Ms2-driven deconvolution of ms1 peaks that are co-eluting and isobaric, for improved accuracy and quantitation of compounds

Abstract

In one aspect, a method of performing mass spectrometry is disclosed, which includes ionizing a sample received from an analyte-delivery device to generate one or more precursor ions, acquiring a precursor ion signal associated with said one or more precursor ions, passing the plurality of precursor ions through a mass filter as an m / z window of the mass filter is scanned so as to select different subsets of the precursor ions having m / z values within different m / z ranges of the scanning m / z window, generating one or more derivative ions of said subsets of the precursor ions exiting the mass filter, acquiring at least one derivative ion signal associated with said one or more derivative ions, and deconvolving the at least one precursor ion signal utilizing the at least one precursor ion signal and the at least one derivative ion signal, to produce a deconvolved precursor ion signal.

Description

MS2-DRIVEN DECONVOLUTION OF MSI PEAKS THAT ARE CO-ELUTING AND ISOBARIC, FOR IMPROVED ACCURACY AND QUANTITATION OF COMPOUNDSTECHNICAL FIELD

[0001] The present disclosure relates generally to mass spectrometry and in particular to methods and systems for analysis of mass spectral data.BACKGROUND

[0002] Mass spectrometry (MS) is an analytical technique for determining the structure of test chemical substances with both qualitative and quantitative applications. MS can be useful for identifying unknown compounds, determining the composition of atomic elements in a molecule, determining the structure of a compound by observing its fragmentation, and quantifying the amount of a particular chemical compound in a mixed sample. Mass spectrometers detect chemical entities as ions such that a conversion of the analytes to charged ions must occur.

[0003] An advanced type of mass spectrometry, generally known as tandem mass spectrometry, employs multiple stages of mass analysis for providing detailed structural information about molecules. In one example of a two-stage mass spectrometry, one or more analytes within a sample under analysis are ionized to generate a plurality of precursor ions and a mass filter is utilized to select those precursor ions having mass-to-charge ratios within a bandpass of the mass filter. Subsequently, the selected precursor ions are fragmented to generate fragment ions and a mass spectrum of the fragment ions is acquired and analyzed to obtain information about the analytes.

[0004] Recent advances in mass spectrometry have allowed its use in analysis of complex samples, e.g., in proteomic and metabolomic analysis. Complex samples, however, typically contain analytes with highly similar masses. Depending on the chromatographic and MS acquisition methods employed for analysis, such samples may exhibit overlapping elution times, which may result in co-fragmentation of the respective precursor ions and hence result in chimeric MS2 spectra.

[0005] Although several techniques are known for the deconvolution of such chimeric MS2 spectra and thus enable annotation and quantification of the analytes based on MS214913-8006-3335, v. 2spectra, there is still a need for enhanced methods and systems for analysis of complex samples using mass spectrometry.SUMMARY

[0006] In one aspect, a method for mass spectral data analysis is disclosed, which includes acquiring at least one precursor ion signal associated with one or more precursor ions, acquiring at least one derivative ion signal associated with one or more derivative ions of said one or more precursor ions, and deconvolving the at least one precursor ion signal utilizing the at least one precursor ion signal and the at least one derivative ion signal, to produce a deconvolved precursor ion signal.

[0007] In various embodiments, the deconvolution of the at least one precursor ion signal can provide information regarding precursor ion purity, e.g., whether a sample under analysis includes a single precursor ion or multiple precursor ions. In various embodiments, such information can be utilized to set a precursor ion tolerance (uncertainty) for a set of fragment ions that are related to the precursor ion, which can in turn be utilized in downstream processing to improve compound identification, e.g., by assigning a “quality measure” for precursor ion m / z or precursor ion quantity.

[0008] In various embodiments, the at least one derivative ion signal corresponds to one or more ion fragments generated due to dissociation of said one or more precursor ions.

[0009] In various embodiments, the at least one derivative ion signal corresponds to at least one neutral loss ion from at least one of the derivative ions.

[0010] In various embodiments, the at least one derivative ion signal corresponds to at least one adduct ion.

[0011] In various embodiments, the step of utilizing the at least one precursor ion signal and the at least one derivative ion signal to deconvolve the at least one precursor ion signal includes deriving a set of basis derivative ion signal profiles suitable for representing said at least one derivative ion signal as a linear combination of the basis derivative ion signal profiles and utilizing the basis derivative ion signal profiles to deconvolve said at least one precursor ion signal.24913-8006-3335, v. 2

[0012] In various embodiments, the step of deconvolving said at least one precursor ion signal includes determining a number of distinct types of precursor ions in said one or more precursor ions and a relative abundance of each of said distinct types of the precursor ions.

[0013] In various embodiments, the at least one precursor ion signal can be represented as a linear combination of the basis derivative ion signal profiles. The coefficients of the linear combination of the basis derivative ion signal profiles can be employed to determine the relative abundance of the distinct types of the precursor ions.

[0014] In various embodiments, the step of deconvolving the at least one precursor ion signal includes determining an elution time of at least one of the plurality of precursor ions from a chromatography device, such as a liquid chromatography column.

[0015] In various embodiments, the step of deconvolving the at least one precursor ion signal includes determining an m / z value of at least one of the plurality of precursor ions. For example, the deconvolved precursor ion signal can be employed to acquire more accurate m / z values for the plurality of precursor ions. By way of example, in some embodiments, a two- dimensional precursor ion signal in which one of the dimensions is the mass-to-charge ratio (m / z) may be deconvolved based on a respective two-dimensional fragment ion signal and the deconvolved precursor ion signal may be employed to derive more accurate values for the m / z ratios of the precursor ions.

[0016] In various embodiments, the accurate values of the m / z ratios of the precursor ions can be employed to identify one or more of those precursor ions. By way of example, such identification of the precursor ions can be achieved by using a reference compound library. The more accurate m / z ratios facilitate the identification of the precursor ions in the library, and in some cases, can allow distinguishing the precursor ion from another compound with a similar m / z ratio.

[0017] In various embodiments, the at least one precursor ion signal provides at least one precursor ion intensity as a function of a variable. Further, in various embodiments, the at least one derivative ion signal provides at least one derivative ion intensity as a function of that variable. By way of example, and without limitation, the variable can be any of time, m / z and ion mobility.

[0018] In various embodiments, the at least one derivative ion signal can include a plurality of derivative ion intensity peaks. In some such embodiments, such derivative ion34913-8006-3335, v. 2intensity peaks can be segregated into two or more subsets such that each subset is associated with a different setting of a measurement parameter associated with the precursor ions. By way of example, the measurement parameter can be any of a mass-to-charge ratio (m / z) and an ion mobility of the precursor ions. For example, a setting of the m / z can correspond to a specific value or a range of values for m / z associated with at least a portion of the plurality of the precursor ions. By way of another example, a setting of the ion mobility can correspond to a specific value or a range of values for ion mobility associated with at least a portion of the plurality of the precursor ions.

[0019] In various embodiments, a plurality of representative derivative ion signal profiles is generated, where each representative profile corresponds to one of the subsets of the segregated derivative ion signal profiles. In some such embodiments, the derivative ion basis profiles can be generated based on the representative derivative ion signal profiles. In various embodiments, the on

[0020] or more derivative ions can include one or more fragment ions of the precursor ions and the fragment ion mass peaks in each subset of the segregated fragment ion mass peaks are associated with the same (or substantially the same) or a different m / z setting of a mass filter providing the precursor ions. By way of example, the m / z setting of the mass filter can correspond to an m / z bandpass of the mass filter, which can be, for example, a quadrupole or a hexapole mass filter. In particular, the m / z setting of a mass filter can be the same or substantially the same for two isobaric precursor ions. In various embodiments, the methods of the present teachings allow the deconvolution of MS 1 spectrum of such isobaric species based on the MS2 data.

[0021] In various embodiments, the at least one precursor ion signal includes an extracted ion chromatogram associated with the one or more precursor ions (“precursor ions XIC”). Further, in various such embodiments, the at least one fragment ion signal includes an extracted ion chromatogram associated with the one or more fragment ions (“fragment ions XIC”).

[0022] In various embodiments, the one or more precursor ions are generated via ionization of one or more analytes provided by an analyte delivery device. By way of example, and without limitation, such an analyte delivery device can be a liquid chromatography (LC) column, and / or an open port interface (OPI).4913-8006-3335, v. 2

[0023] In various embodiments, the one or more precursor ions are received from an ion separation device. By way of example, such an ion separation device can be any of an ion mobility spectrometer (IMS), a mass filter and a combination thereof.

[0024] In various embodiments, a digital data processor is employed to perform the deconvolution of the at least one precursor ion signal based one the data contained in one or more derivative ion signals. The deconvolved precursor ion signals and / or information regarding the precursor ions, such as the number of distinct precursor ions and relative abundances, can be presented to a user.

[0025] In various embodiments, the methods according to the present teachings are particularly useful for the deconvolution of precursor ion signal generated by isobaric compounds, e.g., those eluting from a chromatographic separation device during overlapping temporal periods.

[0026] In a related aspect, a computer program product is disclosed, which includes a non-transitory and tangible computer readable storage medium storing a program with instructions for execution on a processor so as to perform a method for analysis of mass spectral data. The method performed by the computer program product in turn includes receiving at least one precursor ion signal associated with one or more precursor ions, receiving at least one derivative ion signal associated with one or more derivative ions of said one or more precursor ions, and deconvolving the at least one precursor ion signal utilizing the at least one precursor ion signal and the at least one derivative ion signal, to produce a deconvolved precursor ion signal.

[0027] In various embodiments of the computer program product, the step of utilizing the at least one precursor ion signal and the at least one derivative ion signal to deconvolve the at least one precursor ion signal includes deriving a set of basis derivative ion signal profiles suitable for representing said at least one derivative ion signal as a linear combination of the basis derivative ion signal profiles, and utilizing the basis derivative ion signal profiles to deconvolve said at least one precursor ion signal.

[0028] In various embodiments of the computer program product, the step of deconvolving the at least one precursor ion signal can include determining a number of distinct types of precursor ions associated with the one or more precursor ions and a relative abundance of each of said distinct types of the precursor ions.54913-8006-3335, v. 2

[0029] In various embodiments of the computer program product, the method further includes representing the at least one precursor ion signal as a linear combination of the basis derivative ion signal profiles and utilizing coefficients of the linear combination to determine the relative abundance of each of said distinct types of the precursor ions.

[0030] In various embodiments of the computer program product, the step of deconvolving the at least one precursor ion signal includes determining an elution time of at least one of said plurality of precursor ions from a chromatography device, e.g., from a liquid chromatography column.

[0031] In various embodiments of the computer program product, the at least one precursor ion signal and the at least one derivative ion signal are two-dimensional ion signals, where one dimension corresponds to the m / z of the ions.

[0032] In various embodiments of the computer program product, the at least one precursor ion signal provides at least one precursor ion intensity as a function of a variable, e.g., as a function of m / z or ion mobility. Further, the least one derivative ion signal can be in the form of a derivative ion intensity as a function of that variable, e.g., as a function of m / z or ion mobility.

[0033] By way of example, such a derivative ion signal can be represented as a plurality of derivative ion intensity peaks as a function of that variable. In various embodiments of the computer program product, the method can further include segregating the derivative ion intensity peaks into two or more subsets such that each subset is associated with a different setting of at least one measurement parameter, such as m / z or ion mobility. By way of example, the m / z parameter can specify a specific value or a range of values of m / z associated with at least a portion of said plurality of precursor ions. By way of another example, the ion mobility parameter can specify a specific value or a range of values for ion mobility associated with at least a portion of said plurality of precursor ions.

[0034] In various embodiments of the computer program product, the method can further include generating a plurality of representative derivative ion signal profiles each corresponding to one of said subsets and deriving said derivative ion basis profiles from said plurality of representative derivative ion signal profiles. By way of example, the one or more derivative ions can include one or more fragment ions of the precursor ions and the fragment ion mass peaks in each of the subsets can be associated with the same (or substantially the same) or a different m / z setting of a mass filter providing the one or more precursor ions. By64913-8006-3335, v. 2way of example, the m / z setting of the mass filter can correspond to an m / z bandpass of the mass filter (e.g., a quadrupole or a hexapole mass filter).

[0035] In a related aspect, a method of performing mass spectrometry is disclosed, which includes ionizing a sample received from an analyte-delivery device to generate one or more precursor ions, acquiring a precursor ion signal associated with said one or more precursor ions, passing the plurality of precursor ions through a mass filter as an m / z window of the mass filter is scanned so as to select different subsets of the precursor ions having m / z values within different m / z ranges of the scanning m / z window, generating one or more derivative ions of said subsets of the precursor ions exiting the mass filter, acquiring at least one derivative ion signal associated with said one or more derivative ions, and deconvolving the at least one precursor ion signal utilizing the at least one precursor ion signal and the at least one derivative ion signal, to produce a deconvolved precursor ion signal.

[0036] In various aspects of the above method, the step of utilizing the at least one precursor ion signal and the at least one derivative ion signal to deconvolve the at least one precursor ion signal includes deriving a set of basis derivative ion signal profiles suitable for representing said at least one derivative ion signal as a linear combination of the basis derivative ion signal profiles, and utilizing said basis derivative ion signal profiles to deconvolve said at least one precursor ion signal. By way of example, the analyte-delivery device can include a liquid chromatography column and / or an open port interface (OPI).

[0037] In various embodiments of the above method, the derivative ions can include fragment ions that are generated via fragmentation of the subsets of the precursor ions exiting the mass filter.

[0038] In various embodiments, the derivative ions can include fragment ions that are generated via fragmentation of the subsets of the precursor ions exiting the mass filter and the derivative ion signal can be a fragment ions signal including one or more ion intensity peaks. In various embodiments, the fragment ions intensity peaks can be segregated into one or more fragment ion signal subsets such that each of the fragment ions signal subsets is associated with one of the subsets of the precursor ions. In some such cases, a representative fragment ions signal profile for each of the fragment ions signal subsets can be determined to produce a plurality of representative fragment ions signal profiles. The representative fragment ions signal profiles can then be utilized to derive the set of basis derivative ion signal profiles.74913-8006-3335, v. 2

[0039] In a related aspect, a mass spectrometer is disclosed, which includes an ion source for ionizing a sample to generate a plurality of precursor ions, a mass filter configured to allow passage of at least one subset of the plurality of precursor ions having one or more m / z ratios within an m / z window of the mass filter therethrough, a device for receiving said at least one subset of the precursor ions and generating one or more derivative ions of said precursor ions, a mass analyzer configured to generate at least one precursor ions signal associated with said precursor ions and at least one derivative ions signal associated with said derivative ions, and a data analysis module. The data analysis module is configured to receive the at least one precursor ions signal and the at least one fragment ions signal, and deconvolve the at least one precursor ions signal utilizing the at least one precursor ions signal and the at least one derivative ion signal, to produce a deconvolved precursor ions signal.

[0040] In various embodiments of the mass spectrometer, the device for generating the derivative ions comprises an ion fragmentation device.

[0041] In various embodiments, the mass spectrometer can further include a controller that is in communication with the mass filter to cause scanning an m / z window associated with the mass filter over an m / z range.

[0042] Further understanding of various aspects of the present teachings can be obtained with reference to the following detailed description in conjunction with the associated drawings, which are described briefly below.BRIEF DESCRIPTION OF THE DRAWINGS

[0043] FIG. 1 is a flow chart depicting various steps of an embodiment of a computer- implemented method according to the present teachings for analysis of mass spectral data,

[0044] FIG. 2 schematically depicts the representation of a precursor ions profile as a linear combination of a plurality of basis ion profiles,

[0045] FIG. 3A shows a survey (MSI) mass spectrum corresponding to a plurality of precursor ions generated via ionization of a plurality of analytes in a sample under analysis,

[0046] FIG. 3B shows an XIC signal associated with the precursor ions depicted in FIG. 3A,84913-8006-3335, v. 2

[0047] FIG. 3C shows a tandem (MS2) spectrum as a plot of intensity of fragment ions generated due to dissociation of the precursor ions identified in the survey spectrum of FIG. 3A as a function of their m / z values,

[0048] FIG. 3D shows the segregation of the fragment ion peaks depicted in FIG. 3C into two groups via correlating the variation of the intensity of the peaks with an m / z associated with the scanning transmission window of a mass filter,

[0049] FIGS. 3E and 3F show correlation plots depicting association of each of the fragment ion signals depicted in FIGS. 3C and 3D with a precursor ion,

[0050] FIGS. 3G and 3H show XIC signals corresponding to the two groups of the fragment ions identified in FIG. 3D,

[0051] FIG. 4A shows a heat map of two convolved precursor ions,

[0052] FIG. 4B shows measured spectral peak centroids across LC time as well as true m / z ratios of the two precursors ions associated with the heat map of FIG. 4A,

[0053] FIG. 4C shows measured and deconvolved spectra of the two precursor ions corresponding to LC peak apex,

[0054] FIG. 4D shows the LC profile of the measured and deconvolved precursor ions,

[0055] FIG. 5 is a block diagram of a computer system configured to implement spectral analysis methods according to various embodiments of the present teachings,

[0056] FIG. 6 schematically depicts a mass spectrometer according to an embodiment of the present teachings, and

[0057] FIG. 7 shows a schematic pictorial example of the use of the present teachings for deconvolving a precursor ion signal associated with a plurality of precursor ions.DETAILED DESCRIPTION

[0058] It will be appreciated that for clarity, the following discussion will explicate various aspects of embodiments of the applicant’s teachings, while omitting certain specific details wherever convenient or appropriate to do so. For example, discussion of like or analogous features in alternative embodiments may be somewhat abbreviated. Well-known ideas or concepts may also for brevity not be discussed in any great detail. The skilled person will recognize that some embodiments of the applicant’s teachings may not require certain of94913-8006-3335, v. 2the specifically described details in every implementation, which are set forth herein only to provide a thorough understanding of the embodiments. Similarly, it will be apparent that the described embodiments may be susceptible to alteration or variation according to common general knowledge without departing from the scope of the disclosure. The following detailed description of embodiments is not to be regarded as limiting the scope of the applicant’s teachings in any manner.

[0059] As used herein, the terms "about" and "substantially equal" refer to variations in a numerical quantity that can occur, for example, through measuring or handling procedures in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of compositions or reagents; and the like. Typically, the terms "about" and "substantially" as used herein means 10% greater or less than the value or range of values stated or the complete condition or state. For instance, a concentration value of about 30% or substantially equal to 30% can mean a concentration between 27% and 33%. The terms also refer to variations that would be recognized by one skilled in the art as being equivalent so long as such variations do not encompass known values practiced by the prior art.

[0060] As used herein the term "and / or" includes any and all combinations of one or more of the associated listed items and may be abbreviated as " / ".

[0061] The term “a derivative ion” as used herein refers to an ion that is formed from a precursor ion, e.g., via chemical or physical processes. By way of example, as used herein, product ions generated via dissociation of a precursor ion can be considered as the derivatives of the precursor ion. By way of another example, a charge reduced species generated via a charge reduction of a precursor ion can be considered as a derivative of the precursor ion. By way of further illustration, a derivative ion can be generated via addition of one or more functional groups to a precursor ion.

[0062] In the following discussion, the term “MS 1 spectrum” refers to a spectrum, such as an m / z spectrum of one or more precursor ions generated, e.g., via ionization of one or more analytes in a sample, and the term “MS2 spectrum” refers to a spectrum, such as an m / z spectrum or an XIC, of one or more derivative ions generated from the precursor ions, e.g., via dissociation of the precursor ions.

[0063] In tandem mass spectrometry of complex samples, such as in proteomic or metabolomic studies, analysis of analytes having highly similar masses, such as isobaric104913-8006-3335, v. 2species, can pose certain challenges. For example, an overlap between elution periods of such similar compounds from an LC column (which is herein referred to as co-elution of such compounds) can result in chimeric MS2 spectra (e.g., the fragmentation spectra containing derivative ion signals corresponding to different precursor ions). Further, in some cases, different precursor ions can lead to fragment ions having the same m / z ratios (i.e., shared fragment ions). Further, even though different precursor ions may provide unique derivative ion signals (e.g., non-overlapping derivative ion signals), the derivative ion signals (such as fragment ion signals) corresponding to different precursor ions can result in chimeric MS2 spectra that can be difficult to interpret. As discussed in more detail below, in various embodiments, LC decomposition (or clustering of fragment XICs) can be utilized to separate the spectrum into multiple sets of fragment ion signals, each corresponding to one of the precursor ions. For example, the unique XIC profiles of fragment ions corresponding to each precursor ion can be employed to separate the fragment ions signals into distinct groups, each corresponding to one of the precursor ions.

[0064] Although existing techniques are available for deconvolution of such MS2 spectra, there is a need for methods and systems that would allow deconvolution of MS 1 spectra based only on the analysis of MS2 data and without the need for consulting library databases. In other words, there is a need for methods and systems of mass spectral analysis that can employ information contained in one or more derivative ion signals obtained in tandem mass spectrometry to deconvolve MSI spectra, such as XIC profiles of a set of precursor ions.

[0065] By way of example, the MS 1 elution peak symmetry can be affected by the presence of one or more analytes with similar masses in a narrow elution range. Often, such elution peaks are used to either identify and quantitate a single compound, typically the most abundant compound, or identify multiple compounds with approximated MSI quantities. Alternatively, the asymmetry of the elution peak may be deemed as being due to interference on the primary compound and used to adjust the peak integration or may be removed from further analysis.

[0066] The above shortcomings in the conventional methods for analysis of complex compounds are not limited to tandem mass spectrometry methods that employ chromatographic separation of analytes prior to their mass analysis. For example, analyte ions having similar ion mobilities may not be resolved via passage through an ion mobility114913-8006-3335, v. 2spectrometer (IMS). In such cases, the present teachings can be utilized to deconvolve precursor ions mobility signals based on the information contained in the signals related to derivative ions (e.g., fragment ions) derived from the precursor ions. For example, an MSI spectrum containing mobility data of a plurality of precursor ions can be deconvolved based on the information contained in MS2 spectrum of derivative ions corresponding to those precursor ions.

[0067] As discussed in more detail below, in various embodiments, the information contained within MS2 data can be utilized to explain MSI data. By way of example, in various embodiments, MS2 data can be utilized to elucidate MSI peak properties of precursor ions, such as accurate m / z, time of elution, quantity, etc. For example, the determination of an accurate m / z of one or more precursor ions associated with the precursor ion signal can facilitate identification of those precursor ions, e.g., by using a reference compound library. In various embodiments, the information contained in MS2 data can be utilized to elucidate all precursor ions in a sample, including those precursor ions that can be detected in MS 1 spectra using conventional methods as well as those precursor ions that may not be detectable using conventional methods. For example, the MS2 data can provide evidence for an m / z of a precursor ion, where the MSI precursor ion signal is below the detection limit of a mass spectrometer providing the MS 2 data.

[0068] For example, in embodiments in which chromatographic separation of compounds is used prior to their mass analysis, MS2 attributes of distinct ions populations in the elution region can be utilized to deconvolve MSI elution peak to determine various attributes of the precursor ions, such as the number of distinct precursor ions associated with an elution peak, their relative abundances, their m / z values, elution peak height, etc. In some cases, at least some of these parameters associated with distinct precursor ions can be close, or even identical. For example, two isobaric species can have the same m / z values. By way of example, various embodiments allow accurate identification and MS 1 quantification of all compounds in the elution region with distinct MS2 evidence. Subsequently, additional statistics on peak purity can be derived for each elution peak based on its constituents. By way of example, in various embodiments, the present teachings make it possible to determine whether a peak is a monoisotopic or an isotopic peak.

[0069] By way of example, in data-independent acquisition (DIA), precursor ions can be dissociated to generate fragment ions (e.g., Fl fragments in total). In various cases, some of124913-8006-3335, v. 2the fragment ions are unique to a particular precursor ion type while others are shared among various subsets of the precursor ions. As a result, MS / MS ions can define a set of intensity distributions across a set of measurement dimensions (e.g., LC), where some are unique for single precursors and some are varying linear combinations of the unique ones, where this set of distinct but linearly-dependent intensity distributions can have F2 elements, where F2 <= Fl. In various embodiments, applying any Independent Component Analysis method, a minimal number and distribution patterns can be extracted for this set as “basis components,” where in many cases the number of the basis components F3 is less than F2. (The term “basis component” is also herein referred to as “basis ion signal profile” or “basis derivative ion signal profile”). In various embodiments, the basis components can be utilized to deconvolute MS 1 intensity distributions across one or more measurement dimensions.

[0070] By way of example, referring to the flow chart of FIG. 1, in an embodiment of a computer-implemented method according to the present teachings for analysis of mass spectral data, at least one precursor ion signal associated with one or more precursor ions and at least one derivative ion signal associated with one or more derivative ions of the one or more precursor ions are received by an analysis module, e.g., an analysis module of a mass spectrometer. The information contained in the at least one precursor ion signal and the at least one derivative ion signal can then be utilized to deconvolve the precursor ion signal so as to produce a deconvolved precursor ion signal.

[0071] By way of example, the derivative ion signal can be represented in the form of ion intensity as a function of a variable. By way of example, and without any loss of generality, the derivative ion signal can be in the form of ion intensity as a function of elution time or m / z, or other measurement parameters such as ion mobility. Again, by way of example and without loss of generality, the derivative ions can be fragment ions generated via fragmentation of a plurality of precursor ions generated via ionization of analytes eluting from an LC column.

[0072] In various embodiments, the derivative ion signal can be analyzed to compute, via a processor, a set of basis derivative ion signal profiles. For example, ion intensity peaks associated with the derivative ion signal, e.g., intensity peaks associated with fragment ions as a function of the elution time, can be processed to compute the set of basis derivative ion signal profiles such that each of the intensity peaks can be represented as a linear combination of the basis derivative ion signal profiles.134913-8006-3335, v. 2

[0073] Various methods for processing the derivative ion signal to compute the basis derivative ion signal profiles are known and can be employed in the practice of various embodiments of the present teachings. By way of example, statistical methods such as an Independent Component Analysis (ICA) can be utilized to derive the basis ion signal profiles. By way of example, ICA techniques known in the art, such as those described in Independent Component Analysis published by John Wiley & Sons, Inc. in 2001, which is herein Incorporated by reference in its entirety, can be utilized in the practice of the present teachings. By way of another example, the teachings of U.S. Patent No. 10,732,156 entitled “Multi-Trace Quantitation,” can be utilized to derive the basis ion signal profiles.

[0074] By way of illustration, FIG. 2 shows a precursor ions profile A, which may be, for example, a precursor XIC profile acquired for precursor ions obtained via ionization of an eluate exiting an LC column. Alternatively, the exemplary precursor ions profile A can be a precursor XIC profile obtained for ions exiting an ion mobility spectrometer. In this example, the dissociation of the precursor ions leads to formation of fragment ions exhibiting two sets of fragment ions intensity profiles (herein also referred to as “fragment profiles”) B and C. The segregation of the fragment profiles into the sets B and C can be achieved in a variety of different ways. For example, the fragment ions profiles can be segregated into the sets B and C based on unique XIC profiles of each set.

[0075] In some embodiments, for each of fragment ions sets, a representative profile can be computed, e.g., by averaging of the fragment ions profiles (such as a weighted average of the fragment ions profiles or selecting a profile having maximum XIC in the set, etc.). By way of example, the averaging of the fragment ion profiles can be achieved based on the teachings of an article entitled “Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition,” published in Nature Methods, 10, 1239-1245 (2013), which is herein incorporated by reference in its entirety. By way of another example, the teaching of PCT Application No. PCT / IB2024 / 052652 titled “Systems and methods for purity calculation for the compound QC workflow,” which is herein incorporated by reference in its entirety, as informed by the present teachings can be employed for obtain a representative profile for each of the fragment ions sets.

[0076] Profiles BR and CR are examples of such representative fragment ions profiles corresponding to sets B and C, respectively.144913-8006-3335, v. 2

[0077] In this example, the representative profiles BR and CR can then be employed to compute two basis ion signal profiles Basisl and Basis2. By way of example, an Independent Component Analysis (ICA) can be applied to the representative profiles BR and CR to derive the fragment basis ion signal intensity profiles Basisl and Basis2. Some techniques that can be utilized for processing of the fragment ions signal(s) to arrive at the basis ion signal intensity profiles are disclosed in U.S. Patent Nos. 7,587,285 (“Method for identifying correlated variables”), 8,180,581 (“Systems and methods for identifying correlated variables in large amounts of data”), 10,732,156 (“Multi-Trace Quantitation”), each of which is herein incorporated by reference in its entirety.

[0078] In some embodiments, rather than utilizing a representative of each fragment profile set, all of the fragment ion profiles in each set can be utilized for computing the basis profiles. Although the above example was described in connection with fragment ions signal profiles, the same principles apply to processing of other derivative ions signal profiles, such as adduct ions.

[0079] The precursor ions profile A can then be represented as a linear combination of the basis ion signal profiles (herein also referred to as “basis profiles”) Basisl and Basis2. By way of illustration, the scaling factors applied to the basis profiles Basisl and Basis2 in this example are referred to as al and a2. In various embodiments, in representing the precursor XIC profile A as a linear combination of the basis profiles Basisl and Basis2, for example, the scaling of the fragment basis ions signal profiles and the positioning of each of the basis ion signal profiles with respect to the elution time can be achieved using the methods disclosed, e.g., in U.S. Patent No. 10,732,156 (“the ‘156 Patent”) titled “Multi-Trace Quantitation,” which is herein incorporated by reference in its entirety. For example, an analytical model, such as that disclosed in the ‘156 Patent, can be used to optimize the scaling of the basis ion signal profiles and determine the elution time corresponding to the centroid of each of the basis ion signal profiles Basisl and Basis2 in representing the precursor ion signal profile A.

[0080] As noted above, such representation of the precursor signal profile (which in this example is an XIC signal) can then be utilized to deconvolve the precursor signal profile. More specifically, in this example, the number of basis ion signal profiles (e.g., two in the above example) indicates the presence of two distinct types of precursor ions in the precursor ions giving rise to the precursor signal profile. Moreover, the ratio of the scaling factors for154913-8006-3335, v. 2the two basis ion signal profiles can indicate the relative abundance of each of the precursor ion types. By way of illustration, in this example, the ratio ~~ provides a relativeabundance of one of the precursor ions within the precursor ions associated with the precursor ion signal.

[0081] Moreover, the representation of the ion precursor signal as a linear combination of the Basisl and Basis2 profiles allows a more accurate determination of the retention times associated with each of the two types of the precursor ions in this example. For example, the centroid of a scaled version of the Basisl basis profile providing a portion of the precursor XIC profile can correspond to the retention time of one of the two types of the precursor ions associated with that profile. Similarly, the retention time of the other type of the precursor ions can be determined based on the centroid of the Basis2 basis profile utilized to represent the XIC precursor ion profile. Moreover, as discussed in more detail below, the representation of the precursor ions signal as a linear combination of the basis profiles allows a more accurate determination of the m / z values of the precursor ions.

[0082] In various embodiments, fragment ions signals, e.g., the m / z signals associated with the fragment ions, can be segregated into one or more sets based on one or more correlation variables. For each set, a representative fragment ions signal can be derived and one or more ion basis profiles can be determined based on the representative fragment ion signals. The basis profiles can then be employed to deconvolve the precursor ion signal.

[0083] By way of further illustration, FIG. 3A shows a survey (MSI) mass spectrum corresponding to a plurality of precursor ions generated via ionization of a plurality of analytes in a sample under analysis, where the mass spectrum is represented as a plot of ion intensity as a function of mass-to-charge values at a given time. FIG. 3B, in turn, shows an XIC signal associated with the precursor ions, in a narrow m / z region around 580.82, depicted in FIG. 3A as a plot of ion intensity as a function of retention times of the analytes as the sample passes through an LC column.

[0084] FIG. 3C in turn shows a tandem (MS2) spectrum as a plot of intensity of fragment ions generated due to dissociation of the precursor ions identified as a function of their mass- to-charge values (only a subset of the acquired fragment ions is shown for illustrative purpose). In this example, the MS2 spectrum was generated using the SWATH data acquisition approach, which included scanning the mass transmission window of a mass filter164913-8006-3335, v. 2(herein referred to as the QI mass filter) receiving the precursor ions and fragmenting the ions exiting the mass filter.

[0085] In this example, with reference to FIG. 3D, the fragment ion signals depicted in FIG. 3C can be segregated into two sets, where one set (herein referred to as the first set) includes the fragment ions signals at m / z values of 217.1335, 245.1285 and 916.5098 and the other set (herein referred to as the second set) includes the fragment ion signals at m / z values of 339.1663, 691.3773, 861.4827, and 960.5502. By way of example, the segregation of the fragment ions signals into the two sets can be achieved by using the techniques described in U.S. Patent No. 10,068,753 (the ‘753 Patent) titled “Systems and methods for identifying precursor ions from product ions using arbitrary transmission windowing,” which is herein incorporated by reference in its entirety. In particular, the similarity between the fragment ions signal profiles associated with the same precursor ion and the difference between the fragment ions signal profiles associated with different precursor ions can be employed to segregate the fragment ions signals (e.g., fragment ions mass peaks) into different sets, where each set is associated with a particular precursor ion.

[0086] More specifically, based on the teachings of the ‘753 Patent, the variation of the intensity of each fragment ions signal as a function of an m / z of the transmission window (e.g., the m / z associated with the leading edge of the scanning transmission window) of the mass filter as the ion transmission window is scanned is plotted and the fragment ion signal is associated with a precursor ion having an m / z corresponding to the apex of the plot. FIGS. 3E and 3F depict such plots generated for the fragment ions, where the plots show that the fragment ions signals in the first set are associated with a precursor ion with an m / z of 581.003 and the fragment ions signals in the second set are associated with a precursor ion with an m / z of 580.998.

[0087] FIG. 3G shows the XIC signals corresponding to the fragment ions in the first set and FIG. 3H shows the XIC signals corresponding to the fragment ions in the second set.The segregation of the XIC profiles into two sets can be based on comparison of XIC profiles of the fragment ions. More specifically, XIC signals having the same profiles can be assigned to the same set. In other words, the XIC profiles in each set are similar while the XIC profiles between the two sets are different. The XIC signals in each set can be processed to compute a representative XIC signal for that set. For example, as discussed above, the representative XIC signal can be computed as a weighted average of the XIC signals, or the representative174913-8006-3335, v. 2XIC signal can be a signal with a maximum peak intensity, etc. Further, in some cases, rather than utilizing representative XIC signals from the two sets, all of the XIC signals in each set can be employed for deriving the basis ion signal profiles.

[0088] By way of example, the representative signals for the two sets can then be utilized to determine two basis ion signal profiles that can be in turn employed to deconvolve the precursor XIC signal. In this example, the precursor XIC signal can be represented as a linear combination of the two basis ion signal profiles to generate a deconvolved precursor XIC signal.

[0089] As discussed above, the deconvoluted precursor ion signal can be employed to derive information regarding various measurement parameters associated with the precursor ions signals, such as the number of distinct precursor ions present in the precursor ions giving rise to the precursor ion signal, the elution time (or the ion mobility) corresponding to the precursor ions, the height of elution peaks associated with analytes giving rise to the precursor ions, and more precise m / z values associated with the precursor ions. As noted above, in various embodiments, more precise m / z values can facilitate identification of the precursor ions, e.g., via a reference compound library.

[0090] By way of example, FIG. 4A shows a heat map of two convolved precursor ions (herein referred to as components A and B) with close mass and FIG. 4B shows the measured spectral peak centroids across LC time as well as the true m / z ratios of components A and B. For a given LC time, a vertical axis through the heat map provides an m / z spectrum corresponding to that LC time and for a given m / z value, the sum of heat map values along a horizontal axis provides XIC corresponding to that m / z value. At any point of time during LC, the measured centroid deviates from true values of m / z ratios of individual precursor components A and B. The plot shows that component B dominates in a temporal region around 7.2 minutes as in that region the measured peak centroid is closer to true m / z of component B. By way of comparison, FIG. 4E shows measured and deconvoluted spectra of components A and B corresponding to LC peak apex, illustrating that the deconvolution of the precursor spectrum into spectra corresponding to components A and B in a manner discussed herein allows computing more accurate m / z ratios for those components relative to the m / z ratios that can be derived from the measured convolved spectrum. FIG. 4B shows the representation of precursor ions XIC chromatogram as a linear superposition of the two basis profiles corresponding to A and B components. In other words, FIG. 4B shows that the184913-8006-3335, v. 2measured precursor ion signal constitutes two components as indicated by the component traces, where the precise precursor m / z values of the two components and their LC separation (e.g., based on LC elution time for each component) can be derived from the apex of the deconvoluted traces.

[0091] In above example, an MS 1 region of interest was selected and the MS / MS data was used to further analyze MS 1 data and refine the information gleaned purely from MS 1 data. This technique, which is also herein referred to as MS2 driven analysis, can be beneficial in that the MS2 driven analysis leads to the conclusion that two components are contributing to the MS 1 data, each having its unique signature.

[0092] In various embodiments, a computer system can be employed to implement the present teachings for performing a mass spectral analysis, and in particular for deconvolving an MS 1 spectrum based on spectral data contained in an MS2 spectrum.

[0093] By way of example, FIG. 5 is a block diagram that illustrates such a computer system 100, upon which embodiments of the present teachings may be implemented. Computer system 100 includes a bus 102 or other communication mechanism for communicating information, and a processor 104 coupled with bus 102 for processing information. Computer system 100 also includes a memory 106, which can be a random access memory (RAM) or other dynamic storage device, coupled to bus 102 for determining base calls, and instructions to be executed by processor 104. Memory 106 also may be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor 104. Computer system 100 further includes a read only memory (ROM) 108 or other static storage device coupled to bus 102 for storing static information and instructions for processor 104. A storage device 110, such as a magnetic disk or optical disk, is provided and coupled to bus 102 for storing information and instructions.

[0094] Computer system 100 may be coupled via bus 102 to a display 112, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 114, including alphanumeric and other keys, is coupled to bus 102 for communicating information and command selections to processor 104. Another type of user input device is cursor control 116, such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor 104 and for controlling cursor movement on display 112. This input device194913-8006-3335, v. 2typically has two degrees of freedom in two axes, a first axis (i.e., x) and a second axis (i.e., y), that allows the device to specify positions in a plane.

[0095] A computer system 100 can perform the present teachings. Consistent with certain implementations of the present teachings, results are provided by computer system 100 in response to processor 104 executing one or more sequences of one or more instructions contained in memory 106. Such instructions may be read into memory 106 from another computer-readable medium, such as storage device 110. Execution of the sequences of instructions contained in memory 106 causes processor 104 to perform the process described herein. Alternatively, hard-wired circuitry may be used in place of or in combination with software instructions to implement the present teachings. Thus, implementations of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0096] The term “computer-readable medium” as used herein refers to any media that can participate in providing instructions to processor 104 for execution. Such a medium may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media includes, for example, optical or magnetic disks, such as storage device 110. Volatile media includes dynamic memory, such as memory 106. Transmission media includes coaxial cables, copper wire, and fiber optics, including the wires that comprise bus 102.

[0097] Common forms of computer-readable media include, for example, a floppy disk, a flexible disk, hard disk, magnetic tape, or any other magnetic medium, a CD-ROM, any other optical medium, punch cards, paper tape, any other physical medium with patterns of holes, a RAM, PROM, and EPROM, a FLASH-EPROM, any other memory chip or cartridge, or any other tangible medium from which a computer can read.

[0098] Various forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to processor 104 for execution. For example, the instructions may initially be carried on the magnetic disk of a remote computer. The remote computer can load the instructions into its dynamic memory and send the instructions over a telephone line using a modem. A modem local to computer system 100 can receive the data on the telephone line and use an infra-red transmitter to convert the data to an infra-red signal. An infra-red detector coupled to bus 102 can receive the data carried in the infra-red signal and place the data on bus 102. Bus 102 carries the data to memory 106, from204913-8006-3335, v. 2which processor 104 retrieves and executes the instructions. The instructions received by memory 106 may optionally be stored on storage device 110 either before or after execution by processor 104.

[0099] In accordance with various embodiments, instructions configured to be executed by a processor to perform a method are stored on a computer-readable medium. The computer-readable medium can be a device that stores digital information. For example, a computer-readable medium includes a compact disc read-only memory (CD-ROM) as is known in the art for storing software. The computer-readable medium is accessed by a processor suitable for executing instructions configured to be executed.

[0100] The present teachings for analysis of mass spectral data can be utilized in a variety of different mass spectrometers as well as a variety of data acquisition methods employed in mass spectrometry. In particular, the present methods can be utilized in mass spectrometer systems that employ the SWATH data acquisition methods. By way of example, FIG. 6 schematically depicts a mass spectrometer 600 according to an embodiment that includes an LC column 602 that can receive a sample and separate a plurality of analytes in the sample based on their elution times from the LC column. The mass spectrometer 600 further includes an ion source 604 that receives an eluate exiting the LC column and ionizes one or more analytes contained in the eluate to generate a plurality of precursor ions.

[0101] In many implementations, one or more ion guides 606 receive the precursor ions and provide focusing of the ions to generate an ion beam that is received by a mass filter 608. By way of example, the ion guide(s) can include a plurality of rods arranged in a quadrupole configuration to which RF and DC voltages generated by an RF voltage source 610 and a DC voltage source 612 can be applied in a manner known in the art to provide radial confinement of the received ions.

[0102] In other embodiments, an ion mobility spectrometer (IMS), such as a differential mobility spectrometer (DMS), can be utilized as a separation device to separate ions based on their mobility with the ions exiting the IMS being received by the one or more ion guides 606.

[0103] The mass filter 608 provides an ion transmission window that allows transmission of ions having m / z values within an m / z range through the mass filter. By way of example, the mass filter 608 can include a plurality of rods arranged in a quadrupole configuration to which RF voltages as well as a discriminating DC voltage can be applied via the RF and the214913-8006-3335, v. 2DC voltage sources, respectively, to generate an ion transmission window. In this implementation, the ions passing through the mass filter 608 are received by an ion fragmentation device 614 that causes fragmentation of the precursor ions to generate a plurality of product ions. The product ions are received by a mass analyzer 616, which generates mass signal data associated with the product ions.

[0104] When operating in the SWATH data acquisition mode, a controller 618 can control the operation of the RF and the DC voltage sources to scan the ion transmission window over an m / z range so as to generate a plurality of overlapping ion transmission windows.

[0105] In use, the mass spectrometer can be employed to generate a survey scan of the precursor ions, where the survey scan can contain a plurality of precursor ion signals, such as the precursor survey scan illustrated in FIG. 3A. Subsequently, the mass spectrometer can be operated in a SWATH data acquisition mode in which the mass analyzer 616 generates fragment ions signals. In various embodiments, the XIC associated with the fragment ions can be computed by using the mass spectra of the fragment ions acquired at different elution times.

[0106] An analysis module 620 (herein also referred to as an analysis unit) that is in communication with the mass analyzer 616 and the controller 618, such as the computer system 100 discussed above, can receive the precursor ion signals (e.g., the m / z spectrum of the precursor ions and precursor XIC signal), the fragment ion signals (such as the mass spectrum and the XIC spectrum of the fragment ions) and can operate on those signals in a manner discussed above to deconvolve one or more of the precursor ion signals, e.g., to determine the number of different types of precursor ions and their relative abundances.

[0107] The following example is provided for elucidating various aspects of the present teachings and is not provided to necessarily indicate an optimal way of practicing the present teachings and / or optimal results that can be obtained.

[0108] Example

[0109] FIG. 7 shows a schematic pictorial example of the use of the present teachings for deconvolving a precursor ion signal associated with a plurality of precursor ions based on spectral information associated with a plurality of fragment ions generated via dissociation of the precursor ions. More specifically, FIG. 7 shows a precursor ion signal A obtained via224913-8006-3335, v. 2ionization of a plurality of analytes received from an analyte delivery device. Without any loss of generality, in this example, the analyte delivery device is assumed to be an LC column and the precursor ion signal A is assumed to be a precursor XIC obtained for ions generated via ionization of an eluate exiting the LC column. The XIC is a plot of ion intensity as a function of retention time through the LC column. In this example, there is an overlap between the retention times of a plurality of analytes eluting from the LC column.

[0110] In panel 1, a survey (MSI) spectrum of the precursor ions associated with the XIC profile A is depicted. The MSI spectrum is a plot of ion intensity as a function of the ions’ mass-to-charge ratios (m / z).

[0111] Panel 2 shows a scanning SWATH fragment (MS2) spectrum associated with fragment ions generated via dissociation of the precursor ions. The tandem MS2 spectrum is a plot of fragment ion intensity as a function of mass-to-charge ratios of the fragment ions. The tandem MS2 spectrum can be obtained by scanning an m / z window associated with a mass filter (herein referred to as a QI filter) through which precursor ions pass to reach an ion fragmentation device in which the precursor ions undergo fragmentation. Examples of QI profiles and fragment ions profiles are also depicted.

[0112] With reference to Panels 3 - 6, in this example, the MS2 fragment ions peaks can be segregated into two sets (left and right) based on correlation of the m / z profiles of those peaks with the QI profiles. For example, when the apex of the QI profiles of several fragment ions peaks relates to similar m / z value (centroid) that correlates with a precursor ion m / z of the survey spectrum, it can be concluded that the same precursor m / z is shared by those fragment ions peaks. Although for the sake of simplicity, only two sets of fragment ions peaks are illustrated in this example, in general, the fragment ions peaks can be segregated to any number of sets, where the fragment ions peaks within each set correspond to the same precursor m / z. In this manner, a deconvoluted MS2 spectrum can be derived containing two sets of fragment ions as shown schematically in Panels 7 and 8. The segregation of the fragment ions peaks into two distinct sets indicates that the precursor ion signal A is generated via the overlap of ion signals associated with two distinct types of precursor ions.

[0113] The XICs of the fragment ions within each set can be combined to form a representative XIC profile associated with that set. In this case, two representative XIC profiles B and C are shown, where the representative XIC profile B is associated with the234913-8006-3335, v. 2fragment ion set shown in Panel 7 and the representative XIC profile C is associated with the fragment ion set shown in Panel 8. Two basis ion signal profiles can be computed based on representative XIC profiles B and C, e.g., using ICA, or non-negative matrix factorization (NNMF), independent factor analysis (IFA), among others. The basis ion signal profiles can then be utilized to deconvolve the precursor ion signal A in a manner disclosed herein.

[0114] More specifically, the precursor ion signal profile A can be represented as a linear combination of the basis ion signal profiles B and C. The ratio of the coefficients of basis ion signal profiles B and C in such a linear representation provides a relative abundance of the two distinct types of the precursor ions.

[0115] The above descriptions of various implementations of the present teachings have been presented for purposes of illustration and description. It is not exhaustive and does not limit the present teachings to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practicing of the present teachings. Additionally, the described implementation includes software but the present teachings may be implemented as a combination of hardware and software or in hardware alone. The present teachings may be implemented with both object-oriented and non-object- oriented programming systems.

[0116] Depending on certain implementation requirements, embodiments of the present teachings, the controller can be implemented in hardware, firmware and / or in software.

[0117] In some embodiments, the instructions for operating the optical system can be stored using a non-transitory storage medium such as a digital storage medium, for example a DVD, a Blu- Ray, a CD, a ROM, a PROM, and EPROM, an EEPROM or a FLASH memory, having electronically readable control signals stored thereon, which cooperate (or are capable of cooperating) with a programmable computer system such that the respective method is performed. Therefore, the digital storage medium may be computer readable.

[0118] While various embodiments have been illustrated and described in detail in the drawings and foregoing description, such illustration and description are to be considered illustrative or exemplary and not restrictive; embodiments of the present disclosure are not limited to the disclosed embodiments. Other variations to the disclosed embodiments can be understood and effected by those skilled in the art in practicing embodiments of the present disclosure, from a study of the drawings, the disclosure, and the appended claims.244913-8006-3335, v. 2

[0119] In the claims, the word “comprising” does not exclude other elements or steps, and the indefinite article “a” or “an” does not exclude a plurality. A single processor or other processing unit may fulfill the functions of several items recited in the claims. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measured cannot be used to advantage. Any reference signs in the claims should not be construed as limiting the scope.

[0120] Those having ordinary skill in the art will appreciate that various changes can be made to the above embodiments without departing from the scope of the present teachings.254913-8006-3335, v. 2

Claims

1. What is claimed is:

1. A method for mass spectral data analysis, comprising: acquiring at least one precursor ion signal associated with one or more precursor ions, acquiring at least one derivative ion signal associated with one or more derivative ions of said one or more precursor ions, and deconvolving the at least one precursor ion signal utilizing the at least one precursor ion signal and the at least one derivative ion signal, to produce a deconvolved precursor ion signal.

2. The method of Claim 1, wherein the at least one derivative ion signal corresponds to at least one fragment ion signal corresponding to one or more fragment ions generated due to dissociation of said one or more precursor ions.

3. The method of Claim 1, wherein the at least one derivative ion signal corresponds to at least one neutral loss ion from at least one of the derivative ions.

4. The method of Claim 1, wherein the at least one derivative ion signal corresponds to at least one adduct ion.

5. The method of any one of Claims 1 - 4, wherein the step of utilizing the at least one precursor ion signal and the at least one derivative ion signal to deconvolve the at least one precursor ion signal comprises: deriving a set of basis derivative ion signal profiles suitable for representing said at least one derivative ion signal as a linear combination of the basis derivative ion signal profiles, and utilizing said basis derivative ion signal profiles to deconvolve said at least one precursor ion signal.

6. The method of Claim 5, wherein the step of deconvolving said at least one precursor ion signal comprises determining a number of distinct types of precursor ions in said one or more precursor ions and a relative abundance of each of said distinct types of the precursor ions.264913-8006-3335, v.

27. The method of Claim 6, further comprising representing the at least one precursor ion signal as a linear combination of said basis derivative ion signal profiles and utilizing coefficients of said linear combination to determine said relative abundance of each of said distinct types of the precursor ions.

8. The method of any one of the preceding claims, wherein the step of deconvolving said at least one precursor ion signal comprises determining an elution time of at least one of said plurality of precursor ions from a chromatography device.

9. The method of Claim 8, wherein said chromatography device comprises a liquid chromatography column.

10. The method of any one of the preceding claims, wherein said at least one precursor ion signal and said at least one derivative ion signal are two-dimensional ion signals and wherein one of said dimensions is ion mass-to-charge ratio (m / z).

11. The method of Claim 10, wherein the step of deconvolving said at least one precursor ion signal comprises determining an m / z value of at least one of said plurality of precursor ions.

12. The method of Claim 11, further comprising utilizing said determined m / z value to identify said at least one of said plurality of precursor ions.

13. The method of Claim 12, further comprising utilizing a reference compound library to identify said at least one of said plurality of precursor ions based on said determined m / z.

14. The method of Claim 11, further comprising utilizing said deconvolved precursor ion signal to set a precursor ion tolerance for a set of fragment ions related to at least one of said one or more precursor ions.

15. The method of Claim 14, further comprising utilizing said precursor ion tolerance to improve identification of said at least one of said one or more precursor ions.

16. The method of Claim 1, wherein said at least one precursor ion signal provides at least one precursor ion intensity as a function of a variable.274913-8006-3335, v.

217. The method of Claim 16, wherein said at least one derivative ion signal provides at least one derivative ion intensity as a function of said variable, and wherein optionally said variable comprises any of time, m / z and ion mobility.

18. The method of Claim 13, wherein said at least one derivative ion intensity as a function of said variable comprises a plurality of derivative ion intensity peaks, and further comprising segregating said derivative ion intensity peaks into two or more derivative ion subsets such that each subset is associated with a different setting of a measurement parameter.

19. The method of Claim 18, wherein said measurement parameter comprises any of a mass-to-charge ratio (m / z) and an ion mobility, and wherein optionally a setting of any of said m / z and said ion mobility corresponds, respectively, to a specific value or a range of values of m / z or ion mobility associated with at least a portio of said plurality of precursor ions.

20. The method of Claim 18, further comprising generating a plurality of representative derivative ion signal profiles each corresponding to one of said derivative ion subsets and deriving said derivative ion basis profiles from said plurality of representative derivative ion signal profiles.284913-8006-3335, v. 2

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