CN115453009A - Chemical substance annotation method independent of retention time - Google Patents

Chemical substance annotation method independent of retention time Download PDF

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CN115453009A
CN115453009A CN202211262069.2A CN202211262069A CN115453009A CN 115453009 A CN115453009 A CN 115453009A CN 202211262069 A CN202211262069 A CN 202211262069A CN 115453009 A CN115453009 A CN 115453009A
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CN115453009B (en
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薛靖川
诸嘉民
蔡宴朋
谭倩
杨丹琳
林憶玲
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Guangdong University of Technology
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G01N30/62—Detectors specially adapted therefor
    • G01N30/72—Mass spectrometers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G01N30/86—Signal analysis
    • G01N30/8624—Detection of slopes or peaks; baseline correction
    • G01N30/8631—Peaks
    • G01N30/8634—Peak quality criteria

Abstract

The present invention provides a retention time independent chemical annotation process. The method comprises the following steps: acquiring in-source fragment ion mass spectrum data of a target chemical substance acquired based on an in-ion source high-energy cracking phenomenon, establishing a target chemical substance ion database, and acquiring secondary ion mass spectrum data of a sample chemical substance. And extracting chromatographic data of parent ions of specific target chemical substances from the secondary ion mass spectrum data of the sample chemical substances respectively. Peak detection is performed on the extracted chromatographic data to determine a number of potential material chromatographic peaks and corresponding peak periods. And determining the existing credibility of the specific target chemical substance based on the abundance correlation degree of the parent ions and the target fragment ions corresponding to the chromatographic peaks of the specific potential substance in the fragment ion mass spectrum data of the sample chemical substance in the corresponding peak-appearing time period. The target fragment ions are all fragment ions associated with the parent ions corresponding to the specific potential substance chromatographic peaks in the target chemical substance ion database.

Description

Chemical substance annotation method independent of retention time
Technical Field
The technical scheme provided by the application relates to the field of chemical substance identification/identification, in particular to a novel retention time-independent chemical substance annotation method.
Background
Chemical substance recognition/annotation is an important component of exposition omics studies, including exogenous environmental pollutants and endogenous active metabolites generated by in vivo biochemical reaction processes such as intestinal flora, inflammatory response, and the like. The first difficulty of the chemical exposure group is how to perform rapid detection and analysis on human chemical exposure. Chemical substances such as environmental pollutants exist at a low level in a human body, which brings great challenges to detection and analysis, and an analysis and detection technology with high sensitivity is urgently needed to analyze and identify low-concentration chemical substances in a sample.
Conventional chemical annotation/identification schemes require acquisition of both parent ion Mass Spectrometry (MS) data and fragment ion mass spectrometry data, respectively, by a tandem mass spectrometer. The parent ions, also referred to as precursor ions, are typically generated within the ion source. The generation of fragment ions typically requires the combination of ESI and tandem mass spectrometry (ESI-MS/MS) to generate fragment ions by energetic reaction with inert gas molecules after the parent ions enter the collision chamber. However, scientists have found that even if the in-source fragmentation (ISF) phenomenon is present in so-called "soft ionization" techniques such as ESI (electrospray ionization source), the in-source fragment ions generated by the in-source fragmentation phenomenon are a major cause of erroneous chemical species identification results. The data acquisition modes in the traditional expository-based chemical substance annotation/identification scheme are as follows: a data dependent acquisition mode (DDA) and a data independent acquisition mode (DIA).
The Data Dependent Acquisition (DDA) mode is one of the primary modes of data acquisition in tandem mass spectrometry. In DDA mode, the mass spectrometer will automatically perform MS/MS analysis on a list of parent ions selected from a full scan spectrum when performing an MS full scan. DDA mode has the advantage of high selectivity, but low throughput and difficulty in achieving batch collection of chemical fragment ions.
Independent data acquisition (DIA) is a mode of batch acquisition of chemical fragment ions in mass spectrometry. In this mode, all ions within a selected m/z (mass to charge ratio) range will be fragmented and analyzed in the second stage of tandem mass spectrometry. Tandem mass spectral data is obtained in this mode by fragmentation of all ions entering the mass spectrometer at a given time (called broad spectrum DIA) or by sequential separation and fragmentation of the m/z range. This data acquisition mode, while enabling batch acquisition of chemical species fragment ions, is less selective.
However, the fragment ion generation method based on the collision chamber has a certain requirement on the peak height of the parent ion, and the fragment ion information of low-concentration chemical substances cannot be effectively acquired. The applicant has previously proposed a chemical substance highly sensitive analytical technique (EISA) based on the phenomenon of high-energy fragmentation in a mass spectrometry ion source. The method is used for collecting low-concentration chemical substance fragment ions and realizing identification of low-concentration chemical substances. The method requires that a target chemical substance fragment ion database is firstly constructed, the target chemical substance in the database is taken as a research center, and the retention time in mass spectrum data is combined to identify the target chemical substance in the database which may exist in an EISA spectrogram. For retention time missing/unrecorded mass spectral data, there is no way for this method to perform chemical annotation/identification. If the fragment ion data containing retention time of the target chemical substance is obtained based on the experimental means, a large amount of standard products need to be purchased, and the cost is high. Therefore, it is highly desirable to develop a retention-time-independent chemical substance annotation method based on a spectrum obtained by EISA technology, so as to realize automated identification of sample chemical substances by using the existing in-source fragment ion mass spectrum data of target chemical substances with unrecorded retention time.
Disclosure of Invention
Aiming at the defects of the existing low-concentration chemical substance annotation method, the invention provides a chemical substance annotation method independent of retention time, and realizes the automatic identification of chemical substances.
The technical scheme provided by the invention is realized as follows: a method of retention time independent annotation of a chemical, the method comprising the steps of:
s1, acquiring in-source fragment ion mass spectrum data of a target chemical substance acquired based on a high-energy cracking phenomenon in an ion source, establishing a target chemical substance ion database, and acquiring secondary ion mass spectrum data of a sample chemical substance; the in-source fragment ion mass spectrometry data for the target chemical species comprises: the mass-to-charge ratio of the fragment ions is determined by mass spectrometry data of the parent ions of the target chemical substance with the parent ion mass-to-charge ratio and mass spectrometry data of the fragment ions with the fragment ion mass-to-charge ratio associated with the specific parent ions. The secondary ion mass spectrum data of the sample chemical substance is acquired by a secondary source internal ion mass spectrum data of the sample chemical substance in an ion source generated high-energy cracking phenomenon, or acquired by a tandem mass spectrometer under a data acquisition mode (DDA).
And S2, sequentially extracting chromatographic data corresponding to parent ions of related target chemical substances in the target chemical substance ion database from the secondary ion mass spectrum data of the sample chemical substances. The related target chemical substance refers to a target chemical substance of which the parent ion belongs to a target mass-to-charge ratio range, wherein the target mass-to-charge ratio range is a mass-to-charge ratio interval where all ions in secondary ion mass spectrum data of the sample chemical substance are located.
And S3, carrying out peak detection on the extracted chromatographic data to determine a plurality of potential substance chromatographic peaks and a peak-appearing time period of each potential substance chromatographic peak.
S4, outputting chemical substances possibly contained in the sample chemical substances based on the abundance correlation degree of the parent ions and the target fragment ions corresponding to the specific potential substance chromatographic peaks in the secondary fragment ion mass spectrum data of the sample chemical substances in the corresponding peak-appearing time period; and the target fragment ions are all fragment ions associated with the parent ions corresponding to the chromatographic peaks of the specific potential substances in the target chemical substance ion database.
The step S3 is implemented as: and searching a window with the searching width of 3 data points along the time axis of the extracted chromatographic data for the maximum corresponding to the abundance of the parent ions, namely when the value of the middle data point sampled by the window is greater than the set abundance threshold value and the values of the left data point and the right data point are both less than the value of the middle data point, the value corresponding to the middle data point is the maximum corresponding to the abundance of the parent ions. And when the value corresponding to the middle data point of the window is the maximum value, the window simultaneously increases the search width to the left and the right sides, namely, the window is extended to the left and the right sides so as to obtain the corresponding chromatographic peak and the corresponding peak-appearing time period. When the window simultaneously increases the search width leftwards and rightwards, if a zero value or a data value larger than the maximum value occurs in the range of preset N data points on either side of the left side and the right side of the middle data point, taking the position of the zero value or the data value larger than the maximum value on the time axis of the extracted chromatographic data as the boundary of the either side of a corresponding potential substance chromatographic peak, wherein N is a positive integer larger than 1; otherwise, the position of the Nth data point on either side of the middle data point on the time axis of the extracted chromatographic data is taken as the boundary of the either side of the corresponding potential substance chromatographic peak. And recording the time period defined by the left and right boundaries of the corresponding one potential substance chromatographic peak on the time axis of the extracted chromatographic data as the peak appearance time period of the corresponding one potential substance chromatographic peak. Preferably, when extracting chromatographic data corresponding to parent ions of target chemicals in the target chemical ion database at 1 data point in 1 second at the secondary ion mass spectrometry data of the sample chemicals, the N is set to 15.
The step S4 is implemented as follows: judging whether corresponding target fragment ions exist in the secondary fragment ion mass spectrum data of the sample chemical substance in the peak-appearing time period of a plurality of potential substance chromatographic peaks corresponding to the parent ions of the specific target chemical substance; if not, rejecting corresponding potential substance chromatographic peak; otherwise, calculating the abundance correlation degree of each target fragment ion and the parent ion corresponding to the corresponding potential substance chromatographic peak of the secondary ion mass spectrum data of the sample chemical substance in the peak appearing time period of the corresponding potential substance chromatographic peak. When the abundance correlation degrees are all larger than the threshold value, determining the corresponding target chemical substance as a chemical substance possibly contained in the sample chemical substance and outputting the chemical substance; when the abundance correlations are not satisfied to be all greater than the threshold, recording the corresponding target chemical as a screening target for subsequent further identification.
Further, the abundance correlation degree is a pearson correlation coefficient, and the calculation formula is as follows:
Figure BDA0003891455250000041
wherein r xy The abundance correlation degree of any target fragment ion and the corresponding parent ion of the corresponding potential substance chromatographic peak is determined in the peak-appearing time period of the secondary ion mass spectrum data of the sample chemical substance; x is the number of i The ith abundance data of the parent ion corresponding to the corresponding potential species chromatographic peak,
Figure BDA0003891455250000042
average abundance of parent ion corresponding to the corresponding potential species chromatographic peak, y i (ii) the ith abundance data for the abundance of any of the fragment ions,
Figure BDA0003891455250000043
i is more than or equal to 1 and less than or equal to n, and n is the number of the abundance data of the parent ions in the corresponding potential substance chromatographic peak;
Figure BDA0003891455250000044
Figure BDA0003891455250000045
preferably, the threshold is set to 0.8.
The chemical substance annotation method provided by the invention is combined with a chemical substance high-sensitivity analysis technology (EISA) of a high-energy cracking phenomenon in a mass spectrum ion source, so that the annotation/identification of the sample chemical substance by utilizing the in-source fragment ion mass spectrum data of the target chemical substance without retention time is realized.
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FIG. 1 is a flow chart of a retention time independent chemical annotation process provided by the present invention.
Detailed Description
In order to make the technical problems, technical solutions and advantages solved by the present invention more apparent, the present invention is further described in detail below with reference to the accompanying drawings. It should be understood that the specific embodiments described herein are merely illustrative of the invention and are not intended to limit the invention.
As shown in fig. 1, the method for annotating chemical substances independent of retention time provided by the invention comprises the following steps:
s1, acquiring in-source fragment ion mass spectrum data of a target chemical substance acquired based on a high-energy cracking phenomenon in an ion source, establishing a target chemical substance ion database, and acquiring secondary ion mass spectrum data of a sample chemical substance; the in-source fragment ion mass spectrometry data for the target chemical species comprises: the target chemical substance has parent ion mass spectrum data of parent ion mass-to-charge ratio, and fragment ion mass spectrum data of specific parent ion associated mass-to-charge ratio of fragment ions. The fragment ion mass spectrum data in the source of the target chemical substance can be obtained through website downloading or other previous experimental data collection, and the specific acquisition channel is not limited here. The secondary ion mass spectrum data of the sample chemical substance is acquired by a secondary source internal ion mass spectrum data of the sample chemical substance in an ion source generated high-energy cracking phenomenon, or acquired by a tandem mass spectrometer under a data acquisition mode (DDA).
And S2, sequentially extracting chromatographic data corresponding to parent ions of related target chemical substances in the target chemical substance ion database from the secondary ion mass spectrum data of the sample chemical substances. From the secondary ion mass spectral data of the sample chemical species, the mass-to-charge ratio range of the ions therein can be determined, where the target chemical species of interest refers to the target chemical species whose parent ions fall within the mass-to-charge ratio range. Here, extraction of corresponding chromatographic data for parent ions of each target chemical from secondary ion mass spectrum data of the sample chemical is avoided, and annotation/identification efficiency of the sample chemical is improved.
And S3, carrying out peak detection on the extracted chromatographic data to determine a plurality of potential substance chromatographic peaks and a peak-appearing time period of each potential substance chromatographic peak.
The step is realized specifically as follows: and searching the maximum value corresponding to the abundance of the parent ion along the time axis of the extracted chromatographic data by using a window with 3 data point search widths, namely when the value of the middle data point sampled by the window is greater than the set abundance threshold value and the values of the left data point and the right data point are less than the value of the middle data point, the value corresponding to the middle data point is the maximum value corresponding to the abundance of the parent ion. And when the value corresponding to the middle data point of the window is the maximum value, the window simultaneously increases the search width to the left and the right, namely, the window is extended to the left and the right so as to obtain the corresponding chromatographic peak and the corresponding peak-appearing time period. The searching process comprises the following steps: when the window is simultaneously increased in the search width towards the left and the right, in the range of preset N data points on either one of the left and the right sides of the middle data point, if a zero value or a data value larger than the maximum value occurs, taking the position of the zero value or the data value larger than the maximum value on the time axis of the extracted chromatographic data as the boundary of the corresponding one of the one sides of the potential substance chromatographic peak, and otherwise, taking the position of the Nth data point on the either one side of the middle data point on the time axis of the extracted chromatographic data as the boundary of the corresponding one of the one side of the potential substance chromatographic peak; n is a positive integer greater than 1, and the specific numerical value of N can be set according to actual requirements. And recording the time period defined by the left and right boundaries of the corresponding one potential substance chromatographic peak on the time axis of the extracted chromatographic data as the peak appearing time period of the corresponding one potential substance chromatographic peak. In one embodiment, 1 data point per second extracts chromatographic data corresponding to parent ions of target chemistry in the target chemistry ion database at 1 second of the secondary ion mass spectral data of the sample chemistry, and N is correspondingly set to 15.
S4, outputting chemical substances possibly contained in the sample chemical substances based on the abundance correlation degree of the parent ions and the target fragment ions corresponding to the specific potential substance chromatographic peaks in the secondary ion mass spectrum data of the sample chemical substances in the corresponding peak-appearing time periods; and the target fragment ions are all fragment ions associated with the parent ions corresponding to the chromatographic peaks of the specific potential substances in the target chemical substance ion database.
This step is specifically realized as follows: judging whether target fragment ions exist in secondary ion mass spectrum data of the sample chemical substance in the peak-appearing time periods of a plurality of potential substance chromatographic peaks corresponding to parent ions of specific target chemical substances; if not, rejecting corresponding potential substance chromatographic peaks; and if the target fragment ions exist, calculating the abundance correlation degree of each target fragment ion and the parent ion corresponding to the corresponding potential substance chromatographic peak of the secondary ion mass spectrum data of the sample chemical substance in the peak-appearing time period of the corresponding potential substance chromatographic peak. When the abundance correlation degrees are all larger than the threshold value, determining the corresponding target chemical substance as the chemical substance possibly contained in the sample chemical substance and outputting the chemical substance; when the abundance correlations are not satisfied to be all greater than the threshold, recording the corresponding target chemical as a screening target for subsequent further identification. Preferably, the threshold corresponding to the abundance correlation is set to 0.8.
Further, the abundance correlation degree is a pearson correlation coefficient, and the calculation formula is as follows:
Figure BDA0003891455250000071
wherein, r xy The abundance correlation degree of any target fragment ion and the parent ion corresponding to the corresponding potential substance chromatographic peak is obtained when the secondary ion mass spectrum data of the sample chemical substance is in the peak appearing time period of the corresponding potential substance chromatographic peak; x is a radical of a fluorine atom i The ith abundance data of the parent ion corresponding to the corresponding potential species chromatographic peak,
Figure BDA0003891455250000072
chromatography of the corresponding potential substanceAverage abundance of parent ion, y, corresponding to peak i (ii) an ith abundance data that is the abundance of any of the fragment ions,
Figure BDA0003891455250000073
i is more than or equal to 1 and less than or equal to n, wherein n is the number of the mother ion abundance data in the corresponding potential substance chromatographic peak;
Figure BDA0003891455250000074
Figure BDA0003891455250000075
in correspondence with the above method, the present invention also provides a computer-readable storage medium having stored thereon a program code, which is executed by a computer to implement the above retention time-independent chemical substance annotation method.
The above-mentioned embodiments are only used for illustrating the technical solutions of the present application, and not for limiting the same; although the present application has been described in detail with reference to the foregoing embodiments, it should be understood by those of ordinary skill in the art that: the technical solutions described in the foregoing embodiments may still be modified, or some technical features may be equivalently replaced; such modifications and substitutions do not substantially depart from the spirit and scope of the embodiments of the present application and are intended to be included within the scope of the present application.

Claims (6)

1. A method for retention time independent annotation of chemical substances, the method comprising the steps of:
s1, acquiring in-source fragment ion mass spectrum data of a target chemical substance acquired based on a high-energy cracking phenomenon in an ion source, establishing a target chemical substance ion database, and acquiring secondary ion mass spectrum data of a sample chemical substance; the in-source fragment ion mass spectrometry data for the target chemical species comprises: the mass spectrum data of the parent ions of the target chemical substances with the parent ion mass-to-charge ratios and the mass spectrum data of the fragment ions of the specific parent ion-related mass-to-charge ratios with the fragment ions; the secondary ion mass spectrum data of the sample chemical substance is acquired by a secondary source internal ion mass spectrum data of the sample chemical substance in an ion source generated high-energy cracking phenomenon or acquired by a tandem mass spectrometer in a data acquisition mode;
s2, sequentially extracting chromatographic data corresponding to parent ions of related target chemical substances in the target chemical substance ion database from secondary ion mass spectrum data of the sample chemical substances; the related target chemical substance refers to a target chemical substance of which the parent ions belong to a target mass-to-charge ratio range, wherein the target mass-to-charge ratio range is a mass-to-charge ratio interval in which all ions in secondary ion mass spectrum data of the sample chemical substance are located;
s3, performing peak detection on the extracted chromatographic data to determine a plurality of potential substance chromatographic peaks and a peak emergence time period of each potential substance chromatographic peak;
s4, outputting chemical substances possibly contained in the sample chemical substances based on the abundance correlation degree of the parent ions and the target fragment ions corresponding to the specific potential substance chromatographic peaks in the secondary ion mass spectrum data of the sample chemical substances in the corresponding peak-appearing time periods; and the target fragment ions are all fragment ions associated with the parent ions corresponding to the chromatographic peaks of the specific potential substances in the target chemical substance ion database.
2. The chemical substance annotation method of claim 1, wherein said step S3 is implemented as: searching a maximum value corresponding to the abundance of the parent ion along a time axis of the extracted chromatographic data by using a window with 3 data point searching widths, namely when the value of a middle data point sampled by the window is greater than a set abundance threshold value and the values of the left data point and the right data point are both less than a middle data point value, the value corresponding to the middle data point is the maximum value corresponding to the abundance of the parent ion;
when the value corresponding to the middle data point of the window is the maximum value, the window simultaneously increases the search width of the window to the left and the right; when the window simultaneously increases the search width leftwards and rightwards, in the range of N data points on any one side of the left side and the right side of the middle data point, if a zero value or a data value larger than the maximum value occurs, taking the position of the zero value or the data value larger than the maximum value on the time axis of the extracted chromatographic data as the boundary of the corresponding one side of a potential substance chromatographic peak, wherein N is a positive integer larger than 1; otherwise, the position of the Nth data point on either side of the middle data point on the time axis of the extracted chromatographic data is taken as the boundary of the either side of the corresponding one potential substance chromatographic peak; recording a time period defined by the left and right boundaries of the corresponding one of the potential substance chromatographic peaks on the time axis of the extracted chromatographic data as a peak appearing period of the corresponding one of the potential substance chromatographic peaks.
3. The chemical substance annotation process of claim 2, wherein said step S4 is implemented as: judging whether target fragment ions exist in secondary ion mass spectrum data of the sample chemical substance in the peak-appearing time periods of a plurality of potential substance chromatographic peaks corresponding to the parent ions of the specific target chemical substance; if not, rejecting corresponding potential substance chromatographic peaks; otherwise, calculating the abundance correlation degree of each target fragment ion and the parent ion corresponding to the corresponding potential substance chromatographic peak of the secondary ion mass spectrum data of the sample chemical substance in the peak-appearing time period of the corresponding potential substance chromatographic peak; and when the abundance correlation degrees are all larger than the threshold value, determining the corresponding specific target chemical substance as the chemical substance possibly contained in the sample chemical substance and outputting the chemical substance.
4. The method of any one of claims 1 to 3, wherein the abundance correlation is a Pearson correlation coefficient and is calculated by the formula:
Figure FDA0003891455240000021
wherein, r xy The method comprises the steps that in the peak-appearing time period of a corresponding potential substance chromatographic peak, the abundance correlation degree of any target fragment ion and a parent ion corresponding to the corresponding potential substance chromatographic peak is obtained from secondary ion mass spectrum data of a sample chemical substance; x is a radical of a fluorine atom i (ii) the ith abundance data of the parent ion corresponding to the corresponding potential species chromatographic peak,
Figure FDA0003891455240000033
is the average abundance, y, of the parent ion corresponding to the corresponding potential species chromatographic peak i (ii) an ith abundance data that is the abundance of any of the fragment ions,
Figure FDA0003891455240000034
i is more than or equal to 1 and less than or equal to n, wherein n is the number of the mother ion abundance data in the corresponding potential substance chromatographic peak;
Figure FDA0003891455240000031
Figure FDA0003891455240000032
5. the method of claim 4, wherein the threshold is set to 0.8.
6. A computer-readable storage medium having stored thereon a program code, the program code being executable by a computer to implement the retention time independent chemical substance annotation process of any one of claims 1 to 5.
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