CN102788849B - Novel method for chromatography-mass spectrometry metabolomics data analysis - Google Patents
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Abstract
The present invention relates to a novel method for chromatography-mass spectrometry metabolomics data analysis, and belongs to the technical field of analytical chemistry. Based on chromatography-mass spectrometry data characteristics, the method establishes a metabolite mass spectrometry database XMet; then the XMet is projected to a statistical analysis model established by samples in the study system, so as to obtain a metabolite projection score matrix TMet; first two columns of the TMet are plotted to obtain metabolites with differentiation; and metabolites with differentiation can be identified through retrieval of the XMet and the mass spectrometry database. Based on the former methods, the invention sets up the novel method for chromatography-mass spectrometry metabolomics data analysis, so as to conveniently screen and directly identify the metabolites with differentiation, thereby effectively solving the problems in the existing gas chromatography-mass spectrometry metabolomics data analysis strategy.
Description
Technical field
The present invention relates to a kind of chromatography-mass spectroscopy metabolism group data analysing method, belong to technical field of analytical chemistry.
Background technology
Metabolism group is the emerging technology in systems biology field, and chromatograph-mass spectrometer coupling (as gas chromatography mass spectrometry GC-MS, LC-MS LC-MS etc.) is the main flow analytical technology in metabolism group research.The chromatograph-mas spectrometer device often produces mass data, how these data is effectively analyzed, thereby is obtained the metabolic profile feature of relevant research object, is gordian technique and the bottleneck problem in this area research at present.
At present, the strategy commonly used of research chromatography-mass spectroscopy metabolism group data be ms fragment peak intensity take retention time Rt-mass-to-charge ratio m/z place as variable, first the mass spectrum fragment peak is detected, aligns, the information after then processing is carried out statistical analysis.But, there is following point in this Stakeout ﹠ Homicide Preservation Strategy: (1) adopts this strategy, each sample can produce and reach thousands of variablees (intensity at ms fragment peak), and in metabolism group research, sample number is generally tens, to cause thus variable number and sample number proportional imbalance, for subsequent analysis is brought problem; (2) this strategy is paid close attention to mass spectra peak information, and mass spectra peak also comprises adduction peak, isotopic peak etc. except comprising fragment ion peak, therefore has approximately 90% redundant information in above-mentioned a large amount of variablees; And variable is generally the strength information at certain mass-to-charge ratio and retention time place record, abovely all makes the later stage become complicated to the qualitative discriminating of otherness metabolin; (3) because the kind of endogenous metabolism thing in metabolism group research is numerous, content does not wait, and the phenomenons such as chromatographic peak is overlapping, distortion sometimes may occur, thereby brings error for data handling procedure, and affects the reliability of follow-up statistic analysis result.
For overcoming the qualitative problem of differentiating difficulty of otherness metabolin in the analysis of nuclear magnetic resonance metabolism group, the Switzerland scholar proposes a kind of novel metabolism group data analysing method---(the Metabolite Projection Analysis of metabolin shadow casting technique, MPA) (F.Dieterle, A.Ross, G.Schlottebeck, H.Senn.Anal.Chem.78 (2006) 3551-3561).At first they collect the nuclear magnetic resonance spectrum of multiple metabolin, then the wave spectrum of these metabolins is projected to the Statistic analysis models of being set up by sample, thereby can directly carries out qualitative discriminating to the otherness metabolin.But the MPA method is set up for nuclear magnetic resonance data, and its necessary condition is the nuclear magnetic resonance spectrum information that obtains metabolin; And biological specimen generally comprises hundreds and thousands of kinds of metabolins, and the spectral information that therefore will collect so many metabolic product is difficult to accomplish.As the main flow analytical technology in metabolism group research, in the chromatography-mass spectroscopy data, itself has just comprised the Information in Mass Spectra of each metabolin.Therefore, the present invention improves and expands the MPA method, has set up a kind of New Policy of studying chromatography-mass spectroscopy metabolism group data, and can effectively solve the problem that exists in existing chromatography-mass spectroscopy metabolism group Stakeout ﹠ Homicide Preservation Strategy.
Summary of the invention
Technical matters to be solved by this invention is to have set up the new method of a kind of chromatography-mass spectroscopy metabolism group data analysis.The method has overcome the shortcoming of background technology, need not to collect in advance the spectral information of metabolin as background technology, can carry out easily data analysis, and the specific metabolic thing is carried out screening and identification.
The invention provides the method for a kind of chromatography-mass spectroscopy metabolism group data analysis, comprise following steps:
(1) identification at metabolin peak
At first take out equal volume (as 20 microlitres) from each sample of the research system that comprises normal group, model group, administration group, set up Quality Control (QC) sample after mixing; Get total ion current chromatogram (TIC) data of QC sample, choose signal to noise ratio (S/N ratio) wherein greater than 3 chromatographic peak, be designated as peak_i, adopt chemometrics method to carry out purity detecting to peak_i: for pure chromatographic peak, record the retention time at left and right border and the peak value place of each chromatographic peak, be designated as respectively L
Peak_i, R
Peak_iAnd A
Peak_iFor be judged to be overlapping chromatographic peak through purity check, adopt chemometrics method to resolve, obtain the pure color that comprises in Resolution of overlapping chromatographic peaks spectrum and pure Information in Mass Spectra;
(2) foundation of the pure mass spectral database of metabolin
Based on the chromatography-mass spectroscopy data of QC sample, for each chromatographic peak peak_i, with it at L
Peak_iAnd R
Peak_iAll mass spectrometric datas in the retention time scope sum up, on average, to obtain to characterize the Information in Mass Spectra of the corresponding metabolin of chromatographic peak peak_i; For Resolution of overlapping chromatographic peaks, the employing chemometrics method is resolved the pure mass spectrum that obtains can be directly as the Information in Mass Spectra that characterizes metabolin that Resolution of overlapping chromatographic peaks comprises; Above-mentioned two part Information in Mass Spectras are merged, can obtain the pure mass spectral database of the metabolin that comprises in the QC sample, be designated as X
MetX
MetIn comprised the pure Information in Mass Spectra of the metabolin of all samples in the research system;
(3) foundation of Statistic analysis models
, for each sample in research system, it is located to record in each mass-to-charge ratio (m/z) chromatographic data that obtains sum up, to obtain its total mass spectrum; Total mass spectrum alignment with all samples, then merge the total mass spectrometric data X that obtains each sample in research system
M * n, wherein m is sample number, n is the mass spectrum port number; To X
M * nCarry out principal component analysis (PCA) (PCA) or offset minimum binary-discriminatory analysis (PLS-DA), set up Statistic analysis models, obtain X
M * nScore matrix T and loading matrix P; The first two row to score matrix T are drawn, and namely observable draws the classification situation of sample in research system;
(4) metabolin Projection Analysis
According to following formula, with X
MetBe projected to the loading matrix P in above-mentioned Statistic analysis models, can obtain X
MetScore matrix T
Met:
T
Met＝X
MetP
With T
MetThe first two row of matrix are drawn, and upper each point of figure characterizes a metabolin, T
MetBe the metabolin of otherness in figure away from the metabolin of initial point, and the first two row of itself and T matrix respectively to organize the direction of sample in drawing consistent; According to T
MetThe numbering of otherness metabolin on figure, can retrieve X
MetDraw corresponding Information in Mass Spectra, can carry out qualitative discriminating to the otherness metabolin by retrieval mass spectrometric data storehouse finally.
Preferably, in said method, the chemometrics method for purity detecting can independently be selected from Heuristic Evolving Latent Projection, evolving factor analysis, principal component analysis (PCA), derivative method or orthographic projection.More preferably, the chemometrics method of purity detecting is Heuristic Evolving Latent Projection.
Preferably, the Chemical Measurement analytic method of the Resolution of overlapping chromatographic peaks described in said method can independently be selected from Heuristic Evolving Latent Projection, slice-scan technique, Window factor analysis, orthographic projection or polynary curve resolution method.More preferably, the Chemical Measurement analytic method of Resolution of overlapping chromatographic peaks is Heuristic Evolving Latent Projection.
Method provided by the invention has following good effect:
1, set up a kind of can be to the new method of chromatography-mass spectroscopy metabolism group data analysis;
2, the metabolism group data analysing method that adopts the present invention to propose, can screen easily the otherness metabolin and can directly carry out qualitative discriminating;
3, the method for the present invention's proposition not only can effectively be identified the otherness metabolin that existing method is found, but also can find some otherness metabolins that existing method can't be found.
Description of drawings
Fig. 1 is in the metabolism group research of rats with myocardial ischemia blood plasma, the shot chart in the PLS-DA model of being set up by the total mass spectrometric data of each sample.
-myocardial ischemia group;
-positive drug group.
The score matrix T of Fig. 2 for adopting this method to draw
MetFigure, each point represents a metabolin, figure below is the enlarged drawing of part in the red frame of upper figure.
Embodiment
Below describe according to drawings and embodiments technical scheme of the present invention in detail, and illustrate good effect of the present invention, but be not construed as limiting the invention.
The metabolism group research of embodiment myocardial ischemia (Myocardial ischemia, MI) rat plasma.
Zoopery: the SD male rat is divided into 3 groups at random, 6 every group: A. sham-operation group; The B.MI group; C. positive drug group.Gastric infusion, A, B group gives solvent, and the C group gives ISDN (5mg/kg/d), continuous 5 days.Set up myocardial infarction and ischemia model after administration last day: after the SD rat anesthesia,, in third and fourth intercostal space,, along left border of sternum 1cm place, cut off wall of the chest muscle and expose thoracic cavity, cut off pericardium, expose heart, between pulmonary conus and left auricle of heart lower edge, with 5-0 suture line following coronary artery occlusion left anterior descending branch (the sham-operation group is omitted this step), immediately heart is put back to, squeeze the thoracic cavity air, use the hemostatic forceps closed-chest, sew up a wound.Postoperative 5 hours, after the intraperitoneal anesthesia animal, femoral artery was got blood 1mL, and separated plasma is standby.
Blood plasma derivatization step:, due to the basic non-volatility of blood plasma intracellular metabolite thing, therefore must carry out derivatization treatment, method is for getting rat plasma 100 μ L, add 900 μ L methyl alcohol, after vortex mixed, ultrasonic extraction, high speed centrifugation is got supernatant in the glass centrifuge tube, with nitrogen, dries up.Add 75 μ L methoxamine pyridine solutions (15mg/mL), vortex mixed, 70 ℃ of reaction 1h, add again 180 μ L derivatization reagent (MSTFA: TMCS=99: 1), 70 ℃ of reaction 1h, then be transferred in centrifuge tube, gets supernatant after centrifuging and carry out the GC-MS analysis.
Experimental apparatus: adopt the silent gas chromatograph-mass spectrometer (GCMS) (Trace Ultra GC-DSQ II system) that flies your company's production of generation of match, chromatographic column: TR-5MS capillary column (30m * 0.25mm * 0.25 μ m), carrier gas: helium, combustion gas: hydrogen, combustion-supporting gas: air.
GC conditions: 270 ℃ of injector temperatures, 70 ℃ of initial temperatures also keep 10min, and then the speed with 10 ℃/min rises to 280 ℃, then keeps 10min; The mass spectrum condition: the EI ion source temperature is 260 ℃, full scan pattern (50～600m/z, per second scanning 5 times), and mass spectrometry is differentiated and is adopted the NIST mass spectral database.The chromatography-mass spectroscopy data that instrument is provided are converted to the Excel form to carry out following data analysis:
(1) identification at metabolin peak
Based on the TIC data of the QC sample of this research system, detect altogether and obtain signal to noise ratio (S/N ratio) greater than 93 of 3 chromatographic peaks, wherein 5 for adopting the HELP method Resolution of overlapping chromatographic peaks to be resolved the metabolin that draws; Preserve its L for pure chromatographic peak
Peak_i, R
Peak_iAnd A
Peak_iRetention time, preserve through HELP and resolve the pure Information in Mass Spectra that draws for Resolution of overlapping chromatographic peaks;
(2) foundation of the pure mass spectral database of metabolin
Based on the chromatography-mass spectroscopy data of QC sample, for each pure chromatographic peak peak_i, with it at L
Peak_iAnd R
Peak_iAll mass spectrometric datas in the retention time scope sum up, on average, to obtain to characterize the Information in Mass Spectra of the corresponding metabolin of chromatographic peak peak_i, the pure mass spectrum that again this information and HELP method is parsed merges, and can obtain the mass spectral database (X of the metabolin that comprises in the QC sample
Met);
(3) foundation of Statistic analysis models
, for each sample of MI group and positive drug group, it is located to record in each mass-to-charge ratio (m/z) chromatographic data that obtains sum up, to obtain its total mass spectrum.With the alignment of the total mass spectrum of each sample, thereby obtain total mass spectrometric data X of each sample in research system
M * n, wherein m is sample number, n is the mass spectrum port number; To X
M * nSet up the PLS-DA Statistic analysis models, obtain X
M * nScore (T) and load (P) matrix; The first two row to score T matrix are drawn (seeing Fig. 1), and visible MI group and positive drug group can obviously be distinguished;
(4) metabolin Projection Analysis
According to formula T
Met=X
MetP, with X
MetBe projected to above-mentioned PLS-DA model, can obtain metabolin projection score matrix T
MetWith T
MetThe first two row of matrix are drawn (seeing Fig. 2), and on figure, each point characterizes a metabolin, and are larger to the classification contribution of sample away from the metabolin of initial point, and it is consistent with the direction of sample in Fig. 1; To retrieve away from the mass spectrum input NIST storehouse of the metabolin of initial point, can directly draw the qualitative authentication information of otherness metabolin.Chromatography-mass spectroscopy metabolism group data analysis new method and present metabolism group data analysis software---XCMS commonly used that table 1 proposes for adopting the present invention, the comparison of the otherness metabolin that draws after this research system is analyzed.
The comparison * of the otherness metabolin that the method that table 1 the present invention proposes and XCMS disclose
* (or the downwards) arrow that makes progress represents that the MI group compares with sham-operation group (or positive drug group and MI group), this metabolite level rising (or reduction);
Compare with the sham-operation group exist significant difference (
#P＜0.05,
##P＜0.01).
By as seen from Table 1, two kinds of strategies have all disclosed the otherness metabolins such as glucose, lactic acid, urea, in addition, the method that the present invention proposes has also been found other otherness metabolins such as alanine, glycocoll, threonine, glycerine, thereby can verify and supplement the otherness metabolin that existing method is found.
Claims (3)
1. the method for chromatography-mass spectroscopy metabolism group data analysis comprises following steps:
(1) identification at metabolin peak
At first take out equal volume from each sample of the research system that comprises normal group, model group, administration group, set up Quality Control (QC) sample after mixing; Get total ion current chromatogram (TIC) data of QC sample, choose signal to noise ratio (S/N ratio) wherein greater than 3 chromatographic peak, be designated as peak_i, adopt chemometrics method to carry out purity detecting to peak_i: for pure chromatographic peak, record the retention time at left and right border and the peak value place of each chromatographic peak, be designated as respectively L
Peak_i, R
Peak_iAnd A
Peak_iFor be judged to be overlapping chromatographic peak through purity check, adopt chemometrics method to resolve, obtain the pure color that comprises in Resolution of overlapping chromatographic peaks spectrum and pure Information in Mass Spectra;
(2) foundation of the pure mass spectral database of metabolin
Based on the chromatography-mass spectroscopy data of QC sample, for each chromatographic peak peak_i, with it at L
Peak_iAnd R
Peak_iAll mass spectrometric datas in the retention time scope sum up, on average, to obtain to characterize the Information in Mass Spectra of the corresponding metabolin of chromatographic peak peak_i; For Resolution of overlapping chromatographic peaks, the employing chemometrics method is resolved the pure mass spectrum that obtains can be directly as the Information in Mass Spectra that characterizes metabolin that Resolution of overlapping chromatographic peaks comprises; Above-mentioned two part Information in Mass Spectras are merged, can obtain the pure mass spectral database of the metabolin that comprises in the QC sample, be designated as X
MetX
MetIn comprised the pure Information in Mass Spectra of the metabolin of all samples in the research system;
(3) foundation of Statistic analysis models
, for each sample in research system, it is located to record in each mass-to-charge ratio (m/z) chromatographic data that obtains sum up, to obtain its total mass spectrum; Total mass spectrum alignment with all samples, then merge the total mass spectrometric data X that obtains each sample in research system
M * n, wherein m is sample number, n is the mass spectrum port number; To X
M * nCarry out principal component analysis (PCA) (PCA) or offset minimum binary-discriminatory analysis (PLS-DA), set up Statistic analysis models, obtain X
M * nScore matrix T and loading matrix P;
(4) metabolin Projection Analysis
According to following formula, with X
MetBe projected to the loading matrix P in above-mentioned Statistic analysis models, can obtain X
MetScore matrix T
Met:
T
Met＝X
MetP
With T
MetThe first two row of matrix are drawn, and upper each point of figure characterizes a metabolin, T
MetBe the metabolin of otherness in figure away from the metabolin of initial point; According to T
MetThe numbering of otherness metabolin on figure, can retrieve X
MetDraw corresponding Information in Mass Spectra, can carry out qualitative discriminating to the otherness metabolin by retrieval mass spectrometric data storehouse finally.
2. the method for claim 1, is characterized in that, described chemometrics method for purity detecting can independently be selected from Heuristic Evolving Latent Projection, evolving factor analysis, principal component analysis (PCA), derivative method or orthographic projection.
3. the method for claim 1, it is characterized in that, the Chemical Measurement analytic method of described Resolution of overlapping chromatographic peaks can independently be selected from Heuristic Evolving Latent Projection, slice-scan technique, Window factor analysis, orthographic projection or polynary curve resolution method.
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