151
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Jacoby RP, Martyn A, Kopriva S. Exometabolomic Profiling of Bacterial Strains as Cultivated Using Arabidopsis Root Extract as the Sole Carbon Source. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:803-813. [PMID: 29457542 DOI: 10.1094/mpmi-10-17-0253-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The ability of microorganisms to use root-derived metabolites as growth substrates is a key trait for success in the rhizospheric niche. However, few studies describe which specific metabolites are consumed or to what degree microbial strains differ in their substrate consumption patterns. Here, we present a liquid chromatography-mass spectrometry (MS) exometabolomic study of three bacterial strains cultivated using either glucose or Arabidopsis thaliana root extract as the sole carbon source. Two of the strains were previously isolated from field-grown Arabidopsis roots, the other is Escherichia coli, included as a comparison. When cultivated on root extract, a set of 62 MS features were commonly taken up by all three strains, with m/z values matching components of central metabolism (including amino acids and purine or pyrimidine derivatives). Escherichia coli took up very few MS features outside this commonly consumed set, whereas the root-inhabiting strains took up a much larger number of MS features, many with m/z values matching plant-specific metabolites. These measurements define the metabolic niche that each strain potentially occupies in the rhizosphere. Furthermore, we document many MS features released by these strains that could play roles in cross-feeding, antibiosis, or signaling. We present our methodological approach as a foundation for future studies of rhizosphere exometabolomics.
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Affiliation(s)
- Richard P Jacoby
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Anna Martyn
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, D-50674 Cologne, Germany
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152
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Liu R, Chou J, Hou S, Liu X, Yu J, Zhao X, Li Y, Liu L, Sun C. Evaluation of two-step liquid-liquid extraction protocol for untargeted metabolic profiling of serum samples to achieve broader metabolome coverage by UPLC-Q-TOF-MS. Anal Chim Acta 2018; 1035:96-107. [PMID: 30224149 DOI: 10.1016/j.aca.2018.07.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 12/22/2022]
Abstract
Untargeted metabolomics studies aim to extract a broad coverage of metabolites from biological samples, which largely depends on the sample preparation protocols used for metabolite extraction. The aim of this study was to evaluate a comprehensive sample pretreatment strategy using two-step liquid-liquid extraction to achieve broader metabolome coverage by ultra-high-performance liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry (UPLC-Q-TOF-MS). We compared four protocols: (A) methanol protein precipitation, (B) Ostro 96-well plates, (C) two-step extraction protocol of CHCL3-MeOH followed by MeOH-H2O, and (D) two-step extraction protocol of CH2CL2-MeOH followed by MeOH-H2O. The number of extracted features, reproducibility and recovery were the major criteria for evaluation. Our results demonstrated that Protocols B, C and D, with approximately similar number of features, extracted more features than Protocol A. Protocols C and D appeared to have similar extraction reproducibility (low coefficient of variation < 30%) and Protocol D enabled an acceptable recovery of serum metabolites. The two-step extraction Protocol D (CH2CL2-MeOH followed by MeOH-H2O) resulted in the greatest improvement in metabolite coverage, satisfactory extraction reproducibility, acceptable recovery and environmental safety. The selected protocol was applied to an obesity metabolomics study to obtain different metabolites between participants with obesity and the controls, and to investigate complex metabolic alterations in obesity during a 2-h oral glucose-tolerance test. Our results suggested that this protocol was useful for analyzing serum metabolome changes in obese individuals in the fasting and postprandial state.
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Affiliation(s)
- Rui Liu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Jing Chou
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Shaoying Hou
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Xiaowei Liu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Jiaying Yu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Xinshu Zhao
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Ying Li
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China
| | - Liyan Liu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China.
| | - Changhao Sun
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, PR China.
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153
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Kirwan JA, Brennan L, Broadhurst D, Fiehn O, Cascante M, Dunn WB, Schmidt MA, Velagapudi V. Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for "Precision Medicine and Pharmacometabolomics Task Group"-The Metabolomics Society Initiative). Clin Chem 2018; 64:1158-1182. [PMID: 29921725 DOI: 10.1373/clinchem.2018.287045] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND The metabolome of any given biological system contains a diverse range of low molecular weight molecules (metabolites), whose abundances can be affected by the timing and method of sample collection, storage, and handling. Thus, it is necessary to consider the requirements for preanalytical processes and biobanking in metabolomics research. Poor practice can create bias and have deleterious effects on the robustness and reproducibility of acquired data. CONTENT This review presents both current practice and latest evidence on preanalytical processes and biobanking of samples intended for metabolomics measurement of common biofluids and tissues. It highlights areas requiring more validation and research and provides some evidence-based guidelines on best practices. SUMMARY Although many researchers and biobanking personnel are familiar with the necessity of standardizing sample collection procedures at the axiomatic level (e.g., fasting status, time of day, "time to freezer," sample volume), other less obvious factors can also negatively affect the validity of a study, such as vial size, material and batch, centrifuge speeds, storage temperature, time and conditions, and even environmental changes in the collection room. Any biobank or research study should establish and follow a well-defined and validated protocol for the collection of samples for metabolomics research. This protocol should be fully documented in any resulting study and should involve all stakeholders in its design. The use of samples that have been collected using standardized and validated protocols is a prerequisite to enable robust biological interpretation unhindered by unnecessary preanalytical factors that may complicate data analysis and interpretation.
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Affiliation(s)
- Jennifer A Kirwan
- Berlin Institute of Health, Berlin, Germany; .,Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Lorraine Brennan
- UCD School of Agriculture and Food Science, Institute of Food and Health, UCD, Dublin, Ireland
| | | | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis, Davis, CA
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine and IBUB, Universitat de Barcelona, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBER-EHD), Madrid, Spain
| | - Warwick B Dunn
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
| | - Michael A Schmidt
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO.,Sovaris Aerospace, LLC, Boulder, CO
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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154
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Johnson AE, Sidwick KL, Pirgozliev VR, Edge A, Thompson DF. Metabonomic Profiling of Chicken Eggs during Storage Using High-Performance Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry. Anal Chem 2018; 90:7489-7494. [DOI: 10.1021/acs.analchem.8b01031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Amy E. Johnson
- School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Kate L. Sidwick
- School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Vasil R. Pirgozliev
- The National Institute of Poultry Husbandry, Harper Adams University, Newport, Shropshire TF10 8NB, United Kingdom
| | - Anthony Edge
- Department of Chemistry, Liverpool University, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - David F. Thompson
- School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
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155
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Pan H, Yao C, Yang W, Yao S, Huang Y, Zhang Y, Wu W, Guo D. An enhanced strategy integrating offline two-dimensional separation and step-wise precursor ion list-based raster-mass defect filter: Characterization of indole alkaloids in five botanical origins of Uncariae Ramulus Cum Unicis as an exemplary application. J Chromatogr A 2018; 1563:124-134. [PMID: 29880214 DOI: 10.1016/j.chroma.2018.05.066] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/20/2018] [Accepted: 05/28/2018] [Indexed: 01/01/2023]
Abstract
Comprehensive chemical profiling is of great significance for understanding the therapeutic material basis and quality control of herbal medicines, which is challenging due to its inherent chemical diversity and complexity, as well as wide concentration range. In this study, we introduced an enhanced strategy integrating offline two-dimensional (2D) separation and the step-wise precursor ion list-based raster-mass defect filter (step-wise PIL-based raster-MDF) scan by tandem LTQ-Orbitrap mass spectrometer. A comprehensive analysis of indole alkaloids in five botanical origins of Uncariae Ramulus Cum Unicis (Gou-Teng) was used as an exemplary application. A positively charged reversed phase (PR) × conventional RP LC system in different pH conditions was constructed with the orthogonality of 74%. A theoretical step-wise PIL among 310-950 Da with the step-size of 2 Da was developed to selectively trigger fragmentations and extend the coverage of potential indole alkaloids. Simultaneously, by defining parent mass width (PMW) of the step-wise PIL to ±55 mDa, a raster-MDF screening was achieved in the acquisition process. Additionally, subtype classification and structural elucidation were facilitated by a four-step interpretation strategy. As a result, a total of 1227 indole alkaloids were efficiently exposed and characterized from five botanical origins of Gou-Teng, which showed high chemical diversity. A systematic comparison among five species was first performed and only 66 indole alkaloids were common. For method validation, three new alkaloid N-oxides were isolated and unambiguously identified by NMR. The present study provides a novel data-dependent acquisition method with improved target coverage and high selectivity. The integrated strategy is practical to efficiently expose and comprehensively characterize complex components in herbal medicines.
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Affiliation(s)
- Huiqin Pan
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China; University of Chinese Academy of Sciences,No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China; University of Chinese Academy of Sciences,No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Wenzhi Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Shuai Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Yong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Yibei Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China
| | - Wanying Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China.
| | - Dean Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Haike Road 501, Shanghai, 201203, People's Republic of China.
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156
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Lee SJ, Yi T, Ahn SH, Lim DK, Kim SN, Lee HJ, Cho YK, Lim JY, Sung JH, Yun JH, Lim J, Song SU, Kwon SW. Comparative study on metabolite level in tissue-specific human mesenchymal stem cells by an ultra-performance liquid chromatography quadrupole time of flight mass spectrometry. Anal Chim Acta 2018; 1024:112-122. [PMID: 29776537 DOI: 10.1016/j.aca.2018.04.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/03/2018] [Accepted: 04/13/2018] [Indexed: 12/21/2022]
Abstract
Mesenchymal stem cells (MSCs) are a promising therapeutic option for cell-based therapy due to their immunomodulatory and regenerative properties. They can be isolated from various adult tissues, including bone marrow, fat, dental tissue, and glandular tissue. Although they share common characteristics, little is known about the biological differences between MSC populations derived from different tissues. In this study, we used MS to compare the endogenous metabolite level in the human MSCs originating from the bone marrow, adipose tissue, periodontal ligaments, and salivary glands. Using an optimized metabolomics technique, we verified that human MSCs exhibit differences in the endogenous metabolite level depending on their source material, while the multivariate analysis showed that 5 lysophosphatidylcholines and 3 lysophosphatidylethanolamines can serve as markers for the discrimination between MSC sources and may be related to differences in their differentiation capacity. These results may significantly contribute to further mechanistic studies on the MSCs and provide novel insights into the properties and optimal usage of MSCs from different tissues.
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Affiliation(s)
- Seul Ji Lee
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | | | - Soo Hyun Ahn
- Department of Mathematics, Ajou University, Suwon, South Korea
| | - Dong Kyu Lim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Si-Na Kim
- SCM Lifescience Co. Ltd., Incheon, South Korea
| | - Hyun-Joo Lee
- Department of Integrated Biomedical Sciences, Inha University School of Medicine, Incheon, South Korea
| | | | - Jae-Yol Lim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong-Hyuk Sung
- College of Pharmacy, Yonsei University, Incheon, South Korea
| | - Jeong-Ho Yun
- Department of Periodontology, College of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju, South Korea
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Sun U Song
- SCM Lifescience Co. Ltd., Incheon, South Korea; Department of Integrated Biomedical Sciences, Inha University School of Medicine, Incheon, South Korea
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul, South Korea; Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea.
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157
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Van Meulebroek L, Wauters J, Pomian B, Vanden Bussche J, Delahaut P, Fichant E, Vanhaecke L. Discovery of urinary biomarkers to discriminate between exogenous and semi-endogenous thiouracil in cattle: A parallel-like randomized design. PLoS One 2018; 13:e0195351. [PMID: 29649241 PMCID: PMC5896977 DOI: 10.1371/journal.pone.0195351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
Abstract
In the European Union, the use of thyreostats for animal fattening purposes has been banned and monitoring plans have been established to detect potential abuse. However, this is not always straightforward as thyreostats such as thiouracil may also have a semi-endogenous origin. Therefore, this study aimed at defining urinary metabolites, which may aid in defining the origin of detected thiouracil. Hereto, a parallel-like randomized in vivo study was conducted in which calves (n = 8) and cows (n = 8) were subjected to either a control treatment, rapeseed-enriched diet to induce semi-endogenous formation, or thiouracil treatment. Urine samples (n = 330) were assessed through metabolic fingerprinting, employing liquid-chromatography and Q-ExactiveTM Orbitrap mass spectrometry. Urinary fingerprints comprised up to 40,000 features whereby multivariate discriminant analysis was able to point out significant metabolome differences between treatments (Q2(Y) ≥ 0.873). Using the validated models, a total of twelve metabolites (including thiouracil) were assigned marker potential. Combining these markers into age-dependent biomarker panels rendered a tool by which sample classification could be improved in comparison with thiouracil-based thresholds, and this during on-going thiouracil treatment (specificities ≥ 95.2% and sensitivities ≥ 85.7%), post-treatment (sensitivities ≥ 80% for ≥ 24 h after last administration), and simulated low-dose thiouracil treatment (exogenous thiouracil below 30 ng μL-1). Moreover, the metabolic relevance of revealed markers was supported by the suggested identities, for which a structural link with thiouracil could be determined in most cases. The proposed biomarker panels may contribute to a more justified decision-making in monitoring thiouracil abuse.
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Affiliation(s)
- Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
- * E-mail:
| | - Jella Wauters
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
| | - Beata Pomian
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
| | - Julie Vanden Bussche
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
| | | | - Eric Fichant
- Health Department, CER Groupe, Rue Point du Jour, Marloie, Belgium
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
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158
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Characterization of bioactive compounds of Annona cherimola L. leaves using a combined approach based on HPLC-ESI-TOF-MS and NMR. Anal Bioanal Chem 2018; 410:3607-3619. [PMID: 29629503 DOI: 10.1007/s00216-018-1051-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/19/2018] [Accepted: 03/29/2018] [Indexed: 12/26/2022]
Abstract
Annona cherimola Mill. (cherimoya) has widely been used as food crop. The leaves of this tree possess several health benefits, which are, in general, attributed mainly to its bioactive composition. However, literature concerning a comprehensive characterization based on a combined approach, which consists of nuclear magnetic resonance (NMR) and high-performance liquid chromatography coupled with time-of-flight mass spectrometry (HPLC-TOF-MS), from these leaves is scarce. Thus, the aim of this work was to study the polar profile of full extracts of cherimoya leaves by using these tools. Thus, a total of 77 compounds have been characterized, 12 of which were identified by both techniques. Briefly, 23 compounds were classified as amino acids, organic acids, carbohydrates, cholines, phenolic acid derivatives, and flavonoids by NMR, while 66 metabolites were divided into sugars, amino acids, phenolic acids and derivatives, flavonoids, phenylpropanoids, and other polar compounds by HPLC-TOF-MS. It is worth mentioning that different solvent mixtures were tested and the total phenolic content in the extracts quantified (TPC via HPLC-TOF-MS). The tendency observed was EtOH/water 80/20 (v/v) (17.0 ± 0.2 mg TPC/g leaf dry weight (d.w.)) ≥ acetone/water 70/30 (v/v) (16.1 ± 0.7 mg TPC/g leaf d.w.) > EtOH/water 70/30 (v/v) (14.0 ± 0.3 mg TPC/g leaf d.w.) > acetone/water 80/20 (v/v) (13.5 ± 0.4 mg TPC/g leaf d.w.). Importantly, flavonoids derivatives were between 63 and 76% of the TPC in those extracts. Major compounds were sucrose, glucose (α and β), and proline, and chlorogenic acid and rutin for NMR and HPLC-TOF-MS, respectively. Graphical abstract The combined use of LC-HRMS and NMR is a potential synergic combination for a comprehensive metabolite composition of cherimoya leaves.
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159
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Abstract
Ischemic stroke is a sudden loss of brain function due to the reduction of blood flow. Brain tissues cease to function with subsequent activation of the ischemic cascade. Metabolomics and lipidomics are modern disciplines that characterize the metabolites and lipid components of a biological system, respectively. Because the pathogenesis of ischemic stroke is heterogeneous and multifactorial, it is crucial to establish comprehensive metabolomic and lipidomic approaches to elucidate these alterations in this disease. Fortunately, metabolomic and lipidomic studies have the distinct advantages of identifying tissue/mechanism-specific biomarkers, predicting treatment and clinical outcome, and improving our understanding of the pathophysiologic basis of disease states. Therefore, recent applications of these analytical approaches in the early diagnosis of ischemic stroke were discussed. In addition, the emerging roles of metabolomics and lipidomics on ischemic stroke were summarized, in order to gain new insights into the mechanisms underlying ischemic stroke and in the search for novel metabolite biomarkers and their related pathways.
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160
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Cai H, Su S, Li Y, Zeng H, Zhu Z, Guo J, Zhu Y, Guo S, Yu L, Qian D, Tang Y, Duan J. Protective effects of Salvia miltiorrhiza on adenine-induced chronic renal failure by regulating the metabolic profiling and modulating the NADPH oxidase/ROS/ERK and TGF-β/Smad signaling pathways. JOURNAL OF ETHNOPHARMACOLOGY 2018; 212:153-165. [PMID: 29032117 DOI: 10.1016/j.jep.2017.09.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/12/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Chronic renal failure (CRF) is defined as a progressive and irreversible loss of renal function and associated with inflammation and oxidative stress. Salvia miltiorrhiza (SM) is an important Chinese herb used in traditional Chinese medicine for treating cardiovascular diseases. The previous studies showed the SM exhibited significant protective effects on CRF. In this present study, the metabolic profiling changes and action mechanism of SM on CRF were explored. AIMS OF THE STUDY The aims of this study were to illustrate the metabolic profiling changes of adenine induced CRF and analyze the protective effects and action mechanisms of SM ethanol extract (SMEE) and water extract (SMWE). MATERIALS AND METHODS The animals were divided into normal group, CRF model group, Huangkui capsule-treated group, SMEE-treated group and SMWE-treated group. The UPLC-QTOFMS coupled with multivariate statistical methods were used to explore the changes of metabolic profile in plasma, urine and renal tissue from CRF rats simultaneously after treatment with SMEE and SMWE. Hematoxylin eosin (HE) staining and Masson staining were applied to observe pathological changes in renal tissue. Biochemical indicators including serum urea nitrogen (BUN), urine protein (UP) and serum creatinine (Scr) were measured according to the manufacturer's instructions of kits. Furthermore, HK-2 cell damaged model induced by ISF was established to access the protective effects and action mechanism. The dichlorodihydrofluorescein diacetate (DCFH-DA) assay was used to determine the reactive oxygen species (ROS) and Western blot was applied to analyze the expression of pathogenesis-related proteins in different groups. RESULTS The results showed that the ethanol extract (SMEE) and water extract (SMWE) of SM significantly inhibited the elevation of serum creatinine (Scr), blood urea nitrogen (BUN), urine protein (UP) and indoxyl sulfate (ISF) in adenine-induced CRF rats, especially SMEE exhibited more significant effects. Moreover, SM extracts obviously improved the symptoms of glomerular and tubular atrophy, focal calcium deposits, interstitial fibrosis, interstitial inflammation, and renal tissues. By metabolomics analysis, fifty-nine metabolites (thirteen in plasma, twenty-seven in urine and nineteen in kidney tissue) were up-regulated or down-regulated and contributed to CRF progress. After treatment of SM extracts, the altered metabolites were restored back to normal level. These potential biomarkers underpinning the metabolic pathways are including phenylalanine metabolism, pyrimidine metabolism, purine metabolism and tryptophan metabolism. Furthermore, SM extracts prevent epithelial-mesenchymal transition (EMT) of human renal tubular epithelial (HK-2) cell by inhibiting NADPH oxidase/ROS/ERK and TGF-β/Smad signaling pathways. CONCLUSIONS SMEE and SMWE can significantly alleviate adenine-induced CRF via regulation of the metabolic profiling and modulation of NADPH oxidase/ROS/ERK and TGF-β/Smad signaling pathways, which provided important supports for the development of protective agent of SM for CRF.
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Affiliation(s)
- Hongdie Cai
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Zhejiang Pharmaceutical College, Ningbo 310053, PR China.
| | - Shulan Su
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Yonghui Li
- Hainan Provincial Key Laboratory of R&D of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, PR China.
| | - Huiting Zeng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Zhenhua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Jianming Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Yue Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Sheng Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Li Yu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Yuping Tang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
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161
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A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage. Talanta 2018; 182:380-390. [PMID: 29501168 DOI: 10.1016/j.talanta.2018.01.084] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/22/2022]
Abstract
Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run. Here, nanoflow liquid chromatography-nanoelectrospray ionisation (nLC-nESI), which has previously been utilised successfully in proteomics, is explored for use in metabolomic and exposomic research. As a discovery based field, the markedly increased sensitivity of these nLC-nESI platforms offer the potential to uncover the roles played by low abundant signalling metabolites (e.g. steroids, eicosanoids) in health and disease studies, and would also enable an improvement in the detection of xenobiotics present at trace levels in biological matrices to better characterise the chemical exposome. This review aims to give an insight into the advantages associated with nLC-nESI for metabolomics-based approaches. Initially we detail the source of improved sensitivity prior to reviewing the available approaches to achieving nanoflow rates and nanospray ionisation for metabolomics. The robustness of nLC-nESI platforms was then assessed using the literature available from a metabolomic viewpoint. We also discuss the challenging point of sample preparation which needs to be addressed to fully enjoy the benefits of these nLC-nESI platforms. Finally, we assess metabolomic analysis utilising nano scale platforms and look ahead to the future of metabolomics using these new highly sensitive platforms.
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162
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Favre L, Ortalo-Magné A, Pichereaux C, Gargaros A, Burlet-Schiltz O, Cotelle V, Culioli G. Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8. BIOFOULING 2018; 34:132-148. [PMID: 29319346 DOI: 10.1080/08927014.2017.1413551] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells.
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Affiliation(s)
- Laurie Favre
- a MAPIEM EA 4323 , Université de Toulon , Toulon , France
| | | | - Carole Pichereaux
- b Fédération de Recherche FR3450 , CNRS , Toulouse , France
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Audrey Gargaros
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Odile Burlet-Schiltz
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Valérie Cotelle
- d Laboratoire de Recherche en Sciences Végétales , Université de Toulouse, CNRS, UPS , Castanet-Tolosan , France
| | - Gérald Culioli
- a MAPIEM EA 4323 , Université de Toulon , Toulon , France
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163
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Tugizimana F, Steenkamp PA, Piater LA, Dubery IA. Mass spectrometry in untargeted liquid chromatography/mass spectrometry metabolomics: Electrospray ionisation parameters and global coverage of the metabolome. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:121-132. [PMID: 28990281 DOI: 10.1002/rcm.8010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Liquid chromatography coupled to mass spectrometry (LC/MS) is a dominant analytical platform in metabolomics, because of the high sensitivity and resolution, thus enabling large-scale coverage of metabolomes. Correspondingly, electrospray ionisation (ESI) is the favoured ionisation method in untargeted LC/MS metabolomics given the ability to produce large numbers of ions. In the workflow of LC/ESI-MS metabolomics, maximising the ionisation efficiency over a wide mass range is inevitably an essential and determining step, subsequently defining the extent of coverage of the metabolome under investigation. Thus in this study, electronic factors related to the functioning of the ESI source, namely the capillary and sample cone voltages, were explored to investigate the influence on the data acquired in metabolomic investigations. METHODS Hydromethanolic samples from an untargeted study (sorghum plants responding dynamically to fungal infection) were analysed on a high-resolution/definition LC/ESI-MS system. Here the capillary and sample cone voltages of the ZSpray™ ESI source were varied between 1.5-3.0 kV and 10.0-40.0 V, respectively. The acquired data were processed with MarkerLynx™ software and analysed using central composite design response surface methodology and chemometric approaches (principal component analysis and orthogonal projection latent structures-discriminant analysis). RESULTS The results evidently demonstrate that both capillary and sampling cone voltages not only significantly influence the recorded MS signals with regard to the number and abundance of features, but also the overall structure of the collected data. This consequently impacts on the information extracted from the data and thus affects coverage of the metabolome. CONCLUSIONS The observations postulate in that, untargeted LC/MS metabolomics, 'what you see is what you ionise'. Although there is convergence of collected data under different ESI conditions, the nuances observed indicate that the exploration of different ion source settings could be the best trade-off in expanding and maximising the metabolome coverage in untargeted metabolomic experiments.
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Affiliation(s)
- Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Paul A Steenkamp
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Lizelle A Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
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164
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Zhang X, Hou H, Chen H, Liu Y, Wang A, Hu Q. Serum metabolomics of laryngeal cancer based on liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Biomed Chromatogr 2018; 32:e4181. [PMID: 29272549 DOI: 10.1002/bmc.4181] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/27/2017] [Accepted: 12/13/2017] [Indexed: 12/23/2022]
Abstract
The discovery of new laryngeal cancer-related metabolite biomarkers could help to facilitate early diagnosis. A serum metabolomics study from laryngeal cancer patients and healthy individuals was conducted using liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Univariate and multivariate statistics were used to discriminate laryngeal cancer patients and healthy individuals. 1-Palmitoyl-sn-glycero-3-phosphocholine (LysoPC 16:0), 1-o-hexadecyl-2-acetyl-sn-glycero-3-phosphocholine (PAF) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine were found to be significantly different between the laryngeal cancer group and the healthy group. They are mainly involved in phospholipids catabolism, linoleic acid metabolism, α-linoleic acid metabolism and arachidonic acid metabolism. The area under the curve of the biomarker combined by two metabolites (LysoPC 16:0 and PAF) was 0.935, the sensitivity was 0.962 and the specificity was 0.825. LysoPC 16:0 and PAF may show diagnostic potential for laryngeal carcinoma.
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Affiliation(s)
- Xiaotao Zhang
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, Zhengzhou, China.,Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, Zhengzhou, China
| | - Huan Chen
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, Zhengzhou, China
| | - Yong Liu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - An Wang
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Qingyuan Hu
- China National Tobacco Quality Supervision and Test Center, Zhengzhou High and New Technology Industries Development Zone, Zhengzhou, China.,Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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165
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Gao X, Liang M, Fang Y, Zhao F, Tian J, Zhang X, Qin X. Deciphering the Differential Effective and Toxic Responses of Bupleuri Radix following the Induction of Chronic Unpredictable Mild Stress and in Healthy Rats Based on Serum Metabolic Profiles. Front Pharmacol 2018; 8:995. [PMID: 29379441 PMCID: PMC5775221 DOI: 10.3389/fphar.2017.00995] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022] Open
Abstract
The petroleum ether fraction of Bupleuri Radix which is contained in the traditional Chinese medicine prescription of Xiaoyaosan (XYS) may have a therapeutic effect in depressed subjects based on the results of our previous study. It has been reported that Bupleuri Radix can cause liver toxicity following overdosing or long-term use. Therefore, this study aimed to decipher the differential effective and toxic responses of Bupleuri Radix in chronic unpredictable mild stress (CUMS) (with depression) and healthy rats based on serum metabolic profiles. Serum metabolic profiles were obtained using the UHPLC- Q Exactive Orbitrap-MS technique. Our results demonstrated that the petroleum ether fraction of Bupleuri Radix (PBR) produces an antidepressant effect through regulating glycometabolism, amino acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism, and fatty acid metabolism. It also induces more severe toxic reactions in the liver or kidney in healthy rats than in CUMS rats, which exhibited a comparatively mild drug-induced toxic reaction. The altered lysine degradation, sphingolipid metabolism, glycerophospholipid metabolism, fatty acid metabolism, and bile acid metabolism could be at least partly responsible for the PBR toxic responses in healthy rats. The differential effective and toxic response of PBR in CUMS rats and healthy rats provide a new standard for the more rational and safer application of clinical drugs in the future.
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Affiliation(s)
- Xiaoxia Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Meili Liang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, China
| | - Yuan Fang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Fang Zhao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Junsheng Tian
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Xiang Zhang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
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166
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Blum BC, Mousavi F, Emili A. Single-platform ‘multi-omic’ profiling: unified mass spectrometry and computational workflows for integrative proteomics–metabolomics analysis. Mol Omics 2018; 14:307-319. [DOI: 10.1039/c8mo00136g] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Advances in instrumentation and analysis tools are permitting evermore comprehensive interrogation of diverse biomolecules and allowing investigators to move from linear signaling cascades to network models, which more accurately reflect the molecular basis of biological systems and processes.
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Affiliation(s)
- Benjamin C. Blum
- Center for Network Systems Biology
- Boston University School of Medicine
- Boston
- USA
- Department of Biochemistry
| | - Fatemeh Mousavi
- Donnelly Centre
- Department of Molecular Genetics
- University of Toronto
- Toronto
- Canada
| | - Andrew Emili
- Center for Network Systems Biology
- Boston University School of Medicine
- Boston
- USA
- Department of Biochemistry
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167
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Deng J, Zhang G, Neubert TA. Metabolomic Analysis of Glioma Cells Using Nanoflow Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol 2018; 1741:125-134. [PMID: 29392696 DOI: 10.1007/978-1-4939-7659-1_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mass spectrometry (MS)-based techniques have been finding utility as sensitive, high throughput metabolite analysis tools for complex biological samples. We describe here a nanoflow liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) system we developed and applied to metabolic profiling of human cells. Metabolites are extracted from cells using methanol, and filtered through a C18 StageTip to remove large particles. Metabolite samples are separated by HPLC at a flow rate of 400-500 nl/min, then analyzed in both positive and negative ion modes in an LTQ-Orbitrap MS. Metabolite identification and differential analysis are performed using commercial or open source software. Protocols outlined in this chapter describe how nano-LC-MS can be applied to investigate metabolic profiling with limited biomass amount.
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Affiliation(s)
- Jingjing Deng
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA.
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168
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Cheng J, Lan W, Zheng G, Gao X. Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration. Methods Mol Biol 2018. [PMID: 29536449 DOI: 10.1007/978-1-4939-7717-8_16] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolomics aims to quantitatively measure small-molecule metabolites in biological samples, such as bodily fluids (e.g., urine, blood, and saliva), tissues, and breathe exhalation, which reflects metabolic responses of a living system to pathophysiological stimuli or genetic modification. In the past decade, metabolomics has made notable progresses in providing useful systematic insights into the underlying mechanisms and offering potential biomarkers of many diseases. Metabolomics is a complementary manner of genomics and transcriptomics, and bridges the gap between genotype and phenotype, which reflects the functional output of a biological system interplaying with environmental factors. Recently, the technology of metabolomics study has been developed quickly. This review will discuss the whole pipeline of metabolomics study, including experimental design, sample collection and preparation, sample detection and data analysis, as well as mechanism interpretation, which can help understand metabolic effects and metabolite function for living organism in system level.
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Affiliation(s)
- Jing Cheng
- Department of Medical Instrument, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Wenxian Lan
- State Key Laboratory of Bio-Organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Guangyong Zheng
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Xianfu Gao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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169
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Ren JL, Zhang AH, Kong L, Wang XJ. Advances in mass spectrometry-based metabolomics for investigation of metabolites. RSC Adv 2018; 8:22335-22350. [PMID: 35539746 PMCID: PMC9081429 DOI: 10.1039/c8ra01574k] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Abstract
Metabolomics is the systematic study of all the metabolites present within a biological system, which consists of a mass of molecules, having a variety of physical and chemical properties and existing over an extensive dynamic range in biological samples. Diverse analytical techniques are needed to achieve higher coverage of metabolites. The application of mass spectrometry (MS) in metabolomics has increased exponentially since the discovery and development of electrospray ionization and matrix-assisted laser desorption ionization techniques. Significant advances have also occurred in separation-based MS techniques (gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, capillary electrophoresis-mass spectrometry, and ion mobility-mass spectrometry), as well as separation-free MS techniques (direct infusion-mass spectrometry, matrix-assisted laser desorption ionization-mass spectrometry, mass spectrometry imaging, and direct analysis in real time mass spectrometry) in the past decades. This review presents a brief overview of the recent advanced MS techniques and their latest applications in metabolomics. The software/websites for MS result analyses are also reviewed. Metabolomics is the systematic study of all the metabolites present within a biological system, supply functional information and has received extensive attention in the field of life sciences.![]()
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Affiliation(s)
- Jun-Ling Ren
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Ai-Hua Zhang
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Ling Kong
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Xi-Jun Wang
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
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170
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Abstract
Metabolic profiling has advanced greatly in the past decade and evolved from the status of a research topic of a small number of highly specialized laboratories to the status of a major field applied by several hundreds of laboratories, numerous national centers, and core facilities. The present chapter provides our view on the status of the remaining challenges and a perspective of this fascinating research area.
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Affiliation(s)
- Helen G Gika
- School of Medicine, Aristotle University, Thessaloniki, Greece.
| | | | - Ian D Wilson
- Department of Surgery and Cancer, Imperial College London, London, UK
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171
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Abstract
This chapter describes a protocol for the analysis of the metabolomic fingerprint of wine by liquid chromatography-mass spectrometry. The straightforward, optimized sample preparation procedure is limited to a single-step dilution with water or acetonitrile. The separation of wine analytes is carried out by two columns with orthogonal selectivity, including both reversed-phase (C18) and hydrophilic interaction (HILIC) chromatography, while the detection is assured by a high-resolution quadrupole time-of-flight mass spectrometer operating in negative and positive electrospray ionization mode, in order to obtain four different chromatograms for each sample. This validated protocol, or parts of it, could be applied in several oenological topic experimental designs, including wine quality and wine authenticity.
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Affiliation(s)
- Panagiotis Arapitsas
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- Center Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy
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172
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Supercritical fluid chromatography: a promising alternative to current bioanalytical techniques. Bioanalysis 2017; 10:107-124. [PMID: 29236519 DOI: 10.4155/bio-2017-0211] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
During the last years, chemistry was involved in the worldwide effort toward environmental problems leading to the birth of green chemistry. In this context, green analytical tools were developed as modern Supercritical Fluid Chromatography in the field of separative techniques. This chromatographic technique knew resurgence a few years ago, thanks to its high efficiency, fastness and robustness of new generation equipment. These advantages and its easy hyphenation to MS fulfill the requirements of bioanalysis regarding separation capacity and high throughput. In the present paper, the technical aspects focused on bioanalysis specifications will be detailed followed by a critical review of bioanalytical supercritical fluid chromatography methods published in the literature.
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173
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Microscale differential ion mobility spectrometry for field deployable chemical analysis. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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174
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Microdosing, isotopic labeling, radiotracers and metabolomics: relevance in drug discovery, development and safety. Bioanalysis 2017; 9:1913-1933. [PMID: 29171759 DOI: 10.4155/bio-2017-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This review discusses the use of stable (13C, 2D) or radioactive isotopes (14C, 11C, 18F, 131I, 64Cu, 68Ga) incorporated into the molecular structure of new drug entities for the purpose of pharmacokinetic or -dynamic studies. Metabolite in safety testing requires the administration of pharmacologically active doses. In such studies, radiotracers find application mainly in preclinical animal investigations, whereby LC-MS/MS is used to identify metabolite structure and drug-related effects. In contrast, first-in-human metabolite studies have to be carried out at nonpharmacological doses not exceeding 100 μg (microdose), which is generally too low for metabolite detection by LC-MS/MS. This short-coming can be overcome by specific radio- or isotopic labeling of the drug of interest and measurements using accelerator mass spectroscopy, single-photon emission computed tomography and positron emission tomography. Such combined radioisotope-based approaches permit Phase 0, first-in-human metabolite study.
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175
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Sidwick KL, Johnson AE, Adam CD, Pereira L, Thompson DF. Use of Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry and Metabonomic Profiling To Differentiate between Normally Slaughtered and Dead on Arrival Poultry Meat. Anal Chem 2017; 89:12131-12136. [DOI: 10.1021/acs.analchem.7b02749] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kate L. Sidwick
- School
of Chemical and Physical Sciences, Keele University, Keele,
Staffordshire, United Kingdom ST5 5BG
| | - Amy E. Johnson
- School
of Chemical and Physical Sciences, Keele University, Keele,
Staffordshire, United Kingdom ST5 5BG
| | - Craig D. Adam
- School
of Chemical and Physical Sciences, Keele University, Keele,
Staffordshire, United Kingdom ST5 5BG
| | - Luisa Pereira
- Thermo Fisher Scientific, Manor Park, Tudor Road, Runcorn, United Kingdom WA7 1TA
| | - David F. Thompson
- School
of Chemical and Physical Sciences, Keele University, Keele,
Staffordshire, United Kingdom ST5 5BG
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176
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Enhanced MS/MS coverage for metabolite identification in LC-MS-based untargeted metabolomics by target-directed data dependent acquisition with time-staggered precursor ion list. Anal Chim Acta 2017; 992:67-75. [DOI: 10.1016/j.aca.2017.08.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 11/20/2022]
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177
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Moosmang S, Pitscheider M, Sturm S, Seger C, Tilg H, Halabalaki M, Stuppner H. Metabolomic analysis-Addressing NMR and LC-MS related problems in human feces sample preparation. Clin Chim Acta 2017; 489:169-176. [PMID: 29097223 DOI: 10.1016/j.cca.2017.10.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/12/2017] [Accepted: 10/29/2017] [Indexed: 02/06/2023]
Abstract
Metabolomics is a well-established field in fundamental clinical research with applications in different human body fluids. However, metabolomic investigations in feces are currently an emerging field. Fecal sample preparation is a demanding task due to high complexity and heterogeneity of the matrix. To gain access to the information enclosed in human feces it is necessary to extract the metabolites and make them accessible to analytical platforms like NMR or LC-MS. In this study different pre-analytical parameters and factors were investigated i.e. water content, different extraction solvents, influence of freeze-drying and homogenization, ratios of sample weight to extraction solvent, and their respective impact on metabolite profiles acquired by NMR and LC-MS. The results indicate that profiles are strongly biased by selection of extraction solvent or drying of samples, which causes different metabolites to be lost, under- or overstated. Additionally signal intensity and reproducibility of the measurement were found to be strongly dependent on sample pre-treatment steps: freeze-drying and homogenization lead to improved release of metabolites and thus increased signals, but at the same time induced variations and thus deteriorated reproducibility. We established the first protocol for extraction of human fecal samples and subsequent measurement with both complementary techniques NMR and LC-MS.
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Affiliation(s)
- Simon Moosmang
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Maria Pitscheider
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Sonja Sturm
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Christoph Seger
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; Labormedizinisches Zentrum Dr Risch Ostschweiz AG, Lagerstrasse 30, 9470 Buchs, Switzerland.
| | - Herbert Tilg
- Department of Internal Medicine 1, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria.
| | - Maria Halabalaki
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece.
| | - Hermann Stuppner
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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178
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Roullier-Gall C, Heinzmann SS, Garcia JP, Schmitt-Kopplin P, Gougeon RD. Chemical messages from an ancient buried bottle: metabolomics for wine archeochemistry. NPJ Sci Food 2017; 1:1. [PMID: 31304243 PMCID: PMC6548415 DOI: 10.1038/s41538-017-0001-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 03/07/2017] [Accepted: 03/24/2017] [Indexed: 11/09/2022] Open
Abstract
Restoration works in the old Clunisian Saint-Vivant monastery in Burgundy revealed an unidentified wine bottle (SV1) dating between 1772 and 1860. Chemical evidence for SV1 origin and nature are presented here using non-targeted Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Nuclear Magnetic Resonance analyses. The SV1 chemical diversity was compared to red wines (Pinot Noir) from the Romanée Saint Vivant appellation and from six different vintages spanning from 1915 to 2009. The close metabolomic signature between SV1 and Romanée Saint Vivant wines spoke in favor of a filiation between these wines, in particular considering the Pinot noir grape variety. A further statistical comparison with up to 77 Pinot noir wines from Burgundy and vintages from nearly all the 20th century, confirmed that SV1 must have been made more than one hundred years ago. The increasing number of detected high masses and of nitrogen containing compounds with the ageing of the wine was in accordance with known ageing mechanisms. Besides, resveratrol was shown here to be preserved for more than one hundred years in wine. For the first time, the age of an old unknown wine along with its grape variety have been assessed through non-targeted metabolomic analyses. For the first time, non-targeted metabolomics analyses were employed to assess the age of an unlabeled old wine together with its grape variety. Roullier-Gall at the Technische Universitat Munchen and coworkers from both Germany and France identified the metabolomics of unknown wine SV1 using high resolution FT-ICR Mass Spectrometry in combination with NMR. By comparing the metabolic signature of SV1 with the reference wines, it was found the SV1 wine was more than 100 years old and its grape variety was close to the Pinot Noir from the Romanée Saint Vivant appellation. Moreover, this was the first time that resveratrol was observed in wines of more than one hundred years. This archeochemical method can serve as an alternative approach to the commonly used genetic-based techniques on the wine authentication.
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Affiliation(s)
- Chloé Roullier-Gall
- 1Technische Universitat Munchen, Chair of Analytical Food Chemistry, Alte Akademie 10, 85354 Freising-Weihenstephan, Germany.,2German Research Center for Environmental Health, Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstadter Landstrasse. 1, 85764 Neuherberg, Germany
| | - Silke S Heinzmann
- 2German Research Center for Environmental Health, Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstadter Landstrasse. 1, 85764 Neuherberg, Germany
| | - Jean-Pierre Garcia
- 3UMR 6298 ARTEHIS, Université de Bourgogne/CNRS/culture, Université de Bourgogne, 6 bd Gabriel, 21000 Dijon, France
| | - Philippe Schmitt-Kopplin
- 1Technische Universitat Munchen, Chair of Analytical Food Chemistry, Alte Akademie 10, 85354 Freising-Weihenstephan, Germany.,2German Research Center for Environmental Health, Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstadter Landstrasse. 1, 85764 Neuherberg, Germany
| | - Régis D Gougeon
- UMR A 02.102 PAM Université de Bourgogne/Agrosup Dijon, Equipe PCAV, Institut Universitaire de la Vigne et du Vin, Jules Guyot, Rue Claude Ladrey, BP 27877 Dijon Cedex, France
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179
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Discovery of Antimalarial Drugs from Streptomycetes Metabolites Using a Metabolomic Approach. J Trop Med 2017; 2017:2189814. [PMID: 29123551 PMCID: PMC5662797 DOI: 10.1155/2017/2189814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/30/2017] [Indexed: 12/05/2022] Open
Abstract
Natural products continue to play an important role as a source of biologically active substances for the development of new drug. Streptomyces, Gram-positive bacteria which are widely distributed in nature, are one of the most popular sources of natural antibiotics. Recently, by using a bioassay-guided fractionation, an antimalarial compound, Gancidin-W, has been discovered from these bacteria. However, this classical method in identifying potentially novel bioactive compounds from the natural products requires considerable effort and is a time-consuming process. Metabolomics is an emerging “omics” technology in systems biology study which integrated in process of discovering drug from natural products. Metabolomics approach in finding novel therapeutics agent for malaria offers dereplication step in screening phase to shorten the process. The highly sensitive instruments, such as Liquid Chromatography-Mass Spectrophotometry (LC-MS), Gas Chromatography-Mass Spectrophotometry (GC-MS), and Nuclear Magnetic Resonance (1H-NMR) spectroscopy, provide a wide range of information in the identification of potentially bioactive compounds. The current paper reviews concepts of metabolomics and its application in drug discovery of malaria treatment as well as assessing the antimalarial activity from natural products. Metabolomics approach in malaria drug discovery is still new and needs to be initiated, especially for drug research in Malaysia.
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180
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Analysis and identification of chemical constituents of fenugreek by UPLC-IT-MS
n
and UPLC-Q-TOF-MS. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-7136-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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181
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La Barbera G, Capriotti AL, Cavaliere C, Montone CM, Piovesana S, Samperi R, Zenezini Chiozzi R, Laganà A. Liquid chromatography-high resolution mass spectrometry for the analysis of phytochemicals in vegetal-derived food and beverages. Food Res Int 2017; 100:28-52. [PMID: 28873689 DOI: 10.1016/j.foodres.2017.07.080] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 01/04/2023]
Abstract
The recent years witnessed a change in the perception of nutrition. Diet does not only provide nutrients to meet the metabolic requirements of the body, but it also constitutes an active way for the consumption of compounds beneficial for human health. Fruit and vegetables are an excellent source of such compounds, thus the growing interest in characterizing phytochemical sources, structures and activities. Given the interest for phytochemicals in food, the development of advanced and suitable analytical techniques for their identification is fundamental for the advancement of food research. In this review, the state of the art of phytochemical research in food plants is described, starting from sample preparation, throughout extract clean-up and compound separation techniques, to the final analysis, considering both qualitative and quantitative investigations. In this regard, from an analytical point of view, fruit and vegetable extracts are complex matrices, which greatly benefit from the use of modern hyphenated techniques, in particular from the combination of high performance liquid chromatography separation and high resolution mass spectrometry, powerful tools which are being increasingly used in the recent years. Therefore, selected applications to real samples are presented and discussed, in particular for the analysis of phenols, polyphenols and phenolic acids. Finally, some hot points are discussed, such as waste characterization for high value-compounds recovery and the untargeted metabolomics approach.
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Affiliation(s)
- Giorgia La Barbera
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Anna Laura Capriotti
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Chiara Cavaliere
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmela Maria Montone
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Susy Piovesana
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Roberto Samperi
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | | | - Aldo Laganà
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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182
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Cross-platform metabolomics investigating the intracellular metabolic alterations of HaCaT cells exposed to phenanthrene. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1060:15-21. [DOI: 10.1016/j.jchromb.2017.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/24/2017] [Accepted: 05/22/2017] [Indexed: 12/25/2022]
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183
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Abstract
Metabolomics is the newest addition to the "omics" disciplines and has shown rapid growth in its application to human health research because of fundamental advancements in measurement and analysis techniques. Metabolomics has unique and proven advantages in systems biology and biomarker discovery. The next generation of analysis techniques promises even richer and more complete analysis capabilities that will enable earlier clinical diagnosis, drug refinement, and personalized medicine. A review of current advancements in methodologies and statistical analysis that are enhancing and improving the performance of metabolomics is presented along with highlights of some recent successful applications.
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Affiliation(s)
- Eli Riekeberg
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
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184
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Hrbek V, Krtkova V, Rubert J, Chmelarova H, Demnerova K, Ovesna J, Hajslova J. Metabolomic Strategies Based on High-Resolution Mass Spectrometry as a Tool for Recognition of GMO (MON 89788 Variety) and Non-GMO Soybean: a Critical Assessment of Two Complementary Methods. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0929-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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185
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Suzuki M, Nishiumi S, Kobayashi T, Sakai A, Iwata Y, Uchikata T, Izumi Y, Azuma T, Bamba T, Yoshida M. Use of on-line supercritical fluid extraction-supercritical fluid chromatography/tandem mass spectrometry to analyze disease biomarkers in dried serum spots compared with serum analysis using liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:886-894. [PMID: 28332299 DOI: 10.1002/rcm.7857] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/14/2017] [Accepted: 03/19/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE The analytical stability and throughput of biomarker assays based on dried serum spots (DSS) are strongly dependent on the extraction process and determination method. In the present study, an on-line system based on supercritical fluid extraction-supercritical fluid chromatography coupled with tandem mass spectrometry (SFE-SFC/MS/MS) was established for analyzing the levels of disease biomarkers in DSS. METHODS The chromatographic conditions were investigated using the ODS-EP, diol, and SIL-100A columns. Then, we optimized the SFE-SFC/MS/MS method using the diol column, focusing on candidate biomarkers of oral, colorectal, and pancreatic cancer that were identified using liquid chromatography (LC)/MS/MS. RESULTS By using this system, four hydrophilic metabolites and 17 hydrophobic metabolites were simultaneously detected within 15 min. In an experiment involving clinical samples, PC 16:0-18:2/16:1-18:1 exhibited 93.8% sensitivity and 64.3% specificity, whereas PC 17:1-18:1/17:0-18:2 showed 81.3% sensitivity and 92.9% specificity for detecting oral cancer. In addition, assessments of the creatine levels demonstrated 92.3% sensitivity and 78.6% specificity for detecting colorectal cancer. CONCLUSIONS The results of this study indicate that our method has great potential for clinical diagnosis and would be suitable for large-scale screening. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Makoto Suzuki
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Takashi Kobayashi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Arata Sakai
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Yosuke Iwata
- Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Takato Uchikata
- Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Yoshihiro Izumi
- Medical Institute of Bioregulation, Kyusyu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Azuma
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Takeshi Bamba
- Medical Institute of Bioregulation, Kyusyu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
- Division of Metabolomics Research, Department of Internal Related, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
- AMED-CREST, AMED, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
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186
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Zhao S, Dawe M, Guo K, Li L. Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Carbonyl Submetabolome. Anal Chem 2017; 89:6758-6765. [PMID: 28505421 DOI: 10.1021/acs.analchem.7b01098] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential 12C- and 13C-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with 12C-labeling and spiked with a 13C-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 12C-/13C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl metabolites with each containing MS, retention time (RT), and MS/MS information. This library and an online search program for labeled carbonyl metabolite identification based on MS, RT, and MS/MS matches have been implemented in a freely available Website, www.mycompoundid.org . Using this library, out of the 1737 peak pairs detected in urine, 33 metabolites were positively identified. In addition, 1333 peak pairs could be matched to the metabolome databases with most of them belonging to the carbonyl metabolites. These results show that 12C-/13C-DnsHz labeling LC-MS is a useful tool for profiling the carbonyl submetabolome of complex samples with high coverage.
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Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Margot Dawe
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Kevin Guo
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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187
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Catalán Ú, Barrubés L, Valls RM, Solà R, Rubió L. In vitro Metabolomic Approaches to Investigating the Potential Biological Effects of Phenolic Compounds: An Update. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:236-245. [PMID: 28549934 PMCID: PMC5582796 DOI: 10.1016/j.gpb.2016.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 12/15/2016] [Accepted: 12/22/2016] [Indexed: 12/29/2022]
Abstract
Dietary phenolic compounds (PCs) have been receiving interest for their presumed roles in disease prevention. However, there is a lack of studies on the underlying molecular mechanisms. In this regard, in vitrometabolomic approaches are suitable for the investigation of the molecular changes in response to PC exposure. Up to date, the biological effects of PCs have only been examined for PCs from rosemary (Rosmarinus officinalis), olive oil, and resveratrol using cell-based metabolomic approach, although transcriptomic and/or proteomic studies have also been conducted in the same in vitro cell experiment in some cases. Our integral analysis of the reviewed studies suggest that PCs may be involved not only in basic cellular processes or macro- and micro-nutrient metabolism, but also in specific metabolic pathways that have been thoroughly investigated. These modulated pathways could have a clinical impact on neurodegenerative diseases, type 2 diabetes, cancer, and cardiovascular diseases. In conclusion, the in vitro metabolomic approaches provide additional information of the molecular mechanisms involved in disease risk reduction of dietary PCs. In order to elucidate the mechanisms of action of PCs, more metabolomic cell-based studies are needed and testing the physiological conjugated forms of PCs in these cell systems could be of special interest.
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Affiliation(s)
- Úrsula Catalán
- Functional Nutrition, Oxidation and Cardiovascular Diseases Group (NFOC-Salut), Technological Center of Nutrition and Health (CTNS), Institut d'Investigació Sanitària Pere Virgili (IISPV), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus 43201, Spain
| | - Laura Barrubés
- Functional Nutrition, Oxidation and Cardiovascular Diseases Group (NFOC-Salut), Technological Center of Nutrition and Health (CTNS), Institut d'Investigació Sanitària Pere Virgili (IISPV), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus 43201, Spain
| | - Rosa Maria Valls
- Functional Nutrition, Oxidation and Cardiovascular Diseases Group (NFOC-Salut), Technological Center of Nutrition and Health (CTNS), Institut d'Investigació Sanitària Pere Virgili (IISPV), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus 43201, Spain
| | - Rosa Solà
- Functional Nutrition, Oxidation and Cardiovascular Diseases Group (NFOC-Salut), Technological Center of Nutrition and Health (CTNS), Institut d'Investigació Sanitària Pere Virgili (IISPV), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus 43201, Spain.
| | - Laura Rubió
- Functional Nutrition, Oxidation and Cardiovascular Diseases Group (NFOC-Salut), Technological Center of Nutrition and Health (CTNS), Institut d'Investigació Sanitària Pere Virgili (IISPV), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus 43201, Spain; Food Technology Department, Universitat de Lleida-AGROTECNIO Center, Lleida 25198, Spain
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188
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LC-Mass Spectrometry for Metabolomics. Methods Mol Biol 2017. [PMID: 28502010 DOI: 10.1007/978-1-4939-6990-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The field of metabolomics is greatly being refined by the addition of new technologies. LC-MS has allowed researchers to explore additional metabolites which were not originally captured through GC-MS. Through the customizability of the LC columns and mass spectrometer, it is now easier to tailor the instrument to your research needs. Herein, we describe a protocol for sample preparation and data acquisition for a global metabolomic analysis of tissues or feces.
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189
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Lee S, Jang WJ, Choi B, Joo SH, Jeong CH. Comparative metabolomic analysis of HPAC cells following the acquisition of erlotinib resistance. Oncol Lett 2017; 13:3437-3444. [PMID: 28529573 PMCID: PMC5431587 DOI: 10.3892/ol.2017.5940] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/17/2017] [Indexed: 12/30/2022] Open
Abstract
Pancreatic cancer is one of the most lethal types of cancer, due to difficulty in early detection and the limited efficacy of available treatments. Erlotinib is used to inhibit the epidermal growth factor receptor for the treatment of pancreatic cancer; however, erlotinib resistance is a major issue and the mechanisms underlying the development of erlotinib resistance remain unclear. To better understand the alterations in tumor metabolism by acquired resistance to erlotinib, an erlotinib-resistant pancreatic cancer cell line (HPAC-ER) was established, followed by a comparison of the metabolic characteristics between these cells and their erlotinib-sensitive parental cells (HPAC). This comparison was accomplished through mass spectrometry-based targeted metabolic profiling. Five metabolite groups (acylcarnitines, amino acids and biogenic amines, glycerophospholipids, sphingolipids and monosaccharides) were semi-quantified and compared statistically. These results revealed significant differences between the two groups of cells. A significant increase in the level of short-chain acylcarnitines and selected lysophosphatidylcholines, and a significant decrease in the level of acyl-alkyl-phosphatidylcholines and one sphingolipid, were observed in the HPAC-ER cells compared with the HPAC cells. The metabolic changes observed in the present study support the theory that there are increased metabolic demands in erlotinib-resistant cancer, reflecting the changes in acetyl-CoA-associated and choline phospholipid metabolism. These findings will aid in elucidating the changes that occur in pancreatic cancer metabolism through the acquired resistance to erlotinib, and in the identification of biomarkers for the early detection of pancreatic cancer.
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Affiliation(s)
- Sooyeun Lee
- College of Pharmacy, Keimyung University, Dalseo, Daegu 42601, Republic of Korea
| | - Won-Jun Jang
- College of Pharmacy, Keimyung University, Dalseo, Daegu 42601, Republic of Korea
| | - Boyeon Choi
- College of Pharmacy, Keimyung University, Dalseo, Daegu 42601, Republic of Korea
| | - Sang Hoon Joo
- Department of Pharmacy, Catholic University of Daegu, Gyeongsan-si, Gyeongbuk 38430, Republic of Korea
| | - Chul-Ho Jeong
- College of Pharmacy, Keimyung University, Dalseo, Daegu 42601, Republic of Korea
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190
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Khamis MM, Adamko DJ, El-Aneed A. Mass spectrometric based approaches in urine metabolomics and biomarker discovery. MASS SPECTROMETRY REVIEWS 2017; 36:115-134. [PMID: 25881008 DOI: 10.1002/mas.21455] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 05/25/2023]
Abstract
Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.
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Affiliation(s)
- Mona M Khamis
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
- Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Darryl J Adamko
- Department of Pediatrics, College of Medicine, University of Saskatchewan, 103 Hospital Drive, Saskatoon, SK, Canada
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
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191
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Breitkopf SB, Ricoult SJH, Yuan M, Xu Y, Peake DA, Manning BD, Asara JM. A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source. Metabolomics 2017; 13:30. [PMID: 28496395 PMCID: PMC5421409 DOI: 10.1007/s11306-016-1157-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/21/2016] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Advances in high-resolution mass spectrometry have created renewed interest for studying global lipid biochemistry in disease and biological systems. OBJECTIVES Here, we present an untargeted 30 min. LC-MS/MS platform that utilizes positive/negative polarity switching to perform unbiased data dependent acquisitions (DDA) via higher energy collisional dissociation (HCD) fragmentation to profile more than 1000-1500 lipid ions mainly from methyl-tert-butyl ether (MTBE) or chloroform:methanol extractions. METHODS The platform uses C18 reversed-phase chromatography coupled to a hybrid QExactive Plus/HF Orbitrap mass spectrometer and the entire procedure takes ~10 h from lipid extraction to identification/quantification for a data set containing 12 samples (~4 h for a single sample). Lipids are identified by both accurate precursor ion mass and fragmentation features and quantified using Lipid-Search and Elements software. RESULTS Using this approach, we are able to profile intact lipid ions from up to 18 different main lipid classes and 66 subclasses. We show several studies from different biological sources, including cultured cancer cells, resected tissues from mice such as lung and breast tumors and biological fluids such as plasma and urine. CONCLUSIONS Using mouse embryonic fibroblasts, we showed that TSC2-/- KD significantly abrogates lipid biosynthesis and that rapamycin can rescue triglyceride (TG) lipids and we show that SREBP-/- shuts down lipid biosynthesis significantly via mTORC1 signaling pathways. We show that in mouse EGFR driven lung tumors, a large number of TGs and phosphatidylmethanol (PMe) lipids are elevated while some phospholipids (PLs) show some of the largest decrease in lipid levels from ~ 2000 identified lipid ions. In addition, we identified more than 1500 unique lipid species from human blood plasma.
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Affiliation(s)
- Susanne B Breitkopf
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Stéphane J H Ricoult
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Min Yuan
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ying Xu
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - David A Peake
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA 95134, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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192
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Engskog MKR, Ersson L, Haglöf J, Arvidsson T, Pettersson C, Brittebo E. β-N-Methylamino-L-alanine (BMAA) perturbs alanine, aspartate and glutamate metabolism pathways in human neuroblastoma cells as determined by metabolic profiling. Amino Acids 2017; 49:905-919. [PMID: 28161796 PMCID: PMC5383692 DOI: 10.1007/s00726-017-2391-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/28/2017] [Indexed: 12/15/2022]
Abstract
β-Methylamino-L-alanine (BMAA) is a non-proteinogenic amino acid that induces long-term cognitive deficits, as well as an increased neurodegeneration and intracellular fibril formation in the hippocampus of adult rodents following short-time neonatal exposure and in vervet monkey brain following long-term exposure. It has also been proposed to be involved in the etiology of neurodegenerative disease in humans. The aim of this study was to identify metabolic effects not related to excitotoxicity or oxidative stress in human neuroblastoma SH-SY5Y cells. The effects of BMAA (50, 250, 1000 µM) for 24 h on cells differentiated with retinoic acid were studied. Samples were analyzed using LC-MS and NMR spectroscopy to detect altered intracellular polar metabolites. The analysis performed, followed by multivariate pattern recognition techniques, revealed significant perturbations in protein biosynthesis, amino acid metabolism pathways and citrate cycle. Of specific interest were the BMAA-induced alterations in alanine, aspartate and glutamate metabolism and as well as alterations in various neurotransmitters/neuromodulators such as GABA and taurine. The results indicate that BMAA can interfere with metabolic pathways involved in neurotransmission in human neuroblastoma cells.
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Affiliation(s)
- Mikael K R Engskog
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden.
| | - Lisa Ersson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 23, Uppsala, Sweden
| | - Jakob Haglöf
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden
| | - Torbjörn Arvidsson
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden.,Medical Product Agency, Box 26, Dag Hammarskjölds väg 42, 751 03, Uppsala, Sweden
| | - Curt Pettersson
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden
| | - Eva Brittebo
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 23, Uppsala, Sweden
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193
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Influence of chromatogram baseline shifts and exogenous metabolite signals on metabolic profiles of traditional Chinese medicine Chaihu and its liver toxicity metabonomics. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6302-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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194
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Metabolomics: Definitions and Significance in Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:3-17. [DOI: 10.1007/978-3-319-47656-8_1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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195
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Collection and Preparation of Clinical Samples for Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:19-44. [DOI: 10.1007/978-3-319-47656-8_2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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196
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Jin S, Song C, Jia S, Li S, Zhang Y, Chen C, Feng Y, Xu Y, Xiong C, Xiang Y, Jiang H. An integrated strategy for establishment of curcuminoid profile in turmeric using two LC–MS/MS platforms. J Pharm Biomed Anal 2017; 132:93-102. [DOI: 10.1016/j.jpba.2016.09.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/11/2016] [Accepted: 09/25/2016] [Indexed: 10/20/2022]
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197
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Mohyuddin A, Hussain D, Najam-ul-Haq M. Polydopamine assisted functionalization of boronic acid on magnetic nanoparticles for the selective extraction of ribosylated metabolites from urine. RSC Adv 2017. [DOI: 10.1039/c6ra28369a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A novel strategy for the rapid and selective extraction of ribosylated metabolites by dopamine assisted functionalization of boronic acid on magnetic (Fe3O4@PDA-FPBA) nanoparticles has been demonstrated under optimized conditions.
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Affiliation(s)
- Abrar Mohyuddin
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Dilshad Hussain
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
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198
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Begou O, Gika HG, Wilson ID, Theodoridis G. Hyphenated MS-based targeted approaches in metabolomics. Analyst 2017; 142:3079-3100. [DOI: 10.1039/c7an00812k] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Review of targeted metabolomics, with a focus on the description of analytical methods.
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Affiliation(s)
- O. Begou
- Department of Chemistry
- Aristotle University
- 54124 Thessaloniki
- Greece
| | - H. G. Gika
- Department of Medicine
- Aristotle University
- 54124 Thessaloniki
- Greece
| | - I. D. Wilson
- Division of Computational and Systems Medicine
- Department of Surgery and Cancer
- Imperial College
- London
- UK
| | - G. Theodoridis
- Department of Chemistry
- Aristotle University
- 54124 Thessaloniki
- Greece
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199
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Chen W, Liu Y, Wei M, Shi L, Wu Y, Liu Z, Liu S, Song F, Liu Z. Studies on effect of Ginkgo biloba L. leaves in acute gout with hyperuricemia model rats by using UPLC-ESI-Q-TOF/MS metabolomic approach. RSC Adv 2017. [DOI: 10.1039/c7ra08519b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The therapeutic effects of GBE on acute gout with hyperuricemia rats were investigated by using a metabolomic approach.
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Affiliation(s)
- WeiJia Chen
- School of Pharmaceutical Sciences
- Jilin University
- Changchun 130021
- China
| | - Yuanyuan Liu
- School of Pharmaceutical Sciences
- Jilin University
- Changchun 130021
- China
| | - Mengying Wei
- School of Pharmaceutical Sciences
- Jilin University
- Changchun 130021
- China
| | - Liqiang Shi
- School of Pharmaceutical Sciences
- Jilin University
- Changchun 130021
- China
| | - Yi Wu
- School of Pharmaceutical Sciences
- Jilin University
- Changchun 130021
- China
| | - ZhongYing Liu
- School of Pharmaceutical Sciences
- Jilin University
- Changchun 130021
- China
| | - Shu Liu
- National Center of Mass Spectrometry in Changchun
- Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry
- Chemical Biology Laboratory
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
| | - FengRui Song
- National Center of Mass Spectrometry in Changchun
- Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry
- Chemical Biology Laboratory
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
| | - ZhiQiang Liu
- National Center of Mass Spectrometry in Changchun
- Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry
- Chemical Biology Laboratory
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
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200
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Zhang X, Romm M, Zheng X, Zink EM, Kim YM, Burnum-Johnson KE, Orton DJ, Apffel A, Ibrahim YM, Monroe ME, Moore RJ, Smith JN, Ma J, Renslow RS, Thomas DG, Blackwell AE, Swinford G, Sausen J, Kurulugama RT, Eno N, Darland E, Stafford G, Fjeldsted J, Metz TO, Teeguarden JG, Smith RD, Baker ES. SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. CLINICAL MASS SPECTROMETRY 2016; 2:1-10. [PMID: 29276770 PMCID: PMC5739065 DOI: 10.1016/j.clinms.2016.11.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.
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Affiliation(s)
- Xing Zhang
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michelle Romm
- Agilent Technologies, Santa Clara, CA, United States
| | - Xueyun Zheng
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Daniel J Orton
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Alex Apffel
- Agilent Technologies, Santa Clara, CA, United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Matthew E Monroe
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J Moore
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jordan N Smith
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian Ma
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ryan S Renslow
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dennis G Thomas
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | | | | | - John Sausen
- Agilent Technologies, Santa Clara, CA, United States
| | | | - Nathan Eno
- Agilent Technologies, Santa Clara, CA, United States
| | - Ed Darland
- Agilent Technologies, Santa Clara, CA, United States
| | | | | | - Thomas O Metz
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Justin G Teeguarden
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Richard D Smith
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erin S Baker
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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