Patent Publication Number: US-2022237261-A1

Title: Method for analyzing data determined by two variables

Description:
TECHNICAL FIELD 
     The present invention relates to a method for analyzing data of a component that is the target of a measurement determined by two variables including a first variable and a second variable which is another variable. For example, in the case of the data of a detection intensity acquired at each m/z (mass-to-charge ratio) and at each retention time by a chromatograph mass spectrometer, the m/z (mass-to-charge ratio) corresponds to the first variable, and the retention time corresponds to the second variable. In the case of the data of an m/z intensity acquired at each position by an imaging mass spectrometer, the m/z corresponds to the first variable, and the position corresponds to the second variable. In the case of the data of the absorption spectrum acquired at each position by an imaging FT-IR (Fourier transform infrared spectrophotometer), the absorption wavelength corresponds to the first variable, and the position corresponds to the second variable. 
     BACKGROUND ART 
     A set of data determined by two variables in the previously described manner can be represented by a data matrix with N rows and M columns in which the N rows of data differ from each other in the value of the first variable, while the M columns of data differ from each other in the value of the second variable, where N and M are natural numbers. For example, in a chromatograph mass spectrometer, such as a liquid chromatograph mass spectrometer (LC/MS) or gas chromatograph mass spectrometer (GC/MS), a mass spectrum formed by N pieces of data representing detection sensitivities at N m/z values is acquired at one retention time, and those N pieces of data form one column of the data matrix. There are M different retention times, and one mass spectrum is acquired at each retention time, so that M columns each of which includes N pieces of data are obtained. Consequently, a data matrix with N rows and M columns is obtained. 
     A sample to be subjected to a measurement by a chromatograph mass spectrometer contains one or more components. A “component” contained in a sample in the present context means a significant component that forms a peak whose height (or magnitude) on a chromatogram or mass spectrum is equal to or greater than a predetermined level. If K components (where K is a natural number) are contained in the sample, a mass spectrum obtained at each retention time or mass chromatogram obtained at each m/z value will be a superposition of mass spectra or mass chromatograms which respectively result from the K components. If the mass spectrum or mass chromatogram in the superposed form can be separated into K mass spectra or mass chromatograms corresponding to the individual components, it will be possible to obtain information on each individual component. To this end, a technique called “matrix factorization” can be used (for example, see Patent Literature 1). 
     In the matrix factorization, a spectrum matrix S with N rows and K columns and a profile matrix P with K rows and M columns are determined so that the aforementioned data matrix X with N rows and M columns can be expressed by SP, i.e., the product of the spectrum matrix S and the profile matrix P. As noted earlier, K corresponds to the number of components contained in the sample. This number is called the “factor number” in the technique of matrix factorization. Each column of the spectrum matrix S corresponds to one of the mass spectra of the K components, while each row of the profile matrix P corresponds to one of the chromatograms of the K components. 
     In most cases, it is impossible to analytically determine the spectrum matrix S and profile matrix P. To address this problem, a computer-based method is used as follows: A plurality of candidates of the spectrum matrix S and profile matrix P are prepared. For each combination of a candidate of the spectrum matrix S and that of the profile matrix P, a predetermined function D(x|y) which shows an error between a matrix element in the product SP and the corresponding matrix element in the data matrix X in question is defined for each matrix element (this function is also called the “distance function” or “divergence”). The errors respectively obtained for the matrix elements are totaled. The spectrum matrix S and profile matrix P are determined so that the total error is minimized Examples of the distance function D(x|y) include a Euclidean distance expressed by (x−y) 2 , generalized KL (Kullback-Leibler) divergence expressed by x log(x/y)−(x−y), IS (Itakura-Saito) divergence expressed by (x/y)−log(x/y)−1, and β divergence, which is a generalization of the previously mentioned divergences and expressed as follows: 
     
       
         
           
             
               
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     The total of the values of the function respectively obtained for the matrix elements, D(X|SP)=Σ n,m D(λ nm |(SP) nm ), represents the degree of difference between the data matrix X and the product SP. It should be noted that (SP) nm  represents a matrix element in the matrix given by the product SP. 
     On the other hand, for an estimation problem of a parameter of a probability distribution, a maximum likelihood method is often used to obtain an estimated value of the parameter. Specifically, in a probability distribution having parameter θ (this may be a vector having multiple dimensions), a value of θ is determined which gives the largest value of a likelihood function p(x|θ) which expresses the likelihood of parameter θ for data x. It should be noted that an estimated value of parameter θ obtained by the maximization of the likelihood is equal to that of parameter θ obtained by the minimization of a negative log likelihood function, −log p(x|θ). Since the minimization of the negative logarithmic likelihood is easier to calculate, this technique is more frequently used. 
     The matrix factorization can also be considered as a problem of the maximum likelihood estimation. In that case, the problem of determining the matrices S and P so as to minimize the distance function D(X|SP) is identical to the problem of deducing, for each element of the matrix, a probability distribution and likelihood function p(X nm |(SP) nm ) which correspond to the distance function. Specifically, consider four examples of the probability distribution: (i) Gaussian distribution, (ii) Poisson distribution, (iii) exponential distribution and (iv) Tweedie distribution. The negative log likelihood functions of these distributions respectively correspond to (i) Euclidean distance, (ii) generalized KL divergence, (iii) IS divergence and (iv) β divergence (for example, see Non Patent Literature 1). Other than the four aforementioned examples of the correspondence relationship between the probability distribution and the distance function, it is generally possible to perform a similar estimation for any probability distribution by using its negative log likelihood function as the distance function. 
     In the area of the sparce modelling, a technique for obtaining a sparce set of estimated values of the parameter (e.g., a matrix in which a considerable number of matrix elements have a value of zero) is used. An example of such a technique is LASSO (least absolute shrinkage and selection operator), in which a loss function is defined by adding, to the distance function, an L1-norm or similar regularization term for inducing sparsity of the solution, and this loss function is minimized to obtain a solution in which unnecessary parameters have an estimated value of zero. 
     CITATION LIST 
     Patent Literature 
     
         
         Patent Literature 1: US 2009/0121125 A 
       
    
     Non Patent Literature 
     
         
         Non Patent Literature 1: Kazuyoshi Yoshii and three other authors, “NMF vs PLCA: Tajuuon Seisei Katei No Tame No Mugen Inshi Modem To Mugen Kongou Modem (NMF vs PLCA: Infinite Factor Model and Infinite Mixture Model for Multiple Sound Generation Process)”,  IPSJ SIG Technical Report MUS  ( Musical Informatics ), Vol. 2016-MUS-112, No. 21, pp. 1-10, Aug. 1, 2016 
       
    
     SUMMARY OF INVENTION 
     Technical Problem 
     In order to perform a matrix factorization on a data matrix X, it is necessary determine the factor number K. If the number of components contained in the sample is previously known, that number can be used as the factor number K. However, in many cases, that number is unknown. When the number of components contained in the sample is unknown, it is difficult to appropriately determine the factor number K, so that it is also difficult to appropriately determine the spectrum matrix S and profile matrix P based on the data matrix X. Similarly, as in the case of the sparse modeling, when a regularization term for inducing sparsity of the solution is added to the loss function, it is difficult to appropriately determine the value of the regularization parameter. 
     The problem to be solved by the present invention is to provide a data analysis method by which a spectrum matrix S and profile matrix P whose factor number K is appropriate and close to the number of components contained in a sample can be determined based on a data matrix X obtained by a measurement on the sample, even when the number of components is unknown. 
     Solution to Problem 
     A method for analyzing data which depend on two variables according to the present invention developed for solving the previously described problem is a method for determining a first matrix S with N rows and K columns and a second matrix P with K rows and M columns based on a data matrix X in which a set of data obtained from an analyzing device are arranged in N rows and M columns, where the N rows of data differ from each other in the value of a first variable, the M columns of data differ from each other in the value of a second variable, and the first matrix S and the second matrix P are determined so that the product SP approximates to the data matrix X, the method including: 
     a regularization parameter-regularization function preparation process for preparing a plurality of regularization-parameter candidates λr (where r is a natural number from 1 to r max ) and one regularization function R(S, P) which induces sparsity of the solution; 
     a matrix candidate determination process for solving an optimization problem for each of the plurality of regularization-parameter candidates λr so as to determine a matrix Srt as a candidate Sr of the first matrix S and a matrix Prt as a candidate Pr of the second matrix P, where the matrices Srt and Prt are determined so as to minimize the value of a loss function L(S, P)=D(X|SP)+λrR(S, P), where D(X|SP) is a distance function expressing the degree of difference between the data matrix X and the product SP, while λrR(S, P) is the product of the regularization-parameter candidate λr and the regularization function R(S, P); 
     a probability distribution transform process for determining, for each of the plurality of regularization-parameter candidates λr, a transformed value y nm =F nm (X nm |(SrPr) nm ) by a variable transform into a common probability distribution Pcommon for each combination of a matrix element X nm  of the data matrix X and a corresponding matrix element (SrPr) nm  of the product SrPr of the first-matrix candidate Sr and the second-matrix candidate Pr, using F nm  which is a function for the variable transform from a probability distribution P nm  corresponding to the distance function D(X nm |(SP) nm ) into the common probability distribution Pcommon; 
     a goodness-of-fit calculation process for determining, for each of the plurality of regularization-parameter candidates λr, a goodness of fit between the transformed value y nm  and a cumulative distribution function of the probability distribution Pcommon; and 
     a matrix determination process for selecting, as the first matrix S and the second matrix P, the first-matrix candidate Sr and the second-matrix candidate Pr determined for a regularization-parameter candidate λr which yields the highest value of the goodness of fit among the plurality of regularization-parameter candidates λr, or a regularization-parameter candidate λr which yields the goodness of fit higher than a predetermined threshold and also has the largest value of λr. 
     In the present description, for convenience, the first matrix is denoted by the same sign as the spectrum matrix, “S”, while the second matrix is denoted by the same sign as the profile matrix, “P”. In practice, the first and second matrices may be spectrum and profile matrices, respectively, as suggested by their respective signs, or the first and second matrices may be profile and spectrum matrices, respectively, as opposed to their respective signs. In the latter case, unlike the previously described definition, the spectrum matrix should be defined as a matrix with K rows and M columns, while the profile matrix should be defined as a matrix with N rows and K columns. 
     According to the present method, even when the number of components contained in the sample is unknown, a first-matrix candidate Sr in which all elements in one or more columns corresponding to unnecessary factors have a value of zero, and a second-matrix candidate Pr in which all elements in one or more rows corresponding to unnecessary factors have a value of zero, can be prepared due to the effect of the regularization which induces sparsity of the solution. However, if the value of the regularization parameter is too small, the number of columns having non-zero values (i.e., the estimated factor number K) in the matrix S will be too large, causing the problem of “overfitting” (also called the “overtraining”, which is a situation in which even a model that is unreasonable and incorrect shows a high level of goodness of fit with data in question if the used model is complex). Conversely, if the value of the regularization parameter is too large, the estimated factor number K will be too small, causing the problem of “underfitting” (or “undertraining”) which prevents the model from being satisfactorily fitted to the data. 
     According to the present invention, one pair of candidates (Sr, Pr) is determined for each of the plurality of regularization-parameter candidates λr in the matrix candidate determination process. The processes from the probability distribution transform process through the matrix determination process are performed on those candidates (Sr, Pr) to narrow down the candidates using the goodness of fit with an ideal distribution (this will be described later in detail) and ultimately obtain one pair of the first matrix S and second matrix P (and one factor number K corresponding to them). Thus, both the overfitting and underfitting are prevented. In other words, the setting of a factor number K larger than the actual number of components can be prevented, and the first matrix S and second matrix P having an appropriate factor number K can be determined. 
     Commonly known examples of the regularization function for inducing sparsity of the solution include “L1-norm”, “linear combination of L1-norm and L2-norm”, and “volume constraint”. In the regularization function R(S, P) in the present invention, the linear combination of L1-norm and L2-norm is expressed by R(S, P)=α(|S| 1 +|P| 1 )+(1−α)(|S| 2   2 +|P| 2   2 ), where |S| 1 =Σ i,j S i,j , |P| 1 =Σ i,j P i,j , |S| 2 =(Σ i,j S i,j   2 ) 1/2 , |P| 2 =(Σ i,j P i,j   2 ) 1/2 , and α is a constant between 0 and 1. L1-norm corresponds to the case of α=1. In the “volume constraint”, a constraint is placed on the solution so that the total of the values in each column of the matrix P does not exceed 1, and a trace norm (Schatten-1-norm), det|S T S| or log det|S T S+δI| is applied to the matrix S (where I is a unit matrix, and δ is a hyperparameter for controlling the regularization function). 
     The cumulative distribution function of the probability distribution (this function is hereinafter expressed as f(x) using a generalized variable x) is a function given by the following equation: 
         f ( x )=∫ −∞   x   p ( x ′) dx′ 
 
     where p(x) is a probability density function expressing the probability distribution of the data on which f(x) is based. Examples of the probability density function p(x) include the previously mentioned functions: (i) Gaussian distribution, (ii) Poisson distribution, (iii) exponential distribution, and (iv) Tweedie distribution. The cumulative distribution functions f(x) corresponding to the four aforementioned examples of the probability density functions p(x) respectively correspond to (i) Euclidean distance, (ii) generalized KL divergence, (iii) IS divergence and (iv) β divergence mentioned earlier. 
     The transformed value y nm =F nm (X nm |(SrPr) nm ) obtained in the probability distribution transform process is determined so that a variable transform is achieved in which the probability distribution Pnm corresponding to each matrix element X nm  of the data and each matrix element (SrPr) nm  of the product SrPr is transformed into a common probability distribution Pcommon. For example, when the generalized KL divergence is used as the distance function, the corresponding probability distribution Pnm becomes a Poisson distribution. In this case, it is possible to obtain Pcommon in the form of a standard uniform distribution by using a cumulative distribution function as F nm , utilizing the fact that any random variable shows a standard uniform distribution after being subjected to a variable transform using a cumulative distribution function (this fact is known as a “probability integral transform”). The more appropriate the matrix factorization is, the higher the goodness of fit is between the empirical distribution function formed by the transformed value y nm  after the variable transform into the standard uniform distribution and the cumulative distribution function of the assumed probability distribution Pcommon. Accordingly, in the goodness-of-fit calculation process, the goodness of fit between the transformed value y nm  and the cumulative distribution function of the probability distribution Pcommon is determined for each of the plurality of regularization-parameter candidates λr. As for the goodness of fit, any known type of goodness of fit can be used, such as a Kolmogorov-Smirnov statistic. As another specific example, when the variance σ nm   2  of the noise in each matrix element X nm  of the data is previously known, the probability distribution Pcommon can be defined as a standard normal distribution, the cumulative distribution function F nm (X nm |(SrPr) nm ) can be defined as (X nm −(SrPr) nm )/σ nm , and −|σ y   2 −1| can be used as the goodness of fit, where σ y   2  is given by: 
     
       
         
           
             
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     which is the unbiased variance of the transformed value y nm  whose mean value is assumed to be zero. The goodness of fit in this example indicates whether or not the unbiased variance is close to 1. 
     After the goodness of fit has been calculated in the previously described manner, the matrix determination process is performed to select, as the first matrix S and second matrix P, the first-matrix candidate Sr and second-matrix candidate Pr determined for (i) a regularization-parameter candidate λr that yields the highest value of the goodness of fit or (ii) a regularization-parameter candidate λr that yields the goodness of fit higher than a predetermined threshold and also has the largest value of the regularization parameter. Condition (ii) is based on the reasoning that a simpler model (having a smaller value of K) is likely to yield a more accurate result, provided that its goodness of fit is at a certainly high level (equal to or higher than a predetermined threshold). 
     Advantageous Effects of Invention 
     According to the present invention, a spectrum matrix (first or second matrix) and profile matrix (second or first matrix) whose factor number K is appropriate and close to the number of components contained in a sample can be determined based on a data matrix X obtained by a measurement on the sample, even when the number of components is unknown. 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
         FIG. 1  is a schematic configuration diagram showing one embodiment of a chromatograph mass spectrometer in which a data analysis method according to one embodiment of the present invention is carried out. 
         FIG. 2  is a flowchart showing an operation of the chromatograph mass spectrometer shown in  FIG. 1 . 
         FIG. 3  is a diagram conceptually illustrating a data matrix as well as a spectrum matrix and profile matrix, using one example of the three-dimensional data as well as the data of mass spectra and chromatograms. 
         FIG. 4  is a flowchart showing details of an operation in the data analysis method according to the present embodiment, which is a portion of the operation of the chromatograph mass spectrometer shown in  FIG. 1 . 
         FIG. 5  is a diagram showing measurement data in the form of chromatograms and mass spectra which give the data matrix used in an example of the calculation of the matrix factorization performed in the data analysis method according to the present embodiment. 
         FIG. 6  is a diagram in which measurement data which give a data matrix is shown as a superposition of a plurality of mass chromatograms. 
         FIG. 7  is a diagram showing an example of the result of a calculation of mass spectra and chromatograms obtained in a matrix factorization in which the regularization is insufficient due to λr being too small. 
         FIG. 8  is a diagram showing an example of the result of a calculation of mass spectra and chromatograms obtained in a matrix factorization in which the regularization is insufficient due to λr being too large. 
         FIG. 9  is a diagram showing an example of the result of a calculation of mass spectra and chromatograms obtained in a matrix factorization in which the regularization is appropriately performed using an optimum value of λr. 
     
    
    
     DESCRIPTION OF EMBODIMENTS 
     One embodiment of the data analysis method according to the present invention, and a chromatograph mass spectrometer in which the data analysis method is carried out, are hereinafter described using  FIGS. 1-9 . 
     (1) Configuration of Chromatograph Mass Spectrometer in which Data Analysis Method According to Present Embodiment is Carried Out 
       FIG. 1  shows the configuration of the main components of a liquid chromatograph/ion trap time-of-flight mass spectrometer (LC/IT-TOFMS)  10  in which the data analysis method according to the present embodiment is carried out. This LC/IT-TOFMS  1  is roughly divided into a liquid chromatograph (LC) unit  10 , mass spectrometry (MS) unit  20 , data processing unit  40  and analysis control unit  50 . 
     The LC unit  10  includes a mobile phase container  11 , liquid supply pump  12 , injector  13 , and column  14 . The mobile phase container  11  is used for storing a mobile phase. The liquid supply pump  12  is configured to draw the mobile phase from the mobile phase container  11  and supply it to the injector  13  at a constant flow rate. The injector  13 , which includes an autosampler, is configured to automatically select one of the prepared samples and injects a predetermined volume of the sample into the mobile phase at a predetermined timing. When a sample is injected from the injector  13  into the mobile phase, the sample is carried by the mobile phase and introduced into the column  14 . While the sample is passing through the column  14 , the various components in the sample are separated from each other and exit from the outlet end of the column  14  in a temporally separated form, to be introduced into the MS unit  20 . 
     The MS unit  20  includes an ionization chamber  21  to be maintained at atmospheric pressure, and an analysis chamber  29  to be maintained at a high degree of vacuum by being evacuated by a turbo molecular pump (not shown). A first-stage intermediate vacuum chamber  24  and second-stage intermediate vacuum chamber  27 , with their degrees of vacuum increased in a stepwise manner, are provided between the ionization chamber  21  and analysis chamber  29 . The ionization chamber  21  communicates with the first-stage intermediate vacuum chamber  24  through a thin desolvation tube  23 . The first-stage intermediate vacuum chamber  24  communicates with the second-stage intermediate vacuum chamber  27  through an orifice of a small diameter bored at the apex of a conical skimmer  26 . A first ion guide  25  and second ion guide  28  are arranged within the first-stage intermediate vacuum chamber  24  and second-stage intermediate vacuum chamber  27 , respectively. 
     The ionization chamber  21  is equipped with an ESI nozzle  22  as the ion source. The ESI nozzle  22  is configured to be supplied with an eluate containing sample components from the LC unit  10  and spray the eluate into the ionization chamber  21  in the form of droplets while electrically charging the droplets by a high DC voltage applied from a high voltage source (not shown). The electrically charged droplets collide with gas molecules of atmospheric origin and are thereby broken into even smaller droplets, which are quickly dried (desolvated), leaving sample molecules in a gas state. Those sample molecules are ionized through ion evaporation. The droplets containing the resultant ions are drawn into the desolvation tube  23  by the pressure difference between the ionization chamber  21  and the first-stage intermediate vacuum chamber  24 . While passing through the desolvation tube  23 , the droplets further undergo desolvation and produce more ions. It should be noted that the method for ionizing sample molecules is not limited to the electrospray ionization (ESI) described in this paragraph; for example, an atmospheric pressure chemical ionization (APCI) or atmospheric pressure photoionization (APPI) can also be used. 
     The ions which have passed through the desolvation tube  23  travel through the first-stage and second-stage intermediate vacuum chambers  24  and  27  while being converged by the first and second ion guides  25  and  28 , and are sent into the analysis chamber  29 . 
     The analysis chamber  29  contains an ion trap  30 , time-of-flight mass separator (TOF)  31  as the mass separator, and ion detector  33 . 
     Within the ion trap  30 , the ions are temporarily captured and accumulated by a quadrupole electric field created by radio-frequency voltages respectively applied from a power source (not shown) to the electrodes. The various ions accumulated within the ion trap  30  are simultaneously given kinetic energy at a predetermined timing and thereby ejected from the ion trap  30  into the TOF  31 . 
     Additionally, as shown in  FIG. 1 , the ion trap  30  can be supplied with a collision induced dissociation (CID) gas, such as argon. This allows the ions accumulated within the ion trap  30  to be fragmented into product ions by CID. In the case of an MS 2  analysis, after the various ions have been accumulated within the ion trap  30 , the voltages applied to the electrodes are controlled so that an ion having a specific m/z among those ions will be selectively retained as a precursor ion. The CID gas is subsequently introduced into the ion trap  30  to promote the fragmentation of the precursor ion. The resultant product ions are simultaneously ejected from the ion trap  30  toward the TOF  31  at a predetermining timing. 
     The TOF  31  includes a reflectron electrode  32  to which a DC voltage is applied from a DC power source (not shown). Due to the effect of the thereby created DC electric field, the ions are returned and reach the ion detector  33 . Among the ions which have been simultaneously ejected from the ion trap  30 , an ion having a smaller m/z flies at a higher speed. Consequently, the ions separately reach the ion detector  33 , having temporal differences according to their m/z values. The ion detector  33  produces, as a detection signal, an electric current corresponding to the number of ions arriving at the detector. 
     An analogue-to-digital (A/D) converter  34  for converting the detection signal into a digital value is connected to the ion detector  33 . After the conversion by the A/D converter  34 , the detection signal is sent to the data processing unit  40 . 
     The data processing unit  40  includes a data matrix creator  41 , matrix factorization executer  42 , m/z detector  43 , retention time detector  44 , and MS 2  analysis execution condition determiner  45 . The matrix factorization executer  42  includes a regularization parameter-regularization function preparer  421 , matrix candidate determiner  422 , probability distribution transformer  423 , goodness-of-fit calculator  424 , and matrix determiner  425 . Details of those components will be described later. The data processing unit  40  is connected to a storage unit  61 . 
     The analysis control unit  50  is configured to control the components of the LC unit  10  and MS unit  20  so as to perform an LC/MS analysis and LC/MS 2  analysis. It includes an LC/MS analysis executer  51  and LC/MS 2  analysis executer  52 . 
     The data processing unit  40  and analysis control unit  50  are embodied by a personal computer (PC) on which predetermined controlling-and-processing software is installed. The storage unit  61  is embodied by a hard disk drive, solid state drive or other types of storage devices provided in or for the PC. The PC also has a display unit  62  as well as an operation unit  63  including a keyboard, mouse, touch panel and/or other devices. 
     (2) Operation of LC/IT-TOFMS  1  Including Data Processing Method According to Present Embodiment 
     An operation of the LC/IT-TOFMS  1  including the data analysis method according to the present embodiment is hereinafter described using  FIGS. 2 and 3 . The functions of the components in the data processing unit  40  will also be described. 
     Initially, an operator using the operation unit  63  performs a predetermined operation to initiate a measurement. In response to this operation, the LC/MS analysis executer  51  in the LC/IT-TOFMS  1  begins to control the components of the LC/IT-TOFMS  1  to conduct an LC/MS analysis for a target sample, as will be described later (Step  1 ). The target sample injected from the injector  13  into the mobile phase is thereby sent into the column  14 , and the eluate from the column  14  is introduced into the MS unit  20 , which repeatedly performs a mass spectrometric analysis of the eluate. The detection signals produced by the ion detector  33  in the MS unit  20  are converted into digital values by the A/D converter  34  and sent to the data matrix creator  41  in the data processing unit  40 . 
     In the data matrix creator  41 , N signals obtained at each m/z within a predetermined m/z range as a result of one ejection of ions from the ion trap  30  are acquired as the values of N matrix elements to be included in one column of a data matrix X with N rows and M columns The data acquisition is similarly performed for each of the M ejections of ions performed at intervals of time. Based on those data, the data matrix X with N rows and M columns as shown below is created (Step  2 ). 

 
     Each matrix element X nm  of the data matrix X (where n is an integer from 1 to N, while m is an integer from 1 to M) indicates the intensity detected at the n-th m/z within the aforementioned m/z range as well as at the m-th ion ejection (which corresponds to the retention time). Each matrix element X nm  of the data matrix X has a value of zero or positive value (non-negative value). 
     Next, the matrix factorization executer  42  performs a matrix factorization by a method which will be described later (in “(3) Details of Data Analysis Method (Operation of Matrix Factorization) According to Present Embodiment”) to determine a spectrum matrix S with N rows and K columns as well as a profile matrix (also called a “chromatogram matrix”) P with K rows and M columns so that their product SP approximates to the data matrix X (Step  3 ). The spectrum matrix S corresponds to the first matrix S mentioned earlier, while the profile matrix P corresponds to the second matrix P. The spectrum matrix S and profile matrix P can be expressed as follows: 

 
     Each matrix element s nk  of the spectrum matrix S (where n is an integer from 1 to N, while k is an integer from 1 to K) indicates the intensity at one m/z value in a mass spectrum originating from one of the K components contained in a sample (this component is hereinafter called the “k-th component”). Similarly, each matrix element p km  of the profile matrix P indicates the intensity at one retention time in the chromatogram originating from the k-th component. In other words, each set of matrix elements surrounded by the broken line in the above spectrum matrix S shows a mass spectrum of one component, while each set of matrix elements surrounded by the broken line in the above profile matrix P shows a chromatogram of one component. Each of the matrix elements s nk  of the spectrum matrix S and the matrix elements p km  of the profile matrix P has a value of zero or positive value (non-negative value).  FIG. 3  conceptually illustrates the data matrix X as well as the spectrum matrix S and profile matrix P, using one example of the three-dimensional data  71  as well as the data of the mass spectra  72  and chromatograms  73 . 
     Next, the m/z detector  43  performs a peak-detecting operation for each column of the obtained spectrum matrix S (i.e., for each value of k from 1 to K), including the steps of detecting one or more peaks from the mass spectrum in the k-th column of the spectrum matrix S and determining the m/z values corresponding to those peaks (Step  4 ). The m/z values corresponding to those peaks will be the candidates of the m/z value of the precursor ion originating from the k-th component contained in the target sample. Similarly, the retention time detector  44  performs a peak-detecting operation for each row of the obtained profile matrix P (i.e., for each value of k from 1 to K), including the steps of detecting one or more peaks from the chromatogram in the k-th row of the profile matrix P and determining the retention times corresponding to those peaks (Step  5 ). The retention times corresponding to those peaks will be the candidates of the retention time of the k-th component contained in the target sample. 
     Based on the candidates of the m/z in the k-th column of the spectrum matrix S obtained in Step  4  and those of the retention time in the k-th row of the profile matrix P obtained in Step  5 , the MS 2  analysis execution condition determiner  45  creates a precursor-ion list L for each value of k from 1 to K (i.e., for each component contained in the target sample), where each item of the list consists of one candidate of the m/z of the precursor ion paired with one candidate of the retention time (Step  6 ). 
     In the case where the LC/MS data of a background with no sample has been acquired beforehand, the MS 2  analysis execution condition determiner  45  may additionally perform, based on the background data, a selecting operation in which all pairs of the m/z candidate and retention-time candidate originating from the background are removed from the precursor-ion list L, and the remaining candidate pairs are selected as new pairs of the m/z candidate and retention-time candidate (Step  7 ). As another possibility, the previously described operation in Step  7  may be replaced by a selecting operation based on the background data in which only the pairs of the m/z candidate and retention-time candidate that fall within an m/z range and retention-time range which are free from the influence of the background are selected as new pairs of the m/z candidate and the retention-time candidate. These operations in Step  7  may be omitted. 
     Based on the obtained precursor-ion list L (after the removal of the pairs of the m/z candidate and retention-time candidate originating from the background if Step  7  is carried out), the MS 2  analysis execution condition determiner  45  determines execution conditions of an MS 2  analysis (MS 2  analysis method) including the selection and fragmentation of the precursor ion of a component contained in the sample (Step  8 ). In most MS 2  analyses, this type of analysis method is previously known for each component. Therefore, the known analysis methods can be previously stored in the storage unit  61  so that the MS 2  analysis execution condition determiner  45  can retrieve an appropriate analysis method from the storage unit  61  based on the information concerning the candidates of the m/z and retention time in the precursor-ion list L. 
     In the process of determining an analysis method, the analysis method for an MS 2  analysis of one sample may be divided into a plurality of analysis methods so that the loop time (sampling interval) for one MS 2  analysis will be equal to or less than a predetermined value. This ensures a sufficiently high sampling rate and improves the sensitivity of the quantitative determination. 
     The process of determining an analysis method may allow the setting of a different level of collision energy for each component to be analyzed. This allows an analysis of each component to be more appropriately performed when an appropriate level of collision energy for each component is previously known. As another possibility, a plurality of levels of collision energy may be set for each component to be analyzed. This allows an analysis to be performed using multiple levels of collision energy to determine an optimum fragmentation condition when an appropriate level of collision energy for each component is unknown. 
     Based on the analysis method thus determined, the LC/MS 2  analysis executer  52  in the LC/IT-TOFMS  1  controls each component of the LC/IT-TOFMS  1  to perform an LC/MS 2  analysis (Step  9 ). The LC/MS 2  analysis is performed at all retention times included in the precursor-ion list L. After the LC/MS 2  analyses at all retention times have been completed, the entire sequence of operations of the LC/IT-TOFMS  1  is discontinued. 
     (3) Details of Data Analysis Method (Operation of Matrix Factorization) According to Present Embodiment 
     Next, using  FIG. 4 , details of the operation of the matrix factorization (Step  3 ) which is a data analysis method according to the present embodiment and is performed in the matrix factorization executer  42  will be described along with the functions of the components in the matrix factorization executer  42 . 
     Initially, the regularization parameter-regularization function preparer  421  prepares a plurality of regularization-parameter candidates λr (in the present case, there are b candidates, where b is a natural number) and one regularization function R(S, P) (Step  31 ; regularization parameter-regularization function preparation process). The regularization function R(S, P) used in the present embodiment is the sum of the L1-norm of the matrix S and that of the matrix P, i.e., R(S, P)=|S| 1 +|P| 1 . The L1-norm of a matrix means the sum of all matrix elements in the matrix. As for the regularization-parameter candidates λr, a plurality of positive real numbers are appropriately selected. 
     Next, for each of the b regularization-parameter candidates λr, the matrix candidate determiner  422  determines spectrum and profile matrices Srt and Prt which minimize the value of the loss function L(S, P)=D(X|SP)+λrR(S, P) (Step  32 ). The distance function D(X|SP)=Σ n,m D(X nm |(SP) nm ) is the total of the distances between the matrix elements X nm  of the data matrix X and the corresponding matrix elements (SP) nm  of the product SP. This function represents the degree of difference between the matrix elements of the data matrix X and those of the product SP. In the present embodiment, the generalized KL divergence D KL (x|y)=x log(x/y)−(x−y) is used as the distance function D(x|y) for each element. 
     The matrix candidate determiner  422  further determines a spectrum matrix candidate (first-matrix candidate) Sr and profile matrix candidate (second-matrix candidate) Pr for each regularization-parameter candidate λr by one of the following two methods (matrix candidate determination process). In the first method, the combination of the temporary candidates (Srt, Prt) are directly selected as a spectrum matrix candidate Sr and profile matrix candidate Pr (Step  33 ). 
     In the second method, the following operations are performed in place of Step  33 . Using Srt and Prt as the initial values, matrices Srt 2  and Prt 2  which minimize the value of a second loss function having no regularization term, L 2 (S, P)=D(X|SP), are determined (Step  33 - 1 ). These matrices Srt 2  and Prt 2  are selected as a spectrum matrix candidate Sr and profile matrix candidate Pr (Step  33 - 2 ). 
     After the combination (Sr, Pr) of the candidates of the spectrum matrix S and profile matrix P has been determined by one of the two methods, the probability distribution transformer  423  prepares a cumulative distribution function F nm  of the probability distribution corresponding to the distance function D(X nm |(SP) nm ) for each of the b regularization-parameter candidates λr (Step  34 ). Then, for each of the b regularization-parameter candidates λr as well as for each combination (X nm , (SrPr) nm ) of the matrix element X nm  of the data matrix X and the corresponding matrix element (SrPr) nm  of the product SrPr of the spectrum matrix candidate Sr and profile matrix candidate Pr, the probability distribution transformer  423  substitutes the values of those matrix elements into the cumulative distribution function F nm  to determine y nm =F nm (X nm |(SrPr) nm ) which is expected to show a standard uniform distribution (Step  35 ). It is commonly known that the cumulative distribution function F(X|SP) corresponding to the generalized KL divergence D KL (X|SP)=X log(X/SP)−(X−SP), which is the loss function used in the present embodiment, is a cumulative distribution function of a Poisson distribution. 
     Next, the goodness-of-fit calculator  424  calculates the goodness of fit between the empirical distribution y nm =F nm (X nm |(SrPr) nm ) determined by the probability distribution transformer  423  for each of the b regularization-parameter candidates λr and the cumulative distribution function of a standard uniform distribution (Step  36 ; goodness-of-fit calculation process). For the calculation of the goodness of fit, commonly known methods for calculating the goodness of fit in statistics are available, such as a Kolmogorov-Smirnov (KS) statistic, Cramer-von Mises statistic, or Anderson-Darling statistic. 
     Subsequently, the matrix determiner  425  compares the values of the goodness of fit respectively calculated for the regularization-parameter candidates λr, and selects, as the spectrum matrix S and profile matrix P, the spectrum matrix candidate Sr and profile matrix candidate Pr corresponding to the regularization-parameter candidate λr which yields the highest value of the goodness of fit (Step  37 ; matrix determination process). In place of the spectrum and profile matrices corresponding to the regularization-parameter candidate λr which yields the highest value of the goodness of fit, the spectrum matrix candidate Sr and profile matrix candidate Pr corresponding to the largest value of the regularization parameter λr among the regularization-parameter candidates λr which yield the values of the goodness of fit equal to or greater than a predetermined threshold may be selected as the spectrum matrix S and profile matrix P. Thus, the operation of the matrix factorization is completed. 
     (4) Example of Calculation of Matrix Factorization 
     An example of the calculation of the matrix factorization using the chromatograms shown in the left section of  FIG. 5  and the mass spectra shown in the right section of  FIG. 5  is hereinafter described. In the left section of the drawing, a chromatogram acquired by one measurement is divided into five chromatograms showing four peaks originating from four components and the background (BG). Each of the five chromatograms corresponds to one row of a data matrix. Accordingly, in the present example, the value of K in the actual data (obtained by an experiment) is five. The right section of  FIG. 5  shows five mass spectra which correspond to the five chromatograms, respectively. 
       FIG. 6  shows a large number of mass chromatograms acquired at different m/z values from the actual data (obtained by an experiment). This diagram shows the entire information held in the data matrix X. More specifically, one set of intensity values at a number of retention times in one mass chromatogram corresponds to one set of values of the matrix elements in one row of the data matrix X. On the other hand, one set of intensity values on the large number of mass chromatograms at one retention time corresponds to one set of values of the matrix elements in one column of the data matrix X. 
     For this data matrix X, a spectrum matrix candidate Sr and profile matrix candidate Pr were determined for three values of λr (1, 256 and 512) by the matrix factorization according to the present embodiment, and the goodness of fit was calculated for each case. 
       FIG. 7  shows the result obtained in the case of λr=1, where the chromatograms (left section) correspond to the rows of the matrix elements of the profile matrix candidate Pr, while the mass spectra (right section) correspond to the columns of the matrix elements of the spectrum matrix candidate Sr. Similarly,  FIG. 8  shows chromatograms and mass spectra obtained in the case of λr=512, and  FIG. 9  shows chromatograms and mass spectra obtained in the case of λr=256. The calculated value of the KS statistic is also shown in  FIGS. 7-9 . The KS statistic is a numerical value obtained by the Kolmogorov-Smirnov (KS) test. The smaller the numerical value is, the higher the goodness of fit is. 
     In the case of λr=1 ( FIG. 7 ), the KS statistic is 0.0924. The value of K in the determined profile matrix candidate Pr and spectrum matrix candidate Sr is 7, which is greater than the actual value (K=5). This means that the regularization was insufficient due to the too small value of λr. As a matter of fact, it is obvious that the obtained chromatograms and mass spectra do not agree with the actual data ( FIG. 5 ). 
     In the case of λr=512 ( FIG. 8 ), the KS statistic is 0.2652. The value of K in the determined profile matrix candidate Pr and spectrum matrix candidate Sr is 2, which is smaller than the actual value. This means that the regularization had an excessive effect due to the too large value of λr. It is obvious that the obtained chromatograms and mass spectra do not agree with the actual data ( FIG. 5 ). 
     On the other hand, in the case of λr=256 ( FIG. 9 ), the KS statistic is 0.0164, which is the lowest value among the three candidates. This means the highest goodness of fit among the three candidates. Accordingly, the profile matrix candidate Pr and spectrum matrix candidate Sr in the case of λr=256 should be selected as the profile matrix P and spectrum matrix S from the three candidates. The value of K in the obtained profile matrix candidate Pr and spectrum matrix candidate Sr is 5, which agrees with the actual data. The chromatograms and mass spectra obtained from the profile matrix P and spectrum matrix S are approximate to the actual data ( FIG. 5 ). 
     In the previously described example, there were three regularization-parameter candidates λr, from each of which a profile matrix candidate Pr and spectrum matrix candidate Sr were obtained and shown in the form of chromatograms and mass spectra. The number of regularization-parameter candidates λr is not limited to three. The larger the number of the regularization-parameter candidates λ is, the more accurate the ultimately obtained profile matrix P and spectrum matrix S will be. 
     (5) Other Notes 
     In the previous embodiment, the data matrix X is defined as a matrix with N rows and M columns, the spectrum matrix S is defined as a matrix with N rows and K columns, and the profile matrix P is defined as a matrix with K rows and M columns It is also possible to define the data matrix X as a matrix with M rows and N columns, the spectrum matrix S as a matrix with K rows and N columns, and the profile matrix P as a matrix with M rows and K columns. In that case, the profile matrix P corresponds to the first matrix, and the spectrum matrix S corresponds to the second matrix. The product PS should be used in place of the product SP (it should be noted that S and P in the present context do not represent the first and second matrices, but the spectrum and profile matrices in the present example). 
     The configuration of the chromatograph mass spectrometer is not limited to that of the previously described TOFMS  1 . For example, the present invention can also be applied in a chromatograph mass spectrometer which includes the combination of a mass filter (e.g., a quadrupole mass filter) and a collision cell in place of the ion trap  30  used in the previous embodiment, as well as an orthogonal acceleration TOF in place of the TOF  31  used in the previous embodiment. Furthermore, the present invention is not limited to TOFMSs but is also applicable in other types of chromatograph mass spectrometers. 
     The present invention can also be applied to an analysis of data acquired with an imaging mass spectrometer, imaging FT-IR or similar device other than the data acquired with chromatograph mass spectrometers. In the case of the imaging mass spectrometer, one of the first and second variables is m/z, and the other variable corresponds to a numerical value representing a position. In the case of the imaging FT-IR, one of the first and second variables is absorption wavelength, and the other variable corresponds to a numerical value representing a position. 
     In addition, it is needless to say that the present invention is not limited to the previous embodiment but can be changed or modified in various forms. 
     Modes of Invention 
     A person skilled in the art can understand that the previously described illustrative embodiment is a specific example of the following modes of the present invention. 
     (Clause 1) 
     A data analysis method according to Clause 1 is a method for determining a first matrix S with N rows and K columns and a second matrix P with K rows and M columns based on a data matrix X in which a set of data obtained from an analyzing device are arranged in N rows and M columns, where the N rows of data differ from each other in the value of a first variable, the M columns of data differ from each other in the value of a second variable, and the first matrix S and the second matrix P are determined so that the product SP approximates to the data matrix X, the method including: 
     a regularization parameter-regularization function preparation process for preparing a plurality of regularization-parameter candidates λr (where r is a natural number from 1 to r max ) and one regularization function R(S, P) which induces sparsity of the solution; 
     a matrix candidate determination process for solving an optimization problem for each of the plurality of regularization-parameter candidates λr so as to determine a matrix Srt as a candidate Sr of the first matrix S and a matrix Prt as a candidate Pr of the second matrix P, where the matrices Srt and Prt are determined so as to minimize the value of a loss function L(S, P)=D(X|SP)+λrR(S, P), where D(X|SP) is a distance function expressing the degree of difference between the data matrix X and the product SP, while λrR(S, P) is the product of the regularization-parameter candidate λr and the regularization function R(S, P); 
     a probability distribution transform process for determining, for each of the plurality of regularization-parameter candidates λr, a transformed value y nm =F nm (X nm |(SrPr) nm ) by a variable transform into a common probability distribution Pcommon for each combination of a matrix element X nm  of the data matrix X and a corresponding matrix element (SrPr) nm  of the product SrPr of the first-matrix candidate Sr and the second-matrix candidate Pr, using F nm  which is a function for the variable transform from a probability distribution P nm  corresponding to the distance function D(X nm |(SP) nm ) into the common probability distribution Pcommon; 
     a goodness-of-fit calculation process for determining, for each of the plurality of regularization-parameter candidates λr, a goodness of fit between the transformed value y nm  and a cumulative distribution function of the probability distribution Pcommon; and 
     a matrix determination process for selecting, as the first matrix S and the second matrix P, the first-matrix candidate Sr and the second-matrix candidate Pr determined for a regularization-parameter candidate λr which yields the highest value of the goodness of fit among the plurality of regularization-parameter candidates λr, or a regularization-parameter candidate λr which yields the goodness of fit higher than a predetermined threshold and also has the largest value of λr. 
     By the data analysis method according to Clause 1, a first matrix S and second matrix P whose factor number K is appropriate and close to the number of components contained in a sample can be determined based on a data matrix X obtained by a measurement on the sample, even when the number of components is unknown. 
     (Clause 2) 
     In the data analysis method according to Clause 2, the matrix candidate determination process in the data analysis method according to Clause 1 uses the matrix Srt and the matrix Prt as initial values for determining a matrix Srt 2  and a matrix Prt 2  which minimize the value of a second loss function with no regularization term, L2(S, P)=D(X|SP), and selects the matrix Srt 2  and the matrix Prt 2  as the first matrix candidate Sr and the second matrix candidate Pr, instead of selecting the matrix Srt and the matrix Prt as the first matrix candidate Sr and the second matrix candidate Pr. 
     In the data analysis method according to Clause 2, the matrices Srt and Prt which have been determined so as to minimize the value of the loss function L(S, P)=D(X|SP)+λrR(S, P) are used as initial values for making an additional determination for a second optimization which does not include the regularization term. This operation corrects a bias of the residual due to the regularization and enables the selection of first and second matrix candidates Sr and Pr which are closer to the actual data. Consequently, the first and second matrices S and P to be ultimately obtained will be more accurate. 
     (Clause 3) 
     In the data analysis method according to Clause 3, which is one mode of the data analysis method according to Clause 1 or 2, the regularization function R(S, P) is L1-norm, or a linear combination of L1-norm and L2-norm, or a function which applies a trace norm, det|S T S| or log det|S T S+δI| to the matrix S (where I is a unit matrix, and δ is a hyperparameter for controlling the regularization function) while placing a constraint on the solution so that the total of the values in each column of the matrix P should not exceed 1. 
     (Clause 4) 
     In the data analysis method according to Clause 4, which is one mode of the data analysis method according to one of Clauses 1-3, the cumulative distribution function is a function selected from a cumulative distribution function of a Gaussian distribution, a cumulative distribution function of a Poisson distribution, a cumulative distribution function of an exponential distribution, and a cumulative distribution function of a Tweedie distribution. 
     (Clause 5) 
     In the data analysis method according to Clause 5, which is one mode of the data analysis method according to one of Clauses 1-4, the goodness of fit is determined by a test selected from a Kolmogorov-Smirnov test, a Cramer-von Mises test, and an Anderson-Darling test. 
     (Clause 6) 
     In the data analysis method according to Clause 6, which is one mode of the data analysis method according to one of Clauses 1-4, when the variance σ nm   2  of the noise in each matrix element X nm  is previously known, the probability distribution Pcommon is defined as a standard normal distribution, the cumulative distribution function F nm (X nm |(SrPr) nm ) is defined as (X nm −(SrPr) nm )/∝ nm , and −|σ y   2 −1| is used as the goodness of fit, where σ y   2  is given by: 
     
       
         
           
             
               σ 
               y 
               2 
             
             = 
             
               
                 1 
                 
                   
                     N 
                     ⁢ 
                     M 
                   
                   - 
                   1 
                 
               
               ⁢ 
               
                 
                   ∑ 
                   
                     n 
                     , 
                     m 
                   
                 
                 ⁢ 
                 
                   y 
                   
                     n 
                     ⁢ 
                     m 
                   
                   2 
                 
               
             
           
         
       
     
     which is the unbiased variance of the transformed value y nm  whose mean value is assumed to be zero. 
     In the present invention, the various regularization functions R(S, P) mentioned in Clause 3 and the various cumulative functions F(X|SP) mentioned in Clause 4 can be appropriately used. For the calculation of the goodness of fit, the various methods mentioned in Clause 5 or 6, which are commonly known in the area of statistics, can be appropriately used. 
     (Clause 7) 
     In the data analysis method according to Clause 7, which is one mode of the data analysis method according to one of Clauses 1-6, the analyzing device is a chromatograph mass spectrometer, one of the first and second variables is m/z, and the other variable is a retention time. 
     (Clause 8) 
     In the data analysis method according to Clause 8, which is one mode of the data analysis method according to one of Clauses 1-6, the analyzing device is an imaging mass spectrometer, one of the first and second variables is m/z, and the other variable is a numerical value representing a position. 
     (Clause 9) 
     In the data analysis method according to Clause 9, which is one mode of the data analysis method according to one of Clauses 1-6, the analyzing device is an imaging Fourier transform infrared spectrophotometer, one of the first and second variables is absorption wavelength, and the other variable is a numerical value representing a position. 
     As described in Clauses 7-9, the present invention is suitably applicable to an analysis of data acquired by a chromatograph mass spectrometer, imaging mass spectrometer or imaging Fourier transform infrared spectrophotometer. 
     REFERENCE SIGNS LIST 
     
         
           1  . . . Liquid Chromatograph/Ion Trap Time-of-Flight Mass Spectrometer 
           10  . . . Liquid Chromatograph (LC) Unit 
           11  . . . Mobile Phase Container 
           12  . . . Liquid Supply Pump 
           13  . . . Injector 
           14  . . . Column 
           20  . . . Mass Spectrometry (MS) Unit 
           21  . . . Ionization Chamber 
           22  . . . ESI Nozzle 
           23  . . . Desolvation Tube 
           24  . . . First-Stage Intermediate Vacuum Chamber 
           25  . . . First Ion Guide 
           26  . . . Skimmer 
           27  . . . Second-Stage Intermediate Vacuum Chamber 
           28  . . . Second Ion Guide 
           29  . . . Analysis Chamber 
           30  . . . Ion Trap 
           31  . . . Time-of-Flight (TOF) Mass Separator 
           32  . . . Reflectron Electrode 
           33  . . . Ion Detector 
           34  . . . Analogue-to-Digital (A/D) Converter 
           40  . . . Data Processing Unit 
           41  . . . Data Matrix Creator 
           42  . . . Matrix Factorization Executer 
           421  . . . Regularization Parameter-Regularization Function Preparer 
           422  . . . Matrix Candidate Determiner 
           423  . . . Probability Distribution Transformer 
           424  . . . Goodness-of-Fit Calculator 
           425  . . . Matrix Determiner 
           43  . . . m/z Detector 
           44  . . . Retention Time Detector 
           45  . . . MS 2  Analysis Execution Condition Determiner 
           50  . . . Analysis Control Unit 
           51  . . . LC/MS Analysis Executer 
           52  . . . LC/MS 2  Analysis Executer 
           61  . . . Storage Unit 
           62  . . . Display Unit 
           63  . . . Operation Unit 
           71  . . . Three-Dimensional Data 
           72  . . . Mass Spectrum 
           73  . . . Chromatogram