CN114137103A - Method for converting liquid chromatography diode array data into fingerprint - Google Patents
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Abstract
The invention relates to a method for converting liquid chromatography diode array data into a fingerprint spectrum, which is convenient for comparison and finding out the difference between results. The method belongs to the field of data processing, and specifically comprises the following steps: the method comprises the steps of screening original data, zeroing a base line, eliminating negative peaks, performing noise reduction treatment, finding out peak values, correcting peak retention time, drawing fingerprint two-dimensional codes and performing matrix addition comparison, wherein the zeroing of the base line can correct base line offset of liquid chromatogram data, the noise reduction treatment reduces interference of noise on the data, the peak correction treatment improves accuracy of results, and the matrix addition comparison can accurately find out differences among liquid chromatogram results so as to find out component differences among different samples.
Description
Technical Field
The invention relates to a method for converting liquid chromatography diode array data into a fingerprint, and belongs to the technical field of fingerprint data processing.
Background
Liquid chromatography is a chromatographic analysis technology using liquid as a mobile phase, has the advantages of high separation efficiency, good selectivity, high detection sensitivity, no limitation by volatility and thermal stability of a sample and the like, and is commonly used for qualitative and quantitative analysis. The fingerprint is combined according to chromatographic data or spectral data of the liquid chromatogram, and a type of spectrum capable of marking chemical characteristics of the fingerprint is obtained through statistical processing, so that the fingerprint is widely applied to researches such as identification, traceability and evaluation of traditional Chinese medicinal materials, foods and agricultural products.
On the other hand, however, due to the problems of noise interference, spectrum peak drift, difficult difference discrimination and the like existing in the chromatogram, the comparison difficulty of fingerprint analysis is high, and the application is limited.
Disclosure of Invention
The invention aims at the problems of noise, electrical disturbance and the like in the chromatographic acquisition process, establishes a rapid analysis algorithm for converting data acquired by a liquid chromatogram-diode array detector into a fingerprint spectrum by sorting, noise reduction, spectrum peak identification and correction of the data, and realizes rapid comparison of fingerprints of multi-wavelength samples. In the correction process, the method determines the next standard value for the retention time of all peaks through calculation so as to accurately correct the peaks of the sample.
The technical scheme adopted by the invention for realizing the purpose is as follows:
a method for converting data of a liquid chromatography diode array into a fingerprint comprises the following steps:
step one, data acquisition: collecting three-dimensional chromatographic data in a certain wavelength range on a liquid chromatogram provided with a diode array detector;
in the step, the acquired three-dimensional chromatographic data can be subjected to data reduction, and the fingerprint accuracy is adjusted by adjusting the data sampling interval of the chromatographic retention time according to the requirement of analysis accuracy to obtain the reduced three-dimensional chromatographic data; the screening formula for data reduction is Excel as an example, and an OFFSET function is used, and the formula is as follows:
X=OFFSET(reference,n*rows(),m*cols());
wherein, X is the data point after screening, reference is the reference system, n × rows () is the row offset, and m × cols () is the column offset.
And step two, data noise reduction is carried out by the following two steps:
(2.1): baseline drift is eliminated. The calculation formula is as follows:
X(i)'=X(i+m)-X(i)
wherein, X(i)The absorbance value representing the ith retention time, m being the retention time interval, m being generally determined by the half-width of the chromatographic peak, X(i+m)Absorbance value, X, representing the i + m retention time(i)' Replacing original X for chromatographic data after flattening baseline(i);
(2.2): and removing noise. One or more noise values S are taken, the value of the noise values S is determined according to actual requirements, and the calculation formula is as follows:
X'=X-S
when X '<0, X' ═ 0
When X ' >0, X ' ═ X '
Wherein, X' is data after removing noise, X is data before removing noise, and S is set noise value. And subtracting the noise value S from all the data, zeroing the data which are smaller than zero after calculation, and reserving the original value for the data which are larger than zero to obtain the chromatogram after filtering different noise values.
Step three, confirming a spectrum peak: a chromatographic peak retention time acquisition method adopts a peak positioning method published in 2018 by Tom O' Haver, and confirms a chromatographic peak and retention time thereof according to a formula by setting 3 parameters such as peak height, peak width, first-order derivative of a zeroing-tendency spectral peak and the like.
Step four, correcting a spectrum peak: this step is divided into two parts, internal standard determination and peak retention time correction.
In the first part, an internal standard set N and a fluctuation range of a chromatographic peak are obtained by comprehensively calculating all samples, and the internal standard set N is used as an internal standard to correct the retention time of a sample peak, and is determined by the following steps:
(4.1.1): counting the retention time of all peaks of all samples, and sorting according to the size;
(4.1.2): sequentially solving the standard deviation R of the adjacent n retention times, and if the standard deviation R is smaller than a set certain value algebraic value R', taking the corresponding retention time as the retention time of the same peak, and classifying the retention time into a group, wherein the calculation formula is as follows;
wherein R' is a set numerical value, R is a calculated standard deviation value, n is a selected retention time number for solving the standard deviation,as the mean value of the selected retention times, xiFor the ith of the selected retention times;
(4.1.3): taking the median of each group retention time, and setting the collection of median as an internal standard set N for correcting the sample peak retention time.
In the second part, the peak retention time correction method is divided into the following two steps:
(4.2.1): retention time in internal standard aiSample peak retention time b for the first row of the matrixjAs the first column of the matrix, the rest position of the matrix is formed by delta tijCorrespondingly filling;
(4.2.2): judging the difference value delta tijIf the peak spectrum is smaller than the threshold Q, if the peak spectrum is smaller than the threshold Q and the corresponding peak spectrum is basically consistent with the peak spectrum, corresponding to bjCan be regarded as aiOf the same chromatographic peak, bjThe retention time is replaced by ai. If Δ tijIf the value is greater than the threshold value Q, the difference is a peak, not bjAnd (6) carrying out correction. The chromatographic peak retention time correction calculation formula is as follows:
Δtij=ai-bj
when Δ t is reachedij≤Q,bj’=ai;
When Δ t is reachedij>Q,bj’=bj。
Wherein, Δ tijRepresents two chromatographic peaks aiAnd bjThe difference between retention times, i, j represents the serial number of the retention time of the chromatographic peak in the retention time of all peaks, aiRepresenting the retention time of the ith chromatographic peak of the internal standard, bjRepresents the retention time of the jth chromatographic peak of the sample, bj' represents bjThe corrected retention time, Q, is the fluctuation threshold of the peak retention time. The magnitude of the fluctuation threshold Q affects the accuracy of the correction, and therefore, it is necessary to set an appropriate threshold so that it can distinguish different peaks without separating the same peak.
Step five, establishing a fingerprint spectrum, which comprises the following two steps:
(5.1): taking the peak retention time in the internal standard set N as the first column of the matrix, and taking each wavelength AkThe corresponding number sets form the subsequent k columns of the matrix;
(5.2):Akand the corresponding number set consists of whether the wavelength has peaks at different retention times, if the corresponding wavelength and the retention time have peaks, the position is filled with 1, otherwise, the position is filled with 0, and different colors are set for different data to enable the result to be visualized.
Step six: calculating comparison of the fingerprint, and visualizing the difference by matrix addition or subtraction, wherein the method comprises the following specific steps:
(6.1): and (5) adding and comparing. Analyzing common peaks and difference peaks between the sample and the standard, correspondingly adding the fingerprint matrix data of different samples to obtain three data of 0, 1 and 2, wherein 0 represents that no peak exists between the sample and the standard, 1 represents that a difference peak exists between the sample and the standard, 2 represents that a common peak exists between the sample and the standard, and different colors are set for different data to visualize the result. The step can quickly find and locate the difference peak and the common peak among different samples, but cannot distinguish the increase of the peak and the decrease of the peak;
(6.2): and (5) subtracting and comparing. Analyzing the peak increase and peak lack in the difference peak, and subtracting the standard data from the sample fingerprint matrix data to obtain three data of-1, 0 and 1, wherein, -1 represents the sample is "peak lack" relative to the standard, 0 represents the sample and the standard are "no peak or common peak", and 1 represents the sample is "peak increase" relative to the standard. This step is complementary to the first step, with different data set with different colors to visualize the results.
Compared with the prior art, the invention has the beneficial effects that:
firstly, the method for converting the liquid chromatography diode array data into the fingerprint spectrum is based on data noise reduction, spectrum peak correction and difference visualization algorithms, a next standard value is determined for the retention time of all peaks in the correction process, the sample is accurately corrected, and the method for rapidly positioning the difference peak and the same peak of the fingerprint spectrum based on the liquid chromatography is realized.
Secondly, after the chromatographic data is converted into the fingerprint, the difference between the liquid chromatogram peaks can be found out through the addition and subtraction of the matrixes, and the difference between the results can be found out through comparison more easily, so that the difference between different liquid chromatogram results can be analyzed in a shorter time, the difference between components of different samples can be found out, the complicated comparison between single peak values is not needed, and the speed of analyzing the difference between the liquid chromatogram results is improved. The method is suitable for rapid comparison of fingerprint spectra of food or agricultural products, improves analysis efficiency, and promotes automatic identification.
Drawings
FIG. 1 is a flow chart of a method for converting liquid chromatography diode array data into a fingerprint according to the present invention;
FIG. 2 is the chromatographic data of E1 and K7190 after function screening;
FIG. 3 is chromatographic data after baseline flattening for E1 and K7190;
FIG. 4 is the chromatographic data of E1 and K7190 after noise reduction;
FIG. 5 calculated peak retention times for E1 and K7190;
FIG. 6 is a schematic diagram of a peak correction calculation method;
FIG. 7 is a schematic diagram of a K7190 peak correction case;
FIG. 8 is a fingerprint of the corrected original strain;
FIG. 9 is a fingerprint of the knockdown after correction;
FIG. 10 is a schematic diagram of matrix addition;
FIG. 11 is a schematic diagram of matrix subtraction;
FIG. 12 is a graph of the difference obtained by matrix addition comparison;
fig. 13 is a difference diagram obtained by matrix subtraction comparison.
Detailed Description
It should be noted that the following detailed description is exemplary and is intended to provide further explanation of the disclosure. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs.
It is noted that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of example embodiments according to the present application. The technical solution of the present invention is further described in detail with reference to the accompanying drawings and specific embodiments.
The invention mainly relates to the processing of ultra-high performance liquid chromatography-diode array original data, provides a liquid chromatography result rapid analysis method based on data processing, and particularly relates to a method for converting liquid chromatography diode array data into a fingerprint. The liquid chromatography method based on data analysis is used for processing the original data of the liquid chromatography, and quickly and conveniently analyzing the component difference among samples.
Examples
In order to show the whole process of the method, the Eurotium cristatum E1 (the preservation number is CCTCC: NO. M20211112) strain of a certain filamentous fungus and a single gene knockout K7190 thereof are selected in the embodiment, a metabolite obtained by extracting mycelia with methanol is taken as an example sample, an ultra high performance liquid chromatography-diode array detection method is adopted, a three-dimensional chromatogram is obtained by collection, and the product difference among the samples is analyzed by the method. The specific process is as follows:
the method comprises the following steps: and (6) data acquisition. Three-dimensional chromatographic data in the wavelength range of 200-600nm is collected on a liquid chromatogram equipped with a diode array detector.
Step two: data reduction (optional). According to the requirement of analysis precision, sample data is reduced in proportion by adjusting the data sampling interval of the chromatographic retention time to obtain the reduced three-dimensional chromatographic data, and the time interval selected in the embodiment is 0.01 s.
Step three: and (6) reducing noise of the data. Generally, the method comprises two steps:
(3.1): eliminating the baseline drift, and calculating the formula as follows:
X(i)’=X(i+m)-X(i)
wherein, X(i)The absorbance value representing the ith retention time, m being the retention time interval, determined by the half-peak width of the chromatographic peak, X(i)' Replacing original X for chromatographic data after flattening baseline(i)Before calculation, as shown in fig. 2, there is a certain baseline shift, and after calculation, as shown in fig. 3, the baseline shift is successfully eliminated.
(3.2): removing noise, and taking a noise value of 0.01, wherein the noise reduction calculation formula is as follows:
X’=X-S
when X '<0, X' ═ 0
When X ' >0, X ' ═ X '
Wherein, X' is data after noise removal; x is data before noise removal after baseline drift elimination; s is the set noise value. Subtracting the noise value S from all the data, zeroing the data smaller than zero after calculation, and keeping the original value of the data larger than zero to obtain the chromatogram after filtering different noise values, as shown in FIG. 4, and removing noise interference from the data by noise reduction.
Step four: and (5) confirming a spectrum peak. The chromatographic peak retention time acquisition method adopts a peak positioning method published in 2018 by Tom O' Haver, confirms a chromatographic peak and retention time thereof according to a publication method by setting 3 parameters of a peak height of more than 0.01, a peak width of less than 0.01 and a zeroing spectrum peak first-order derivative, and the peak retention time is calculated in an embodiment shown in FIG. 5.
Step five: and correcting a spectrum peak. The spectral peak correction is divided into two parts of internal standard determination and peak retention time correction. The chromatographic peak internal standard set N and the fluctuation range are obtained by comprehensively calculating all samples, the sample peak retention time is corrected by taking the chromatographic peak internal standard set N as a reference, and the internal standard set N is determined to be divided into the following steps:
(5.1): counting the peak retention time of all samples, and sorting according to the size;
(5.2): and sequentially solving the standard deviation R of the adjacent n retention times, and if the standard deviation R is smaller than a set certain value algebraic value R ', taking the corresponding retention time as the retention time of the same peak, and classifying the retention time into a group, wherein R' is 0.01 in the embodiment. The calculation formula is as follows:
wherein R is the calculated standard deviation value, n is the selected retention time number for standard deviation,as the mean value of the selected retention times, xiFor the ith of the selected retention times, n in the example is 2;
(5.3): taking the median of each group retention time, obtaining a median set N {0.115146, 0.726526, 0.899511, 0.951919, 1.196531, 1.330706, 1.354479, 1.420423, 1.691122, 1.800919, 1.981347, 2.469146, 2.540331, 2.721936, 3.342319, 3.576133, 3.928523, 4.418416, 4.618703, 4.833786, 5.080974, 5.202326, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, 5.961394, a peak time set for a sample retention time, 5.961394, an internal standard set.
The calculation method of the peak retention time correction is shown in fig. 6, and includes the following two steps:
(5.4): retention time in internal standard aiSample peak retention time b for the first row of the matrixjAnd as the first column of the matrix, the rest positions of the matrix are correspondingly filled by the difference values of the rest positions.
(5.5): judging whether the difference is less than the threshold value of 0.02, if so, corresponding to bjCan be regarded as aiOf the same chromatographic peak, bjThe retention time is replaced by ai. If the difference is greater than the threshold value of 0.02, the difference is a difference peak, not for bjAnd (6) carrying out correction. The size of the threshold affects the accuracy of the correction, and therefore, it is necessary to set an appropriate threshold so that it can distinguish different peaks without separating the same peak. As shown in fig. 7, when the retention time of the K7190 peak was corrected by using E1 as a standard, it was found that the orange portion value was less than the threshold value of 0.02, which represents that the corresponding peak was a common peak, and the correction result is also shown in fig. 7.
Step six: and establishing a fingerprint. The method for drawing the fingerprint spectrum comprises the following specific steps:
(6.1): taking the peak retention time in the internal standard set N as the first column of the matrix, and taking each wavelength AkThe corresponding number sets form the subsequent k columns of the matrix;
(6.2):Akand the corresponding number set consists of whether the wavelength has peaks at different retention times, if the corresponding wavelength and the retention time have peaks, the position is filled with 1, otherwise, the position is filled with 0, and different colors are set for different data to enable the result to be visualized. The E1 fingerprint is shown in figure 8, the K7190 fingerprint is shown in figure 9, the yellow part has a chromatographic peak, and the white part has no chromatographic peak.
Step seven: the fingerprint comparison comprises the following steps:
(7.1): and (5) adding and comparing. Analyzing common peaks and difference peaks between samples and standards, correspondingly adding matrix data of different samples, as shown in fig. 10, obtaining three kinds of data of 0, 1 and 2 from only 0 and 1 data originally, wherein 0 represents that no peak exists between the samples and the standards, 1 represents that a difference peak exists between the samples and the standards, and 2 represents that a common peak exists between the samples and the standards, and the three kinds of data correspond to white, yellow and orange respectively, and the difference of different data can be obviously seen in the figure. The step can quickly find and locate the difference peak and the common peak among different samples, but cannot distinguish the increase of the peak and the decrease of the peak;
(7.2): and (5) subtracting and comparing. Analyzing the peak increase and the peak lack in the difference peak, subtracting the standard data from the sample fingerprint matrix data, as shown in fig. 11, obtaining three data of-1, 0 and 1 from the original data only having two kinds of 0 and 1, wherein, -1 represents that the sample is "peak lack" relative to the standard, 0 represents that the sample and the standard are "peak absence or common peak presence", 1 represents that the sample is "peak increase" relative to the standard, and the three data correspond to green, white and yellow respectively, and the difference of the different data can be obviously seen in the figure.
As shown in fig. 12, orange is a common peak, yellow is a difference peak, clicking can amplify the region, the wavelength and retention time that are desired to be viewed can be selected, clicking can be used to view chromatogram comparison, subtracting can be used to obtain a fingerprint, as shown in fig. 13, green is a lack of peak, orange is an increase of peak, clicking can amplify the region, and the wavelength and retention time that are desired to be viewed can be selected, so that the peak difference between the two samples can be identified.
Although the embodiments of the present invention have been described with reference to the accompanying drawings, it is not intended to limit the scope of the present invention, and it should be understood by those skilled in the art that various modifications and variations can be made without inventive efforts by those skilled in the art based on the technical solution of the present invention.
Claims (7)
1. A method for converting liquid chromatography diode array data into a fingerprint spectrum is characterized by comprising the following steps:
step one, data acquisition: collecting the liquid chromatogram diode array data of all samples to be analyzed;
step two, data denoising: eliminating baseline drift of the liquid chromatogram data collected in the step one, and then removing noise to obtain a chromatogram after filtering different noise values;
step three, confirming a spectrum peak: confirming chromatographic peaks and retention time thereof in the chromatogram obtained in the step two by adopting a peak positioning method;
step four, correcting a spectrum peak: comprehensively calculating all peak retention times of all samples to be analyzed to obtain a chromatographic peak internal standard set N, and correcting the chromatographic peak retention time of the samples by taking the chromatographic peak internal standard set N as an internal standard;
step five, establishing a fingerprint spectrum: taking the peak retention time in the chromatographic peak internal standard set N as a first column of a matrix, wherein each wavelength AkThe corresponding number sets form the subsequent k columns of the matrix; a. thekAnd the corresponding number set consists of whether peaks exist at different retention time positions of the wavelength or not, if the peaks exist at the corresponding wavelength and the retention time positions, the position is filled with 1, otherwise, 0 is filled, different colors are set for different data, and a visual fingerprint is obtained, so that the conversion of the liquid chromatogram diode array data to the fingerprint is realized.
2. The method for converting data of the liquid chromatography diode array into the fingerprint as claimed in claim 1, further comprising a sixth step of fingerprint comparison: and D, calculating and comparing the fingerprint obtained in the step five, and visualizing the difference between different liquid chromatogram results through matrix addition or subtraction.
3. The method for converting data of the liquid chromatography diode array into the fingerprint as claimed in claim 2, wherein the specific process of the fingerprint comparison method comprises the following two steps:
the first step is as follows: correspondingly adding the fingerprint matrix data of different samples to be analyzed according to the common peak and the difference peak between the samples to be analyzed and the standard products to obtain three data of 0, 1 and 2, wherein 0 represents that no peak exists between the samples to be analyzed and the standard products, 1 represents that a difference peak exists between the samples to be analyzed and the standard products, and 2 represents that a common peak exists between the samples to be analyzed and the standard products, different colors are set for the different data to enable the analysis results of the different samples to be analyzed to be visualized, so that the difference peak and the common peak between the different samples to be analyzed are found and positioned, but the increase of the peak and the decrease of the peak cannot be distinguished;
the second step is that: subtracting the fingerprint matrix data of the standard product from the fingerprint matrix data of the sample to be analyzed according to the increase and the lack of the peaks in the difference peaks to obtain three data of-1, 0 and 1, wherein, -1 represents that the sample to be analyzed is lack of peaks relative to the standard product, 0 represents that the sample to be analyzed and the standard product do not have peaks or have common peaks, and 1 represents that the sample to be analyzed is increased of peaks relative to the standard product; this step is complementary to the first step, where different colors are set for different data to visualize the analysis results for different samples to be analyzed.
4. The method for converting data of a liquid chromatography diode array into a fingerprint as claimed in claim 1, wherein the data noise reduction is performed in two steps as follows:
the first step, eliminating the baseline drift, the calculation formula is:
X(i)'=X(i+m)-X(i)
wherein, X(i)Denotes the absorbance value of the ith retention time, m is the retention time interval, X(i+m)An absorbance value representing the i + m retention time; x(i)' Replacing original X for chromatographic data after flattening baseline(i);
Step two, noise removal: one or more noise values S are taken, and the calculation formula is as follows:
X'=X-S
when X '<0, X' ═ 0
When X ' >0, X ' ═ X '
Wherein, X' is data after noise removal, X is data before noise removal, and S is a set noise value;
and subtracting the noise value S from all the data, zeroing the data which are smaller than zero after calculation, and reserving the original value for the data which are larger than zero to obtain the chromatogram after filtering different noise values.
5. The method for converting data of a liquid chromatography diode array into a fingerprint spectrum as claimed in claim 1, wherein the determination of the internal standard set N of the chromatographic peak comprises the following steps:
step one, counting the retention time of all peaks of all samples, and sorting according to the size;
secondly, solving the standard deviation of n adjacent retention times in sequence, and if the standard deviation is smaller than a set algebraic value R, regarding the corresponding retention time as the retention time of the same peak, and classifying the retention time into a group, wherein the calculation formula is as follows;
wherein R is a set algebraic value, n is a selected number of retention times to standard deviation,as the mean value of the selected retention times, xiFor the ith of the selected retention times;
and thirdly, taking the median of each group of retention time, setting the collection of the median as a chromatographic peak internal standard set N, and using the internal standard set N as a correction standard for correcting the retention time of chromatographic peaks of all samples.
6. The method for converting data of a liquid chromatography diode array into a fingerprint as claimed in claim 1, wherein the method for correcting retention time of chromatographic peaks comprises the following two steps:
first step, retention time in subscript aiSample peak retention time b for the first row of the matrixjAs the first column of the matrix, the rest position of the matrix is formed by delta tijCorrespondingly filling;
second, the difference value Deltat is judgedijIf the peak spectrum is smaller than the threshold Q, if the peak spectrum is smaller than the threshold Q and the corresponding peak spectrum is basically consistent with the peak spectrum, corresponding to bjCan be regarded as aiOf the same chromatographic peak, bjThe retention time is replaced by ai(ii) a If Δ tijIf the value is greater than the threshold value Q, the difference is a peak, not bjCarrying out correction;
i.e. atij=ai-bj
When Δ t is reachedij≤Q,bj’=ai
When Δ t is reachedij>Q,bj’=bj
Wherein, Δ tijRepresents two chromatographic peaks aiAnd bjThe difference between retention times, i, j represents the serial number of the retention time of the chromatographic peak in the retention time of all peaks, aiRepresenting the retention time of the ith chromatographic peak of the internal standard, bjRepresents the retention time of the jth chromatographic peak of the sample, bj' represents bjThe corrected retention time, Q, is the fluctuation threshold of the peak retention time.
7. The method for converting data of the liquid chromatography diode array into the fingerprint as claimed in claim 1, wherein a data reduction step is further included between the first step and the third step, and specifically comprises: and according to the requirement of analysis precision, sample data is reduced in proportion by adjusting the data sampling interval of the chromatographic retention time, and the reduced data of the liquid chromatography diode array is obtained for subsequent steps.
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