Mass spectrometry data display and processing device and computer readable medium

Abstract

A mass spectrometry data display processing device and a computer-readable medium are provided to present the mass spectrum of a microorganism to be tested and the existing genome association information so that the relationship between the two can be easily understood. A spectrum acquisition unit (41) is provided in the mass spectrometry data display processing device to acquire the mass spectrum (80) of the microorganism to be tested; a genome association information acquisition unit (42) to acquire the genome association information of a known microorganism estimated to be the same as or related to the microorganism to be tested based on the mass spectrum; a correspondence determination unit (43) to determine the correspondence between the peak on the mass spectrum and the protein expressed in the known microorganism based on the mass spectrum and the genome association information; and a display control unit (45) to display an identifier (81) and a genome map (70) together with the mass spectrum on a display device, wherein the identifier (81) indicates which protein the peak corresponds to, and the genome map (70) indicates the position of the gene encoding each protein on the genome.

Description

Technical Field

[0001] The invention relates to a mass spectrum analysis data display and processing device. Background Art

[0002] In recent years, a method for identifying microorganisms using mass spectrometry has been developed. In this method, first, a solution containing proteins extracted from the microorganism to be tested or a suspension of the microorganism to be tested is analyzed using a mass spectrometry device that uses a soft ionization method such as MALDI (Matrix Assisted Laser Desorption / Ionization). In addition, a "soft" ionization method refers to an ionization method in which high molecular weight compounds are not easily decomposed. Then, by comparing the obtained mass spectrum with the mass spectrum of known microorganisms, the genus, species or strain of the microorganism to be tested is determined. This method uses the mass spectrum pattern as information unique to each microorganism (i.e., fingerprint), so it is called the fingerprint method.

[0003] However, in the fingerprint method, it is not determined which protein each peak appearing on the mass spectrum originates from, which has problems in the theoretical basis and reliability of identification. Therefore, in order to solve this problem, the following method has been developed: using the fact that about half of the peaks obtained by mass spectrometry analysis of microorganisms are derived from ribosomal proteins, the mass-to-charge ratio of the peak obtained by mass spectrometry is associated with the calculated mass inferred from the amino acid sequence obtained by translating the base sequence information of the ribosomal protein gene, thereby attributing the type of protein that is the source of the peak to the peak (for example, refer to Patent Document 1). According to this method, mass spectrometry can be used to perform microbial identification with high reliability based on theoretical basis.

[0004] Prior art literature

[0005] Patent Literature

[0006] Patent Document 1: Japanese Patent Application Laid-Open No. 2007-316063 Summary of the invention

[0007] Problem that the invention aims to solve

[0008] In order to attribute the type of protein that is the source of a mass spectrum peak to the mass spectrum peak, genome information or protein information of various microorganisms is required. In recent years, genome analysis of microorganisms has been developing. If the species of a microorganism is known, it is easy to know the genome base sequence of the microorganism, the position of each gene on the genome base sequence, the base sequence of each gene, the name of the protein encoded by each gene, the amino acid sequence of each protein, and other information (hereinafter referred to as "genome-related information").

[0009] However, conventional microbial analysis using mass spectrometry has a problem in that it is difficult for an analyst to intuitively understand the relationship between a mass spectrum obtained by mass spectrometry analysis of a test microorganism and the above-mentioned existing genome-related information.

[0010] The present invention has been made in view of the above-mentioned problems, and an object of the present invention is to present the mass spectrum of a test microorganism and existing genome correlation information so that an analyst can easily understand the relationship between the two.

[0011] Solutions for solving problems

[0012] The mass spectrometry data display processing device according to the present invention, which has been completed in order to solve the above-mentioned problems, displays data obtained by mass spectrometry on a screen of a display device, and the mass spectrometry data display processing device comprises:

[0013] a spectrum acquisition unit that acquires a mass spectrum obtained by performing mass spectrometry analysis on the microorganism to be tested;

[0014] a genome association information acquisition unit that acquires genome association information, the genome association information including information on a plurality of proteins encoded by a genome of a known microorganism estimated to be identical to or related to the microorganism to be tested based on the mass spectrum, and information indicating positions on the genome of a plurality of genes encoding each of the plurality of proteins;

[0015] a correspondence determination unit, which determines the correspondence between the plurality of peaks on the mass spectrum and the plurality of proteins based on the mass spectrum and the genome association information; and

[0016] A display control unit displays an identifier and a genome map together with the mass spectrum on the screen, wherein the identifier is an identifier assigned to at least a part of the multiple peaks and indicates a correspondence between the assigned peak and one of the multiple proteins determined by the correspondence determination unit, and the genome map is a genome map produced based on the genome association information and indicating the positions of the multiple genes on the genome.

[0017] Effects of the Invention

[0018] According to the mass spectrometry data display processing device of the present invention, the mass spectrum of the microorganism to be tested and the existing genome correlation information can be presented so that the analysis person can easily understand the relationship between the two. BRIEF DESCRIPTION OF THE DRAWINGS

[0019] Figure 1 It is a schematic configuration diagram of a mass spectrometry system according to one embodiment of the present invention.

[0020] Figure 2 : is a flowchart showing the processing procedure of the mass spectrometry system involved in this embodiment.

[0021] Figure 3 This is a diagram showing an example of screen display in this embodiment.

[0022] Figure 4 FIG. 1 is a diagram showing an example of a screen display after a peak selection is performed by the user in this embodiment.

[0023] Description of Reference Numerals

[0024] 10: mass spectrometry analysis unit; 20: analysis unit; 30: storage unit; 32: spectrum creation program; 33: microorganism identification program; 34: database for microorganism identification; 35: display processing program; 36: correspondence storage unit; 41: spectrum acquisition unit; 42: genome association information acquisition unit; 43: correspondence determination unit; 44: genome map generation unit; 45: display control unit; 52: genome database; 60: display screen; 70: genome map; 80: mass spectrum; 81: peak label; 82: mark; 90: protein information display column. DETAILED DESCRIPTION

[0025] Hereinafter, a mode for carrying out the present invention will be described with reference to the drawings. Figure 1 1 is a schematic diagram of the mass spectrometry system according to the present embodiment. The mass spectrometry system includes a mass spectrometry unit 10 and an analysis unit 20 (as one embodiment of the mass spectrometry data display processing device according to the present invention).

[0026] The mass spectrometer 10 includes: an ionization unit 11, which ionizes molecules and atoms in a sample by matrix-assisted laser desorption ionization (MALDI); and a time-of-flight mass separator (TOF) 12, which separates various ions ejected from the ionization unit 11 according to the mass-to-charge ratio. The TOF 12 includes: an extraction electrode 13, which is used to extract ions from the ionization unit 11 and introduce them into the ion flight space in the TOF 12; and a detector 14, which detects the ions after mass separation in the ion flight space. However, the structure of the mass spectrometer 10 is not limited to this, and various modifications can be made.

[0027] The entity of the analysis unit 20 is a computer such as a workstation or a personal computer, and a CPU (Central Processing Unit) 21 as a central processing unit is connected to a memory 22, a display unit 23 composed of an LCD (Liquid Crystal Display), etc., an input unit 24 composed of a keyboard, a mouse, etc., and a storage unit 30 composed of a large-capacity storage device such as a hard disk and an SSD (Solid State Drive). The storage unit 30 stores an OS (Operating System) 31, a spectrum creation program 32, a microorganism identification program 33, and a display processing program 35 (as one form of the program involved in the present invention). In addition, a microorganism identification database 34 is stored in the storage unit 30, and a corresponding relationship storage unit 36 ​​is provided. The analysis unit 20 also has an interface (I / F) 25, which is used for direct connection with an external device or connection with an external device via a network such as a LAN (Local Area Network) or the Internet. The analysis unit 20 is connected to the mass spectrometry analysis unit 10 and the genome database 52 through the interface 25 via a network cable NW (or wireless LAN) or the Internet 51.

[0028] exist Figure 1 , a spectrum acquisition unit 41, a genome association information acquisition unit 42, a correspondence determination unit 43, a genome map generation unit 44, and a display control unit 45 are shown in association with the display processing program 35. They are basically functional units implemented in the form of software by the CPU 21 executing the display processing program 35. In addition, the display processing program 35 does not necessarily need to be a single program, for example, it can also be a function embedded in the microorganism identification program 33 or embedded in a part of the program for controlling the mass spectrometry analysis unit 10, and its form is not particularly limited. In addition, as the microorganism identification program 33, for example, a program for performing microorganism identification by an existing fingerprint method can be used.

[0029] In addition, Figure 1 The structure is set as follows: the spectrum creation program 32, the microorganism identification program 33, the display processing program 35, the microorganism identification database 34 and the correspondence storage unit 36 ​​are installed in the terminal operated by the user, but it can also be set as the following structure: a part or all of the programs except the display processing program 35 are set in other devices connected to the terminal through a computer network, and the processing based on the programs set in the other devices and / or the access to the database are executed according to the instructions from the terminal. In addition, Figure 1In the figure, the genome database 52 is connected to the terminal operated by the user via the Internet 51, but is not limited to this. The genome database 52 can also be installed in other terminals configured in the same facility as the terminal operated by the user, or in the storage unit 30 set in the terminal operated by the user.

[0030] A mass list related to a plurality of known microorganisms is registered in the database 34 for microorganism identification. The mass list is a list of m / z of ions detected when mass spectrometry is performed on each known microorganism. In addition to the value of the m / z, the mass list also contains at least information (classification information) of the taxonomic group (family, genus, species or strain, etc.) to which the known microorganism belongs. Such a mass list can be prepared based on data (measured data) obtained by actually performing mass spectrometry on various known microorganisms in advance by the same ionization method and mass separation method as the method used by the mass spectrometry analysis unit 10. When the mass list is prepared based on the measured data, first, the peaks appearing in the specified m / z range are extracted from the mass spectrum obtained as the measured data. At this time, by setting the m / z range to about 2,000 to 35,000, peaks mainly derived from proteins can be extracted. In addition, by extracting only peaks whose peak heights (relative intensities) are above a specified threshold, undesirable peaks (noise) can be excluded. In addition, since the ribosomal protein group is expressed in large quantities in cells, by appropriately setting the threshold, most of the m / z recorded in the mass list can be set as the part derived from the ribosomal protein. Then, the m / z of the peak extracted in the above manner and the intensity of the peak are listed for each of the known microorganisms, and registered in the microorganism identification database 34 after adding the classification information, etc. In addition, in order to suppress the deviation of gene expression caused by the culture conditions, it is desirable to standardize the culture conditions of each known microorganism used to collect the measured data in advance.

[0031] In the genome database 52, multiple genome association information related to each of the multiple known microorganisms is registered. The genome association information includes, for example, the genome base sequence, the position of each gene on the genome base sequence, the base sequence of each gene, the name of the protein encoded by each gene, and the amino acid sequence of these proteins. These genome association information are stored in association with the identifier of the known microorganism (for example, the registration number of the microorganism, etc.), the name of the microorganism (genus name, species name or strain name, etc.). As such a genome database 52, for example, a public database provided by an international organization (GenBank, EMBL or DDBJ, etc.) can be used.

[0032] Reference Figure 2The flowchart of FIG. 1 illustrates a process of analyzing microorganisms using the mass spectrometry system according to the present embodiment and a process of displaying mass spectrometry data.

[0033] First, the user prepares a sample containing constituent components of the microorganism to be tested, and places the sample in the ionization unit 11 of the mass spectrometry unit 10 to perform mass spectrometry analysis. At this time, as the sample, in addition to using a microbial extract of the microorganism to be tested or a substance obtained by purifying cell constituent components such as ribosomal proteins from a microbial extract, it is also possible to use microorganisms or cell suspensions directly.

[0034] When the mass spectrometer 10 analyzes the sample, the spectrum creation program 32 of the analyzer 20 acquires the detection signal acquired by the detector 14 of the mass spectrometer 10 via the interface 25 and creates a mass spectrum of the microorganism based on the detection signal (step S11).

[0035] Next, the microorganism identification program 33 compares the mass spectrum of the microorganism to be tested generated in step S11 with the mass list of each known microorganism included in the microorganism identification database 34, and extracts a mass list having an m / z pattern similar to the mass spectrum of the microorganism to be tested, for example, a mass list containing a large number of ions whose m / z is consistent with each peak in the mass spectrum of the microorganism to be tested within a specified error range (step S12).

[0036] Next, the microorganism identification program 33 refers to the classification information stored in the microorganism identification database 34 corresponding to the mass list extracted in step S12 to identify the classification (for example, species or genus) of the known microorganism corresponding to the mass list (step S13).

[0037] When the classification of the detected microorganism is determined in advance by other methods, the process by the microorganism identification program 33 (ie, steps S12 and S13) may be skipped and the process by the display processing program 35 (ie, steps S14 to S19) may be entered.

[0038] Next, the spectrum acquisition unit 41 of the display processing program 35 acquires the mass spectrum of the test microorganism generated in step S11.

[0039] Next, the genome association information acquisition unit 42 accesses the genome database 52 via the interface 25 and the Internet 51 to acquire the genome association information of the known microorganism corresponding to the classification determined in step S13 (i.e., the known microorganism estimated to be the same as or related to the microorganism to be tested) (step S14). Specifically, for example, when the species to which the microorganism to be tested belongs is determined in step S13, the genome association information acquisition unit 42 searches the genome database 52 using the species name as a query condition to acquire the genome association information of the known microorganism belonging to the species.

[0040] In addition, in the case where genome association information related to multiple microbial species or multiple microbial strains belonging to the classification determined in step S13 is registered in the genome database 52, genome association information related to the type species (Type species) or type strain (Type strain) in the multiple microbial species or microbial strains is obtained. In addition, in the case where information representing the reliability of genome association information related to each known microorganism is registered in the genome database, the information with the highest reliability in the genome association information of the multiple microbial species or microbial strains can be obtained. For example, status information such as "Finished (finished)", "Permanent draft (permanent draft)" or "Draft (draft)" representing the progress of the genome analysis of each microbial strain is sometimes registered in the above-mentioned public database. In this case, the reliability of the genome association information is in the order of "Finished", "Permanent draft", and "Draft" from high to low. In addition, in the case where there are multiple microbial species or microbial strains whose reliability of genome association information is the same, the genome association information of the type species or type strain can be obtained.

[0041] In addition, here, in step S14, it is set that the genome association information acquisition unit 42 automatically searches the genome database 52 to obtain appropriate genome association information, but it is not limited to this. It can also be set that the user uses the input unit 24 to perform a prescribed operation to search the genome database 52 with the classification name determined in step S13 as the query condition, and the genome association information acquisition unit 42 obtains the genome association information related to the known microorganism selected by the user from the search results from the genome database 52.

[0042] In addition, Figure 1 Although only a single genome database 52 is shown in the figure, the genome association information acquisition unit 42 of this embodiment can also acquire the above-mentioned genome association information from multiple genome databases independent of each other (for example, databases provided by different organizations, etc.).

[0043] Next, the correspondence determination unit 43 determines the correspondence between each peak on the mass spectrum and the protein expressed (or estimated to be expressed) in the known microorganism based on the mass spectrum generated in step S11 and the genome association information obtained in step S14 (step S15). Specifically, first, the correspondence determination unit 43 extracts the amino acid sequence of the specified protein from the genome association information obtained in step S14. In addition, the specified protein can be all proteins registered in the genome database 52 in association with the known microorganism, or a part of the protein pre-specified by the user (for example, all or part of the ribosomal protein). Next, the correspondence determination unit 43 calculates the calculated molecular weight of the specified protein by calculation based on the amino acid sequence, and then converts the calculated molecular weight into the theoretical m / z of the specified protein. Here, the theoretical m / z refers to the m / z of the ion that is presumed to be detected when the protein is subjected to mass spectrometry analysis. It is known that when analyzing a biological sample by mass spectrometry accompanied by ionization of the sample based on MALDI, [M+H] is mainly detected. + (M is a molecule, H is a hydrogen atom), [MH] - or[M+Na] + (Na is a sodium atom) and other molecular weight associated ions. Therefore, as long as the mass spectrometry analysis conditions are determined, the conversion from the calculated molecular weight of each protein to the theoretical m / z can be easily performed. In addition, in the case where the calculated molecular weight of the protein expressed (or estimated to be expressed) in the known microorganism is included in the genome database 52, the calculated molecular weight can also be used to calculate the theoretical m / z. Next, the correspondence determination unit 43 searches for a peak consistent with the theoretical m / z obtained above within a specified error range from the mass spectrum of the test sample for each of the specified proteins. Then, for the protein for which a consistent peak is found, it is judged that the protein is the protein corresponding to the peak, and the correspondence between the protein and the peak is stored in the correspondence storage unit 36.

[0044] Next, the genome map generation unit 44 generates a genome map indicating the position of each gene on the genome base sequence of the known microorganism based on the genome association information acquired in step S14 (step S16 ).

[0045] Next, under the control of the display control unit 45, the mass spectrum 80 generated in step S11, the peak label (equivalent to the identifier in the present invention) 81 indicating the correspondence determined in step S15, and the genome map 70 generated in step S16 are displayed on the screen of the display unit 23 (step S17).

[0046] Figure 3An example of the screen display at this time is shown. In the example of this figure, a genome map 70 is displayed on the upper part of the display screen 60, and a mass spectrum 80 of the test microorganism is displayed on the lower part of the display screen 60.

[0047] Furthermore, a peak label 81 indicating the name of the protein corresponding to the peak is displayed at the peak whose corresponding protein is determined in step S15 among the plurality of peaks on the mass spectrum 80. For example, in the example of the figure, the peak label 81 indicated by the character string "L36" means that the peak is a peak corresponding to "ribosomal protein L36".

[0048] When the user selects a peak on the mass spectrum 80 via the input unit 24 (“Yes” in step S18), the display screen 60 is displayed on the display unit 23. Figure 4 The peak (hereinafter referred to as the "selected peak") is highlighted on the display screen 60 as shown (i.e., a mark 82 is displayed near the selected peak), and when the protein corresponding to the selected peak is determined in step S15, a protein information display bar 90 is displayed on the upper right side of the display screen 60, and the protein information display bar 90 is used to display information related to the protein corresponding to the selected peak (hereinafter referred to as the "selected protein") (step S19). In addition, the user selects the peak by, for example, clicking on any peak or peak label 81 on the display screen 60. Here, the display control unit 45 and the input unit 24 of this embodiment correspond to the peak selection receiving unit in the present invention.

[0049] In addition, Figure 4 In FIG. 7 , as an example of the highlighted display, a mark 82 indicating that the peak is a selected peak is assigned near the selected peak, but the highlighted display is not limited thereto. For example, the selected peak may be displayed in a color or thickness different from other peaks, or the peak label assigned to the selected peak may be displayed in a color or font different from other peak labels. In addition to the highlighted display of the selected peak, the position of the gene encoding the selected protein on the genome map 70 may also be highlighted.

[0050] The protein information display column 90 has a dialog box shape extending from the position of the gene encoding the selected protein on the genome map 70. The protein information display column 90 displays information related to the selected protein, such as the name of the selected protein, the base sequence of the gene encoding the selected protein, the identification number of the gene on the genome database 52, the amino acid sequence and theoretical m / z of the selected protein, and the identification number of the selected protein on the genome database 52.

[0051] Thus, according to the mass spectrometry analysis system involved in this embodiment, the mass spectrum of the tested microorganism and the existing genome association information are displayed in a manner that allows the user to easily understand the relationship between the two. Therefore, for example, even a microbiological researcher who is not proficient in mass spectrometry analysis can easily grasp the mass spectrometry analysis results of the tested microorganism.

[0052] [Various methods]

[0053] It will be understood by those skilled in the art that the above-described exemplary embodiments are specific examples of the following aspects.

[0054] (Item 1) A mass spectrometry data display processing device according to one embodiment of the present invention displays data obtained by mass spectrometry on a screen of a display device, the mass spectrometry data display processing device comprising:

[0055] a spectrum acquisition unit that acquires a mass spectrum obtained by performing mass spectrometry analysis on the microorganism to be tested;

[0056] a genome association information acquisition unit that acquires genome association information, the genome association information including information on a plurality of proteins encoded by a genome of a known microorganism estimated to be identical to or related to the microorganism to be tested based on the mass spectrum, and information indicating positions on the genome of a plurality of genes encoding each of the plurality of proteins;

[0057] a correspondence determination unit, which determines the correspondence between the plurality of peaks on the mass spectrum and the plurality of proteins based on the mass spectrum and the genome association information; and

[0058] A display control unit displays an identifier and a genome map together with the mass spectrum on the screen, wherein the identifier is an identifier assigned to at least a part of the multiple peaks and indicates a correspondence between the assigned peak and one of the multiple proteins determined by the correspondence determination unit, and the genome map is a genome map produced based on the genome association information and indicating the positions of the multiple genes on the genome.

[0059] According to the mass spectrum analysis data display processing device described in the first item, the user can grasp at once which protein each peak of the mass spectrum corresponds to and where the gene encoding the protein exists on the genome.

[0060] (Item 2) Regarding a mass spectrometry data display and processing device according to another embodiment of the present invention, in the mass spectrometry data display and processing device described in Item 1,

[0061] The method further comprises a peak selection accepting unit configured to allow a user to select a peak from among the plurality of peaks on the mass spectrum displayed on the screen,

[0062] When the peak selection accepting unit selects the one peak, the display control unit emphatically displays the position of a gene encoding a protein corresponding to the peak among the plurality of proteins on the genome map.

[0063] According to the mass spectrometry data display processing device described in the second item, the user can intuitively understand the position of the gene corresponding to a peak on the genome simply by selecting the peak.

[0064] (Item 3) Regarding a mass spectrometry data display and processing device according to another embodiment of the present invention, in the mass spectrometry data display and processing device described in Item 1,

[0065] The method further comprises a peak selection accepting unit configured to allow a user to select a peak from among the plurality of peaks on the mass spectrum displayed on the screen,

[0066] The genome association information also includes information on the amino acid sequences of the plurality of proteins or the base sequences of the genes encoding the proteins.

[0067] When the peak selection accepting unit selects the one peak, the display control unit further displays on the screen an amino acid sequence of a protein corresponding to the peak among the plurality of proteins or a base sequence of a gene encoding the protein.

[0068] According to the mass spectrum analysis data display processing device described in the third aspect, the user can easily refer to the amino acid sequence of the protein or the base sequence of the gene corresponding to a certain peak simply by selecting the peak.

[0069] (Item 4) A program according to another aspect of the present invention is a program for causing a computer to function as the mass spectrometry data display processing device according to any one of Items 1 to 3.

Claims

1. A mass spectrometry data display processing device, which displays data obtained through mass spectrometry on a screen of a display device, the mass spectrometry data display processing device comprising: a spectrum acquisition unit that acquires a mass spectrum obtained by performing mass spectrometry analysis on the microorganism to be tested; a genome association information acquisition unit that acquires genome association information, the genome association information including information on a plurality of proteins encoded by a genome of a known microorganism estimated to be identical to or related to the microorganism to be tested based on the mass spectrum, and information indicating positions on the genome of a plurality of genes encoding each of the plurality of proteins; a correspondence determination unit, which determines the correspondence between the plurality of peaks on the mass spectrum and the plurality of proteins based on the mass spectrum and the genome association information; A genome map generating unit, which generates a genome map indicating the positions of the plurality of genes on the genome based on the genome association information; as well as a display control unit that causes an identifier and the genome map to be displayed on the screen together with the mass spectrum, wherein the identifier is an identifier assigned to at least a portion of the plurality of peaks and indicates a correspondence between the assigned peak and one of the plurality of proteins determined by the correspondence determination unit, The mass spectrum analysis data display processing device further comprises a peak selection accepting unit, the peak selection accepting unit being used to allow a user to select a peak from the plurality of peaks on the mass spectrum displayed on the screen. When the peak selection accepting unit selects the one peak, the display control unit emphatically displays the position of a gene encoding a protein corresponding to the peak among the plurality of proteins on the genome map.

2. The mass spectrometry data display and processing device according to claim 1, characterized in that: The method further comprises a peak selection accepting unit configured to allow a user to select a peak from among the plurality of peaks on the mass spectrum displayed on the screen, The genome association information also includes information on the amino acid sequences of the plurality of proteins or the base sequences of the genes encoding the proteins. When the peak selection accepting unit selects the peak, the display control unit further displays on the screen an amino acid sequence of a protein corresponding to the peak among the plurality of proteins or a base sequence of a gene encoding the protein.

3. A non-transitory computer-readable medium, The non-transitory computer-readable medium records a program for causing a computer to function as the mass spectrometry data display processing device according to claim 1 or 2.

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