CN114137103B - 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 comprises the following specific steps: the method comprises the steps of screening original data, resetting a base line, eliminating negative peaks, carrying out noise reduction treatment, finding out peaks, correcting peak retention time, drawing fingerprint two-dimensional codes and carrying out matrix addition comparison, wherein the base line can correct base line deviation of liquid chromatography 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 chromatography results, so that differences of components among different samples are found out.
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
The 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 of sample volatility and thermal stability and the like, and is commonly used for qualitative and quantitative analysis. The fingerprint is subjected to statistical treatment according to chromatographic data or spectral data combination of liquid chromatography to obtain a type of fingerprint capable of marking chemical characteristics of the fingerprint, and the fingerprint is widely applied to researches such as identification, tracing and evaluation of traditional Chinese medicinal materials, foods and agricultural products.
However, on the other hand, due to the problems of noise interference, spectral peak drift, indistinguishable difference and the like in the chromatograph, the fingerprint analysis and comparison are difficult, and the application is limited.
Disclosure of Invention
The invention establishes a rapid analysis algorithm for converting data collected by a liquid chromatograph-diode array detector into fingerprints by sorting, reducing noise and identifying and correcting spectral peaks of the data, and realizes rapid comparison of fingerprints of multi-wavelength samples aiming at the problems of noise, electric disturbance and the like in the chromatographic collection process. In the correction process, the method of the invention determines the next standard value for all the peak retention time through calculation so as to accurately correct the sample peak.
The technical scheme adopted by the invention for achieving the purpose is as follows:
a method for converting liquid chromatography diode array data into fingerprint comprises the following steps:
step one, data acquisition: collecting three-dimensional chromatographic data in a certain wavelength range on liquid chromatograph equipped with a diode array detector;
in the step, the acquired three-dimensional chromatographic data can be subjected to data reduction, and the fingerprint precision is adjusted by adjusting the data sampling interval of the chromatographic retention time according to the analysis precision requirement, so as to obtain the reduced three-dimensional chromatographic data; the screening formula of data reduction takes Excel as an example, and uses an OFFSET function, and the formula is as follows:
X＝OFFSET(reference,n*rows(),m*cols())；
where X is the data point after screening, reference is the reference frame, n rows () is the row offset, and m cols () is the column offset.
Step two, data noise reduction is carried out in the following two steps:
(2.1): baseline wander is eliminated. The calculation formula is as follows:
X (i) '＝X (i+m) -X (i)
wherein X is (i) Absorbance value representing the ith retention time, m is retentionThe time interval, m, is generally determined by the half-width of the chromatographic peak, X (i+m) Absorbance, X, representing the i+mth retention time (i) ' replace original X for chromatographic data after baseline flattening (i) ；
(2.2): noise is removed. And taking one or more noise values S, wherein the values are 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 the data after noise removal, X is the data before noise removal, and S is the set noise value. And subtracting the noise value S from all the data, returning the calculated data smaller than zero to zero, and keeping the original value of the data larger than zero to obtain chromatograms after filtering different noise values.
Step three, spectral peak confirmation: the chromatographic peak retention time acquisition method adopts a peak positioning method published in 2018 by Tom O' Haver, and confirms the chromatographic peak and the retention time thereof according to a formula by setting 3 parameters such as peak height, peak width, first derivative of zeroing spectral peak and the like.
Step four, spectral peak correction: this step is divided into two parts, internal standard determination and peak retention time correction.
In the first part, the chromatographic peak internal standard set N and the fluctuation range are comprehensively calculated by all samples, the chromatographic peak internal standard set N is used as an internal standard to correct the sample peak retention time, and the determination of the internal standard set N is divided into the following steps:
(4.1.1): counting all peak retention times of all samples, and sorting according to the sizes;
(4.1.2): the standard deviation R is calculated for n adjacent retention times in sequence, if the standard deviation R is smaller than the set value of the value R', the corresponding retention time is regarded as the same peak retention time, and the retention time is classified into a group, and the calculation formula is as follows;
wherein R' is a set value, R is calculatedN is the number of standard deviation retention times selected,
x is the average of the selected retention times i An ith of the selected retention times;
(4.1.3): taking the median value of each group of retention time, the aggregate set of median values is set as an internal standard set N for correction of the sample peak retention time.
The second part, the peak retention time correction method, is divided into two steps:
(4.2.1): internal standard retention time a i Sample peak retention time b for the first row of the matrix j As the first column of the matrix, the rest of the matrix is represented by Δt ij Filling correspondingly;
(4.2.2): determining the difference Deltat ij If the spectrum is smaller than the threshold value Q, and if the spectrum is smaller than Q and the corresponding peak spectrum is basically consistent, the spectrum corresponds to b j Can be regarded as a i Is the same as the chromatographic peak of B j Retention time is replaced by a i . If delta t ij If the value is greater than the threshold value Q, the value is a difference peak, and the value is not equal to b j Correction is performed. The chromatographic peak retention time correction calculation formula is as follows:
Δt ij ＝a i -b j
when Deltat ij ≤Q,b j ’＝a i ；
When Deltat ij ＞Q,b j ’＝b j 。
Wherein Δt is ij Representing two chromatographic peaks a i And b j The difference in retention time between i, j represent the number of the retention time of the chromatographic peak in the total retention time of the peaks, a i Represents the retention time of the ith chromatographic peak of the internal standard, b j Represents the sample jth chromatographic peak retention time, b j ' represents b j Corrected retention time, Q, is the fluctuating threshold of peak retention time. The magnitude of the fluctuation threshold Q affects the accuracy of correction, and therefore, an appropriate threshold needs to be set so that it can distinguish different peaks without separating the same peak.
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 each wavelength A k The corresponding number sets form the subsequent k columns of the matrix;
(5.2)：A k the corresponding data 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 0, and different data sets with different colors to visualize the result.
Step six: fingerprint spectrum calculation contrast, the difference is visualized through matrix addition or subtraction, and the specific steps are as follows:
(6.1): and (5) adding and comparing. And analyzing the common peak and the differential peak between the sample and the standard, correspondingly adding fingerprint spectrum matrix data of different samples, and obtaining three data of 0, 1 and 2, wherein 0 represents that the sample and the standard are both in a non-existence state, 1 represents that the sample and the standard are in a differential peak state, 2 represents that the sample and the standard are in a common peak state, and different colors are set for the different data to enable the result to be visualized. The step can quickly find and locate the difference peaks and the common peaks among different samples, but cannot distinguish the increase of the peaks and the decrease of the peaks;
(6.2): and subtracting the comparison. And analyzing the peak increase and the peak lack in the difference peaks, and subtracting the standard data from the fingerprint matrix data of the sample to obtain three data of-1, 0 and 1, wherein-1 represents the peak lack of the sample relative to the standard, 0 represents the absence or the presence of a common peak of the sample and the standard, and 1 represents the peak increase of the sample relative to the standard. This step is complementary to the first step, with different data being set to 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 the data noise reduction, spectral peak correction and difference visualization algorithm, and the next standard value is set for all peak retention time in the correction process, so that the sample is accurately corrected, and the method for rapidly positioning the difference peak and the same peak based on the fingerprint spectrum of the liquid chromatography is realized.
Secondly, after the chromatographic data are converted into the fingerprint, the differences among the liquid chromatographic peaks can be found out through the addition and subtraction of the matrixes, and the differences among the results can be found out more easily through comparison, so that the differences among different liquid chromatographic results can be analyzed in a shorter time, the differences of components among different samples can be found out, complicated comparison among single peaks is not needed, and the speed of analyzing the differences among the liquid chromatographic results is improved. The method is suitable for the pairwise rapid comparison of the fingerprints of the food or agricultural products, improves the analysis efficiency and promotes the automatic identification.
Drawings
FIG. 1 is a flow chart of a method for converting liquid chromatography diode array data into a fingerprint;
FIG. 2 shows chromatographic data of E1 and K7190 subjected to function screening;
FIG. 3 is chromatographic data after E1 and K7190 flatten the baseline;
FIG. 4 is a graph of the noise reduction of the chromatographic data of E1 and K7190;
FIG. 5 shows the 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 original strain after correction;
FIG. 9 is a fingerprint of the corrected knockouts;
FIG. 10 is a schematic diagram of matrix addition;
FIG. 11 is a schematic diagram of matrix subtraction;
FIG. 12 is a difference plot obtained by matrix addition comparison;
fig. 13 is a difference chart obtained by matrix subtraction.
Detailed Description
It should be noted that the following detailed description is illustrative and is intended to provide further explanation of the present application. 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 in accordance with the present application. The technical scheme of the invention is further described in detail below with reference to the attached drawings and specific embodiments.
The invention mainly relates to the processing of ultra-high performance liquid chromatography-diode array raw 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 liquid chromatography raw data and rapidly and conveniently analyzing component differences among samples.
Examples
In order to show the whole process, a strain E1 (preservation number CCTCC: no. M20211112) of a certain filamentous fungus and a single gene knockout K7190 thereof are selected in the embodiment, a metabolite obtained by extracting mycelium 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 acquired, and the product difference between the samples is analyzed by the method. The specific process is as follows:
step one: and (5) data acquisition. Three-dimensional chromatographic data in the wavelength range of 200-600nm were collected on a liquid chromatograph equipped with a diode array detector.
Step two: data reduction (optional). According to the analysis precision requirement, the sample data is reduced proportionally 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 0.01s.
Step three: and (5) data noise reduction. Generally, the method comprises two steps, namely:
(3.1): baseline drift was eliminated as follows:
X (i) ’＝X (i+m) -X (i)
wherein X is (i) The absorbance value representing the ith retention time, m being the retention time interval, according to the half-width of the chromatographic peakDetermination of X (i) ' replace original X for chromatographic data after baseline flattening (i) The baseline wander was successfully eliminated as shown in figure 3 after calculation with some degree of baseline wander as shown in figure 2 before calculation.
(3.2): removing noise, taking a noise value of 0.01, and adopting a noise reduction calculation formula 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 is removed after baseline drift is eliminated; s is the set noise value. And subtracting the noise value S from all the data, returning the calculated data smaller than zero to zero, and keeping the data larger than zero to obtain chromatograms with different filtered noise values, wherein the data is subjected to noise reduction to remove noise interference as shown in fig. 4.
Step four: and confirming a spectrum peak. According to the chromatographic peak retention time acquisition method, a peak positioning method published in 2018 by Tom O' Haver is adopted, the chromatographic peak and the retention time thereof are confirmed according to the published method by setting 3 parameters of peak height greater than 0.01, peak width less than 0.01 and first derivative of zeroing spectral peak, and the obtained peak retention time is calculated in the embodiment shown in fig. 5.
Step five: and (5) correcting a spectrum peak. The spectral peak correction is divided into two parts, namely internal standard determination and peak retention time correction. The chromatographic peak internal standard set N and the fluctuation range are obtained by comprehensive calculation of all samples, the retention time of the sample peak is corrected by taking the chromatographic peak internal standard set N as a reference, and the determination of the internal standard set N is divided into the following steps:
(5.1): counting the peak retention time of all samples, and sorting according to the size;
(5.2): and (3) sequentially solving standard deviation R for n adjacent retention times, and if the standard deviation R is smaller than a set value of a value R ', regarding the corresponding retention time as the same peak retention time, and classifying the same peak retention time into one group, wherein R' is 0.01 in the embodiment. The calculation formula is as follows:
wherein R is the standard deviation value obtained by calculation, n is the retention time quantity of the standard deviation,
x is the average of the selected retention times i For the ith of the selected retention times, n is 2 in the example;
(5.3): taking the median value of each set of retention times, we obtain the median set N {0.115146,0.726526,0.899511,0.951919,1.196531,1.330706,1.354479,1.420423,1.691122,1.800919,1.981347,2.469146,2.540331,2.721936,3.342319,3.576133,3.928523,4.418416,4.618703,4.833786,5.080974,5.202326,5.961394,6.251355,6.515896,6.81018,6.890687,7.052432,8.256224,8.318162,8.778295,9.397981,9.539001,9.872432,9.904062, 10.25509, 10.4201, 10.56877, 10.80861, 11.54996, 12.05954, 12.87973, 13.00961, 13.20177, 13.73844, 14.29435, 14.58056, 14.85723, 15.38743, 15.99942, 16.79521, 17.06683, 17.1167, 17.16048, 17.30226, 17.45879, 17.51757, 17.65166, 18.32486, 18.38244, 18.61797, 18.6562, 18.79465, 19.92223, 20.33528, 20.36224, 20.70383, 20.93617, 20.95951, 21.20727, 21.99564, 22.57375, 23.36959, 23.41928, 23.45703, 23.73129, 24.06929}, set N being the internal standard for correction of sample peak retention times.
The peak retention time correction calculation method is shown in fig. 6, and is divided into the following two steps:
(5.4): internal standard retention time a i Sample peak retention time b for the first row of the matrix j As the first column of the matrix, the rest of the matrix is filled by its difference.
(5.5): judging whether the difference is smaller than the threshold value 0.02, if so, the corresponding peak spectrogram is basically consistent, corresponding to b j Can be regarded as a i Is the same as the chromatographic peak of B j Retention time is replaced by a i . If the difference is greater than the threshold value of 0.02, the difference is a difference peak, and the difference is not equal to b j Correction is performed. The magnitude of the threshold will be a shadowThe accuracy of the correction is thus such that it is necessary to set a suitable threshold value so that it can distinguish between different peaks without separating the same peak. As shown in fig. 7, the retention time of the peak K7190 was corrected using E1 as a standard, and it can be seen that the orange fraction value is less than the threshold value of 0.02, representing that the corresponding peak is a common peak, and the correction result is also shown in fig. 7.
Step six: and establishing a fingerprint. The fingerprint drawing method 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 each wavelength A k The corresponding number sets form the subsequent k columns of the matrix;
(6.2)：A k the corresponding data 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 0, and different data sets with different colors to visualize the result. E1 fingerprint is shown in FIG. 8, K7190 fingerprint is shown in FIG. 9, and the yellow part has chromatographic peaks and the white part has no chromatographic peaks.
Step seven: fingerprint comparison, the steps are divided into the following two steps:
(7.1): and (5) adding and comparing. The common peak and the difference peak between the sample and the standard are analyzed, matrix data of different samples are correspondingly added, as shown in fig. 10, three data of 0, 1 and 2 are obtained by only 0 and 1, wherein 0 indicates that the sample and the standard are both in the absence of the peak, 1 indicates that the sample and the standard are in the presence of the difference peak, 2 indicates that the sample and the standard are in the presence of the common peak, the three data are respectively corresponding to white, yellow and orange, and the difference of the different data can be obviously seen in the graph. The step can quickly find and locate the difference peaks and the common peaks among different samples, but cannot distinguish the increase of the peaks and the decrease of the peaks;
(7.2): and subtracting the comparison. Analyzing the peak increase and the peak lack in the difference peaks, subtracting the standard data from the fingerprint matrix data of the sample, and obtaining three data of-1, 0 and 1 from only 0 and 1, wherein, -1 represents the peak lack of the sample relative to the standard, 0 represents the absence or the presence of the common peak of the sample and the standard, 1 represents the peak increase of the sample relative to the standard, and the three data respectively correspond to green, white and yellow, 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 a region, clicking can select a wavelength and a retention time to be checked, clicking can check a chromatogram contrast, subtracting to obtain a fingerprint, as shown in fig. 13, green is a lack of a peak, orange is a peak increase, clicking can amplify a region, and clicking can select a wavelength and a retention time to be checked, thereby identifying a peak difference between two samples.
While the foregoing description of the embodiments of the present invention has been presented in conjunction with the drawings, it should be understood that it is not intended to limit the scope of the invention, but rather, it is intended to cover all modifications or variations within the scope of the invention as defined by the claims of the present invention.
Claims (6)
1. The method for converting the liquid chromatography diode array data into the fingerprint is characterized by comprising the following steps of:
step one, data acquisition: collecting liquid chromatographic diode array data of all samples to be analyzed;
step two, data noise reduction: eliminating baseline drift of the liquid chromatography data collected in the first step, and then removing noise to obtain chromatograms with different noise values filtered;
step three, spectral peak confirmation: confirming chromatographic peaks and retention time of the chromatographic peaks obtained in the second step by adopting a peak positioning method;
step four, spectral peak correction: comprehensively calculating all peak retention time of all samples to be analyzed to obtain a chromatographic peak internal standard set N, and correcting the sample chromatographic peak retention time by taking the chromatographic peak internal standard set N as an internal standard;
wherein the method for correcting the retention time of the chromatographic peak comprises the following two steps:
first, with internal standard retention time a i For the first row of the matrix, samplesPeak retention time b j As the first column of the matrix, the rest of the matrix is represented by Δt ij Filling correspondingly;
second, determining the difference Deltat ij If the spectrum is smaller than the threshold value Q, and if the spectrum is smaller than Q and the corresponding peak spectrum is basically consistent, the spectrum corresponds to b j Can be regarded as a i Is the same as the chromatographic peak of B j Retention time is replaced by a i The method comprises the steps of carrying out a first treatment on the surface of the If delta t ij If the value is greater than the threshold value Q, the value is a difference peak, and the value is not equal to b j Correcting;
i.e. Δt ij ＝a i -b j
When Deltat ij ≤Q,b j ’＝a i
When Deltat ij ＞Q,b j ’＝b j
Wherein Δt is ij Representing two chromatographic peaks a i And b j The difference in retention time between i, j represent the number of the retention time of the chromatographic peak in the total retention time of the peaks, a i Represents the retention time of the ith chromatographic peak of the internal standard, b j Represents the sample jth chromatographic peak retention time, b j ' represents b j Corrected retention time, Q is the fluctuating threshold of peak retention time;
step five, establishing a fingerprint spectrum: taking the retention time of the peaks in the chromatographic peak internal standard set N as the first column of the matrix, and each wavelength A k The corresponding number sets form the subsequent k columns of the matrix; a is that k And if the corresponding number set has peaks at different retention times, filling 1 at the position of the corresponding number set, otherwise filling 0, and setting different colors for different data to obtain a visualized fingerprint, thereby realizing conversion of the liquid chromatography diode array data into the fingerprint.
2. The method for converting liquid chromatography diode array data into fingerprint according to claim 1, further comprising the step of comparing the fingerprint with: and D, carrying out calculation contrast on the finger print obtained in the fifth step, and visualizing differences among different liquid chromatographic results through matrix addition or subtraction.
3. The method for converting liquid chromatography diode array data into fingerprint according to claim 2, wherein the specific process of the fingerprint comparison method comprises the following two steps:
the first step: according to the common peak and the difference peak between the sample to be analyzed and the standard, fingerprint spectrum matrix data of different samples to be analyzed are correspondingly added to obtain three data of 0, 1 and 2, wherein 0 represents that the sample to be analyzed and the standard are both 'no peak', 1 represents that the sample to be analyzed and the standard are both 'different peak', 2 represents that the sample to be analyzed and the standard are both 'common peak', and different colors are set for different data to enable analysis results of different samples to be visualized, so that the difference peak and the common peak between different samples to be analyzed are found and positioned, but the increase of the peak and the decrease of the peak cannot be distinguished;
and a second step of: according to the peak increase and the peak lack in the difference peaks, subtracting the fingerprint matrix data of the standard from the fingerprint matrix data of the sample to be analyzed to obtain three data of-1, 0 and 1, wherein-1 represents that the sample to be analyzed is lack of the peak relative to the standard, 0 represents that the sample to be analyzed and the standard are not provided with the peak or are provided with the common peak, and 1 represents that the sample to be analyzed is increased relative to the standard; this step is complementary to the first step in that different data sets are provided with different colors to visualize the analysis results of different samples to be analyzed.
4. The method for converting liquid chromatography diode array data into fingerprint according to claim 1, wherein the data noise reduction is performed in two steps:
the first step, baseline drift is eliminated, and the calculation formula is as follows:
X (i) '＝X (i+m) -X (i)
wherein X is (i) The absorbance value representing the ith retention time, m is the retention time interval, X (i+m) A light absorption value representing the i+mth retention time; x is X (i) ' is chromatographic data after baseline is leveled and replacedReplace the original X (i) ；
Second, noise is removed: taking one or more noise values S, and calculating the following formula:
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, returning the calculated data smaller than zero to zero, and keeping the original value of the data larger than zero to obtain chromatograms after filtering different noise values.
5. The method for converting liquid chromatography diode array data into fingerprint according to claim 1, wherein the determining step of the chromatographic peak internal standard set N is as follows:
the first step, counting all peak retention time of all samples, and sorting according to the size;
secondly, standard deviation is calculated for n adjacent retention times in sequence, if the standard deviation is smaller than the set value R of the code, the corresponding retention time is regarded as the same peak retention time, and the retention time is classified into a group, and the calculation formula is as follows;
wherein R is a set value of a code, n is a selected number of retention times for standard deviation,
x is the average of the selected retention times i An ith of the selected retention times;
and thirdly, taking the median value of each group of retention time, setting the aggregate set of the median values as an internal standard set N of chromatographic peaks, and using the internal standard set N as a correction standard for correction of chromatographic peak retention time of all samples.
6. The method for converting liquid chromatography diode array data into fingerprint according to claim 1, wherein the step of data reduction is further included between the step one and the step three, specifically: according to the analysis precision requirement, sample data is reduced proportionally by adjusting the data sampling interval of the chromatographic retention time, and the reduced liquid chromatographic diode array data is obtained and used for the subsequent steps.
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| JP2006053004A (en) * | 2004-08-11 | 2006-02-23 | Hitachi High-Technologies Corp | Mass spectrometer |
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| CN105891397A (en) * | 2015-01-26 | 2016-08-24 | 大连达硕信息技术有限公司 | Comprehensive-two-dimensional-gas-chromatography peak detecting method |
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