BACKGROUND OF THE DISCLOSURE

Field of the Disclosure

The present disclosure relates to the field of analyzing small molecule components in a complex mixture and, more particularly, to a method and associated apparatus and computer program product for analyzing small molecule components of a complex mixture, with such small molecule analysis including metabolomics, which is the study of small molecules produced by an organism's metabolic processes, or other analysis of small molecules produced through metabolism.

Description of Related Art

Metabolomics is the study of the small molecules, or metabolites, contained in a cell, tissue or organ (including fluids) and involved in primary and intermediary metabolism. The term “metabolome” refers to the collection of metabolites present in an organism. The human metabolome encompasses native small molecules (natively biosynthesizeable, non-polymeric compounds) that are participants in general metabolic reactions and that are required for the maintenance, growth and normal function of a cell. Thus, metabolomics is a direct observation of the status of cellular physiology, and may thus be predictive of disease in a given organism. Subtle biochemical changes (including the presence of selected metabolites) are inherent in a given disease. Therefore, the accurate mapping of these changes to known pathways may allow researchers to build a biochemical hypothesis for a disease. Based on this hypothesis, the enzymes and proteins critical to the disease can be uncovered such that disease targets may be identified for treatment with targeted pharmaceutical compounds or other therapy.

Molecular biology techniques for uncovering the biochemical processes underlying disease have been centered on the genome, which consists of the genes that make up DNA, which is transcribed into RNA and then translated to proteins, which then make up the small molecules of the human metabolome. While genomics (study of the DNA-level biochemistry), transcript profiling (study of the RNA-level biochemistry), and proteomics (study of the protein-level biochemistry) are useful for identification of disease pathways, these methods are complicated by the fact that there exist over 25,000 genes, 100,000 to 200,000 RNA transcripts and up to 1,000,000 proteins in human cells. However, it is estimated that there may be as few as 2,500 small molecules in the human metabolome.

Thus, metabolomic technology provides a significant leap beyond genomics, transcript profiling, and/or proteomics. With metabolomics, metabolites and their role in metabolism may be readily identified. In this context, the identification of disease targets may be expedited with greater accuracy relative to other known methods. The collection of metabolomic data for use in identifying disease pathways is generally known in the art, as described generally, for example, in U.S. Pat. Nos. 7,005,255 and 7,329,489 to Metabolon, Inc., each entitled Methods for Drug Discovery, Disease Treatment, and Diagnosis Using Metabolomics. Additional uses for metabolomics data are described therein and include, for example, determining response to a therapeutic agent (i.e., a drug) or other xenobiotics, monitoring drug response, determining drug safety, and drug discovery. However, the collection and sorting of metabolomic data taken from a variety of samples (e.g., from a patient population) consumes large amounts of time and computational power. For example, according to some known metabolomic techniques, spectrometry data for certain samples is collected and plotted in three (or more) dimensions (i.e., sample properties that can be represented along an axis with respect to other sample properties) and stored in an individual file corresponding to each sample. This data is then, by individual file, compared to data corresponding to a plurality of known metabolites in order to identify known metabolites that may be disease targets. The data may also be used for identification of toxic agents and/or drug metabolites. Furthermore, such data may also be used to monitor the effects of xenobiotics and/or used to monitor/measure/identify the xenobiotics and associated metabolites produced by processing (metabolizing) the xenobiotics. However, such conventional “file-based” methods (referring to the individual data file generated for each sample) require the use of large amounts of computing power and memory capacity to handle the screening of large numbers of known metabolites. Furthermore, “file-based” data handling may not lend itself to the compilation of sample population data across a number of samples because, according to known metabolomic data handling techniques, each sample is analyzed independently, without taking into account subtle changes in metabolite composition that may be more readily detectable across a sample population. Furthermore, existing “file-based” method may have other limitations including: limited security and auditability; and poor data set consistency across multiple file copies. In addition, individual files may not support multiple indices (i.e., day collected, sample ID, control vs. treated, drug dose, etc.) such that all files must be scanned when only a particular subset is desired. Such “file-based” methods may thus be of limited assistance in using previously-collected data to facilitate the analysis of data for new samples.

These limitations in current metabolomic data analysis techniques may lead to the discarding of potentially relevant and/or valuable metabolomic data that may be used to identify and classify particular metabolites as disease targets. Specifically, spectrometry data corresponding to a number of samples (such as tissue samples from individual human subjects) generally results in a large data file corresponding to each sample, wherein each data file must then be subjected to an individual screening process with respect to a library of known metabolites. However, conventional systems do not readily allow for the consolidation of spectrometry data from a number of samples for the subjective evaluation of the data generated by the spectrometry processes. Thus, while a single file corresponding to an individual sample may be inconclusive, such data may be more telling if viewed subjectively in a succinct format with respect to other samples within a sample population.

One particular example of a limitation in current metabolomic data analysis techniques involves the identification of a metabolite in each of a plurality of sample. In some instances, the identification of the metabolite involves analyzing the data file of each sample to determine whether an indication (i.e., an intensity peak for a particular sample ion mass or sample component mass, observed at a particular retention time or range or retention times) of that metabolite exists within the respective data files. However, as previously noted, it may be difficult in “file based” data handling methods to verify whether the determined indication is consistent across samples. For example, it may be difficult to determine whether the identified intensity peaks are aligned with respect to retention time across the samples. Further, there may be instances where the indication (e.g., the intensity peak) is not clearly defined within the data file of one or more samples. In those instances, the indication (e.g., the intensity peak) may actually reflect the presence of more than one sample component and, as such, any analysis of those intensity peaks as a whole may be significantly inaccurate. As such, the various assumptions and estimates, which may be difficult to analyze for individual samples when using a file-base data handling method, may result in an inaccurate indication of factors such as the identification and quantity of that metabolite (or a plurality of metabolites) present over/across the plurality of the sample. In this regard, such inaccuracy introduced into a metabolomics analysis at such an early stage may lead to larger inaccuracies in subsequent steps or analyses.

This collection of metabolomics data, as well as other empirical data representing a knowledge base of metabolites including, for example, individual metabolite characteristics, situational metabolite characteristics, and interactional metabolite characteristics, also provides an opportunity for using this trove of data to predict and/or identify metabolites likely to be present in a particular sample, and/or to facilitate validation of the data collected for a particular sample.

Therefore, there exists a need for an improved apparatus and method for solving the technical issues outlined above that are associated with conventional metabolomic data analysis systems. More particularly, there exists a need for an apparatus and method capable of analyzing spectrometry data over/across samples, with the option of, but not the need for, generating a separate data file for each sample. There also exists a need for an apparatus and method capable of allowing a user to subjectively evaluate spectrometry data across a plurality of samples to identify selected metabolites, for allowing the user to verify or otherwise determine the confidence in the identification of the selected metabolites, for allowing the user to examine the data associated with the identification of the selected metabolites, for example, for sorting, grouping, and/or aligning purposes, and for allowing the user to determine additional information related to the identified selected metabolites, for instance, for quality control and consistency verification purposes. There also exists a need for an improved apparatus and method capable of more accurately identifying sample components over/across samples from the acquired spectrometry data. In addition, there exists a need for better implementation of existing metabolomics data, as well as other available metabolomics information, in the metabolomics analysis of subsequent samples.

SUMMARY OF THE DISCLOSURE

The above and other needs are met by aspects of the present disclosure which, in one aspect, provides a method of analyzing data for a sample having a known characteristic, wherein the data for the sample is obtained from a component separation and mass spectrometer system. Such a method comprises analyzing data obtained from the component separation and mass spectrometer system for a reference ion, to determine a relationship between reference ion mass, retention time, and intensity, including intensity as a function of retention time for the reference ion mass, wherein the reference ion has an intensity maxima at a characteristic retention time for the reference ion mass; adding the analyzed data for the reference ion to an ion data repository, wherein each of the ions in the ion data repository has an intensity maxima within a range of characteristic retention times for a characteristic ion mass; modifying, if the reference ion was previously included in the ion data repository, the range of characteristic retention times of the reference ion in the ion data repository, according to the characteristic retention time of the intensity maxima for the reference ion; selecting, via a user interface, one or more ions from the ion data repository expected to be included in the sample based on the known characteristic of the sample; comparing, on a display associated with the user interface, data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample; and modifying, via the user interface, the range of characteristic retention times of each of the one or more ions determined to be present in the sample, in the data repository, according to the characteristic retention time of the intensity maxima for a respective one of the one or more ions determined to be present in the sample.

Another aspect of the present disclosure provides an apparatus for analyzing data for a sample having a known characteristic, with the data for the sample being obtained from a component separation and mass spectrometer system, wherein the apparatus comprises a processor and a memory storing executable instructions that, in response to execution by the processor, cause the apparatus to at least perform the steps of the method aspect of the present disclosure.

A further aspect of the present disclosure provides a computer program product for analyzing data for a sample having a known characteristic, with the data for the sample being obtained from a component separation and mass spectrometer system, wherein the computer program product comprises at least one non-transitory computer readable storage medium having computer-readable program code stored thereon, the computer-readable program code comprising program code that is executable to at least perform the steps of the method aspect of the present disclosure.

The present disclosure thus includes, without limitation, the following embodiments:

Embodiment 1: A method of analyzing data for a sample having a known characteristic, the data for the sample being obtained from a component separation and mass spectrometer system, said method comprising analyzing data obtained from the component separation and mass spectrometer system for a reference ion, to determine a relationship between reference ion mass, retention time, and intensity, including intensity as a function of retention time for the reference ion mass, the reference ion having an intensity maxima at a characteristic retention time for the reference ion mass; adding the analyzed data for the reference ion to an ion data repository, each of the ions in the ion data repository having an intensity maxima within a range of characteristic retention times for a characteristic ion mass; modifying, if the reference ion was previously included in the ion data repository, the range of characteristic retention times of the reference ion in the ion data repository, according to the characteristic retention time of the intensity maxima for the reference ion; selecting, via a user interface, one or more ions from the ion data repository expected to be included in the sample based on the known characteristic of the sample; comparing, on a display associated with the user interface, data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample; and modifying, via the user interface, the range of characteristic retention times of each of the one or more ions determined to be present in the sample, in the data repository, according to the characteristic retention time of the intensity maxima for a respective one of the one or more ions determined to be present in the sample.
Embodiment 2: The method of any preceding embodiment, or any combination of preceding embodiments, comprising including the reference ion in the sample.

Embodiment 3: The method of any preceding embodiment, or any combination of preceding embodiments, comprising: analyzing data obtained from the component separation and mass spectrometer system for the sample to determine a relationship between sample ion mass, retention time, and intensity, including intensity as a function of retention time for a selected sample ion mass, the selected sample ion mass being selected via the user interface; selecting, via the user interface, an ion present in the data for the sample, the selected ion having an intensity maxima at a characteristic retention time for the selected sample ion mass; comparing the data for the selected ion to the selected one or more ions in the ion data repository expected to be included in the sample based on the known characteristic of the sample, in order to determine an identity of the selected ion; and modifying the range of characteristic retention times of the ion in the ion data repository corresponding to the selected ion, according to the characteristic retention time of the intensity maxima for the selected ion.

Embodiment 4: The method of any preceding embodiment, or any combination of preceding embodiments, wherein selecting one or more ions from the ion data repository expected to be included in the sample based on the known characteristic of the sample comprises querying the ion data repository via the user interface to select the one or more ions therefrom based upon a retention time of an intensity maxima of a selected ion from the data for the sample in relation to the range of characteristic retention times of the intensity maxima of the one or more ions in the ion data repository.
Embodiment 5: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein selecting one or more ions from the ion data repository expected to be included in the sample based on the known characteristic of the sample comprises selecting the one or more ions from the ion data repository in relation to ions determined to be present in a first one of the plurality of samples, the selected one or more ions related to ions determined to be present in a first one of the plurality of samples being used for comparison to the data for a remainder of the samples in the sample run.
Embodiment 6: The method of any preceding embodiment, or any combination of preceding embodiments, wherein comparing, on a display associated with the user interface, data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository comprises comparing, on the display, a two dimensional plot of intensity as a function of retention time for the sample to a two dimensional plot of intensity as a function of retention time for each of the one or more ions selected from the ion data repository so as to provide a visual indication of intensity maxima therebetween for determining whether any of the one or more ions is present in the sample.
Embodiment 7: The method of any preceding embodiment, or any combination of preceding embodiments, wherein modifying, if the reference ion was previously included in the ion data repository, the range of characteristic retention times of the reference ion in the ion data repository, according to the characteristic retention time of the intensity maxima for the reference ion comprises reducing the range of characteristic retention times if the characteristic retention time of the intensity maxima for the reference ion is within the range of characteristic retention times; and determining whether any data deviation factors in the component separation and mass spectrometer system require consideration if the characteristic retention time of the intensity maxima for the reference ion is outside the range of characteristic retention times.
Embodiment 8: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the relationship between reference ion mass, retention time, and intensity, includes intensity as a function of the reference ion mass for a selected retention time, wherein the adding step comprises adding the analyzed data for the reference ion to an ion data repository such that each of the ions in the ion data repository have the intensity maxima within a range of characteristic ion masses for a characteristic retention time, and wherein the modifying step comprises modifying, if the reference ion was previously included in the ion data repository, the range of characteristic ion masses of the reference ion in the ion data repository, according to the characteristic ion mass of the intensity maxima for the reference ion.
Embodiment 9: The method of any preceding embodiment, or any combination of preceding embodiments, wherein selecting one or more ions from the ion data repository comprises comparing the known characteristic to empirical data included in the ion data repository, the empirical data including relational information between known characteristics and ions, and determining therefrom the one or more ions corresponding to the known characteristic of the sample.
Embodiment 10: The method of any preceding embodiment, or any combination of preceding embodiments, wherein, after comparing data for the sample to data for the one or more ions from the ion data repository and determining whether any of the one or more ions is present in the sample, the method comprises adding empirical data associated with the sample to the ion data repository in relation to the any of the one or more ions determined to be present in the sample.
Embodiment 11: The method of any preceding embodiment, or any combination of preceding embodiments, comprising analyzing data obtained from the component separation and mass spectrometer system for an anchor sample, the anchor sample being defined as a consistent, previously-characterized sample, to determine a component ion of the anchor sample and a relationship between component ion mass, retention time, and intensity, including intensity as a function of retention time for the component ion mass, the component ion having an intensity maxima at a characteristic component ion retention time for the component ion mass.
Embodiment 12: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the component ion mass is substantially equal to the characteristic ion mass of one of the one or more ions determined to be in the sample, and the method comprises comparing the intensity maxima for the component ion at the characteristic component ion retention time, to the intensity maxima for the one of the one or more ions determined to be in the sample at the characteristic retention time, wherein if the intensity maxima for the component ion and the one of the one or more ions determined to be in the sample are substantially similar, then the one of the one or more ions determined to be in the sample is designated as an artifact ion in the sample.
Embodiment 13: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the anchor sample comprises water.
Embodiment 14: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, wherein the method comprises analyzing the plurality of samples in the sample run to determine a presence of one of the one or more ions from the ion data repository determined to be present in a first one of the plurality of samples, across the plurality of samples, and wherein if a threshold quantity of the samples in the plurality of samples does not include the one of the one or more ions from the ion data repository determined to be present in the first one of the plurality of samples, then the one of the one or more ions determined to be present in the first one of the plurality of samples is designated as sparse ion in the plurality of samples.
Embodiment 15: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the method comprises analyzing data obtained from the component separation and mass spectrometer system for each sample to determine a relationship between sample ion mass, retention time, and intensity, including intensity as a function of retention time for a selected sample ion mass, the selected sample ion mass being selected via the user interface; analyzing the intensity as the function of retention time for the selected sample ion mass for each of the samples, across the plurality of samples, to identify an intensity maxima within a predicted range of retention times for each sample, the predicted range of retention times including an expected intensity maxima retention time therein for the selected sample ion mass; identifying, for each sample, an actual retention time of the intensity maxima in relation to the expected intensity maxima retention time; and determining whether the actual retention times of the intensity maxima of two or more consecutive samples of the plurality of samples in the sample run demonstrate an identifiable pattern with respect to the expected intensity maxima retention time.
Embodiment 16: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the identifiable pattern of the actual retention times of the intensity maxima of the two or more consecutive samples, with respect to the expected intensity maxima retention time, comprises a shift wherein the actual retention times of the intensity maxima are substantially consistently offset from the expected intensity maxima retention time, or a drift wherein the actual retention times of the intensity maxima are offset by a non-constant function from the expected intensity maxima retention time, and wherein the method comprises correcting the offset of the actual retention time of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern.
Embodiment 17: The method of any preceding embodiment, or any combination of preceding embodiments, wherein the identifiable pattern of the actual retention times of the intensity maxima of the two or more consecutive samples, with respect to the expected intensity maxima retention time, comprises an offset from the expected intensity maxima retention time, the offset differing between two subsets of two or more consecutive samples in the sample run, and wherein the method comprises correcting the offset of the actual retention times of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern of one of the two subsets having a majority of the samples in the sample run.
Embodiment 18: The method of any preceding embodiment, or any combination of preceding embodiments, wherein, if comparing data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample results in none of the one or more ions being present in the sample, then the method comprises resolving an instrument error associated with the component separation and mass spectrometer system and re-running the sample through the component separation and mass spectrometer system to obtain replacement data for the sample.
Embodiment 19: The method of any preceding embodiment, or any combination of preceding embodiments, comprising displaying, on the display associated with the user interface, the corrected offset of the actual retention time of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern to provide a visualization of the corrected actual retention time of the intensity maxima of each of the plurality of samples across the plurality of samples in the sample run.
Embodiment 20: An apparatus for analyzing data for a sample having a known characteristic, the data for the sample being obtained from a component separation and mass spectrometer system, the apparatus comprising a processor and a memory storing executable instructions that, in response to execution by the processor, cause the apparatus to at least perform the steps of analyzing data obtained from the component separation and mass spectrometer system for a reference ion, to determine a relationship between reference ion mass, retention time, and intensity, including intensity as a function of retention time for the reference ion mass, the reference ion having an intensity maxima at a characteristic retention time for the reference ion mass; adding the analyzed data for the reference ion to an ion data repository, each of the ions in the ion data repository having an intensity maxima within a range of characteristic retention times for a characteristic ion mass; modifying, if the reference ion was previously included in the ion data repository, the range of characteristic retention times of the reference ion in the ion data repository, according to the characteristic retention time of the intensity maxima for the reference ion; selecting, via a user interface associated with the apparatus, one or more ions from the ion data repository expected to be included in the sample based on the known characteristic of the sample; comparing, on a display associated with the user interface, data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample; and modifying, via the user interface, the range of characteristic retention times of each of the one or more ions determined to be present in the sample, in the data repository, according to the characteristic retention time of the intensity maxima for a respective one of the one or more ions determined to be present in the sample.
Embodiment 21: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the reference ion is included in the sample.
Embodiment 22: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the steps of analyzing data obtained from the component separation and mass spectrometer system for the sample to determine a relationship between sample ion mass, retention time, and intensity, including intensity as a function of retention time for a selected sample ion mass, the selected sample ion mass being selected via the user interface; selecting, via the user interface, an ion present in the data for the sample, the selected ion having an intensity maxima at a characteristic retention time for the selected sample ion mass; comparing the data for the selected ion to the selected one or more ions in the ion data repository expected to be included in the sample based on the known characteristic of the sample, in order to determine an identity of the selected ion; and modifying the range of characteristic retention times of the ion in the ion data repository corresponding to the selected ion, according to the characteristic retention time of the intensity maxima for the selected ion.
Embodiment 23: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of querying the ion data repository via the user interface to select the one or more ions therefrom based upon a retention time of an intensity maxima of a selected ion from the data for the sample in relation to the range of characteristic retention times of the intensity maxima of the one or more ions in the ion data repository.
Embodiment 24: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of selecting the one or more ions from the ion data repository in relation to ions determined to be present in a first one of the plurality of samples, the selected one or more ions related to ions determined to be present in a first one of the plurality of samples being used for comparison to the data for a remainder of the samples in the sample run.
Embodiment 25: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of comparing, on the display, a two dimensional plot of intensity as a function of retention time for the sample to a two dimensional plot of intensity as a function of retention time for each of the one or more ions selected from the ion data repository so as to provide a visual indication of intensity maxima therebetween for determining whether any of the one or more ions is present in the sample.
Embodiment 26: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the steps of reducing the range of characteristic retention times if the characteristic retention time of the intensity maxima for the reference ion is within the range of characteristic retention times; and determining whether any data deviation factors in the component separation and mass spectrometer system require consideration if the characteristic retention time of the intensity maxima for the reference ion is outside the range of characteristic retention times.
Embodiment 27: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the relationship between reference ion mass, retention time, and intensity, includes intensity as a function of the reference ion mass for a selected retention time, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the steps of adding the analyzed data for the reference ion to an ion data repository such that each of the ions in the ion data repository have the intensity maxima within a range of characteristic ion masses for a characteristic retention time; and modifying, if the reference ion was previously included in the ion data repository, the range of characteristic ion masses of the reference ion in the ion data repository, according to the characteristic ion mass of the intensity maxima for the reference ion.
Embodiment 28: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the steps of comparing the known characteristic to empirical data included in the ion data repository, the empirical data including relational information between known characteristics and ions; and determining therefrom the one or more ions corresponding to the known characteristic of the sample.
Embodiment 29: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of adding empirical data associated with the sample to the ion data repository in relation to the any of the one or more ions determined to be present in the sample, after comparing data for the sample to data for the one or more ions from the ion data repository and determining whether any of the one or more ions is present in the sample.
Embodiment 30: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of analyzing data obtained from the component separation and mass spectrometer system for an anchor sample, the anchor sample being defined as a consistent, previously-characterized sample, to determine a component ion of the anchor sample and a relationship between component ion mass, retention time, and intensity, including intensity as a function of retention time for the component ion mass, the component ion having an intensity maxima at a characteristic component ion retention time for the component ion mass.
Embodiment 31: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the component ion mass is substantially equal to the characteristic ion mass of one of the one or more ions determined to be in the sample, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of comparing the intensity maxima for the component ion at the characteristic component ion retention time, to the intensity maxima for the one of the one or more ions determined to be in the sample at the characteristic retention time, wherein if the intensity maxima for the component ion and the one of the one or more ions determined to be in the sample are substantially similar, then the one of the one or more ions determined to be in the sample is designated as an artifact ion in the sample.
Embodiment 32: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the anchor sample comprises water.
Embodiment 33: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of analyzing the plurality of samples in the sample run to determine a presence of one of the one or more ions from the ion data repository determined to be present in a first one of the plurality of samples, across the plurality of samples, wherein if a threshold quantity of the samples in the plurality of samples does not include the one of the one or more ions from the ion data repository determined to be present in the first one of the plurality of samples, then the one of the one or more ions determined to be present in the first one of the plurality of samples is designated as sparse ion in the plurality of samples.
Embodiment 34: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the steps of analyzing data obtained from the component separation and mass spectrometer system for each sample to determine a relationship between sample ion mass, retention time, and intensity, including intensity as a function of retention time for a selected sample ion mass, the selected sample ion mass being selected via the user interface; analyzing the intensity as the function of retention time for the selected sample ion mass for each of the samples, across the plurality of samples, to identify an intensity maxima within a predicted range of retention times for each sample, the predicted range of retention times including an expected intensity maxima retention time therein for the selected sample ion mass; identifying, for each sample, an actual retention time of the intensity maxima in relation to the expected intensity maxima retention time; and determining whether the actual retention times of the intensity maxima of two or more consecutive samples of the plurality of samples in the sample run demonstrate an identifiable pattern with respect to the expected intensity maxima retention time.
Embodiment 35: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the identifiable pattern of the actual retention times of the intensity maxima of the two or more consecutive samples, with respect to the expected intensity maxima retention time, comprises a shift wherein the actual retention times of the intensity maxima are substantially consistently offset from the expected intensity maxima retention time, or a drift wherein the actual retention times of the intensity maxima are offset by a non-constant function from the expected intensity maxima retention time, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of correcting the offset of the actual retention time of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern.
Embodiment 36: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the identifiable pattern of the actual retention times of the intensity maxima of the two or more consecutive samples, with respect to the expected intensity maxima retention time, comprises an offset from the expected intensity maxima retention time, the offset differing between two subsets of two or more consecutive samples in the sample run, and wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of correcting the offset of the actual retention times of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern of one of the two subsets having a majority of the samples in the sample run.
Embodiment 37: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein, if comparing data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample results in none of the one or more ions being present in the sample, the memory stores executable instructions that, in response to execution by the processor, then cause the apparatus to further perform the step of resolving an instrument error associated with the component separation and mass spectrometer system and re-running the sample through the component separation and mass spectrometer system to obtain replacement data for the sample.
Embodiment 38: The apparatus of any preceding embodiment, or any combination of preceding embodiments, wherein the memory stores executable instructions that, in response to execution by the processor, cause the apparatus to further perform the step of displaying, on the display associated with the user interface, the corrected offset of the actual retention time of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern to provide a visualization of the corrected actual retention time of the intensity maxima of each of the plurality of samples across the plurality of samples in the sample run.
Embodiment 39: A computer program product for analyzing data for a sample having a known characteristic, the data for the sample being obtained from a component separation and mass spectrometer system, the computer program product comprising at least one non-transitory computer readable storage medium having computer-readable program code stored thereon, the computer-readable program code comprising program code for performing the steps of analyzing data obtained from the component separation and mass spectrometer system for a reference ion, to determine a relationship between reference ion mass, retention time, and intensity, including intensity as a function of retention time for the reference ion mass, the reference ion having an intensity maxima at a characteristic retention time for the reference ion mass; adding the analyzed data for the reference ion to an ion data repository, each of the ions in the ion data repository having an intensity maxima within a range of characteristic retention times for a characteristic ion mass; modifying, if the reference ion was previously included in the ion data repository, the range of characteristic retention times of the reference ion in the ion data repository, according to the characteristic retention time of the intensity maxima for the reference ion; selecting, via a user interface associated with the apparatus, one or more ions from the ion data repository expected to be included in the sample based on the known characteristic of the sample; comparing, on a display associated with the user interface, data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample; and modifying, via the user interface, the range of characteristic retention times of each of the one or more ions determined to be present in the sample, in the data repository, according to the characteristic retention time of the intensity maxima for a respective one of the one or more ions determined to be present in the sample.
Embodiment 40: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the reference ion is included in the sample.
Embodiment 41: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for analyzing data obtained from the component separation and mass spectrometer system for the sample to determine a relationship between sample ion mass, retention time, and intensity, including intensity as a function of retention time for a selected sample ion mass, the selected sample ion mass being selected via the user interface; selecting, via the user interface, an ion present in the data for the sample, the selected ion having an intensity maxima at a characteristic retention time for the selected sample ion mass; comparing the data for the selected ion to the selected one or more ions in the ion data repository expected to be included in the sample based on the known characteristic of the sample, in order to determine an identity of the selected ion; and modifying the range of characteristic retention times of the ion in the ion data repository corresponding to the selected ion, according to the characteristic retention time of the intensity maxima for the selected ion.
Embodiment 42: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for querying the ion data repository via the user interface to select the one or more ions therefrom based upon a retention time of an intensity maxima of a selected ion from the data for the sample in relation to the range of characteristic retention times of the intensity maxima of the one or more ions in the ion data repository.
Embodiment 43: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the computer program product comprises program code for selecting the one or more ions from the ion data repository in relation to ions determined to be present in a first one of the plurality of samples, the selected one or more ions related to ions determined to be present in a first one of the plurality of samples being used for comparison to the data for a remainder of the samples in the sample run.
Embodiment 44: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for comparing a two dimensional plot of intensity as a function of retention time for the sample to a two dimensional plot of intensity as a function of retention time for each of the one or more ions selected from the ion data repository so as to provide a visual indication of intensity maxima therebetween for determining whether any of the one or more ions is present in the sample.
Embodiment 45: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for comparing, on the display, a two dimensional plot of intensity as a function of retention time for the sample to a two dimensional plot of intensity as a function of retention time for each of the one or more ions selected from the ion data repository so as to provide a visual indication of intensity maxima therebetween for determining whether any of the one or more ions is present in the sample.
Embodiment 46: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for modifying, if the reference ion was previously included in the ion data repository, the range of characteristic retention times of the reference ion in the ion data repository, according to the characteristic retention time of the intensity maxima for the reference ion comprises reducing the range of characteristic retention times if the characteristic retention time of the intensity maxima for the reference ion is within the range of characteristic retention times; and determining whether any data deviation factors in the component separation and mass spectrometer system require consideration if the characteristic retention time of the intensity maxima for the reference ion is outside the range of characteristic retention times.
Embodiment 47: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the relationship between reference ion mass, retention time, and intensity, includes intensity as a function of the reference ion mass for a selected retention time, and wherein the computer program product comprises program code for adding the analyzed data for the reference ion to an ion data repository such that each of the ions in the ion data repository have the intensity maxima within a range of characteristic ion masses for a characteristic retention time; and modifying, if the reference ion was previously included in the ion data repository, the range of characteristic ion masses of the reference ion in the ion data repository, according to the characteristic ion mass of the intensity maxima for the reference ion.
Embodiment 48: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for comparing the known characteristic to empirical data included in the ion data repository, the empirical data including relational information between known characteristics and ions; and determining therefrom the one or more ions corresponding to the known characteristic of the sample.
Embodiment 49: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein, after comparing data for the sample to data for the one or more ions from the ion data repository and determining whether any of the one or more ions is present in the sample, the computer program product comprises program code for adding empirical data associated with the sample to the ion data repository in relation to the any of the one or more ions determined to be present in the sample.
Embodiment 50: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for analyzing data obtained from the component separation and mass spectrometer system for an anchor sample, the anchor sample being defined as a consistent, previously-characterized sample, to determine a component ion of the anchor sample and a relationship between component ion mass, retention time, and intensity, including intensity as a function of retention time for the component ion mass, the component ion having an intensity maxima at a characteristic component ion retention time for the component ion mass.
Embodiment 51: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the component ion mass is substantially equal to the characteristic ion mass of one of the one or more ions determined to be in the sample, and wherein the computer program product comprises program code for comparing the intensity maxima for the component ion at the characteristic component ion retention time, to the intensity maxima for the one of the one or more ions determined to be in the sample at the characteristic retention time, wherein if the intensity maxima for the component ion and the one of the one or more ions determined to be in the sample are substantially similar, then the one of the one or more ions determined to be in the sample is designated as an artifact ion in the sample.
Embodiment 52: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the anchor sample comprises water.
Embodiment 53: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the computer program product comprises program code for analyzing the plurality of samples in the sample run to determine a presence of one of the one or more ions from the ion data repository determined to be present in a first one of the plurality of samples, across the plurality of samples, wherein if a threshold quantity of the samples in the plurality of samples does not include the one of the one or more ions from the ion data repository determined to be present in the first one of the plurality of samples, then the one of the one or more ions determined to be present in the first one of the plurality of samples is designated as sparse ion in the plurality of samples.
Embodiment 54: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the sample comprises a plurality of samples in a sample run, and wherein the computer program product comprises program code for analyzing data obtained from the component separation and mass spectrometer system for each sample to determine a relationship between sample ion mass, retention time, and intensity, including intensity as a function of retention time for a selected sample ion mass, the selected sample ion mass being selected via the user interface; analyzing the intensity as the function of retention time for the selected sample ion mass for each of the samples, across the plurality of samples, to identify an intensity maxima within a predicted range of retention times for each sample, the predicted range of retention times including an expected intensity maxima retention time therein for the selected sample ion mass; identifying, for each sample, an actual retention time of the intensity maxima in relation to the expected intensity maxima retention time; and determining whether the actual retention times of the intensity maxima of two or more consecutive samples of the plurality of samples in the sample run demonstrate an identifiable pattern with respect to the expected intensity maxima retention time.
Embodiment 55: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the identifiable pattern of the actual retention times of the intensity maxima of the two or more consecutive samples, with respect to the expected intensity maxima retention time, comprises a shift wherein the actual retention times of the intensity maxima are substantially consistently offset from the expected intensity maxima retention time, or a drift wherein the actual retention times of the intensity maxima are offset by a non-constant function from the expected intensity maxima retention time, and wherein the computer program product comprises program code for correcting the offset of the actual retention time of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern.
Embodiment 56: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the identifiable pattern of the actual retention times of the intensity maxima of the two or more consecutive samples, with respect to the expected intensity maxima retention time, comprises an offset from the expected intensity maxima retention time, the offset differing between two subsets of two or more consecutive samples in the sample run, and wherein the computer program product comprises program code for correcting the offset of the actual retention times of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern of one of the two subsets having a majority of the samples in the sample run.
Embodiment 57: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein, if comparing data obtained from the component separation and mass spectrometer system for the sample to data for each of the one or more ions selected from the ion data repository to determine whether any of the one or more ions is present in the sample results in none of the one or more ions being present in the sample, the computer program product comprises program code for then resolving an instrument error associated with the component separation and mass spectrometer system and re-running the sample through the component separation and mass spectrometer system to obtain replacement data for the sample.
Embodiment 58: The computer program product of any preceding embodiment, or any combination of preceding embodiments, wherein the computer program product comprises program code for displaying, on the display associated with the user interface, the corrected offset of the actual retention time of the intensity maxima of each of the plurality of samples in the sample run according to the identifiable pattern to provide a visualization of the corrected actual retention time of the intensity maxima of each of the plurality of samples across the plurality of samples in the sample run.

These and other features, aspects, and advantages of the present disclosure will be apparent from a reading of the following detailed description together with the accompanying drawings, which are briefly described below. The present disclosure includes any combination of two, three, four, or more features or elements set forth in this disclosure or recited in any one or more of the claims, regardless of whether such features or elements are expressly combined or otherwise recited in a specific embodiment description or claim herein. This disclosure is intended to be read holistically such that any separable features or elements of the disclosure, in any of its aspects and embodiments, should be viewed as intended to be combinable, unless the context of the disclosure clearly dictates otherwise.

Thus, the apparatuses, methods, and computer program products for analyzing data for a sample having a known characteristic, with the data being obtained from a component separation and mass spectrometer system and according to aspects of the present disclosure provide these and other advantages, as detailed further herein. Importantly, these advantages include the ability to dynamically and autonomously identify and verify ions, compounds or other components present in a sample having a known characteristic, with increased quality and consistency of analysis results. These advantages also include the capability of increasing curation/verification speed for identified ions, compounds or components of the sample, while lowering the manual manipulation of data required for verification/curation, for example, by providing a visual verification process.

