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Li M, Zhao Z, Zhang Y, Guo X, Zhang Y, Wang J, Liu Y, Yang L, Mou W, Zhang X, Gao H. Chemometrics combined with comprehensive two-dimensional gas chromatography-mass spectrometry for the identification of Baijiu vintage. Food Chem 2024; 444:138690. [PMID: 38354654 DOI: 10.1016/j.foodchem.2024.138690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
The identification of baijiu vintage is crucial for quality assessment and economic value determination. However, its complex composition and multifaceted influences pose significant technical challenges, necessitating research into its aging mechanisms and the development of related identification methods. This study utilized Chemometrics in conjunction with GC × GC-TOFMS for Baijiu Vintage identification. Data compression achieved a reduction of over 1000-fold without compromising key information, enabling analysis on many samples and get their changing regular in a big matrix by MCR. Subsequently, MCR-ALS facilitated the extraction of physical and chemical meaningful information related to baijiu vintage. Key MCR principal components suitable for qualitative and quantitative assessments were selected using CARS-PLS. The regression model demonstrated errors of less than one year. Furthermore, a PLS-DA model provided 30 MCR principal components as potential markers. The research results provide technical support for baijiu vintage identification and lay the groundwork for studying the changing patterns of flavor compounds in baijiu.
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Affiliation(s)
- Miao Li
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Zhengyu Zhao
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Yusong Zhang
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Xinguang Guo
- China National Research Institute of Food & Fermentation Industries Co., Ltd, Beijing 100016, China
| | - Yu Zhang
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Jian Wang
- China National Research Institute of Food & Fermentation Industries Co., Ltd, Beijing 100016, China
| | - Yangqingxue Liu
- China National Research Institute of Food & Fermentation Industries Co., Ltd, Beijing 100016, China
| | - Lihua Yang
- Guangzhou Hexin Instrument Co. Ltd., Guangzhou 510535, China
| | - Wenlong Mou
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Xin Zhang
- Department of Chemistry, Capital Normal University, Beijing 100048, China.
| | - Hongbo Gao
- China National Research Institute of Food & Fermentation Industries Co., Ltd, Beijing 100016, China.
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Reuschenbach M, Drees F, Leupold MS, Tintrop LK, Schmidt TC, Renner G. qPeaks: A Linear Regression-Based Asymmetric Peak Model for Parameter-Free Automatized Detection and Characterization of Chromatographic Peaks in Non-Target Screening Data. Anal Chem 2024; 96:7120-7129. [PMID: 38666514 DOI: 10.1021/acs.analchem.4c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
We present qPeaks (quality peaks), a novel, user-parameter-free algorithm for peak detection and peak characterization applicable to chromatographic data. The algorithm is based on a linearizable regression model that analyzes asymmetric peaks and estimates the specific uncertainties associated with the peak regression parameters. The uncertainties of the parameters are used to derive a data quality score DQSpeak, rendering low reliability results more transparent during processing and allowing for the prioritization of generated features. High DQSpeak chromatographic peaks have a lower chance of being classified as false-positive and show higher repeatability over multiple measurements. The high efficiency of the algorithm makes it particularly useful for application within processing routines of nontarget screening through chromatography coupled with high-resolution mass spectrometry. qPeaks is integrated into the qAlgorithms nontarget screening processing toolbox and appends a parameter-free chromatographic peak detection and characterization step to it. With qAlgorithms, now high-resolution mass spectra are centroided using the qCentroids algorithms, centroids are clustered to form extracted ion chromatograms (EICs) with the qBinning algorithm, and chromatographic peaks are found on the generated EICs with qPeaks. However, all tools from qAlgorithms can also be used independently.
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Affiliation(s)
- Max Reuschenbach
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr.5, Essen 45141, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr.2, Essen 45141, Germany
| | - Felix Drees
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr.5, Essen 45141, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr.2, Essen 45141, Germany
| | - Michael S Leupold
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr.5, Essen 45141, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr.2, Essen 45141, Germany
| | - Lucie K Tintrop
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr.5, Essen 45141, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr.2, Essen 45141, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr.5, Essen 45141, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr.2, Essen 45141, Germany
- IWW Water Center, Moritzstr.26, Mülheim an der Ruhr 45476, Germany
| | - Gerrit Renner
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr.5, Essen 45141, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr.2, Essen 45141, Germany
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Galineau L, Bourdin-Pintueles A, Bodard S, Busson J, Nadal-Desbarats L, Lefèvre A, Emond P, Mavel S. Temporal metabolomics state in pregnant rat: Analysis of amniotic fluid, placenta, and maternal plasma at embryonic and fetal time points. Placenta 2024; 150:22-30. [PMID: 38581971 DOI: 10.1016/j.placenta.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/08/2024]
Abstract
INTRODUCTION During pregnancy, the dynamic metabolic demands for fetal growth require a continuous supply of essential metabolites. Understanding maternal metabolome changes during gestation is crucial for predicting disease risks in neonates. METHODS The study aimed to characterize the placental and amniotic fluid (AF) metabolomes during gestation in rats at gestational days GD-13 and 19 reflecting the end of the embryonic and fetal periods, respectively, and the maternal plasma, using metabolomics (LC-MS) and chemometrics. The objective was to highlight, through univariate and multivariate analyses, the complementarity of the data obtained from these different biological matrices. RESULTS The biological matrix had more impact on the metabolome composition than the gestational stage. The placental and AF metabolomes showed specific metabolome evolving over the two gestational stages. Analyzing the three targeted metabolomes revealed evolving pathways in arginine and proline metabolism/glutathione metabolism and phenylalanine metabolism; purine metabolism; and carbohydrate metabolism. Significantly, lipid metabolism in the placenta exhibited substantial changes with higher levels of certain phosphatidylethanolamine and sphingomyelins at GD19 while some cholesteryl esters and some glycosphingolipids levels being in higher levels at GD13. DISCUSSION These data highlight the metabolic gradients (mainly in placenta, also in AF, but only a few in plasma) observed through embryonic patterning and organ development during mid-to late gestation.
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Affiliation(s)
- Laurent Galineau
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | | | - Sylvie Bodard
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | - Julie Busson
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | - Lydie Nadal-Desbarats
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France; PST-ASB, Université de Tours, France
| | - Antoine Lefèvre
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France; PST-ASB, Université de Tours, France
| | - Patrick Emond
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France; PST-ASB, Université de Tours, France; Service de Médecine Nucléaire In Vitro, CHRU Tours, Tours, France
| | - Sylvie Mavel
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France.
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Zeng J, Li Y, Wang C, Fu S, He M. Combination of in silico prediction and convolutional neural network framework for targeted screening of metabolites from LC-HRMS fingerprints: A case study of "Pericarpium Citri Reticulatae - FructusAurantii". Talanta 2024; 269:125514. [PMID: 38071769 DOI: 10.1016/j.talanta.2023.125514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
In this study, a novel approach is introduced, merging in silico prediction with a Convolutional Neural Network (CNN) framework for the targeted screening of in vivo metabolites in Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) fingerprints. Initially, three predictive tools, supplemented by literature, identify potential metabolites for target prototypes derived from Traditional Chinese Medicines (TCMs) or functional foods. Subsequently, a CNN is developed to minimize false positives from CWT-based peak detection. The Extracted Ion Chromatogram (EIC) peaks are then annotated using MS-FINDER across three levels of confidence. This methodology focuses on analyzing the metabolic fingerprints of rats administered with "Pericarpium Citri Reticulatae - Fructus Aurantii" (PCR-FA). Consequently, 384 peaks in positive mode and 282 in negative mode were identified as true peaks of probable metabolites. By contrasting these with "blank serum" data, EIC peaks of adequate intensity were chosen for MS/MS fragment analysis. Ultimately, 14 prototypes (including flavonoids and lactones) and 40 metabolites were precisely linked to their corresponding EIC peaks, thereby providing deeper insight into the pharmacological mechanism. This innovative strategy markedly enhances the chemical coverage in the targeted screening of LC-HRMS metabolic fingerprints.
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Affiliation(s)
- Jun Zeng
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Xiangtan University, Xiangtan 411105, China
| | - Yaping Li
- Department of Quality Control, Xiangtan Central Hospital, Xiangtan 411100, China
| | - Chuanlin Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Xiangtan University, Xiangtan 411105, China
| | - Sheng Fu
- Hunan prevention and treatment institute for occupational disease, Changsha 410007, China
| | - Min He
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Xiangtan University, Xiangtan 411105, China.
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5
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Blanco AM, Antomagesh F, Comesaña S, Soengas JL, Vijayan MM. Chronic cortisol stimulation enhances hypothalamus-specific enrichment of metabolites in the rainbow trout brain. Am J Physiol Endocrinol Metab 2024; 326:E382-E397. [PMID: 38294699 DOI: 10.1152/ajpendo.00410.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
The hypothalamus is a key integrating center that is involved in the initiation of the corticosteroid stress response, and in regulating nutrient homeostasis. Although cortisol, the principal glucocorticoid in humans and teleosts, plays a central role in feeding regulation, the mechanisms are far from clear. We tested the hypothesis that the metabolic changes to cortisol exposure signal an energy excess in the hypothalamus, leading to feeding suppression during stress in fish. Rainbow trout (Oncorhynchus mykiss) were administered a slow-release cortisol implant for 3 days, and the metabolite profiles in the plasma, hypothalamus, and the rest of the brain were assessed. Also, U-13C-glucose was injected into the hypothalamus by intracerebroventricular (ICV) route, and the metabolic fate of this energy substrate was followed in the brain regions by metabolomics. Chronic cortisol treatment reduced feed intake, and this corresponded with a downregulation of the orexigenic gene agrp, and an upregulation of the anorexigenic gene cart in the hypothalamus. The U-13C-glucose-mediated metabolite profiling indicated an enhancement of glycolytic flux and tricarboxylic acid intermediates in the rest of the brain compared with the hypothalamus. There was no effect of cortisol treatment on the phosphorylation status of AMPK or mechanistic target of rapamycin in the brain, whereas several endogenous metabolites, including leucine, citrate, and lactate were enriched in the hypothalamus, suggesting a tissue-specific metabolic shift in response to cortisol stimulation. Altogether, our results suggest that the hypothalamus-specific enrichment of leucine and the metabolic fate of this amino acid, including the generation of lipid intermediates, contribute to cortisol-mediated feeding suppression in fish.NEW & NOTEWORTHY Elevated cortisol levels during stress suppress feed intake in animals. We tested whether the feed suppression is associated with cortisol-mediated alteration in hypothalamus metabolism. The brain metabolome revealed a hypothalamus-specific metabolite profile suggesting nutrient excess. Specifically, we noted the enrichment of leucine and citrate in the hypothalamus, and the upregulation of pathways involved in leucine metabolism and fatty acid synthesis. This cortisol-mediated energy substrate repartitioning may modulate the feeding/satiety centers leading to the feeding suppression.
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Affiliation(s)
- Ayelén M Blanco
- Centro de Investigación Mariña, Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
| | | | - Sara Comesaña
- Centro de Investigación Mariña, Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
| | - José L Soengas
- Centro de Investigación Mariña, Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
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Kumari M, Yagnik KN, Gupta V, Singh IK, Gupta R, Verma PK, Singh A. Metabolomics-driven investigation of plant defense response against pest and pathogen attack. PHYSIOLOGIA PLANTARUM 2024; 176:e14270. [PMID: 38566280 DOI: 10.1111/ppl.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Kalpesh Nath Yagnik
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, Republic of Korea
| | - Praveen K Verma
- Plant-Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, India
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Zhang Y, Zhao H, Zhao J, Lv W, Jia X, Lu X, Zhao X, Xu G. Quantified Metabolomics and Lipidomics Profiles Reveal Serum Metabolic Alterations and Distinguished Metabolites of Seven Chronic Metabolic Diseases. J Proteome Res 2024. [PMID: 38407022 DOI: 10.1021/acs.jproteome.3c00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The co-occurrence of multiple chronic metabolic diseases is highly prevalent, posing a huge health threat. Clarifying the metabolic associations between them, as well as identifying metabolites which allow discrimination between diseases, will provide new biological insights into their co-occurrence. Herein, we utilized targeted serum metabolomics and lipidomics covering over 700 metabolites to characterize metabolic alterations and associations related to seven chronic metabolic diseases (obesity, hypertension, hyperuricemia, hyperglycemia, hypercholesterolemia, hypertriglyceridemia, fatty liver) from 1626 participants. We identified 454 metabolites were shared among at least two chronic metabolic diseases, accounting for 73.3% of all 619 significant metabolite-disease associations. We found amino acids, lactic acid, 2-hydroxybutyric acid, triacylglycerols (TGs), and diacylglycerols (DGs) showed connectivity across multiple chronic metabolic diseases. Many carnitines were specifically associated with hyperuricemia. The hypercholesterolemia group showed obvious lipid metabolism disorder. Using logistic regression models, we further identified distinguished metabolites of seven chronic metabolic diseases, which exhibited satisfactory area under curve (AUC) values ranging from 0.848 to 1 in discovery and validation sets. Overall, quantitative metabolome and lipidome data sets revealed widespread and interconnected metabolic disorders among seven chronic metabolic diseases. The distinguished metabolites are useful for diagnosing chronic metabolic diseases and provide a reference value for further clinical intervention and management based on metabolomics strategy.
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Affiliation(s)
- Yuqing Zhang
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Hui Zhao
- Department of the Health Checkup Center, The Second Hospital of Dalian Medical University, Dalian 116023, P. R. China
| | - Jinhui Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Science, Beijing 100049, P. R. China
| | - Wangjie Lv
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Science, Beijing 100049, P. R. China
| | - Xueni Jia
- Department of the Health Checkup Center, The Second Hospital of Dalian Medical University, Dalian 116023, P. R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guowang Xu
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Science, Beijing 100049, P. R. China
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8
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Gowda SGB, Hou F, Gowda D, Chiba H, Kawakami K, Fukiya S, Yokota A, Hui SP. Synthesis and quantification of short-chain fatty acid esters of hydroxy fatty acids in rat intestinal contents and fecal samples by LC-MS/MS. Anal Chim Acta 2024; 1288:342145. [PMID: 38220280 DOI: 10.1016/j.aca.2023.342145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024]
Abstract
Short-chain fatty acid esters of hydroxy fatty acids (SFAHFAs) are a new class of endogenous lipids belonging to the fatty acid esters of the hydroxy fatty acid family. We previously uncovered their chemical structure and discussed their potential biological significance. We anticipate an increased need for SFAHFA measurements as markers of metabolic and inflammatory health. In this study, we synthesized sixty isomeric SFAHFAs by combining 12 hydroxy fatty acids (C16-C24) and five short-chain fatty acids (C2-C6) including a labelled internal standard. SFAHFA enrichment was achieved by solid-phase extraction and established a sensitive method for their quantitation by targeted LC-MS/MS. The method was applied to profile SFAHFAs in intestinal contents and fecal samples collected from rats fed a high-fat diet (HFD). The results demonstrated a significant decrease in SFAHFAs in the intestinal contents of the HFD group compared with the control group. The fecal time course (0-8 weeks) profile of SFAHFAs showed significant downregulation of acetic and propanoic acid esters in just 2 weeks after HFD administration. This study offers the first synthesis and quantitation method for SFAHFAs, demonstrating their potential use in elucidating SFAHFA sources, their role in various diseases, and potential biochemical signalling pathways.
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Affiliation(s)
- Siddabasave Gowda B Gowda
- Faculty of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Kita-ku, Sapporo, 060-0812, Japan; Graduate School of Global Food Resources, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-0809, Japan
| | - Fengjue Hou
- Graduate School of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Kita-ku, Sapporo, 060-0812, Japan
| | - Divyavani Gowda
- Faculty of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Kita-ku, Sapporo, 060-0812, Japan
| | - Hitoshi Chiba
- Department of Nutrition, Sapporo University of Health Sciences, Nakanuma, Nishi-4-3-1-15, Higashi-ku, Sapporo, 007-0894, Japan
| | - Kentaro Kawakami
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Satoru Fukiya
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Atsushi Yokota
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Shu-Ping Hui
- Faculty of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Kita-ku, Sapporo, 060-0812, Japan.
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9
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Vosough M, Salemi A, Rockel S, Schmidt TC. Enhanced efficiency of MS/MS all-ion fragmentation for non-targeted analysis of trace contaminants in surface water using multivariate curve resolution and data fusion. Anal Bioanal Chem 2024; 416:1165-1177. [PMID: 38206346 PMCID: PMC10850027 DOI: 10.1007/s00216-023-05102-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
Data-independent acquisition-all-ion fragmentation (DIA-AIF) mode of mass spectrometry can facilitate wide-scope non-target analysis of contaminants in surface water due to comprehensive spectral identification. However, because of the complexity of the resulting MS2 AIF spectra, identifying unknown pollutants remains a significant challenge, with a significant bottleneck in translating non-targeted chemical signatures into environmental impacts. The present study proposes to process fused MS1 and MS2 data sets obtained from LC-HRMS/MS measurements in non-targeted AIF workflows on surface water samples using multivariate curve resolution-alternating least squares (MCR-ALS). This enables straightforward assignment between precursor ions obtained from resolved MS1 spectra and their corresponding MS2 spectra. The method was evaluated for two sets of tap water and surface water contaminated with 14 target chemicals as a proof of concept. The data set of surface water samples consisting of 3506 MS1 and 2170 MS2 AIF mass spectral features was reduced to 81 components via a fused MS1-MS2 MCR model that describes at least 98.8% of the data. Each component summarizes the distinct chromatographic elution of components together with their corresponding MS1 and MS2 spectra. MS2 spectral similarity of more than 82% was obtained for most target chemicals. This highlights the potential of this method for unraveling the composition of MS/MS complex data in a water environment. Ultimately, the developed approach was applied to the retrospective non-target analysis of an independent set of surface water samples.
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Affiliation(s)
- Maryam Vosough
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany.
- Department of Clean Technologies, Chemistry and Chemical Engineering Research Center of Iran, P.O. Box 14335-186, Tehran, Iran.
| | - Amir Salemi
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
| | - Sarah Rockel
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
- IWW Water Centre, Moritzstr. 26, Mülheim an der Ruhr, 45476, Germany
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10
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Thukral M, Allen AE, Petras D. Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics. THE ISME JOURNAL 2023; 17:2147-2159. [PMID: 37857709 PMCID: PMC10689791 DOI: 10.1038/s41396-023-01532-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Advances in bioanalytical technologies are constantly expanding our insights into complex ecosystems. Here, we highlight strategies and applications that make use of non-targeted metabolomics methods in aquatic chemical ecology research and discuss opportunities and remaining challenges of mass spectrometry-based methods to broaden our understanding of environmental systems.
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Affiliation(s)
- Monica Thukral
- University of California San Diego, Scripps Institution of Oceanography, La Jolla, CA, USA
- J. Craig Venter Institute, Microbial and Environmental Genomics Group, La Jolla, CA, USA
| | - Andrew E Allen
- University of California San Diego, Scripps Institution of Oceanography, La Jolla, CA, USA
- J. Craig Venter Institute, Microbial and Environmental Genomics Group, La Jolla, CA, USA
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Tuebingen, Germany.
- University of California Riverside, Department of Biochemistry, Riverside, CA, USA.
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Ivanic FM, Butler M, Borón CI, Candal RJ. Assessing the transformation products and fate of Oxytetracycline by simulated aerobic degradation tests. CHEMOSPHERE 2023; 343:140284. [PMID: 37758075 DOI: 10.1016/j.chemosphere.2023.140284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/01/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
Oxytetracycline (OTC) is a widely used broad-spectrum antibiotic, whose presence in water and sediments was reported in various regions of the world. The effects of OTC and other tetracyclines on the environment have been intensively studied although many of their transformation products (TPs) formed in the environment and their impact have not been yet fully characterized. Abiotic and biotic degradation tests under aerobic conditions at two pH values were carried out using OTC in artificial water/sediment systems to assess the effect of these variables on the environmental fate of the pollutant. HPLC-MSn was employed to detect and identify the main degradation products and pathways. Several transformations involved in the process were identified including alcohol oxidation, decarbonylation and hydroxylation. Differences in TPs and kinetics were found among degradation conditions, remarking a faster degradation of both OTC and TPs in the presence of microorganisms and at lower pH values. In summary, a total of 44 TPs were detected and structures were proposed for 20 of them, none of them having been previously reported. Furthermore, OTC degradation generated 24 TPs which remained in either solution or sediment, although none of them displayed higher algae toxicity than OTC. These results might be useful for planning future remediation and monitoring strategies.
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Affiliation(s)
- Federico M Ivanic
- IIIA-UNSAM-CONICET, Instituto de Investigación e Ingeniería Ambiental, Escuela de Hábitat y Sostenibilidad (EHyS), Universidad Nacional de San Martín (UNSAM), Campus Miguelete, 25 de mayo y Francia, 1650-San Martín, Provincia de Buenos Aires, Argentina
| | - Matías Butler
- IIIA-UNSAM-CONICET, Instituto de Investigación e Ingeniería Ambiental, Escuela de Hábitat y Sostenibilidad (EHyS), Universidad Nacional de San Martín (UNSAM), Campus Miguelete, 25 de mayo y Francia, 1650-San Martín, Provincia de Buenos Aires, Argentina.
| | - Carlos I Borón
- IIIA-UNSAM-CONICET, Instituto de Investigación e Ingeniería Ambiental, Escuela de Hábitat y Sostenibilidad (EHyS), Universidad Nacional de San Martín (UNSAM), Campus Miguelete, 25 de mayo y Francia, 1650-San Martín, Provincia de Buenos Aires, Argentina
| | - Roberto J Candal
- IIIA-UNSAM-CONICET, Instituto de Investigación e Ingeniería Ambiental, Escuela de Hábitat y Sostenibilidad (EHyS), Universidad Nacional de San Martín (UNSAM), Campus Miguelete, 25 de mayo y Francia, 1650-San Martín, Provincia de Buenos Aires, Argentina
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12
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Fuica-Carrasco C, Toro-Núñez Ó, Lira-Noriega A, Pérez AJ, Hernández V. Metabolome expression in Eucryphia cordifolia populations: Role of seasonality and ecological niche centrality hypothesis. JOURNAL OF PLANT RESEARCH 2023; 136:827-839. [PMID: 37486392 DOI: 10.1007/s10265-023-01483-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The ecological niche centrality hypothesis states that population abundance is determined by the position in the ecological niche, expecting higher abundances towards the center of the niche and lower at the periphery. However, the variations in the conditions that favor the persistence of populations between the center and the periphery of the niche can be a surrogate of stress factors that are reflected in the production of metabolites in plants. In this study we tested if metabolomic similarity and diversity in populations of the tree species Eucryphia cordifolia Cav. vary according to their position with respect to the structure of the ecological niche. We hypothesize that populations growing near the centroid should exhibit lower metabolites diversity than plants growing at the periphery of the niche. The ecological niche of the species was modeled using correlative approaches and bioclimatic variables to define central and peripheral localities from which we chose four populations to obtain their metabolomic information using UHPLC-DAD-QTOF-MS. We observed that populations farther away from the centroid tend to have higher metabolome diversity, thus supporting our expectation of the niche centrality hypothesis. Nonetheless, the Shannon index showed a marked variation in metabolome diversity at the seasonal level, with summer and autumn being the periods with higher metabolite diversity compared to winter and spring. We conclude that both the environmental variation throughout the year in combination with the structure of the ecological niche are relevant to understand the variation in expression of metabolites in plants.
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Affiliation(s)
- Camila Fuica-Carrasco
- Laboratorio de Química de Productos Naturales, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile.
| | - Óscar Toro-Núñez
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile
| | - Andrés Lira-Noriega
- CONAHCyT Research Fellow, Red de Estudios Moleculares Avanzados, Instituto de Ecología, Mexico City, A.C, México
| | - Andy J Pérez
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile
| | - Víctor Hernández
- Laboratorio de Química de Productos Naturales, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile
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13
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Chen YC, Hsu JF, Chang CW, Li SW, Yang YC, Chao MR, Chen HJC, Liao PC. Connecting chemical exposome to human health using high-resolution mass spectrometry-based biomonitoring: Recent advances and future perspectives. MASS SPECTROMETRY REVIEWS 2023; 42:2466-2486. [PMID: 36062854 DOI: 10.1002/mas.21805] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
Compared with the rapid advances in genomics leading to broad understanding of human disease, the linkage between chemical exposome and diseases is still under investigation. High-resolution mass spectrometry (HRMS) is expected to accelerate the process via relatively accurate and precise biomonitoring of human exposome. This review covers recent advancements in biomonitoring of exposed environmental chemicals (chemical exposome) using HRMS described in the 124 articles that resulted from a systematic literature search on Medline and Web of Science databases. The analytical strategic aspects, including the selection of specimens, sample preparation, instrumentation, untargeted versus targeted analysis, and workflows for MS-based biomonitoring to explore the environmental chemical space of human exposome, are deliberated. Applications of HRMS in human exposome investigation are presented by biomonitoring (1) exposed chemical compounds and their biotransformation products; (2) DNA/protein adducts; and (3) endogenous compound perturbations. Challenges and future perspectives are also discussed.
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Affiliation(s)
- Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Jing-Fang Hsu
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Shih-Wen Li
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Ya-Chi Yang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hauh-Jyun C Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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14
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McMillen TS, Leslie A, Chisholm K, Penny S, Gallant J, Cohen A, Drucker A, Fawcett JP, Pinto DM. A large-scale, targeted metabolomics method for the analysis and quantification of metabolites in human plasma via liquid chromatography-mass spectrometry. Anal Chim Acta 2023; 1279:341791. [PMID: 37827685 DOI: 10.1016/j.aca.2023.341791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Metabolomics is the study of small molecules, primarily metabolites, that are produced during metabolic processes. Analysis of the composition of an organism's metabolome can yield useful information about an individual's health status at any given time. In recent years, the development of large-scale, targeted metabolomic methods has allowed for the analysis of biological samples using analytical techniques such as LC-MS/MS. This paper presents a large-scale metabolomics method for analysis of biological samples, with a focus on quantification of metabolites found in blood plasma. The method comprises a 10-min chromatographic separation using HILIC and RP stationary phases combined with positive and negative electrospray ionization in order to maximize metabolome coverage. Complete analysis of a single sample can be achieved in as little as 40 min using the two columns and dual modes of ionization. With 540 metabolites and the inclusion of over 200 analytical standards, this method is comprehensive and quantitatively robust when compared to current targeted metabolomics methods. This study uses a large-scale evaluation of metabolite recovery from plasma that enables absolute quantification of metabolites by correcting for analyte loss throughout processes such as extraction, handling, or storage. In addition, the method was applied to plasma collected from adjuvant breast cancer patients to confirm the suitability of the method to clinical samples.
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Affiliation(s)
- Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia Canada
| | - Andrew Leslie
- National Research Council Canada, Health and Human Therapeutics, Halifax, Nova Scotia Canada
| | - Kenneth Chisholm
- National Research Council Canada, Health and Human Therapeutics, Halifax, Nova Scotia Canada
| | - Susanne Penny
- National Research Council Canada, Health and Human Therapeutics, Halifax, Nova Scotia Canada
| | - Jeffrey Gallant
- National Research Council Canada, Health and Human Therapeutics, Halifax, Nova Scotia Canada
| | - Alejandro Cohen
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia Canada
| | - Arik Drucker
- Division of Medical Oncology, Nova Scotia Health Authority, Halifax, Nova Scotia Canada
| | - James P Fawcett
- Department of Pharmacology, Dalhousie University, Nova Scotia Canada; Department of Surgery, Dalhousie University, Nova Scotia Canada
| | - Devanand M Pinto
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia Canada; National Research Council Canada, Health and Human Therapeutics, Halifax, Nova Scotia Canada.
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15
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Subrahmaniam HJ, Lind Salomonsen C, Radutoiu S, Ehlers BK, Glasius M. Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana. OPEN RESEARCH EUROPE 2023; 3:12. [PMID: 37645513 PMCID: PMC10445920 DOI: 10.12688/openreseurope.15377.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 08/31/2023]
Abstract
Background Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions. Methods Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions. Results Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software. Conclusions The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.
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Affiliation(s)
- Harihar Jaishree Subrahmaniam
- Department of Ecoscience, Aarhus University, 8000 Aarhus C, Denmark
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics - Plant Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Simona Radutoiu
- Department of Molecular Biology and Genetics - Plant Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Bodil K. Ehlers
- Department of Ecoscience, Aarhus University, 8000 Aarhus C, Denmark
| | - Marianne Glasius
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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16
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Vrobel O, Tarkowski P. Can plant hormonomics be built on simple analysis? A review. PLANT METHODS 2023; 19:107. [PMID: 37833752 PMCID: PMC10576392 DOI: 10.1186/s13007-023-01090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
The field of plant hormonomics focuses on the qualitative and quantitative analysis of the hormone complement in plant samples, akin to other omics sciences. Plant hormones, alongside primary and secondary metabolites, govern vital processes throughout a plant's lifecycle. While active hormones have received significant attention, studying all related compounds provides valuable insights into internal processes. Conventional single-class plant hormone analysis employs thorough sample purification, short analysis and triple quadrupole tandem mass spectrometry. Conversely, comprehensive hormonomics analysis necessitates minimal purification, robust and efficient separation and better-performing mass spectrometry instruments. This review summarizes the current status of plant hormone analysis methods, focusing on sample preparation, advances in chromatographic separation and mass spectrometric detection, including a discussion on internal standard selection and the potential of derivatization. Moreover, current approaches for assessing the spatiotemporal distribution are evaluated. The review touches on the legitimacy of the term plant hormonomics by exploring the current status of methods and outlining possible future trends.
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Affiliation(s)
- Ondřej Vrobel
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic.
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic.
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17
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Smith E, Lewis A, Narine SS, Emery RJN. Unlocking Potentially Therapeutic Phytochemicals in Capadulla ( Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics. Metabolites 2023; 13:1050. [PMID: 37887375 PMCID: PMC10608729 DOI: 10.3390/metabo13101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to identify therapeutic biofingerprints for conditions, such as erectile dysfunction, in men. This study executes a preliminary phytochemical screening of the woody vine of two ecotypes of D. dentatus with renowned differences in therapeutic potential for erectile dysfunction. Liquid chromatography-mass spectrometry-based metabolomics was used to screen for flavonoids, terpenoids, and other chemical classes found to contrast between red and white ecotypes. Among the metabolite chemodiversity found in the ecotype screens, using a combination of GNPS, MS-DIAL, and SIRIUS, approximately 847 compounds were annotated at levels 2 to 4, with the majority of compounds falling under lipid and lipid-like molecules, benzenoids and phenylpropanoids, and polyketides, indicative of the contributions of the flavonoid, shikimic acid, and terpenoid biosynthesis pathways. Despite the extensive annotation, we report on 138 tentative compound identifications of potentially therapeutic compounds, with 55 selected compounds at a level-2 annotation, and 22 statistically significant therapeutic biomarkers, the majority of which were polyphenols. Epicatechin methyl gallate, catechin gallate, and proanthocyanidin A2 had the greatest significant differences and were also relatively abundant among the red and white ecotypes. These putatively identified compounds reportedly act as antioxidants, neutralizing damaging free radicals, and lowering cell oxidative stress, thus aiding in potentially preventing cellular damage and promoting overall well-being, especially for treating erectile dysfunction (ED).
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Affiliation(s)
- Ewart Smith
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 0G2, Canada
| | - Ainsely Lewis
- Department of Biology, Trent University, Peterborough, ON K9J 0G2, Canada
| | - Suresh S. Narine
- Trent Centre for Biomaterials Research, Trent University, Peterborough, ON K9J 0G2, Canada
- Departments of Physics & Astronomy and Chemistry, Trent University, Peterborough, ON K9J 0G2, Canada
| | - R. J. Neil Emery
- Department of Biology, Trent University, Peterborough, ON K9J 0G2, Canada
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18
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Queral-Beltran A, Marín-García M, Lacorte S, Tauler R. UV-Vis absorption spectrophotometry and LC-DAD-MS-ESI(+)-ESI(-) coupled to chemometrics analysis of the monitoring of sulfamethoxazole degradation by chlorination, photodegradation, and chlorination/photodegradation. Anal Chim Acta 2023; 1276:341563. [PMID: 37573101 DOI: 10.1016/j.aca.2023.341563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 06/25/2023] [Indexed: 08/14/2023]
Abstract
Sulfamethoxazole (SMX) is one of the most widely used antibiotics worldwide and has been detected at high concentrations in wastewater treatment plant effluents and river waters. In this study, the SMX degradation process combining the simultaneous chlorine oxidation and UV photodegradation is assessed and compared with both photodegradation and chlorine oxidation processes individually. Photodegradation and Chlorine/UV tests were performed using Suntest CPS equipment. Different experimental techniques, including UV-Visible spectrophotometry and liquid chromatography coupled to a diode array detector and positive and negative ionization mass spectrometry (LC-DAD-MS-ESI(+)-ESI(-)), were used to evaluate the degradation reaction of SMX. All the analytical data generated have been processed with the Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) method to monitor, resolve, and identify the several transformation products generated during the studied degradation processes. A new data fusion analysis strategy is proposed to examine the three processes simultaneously (with only photodegradation, only chlorination, and simultaneous chlorination+photodegradation). Combined with the analysis of different analytical techniques individually (spectrophotometry, LC-DAD, and LC-MS), the fusion of all generated data improved the description of the degradation processes. Detection using DAD allowed a better correspondence among the species monitored spectrophotometrically (UV-Vis) with those analyzed chromatographically. On the other side, detection using MS in both positive and negative acquisition modes allowed resolving a larger number of chemical compounds (specially SMX degradation subproducts) that could not be detected by UV-Vis spectrometry. The results obtained permitted the comparison of the effects produced by the three different degradation processes.
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Affiliation(s)
- Aina Queral-Beltran
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034, Barcelona, Catalonia, Spain
| | - Marc Marín-García
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034, Barcelona, Catalonia, Spain; Department of Analytical and Applied Chemistry, School of Engineering, Institut Químic de Sarrià-Universitat Ramon Llull (IQS-URL), Via Augusta 390, 08017, Barcelona, Spain
| | - Silvia Lacorte
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034, Barcelona, Catalonia, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034, Barcelona, Catalonia, Spain.
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19
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Yamamoto FY, Pérez-López C, Lopez-Antia A, Lacorte S, de Souza Abessa DM, Tauler R. Linking MS1 and MS2 signals in positive and negative modes of LC-HRMS in untargeted metabolomics using the ROIMCR approach. Anal Bioanal Chem 2023; 415:6213-6225. [PMID: 37587312 PMCID: PMC10558381 DOI: 10.1007/s00216-023-04893-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Data-independent acquisition (DIA) mode in liquid chromatography (LC) high-resolution mass spectrometry (HRMS) has emerged as a powerful strategy in untargeted metabolomics for detecting a broad range of metabolites. However, the use of this approach also represents a challenge in the analysis of the large datasets generated. The regions of interest (ROI) multivariate curve resolution (MCR) approach can help in the identification and characterization of unknown metabolites in their mixtures by linking their MS1 and MS2 DIA spectral signals. In this study, it is proposed for the first time the analysis of MS1 and MS2 DIA signals in positive and negative electrospray ionization modes simultaneously to increase the coverage of possible metabolites present in biological systems. In this work, this approach has been tested for the detection and identification of the amino acids present in a standard mixture solution and in fish embryo samples. The ROIMCR analysis allowed for the identification of all amino acids present in the analyzed mixtures in both positive and negative modes. The methodology allowed for the direct linking and correspondence between the MS signals in their different acquisition modes. Overall, this approach confirmed the advantages and possibilities of performing the proposed ROIMCR simultaneous analysis of mass spectrometry signals in their differing acquisition modes in untargeted metabolomics studies.
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Affiliation(s)
- Flávia Yoshie Yamamoto
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
- Institute of Biosciences, São Paulo State University, São Vicente, Brazil
| | - Carlos Pérez-López
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Ana Lopez-Antia
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Silvia Lacorte
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | | | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain.
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20
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Hao JD, Chen YY, Wang YZ, An N, Bai PR, Zhu QF, Feng YQ. Novel Peak Shift Correction Method Based on the Retention Index for Peak Alignment in Untargeted Metabolomics. Anal Chem 2023; 95:13330-13337. [PMID: 37609864 DOI: 10.1021/acs.analchem.3c02583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Peak alignment is a crucial step in liquid chromatography-mass spectrometry (LC-MS)-based large-scale untargeted metabolomics workflows, as it enables the integration of metabolite peaks across multiple samples, which is essential for accurate data interpretation. Slight differences or fluctuations in chromatographic separation conditions, however, can cause the chromatographic retention time (RT) shift between consecutive analyses, ultimately affecting the accuracy of peak alignment between samples. Here, we introduce a novel RT shift correction method based on the retention index (RI) and apply it to peak alignment. We synthesized a series of N-acyl glycine (C2-C23) homologues via the amidation reaction between glycine with normal saturated fatty acids (C2-C23) as calibrants able to respond proficiently in both mass spectrometric positive- and negative-ion modes. Using these calibrants, we established an N-acyl glycine RI system. This RI system is capable of covering a broad chromatographic space and addressing chromatographic RT shift caused by variations in flow rate, gradient elution, instrument systems, and LC separation columns. Moreover, based on the RI system, we developed a peak shift correction model to enhance peak alignment accuracy. Applying the model resulted in a significant improvement in the accuracy of peak alignment from 15.5 to 80.9% across long-term data spanning a period of 157 days. To facilitate practical application, we developed a Python-based program, which is freely available at https://github.com/WHU-Fenglab/RI-based-CPSC.
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Affiliation(s)
- Jun-Di Hao
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yao-Yu Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yan-Zhen Wang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Na An
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Pei-Rong Bai
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Quan-Fei Zhu
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
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21
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Jin Y, Chi J, LoMonaco K, Boon A, Gu H. Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome. Trends Analyt Chem 2023; 166:117155. [PMID: 37484879 PMCID: PMC10361410 DOI: 10.1016/j.trac.2023.117155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.
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Affiliation(s)
- Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jinhua Chi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Kaelene LoMonaco
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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Badillo-Sanchez D, Serrano Ruber M, Davies-Barrett A, Jones DJ, Hansen M, Inskip S. Metabolomics in archaeological science: A review of their advances and present requirements. SCIENCE ADVANCES 2023; 9:eadh0485. [PMID: 37566664 PMCID: PMC10421062 DOI: 10.1126/sciadv.adh0485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/11/2023] [Indexed: 08/13/2023]
Abstract
Metabolomics, the study of metabolites (small molecules of <1500 daltons), has been posited as a potential tool to explore the past in a comparable manner to other omics, e.g., genomics or proteomics. Archaeologists have used metabolomic approaches for a decade or so, mainly applied to organic residues adhering to archaeological materials. Because of advances in sensitivity, resolution, and the increased availability of different analytical platforms, combined with the low mass/volume required for analysis, metabolomics is now becoming a more feasible choice in the archaeological sector. Additional approaches, as presented by our group, show the versatility of metabolomics as a source of knowledge about the human past when using human osteoarchaeological remains. There is tremendous potential for metabolomics within archaeology, but further efforts are required to position it as a routine technique.
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Affiliation(s)
| | - Maria Serrano Ruber
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Anna Davies-Barrett
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Donald J. L. Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester, UK
- The Leicester van Geest MultiOmics Facility, University of Leicester, Leicester, UK
| | - Martin Hansen
- Environmental Metabolomics Lab, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Sarah Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
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23
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Borras E, McCartney MM, Rojas DE, Hicks TL, Tran NK, Tham T, Juarez MM, Franzi L, Harper RW, Davis CE, Kenyon NJ. Oxylipin concentration shift in exhaled breath condensate (EBC) of SARS-CoV-2 infected patients. J Breath Res 2023; 17:10.1088/1752-7163/acea3d. [PMID: 37489864 PMCID: PMC10446499 DOI: 10.1088/1752-7163/acea3d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Infection of airway epithelial cells with severe acute respiratory coronavirus 2 (SARS-CoV-2) can lead to severe respiratory tract damage and lung injury with hypoxia. It is challenging to sample the lower airways non-invasively and the capability to identify a highly representative specimen that can be collected in a non-invasive way would provide opportunities to investigate metabolomic consequences of COVID-19 disease. In the present study, we performed a targeted metabolomic approach using liquid chromatography coupled with high resolution chromatography (LC-MS) on exhaled breath condensate (EBC) collected from hospitalized COVID-19 patients (COVID+) and negative controls, both non-hospitalized and hospitalized for other reasons (COVID-). We were able to noninvasively identify and quantify inflammatory oxylipin shifts and dysregulation that may ultimately be used to monitor COVID-19 disease progression or severity and response to therapy. We also expected EBC-based biochemical oxylipin changes associated with COVID-19 host response to infection. The results indicated ten targeted oxylipins showing significative differences between SAR-CoV-2 infected EBC samples and negative control subjects. These compounds were prostaglandins A2 and D2, LXA4, 5-HETE, 12-HETE, 15-HETE, 5-HEPE, 9-HODE, 13-oxoODE and 19(20)-EpDPA, which are associated with specific pathways (i.e. P450, COX, 15-LOX) related to inflammatory and oxidative stress processes. Moreover, all these compounds were up-regulated by COVID+, meaning their concentrations were higher in subjects with SAR-CoV-2 infection. Given that many COVID-19 symptoms are inflammatory in nature, this is interesting insight into the pathophysiology of the disease. Breath monitoring of these and other EBC metabolites presents an interesting opportunity to monitor key indicators of disease progression and severity.
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Affiliation(s)
- Eva Borras
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, University of California Davis, CA
- These authors contributed equally: Eva Borras, Mitchell M. McCartney
| | - Mitchell M. McCartney
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, University of California Davis, CA
- VA Northern California Health Care System, 10535 Hospital Way, Mather, CA 95655, USA
- These authors contributed equally: Eva Borras, Mitchell M. McCartney
| | - Dante E. Rojas
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, University of California Davis, CA
| | - Tristan L Hicks
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, University of California Davis, CA
| | - Nam K Tran
- UC Davis Lung Center, University of California Davis, CA
- Department of Pathology and Laboratory Medicine, UC Davis, Sacramento CA, USA
| | - Tina Tham
- UC Davis Lung Center, University of California Davis, CA
- Department of Internal Medicine, 4150 V Street, Suite 3400, University of California, Davis, Sacramento, CA 95817, USA
| | - Maya M Juarez
- UC Davis Lung Center, University of California Davis, CA
- Department of Internal Medicine, 4150 V Street, Suite 3400, University of California, Davis, Sacramento, CA 95817, USA
| | - Lisa Franzi
- UC Davis Lung Center, University of California Davis, CA
- Department of Internal Medicine, 4150 V Street, Suite 3400, University of California, Davis, Sacramento, CA 95817, USA
| | - Richart W. Harper
- UC Davis Lung Center, University of California Davis, CA
- VA Northern California Health Care System, 10535 Hospital Way, Mather, CA 95655, USA
- Department of Internal Medicine, 4150 V Street, Suite 3400, University of California, Davis, Sacramento, CA 95817, USA
| | - Cristina E. Davis
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, University of California Davis, CA
- VA Northern California Health Care System, 10535 Hospital Way, Mather, CA 95655, USA
| | - Nicholas J. Kenyon
- UC Davis Lung Center, University of California Davis, CA
- VA Northern California Health Care System, 10535 Hospital Way, Mather, CA 95655, USA
- Department of Pathology and Laboratory Medicine, UC Davis, Sacramento CA, USA
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24
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Jafari JM, Casas J, Barata C, Abdollahi H, Tauler R. Non-target ROIMCR LC-MS analysis of the disruptive effects of TBT over time on the lipidomics of Daphnia magna. Metabolomics 2023; 19:70. [PMID: 37548829 PMCID: PMC10406683 DOI: 10.1007/s11306-023-02030-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
INTRODUCTION This study has investigated the temporal disruptive effects of tributyltin (TBT) on lipid homeostasis in Daphnia magna. To achieve this, the study used Liquid Chromatography-Mass Spectrometry (LC-MS) analysis to analyze biological samples of Daphnia magna treated with TBT over time. The resulting data sets were multivariate and three-way, and were modeled using bilinear and trilinear non-negative factor decomposition chemometric methods. These methods allowed for the identification of specific patterns in the data and provided insight into the effects of TBT on lipid homeostasis in Daphnia magna. OBJECTIVES Investigation of how are the changes in the lipid concentrations of Daphnia magna pools when they were exposed with TBT and over time using non-targeted LC-MS and advanced chemometric analysis. METHODS The simultaneous analysis of LC-MS data sets of Daphnia magna samples under different experimental conditions (TBT dose and time) were analyzed using the ROIMCR method, which allows the resolution of the elution and mass spectra profiles of a large number of endogenous lipids. Changes obtained in the peak areas of the elution profiles of these lipids caused by the dose of TBT treatment and the time after its exposure are analyzed by principal component analysis, multivariate curve resolution-alternative least square, two-way ANOVA and ANOVA-simultaneous component analysis. RESULTS 87 lipids were identified. Some of these lipids are proposed as Daphnia magna lipidomic biomarkers of the effects produced by the two considered factors (time and dose) and by their interaction. A reproducible multiplicative effect between these two factors is confirmed and the optimal approach to model this dataset resulted to be the application of the trilinear factor decomposition model. CONCLUSION The proposed non-targeted LC-MS lipidomics approach resulted to be a powerful tool to investigate the effects of the two factors on the Daphnia magna lipidome using chemometric methods based on bilinear and trilinear factor decomposition models, according to the type of interaction between the design factors.
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Affiliation(s)
| | - Josefina Casas
- RUBAM, Institute for Advanced Chemistry (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Center (CIBEREHD), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Carlos Barata
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish Research Council (IDAEA-CSIC), Barcelona, Spain
| | - Hamid Abdollahi
- Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish Research Council (IDAEA-CSIC), Barcelona, Spain.
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25
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Oesterle I, Pristner M, Berger S, Wang M, Verri Hernandes V, Rompel A, Warth B. Exposomic Biomonitoring of Polyphenols by Non-Targeted Analysis and Suspect Screening. Anal Chem 2023; 95:10686-10694. [PMID: 37409760 PMCID: PMC10357401 DOI: 10.1021/acs.analchem.3c01393] [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] [Received: 03/31/2023] [Accepted: 06/16/2023] [Indexed: 07/07/2023]
Abstract
Polyphenols, prevalent in plants and fungi, are investigated intensively in nutritional and clinical settings because of their beneficial bioactive properties. Due to their complexity, analysis with untargeted approaches is favorable, which typically use high-resolution mass spectrometry (HRMS) rather than low-resolution mass spectrometry (LRMS). Here, the advantages of HRMS were evaluated by thoroughly testing untargeted techniques and available online resources. By applying data-dependent acquisition on real-life urine samples, 27 features were annotated with spectral libraries, 88 with in silico fragmentation, and 113 by MS1 matching with PhytoHub, an online database containing >2000 polyphenols. Moreover, other exogenous and endogenous molecules were screened to measure chemical exposure and potential metabolic effects using the Exposome-Explorer database, further annotating 144 features. Additional polyphenol-related features were explored using various non-targeted analysis techniques including MassQL for glucuronide and sulfate neutral losses, and MetaboAnalyst for statistical analysis. As HRMS typically suffers a sensitivity loss compared to state-of-the-art LRMS used in targeted workflows, the gap between the two instrumental approaches was quantified in three spiked human matrices (urine, serum, plasma) as well as real-life urine samples. Both instruments showed feasible sensitivity, with median limits of detection in the spiked samples being 10-18 ng/mL for HRMS and 4.8-5.8 ng/mL for LRMS. The results demonstrate that, despite its intrinsic limitations, HRMS can readily be used for comprehensively investigating human polyphenol exposure. In the future, this work is expected to allow for linking human health effects with exposure patterns and toxicological mixture effects with other xenobiotics.
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Affiliation(s)
- Ian Oesterle
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Fakultät
für Chemie, Institut für Biophysikalische Chemie, Universität Wien, Wien 1090, Austria
- Doctoral
School of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Manuel Pristner
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Doctoral
School of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Sabrina Berger
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Mingxun Wang
- Department
of Computer Science, University of California
Riverside, Riverside, California 92521, United States
| | - Vinicius Verri Hernandes
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Exposome
Austria, Research Infrastructure and National EIRENE Hub, Vienna 1090, Austria
| | - Annette Rompel
- Fakultät
für Chemie, Institut für Biophysikalische Chemie, Universität Wien, Wien 1090, Austria
| | - Benedikt Warth
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Exposome
Austria, Research Infrastructure and National EIRENE Hub, Vienna 1090, Austria
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26
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Fothergill DM, Borras E, McCartney MM, Schelegle E, Davis CE. Exhaled breath condensate profiles of U.S. Navy divers following prolonged hyperbaric oxygen (HBO) and nitrogen-oxygen (Nitrox) chamber exposures. J Breath Res 2023; 17:10.1088/1752-7163/acd715. [PMID: 37207635 PMCID: PMC11057948 DOI: 10.1088/1752-7163/acd715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/19/2023] [Indexed: 05/21/2023]
Abstract
Prolonged exposure to hyperbaric hyperoxia can lead to pulmonary oxygen toxicity (PO2tox). PO2tox is a mission limiting factor for special operations forces divers using closed-circuit rebreathing apparatus and a potential side effect for patients undergoing hyperbaric oxygen (HBO) treatment. In this study, we aim to determine if there is a specific breath profile of compounds in exhaled breath condensate (EBC) that is indicative of the early stages of pulmonary hyperoxic stress/PO2tox. Using a double-blind, randomized 'sham' controlled, cross-over design 14 U.S. Navy trained diver volunteers breathed two different gas mixtures at an ambient pressure of 2 ATA (33 fsw, 10 msw) for 6.5 h. One test gas consisted of 100% O2(HBO) and the other was a gas mixture containing 30.6% O2with the balance N2(Nitrox). The high O2stress dive (HBO) and low O2stress dive (Nitrox) were separated by at least seven days and were conducted dry and at rest inside a hyperbaric chamber. EBC samples were taken immediately before and after each dive and subsequently underwent a targeted and untargeted metabolomics analysis using liquid chromatography coupled to mass spectrometry (LC-MS). Following the HBO dive, 10 out of 14 subjects reported symptoms of the early stages of PO2tox and one subject terminated the dive early due to severe symptoms of PO2tox. No symptoms of PO2tox were reported following the nitrox dive. A partial least-squares discriminant analysis of the normalized (relative to pre-dive) untargeted data gave good classification abilities between the HBO and nitrox EBC with an AUC of 0.99 (±2%) and sensitivity and specificity of 0.93 (±10%) and 0.94 (±10%), respectively. The resulting classifications identified specific biomarkers that included human metabolites and lipids and their derivatives from different metabolic pathways that may explain metabolomic changes resulting from prolonged HBO exposure.
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Affiliation(s)
| | - Eva Borras
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, One Shields Avenue, University of California, Davis, Davis, California, USA
| | - Mitchell M. McCartney
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, One Shields Avenue, University of California, Davis, Davis, California, USA
- VA Northern California Health Care System, Mather, California, USA
| | - Edward Schelegle
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Cristina E. Davis
- Mechanical and Aerospace Engineering, One Shields Avenue, University of California, Davis, Davis, California, USA
- UC Davis Lung Center, One Shields Avenue, University of California, Davis, Davis, California, USA
- VA Northern California Health Care System, Mather, California, USA
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27
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Wang W, Zheng Z, Chen J, Duan T, He H, Tang S. Characterization of metabolite landscape distinguishes wild from cultivated Polygonati Rhizomes by UHPLC-Q-TOF-MS untargeted metabolomics. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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28
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Chen LH, Zhang YB, Yang XW, Xu J, Wang ZJ, Sun YZ, Xu W, Wang YP. Application of UPLC-Triple TOF-MS/MS metabolomics strategy to reveal the dynamic changes of triterpenoid saponins during the decocting process of Asian ginseng and American ginseng. Food Chem 2023; 424:136425. [PMID: 37263091 DOI: 10.1016/j.foodchem.2023.136425] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/23/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
Triterpenoid saponins are the main bioactive components contributed to the nutritional value of ginseng, and different process conditions will affect their content and quality. To study the holistic characterization and dynamic changes of triterpenoid saponins in Asian ginseng (ASG) and American ginseng (AMG) during soaking and decoction, a UPLC-Triple TOF-MS/MS-based metabolomics strategy was used to characterize and discover differential saponin markers. In total, 739 triterpenoid saponins (including 225 potential new saponins) were identified from ASG and AMG in untargeted metabolomics. Based on PCA and OPLS-DA, 51 and 48 saponin markers were screened from soaked and decocted ASG and AMG, respectively. Additionally, targeted metabolomics analysis and HCA of 22 ginsenoside markers suggested that decoction of ASG and AMG for 2 h to 4 h could significantly increase the contents of rare ginsenosides (G), such as G-Rg3, G-Rg5, G-F4. This study provides a scientific insight that high boiling combined with simmering enriches ASG and AMG extracts with rich rare ginsenosides that are more beneficial to human health.
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Affiliation(s)
- Li-Hua Chen
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - You-Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiu-Wei Yang
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Jing Xu
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhao-Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yi-Zheng Sun
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Wei Xu
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ying-Ping Wang
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, International Joint Research Center of Plants of the Genus Panax, Jilin Agricultural University, Changchun 130118, China
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29
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Dagan S, Marder D, Tzanani N, Drug E, Prihed H, Yishai-Aviram L. Evaluation of Matrix Complexity in Nontargeted Analysis of Small-Molecule Toxicants by Liquid Chromatography-High-Resolution Mass Spectrometry. Anal Chem 2023; 95:7924-7932. [PMID: 37167435 DOI: 10.1021/acs.analchem.3c00413] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Complex mixtures, characterized by high density of compounds, challenge trace detection and identification. This is further exacerbated in nontargeted analysis, where a compound of interest may be well hidden under thousands of matrix compounds. We studied the effect of matrix complexity on nontargeted detection (peak picking) by LC-MS/MS (Orbitrap) analysis. A series of ∼20 drugs, V-type chemical warfare agents and pesticides, simulating toxic unknowns, were spiked at various concentrations in several complex matrices including urine, rosemary leaves, and soil extracts. Orbitrap "TraceFinder" software was used to explore their peak intensities in relation to the matrix (peak location in an intensity-sorted list). Average practical detection limits of nontargets were determined. While detection among the first 10,000 peaks was achieved at 0.3-1 ng/mL levels in the extract, for the more realistic "top 1000" list, much higher concentrations were required, approaching 10-30 ng/mL. A negative power law functional dependence between the peak location in an intensity-sorted suspect list and the nontarget concentration is proposed. Controlled complexity was explored with a series of urine dilutions, resulting in an excellent correlation between the power law coefficient and dilution factor. The intensity distribution of matrix peaks was found to spread (unevenly) on a broad range, fitting well the Weibull distribution function with all matrices and extracts. The quantitative approach demonstrated here gives a measure of the actual capabilities and limitations of LC-MS in the analysis of nontargets in complex matrices. It may be used to estimate and compare the complexity of matrices and predict the typical detection limits of unknowns.
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Affiliation(s)
- Shai Dagan
- Analytical Chemistry Department, Israel Institute for Biological Research (IIBR), Ness Ziona 7410001, Israel
| | - Dana Marder
- Analytical Chemistry Department, Israel Institute for Biological Research (IIBR), Ness Ziona 7410001, Israel
| | - Nitzan Tzanani
- Analytical Chemistry Department, Israel Institute for Biological Research (IIBR), Ness Ziona 7410001, Israel
| | - Eyal Drug
- Analytical Chemistry Department, Israel Institute for Biological Research (IIBR), Ness Ziona 7410001, Israel
| | - Hagit Prihed
- Analytical Chemistry Department, Israel Institute for Biological Research (IIBR), Ness Ziona 7410001, Israel
| | - Lilach Yishai-Aviram
- Analytical Chemistry Department, Israel Institute for Biological Research (IIBR), Ness Ziona 7410001, Israel
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30
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Chang CW, Hsu JY, Su YH, Chen YC, Hsiao PZ, Liao PC. Monitoring long-term chemical exposome by characterizing the hair metabolome using a high-resolution mass spectrometry-based suspect screening approach. CHEMOSPHERE 2023; 332:138864. [PMID: 37156292 DOI: 10.1016/j.chemosphere.2023.138864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Hair has recently emerged as a biospecimen for characterizing the long-term chemical exposome in biomonitoring investigations spanning several months, as chemical compounds circulating in the bloodstream accumulate in hair. Although there has been interest in using human hair as a biospecimen for exposome studies, it has yet to be widely adopted compared to blood and urine. Here, we applied a high-resolution mass spectrometry (HRMS)-based suspect screening strategy to characterize the long-term chemical exposome in human hair. Hair samples were collected from 70 subjects and cut into 3 cm segments, which were then mixed to prepare pooled samples. The pooled hair samples underwent a sample preparation procedure, and the hair extracts were further analyzed using an HRMS-based suspect screening approach. An in-house chemical suspect list containing 1227 chemical entries from National Report on Human Exposure to Environmental Chemicals (Report) published by the U.S. CDC and the Exposome-Explorer 3.0 database developed by the WHO was subsequently used to screen and filter the suspect features against the HRMS dataset. Overall, we matched 587 suspect features in the HRMS dataset to 246 unique chemical formulas in the suspect list, and the structures of 167 chemicals were further identified through a fragmentation analysis. Among these, chemicals such as mono-2-ethylhexyl phthalate, methyl paraben, and 1-naphthol, which have been detected in the urine or blood for exposure assessment, were also identified in human hair. This suggests that hair reflects the accumulation of environmental compounds to which an individual is exposed. Exposure to exogenous chemicals may exert adverse effects on cognitive function, and we discovered 15 chemicals in human hair that may contribute to the pathogenesis of Alzheimer's disease. This finding suggests that human hair may be a promising biospecimen for monitoring long-term exposure to multiple environmental chemicals and perturbations in endogenous chemicals in biomonitoring investigations.
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Affiliation(s)
- Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Yi Hsu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Hsiang Su
- Division of Neurology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, 60002, Taiwan
| | - Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Zu Hsiao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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31
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Wang XC, Ma XL, Liu JN, Zhang Y, Zhang JN, Ma MH, Ma FL, Yu YJ, She Y. A comparison of feature extraction capabilities of advanced UHPLC-HRMS data analysis tools in plant metabolomics. Anal Chim Acta 2023; 1254:341127. [PMID: 37005031 DOI: 10.1016/j.aca.2023.341127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
Data analysis of ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is an essential and time-consuming step in plant metabolomics and feature extraction is the fundamental step for current tools. Various methods lead to different feature extraction results in practical applications, which may puzzle users for selecting adequate data analysis tools to deal with collected data. In this work, we provide a comprehensive method evaluation for some advanced UHPLC-HRMS data analysis tools in plant metabolomics, including MS-DIAL, XCMS, MZmine, AntDAS, Progenesis QI, and Compound Discoverer. Both mixtures of standards and various complex plant matrices were specifically designed for evaluating the performances of the involved method in analyzing both targeted and untargeted metabolomics. Results indicated that AntDAS provide the most acceptable feature extraction, compound identification, and quantification results in targeted compound analysis. Concerning the complex plant dataset, both MS-DIAL and AntDAS can provide more reliable results than the others. The method comparison is maybe useful for the selection of suitable data analysis tools for users.
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Affiliation(s)
- Xing-Cai Wang
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Xing-Ling Ma
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Jia-Nan Liu
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Yang Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Jia-Ni Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Meng-Han Ma
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Feng-Lian Ma
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Yong-Jie Yu
- College of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
| | - Yuanbin She
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310032, China.
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32
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Ccana-Ccapatinta GV, Padilla-Gonzalez GF, Ferreira PL, Monge M, Semir J, Groppo M, Da Costa FB. High-Resolution Liquid Chromatography-Mass Spectrometry-Based Metabolomics for the Classification of Chuquiraga (Barnadesioideae, Asteraceae): New Phenylpropanoid Derivatives as Chemical Markers for Chuquiraga spinosa. JOURNAL OF NATURAL PRODUCTS 2023; 86:683-693. [PMID: 36913505 DOI: 10.1021/acs.jnatprod.2c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Despite their relatively poorly investigated phytochemistry, species of the genus Chuquiraga are widely commercialized. The present study reports the use of a high-resolution liquid chromatography-mass spectrometry-based metabolomics approach coupled with exploratory and supervised multivariate statistical analyses for species classification and chemical marker identification of four species of Chuquiraga (C. jussieui, C. weberbaueri, C. spinosa, and Chuquiraga sp.) from Ecuador and Peru. Based on these analyses, a high percentage of correct classifications (87% to 100%) allowed the prediction of the taxonomic identity of Chuquiraga species. Through the metabolite selection process, several key constituents with the potential to be chemical markers were identified. Samples of C. jussieui displayed alkyl glycosides and triterpenoid glycosides as discriminating metabolites, while Chuquiraga sp. displayed high concentrations of p-hydroxyacetophenone, p-hydroxyacetophenone 4-O-glucoside, p-hydroxyacetophenone 4-O-(6-O-apiosyl)-glucoside, and quinic acid ester derivatives as the main metabolites. Caffeic acid was characteristic for C. weberbaueri samples, whereas C. spinosa displayed higher concentrations of the following new phenylpropanoid ester derivatives: 2-O-caffeoyl-4-hydroxypentanedioic acid (24), 2-O-p-coumaroyl-4-hydroxypentanedioic acid (34), 2-O-feruloyl-4-hydroxypentanedioic acid (46), 2,4-O-dicaffeoylpentanedioic acid (71), and 2-O-caffeoyl-4-O-feruloylpentanedioic acid (77).
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Affiliation(s)
- Gari V Ccana-Ccapatinta
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Guillermo F Padilla-Gonzalez
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Paola L Ferreira
- Laboratory of Plant Systematics, Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, USP, Ribeirão Preto 14040-901, Brazil
| | - Marcelo Monge
- Graduate Program of Plant Biology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Joao Semir
- Graduate Program of Plant Biology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Milton Groppo
- Laboratory of Plant Systematics, Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, USP, Ribeirão Preto 14040-901, Brazil
| | - Fernando B Da Costa
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
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Pérez-López C, Ginebreda A, Barcelo D, Tauler R. SigSel: A MATLAB package for the pre and post-treatment of high-resolution mass spectrometry signals using the ROIMCR methodology. MethodsX 2023; 10:102199. [PMID: 37424752 PMCID: PMC10326443 DOI: 10.1016/j.mex.2023.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/24/2023] [Indexed: 07/11/2023] Open
Abstract
The Regions of Interest Multivariate curve Resolution (ROIMCR) methodology has gained significance for analyzing mass spectrometry data. The new SigSel package improves the ROIMCR methodology by providing a filtering step to reduce computational costs and to identify chemical compounds giving low-intensity signals. SigSel allows the visualization and assessment of ROIMCR results and filters out components resolved as interferences and background noise. This improves the analysis of complex mixtures and facilitates the identification of chemical compounds for statistical or chemometrics analysis. SigSel has been tested using metabolomics samples of mussels exposed to the sulfamethoxazole antibiotic. It begins by analyzing the data according to their charge state, eliminating signals considered background noise, and reducing the size of the datasets. In the ROIMCR analysis, the resolution of 30 ROIMCR components was achieved. After evaluating these components, 24 were ultimately selected explaining 99.05% of the total data variance. From ROIMCR results, chemical annotation is performed using different methods: •Generating a list of signals and reanalyzing them in a data-dependent analysis.•Comparing the ROIMCR resolved mass spectra to those stored in online repositories.•Searching MS signals of chemical compounds in the ROIMCR resolved spectra profiles.
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Affiliation(s)
- Carlos Pérez-López
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Department of Environmental Chemistry, Jordi Girona 18–26, Barcelona 08034, Spain
| | - Antoni Ginebreda
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Department of Environmental Chemistry, Jordi Girona 18–26, Barcelona 08034, Spain
| | - Damia Barcelo
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Department of Environmental Chemistry, Jordi Girona 18–26, Barcelona 08034, Spain
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, Parc Científic i Tecnològic de la Universitat de Girona, Edifici H2O, Girona 17003, Spain
| | - Roma Tauler
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Department of Environmental Chemistry, Jordi Girona 18–26, Barcelona 08034, Spain
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Rischke S, Hahnefeld L, Burla B, Behrens F, Gurke R, Garrett TJ. Small molecule biomarker discovery: Proposed workflow for LC-MS-based clinical research projects. J Mass Spectrom Adv Clin Lab 2023; 28:47-55. [PMID: 36872952 PMCID: PMC9982001 DOI: 10.1016/j.jmsacl.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Mass spectrometry focusing on small endogenous molecules has become an integral part of biomarker discovery in the pursuit of an in-depth understanding of the pathophysiology of various diseases, ultimately enabling the application of personalized medicine. While LC-MS methods allow researchers to gather vast amounts of data from hundreds or thousands of samples, the successful execution of a study as part of clinical research also requires knowledge transfer with clinicians, involvement of data scientists, and interactions with various stakeholders. The initial planning phase of a clinical research project involves specifying the scope and design, and engaging relevant experts from different fields. Enrolling subjects and designing trials rely largely on the overall objective of the study and epidemiological considerations, while proper pre-analytical sample handling has immediate implications on the quality of analytical data. Subsequent LC-MS measurements may be conducted in a targeted, semi-targeted, or non-targeted manner, resulting in datasets of varying size and accuracy. Data processing further enhances the quality of data and is a prerequisite for in-silico analysis. Nowadays, the evaluation of such complex datasets relies on a mix of classical statistics and machine learning applications, in combination with other tools, such as pathway analysis and gene set enrichment. Finally, results must be validated before biomarkers can be used as prognostic or diagnostic decision-making tools. Throughout the study, quality control measures should be employed to enhance the reliability of data and increase confidence in the results. The aim of this graphical review is to provide an overview of the steps to be taken when conducting an LC-MS-based clinical research project to search for small molecule biomarkers.
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Key Words
- (U)HPLC (Ultra-), High pressure liquid chromatography
- Biomarker Discovery Study
- HILIC, Hydrophilic interaction liquid chromatography
- HRMS, High resolution mass spectrometry
- LC-MS, Liquid chromatography – mass spectrometry
- LC-MS-Based Clinical Research
- Lipidomics
- MRM, Multiple reaction monitoring
- Metabolomics
- PCA, Principal component analysis
- QA, Quality assurance
- QC, Quality control
- RF, Random Forest
- RP, Reversed phase
- SVA, Support vector machine
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Affiliation(s)
- S Rischke
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - L Hahnefeld
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - B Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - F Behrens
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.,Division of Rheumatology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - R Gurke
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - T J Garrett
- Department of Pathology, Immunology and Laboratory Medicine and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32611, USA
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Gajula SNR, Khairnar AS, Jock P, Kumari N, Pratima K, Munjal V, Kalan P, Sonti R. LC-MS/MS: A sensitive and selective analytical technique to detect COVID-19 protein biomarkers in the early disease stage. Expert Rev Proteomics 2023; 20:5-18. [PMID: 36919634 DOI: 10.1080/14789450.2023.2191845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION The COVID-19 outbreak has put enormous pressure on the scientific community to detect infection rapidly, identify the status of disease severity, and provide an immediate vaccine/drug for the treatment. Relying on immunoassay and a real-time reverse transcription polymerase chain reaction (rRT-PCR) led to many false-negative and false-positive reports. Therefore, detecting biomarkers is an alternative and reliable approach for determining the infection, its severity, and disease progression. Recent advances in liquid chromatography and mass spectrometry (LC-MS/MS) enable the protein biomarkers even at low concentrations, thus facilitating clinicians to monitor the treatment in hospitals. AREAS COVERED This review highlights the role of LC-MS/MS in identifying protein biomarkers and discusses the clinically significant protein biomarkers such as Serum amyloid A, Interleukin-6, C-Reactive Protein, Lactate dehydrogenase, D-dimer, cardiac troponin, ferritin, Alanine transaminase, Aspartate transaminase, gelsolin and galectin-3-binding protein in COVID-19, and their analysis by LC-MS/MS in the early stage. EXPERT OPINION Clinical doctors monitor significant biomarkers to understand, stratify, and treat patients according to disease severity. Knowledge of clinically significant COVID-19 protein biomarkers is critical not only for COVID-19 caused by the coronavirus but also to prepare us for future pandemics of other diseases in detecting by LC-MS/MS at the early stages.
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Affiliation(s)
- Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Ankita Sahebrao Khairnar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Pallavi Jock
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Nikita Kumari
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Kendre Pratima
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Vijay Munjal
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Pavan Kalan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
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Tran TLC, Callahan DL, Islam MT, Wang Y, Arioli T, Cahill D. Comparative metabolomic profiling of Arabidopsis thaliana roots and leaves reveals complex response mechanisms induced by a seaweed extract. FRONTIERS IN PLANT SCIENCE 2023; 14:1114172. [PMID: 36968386 PMCID: PMC10035662 DOI: 10.3389/fpls.2023.1114172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Seaweed extracts are a prominent class of biostimulants that enhance plant health and tolerance to biotic and abiotic stresses due to their unique bioactive components. However, the mechanisms of action of biostimulants are still unknown. Here, we have used a metabolomic approach, a UHPLC-MS method, to uncover the mechanisms induced following application to Arabidopsis thaliana of a seaweed extract derived from Durvillaea potatorum and Ascophyllum nodosum. We have identified, following the application of the extract, key metabolites and systemic responses in roots and leaves across 3 timepoints (0, 3, 5 days). Significant alterations in metabolite accumulation or reduction were found for those belonging to broad groups of compounds such as lipids, amino acids, and phytohormones; and secondary metabolites such as phenylpropanoids, glucosinolates, and organic acids. Strong accumulations of TCA cycle and N-containing and defensive metabolites such as glucosinolates were also found revealing the enhancement of carbon and nitrogen metabolism and defence systems. Our study has demonstrated that application of seaweed extract dramatically altered the metabolomic profiles of Arabidopsis and revealed differences in roots and leaves that varied across the timepoints tested. We also show clear evidence of systemic responses that were initiated in the roots and resulted in metabolic alterations in the leaves. Collectively, our results suggest that this seaweed extract promotes plant growth and activates defence systems by altering various physiological processes at the individual metabolite level.
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Affiliation(s)
- Thi Linh Chi Tran
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Damien L. Callahan
- School of Life and Environmental Sciences, Centre for Cellular and Molecular Biology, Deakin University, Burwood, VIC, Australia
| | - Md Tohidul Islam
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Yichao Wang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Tony Arioli
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Seasol International R&D Department, Bayswater, VIC, Australia
| | - David Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
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Fabrile MP, Ghidini S, Conter M, Varrà MO, Ianieri A, Zanardi E. Filling gaps in animal welfare assessment through metabolomics. Front Vet Sci 2023; 10:1129741. [PMID: 36925610 PMCID: PMC10011658 DOI: 10.3389/fvets.2023.1129741] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Sustainability has become a central issue in Italian livestock systems driving food business operators to adopt high standards of production concerning animal husbandry conditions. Meat sector is largely involved in this ecological transition with the introduction of new label claims concerning the defense of animal welfare (AW). These new guarantees referred to AW provision require new tools for the purpose of authenticity and traceability to assure meat supply chain integrity. Over the years, European Union (EU) Regulations, national, and international initiatives proposed provisions and guidelines for assuring AW introducing requirements to be complied with and providing tools based on scoring systems for a proper animal status assessment. However, the comprehensive and objective assessment of the AW status remains challenging. In this regard, phenotypic insights at molecular level may be investigated by metabolomics, one of the most recent high-throughput omics techniques. Recent advances in analytical and bioinformatic technologies have led to the identification of relevant biomarkers involved in complex clinical phenotypes of diverse biological systems suggesting that metabolomics is a key tool for biomarker discovery. In the present review, the Five Domains model has been employed as a vademecum describing AW. Starting from the individual Domains-nutrition (I), environment (II), health (III), behavior (IV), and mental state (V)-applications and advances of metabolomics related to AW setting aimed at investigating phenotypic outcomes on molecular scale and elucidating the biological routes most perturbed from external solicitations, are reviewed. Strengths and weaknesses of the current state-of-art are highlighted, and new frontiers to be explored for AW assessment throughout the metabolomics approach are argued. Moreover, a detailed description of metabolomics workflow is provided to understand dos and don'ts at experimental level to pursue effective results. Combining the demand for new assessment tools and meat market trends, a new cross-strategy is proposed as the promising combo for the future of AW assessment.
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Affiliation(s)
| | - Sergio Ghidini
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Mauro Conter
- Department of Veterinary Science, University of Parma, Parma, Italy
| | | | - Adriana Ianieri
- Department of Food and Drug, University of Parma, Parma, Italy
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Khodadadi Karimvand S, Mohammad Jafari J, Vali Zade S, Abdollahi H. Practical and comparative application of efficient data reduction - Multivariate curve resolution. Anal Chim Acta 2023; 1243:340824. [PMID: 36697179 DOI: 10.1016/j.aca.2023.340824] [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: 08/21/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
The term 'Big Data' has recently attracted much attention in science. Working with big data sets can be both challenging and rewarding. The complexity and big data sets make the analysis difficult to deal with, and the increasing volume of data sets requires the development of new practical methods for their handling. In this contribution, we explored the efficient data reduction-multivariate curve resolution (EDR-MCR) strategy based on the convex hull theory for quantitative and qualitative analysis of large chemical data sets. For the quantitative example, the potential of the EDR-MCR method for selecting a representative calibration set was investigated, and the results were compared with the widely used Kennard-Stone (KS) algorithm. The EDR-MCR strategy strongly limits the number of calibration samples with a high potency of prediction performance. The priority of EDR-MCR over KS is its ability to find informative variables and eliminate redundant features. Moreover, the EDR-MCR strategy was also applied for the qualitative analysis of a large-scale metabolomic data set. The comparable analysis results of EDR-MCR with the region of interest (ROI) method confirmed the ability of this method for quantitative analysis of big mass spectrophotometer data sets.
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Affiliation(s)
| | - Jamile Mohammad Jafari
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran
| | - Somaye Vali Zade
- Halal Research Center of IRI, Food and Drug Administration, Ministry of Health and Medical Education, Tehran, Iran
| | - Hamid Abdollahi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran.
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Krausová M, Braun D, Buerki-Thurnherr T, Gundacker C, Schernhammer E, Wisgrill L, Warth B. Understanding the Chemical Exposome During Fetal Development and Early Childhood: A Review. Annu Rev Pharmacol Toxicol 2023; 63:517-540. [PMID: 36202091 DOI: 10.1146/annurev-pharmtox-051922-113350] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Early human life is considered a critical window of susceptibility to external exposures. Infants are exposed to a multitude of environmental factors, collectively referred to as the exposome. The chemical exposome can be summarized as the sum of all xenobiotics that humans are exposed to throughout a lifetime. We review different exposure classes and routes that impact fetal and infant metabolism and the potential toxicological role of mixture effects. We also discuss the progress in human biomonitoring and present possiblemodels for studying maternal-fetal transfer. Data gaps on prenatal and infant exposure to xenobiotic mixtures are identified and include natural biotoxins, in addition to commonly reported synthetic toxicants, to obtain a more holistic assessment of the chemical exposome. We highlight the lack of large-scale studies covering a broad range of xenobiotics. Several recommendations to advance our understanding of the early-life chemical exposome and the subsequent impact on health outcomes are proposed.
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Affiliation(s)
- Magdaléna Krausová
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria; , ,
| | - Dominik Braun
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria; , ,
| | - Tina Buerki-Thurnherr
- Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Particles Biology Interactions, St. Gallen, Switzerland;
| | - Claudia Gundacker
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria; .,Exposome Austria, Research Infrastructure and National EIRENE Hub, Austria
| | - Eva Schernhammer
- Exposome Austria, Research Infrastructure and National EIRENE Hub, Austria.,Center for Public Health, Department of Epidemiology, Medical University of Vienna, Vienna, Austria; .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Lukas Wisgrill
- Exposome Austria, Research Infrastructure and National EIRENE Hub, Austria.,Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria;
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria; , , .,Exposome Austria, Research Infrastructure and National EIRENE Hub, Austria
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Salem MA, Wang JY, Al-Babili S. Metabolomics of plant root exudates: From sample preparation to data analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1062982. [PMID: 36561464 PMCID: PMC9763704 DOI: 10.3389/fpls.2022.1062982] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Plants release a set of chemical compounds, called exudates, into the rhizosphere, under normal conditions and in response to environmental stimuli and surrounding soil organisms. Plant root exudates play indispensable roles in inhibiting the growth of harmful microorganisms, while also promoting the growth of beneficial microbes and attracting symbiotic partners. Root exudates contain a complex array of primary and specialized metabolites. Some of these chemicals are only found in certain plant species for shaping the microbial community in the rhizosphere. Comprehensive understanding of plant root exudates has numerous applications from basic sciences to enhancing crop yield, production of stress-tolerant crops, and phytoremediation. This review summarizes the metabolomics workflow for determining the composition of root exudates, from sample preparation to data acquisition and analysis. We also discuss recent advances in the existing analytical methods and future perspectives of metabolite analysis.
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Affiliation(s)
- Mohamed A. Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, Biological and Environment Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, Biological and Environment Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Abstract
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing.
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Affiliation(s)
- Jarod Rutledge
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamilton Oh
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Mendes MPR, Paiva MJN, Costa-Amaral IC, Carvalho LVB, Figueiredo VO, Gonçalves ES, Larentis AL, André LC. Metabolomic Study of Urine from Workers Exposed to Low Concentrations of Benzene by UHPLC-ESI-QToF-MS Reveals Potential Biomarkers Associated with Oxidative Stress and Genotoxicity. Metabolites 2022; 12:metabo12100978. [PMID: 36295880 PMCID: PMC9611274 DOI: 10.3390/metabo12100978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/23/2022] Open
Abstract
Benzene is a human carcinogen whose exposure to concentrations below 1 ppm (3.19 mg·m-3) is associated with myelotoxic effects. The determination of biomarkers such as trans-trans muconic acid (AttM) and S-phenylmercapturic acid (SPMA) show exposure without reflecting the toxic effects of benzene. For this reason, in this study, the urinary metabolome of individuals exposed to low concentrations of benzene was investigated, with the aim of understanding the biological response to exposure to this xenobiotic and identifying metabolites correlated with the toxic effects induced by it. Ultra-efficient liquid chromatography coupled to a quadrupole-time-of-flight mass spectrometer (UHPLC-ESI-Q-ToF-MS) was used to identify metabolites in the urine of environmentally (n = 28) and occupationally exposed (n = 32) to benzene (mean of 22.1 μg·m-3 and 31.8 μg·m-3, respectively). Non-targeted metabolomics analysis by PLS-DA revealed nine urinary metabolites discriminating between groups and statistically correlated with oxidative damage (MDA, thiol) and genetic material (chromosomal aberrations) induced by the hydrocarbon. The analysis of metabolic pathways revealed important alterations in lipid metabolism. These results point to the involvement of alterations in lipid metabolism in the mechanisms of cytotoxic and genotoxic action of benzene. Furthermore, this study proves the potential of metabolomics to provide relevant information to understand the biological response to exposure to xenobiotics and identify early effect biomarkers.
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Affiliation(s)
- Michele P. R. Mendes
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
| | - Maria José N. Paiva
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
| | - Isabele C. Costa-Amaral
- Center for the Study of Occupational Health and Human Ecology (CESTEH), Sergio Arouca National School of Public Health (ENSP), Oswaldo Cruz Foundation (Fiocruz), Rua Leopoldo Bulhões 1480, Manguinhos, Rio de Janeiro 21041-210, RJ, Brazil
| | - Leandro V. B. Carvalho
- Center for the Study of Occupational Health and Human Ecology (CESTEH), Sergio Arouca National School of Public Health (ENSP), Oswaldo Cruz Foundation (Fiocruz), Rua Leopoldo Bulhões 1480, Manguinhos, Rio de Janeiro 21041-210, RJ, Brazil
| | - Victor O. Figueiredo
- Center for the Study of Occupational Health and Human Ecology (CESTEH), Sergio Arouca National School of Public Health (ENSP), Oswaldo Cruz Foundation (Fiocruz), Rua Leopoldo Bulhões 1480, Manguinhos, Rio de Janeiro 21041-210, RJ, Brazil
| | - Eline S. Gonçalves
- Center for the Study of Occupational Health and Human Ecology (CESTEH), Sergio Arouca National School of Public Health (ENSP), Oswaldo Cruz Foundation (Fiocruz), Rua Leopoldo Bulhões 1480, Manguinhos, Rio de Janeiro 21041-210, RJ, Brazil
| | - Ariane L. Larentis
- Center for the Study of Occupational Health and Human Ecology (CESTEH), Sergio Arouca National School of Public Health (ENSP), Oswaldo Cruz Foundation (Fiocruz), Rua Leopoldo Bulhões 1480, Manguinhos, Rio de Janeiro 21041-210, RJ, Brazil
| | - Leiliane C. André
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
- Correspondence: ; Tel.: +55-31-9238-3636
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Kronik OM, Liang X, Nielsen NJ, Christensen JH, Tomasi G. Obtaining clean and informative mass spectra from complex chromatographic and high-resolution all-ions-fragmentation data by nonnegative parallel factor analysis 2. J Chromatogr A 2022; 1682:463501. [PMID: 36155072 DOI: 10.1016/j.chroma.2022.463501] [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: 07/31/2022] [Revised: 08/30/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
A major challenge in processing of complex data obtained from chromatography hyphenated to mass spectrometry is to resolve chromatographically co-eluting compounds. In this study, we present a workflow for the resolution of ultra-high pressure liquid chromatography high-resolution mass spectrometry data obtained by the broadband data-independent acquisition MSE operation (UHPLCHRMSE). The workflow is based on a recently introduced algorithm for Parallel Factor Analysis 2 (PARAFAC2) that allows to enforce non-negativity on all the model coefficients. The workflow was tested on three sets of UHPLC-HRMSE measurements from a Lupinus angustifolius L. crop field study, which included plant tissue samples, soil samples and samples from drainage water as well as stream water close to the field. The three datasets included 93, 59, and 75 chromatographic runs in total for the plant, soil and water batches, respectively. Nonnegative-PARAFAC2 models were fitted on the summed high and low energy (HE and LE) traces on chromatographic intervals corresponding to spiked standard for the three sample sets independently. In soil and plant samples, 13 out of 14 spiked standards were resolved by NN-PARAFAC2 even in presence of chromatographic co-elution, and their mass spectral loadings could be matched to a reference spectrum. In contrast, only seven spiked standards were correctly resolved and matched for the water samples because a higher chromatographic baseline rendered the data noisier. The results show that the workflow we present can provide improved mass spectral selectivity for data-independent acquisition compared to using the raw mass spectra and can be used to match fragment ions from the HE trace, and precursor and adduct ions from the LE trace even in presence of co-eluting compounds.
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Affiliation(s)
- Oskar Munk Kronik
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark.
| | - Xiaomeng Liang
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Nikoline Juul Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Jan H Christensen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Giorgio Tomasi
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
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Dehghani F, Yousefinejad S, Walker DI, Omidi F. Metabolomics for exposure assessment and toxicity effects of occupational pollutants: current status and future perspectives. Metabolomics 2022; 18:73. [PMID: 36083566 DOI: 10.1007/s11306-022-01930-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Work-related exposures to harmful agents or factors are associated with an increase in incidence of occupational diseases. These exposures often represent a complex mixture of different stressors, challenging the ability to delineate the mechanisms and risk factors underlying exposure-disease relationships. The use of omics measurement approaches that enable characterization of biological marker patterns provide internal indicators of molecular alterations, which could be used to identify bioeffects following exposure to a toxicant. Metabolomics is the comprehensive analysis of small molecule present in biological samples, and allows identification of potential modes of action and altered pathways by systematic measurement of metabolites. OBJECTIVES The aim of this study is to review the application of metabolomics studies for use in occupational health, with a focus on applying metabolomics for exposure monitoring and its relationship to occupational diseases. METHODS PubMed, Web of Science, Embase and Scopus electronic databases were systematically searched for relevant studies published up to 2021. RESULTS Most of reviewed studies included worker populations exposed to heavy metals such as As, Cd, Pb, Cr, Ni, Mn and organic compounds such as tetrachlorodibenzo-p-dioxin, trichloroethylene, polyfluoroalkyl, acrylamide, polyvinyl chloride. Occupational exposures were associated with changes in metabolites and pathways, and provided novel insight into the relationship between exposure and disease outcomes. The reviewed studies demonstrate that metabolomics provides a powerful ability to identify metabolic phenotypes and bioeffect of occupational exposures. CONCLUSION Continued application to worker populations has the potential to enable characterization of thousands of chemical signals in biological samples, which could lead to discovery of new biomarkers of exposure for chemicals, identify possible toxicological mechanisms, and improved understanding of biological effects increasing disease risk associated with occupational exposure.
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Affiliation(s)
- Fatemeh Dehghani
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Research Center for Health Sciences, Research Institute for Health, Department of Occupational Health and Safety Engineering, School of Health Shiraz, University of Medical Sciences, Shiraz, Iran
| | - Saeed Yousefinejad
- Research Center for Health Sciences, Research Institute for Health, Department of Occupational Health and Safety Engineering, School of Health Shiraz, University of Medical Sciences, Shiraz, Iran.
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fariborz Omidi
- Research Center for Environmental Determinants of Health (RCEDH), Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Dinis K, Tsamba L, Thomas F, Jamin E, Camel V. Preliminary authentication of apple juices using untargeted UHPLC-HRMS analysis combined to chemometrics. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Harlina PW, Maritha V, Musfiroh I, Huda S, Sukri N, Muchtaridi M. Possibilities of Liquid Chromatography Mass Spectrometry
(LC-MS)-Based Metabolomics and Lipidomics in the Authentication of Meat
Products: A Mini Review. Food Sci Anim Resour 2022; 42:744-761. [PMID: 36133639 PMCID: PMC9478982 DOI: 10.5851/kosfa.2022.e37] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Putri Widyanti Harlina
- Department of Food Industrial Technology,
Faculty of Agro-Industrial Technology, Universitas
Padjadjaran, Bandung 45363, Indonesia
- Corresponding author: Putri
Widyanti Harlina, Department of Food Industrial Technology, Faculty of
Agro-Industrial Technology, Universitas Padjadjaran, Bandung 45363, Indonesia,
Tel: +62-22-7798844, E-mail:
| | - Vevi Maritha
- Department of Pharmaceutical Analysis and
Medicinal Chemistry, Faculty of Pharmacy, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Ida Musfiroh
- Department of Pharmaceutical Analysis and
Medicinal Chemistry, Faculty of Pharmacy, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Syamsul Huda
- Department of Food Industrial Technology,
Faculty of Agro-Industrial Technology, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Nandi Sukri
- Department of Food Industrial Technology,
Faculty of Agro-Industrial Technology, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Muchtaridi Muchtaridi
- Department of Pharmaceutical Analysis and
Medicinal Chemistry, Faculty of Pharmacy, Universitas
Padjadjaran, Bandung 45363, Indonesia
- Corresponding author:
Muchtaridi Muchtaridi, Department of Pharmaceutical Analysis and Medicinal
Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363,
Indonesia, Tel: +62-22-8784288888 (ext. 3210), E-mail:
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Untargeted Metabolomics Analysis of Crocus cancellatus subsp. damascenus (Herb.) B. Mathew Stigmas and Their Anticarcinogenic Effect on Breast Cancer Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3861783. [PMID: 36016682 PMCID: PMC9398734 DOI: 10.1155/2022/3861783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/01/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022]
Abstract
Safranal, crocin, crocetin, and picrocrocin are major known compounds in the stigma extract of Crocus sativus with various medicinal properties. Crocus cancellatus is another Crocus species that grows extensively in Iran’s various regions, such as the Kurdistan province. The predominant metabolites and biological properties of C. cancellatus have not yet been investigated. The ingredients of the stigma ethanol extract of C. cancellatus were investigated using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography with tandem mass spectrometry (LC-MS). The ROIMCR approach was performed to analyze the LC-MS full scan data sets. This method searches the MS regions of interest (ROI) data in the m/z domain and analyses the results using the multivariate curve-resolution alternating least squares (MCR-ALS) chemometrics technique for simultaneous resolution of two extracts. Also, the antiproliferative properties of C. cancellatus against MDA-MB-231 and MCF-7 cancer cells were examined by MTT, dual acridine orange/ethidium bromide test, Annexin V-FITC/PI, and zymography. The GC-MS and LC-MS untargeted metabolomics data analysis of the extract indicated the presence of cytotoxic agents including safranal, crocin, picrocrocin, and crocetin in the stigma ethanol extract of C. cancellatus. Biological tests showed that the viability of MDA-MB-231 and MCF-7 cancer cells is decreased following C. cancellatus treatment in a time- and dose-dependent way in both monolayer and 3D cell cultures. The MCF-7 cell spheroids had greater resistance to the cytotoxic activity of the extract in 3D cell culture than the MDA-MB-231 cell spheroids. The morphological changes of the cells treated with C. cancellatus stigmas extract were indicative of apoptosis. Zymography analysis revealed a similar trend of matrix metallopeptidase-2 (MMP-2) and matrix metallopeptidase-9 (MMP-9) activity in the treated cells with C. cancellatus extract in comparison with doxorubicin treatment as a positive control. The findings of this research indicate that the ethanolic extract of C. cancellatus stigmas was a good source of bioactive metabolites with anticancer activity.
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Pérez-López C, Rodríguez-Mozaz S, Serra-Compte A, Alvarez-Muñoz D, Ginebreda A, Barceló D, Tauler R. Effects of sulfamethoxazole exposure on mussels (Mytilus galloprovincialis) metabolome using retrospective non-target high-resolution mass spectrometry and chemometric tools. Talanta 2022; 252:123804. [DOI: 10.1016/j.talanta.2022.123804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/28/2022]
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50
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Chang WH, Ling YS, Wang KC, Nan FH, Chen WL. Discrimination of Atlantic salmon origins using untargeted chemical fingerprinting. Food Chem 2022; 394:133538. [PMID: 35759841 DOI: 10.1016/j.foodchem.2022.133538] [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: 02/02/2022] [Revised: 05/27/2022] [Accepted: 06/18/2022] [Indexed: 11/15/2022]
Abstract
Mislabelling the geographic origin of same-species aquaculture products is difficult to identify. This study applied untargeted small-molecule fingerprinting to discriminating between Atlantic salmon originating from Chile and Norway. The acquired liquid chromatography-high-resolution mass spectrometry data from Chilean (n = 32) and Norwegian (n = 29) salmon were chemometrically processed. The partial least squares discriminant analysis (PLS-DA) models successfully discriminated between Chilean and Norwegian salmon at both positive and negative ionisation modes (R2 > 0.96, Q2 > 0.81). Univariate analyses facilitated the selection of approximately 100 candidate markers with high statistical confidence (> 95%). Of these, 37 confirmed markers of Chilean and Norwegian salmon were primarily associated with feed formulations, including lipid derivatives and feed additives. None of the markers were residues or contaminants of potential food safety concern.
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Affiliation(s)
- Wen-Hsin Chang
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, 17 Xuzhou Rd., Taipei 100, Taiwan
| | - Yee Soon Ling
- CAIQ Certification Sdn Bhd, Suite D-4-1, Block D, 4th Fl., Plaza Tanjung Aru, 88100 Kota Kinabalu, Sabah, Malaysia
| | - Ko-Chih Wang
- Department of Computer Science and Information Engineering, College of Science, National Taiwan Normal University, 162, Sec. 1, Heping E. Rd., Taipei 106, Taiwan.
| | - Fan-Hua Nan
- Department of Aquaculture, College of Life Sciences, National Taiwan Ocean University, 2, Beining Rd., Keelung 202, Taiwan.
| | - Wen-Ling Chen
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, 17 Xuzhou Rd., Taipei 100, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, 17 Xuzhou Rd., Taipei 100, Taiwan; Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
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