1
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Barchanska H, Malejka A, Płonka J. Non-target metabolomics approach for the investigation of the hidden effects induced by atrazine and its degradation products on plant metabolism. CHEMOSPHERE 2024; 359:142298. [PMID: 38729438 DOI: 10.1016/j.chemosphere.2024.142298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/12/2024]
Abstract
Japanese radish (Raphanus sativus var. longipinnatus) plants grown under laboratory conditions were individually exposed to the same doses of atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine, ATR) or its main degradation products: either 2-amino-4-chloro-6-isopropylamino-1,3,5-triazine (DEA) or 2-amino-4-chloro-6-ethylamino-1,3,5-triazine (DIA) or desethyl-desisopropyl-atrazine (DEDIA) or 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine (HA), respectively. One week after treatment in plants exposed to ATR, DIA, and DEA, their concentrations were 7.8 μg/g, 9.7 μg/g, and 14.5 μg/g, respectively, while those treated with DEDIA and HA did not contain these compounds. These results were correlated with plant amino acid profile obtained by suspect screening analysis and metabolomic "fingerprint" based on non-target analysis, obtained by liquid chromatography coupled with QTRAP triple quadrupole mass spectrometer. In all cases, both ATR and its by-products were found to interfere with the plant's amino acid profile and modify its metabolic "fingerprint". Therefore, we proved that the non-target metabolomics approach is an effective tool for investigating the hidden effects of pesticides and their transformation products, which is particularly important as these compounds may reduce the quality of edible plants.
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Affiliation(s)
- Hanna Barchanska
- Department of Inorganic Chemistry, Analytical Chemistry and Electrochemistry, Silesian University of Technology, Poland
| | - Anna Malejka
- Department of Inorganic Chemistry, Analytical Chemistry and Electrochemistry, Silesian University of Technology, Poland
| | - Joanna Płonka
- Department of Inorganic Chemistry, Analytical Chemistry and Electrochemistry, Silesian University of Technology, Poland; Biotechnology Centre, Silesian University of Technology, Poland.
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2
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Murray KJ, Villalta PW, Griffin TJ, Balbo S. Discovery of Modified Metabolites, Secondary Metabolites, and Xenobiotics by Structure-Oriented LC-MS/MS. Chem Res Toxicol 2023; 36:1666-1682. [PMID: 37862059 DOI: 10.1021/acs.chemrestox.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Exogenous compounds and metabolites derived from therapeutics, microbiota, or environmental exposures directly interact with endogenous metabolic pathways, influencing disease pathogenesis and modulating outcomes of clinical interventions. With few spectral library references, the identification of covalently modified biomolecules, secondary metabolites, and xenobiotics is a challenging task using global metabolomics profiling approaches. Numerous liquid chromatography-coupled mass spectrometry (LC-MS) small molecule analytical workflows have been developed to curate global profiling experiments for specific compound groups of interest. These workflows exploit shared structural moiety, functional groups, or elemental composition to discover novel and undescribed compounds through nontargeted small molecule discovery pipelines. This Review introduces the concept of structure-oriented LC-MS discovery methodology and aims to highlight common approaches employed for the detection and characterization of covalently modified biomolecules, secondary metabolites, and xenobiotics. These approaches represent a combination of instrument-dependent and computational techniques to rapidly curate global profiling experiments to detect putative ions of interest based on fragmentation patterns, predictable phase I or phase II metabolic transformations, or rare elemental composition. Application of these methods is explored for the detection and identification of novel and undescribed biomolecules relevant to the fields of toxicology, pharmacology, and drug discovery. Continued advances in these methods expand the capacity for selective compound discovery and characterization that promise remarkable insights into the molecular interactions of exogenous chemicals with host biochemical pathways.
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Affiliation(s)
- Kevin J Murray
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Silvia Balbo
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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3
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Huang AX, Li JM, Yang L, Chen L, Zhou ZH, Li P, Gao W. A mass defect filtering combined background subtraction strategy for rapid screening and identification of metabolites in rat plasma after oral administration of Yindan Xinnaotong soft capsule. J Pharm Biomed Anal 2023; 231:115400. [PMID: 37099978 DOI: 10.1016/j.jpba.2023.115400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/07/2023] [Accepted: 04/15/2023] [Indexed: 04/28/2023]
Abstract
The absorbed prototypes and metabolites of traditional Chinese medicines (TCMs) serves an important part in pharmacological action and clinical effects. However, the comprehensive characterization of which is facing actual or possible rigorous challenges due to the lack of data mining methods and the complexity of metabolite samples. Yindan Xinnaotong soft capsule (YDXNT), a typical traditional Chinese medicine prescription consisting of extracts from 8 herbal medicines, is widely used for the treatment of angina pectoris and ischemic stroke in the clinic. This study established a systematic data mining strategy based on ultra-high performance liquid chromatography tandem quadrupole-time-of-fight mass spectrometry (UHPLC-Q-TOF MS) for comprehensive metabolite profiling of YDXNT in rat plasma after oral administration. The multi-level feature ion filtration strategy was primarily conducted through the full scan MS data of plasma samples. All potential metabolites were rapidly fileted out from the endogenous background interference based on the background subtract and the chemical type specifically mass defect filter (MDF) windows including flavonoids, ginkgolides, phenolic acids, saponins, and tanshinones. As the MDF windows of certain types were overlapped, the screened-out potential metabolites were deeply characterized and identified according to their retention times (RT), integrating neutral loss filtering (NLF), diagnostic fragment ions filtering (DFIF), and further confirmed by reference standards. Thus, a total of 122 compounds, consisting of 29 prototype components (16 confirmed with reference standards) and 93 metabolites had been identified. This study provides a rapid and robust metabolite profiling method for researching complicated traditional Chinese medicine prescriptions.
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Affiliation(s)
- An-Xian Huang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Jun-Ming Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Liu Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Ling Chen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Zi-Han Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China.
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4
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Wu Y, Zhou L, Kang L, Cheng H, Wei X, Pan C. Suspect screening strategy for pesticide application history based on characteristics of trace metabolites. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120557. [PMID: 36328280 DOI: 10.1016/j.envpol.2022.120557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Pesticides are widely used to protect crops but can also threaten public health as they can remain in the environment for a long time. Additionally, some transformation products (TPs) of unknown toxicity, stability, or bioaccumulation properties can further be formed from the hydrolysis, photolysis and biodegradation of pesticides. The identification and quantification of those TPs can be challenging for environmental regulation and risk assessment due to a limited understanding about them. In this study, a suspect screening strategy for pesticide application history was developed and then used to organic products (tea). Liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) was used to screen and identify the TPs in crops and their toxicity was subsequently predicted with the open-source software (ECOSAR and admetSAR). Finally, the SIRIUS software was applied and 142 TPs from 20 pesticides were identified in tea plants based on the fragmentation-degradation relationship. Of these, standards (level 1) and 53 were considered as tentatively identified (levels 2a and 2b). Some TPs were also found to be present in tea plants and soil after 65 days, thus indicating higher persistency or stability than parent pesticides. While others from diafenthiuron and neonicotinoids had higher predicted toxicity of daphnid, and demonstrated positive for honeybee toxicity. Suspect screening is a powerful tool to screen pesticide TPs on the complex matrix of crops. Such screening can provide potential evidence of pesticide application, especially in cases of illegal practices in organic farming.
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Affiliation(s)
- Yangliu Wu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Li Zhou
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Lu Kang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Haiyan Cheng
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xinlin Wei
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Canping Pan
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China.
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Zhou X, Chen X, Fan L, Dong H, Ren Y, Chen X. Stepwise Diagnostic Product Ions Filtering Strategy for Rapid Discovery of Diterpenoids in Scutellaria barbata Based on UHPLC-Q-Exactive-Orbitrap-MS. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238185. [PMID: 36500290 PMCID: PMC9736491 DOI: 10.3390/molecules27238185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022]
Abstract
Diterpenoids are considered the major bioactive components in Scutellaria barbata to treat cancer and inflammation, but few comprehensive profiling studies of diterpenoids have been reported. Herein, a stepwise diagnostic product ions (DPIs) filtering strategy for efficient and targeted profiling of diterpenoids in Scutellaria barbata was developed using UHPLC-Q-Exactive-Orbitrap-MS. After UHPLC-HRMS/MS analysis of six diterpenoid reference standards, fragmentation behaviors of these references were studied to provide DPIs. Then, stepwise DPIs filtering aimed to reduce the potential interferences of matrix ions and achieve more chromatographic peaks was conducted to rapidly screen the diterpenoids. The results demonstrated that stepwise DPIs were capable of simplifying the workload in data post-processing and the effective acquisition of low abundance compounds. Subsequently, DPIs and MS/MS fragment patterns were adopted to identify the targeted diterpenoids. As a result, 381 diterpenoids were unambiguously or tentatively identified, while 141 of them with completely new molecular weights were potential new diterpenoids for Scutellaria barbata. These results demonstrate that the developed stepwise DPIs filtering method could be employed as an efficient, reliable, and valuable strategy to screen and identify the diterpenoid profile in Scutellaria barbata. This might accelerate and simplify target constituent profiling from traditional Chinese medicine (TCM) extracts.
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Cai R, Huang W, Meder M, Bourgain F, Aizikov K, Riva M, Bianchi F, Ehn M. Improving the Sensitivity of Fourier Transform Mass Spectrometer (Orbitrap) for Online Measurements of Atmospheric Vapors. Anal Chem 2022; 94:15746-15753. [DOI: 10.1021/acs.analchem.2c03403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Runlong Cai
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Wei Huang
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Melissa Meder
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Frederic Bourgain
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON, Villeurbanne 69626, France
| | | | - Matthieu Riva
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON, Villeurbanne 69626, France
| | - Federico Bianchi
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Mikael Ehn
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
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7
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Ruan Q, Comstock K. A New Workflow for Drug Metabolite Profiling by Utilizing Advanced Tribrid Mass Spectrometry and Data-Processing Techniques. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2050-2061. [PMID: 33998806 DOI: 10.1021/jasms.0c00436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Drug metabolite profiling utilizes liquid chromatography with tandem mass spectrometry (LC/MS/MS) to acquire ample information for metabolite identification and structural elucidation. However, there are still challenges in detecting and characterizing all potential metabolites that can be masked by a high biological background, especially the unknown and uncommon ones. In this work, a novel metabolite profiling workflow was established on a platform using a state-of-the-art tribrid high-resolution mass spectrometry (HRMS) system. Primarily, an instrumental method was developed based on the novel design of the tribrid system that facilitates in-depth MSn scans with two fragmentation devices. Additionally, different advanced data acquisition techniques were assessed and compared, and automatic background exclusion and deep-scan approaches were adopted to promote assay efficiency and metabolite coverage. Finally, different data-analysis techniques were explored to fully extract metabolite data from the information-rich MS/MS data sets. Overall, a workflow combining tribrid mass spectrometry and advanced acquisition methodology has been developed for metabolite characterization in drug discovery and development. It maximizes the tribrid HRMS platform's utility and enhances the coverage, efficiency, quality, and speed of metabolite profiling assays.
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Affiliation(s)
- Qian Ruan
- Non-clinical Disposition and Bioanalysis, BMS, Princeton, New Jersey 08540, United States
| | - Kate Comstock
- Thermo Fisher Scientific, San Jose, California 95134, United States
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8
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Zuo L, Liu L, Yang Y, Yang J, Chen M, Zhang H, Kang J, Zhang X, Wang J, Sun Z. An Entire Process Optimization Strategy for Comprehensive In Vivo Metabolite Profiling of Prucalopride in Rats Based on Ultra-Performance Liquid Chromatography With Q-Exactive Hybrid Quadrupole-Orbitrap High-Resolution Mass Spectrometry. Front Pharmacol 2021; 12:610226. [PMID: 34025397 PMCID: PMC8138455 DOI: 10.3389/fphar.2021.610226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/17/2021] [Indexed: 11/15/2022] Open
Abstract
Prucalopride was widely used for chronic constipation, which is difficult to be adequately relieved by laxatives in adult patients in clinic. Due to the difficulty in metabolite identification, metabolic process of prucalopride had not been investigated in vivo. In this study, an efficient strategy was proposed for comprehensive metabolite profiling of prucalopride after oral administration in rat plasma, urine, and feces samples. This strategy was composed of five steps. First, the samples at multiple time points after oral administration were collected to increase the representativeness of the samples. Second, different sample preparation methods were investigated to obtain superior extraction efficiency. Third, the raw data of test sample and blank sample were acquired using ultra-performance liquid chromatography with Q-Exactive hybrid quadrupole–orbitrap high-resolution accurate mass spectrometry under the positive and negative full-scan/dd MS2 mode. Fourth, combined mass defect filter with background subtraction model in soft of compound discovery, all peaks were constructed to filter potential metabolites after retention time alignment and ion filtration, which could remove large amounts of interference ions. Besides, it can predict potential biotransformation, promoting to understand how to metabolize the drug. This provides multiple possibilities and prevents us conjecturing the potential metabolites blindly. Finally, the verification procedure was implemented through exporting the structure and MS2 spectrum to the analytical tool of Mass Frontier. The proposed strategy significantly improved the targeted detection and identification for metabolites in vivo. A total of 47 metabolites were tentatively characterized in the plasma, urine, and feces samples after oral administration of prucalopride. This study could provide a valuable reference for systematic metabolite profile of drug in vivo.
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Affiliation(s)
- Lihua Zuo
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
| | - Liwei Liu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
| | - Yantao Yang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
| | - Jie Yang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
| | - Min Chen
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huafeng Zhang
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian Kang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
| | - Xiaojian Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
| | - Jiabo Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhi Sun
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China
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9
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Wei WL, Li HJ, Yang WZ, Qu H, Li ZW, Yao CL, Hou JJ, Wu WY, Guo DA. An integrated strategy for comprehensive characterization of metabolites and metabolic profiles of bufadienolides from Venenum Bufonis in rats. J Pharm Anal 2021; 12:136-144. [PMID: 35573889 PMCID: PMC9073132 DOI: 10.1016/j.jpha.2021.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Comprehensive characterization of metabolites and metabolic profiles in plasma has considerable significance in determining the efficacy and safety of traditional Chinese medicine (TCM) in vivo. However, this process is usually hindered by the insufficient characteristic fragments of metabolites, ubiquitous matrix interference, and complicated screening and identification procedures for metabolites. In this study, an effective strategy was established to systematically characterize the metabolites, deduce the metabolic pathways, and describe the metabolic profiles of bufadienolides isolated from Venenum Bufonis in vivo. The strategy was divided into five steps. First, the blank and test plasma samples were injected into an ultra-high performance liquid chromatography/linear trap quadrupole-orbitrap-mass spectrometry (MS) system in the full scan mode continuously five times to screen for valid matrix compounds and metabolites. Second, an extension-mass defect filter model was established to obtain the targeted precursor ions of the list of bufadienolide metabolites, which reduced approximately 39% of the interfering ions. Third, an acquisition model was developed and used to trigger more tandem MS (MS/MS) fragments of precursor ions based on the targeted ion list. The acquisition mode enhanced the acquisition capability by approximately four times than that of the regular data-dependent acquisition mode. Fourth, the acquired data were imported into Compound Discoverer software for identification of metabolites with metabolic network prediction. The main in vivo metabolic pathways of bufadienolides were elucidated. A total of 147 metabolites were characterized, and the main biotransformation reactions of bufadienolides were hydroxylation, dihydroxylation, and isomerization. Finally, the main prototype bufadienolides in plasma at different time points were determined using LC-MS/MS, and the metabolic profiles were clearly identified. This strategy could be widely used to elucidate the metabolic profiles of TCM preparations or Chinese patent medicines in vivo and provide critical data for rational drug use. Extension-mass defect filter model could reduce about 39% interfering ions. The optimized acquisition mode enhanced about 4 times acquisition capability than regular DDA mode. 147 metabolites were characterized with metabolic network prediction, and the metabolic pathways were deduced in plasmas. The quantitative method of 14 prototypes was established by LC-MS/MS for metabolic profiles study.
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Affiliation(s)
- Wen-Long Wei
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hao-Jv Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Zhi Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hua Qu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhen-Wei Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang-Liang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jin-Jun Hou
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wan-Ying Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Corresponding author.
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Corresponding author. Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
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10
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Wilkinson SD, Martin S, Orton AL, Markandu R, Jones BC. Drug metabolite identification using ultrahigh-performance liquid chromatography-ultraviolet spectroscopy and parallelized scans on a tribrid Orbitrap mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8735. [PMID: 31967694 DOI: 10.1002/rcm.8735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE To capture all metabolites in metabolite identification studies, MS/MS information is required in both positive and negative ionization mode, usually involving several sample injections to gain all information about samples. A high-resolution and high mass accuracy quadrupole/linear trap/Orbitrap tribrid instrument was used to gain this information in a novel single injection 'capture-all' approach to metabolite identification. METHODS Diclofenac, a model compound, was incubated in human and rat hepatocytes. These incubated samples were run using an ultrahigh-performance liquid chromatography/ultraviolet (UHPLC-UV) system coupled to a Thermo Fusion tribrid mass spectrometer. Five parallel scans were used: positive and negative ion full scan, data-dependent MS/MS, both high energy dissociation and collision-induced dissociation, and data-independent all ion fragmentation (AIF) spectra were collected in positive and negative ion mode. RESULTS Nine metabolites were identified; a metabolite observed in the UV trace, but not positive ion full scan MS, was detected in the same sample injection by negative ion full scan MS. This was identified as a sulphate metabolite, and the corresponding negative ion AIF allowed for some structural elucidation. The use of a photo-diode array (PDA) detector allowed for spectral assessment in case of changes in absorbance spectra, and the subsequent semi-quantification of metabolites. CONCLUSIONS This method provided good-quality MS/MS data across the m/z range in both positive and negative ion mode. The addition of both negative ion full scan MS and negative ion MS/MS allowed for the detection and structural elucidation of metabolites not observed in positive ion mode. The use of the PDA detector allowed for the semi-quantification of metabolites.
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Affiliation(s)
- Stephen D Wilkinson
- DMPK/ADME Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Scott Martin
- DMPK/ADME Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Alexandra L Orton
- DMPK/ADME Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Roshini Markandu
- DMPK/ADME Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Barry C Jones
- DMPK/ADME Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
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11
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Wang X, Yu N, Yang J, Jin L, Guo H, Shi W, Zhang X, Yang L, Yu H, Wei S. Suspect and non-target screening of pesticides and pharmaceuticals transformation products in wastewater using QTOF-MS. ENVIRONMENT INTERNATIONAL 2020; 137:105599. [PMID: 32109725 DOI: 10.1016/j.envint.2020.105599] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/16/2020] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
Pesticides and pharmaceuticals are widely used in modern life and are discharged into wastewater after usage. However, a large number of transformation products (TPs) are formed through abiotic (hydrolysis/photolysis, etc.) and biotic (aerobic/anaerobic degradation by micro-organisms) wastewater treatment processes, and the structure and potential risk of TPs are still unclear. In this study, a suspect and non-target screening was performed to monitor these chemicals with HPLC-QTOF-MS. We identified 60 parent compounds by suspect screening in three Chinese wastewater treatment plants with the commercial database of pesticides and pharmaceuticals, and they were confirmed by authentic standards. Then, suspect and non-target screening strategies based on the predicted diagnostic fragment ions were used to screen TPs of the 60 parent compounds. We tentatively identified 50 TPs and confirmed thirteen of them with authentic standards. Among 13 quantified TPs, about 40% of them showed higher concentration than their parent compounds in effluent. Especially, cloquintocet, as a TP of cloquintocet-mexyl, had a concentration ratio TP/parent = 14,809 in effluent. Twenty-five TPs had higher predicted toxicity than the corresponding parent compounds by calculating their LC50 values towards aquatic organisms using toxicity prediction software. Twenty identified TPs were firstly reported in this study. These results indicate the importance of TP analysis in environmental monitoring in wastewater.
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Affiliation(s)
- Xuebing Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Nanyang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Jingping Yang
- Laboratory of Immunology and Reproductive Biology, School of Medicine, Nanjing University, Nanjing, People's Republic of China
| | - Ling Jin
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Huiwei Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Liuyan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Si Wei
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China.
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12
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King A, Baginski M, Morikawa Y, Rainville PD, Gethings LA, Wilson ID, Plumb RS. Application of a Novel Mass Spectral Data Acquisition Approach to Lipidomic Analysis of Liver Extracts from Sitaxentan-Treated Liver-Humanized PXB Mice. J Proteome Res 2019; 18:4055-4064. [DOI: 10.1021/acs.jproteome.9b00334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adam King
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Matthew Baginski
- PhoenixBio USA Corporation, 65 Broadway, Suite 605, New York, New York 10006, United States
| | - Yoshio Morikawa
- PhoenixBio USA Corporation, 65 Broadway, Suite 605, New York, New York 10006, United States
| | - Paul D. Rainville
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, United States
| | | | - Ian D. Wilson
- Department of Surgery and Cancer, Imperial College, Exhibition Road, South Kensington, London SW7 2AZ, U.K
| | - Robert S. Plumb
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, United States
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13
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Li Z, Li Y, Tang YJ, Shui W. Exploiting High-Resolution Mass Spectrometry for Targeted Metabolite Quantification and 13C-Labeling Metabolism Analysis. Methods Mol Biol 2019; 1859:171-184. [PMID: 30421229 DOI: 10.1007/978-1-4939-8757-3_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantification of targeted metabolites, especially trace metabolites and structural isomers, in complex biological materials is an ongoing challenge for metabolomics. In this chapter, we summarize high-resolution mass spectrometry-based approaches mainly used for targeted metabolite and metabolomics analysis, and then introduce an MS1/MS2-combined PRM workflow for quantification of central carbon metabolism intermediates, amino acids, and shikimate pathway-related metabolites. Major steps in the workflow, including cell culture, metabolite extraction, LC-MS analysis and data processing, are described. Furthermore, we adapt this new approach to a dynamic 13C-labeling experiment and demonstrate its unique advantage in capturing and correcting isotopomer labeling curves to facilitate nonstationary 13C-labeling metabolism analysis.
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Affiliation(s)
- Zhucui Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujing Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China.
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14
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Zhu XY, Liu JZ, Dong ZH, Feng F, Liu WY. Identification and screening of cardiac glycosides in Streptocaulon griffithii using an integrated data mining strategy based on high resolution mass spectrometry. Chin J Nat Med 2018; 16:546-560. [PMID: 30080653 DOI: 10.1016/s1875-5364(18)30090-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Indexed: 11/29/2022]
Abstract
The present study was designed to develop a practical strategy to tackle the problem of lacking standard compounds and limited references for identifying structure-related compounds in Streptocaulon griffithii Hook. f., especially those in trace concentrations, with a focus on antitumor activity. The cardiac glycosides (CGs)-enriched part was determined using in vitro bioactive assays in three cancer cell lines and then isolated using macroporous resins. The MS and MS/MS data were acquired using a high performance liquid chromatography coupled with hybrid quadrupole-time of flight (HPLC-Q-TOF-MS) system. To acquire data of trace compound in the extract, a multiple segment program was applied to modify the HPLC-Q-TOF-MS method. A mass defect filter (MDF) approach was employed to make a primary MS data filtration. Utilizing a MATLAB program, the redundant peaks obtained by imprecise MDF template calculated with limited references were excluded by fragment ion classification, which was based on the ion occurrence number in the MDF-filtered total ion chromatograms (TIC). Additionally, the complete cleavage pathways of CG aglycones were proposed to assist the structural identification of 29 common fragment ions (CFIs, ion occurrence number ≥ 5) and diagnostic fragment ions (DFIs, ion occurrence number < 5). As a result, 30 CGs were filtered out from the MDF results, among which 23 were identified. This newly developed strategy may provide a rapid and effective tool for identifying structure-related compounds in herbal medicines.
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Affiliation(s)
- Xiao-Yu Zhu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Zhuo Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen-Huan Dong
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Feng Feng
- Key Laboratory of Biomedical Functional Materials, China Pharmaceutical University, Nanjing 211198, China
| | - Wen-Yuan Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China.
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15
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Zhao X, Zeng Z, Chen A, Lu X, Zhao C, Hu C, Zhou L, Liu X, Wang X, Hou X, Ye Y, Xu G. Comprehensive Strategy to Construct In-House Database for Accurate and Batch Identification of Small Molecular Metabolites. Anal Chem 2018; 90:7635-7643. [DOI: 10.1021/acs.analchem.8b01482] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Zhongda Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- Dalian ChemDataSolution Information Technology Co. Ltd, Dalian 116023, China
| | - Aiming Chen
- Dalian ChemDataSolution Information Technology Co. Ltd, Dalian 116023, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Xiaolin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Xiaoli Hou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yaorui Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
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16
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Pan H, Yao C, Yang W, Yao S, Huang Y, Zhang Y, Wu W, Guo D. An enhanced strategy integrating offline two-dimensional separation and step-wise precursor ion list-based raster-mass defect filter: Characterization of indole alkaloids in five botanical origins of Uncariae Ramulus Cum Unicis as an exemplary application. J Chromatogr A 2018; 1563:124-134. [PMID: 29880214 DOI: 10.1016/j.chroma.2018.05.066] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/20/2018] [Accepted: 05/28/2018] [Indexed: 01/01/2023]
Abstract
Comprehensive chemical profiling is of great significance for understanding the therapeutic material basis and quality control of herbal medicines, which is challenging due to its inherent chemical diversity and complexity, as well as wide concentration range. In this study, we introduced an enhanced strategy integrating offline two-dimensional (2D) separation and the step-wise precursor ion list-based raster-mass defect filter (step-wise PIL-based raster-MDF) scan by tandem LTQ-Orbitrap mass spectrometer. A comprehensive analysis of indole alkaloids in five botanical origins of Uncariae Ramulus Cum Unicis (Gou-Teng) was used as an exemplary application. A positively charged reversed phase (PR) × conventional RP LC system in different pH conditions was constructed with the orthogonality of 74%. A theoretical step-wise PIL among 310-950 Da with the step-size of 2 Da was developed to selectively trigger fragmentations and extend the coverage of potential indole alkaloids. Simultaneously, by defining parent mass width (PMW) of the step-wise PIL to ±55 mDa, a raster-MDF screening was achieved in the acquisition process. Additionally, subtype classification and structural elucidation were facilitated by a four-step interpretation strategy. As a result, a total of 1227 indole alkaloids were efficiently exposed and characterized from five botanical origins of Gou-Teng, which showed high chemical diversity. A systematic comparison among five species was first performed and only 66 indole alkaloids were common. For method validation, three new alkaloid N-oxides were isolated and unambiguously identified by NMR. The present study provides a novel data-dependent acquisition method with improved target coverage and high selectivity. The integrated strategy is practical to efficiently expose and comprehensively characterize complex components in herbal medicines.
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Affiliation(s)
- Huiqin Pan
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China; University of Chinese Academy of Sciences,No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China; University of Chinese Academy of Sciences,No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Wenzhi Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Shuai Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Yong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Yibei Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Wanying Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China.
| | - Dean Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China.
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17
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Noble C, Weihe Dalsgaard P, Stybe Johansen S, Linnet K. Application of a screening method for fentanyl and its analogues using UHPLC-QTOF-MS with data-independent acquisition (DIA) in MSE
mode and retrospective analysis of authentic forensic blood samples. Drug Test Anal 2017; 10:651-662. [DOI: 10.1002/dta.2263] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Carolina Noble
- Section of Forensic Chemistry, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Petur Weihe Dalsgaard
- Section of Forensic Chemistry, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Sys Stybe Johansen
- Section of Forensic Chemistry, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Kristian Linnet
- Section of Forensic Chemistry, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
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18
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DiBattista A, Rampersaud D, Lee H, Kim M, Britz-McKibbin P. High Throughput Screening Method for Systematic Surveillance of Drugs of Abuse by Multisegment Injection–Capillary Electrophoresis–Mass Spectrometry. Anal Chem 2017; 89:11853-11861. [DOI: 10.1021/acs.analchem.7b03590] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alicia DiBattista
- Department
of Chemistry and Chemical Biology, McMaster University, Hamilton L8S 4L8, Canada
| | | | - Howard Lee
- Seroclinix Corporation, Mississauga, ON L4W 5B9, Canada
| | - Marcus Kim
- Agilent Technologies Inc., Mississauga, ON L5N 5M4, Canada
| | - Philip Britz-McKibbin
- Department
of Chemistry and Chemical Biology, McMaster University, Hamilton L8S 4L8, Canada
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19
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Post-acquisition data mining techniques for LC–MS/MS-acquired data in drug metabolite identification. Bioanalysis 2017; 9:1265-1278. [DOI: 10.4155/bio-2017-0046] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Metabolite identification is a crucial part of the drug discovery process. LC–MS/MS-based metabolite identification has gained widespread use, but the data acquired by the LC–MS/MS instrument is complex, and thus the interpretation of data becomes troublesome. Fortunately, advancements in data mining techniques have simplified the process of data interpretation with improved mass accuracy and provide a potentially selective, sensitive, accurate and comprehensive way for metabolite identification. In this review, we have discussed the targeted (extracted ion chromatogram, mass defect filter, product ion filter, neutral loss filter and isotope pattern filter) and untargeted (control sample comparison, background subtraction and metabolomic approaches) post-acquisition data mining techniques, which facilitate the drug metabolite identification. We have also discussed the importance of integrated data mining strategy.
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20
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What can we do to refine the redundant data in LC–MS and GC–MS based metabolomics? Bioanalysis 2017; 9:235-238. [DOI: 10.4155/bio-2016-0272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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21
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Wang G, Fu H, Ye W, Zheng X, Xiao J, Kang D, Rao T, Shao Y, Xie L, Liang Y. Comprehensive characterization of the in vitro and in vivo metabolites of ziyuglycoside I in rat microsome, intestinal flora, excretion specimen and fresh tissues based on LC–Q-TOF/MS. J Pharm Biomed Anal 2016; 128:191-200. [DOI: 10.1016/j.jpba.2016.05.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/20/2022]
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22
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Lai CJS, Zha L, Liu DH, Kang L, Ma X, Zhan ZL, Nan TG, Yang J, Li F, Yuan Y, Huang LQ. Global profiling and rapid matching of natural products using diagnostic product ion network and in silico analogue database: Gastrodia elata as a case study. J Chromatogr A 2016; 1456:187-95. [PMID: 27318507 DOI: 10.1016/j.chroma.2016.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/29/2016] [Accepted: 06/03/2016] [Indexed: 12/25/2022]
Abstract
Rapid discovery of novel compounds of a traditional herbal medicine is of vital significance for pharmaceutical industry and plant metabolic pathway analysis. However, discovery of unknown or trace natural products is an ongoing challenge. This study presents a universal targeted data-independent acquisition and mining strategy to globally profile and effectively match novel natural product analogues from an herbal extract. The famous medical plant Gastrodia elata was selected as an example. This strategy consists of three steps: (i) acquisition of accurate parent and adduct ions (PAIs) and the product ions data of all eluting compounds by untargeted full-scan MS(E) mode; (ii) rapid compound screening using diagnostic product ions (DPIs) network and in silico analogue database with SUMPRODUCT function to find novel candidates; and (iii) identification and isomerism discrimination of multiple types of compounds using ClogP and ions fragment behavior analyses. Using above data mining methods, a total of 152 compounds were characterized, and 70 were discovered for the first time, including series of phospholipids and novel gastroxyl derivatives. Furthermore, a number of gastronucleosides and phase II metabolites of gastrodin and parishins were discovered, including glutathionylated, cysteinylglycinated and cysteinated compounds, and phosphatidylserine analogues. This study extended the application of classical DPIs filter strategy and developed a structure-based screening approach with the potential for significant increase of efficiency for discovery and identification of trace novel natural products.
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Affiliation(s)
- Chang-Jiang-Sheng Lai
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Liangping Zha
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Da-Hui Liu
- Institute of Medicinal Plants, Yunnan Academy of Agriculture Science, Kunming, 650231, PR China
| | - Liping Kang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Xiaojing Ma
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Zhi-Lai Zhan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Tie-Gui Nan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Jian Yang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Fajie Li
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China.
| | - Lu-Qi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijng, 100700, PR China.
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van der Hooft JJJ, Padmanabhan S, Burgess KEV, Barrett MP. Urinary antihypertensive drug metabolite screening using molecular networking coupled to high-resolution mass spectrometry fragmentation. Metabolomics 2016; 12:125. [PMID: 27471437 PMCID: PMC4932139 DOI: 10.1007/s11306-016-1064-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/01/2016] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Mass spectrometry is the current technique of choice in studying drug metabolism. High-resolution mass spectrometry in combination with MS/MS gas-phase experiments has the potential to contribute to rapid advances in this field. However, the data emerging from such fragmentation spectral files pose challenges to downstream analysis, given their complexity and size. OBJECTIVES This study aims to detect and visualize antihypertensive drug metabolites in untargeted metabolomics experiments based on the spectral similarity of their fragmentation spectra. Furthermore, spectral clusters of endogenous metabolites were also examined. METHODS Here we apply a molecular networking approach to seek drugs and their metabolites, in fragmentation spectra from urine derived from a cohort of 26 patients on antihypertensive therapy. The mass spectrometry data was collected on a Thermo Q-Exactive coupled to pHILIC chromatography using data dependent analysis (DDA) MS/MS gas-phase experiments. RESULTS In total, 165 separate drug metabolites were found and structurally annotated (17 by spectral matching and 122 by classification based on a clustered fragmentation pattern). The clusters could be traced to 13 drugs including the known antihypertensives verapamil, losartan and amlodipine. The molecular networking approach also generated clusters of endogenous metabolites, including carnitine derivatives, and conjugates containing glutamine, glutamate and trigonelline. CONCLUSIONS The approach offers unprecedented capability in the untargeted identification of drugs and their metabolites at the population level and has great potential to contribute to understanding stratified responses to drugs where differences in drug metabolism may determine treatment outcome.
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Affiliation(s)
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Karl E. V. Burgess
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Michael P. Barrett
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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