph 6011 illustrate a first peak corresponding to a non-deuterated tag (127c) and a second peak corresponding to a deuterated tag (127d). As can be seen in the graph 6011, the peak corresponding to the deuterated tag (127d) eluted slightly before the peak corresponding to the non- deuterated tag (127c). The chromatographic peaks shown in graph 6012 illustrate a first peak corresponding to a non-deuterated tag (128c) and a second peak corresponding to a deuterated tag (128cd). As can be seen in the graph 6012, the peak corresponding to the deuterated tag (128cd) eluted slightly before the peak corresponding to the non-deuterated tag (128c). The chromatographic peaks shown in graph 6013 illustrate a first peak corresponding to a non-deuterated tag (128c) and a second peak corresponding to a deuterated tag (128cd). As can be seen in the graph 6013, the peak corresponding to the deuterated tag (128cd) eluted slightly before the peak corresponding to the non-deuterated tag (128c).

[0036] The methods and systems disclosed herein enable compensating for deuterium shifts using normalization channels. In TMT quantification, the quantification values are derived from the intensity of reporter peaks of known mass. Based on the masses of the different reporter ion masses, the reporter peaks can be distinguished as having a deuterium-containing label or not, and peaks can be split into two groups (with deuterium and without deuterium).

[0037] The methods and systems disclosed herein may compensate for the above-described shift. A method for such compensation will now be described. In each fragment spectrum of a TMT isobaric mass tag experiment, the intensities of the reporter ions (there is one reporter ion for each channel in the tag experiment) reflect the relationship between the quantification values of the peptide that is associated withthe fragment spectrum. For example, each (pairwise) ratio between two channels reflects the ratio of the amount of peptides contained in the original sample.

[0038] With TMT proD, all peptides that contain Deuterium in their structure are shifted in the retention time. Consequently, all peptides labelled with Deuterium labels carry systematically different values in the height of their reporter ions peaks in the fragment spectrum. The methods and systems disclosed herein can correct the values using the methods and systems disclosed herein.

[0039] The scientific instrument support module 1000 may include first logic 1002, second logic 1004, and third logic 1006. As used herein, the term "logic” may include an apparatus that is to perform a set of operations associated with the logic. For example, any of the logic elements included in the support module 1000 may be implemented by one or more computing devices programmed with instructions to cause one or more processing devices of the computing devices to perform the associated set of operations. In a particular embodiment, a logic element may include one or more non-transitory computer-readable media having instructions thereon that, when executed by one or more processing devices of one or more computing devices, cause the one or more computing devices to perform the associated set of operations. As used herein, the term "module” may refer to a collection of one or more logic elements that, together, perform a function associated with the module. Different ones of the logic elements in a module may take the same form or may take different forms. For example, some logic in a module may be implemented by a programmed general-purpose processing device, while other logic in a module may be implemented by an application-specific integrated circuit (ASIC). In another example, different ones of the logic elements in a module may be associated with different sets of instructions executed by one or more processing devices. A module may not include all of the logic elements depicted in the associated drawing; for example, a module may include a subset of the logic elements depicted in the associated drawing when that module is to perform a subset of the operations discussed herein with reference to that module.

[0040] The first logic 1002 may include setup logic for determining two control channels and adding peptides to the sample preparation process.

[0041] The second logic 1004 may include performing logic for performing a tandem mass spec experiment.

[0042] The third logic 1006 may include analysis logic for processing a report ions quantification workflow, determining the intensity of the two reporter ion peaks that correspond to the two control channels, calculating the ratio between the two channels, raising the intensity of all channels that correspond to the control channel with the lower intensity according to the calculated ratio, and performing the quantification as if there was no systematic error. In at least one instance, the analysis logic lowers the intensity of all channels that correspond to the control channel with the higher intensity according to the calculated ratio, and performing the quantification as if there was no systematic error.

[0043] FIG. 2 is a flow diagram of a method 2000 of performing support operations, in accordance with various embodiments. Although the operations of the method 2000 may be illustrated with reference to particular embodiments disclosed herein (e.g., the scientific instrument support modules 1000 discussedherein with reference to FIG. 1, the GUI 3000 discussed herein with reference to FIG. 5, the computing devices 4000 discussed herein with reference to FIG. 6, and / or the scientific instrument support system 5000 discussed herein with reference to FIG. 7), the method 2000 may be used in any suitable setting to perform any suitable support operations. Operations are illustrated once each and in a particular order in FIG. 2, but the operations may be reordered and / or repeated as desired and appropriate (e.g., different operations performed may be performed in parallel, as suitable).

[0044] At 2002, first operations may be performed. For example, the first logic 1002 of a support module 1000 may perform the operations of 2002. The first operations may include a user defining / determining two control channels, i.e. , chose a control channel from both the deuterated and the non-deuterated set of channels in a TMTProD labelling kit. The first operations further includes the user adding peptides of exactly the same amount labelled with the two control channels, respectively, to the sample preparation process.

[0045] At 2004, second operations may be performed. For example, the second logic 1004 of a support module 1000 may perform the operations of 2004. The second operations may include performing a tandem mass spec experiment using an instrument of choice.

[0046] At 2006, third operations may be performed. For example, the third logic 1006 of a support module 1000 may perform the operations of 2006. The third operations may include, in a data analysis application, such as Proteome Discoverer, for example, processing a Reporter Ions Quantification workflow that uses the control channel correction methods disclosed herein. The third operations further includes determining, for every spectrum, the intensity of the two reporter ion peaks that correspond to the two control channels. The third operations further includes calculating the ratio between the two channels. This ratio is exactly the systematic error that needs to be corrected by the methods and systems disclosed herein. The third operations further includes raising the intensity of all channels that correspond to the control channel with the lower intensity according to the calculated ratio of the previous step. The third operations further includes performing the quantification as if there was no systematic error.

[0047] FIG. 3 is a block diagram of a scientific instrument support module 1010 for performing support operations, in accordance with various embodiments. The scientific instrument support module 1010 may be implemented by circuitry (e.g., including electrical and / or optical components), such as a programmed computing device. The logic of the scientific instrument support module 1010 may be included in a single computing device, or may be distributed across multiple computing devices that are in communication with each other as appropriate. Examples of computing devices that may, singly or in combination, implement the scientific instrument support module 1010 are discussed herein with reference to the computing device 4000 of FIG. 6, and examples of systems of interconnected computing devices, in which the scientific instrument support module 1010 may be implemented across one or more of the computing devices, is discussed herein with reference to the scientific instrument support system 5000 of FIG. 7.

[0048] The scientific instrument support module 1010 may include generating logic 1012, determining logic 1014, and normalizing logic 1016. As used herein, the term "logic” may include an apparatus that is to perform a set of operations associated with the logic. For example, any of the logic elements included in thesupport module 1010 may be implemented by one or more computing devices programmed with instructions to cause one or more processing devices of the computing devices to perform the associated set of operations. In a particular embodiment, a logic element may include one or more non-transitory computer- readable media having instructions thereon that, when executed by one or more processing devices of one or more computing devices, cause the one or more computing devices to perform the associated set of operations. As used herein, the term "module” may refer to a collection of one or more logic elements that, together, perform a function associated with the module. Different ones of the logic elements in a module may take the same form or may take different forms. For example, some logic in a module may be implemented by a programmed general-purpose processing device, while other logic in a module may be implemented by an application-specific integrated circuit (ASIC). In another example, different ones of the logic elements in a module may be associated with different sets of instructions executed by one or more processing devices. A module may not include all of the logic elements depicted in the associated drawing; for example, a module may include a subset of the logic elements depicted in the associated drawing when that module is to perform a subset of the operations discussed herein with reference to that module.

[0049] The generating logic 1012 may include generating mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels. The mass spectrum data may be generated with any suitable mass spectrometer. The plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags. The plurality of non-deuterated channels comprises a non-deuterated control channel corresponding to a first non-deuterated tag and the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag.

[0050] In at least one instance, the support module 1010 further includes setup logic for defining two control channels. Defining the control channels with the support module can occur before and / or after the mass spectrometry experiment occurs. The control channels may correspond to samples prepared by a technician with known parameters such as, for example, quantities of peptides, type of sample, etc. As discussed herein, each sample is tagged with a unique mass tag reagent.

[0051] In at least one instance, a control channel selection input is received by a user to define the control channels. In at least one instance, the user selects two control channels, one corresponding to a non- deuterated tag and one corresponding to a deuterated tag. In at least one instance, the user selects more than two control channels and an average of multiple correction ratios is used as the final correction ratio.

[0052] The determining logic 1014 may include determining, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag. Thus, the reporter ion intensities of the control channels defined by the user are used by the determining logic 1014 to determine the correction ratio. The correction ratio may include a first signal intensity corresponding to reporter ions of the first non-deuterated tag and a second signal intensity corresponding to reporter ions of the first deuterated tag. The ratio of the two intensities is defined as the correction ratio. In at least one instance, this can bereferred to as a signal correction ratio or signal normalization ratio. This ratio represents the variation in ion intensity reading due to the different tags (deuterated relative to non-deuterated). Thus, this ratio is used to correct for the variation by way of the normalizing logic 1016, discussed in greater detail herein.

[0053] The normalizing logic 1016 may include normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio. In at least one instance, the normalizing logic 1016 normalizes reporter ion intensities of all other non-control channels relative to each other. In at least one instance, the normalizing logic 1016 applies the determined correction ratio to ion intensity readings of one set of channels (either the set of channels corresponding to the deuterated tags or the set of channels corresponding to the non-deuterated tags) to normalize (raise or lower according to the determined correction ratio) the signal intensities of the set of channels adjusted relative to the other set of channels with unadjusted signal intensities. This normalization of signal intensities accounts for the variations due to the relative retention time shift between the two sets of channels (due to the Deuterium) so that all of the channels (deuterated and non-deuterated) can be compared with each other, or otherwise used for subsequent analysis such as quantification workflows, for example, in a one for one context (keeping in mind that some of the channels have been normalized).

[0054] In at least one instance, new correction ratios can be determined for each subsequent MS2 trigger. In other words, each time an MS2 scan is triggered during the experiment, a new correction ratio can be determined and signals normalized by the embodiments disclosed herein. In such an instance, the generating logic 1012 is further to generate second mass spectrum data during the tandem mass tag labeling experiment and the determining logic 1014 is further to determine, in the generated second mass spectrum data, a second correction ratio between reporter ion peak intensities of the second mass spectrum data corresponding to the first non-deuterated tag and the first deuterated tag. The normalizing logic 1016 is further to apply the determined second correction ratio to reporter ion peak intensities of the generated second mass spectrum data corresponding to the second non-deuterated tag and the second deuterated tag, wherein the first correction ratio and the second correction ratio are different.

[0055] In at least one instance, the scientific instrument support module further comprises quantification logic to quantify the analyte of each channel using the normalized reporter ion intensities. The quantification logic may include existing data analysis workflows, for example. In such an instance, a user can directly compare the quantity of the analyte in each channel by analyzing the normalized reporter ion intensities of all channels in the tandem mass tag experiment.

[0056] In at least one instance, the normalizing logic 1016 is to apply the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a greater reporter ion intensity is lowered with the correction ratio. In at least one instance, the normalizing logic 1016 is to apply the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a lesser reporter ion intensity is raised with the correction ratio. In at least oneinstance, a user can define whether they want the normalizing logic 1016 to raise all dampened intensity signals or lower all higher intensity signals.

[0057] In at least one instance, the normalizing logic 1016 is further to normalize all of the deuterated channels relative to the deuterated control channel before the normalizing logic 1016 normalizes reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio, and wherein the normalizing logic 1016 is further to normalize all of the nondeuterated channels relative to the non-deuterated control channel before the normalizing logic 1016 normalizes reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio. In such an instance, the resulting correction ratio can be considered a ratio of a ratio where, for both channel sets (deuterated channels and non-deuterated channels), all of the channels of a particular channel set are normalized with respect to at least one channel set control before the channel sets being normalized relative to each other.

[0058] In at least one instance, more than one control channel is selected for one or both of the channel sets. In at least one instance, the non-deuterated control channel comprises a first non-deuterated control channel, wherein the plurality of non-deuterated channels further comprises a second non-deuterated control channel corresponding to a second non-deuterated tag, and wherein the determining logic 1014 is to further average reporter ion peak intensities corresponding to the first non-deuterated tag and the second non-deuterated tag before determining the correction ratio. In at least one instance, the deuterated control channel comprises a first deuterated control channel, wherein the plurality of deuterated channels further comprises a second deuterated control channel, and wherein the determining logic 1014 is to further average reporter ion peak intensities corresponding to the first deuterated tag and the second deuterated tag before determining the correction ratio.

[0059] FIG. 4 is a flow diagram of a method 2010 of performing support operations, in accordance with various embodiments. Although the operations of the method 2010 may be illustrated with reference to particular embodiments disclosed herein (e.g., the scientific instrument support modules 1010 discussed herein with reference to FIG. 3, the GUI 3000 discussed herein with reference to FIG. 5, the computing devices 4000 discussed herein with reference to FIG. 6, and / or the scientific instrument support system 5000 discussed herein with reference to FIG. 7), the method 2010 may be used in any suitable setting to perform any suitable support operations. Operations are illustrated once each and in a particular order in FIG. 4, but the operations may be reordered and / or repeated as desired and appropriate (e.g., different operations performed may be performed in parallel, as suitable).

[0060] At 2012, first operations may be performed. For example, the generating logic 1012 of a support module 1010 may perform the operations of 2012. The first operations may include generating mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, wherein the plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags, wherein the plurality of non- deuterated channels comprises a non-deuterated control channel corresponding to a first non-deuterated tagand the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag.

[0061] At 2014, second operations may be performed. For example, the determining logic 1014 of a support module 1010 may perform the operations of 2014. The second operations may include determining, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag.

[0062] At 2016, third operations may be performed. For example, the normalizing logic 1016 of a support module 1010 may perform the operations of 2016. The third operations may include normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

[0063] In at least one instance, the correction ratio is equivalent to the systematic error that needs to be corrected caused by the relative retention time shift between different sets of channels (deuterated channels and non-deuterated channels).

[0064] The scientific instrument support methods disclosed herein may include interactions with a human user (e.g., via the user local computing device 5020 discussed herein with reference to FIG. 7). These interactions may include providing information to the user (e.g., information regarding the operation of a scientific instrument such as the scientific instrument 5010 of FIG. 7, information regarding a sample being analyzed or other test or measurement performed by a scientific instrument, information retrieved from a local or remote database, or other information) or providing an option for a user to input commands (e.g., to control the operation of a scientific instrument such as the scientific instrument 5010 of FIG. 7, or to control the analysis of data generated by a scientific instrument), queries (e.g., to a local or remote database), or other information. In some embodiments, these interactions may be performed through a graphical user interface (GUI) that includes a visual display on a display device (e.g., the display device 4010 discussed herein with reference to FIG. 6) that provides outputs to the user and / or prompts the user to provide inputs (e.g., via one or more input devices, such as a keyboard, mouse, trackpad, or touchscreen, included in the other I / O devices 4012 discussed herein with reference to FIG. 6). The scientific instrument support systems disclosed herein may include any suitable GUIs for interaction with a user.

[0065] FIG. 5 depicts an example GUI 3000 that may be used in the performance of some or all of the support methods disclosed herein, in accordance with various embodiments. As noted above, the GUI 3000 may be provided on a display device (e.g., the display device 4010 discussed herein with reference to FIG.6) of a computing device (e.g., the computing device 4000 discussed herein with reference to FIG. 6) of a scientific instrument support system (e.g., the scientific instrument support system 5000 discussed herein with reference to FIG. 7), and a user may interact with the GUI 3000 using any suitable input device (e.g., any of the input devices included in the other I / O devices 4012 discussed herein with reference to FIG. 6) and input technique (e.g., movement of a cursor, motion capture, facial recognition, gesture detection, voice recognition, actuation of buttons, etc.).

[0066] The GUI 3000 may include a data display region 3002, a data analysis region 3004, a scientific instrument control region 3006, and a settings region 3008. The particular number and arrangement of regions depicted in FIG. 5 is simply illustrative, and any number and arrangement of regions, including any desired features, may be included in a GUI 3000.

[0067] The data display region 3002 may display data generated by a scientific instrument (e.g., the scientific instrument 5010 discussed herein with reference to FIG. 7).

[0068] The data analysis region 3004 may display the results of data analysis (e.g., the results of analyzing the data illustrated in the data display region 3002 and / or other data). In some embodiments, the data display region 3002 and the data analysis region 3004 may be combined in the GUI 3000 (e.g., to include data output from a scientific instrument, and some analysis of the data, in a common graph or region).

[0069] The scientific instrument control region 3006 may include options that allow the user to control a scientific instrument (e.g., the scientific instrument 5010 discussed herein with reference to FIG. 7).

[0070] The settings region 3008 may include options that allow the user to control the features and functions of the GUI 3000 (and / or other GUIs) and / or perform common computing operations with respect to the data display region 3002 and data analysis region 3004 (e.g., saving data on a storage device, such as the storage device 4004 discussed herein with reference to FIG. 6, sending data to another user, labeling data, etc.).

[0071] As noted above, the scientific instrument support module 1000 may be implemented by one or more computing devices. FIG. 6 is a block diagram of a computing device 4000 that may perform some or all of the scientific instrument support methods disclosed herein, in accordance with various embodiments. In some embodiments, the scientific instrument support module 1000 may be implemented by a single computing device 4000 or by multiple computing devices 4000. Further, as discussed below, a computing device 4000 (or multiple computing devices 4000) that implements the scientific instrument support module 1000 may be part of one or more of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 of FIG. 7.

[0072] The computing device 4000 of FIG. 6 is illustrated as having a number of components, but any one or more of these components may be omitted or duplicated, as suitable for the application and setting. In some embodiments, some or all of the components included in the computing device 4000 may be attached to one or more motherboards and enclosed in a housing (e.g., including plastic, metal, and / or other materials). In some embodiments, some of these components may be fabricated onto a single system-on-a- chip (SoC) (e.g., an SoC may include one or more processing devices 4002 and one or more storage devices 4004). Additionally, in various embodiments, the computing device 4000 may not include one or more of the components illustrated in FIG. 6, but may include interface circuitry (not shown) for coupling to the one or more components using any suitable interface (e.g., a Universal Serial Bus (USB) interface, a High-Definition Multimedia Interface (HDMI) interface, a Controller Area Network (CAN) interface, a Serial Peripheral Interface (SPI) interface, an Ethernet interface, a wireless interface, or any other appropriateinterface) . For example, the computing device 4000 may not include a display device 4010, but may include display device interface circuitry (e.g., a connector and driver circuitry) to which a display device 4010 may be coupled.

[0073] The computing device 4000 may include a processing device 4002 (e.g., one or more processing devices). As used herein, the term "processing device" may refer to any device or portion of a device that processes electronic data from registers and / or memory to transform that electronic data into other electronic data that may be stored in registers and / or memory. The processing device 4002 may include one or more digital signal processors (DSPs), application-specific integrated circuits (ASICs), central processing units (CPUs), graphics processing units (GPUs), cryptoprocessors (specialized processors that execute cryptographic algorithms within hardware), server processors, or any other suitable processing devices.

[0074] The computing device 4000 may include a storage device 4004 (e.g., one or more storage devices). The storage device 4004 may include one or more memory devices such as random access memory (RAM) (e.g., static RAM (SRAM) devices, magnetic RAM (MRAM) devices, dynamic RAM (DRAM) devices, resistive RAM (RRAM) devices, or conductive-bridging RAM (CBRAM) devices), hard drive-based memory devices, solid-state memory devices, networked drives, cloud drives, or any combination of memory devices. In some embodiments, the storage device 4004 may include memory that shares a die with a processing device 4002. In such an embodiment, the memory may be used as cache memory and may include embedded dynamic random access memory (eDRAM) or spin transfer torque magnetic random access memory (STT-MRAM), for example. In some embodiments, the storage device 4004 may include non-transitory computer readable media having instructions thereon that, when executed by one or more processing devices (e.g., the processing device 4002), cause the computing device 4000 to perform any appropriate ones of or portions of the methods disclosed herein.

[0075] The computing device 4000 may include an interface device 4006 (e.g., one or more interface devices 4006). The interface device 4006 may include one or more communication chips, connectors, and / or other hardware and software to govern communications between the computing device 4000 and other computing devices. For example, the interface device 4006 may include circuitry for managing wireless communications for the transfer of data to and from the computing device 4000. The term "wireless" and its derivatives may be used to describe circuits, devices, systems, methods, techniques, communications channels, etc., that may communicate data through the use of modulated electromagnetic radiation through a nonsolid medium. The term does not imply that the associated devices do not contain any wires, although in some embodiments they might not. Circuitry included in the interface device 4006 for managing wireless communications may implement any of a number of wireless standards or protocols, including but not limited to Institute for Electrical and Electronic Engineers (IEEE) standards including Wi-Fi (IEEE 802.11 family), IEEE 802.16 standards (e.g., IEEE 802.16-2005 Amendment), Long-Term Evolution (LTE) project along with any amendments, updates, and / or revisions (e.g., advanced LTE project, ultra mobile broadband (UMB) project (also referred to as "3GPP2"), etc.). In some embodiments, circuitryincluded in the interface device 4006 for managing wireless communications may operate in accordance with a Global System for Mobile Communication (GSM), General Packet Radio Service (GPRS), Universal Mobile Telecommunications System (UMTS), High Speed Packet Access (HSPA), Evolved HSPA (E- HSPA), or LTE network. In some embodiments, circuitry included in the interface device 4006 for managing wireless communications may operate in accordance with Enhanced Data for GSM Evolution (EDGE), GSM EDGE Radio Access Network (GERAN), Universal Terrestrial Radio Access Network (UTRAN), or Evolved UTRAN (E-UTRAN). In some embodiments, circuitry included in the interface device 4006 for managing wireless communications may operate in accordance with Code Division Multiple Access (CDMA), Time Division Multiple Access (TDMA), Digital Enhanced Cordless Telecommunications (DECT), Evolution-Data Optimized (EV-DO), and derivatives thereof, as well as any other wireless protocols that are designated as 3G, 4G, 5G, and beyond. In some embodiments, the interface device 4006 may include one or more antennas (e.g., one or more antenna arrays) to receipt and / or transmission of wireless communications.

[0076] In some embodiments, the interface device 4006 may include circuitry for managing wired communications, such as electrical, optical, or any other suitable communication protocols. For example, the interface device 4006 may include circuitry to support communications in accordance with Ethernet technologies. In some embodiments, the interface device 4006 may support both wireless and wired communication, and / or may support multiple wired communication protocols and / or multiple wireless communication protocols. For example, a first set of circuitry of the interface device 4006 may be dedicated to shorter-range wireless communications such as Wi-Fi or Bluetooth, and a second set of circuitry of the interface device 4006 may be dedicated to longer-range wireless communications such as global positioning system (GPS), EDGE, GPRS, CDMA, WiMAX, LTE, EV-DO, or others. In some embodiments, a first set of circuitry of the interface device 4006 may be dedicated to wireless communications, and a second set of circuitry of the interface device 4006 may be dedicated to wired communications.

[0077] The computing device 4000 may include battery / power circuitry 4008. The battery / power circuitry 4008 may include one or more energy storage devices (e.g., batteries or capacitors) and / or circuitry for coupling components of the computing device 4000 to an energy source separate from the computing device 4000 (e.g., AC line power).

[0078] The computing device 4000 may include a display device 4010 (e.g., multiple display devices). The display device 4010 may include any visual indicators, such as a heads-up display, a computer monitor, a projector, a touchscreen display, a liquid crystal display (LCD), a light-emitting diode display, or a flat panel display.

[0079] The computing device 4000 may include other input / output (I / O) devices 4012. The other I / O devices 4012 may include one or more audio output devices (e.g., speakers, headsets, earbuds, alarms, etc.), one or more audio input devices (e.g., microphones or microphone arrays), location devices (e.g., GPS devices in communication with a satellite-based system to receive a location of the computing device 4000, as known in the art), audio codecs, video codecs, printers, sensors (e.g., thermocouples or other temperature sensors, humidity sensors, pressure sensors, vibration sensors, accelerometers, gyroscopes,etc.), image capture devices such as cameras, keyboards, cursor control devices such as a mouse, a stylus, a trackball, or a touchpad, bar code readers, Quick Response (QR) code readers, or radio frequency identification (RFID) readers, for example.

[0080] The computing device 4000 may have any suitable form factor for its application and setting, such as a handheld or mobile computing device (e.g., a cell phone, a smart phone, a mobile internet device, a tablet computer, a laptop computer, a netbook computer, an ultrabook computer, a personal digital assistant (PDA), an ultra mobile personal computer, etc.), a desktop computing device, or a server computing device or other networked computing component.

[0081] One or more computing devices implementing any of the scientific instrument support modules or methods disclosed herein may be part of a scientific instrument support system. FIG. 7 is a block diagram of an example scientific instrument support system 5000 in which some or all of the scientific instrument support methods disclosed herein may be performed, in accordance with various embodiments. The scientific instrument support modules and methods disclosed herein (e.g., the scientific instrument support module 1000 of FIG. 1 and the method 2000 of FIG. 2) may be implemented by one or more of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 of the scientific instrument support system 5000.

[0082] Any of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 may include any of the embodiments of the computing device 4000 discussed herein with reference to FIG. 6, and any of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 may take the form of any appropriate ones of the embodiments of the computing device 4000 discussed herein with reference to FIG. 6.

[0083] The scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 may each include a processing device 5002, a storage device 5004, and an interface device 5006. The processing device 5002 may take any suitable form, including the form of any of the processing devices 4002 discussed herein with reference to FIG. 6, and the processing devices 5002 included in different ones of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 may take the same form or different forms. The storage device 5004 may take any suitable form, including the form of any of the storage devices 4004 discussed herein with reference to FIG. 6, and the storage devices 5004 included in different ones of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 may take the same form or different forms. The interface device 5006 may take any suitable form, including the form of any of the interface devices 4006 discussed herein with reference to FIG. 6, and the interface devices 5006 included in different ones of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, or the remote computing device 5040 may take the same form or different forms.

[0084] The scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, and the remote computing device 5040 may be in communication with other elements of the scientific instrument support system 5000 via communication pathways 5008. The communication pathways 5008 may communicatively couple the interface devices 5006 of different ones of the elements of the scientific instrument support system 5000, as shown, and may be wired or wireless communication pathways (e.g., in accordance with any of the communication techniques discussed herein with reference to the interface devices 4006 of the computing device 4000 of FIG. 6). The particular scientific instrument support system 5000 depicted in FIG. 7 includes communication pathways between each pair of the scientific instrument 5010, the user local computing device 5020, the service local computing device 5030, and the remote computing device 5040, but this "fully connected” implementation is simply illustrative, and in various embodiments, various ones of the communication pathways 5008 may be absent. For example, in some embodiments, a service local computing device 5030 may not have a direct communication pathway 5008 between its interface device 5006 and the interface device 5006 of the scientific instrument 5010, but may instead communicate with the scientific instrument 5010 via the communication pathway 5008 between the service local computing device 5030 and the user local computing device 5020 and the communication pathway 5008 between the user local computing device 5020 and the scientific instrument 5010.

[0085] The scientific instrument 5010 may include any appropriate scientific instrument, such as a mass spectrometer, for example.

[0086] The user local computing device 5020 may be a computing device (e.g., in accordance with any of the embodiments of the computing device 4000 discussed herein) that is local to a user of the scientific instrument 5010. In some embodiments, the user local computing device 5020 may also be local to the scientific instrument 5010, but this need not be the case; for example, a user local computing device 5020 that is in a user's home or office may be remote from, but in communication with, the scientific instrument 5010 so that the user may use the user local computing device 5020 to control and / or access data from the scientific instrument 5010. In some embodiments, the user local computing device 5020 may be a laptop, smartphone, or tablet device. In some embodiments the user local computing device 5020 may be a portable computing device.

[0087] The service local computing device 5030 may be a computing device (e.g., in accordance with any of the embodiments of the computing device 4000 discussed herein) that is local to an entity that services the scientific instrument 5010. For example, the service local computing device 5030 may be local to a manufacturer of the scientific instrument 5010 or to a third-party service company. In some embodiments, the service local computing device 5030 may communicate with the scientific instrument 5010, the user local computing device 5020, and / or the remote computing device 5040 (e.g., via a direct communication pathway 5008 or via multiple "indirect” communication pathways 5008, as discussed above) to receive data regarding the operation of the scientific instrument 5010, the user local computing device 5020, and / or the remote computing device 5040 (e.g., the results of self-tests of the scientific instrument 5010, calibration coefficients used by the scientific instrument 5010, the measurements of sensors associated with the scientificinstrument 5010, etc.). In some embodiments, the service local computing device 5030 may communicate with the scientific instrument 5010, the user local computing device 5020, and / or the remote computing device 5040 (e.g., via a direct communication pathway 5008 or via multiple "indirect” communication pathways 5008, as discussed above) to transmit data to the scientific instrument 5010, the user local computing device 5020, and / or the remote computing device 5040 (e.g., to update programmed instructions, such as firmware, in the scientific instrument 5010, to initiate the performance of test or calibration sequences in the scientific instrument 5010, to update programmed instructions, such as software, in the user local computing device 5020 or the remote computing device 5040, etc.). A user of the scientific instrument 5010 may utilize the scientific instrument 5010 or the user local computing device 5020 to communicate with the service local computing device 5030 to report a problem with the scientific instrument 5010 or the user local computing device 5020, to request a visit from a technician to improve the operation of the scientific instrument 5010, to order consumables or replacement parts associated with the scientific instrument 5010, or for other purposes.

[0088] The remote computing device 5040 may be a computing device (e.g., in accordance with any of the embodiments of the computing device 4000 discussed herein) that is remote from the scientific instrument 5010 and / or from the user local computing device 5020. In some embodiments, the remote computing device 5040 may be included in a datacenter or other large-scale server environment. In some embodiments, the remote computing device 5040 may include network-attached storage (e.g., as part of the storage device 5004). The remote computing device 5040 may store data generated by the scientific instrument 5010, perform analyses of the data generated by the scientific instrument 5010 (e.g., in accordance with programmed instructions), facilitate communication between the user local computing device 5020 and the scientific instrument 5010, and / or facilitate communication between the service local computing device 5030 and the scientific instrument 5010.

[0089] In some embodiments, one or more of the elements of the scientific instrument support system 5000 illustrated in FIG. 7 may not be present. Further, in some embodiments, multiple ones of various ones of the elements of the scientific instrument support system 5000 of FIG. 7 may be present. For example, a scientific instrument support system 5000 may include multiple user local computing devices 5020 (e.g., different user local computing devices 5020 associated with different users or in different locations). In another example, a scientific instrument support system 5000 may include multiple scientific instruments 5010, all in communication with service local computing device 5030 and / or a remote computing device 5040; in such an embodiment, the service local computing device 5030 may monitor these multiple scientific instruments 5010, and the service local computing device 5030 may cause updates or other information may be "broadcast” to multiple scientific instruments 5010 at the same time. Different ones of the scientific instruments 5010 in a scientific instrument support system 5000 may be located close to one another (e.g., in the same room) or farther from one another (e.g., on different floors of a building, in different buildings, in different cities, etc.). In some embodiments, a scientific instrument 5010 may be connected to an I nternet- of-Things (loT) stack that allows for command and control of the scientific instrument 5010 through a web-based application, a virtual or augmented reality application, a mobile application, and / or a desktop application. Any of these applications may be accessed by a user operating the user local computing device 5020 in communication with the scientific instrument 5010 by the intervening remote computing device 5040. In some embodiments, a scientific instrument 5010 may be sold by the manufacturer along with one or more associated user local computing devices 5020 as part of a local scientific instrument computing unit 5012.

[0090] In some embodiments, different ones of the scientific instruments 5010 included in a scientific instrument support system 5000 may be different types of scientific instruments 5010. In some such embodiments, the remote computing device 5040 and / or the user local computing device 5020 may combine data from different types of scientific instruments 5010 included in a scientific instrument support system 5000.

[0091] In at least one instance, the methods and systems disclosed herein allow for correction of intensity based on the distance from the apex of the elution peak. The shift in reporter ion intensity depends on the position of the ms2 trigger on the elution peak. For all peptides triggered at the apex of the elution peak or very close to it, no shift in intensity may be observed. If the peptide was triggered left of the apex (lower RTs), the deuterated labeled reporter ions are enriched, and for peptides triggered after the apex, the nondeuterated labels are enriched. For each elution peak descriptive parameters (start RT, Apex RT, left RT) are available using a mass trace and elution peak detection algorithm such as Minora, for example. The relative position of the trigger in the peak can be calculated. Assuming a Gaussian peak shape, for example, (actually 2 slightly shifted elution peaks for the deuterated and non-deuterated labels), a correction factor can be calculated for the apex intensity of deuterated and non-deuterated labels that represent the control channels.

[0092] In at least one instance, the methods and systems disclosed herein allow for correction using machine learning. The correction can be viewed as a multivariate regression problem considering peak intensities, peptide RT, elution profile, position of trigger in elution profile, etc. Using multivariate regressors (SVM, KNN based regressors, Decision tree regressors, etc.) can allow for determining peptide-specific correction factors.

[0093] The following paragraphs provide various examples of the embodiments disclosed herein.

[0094] Example A includes any of the scientific instrument support modules disclosed herein.

[0095] Example B includes any of the methods disclosed herein.

[0096] Example C includes any of the GUIs disclosed herein.

[0097] Example D includes any of the scientific instrument support computing devices and systems disclosed herein.

[0098] Example 1 - A scientific instrument support apparatus comprising generating logic to generate mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, wherein the plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags, wherein the plurality of non- deuterated channels comprises a non-deuterated control channel corresponding to a first non-deuterated tagand the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag, determining logic to determine, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag, and normalizing logic to normalize reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

[0099] Example 2 - The scientific instrument support apparatus of Example 1 , wherein the correction ratio comprises a first correction ratio, wherein the generating logic is further to generate second mass spectrum data during the tandem mass tag labeling experiment, the determining logic is further to determine, in the generated second mass spectrum data, a second correction ratio between reporter ion peak intensities of the second mass spectrum data corresponding to the first non-deuterated tag and the first deuterated tag, and wherein the normalizing logic is further to apply the determined second correction ratio to reporter ion peak intensities of the generated second mass spectrum data corresponding to the second non-deuterated tag and the second deuterated tag, and wherein the first correction ratio and the second correction ratio are different.

[0100] Example 3 - The scientific instrument support apparatus of any one of Examples 1 or 2, further comprising defining logic to define which channels of the plurality of channels are to be used as the non- deuterated control channel and the deuterated control channel by receiving a control channel selection input from a user.

[0101] Example 4 - The scientific instrument support apparatus of Example 3, wherein the input from a user comprises at least one of the non-deuterated channels and at least one of the deuterated channels.

[0102] Example 5 - The scientific instrument support apparatus of any one of Examples 1-4, further comprising quantification logic to quantify the analyte of each channel using the normalized reporter ion intensities.

[0103] Example 6 - The scientific instrument support apparatus of any one of Examples 1-5, wherein the normalizing logic is to apply the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a greater reporter ion intensity is lowered with the correction ratio.

[0104] Example 7 - The scientific instrument support apparatus of any one of Examples 1-6, wherein the normalizing logic is to apply the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a lesser reporter ion intensity is raised with the correction ratio.

[0105] Example 8 - The scientific instrument support apparatus of any one of Examples 1-7, wherein the normalizing logic is further to normalize all of the deuterated channels relative to the deuterated control channel before the normalizing logic normalizes reporter ion intensities corresponding to a second non- deuterated tag and a second deuterated tag based on the determined correction ratio, and wherein the normalizing logic is further to normalize all of the non-deuterated channels relative to the non-deuteratedcontrol channel before the normalizing logic normalizes reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

[0106] Example 9 - The scientific instrument support apparatus of any one of Examples 1-8, wherein the non-deuterated control channel comprises a first non-deuterated control channel, wherein the plurality of non-deuterated channels further comprises a second non-deuterated control channel corresponding to a second non-deuterated tag, and wherein the determining logic is to further average reporter ion peak intensities corresponding to the first non-deuterated tag and the second non-deuterated tag before determining the correction ratio.

[0107] Example 10 - A computer-implemented method comprising generating mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, wherein the plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags, wherein the plurality of non-deuterated channels comprises a non-deuterated control channel corresponding to a first non-deuterated tag and the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag, determining, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag, and normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

[0108] Example 11 - The method of Example 10, wherein the correction ratio comprises a first correction ratio, wherein the method further comprises generating second mass spectrum data during the tandem mass tag labeling experiment, determining, in the generated second mass spectrum data, a second correction ratio between reporter ion peak intensities of the second mass spectrum data corresponding to the first non-deuterated tag and the first deuterated tag, and applying the determined second correction ratio to reporter ion peak intensities of the generated second mass spectrum data corresponding to the second non-deuterated tag and the second deuterated tag, and wherein the first correction ratio and the second correction ratio are different.

[0109] Example 12 - The method of any one of Examples 10 or 11, further comprising defining which channels of the plurality of channels are to be used as the non-deuterated control channel and the deuterated control channel by receiving a control channel selection input from a user.

[0110] Example 13 - The method of Example 12, wherein the input from a user comprises at least one of the non-deuterated channels and at least one of the deuterated channels.

[0111] Example 14 - The method of any one of Examples 10-13, further comprising applying the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a greater reporter ion intensity is lowered with the correction ratio.

[0112] Example 15 - The method of any one of Examples 10-14, further comprising applying the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag andthe second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a lesser reporter ion intensity is raised with the correction ratio.

[0113] Example 16 - The method of any one of Examples 10-15, further comprising normalizing all of the deuterated channels relative to the deuterated control channel before normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio and normalizing all of the non-deuterated channels relative to the non-deuterated control channel before normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

[0114] Example 17 - The method of any one of Examples 10-16, wherein the non-deuterated control channel comprises a first non-deuterated control channel, wherein the plurality of non-deuterated channels further comprises a second non-deuterated control channel corresponding to a second non-deuterated tag, and wherein the method further comprises averaging reporter ion peak intensities corresponding to the first non-deuterated tag and the second non-deuterated tag before determining the correction ratio.

Claims

Claims:1 . A scientific instrument support apparatus, comprising: generating logic to generate mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, wherein the plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags, wherein the plurality of non-deuterated channels comprises a non-deuterated control channel corresponding to a first non-deuterated tag and the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag; determining logic to determine, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag; and normalizing logic to normalize reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

2. The scientific instrument support apparatus of Claim 1, wherein the correction ratio comprises a first correction ratio, wherein: the generating logic is further to generate second mass spectrum data during the tandem mass tag labeling experiment; wherein the determining logic is further to determine, in the generated second mass spectrum data, a second correction ratio between reporter ion peak intensities of the second mass spectrum data corresponding to the first non-deuterated tag and the first deuterated tag; and wherein the normalizing logic is further to apply the determined second correction ratio to reporter ion peak intensities of the generated second mass spectrum data corresponding to the second non- deuterated tag and the second deuterated tag, and wherein the first correction ratio and the second correction ratio are different.

3. The scientific instrument support apparatus of Claim 1, further comprising defining logic to define which channels of the plurality of channels are to be used as the non-deuterated control channel and the deuterated control channel by receiving a control channel selection input from a user.

4. The scientific instrument support apparatus of Claim 3, wherein the input from a user comprises at least one of the non-deuterated channels and at least one of the deuterated channels.

5. The scientific instrument support apparatus of Claim 1, further comprising quantification logic to quantify the analyte of each channel using the normalized reporter ion intensities.

6. The scientific instrument support apparatus of Claim 1, wherein the normalizing logic is to apply the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a greater reporter ion intensity is lowered with the correction ratio.

7. The scientific instrument support apparatus of Claim 1, wherein the normalizing logic is to apply the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a lesser reporter ion intensity is raised with the correction ratio.

8. The scientific instrument support apparatus of Claim 1, wherein the normalizing logic is further to normalize all of the deuterated channels relative to the deuterated control channel before the normalizing logic normalizes reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio, and wherein the normalizing logic is further to normalize all of the non-deuterated channels relative to the non-deuterated control channel before the normalizing logic normalizes reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

9. The scientific instrument support apparatus of Claim 1, wherein the non-deuterated control channel comprises a first non-deuterated control channel, wherein the plurality of non-deuterated channels further comprises a second non-deuterated control channel corresponding to a second non-deuterated tag, and wherein the determining logic is to further average reporter ion peak intensities corresponding to the first non-deuterated tag and the second non-deuterated tag before determining the correction ratio.

10. A computer-implemented method, comprising: generating mass spectrum data during a tandem mass tag labeling experiment including a plurality of channels, wherein the plurality of channels comprises a plurality of non-deuterated channels corresponding to non-deuterated tags and a plurality of deuterated channels corresponding to deuterated tags, wherein the plurality of non-deuterated channels comprises a non-deuterated control channel corresponding to a first non-deuterated tag and the plurality of deuterated channels comprises a deuterated control channel corresponding to a first deuterated tag; determining, in the generated mass spectrum data, a correction ratio between a first reporter ion peak intensity corresponding to the first non-deuterated tag and a second reporter ion peak intensity corresponding to the first deuterated tag; and normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.11 . The method of Claim 10, wherein the correction ratio comprises a first correction ratio, wherein the method further comprises: generating second mass spectrum data during the tandem mass tag labeling experiment; determining, in the generated second mass spectrum data, a second correction ratio between reporter ion peak intensities of the second mass spectrum data corresponding to the first non-deuterated tag and the first deuterated tag; and applying the determined second correction ratio to reporter ion peak intensities of the generated second mass spectrum data corresponding to the second non-deuterated tag and the second deuterated tag, and wherein the first correction ratio and the second correction ratio are different.

12. The method of Claim 10, further comprising defining which channels of the plurality of channels are to be used as the non-deuterated control channel and the deuterated control channel by receiving a control channel selection input from a user.

13. The method of Claim 12, wherein the input from a user comprises at least one of the non-deuterated channels and at least one of the deuterated channels.

14. The method of Claim 10, further comprising applying the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a greater reporter ion intensity is lowered with the correction ratio.

15. The method of Claim 10, further comprising applying the determined correction ratio to reporter ion intensities corresponding to the second non-deuterated tag and the second deuterated tag such that the one of the second non-deuterated tag and the second deuterated tag having a lesser reporter ion intensity is raised with the correction ratio.

16. The method of Claim 10, further comprising: normalizing all of the deuterated channels relative to the deuterated control channel before normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio; and normalizing all of the non-deuterated channels relative to the non-deuterated control channel before normalizing reporter ion intensities corresponding to a second non-deuterated tag and a second deuterated tag based on the determined correction ratio.

17. The method of Claim 10, wherein the non-deuterated control channel comprises a first non-deuterated control channel, wherein the plurality of non-deuterated channels further comprises a second non-deuterated control channel corresponding to a second non-deuterated tag, and wherein the method further comprises averaging reporter ion peak intensities corresponding to the first non-deuterated tag and the second non-deuterated tag before determining the correction ratio.

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