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Dos Santos EKP, Canuto GAB. Optimizing XCMS parameters for GC-MS metabolomics data processing: a case study. Metabolomics 2023; 19:26. [PMID: 36976375 DOI: 10.1007/s11306-023-01992-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/05/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND AND AIMS Optimizing metabolomics data processing parameters is a challenging and fundamental task to obtain reliable results. Automated tools have been developed to assist this optimization for LC-MS data. GC-MS data require substantial modifications in processing parameters, as the chromatographic profiles are more robust, with more symmetrical and Gaussian peaks. This work compared an automated XCMS parameter optimization using the Isotopologue Parameter Optimization (IPO) software with manual optimization of GC-MS metabolomics data. Additionally, the results were compared to online XCMS platform. METHODS GC-MS data from control and test groups of intracellular metabolites from Trypanosoma cruzi trypomastigotes were used. Optimizations were performed on the quality control (QC) samples. RESULTS The results in terms of the number of molecular features extracted, repeatability, missing values, and the search for significant metabolites showed the importance of optimizing the parameters for peak detection, alignment, and grouping, especially those related to peak width (fwhm, bw) and noise ratio (snthresh). CONCLUSION This is the first time that a systematic optimization using IPO has been performed on GC-MS data. The results demonstrate that there is no universal approach for optimization but automated tools are valuable at this stage of the metabolomics workflow. The online XCMS proves to be an interesting processing tool, helping, above all, in the choice of parameters as a starting point for adjustments and optimizations. Although the tools are easy to use, there is still a need for technical knowledge about the analytical methods and instruments used.
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Furlani IL, da Cruz Nunes E, Canuto GAB, Macedo AN, Oliveira RV. Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:179-213. [PMID: 34628633 DOI: 10.1007/978-3-030-77252-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Metabolomics is a discipline that offers a comprehensive analysis of metabolites in biological samples. In the last decades, the notable evolution in liquid chromatography and mass spectrometry technologies has driven an exponential progress in LC-MS-based metabolomics. Targeted and untargeted metabolomics strategies are important tools in health and medical science, especially in the study of disease-related biomarkers, drug discovery and development, toxicology, diet, physical exercise, and precision medicine. Clinical and biological problems can now be understood in terms of metabolic phenotyping. This overview highlights the current approaches to LC-MS-based metabolomics analysis and its applications in the clinical research.
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Affiliation(s)
- Izadora L Furlani
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Estéfane da Cruz Nunes
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Adriana N Macedo
- Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Regina V Oliveira
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil.
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Analytical Platforms for Mass Spectrometry-Based Metabolomics of Polar and Ionizable Metabolites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:215-242. [PMID: 34628634 DOI: 10.1007/978-3-030-77252-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Metabolomics studies rely on the availability of suitable analytical platforms to determine a vast collection of chemically diverse metabolites in complex biospecimens. Liquid chromatography-mass spectrometry operated under reversed-phase conditions is the most commonly used platform in metabolomics, which offers extensive coverage for nonpolar and moderately polar compounds. However, complementary techniques are required to obtain adequate separation of polar and ionic metabolites, which are involved in several fundamental metabolic pathways. This chapter focuses on the main mass-spectrometry-based analytical platforms used to determine polar and/or ionizable compounds in metabolomics (GC-MS, HILIC-MS, CE-MS, IPC-MS, and IC-MS). Rather than comprehensively describing recent applications related to GC-MS, HILIC-MS, and CE-MS, which have been covered in a regular basis in the literature, a brief discussion focused on basic principles, main strengths, limitations, as well as future trends is presented in this chapter, and only key applications with the purpose of illustrating important analytical aspects of each platform are highlighted. On the other hand, due to the relative novelty of IPC-MS and IC-MS in the metabolomics field, a thorough compilation of applications for these two techniques is presented here.
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Metabolic profiling by reversed-phase/ion-exchange mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1143:122072. [PMID: 32220802 DOI: 10.1016/j.jchromb.2020.122072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 01/22/2023]
Abstract
Metabolic profiling is commonly achieved by mass spectrometry (MS) following reversed-phase (RP) and hydrophilic interaction chromatography (HILIC) either performed independently, leading to overlapping datasets, or in a coupled configuration, requiring multiple liquid chromatography (LC) systems. To overcome these limitations, we developed a single, 20-minute chromatographic method using an in-line RP-ion-exchange (IEX) column arrangement and a single LC system. This configuration separates clinically significant polar and non-polar compounds without derivatization or ion-pairing reagents, allowing ionization in both polarities. An in-house library was created with 397 authentic standards, including acylcarnitines, amino acids, bile acids, nucleosides, organic acids, steroid hormones, and vitamins. Analysis of pooled plasma and urine samples revealed 5445 and 4111 ion features, leading to 88 and 82 confirmed metabolite identifications, respectively. Metabolites were detected at clinically relevant concentrations with good precision, and good chromatographic separation was demonstrated for clinically significant isomers including methylmalonic acid and succinic acid, as well as alloisoleucine and isoleucine/leucine. Evaluation of the samples by unsupervised principal component analysis showed excellent analytical quality.
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5
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Ritler D, Rufener R, Li JV, Kämpfer U, Müller J, Bühr C, Schürch S, Lundström-Stadelmann B. In vitro metabolomic footprint of the Echinococcus multilocularis metacestode. Sci Rep 2019; 9:19438. [PMID: 31857639 PMCID: PMC6923418 DOI: 10.1038/s41598-019-56073-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Alveolar echinococcosis (AE) is a zoonotic disease that is deadly if left untreated. AE is caused by the larval metacestode stage of the cestode Echinococcus multilocularis. Better knowledge on the host-parasite interface could yield novel targets for improvement of the treatment against AE. We analyzed culture media incubated with in vitro grown E. multilocularis metacestodes by 1H nuclear magnetic resonance spectroscopy to identify the unknown metabolic footprint of the parasite. Moreover, we quantitatively analyzed all amino acids, acetate, glucose, lactate, and succinate in time-course experiments using liquid chromatography and enzymatic assays. The E. multilocularis metacestodes consumed glucose and, surprisingly, threonine and produced succinate, acetate, and alanine as major fermentation products. The metabolic composition of vesicle fluid (VF) from in vitro grown E. multilocularis metacestodes was different from parasite-incubated culture medium with respect to the abundance, but not the spectrum, of metabolites, and some metabolites, in particular amino acids, accumulated in the VF. Overall, this study presents the first characterization of the in vitro metabolic footprint of E. multilocularis metacestodes and VF composition, and it provides the basis for analyses of potentially targetable pathways for future drug development.
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Affiliation(s)
- Dominic Ritler
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland
| | - Reto Rufener
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland
| | - Jia V Li
- Division of Systems and Digestive Medicine, Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Urs Kämpfer
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Joachim Müller
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland
| | - Claudia Bühr
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Stefan Schürch
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Britta Lundström-Stadelmann
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland.
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Sotillo J, Pearson MS, Loukas A. Trematode Genomics and Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1154:411-436. [PMID: 31297769 DOI: 10.1007/978-3-030-18616-6_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Trematode infections are among the most neglected tropical diseases despite their worldwide distribution and extraordinary ability to parasitise many different host species and host tissues. Furthermore, these parasites are of great socioeconomic, medical, veterinary and agricultural importance. During the last 10 years, there have been increasing efforts to overcome the lack of information on different "omic" resources such as proteomics and genomics. Herein, we focus on the recent advances in genomics and proteomics from trematodes of human importance, including liver, blood, intestinal and lung flukes. We also provide information on the latest technologies applied to study the biology of trematodes as well as on the resources available for the study of the molecular aspects of this group of helminths.
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Affiliation(s)
- Javier Sotillo
- Centre for Molecular Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.
| | - Mark S Pearson
- Centre for Molecular Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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Zhao J, Li L, Zhao Y, Zhao C, Chen X, Liu P, Zhou H, Zhang J, Hu C, Chen A, Liu G, Peng X, Lu X, Xu G. Metabolic changes in primary, secondary, and lipid metabolism in tobacco leaf in response to topping. Anal Bioanal Chem 2018; 410:839-851. [PMID: 28929184 DOI: 10.1007/s00216-017-0596-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/25/2017] [Accepted: 08/18/2017] [Indexed: 12/19/2022]
Abstract
As an important cultivation practice used for flue-cured tobacco, topping affects diverse biological processes in the later stages of development and growth. Some studies have focused on using tobacco genes to reflect the physiological changes caused by topping. However, the complex metabolic shifts in the leaf resulting from topping have not yet been investigated in detail. In this study, a comprehensive metabolic profile of primary, secondary, and lipid metabolism in flue-cured tobacco leaf was generated with use of a multiple platform consisting of gas chromatography-mass spectrometry, capillary electrophoresis-mass spectrometry, and liquid chromatography-mass spectrometry/ultraviolet spectroscopy. A total of 367 metabolites were identified and determined. Both principal component analysis and the number of significantly different metabolites indicated that topping had the greatest influence on the upper leaves. During the early stage of topping, great lipid level variations in the upper leaves were observed, and antioxidant defense metabolites were accumulated. This indicated that the topping activated lipid turnover and the antioxidant defense system. At the mature stage, lower levels of senescence-related metabolites and higher levels of secondary metabolites were found in the topped mature leaves. This implied that topping delayed leaf senescence and promoted secondary metabolite accumulation. This study provides a global view of the metabolic perturbation in response to topping. Graphical abstract Metabolic alterations in tobacco leaf in response to topping using a multiplatform metabolomics.
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Affiliation(s)
- Jieyu Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning, 116023, China
| | - Lili Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Yanni Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Xia Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, 450001, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, 450001, China
| | - Huina Zhou
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, 450001, China
| | - Junjie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Aiguo Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, 266101, China
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, 266101, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning, 116023, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, China.
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8
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Fenaille F, Barbier Saint-Hilaire P, Rousseau K, Junot C. Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand? J Chromatogr A 2017; 1526:1-12. [PMID: 29074071 DOI: 10.1016/j.chroma.2017.10.043] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/15/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
Abstract
Typical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools.
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Affiliation(s)
- François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Pierre Barbier Saint-Hilaire
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Kathleen Rousseau
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France.
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Rodrigues KT, Cieslarová Z, Tavares MFM, Simionato AVC. Strategies Involving Mass Spectrometry Combined with Capillary Electrophoresis in Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:99-141. [DOI: 10.1007/978-3-319-47656-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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10
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Yamamoto M, Ly R, Gill B, Zhu Y, Moran-Mirabal J, Britz-McKibbin P. Robust and High-Throughput Method for Anionic Metabolite Profiling: Preventing Polyimide Aminolysis and Capillary Breakages under Alkaline Conditions in Capillary Electrophoresis-Mass Spectrometry. Anal Chem 2016; 88:10710-10719. [DOI: 10.1021/acs.analchem.6b03269] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mai Yamamoto
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Ritchie Ly
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Biban Gill
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Yujie Zhu
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Jose Moran-Mirabal
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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11
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Vorkas PA, Shalhoub J, Lewis MR, Spagou K, Want EJ, Nicholson JK, Davies AH, Holmes E. Metabolic Phenotypes of Carotid Atherosclerotic Plaques Relate to Stroke Risk: An Exploratory Study. Eur J Vasc Endovasc Surg 2016; 52:5-10. [PMID: 27231199 DOI: 10.1016/j.ejvs.2016.01.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Stroke is a major cause of death and disability. That three-quarters of stroke patients will never have previously manifested cerebrovascular symptoms demonstrates the unmet clinical need for new biomarkers able to stratify patient risk and elucidation of the biological dysregulations. In this study, the utility of comprehensive metabolic phenotyping is assessed to provide candidate biomarkers that relate to stroke risk in stenosing carotid plaque tissue samples. METHOD Carotid plaque tissue samples were obtained from patients with cerebrovascular symptoms of carotid origin (n = 5), and from asymptomatic patients (n = 5). Two adjacent biological replicates were obtained from each tissue. Organic and aqueous metabolite extracts were obtained separately and analysed using two ultra performance liquid chromatography coupled to mass spectrometry metabolic profiling methods. Multivariate and univariate tools were used for statistical analysis. RESULTS The two study groups demonstrated distinct plaque phenotypes using multivariate data analysis. Univariate statistics also revealed metabolites that differentiated the two groups with a strong statistical significance (p = 10(-4)-10(-5)). Specifically, metabolites related to the eicosanoid pathway (arachidonic acid and arachidonic acid precursors), and three acylcarnitine species (butyrylcarnitine, hexanoylcarnitine, and palmitoylcarnitine), intermediates of the β-oxidation, were detected in higher intensities in symptomatic patients. However, metabolites implicated in the process of cell death, a process known to be upregulated in the formation of the vulnerable plaque, were unaffected. CONCLUSIONS Discrimination between symptomatic and asymptomatic carotid plaque tissue is demonstrated for the first time using metabolic profiling technologies. Two biological pathways (eicosanoid and β-oxidation) were implicated in differentiating symptomatic from asymptomatic patients and will be further investigated. These results indicate that metabolic phenotyping should be further explored to investigate the chemistry of the unstable plaque, in the pursuit of candidate biomarkers for risk-stratification and targets for pharmacotherapeutic intervention.
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Affiliation(s)
- P A Vorkas
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - J Shalhoub
- Academic Section of Vascular Surgery, Division of Surgery, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - M R Lewis
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - K Spagou
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - E J Want
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - J K Nicholson
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - A H Davies
- Academic Section of Vascular Surgery, Division of Surgery, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK
| | - E Holmes
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, UK.
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The omic approach to parasitic trematode research—a review of techniques and developments within the past 5 years. Parasitol Res 2016; 115:2523-43. [DOI: 10.1007/s00436-016-5079-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/26/2022]
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13
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Zhao J, Zhao Y, Hu C, Zhao C, Zhang J, Li L, Zeng J, Peng X, Lu X, Xu G. Metabolic Profiling with Gas Chromatography-Mass Spectrometry and Capillary Electrophoresis-Mass Spectrometry Reveals the Carbon-Nitrogen Status of Tobacco Leaves Across Different Planting Areas. J Proteome Res 2016; 15:468-76. [PMID: 26784525 DOI: 10.1021/acs.jproteome.5b00807] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The interaction between carbon (C) and nitrogen (N) metabolism can reflect plant growth status and environmental factors. Little is known regarding the connections between C-N metabolism and growing regions under field conditions. To comprehensively investigate the relationship in mature tobacco leaves, we established metabolomics approaches based on gas chromatography-mass spectrometry (GC-MS) and capillary electrophoresis-time-of-flight-mass spectrometry (CE-TOF-MS). Approximately 240 polar metabolites were determined. Multivariate statistical analysis revealed that the growing region greatly influenced the metabolic profiles of tobacco leaves. A metabolic correlation network and related pathway maps were used to reveal the global overview of the alteration of C-N metabolism across three typical regions. In Yunnan, sugars and tricarboxylic acid (TCA) cycle intermediates were closely correlated with amino acid pools. Henan tobacco leaves showed positive correlation between the pentose phosphate pathway (PPP) intermediates and C-rich secondary metabolism. In Guizhou, the proline and asparagine had significant links with TCA cycle intermediates and urea cycle, and antioxidant accumulation was observed in response to drought. These results demonstrate that combined analytical approaches have great potential to detect polar metabolites and provide information on C-N metabolism related to planting regional characteristics.
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Affiliation(s)
- Jieyu Zhao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116023, China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Yanni Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Chunxiu Hu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Chunxia Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Junjie Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Lili Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Jun Zeng
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116023, China
| | - Xin Lu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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14
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Extending metabolome coverage for untargeted metabolite profiling of adherent cultured hepatic cells. Anal Bioanal Chem 2016; 408:1217-30. [DOI: 10.1007/s00216-015-9227-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/24/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023]
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15
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16
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Application of CE-MS to a metabonomics study of human urine from cigarette smokers and non-smokers. Bioanalysis 2015; 6:2733-49. [PMID: 25413705 DOI: 10.4155/bio.14.136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Novel biomarkers of exposure and early adverse effects are needed for comparative studies of combustible and non-combustible tobacco products for regulatory authority evaluation. Metabolic biomarkers reflect both gene and environmental effects. RESULTS CE-MS has been applied to human urine samples from non-smokers and smokers of cigarettes at two tar levels. Validated chemometric models were able to separate smokers from non-smokers, with discrimination mainly based on the presence of nicotine metabolites. With these removed, it still proved possible to discriminate smokers from non-smokers with models now based on endogenous metabolites. The biochemical relevance of these biomarkers is discussed. CONCLUSION This proof-of-principle metabonomics study illustrates the potential of CE-MS to discover novel biomarkers in urine from tobacco users.
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Probert F, Rice P, Scudamore CL, Wells S, Williams R, Hough TA, Cox IJ. 1H NMR Metabolic Profiling of Plasma Reveals Additional Phenotypes in Knockout Mouse Models. J Proteome Res 2015; 14:2036-45. [DOI: 10.1021/pr501039k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fay Probert
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
- Institute of Hepatology, Foundation for Liver Research, 69-75 Chenies Mews, London WC1E 6HX, United Kingdom
| | - Paul Rice
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
| | | | - Sara Wells
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
| | - Roger Williams
- Institute of Hepatology, Foundation for Liver Research, 69-75 Chenies Mews, London WC1E 6HX, United Kingdom
| | - Tertius A. Hough
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
| | - I. Jane Cox
- Institute of Hepatology, Foundation for Liver Research, 69-75 Chenies Mews, London WC1E 6HX, United Kingdom
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Vorkas PA, Isaac G, Anwar MA, Davies AH, Want EJ, Nicholson JK, Holmes E. Untargeted UPLC-MS profiling pipeline to expand tissue metabolome coverage: application to cardiovascular disease. Anal Chem 2015; 87:4184-93. [PMID: 25664760 PMCID: PMC4407508 DOI: 10.1021/ac503775m] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Metabolic
profiling studies aim to achieve broad metabolome coverage
in specific biological samples. However, wide metabolome coverage
has proven difficult to achieve, mostly because of the diverse physicochemical
properties of small molecules, obligating analysts to seek multiplatform
and multimethod approaches. Challenges are even greater when it comes
to applications to tissue samples, where tissue lysis and metabolite
extraction can induce significant systematic variation in composition.
We have developed a pipeline for obtaining the aqueous and organic
compounds from diseased arterial tissue using two consecutive extractions,
followed by a different untargeted UPLC-MS analysis method for each
extract. Methods were rationally chosen and optimized to address the
different physicochemical properties of each extract: hydrophilic
interaction liquid chromatography (HILIC) for the aqueous extract
and reversed-phase chromatography for the organic. This pipeline can
be generic for tissue analysis as demonstrated by applications to
different tissue types. The experimental setup and fast turnaround
time of the two methods contributed toward obtaining highly reproducible
features with exceptional chromatographic performance (CV % < 0.5%),
making this pipeline suitable for metabolic profiling applications.
We structurally assigned 226 metabolites from a range of chemical
classes (e.g., carnitines, α-amino acids, purines, pyrimidines,
phospholipids, sphingolipids, free fatty acids, and glycerolipids)
which were mapped to their corresponding pathways, biological functions
and known disease mechanisms. The combination of the two untargeted
UPLC-MS methods showed high metabolite complementarity. We demonstrate
the application of this pipeline to cardiovascular disease, where
we show that the analyzed diseased groups (n = 120)
of arterial tissue could be distinguished based on their metabolic
profiles.
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Affiliation(s)
- Panagiotis A Vorkas
- †Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, U.K
| | - Giorgis Isaac
- ‡Pharmaceutical Discovery and Life Sciences, Waters Corporations, Milford, Massachusetts 01757, United States
| | - Muzaffar A Anwar
- §Academic Section of Vascular Surgery, Division of Surgery, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London W6 8RF, U.K
| | - Alun H Davies
- §Academic Section of Vascular Surgery, Division of Surgery, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London W6 8RF, U.K
| | - Elizabeth J Want
- †Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, U.K
| | - Jeremy K Nicholson
- †Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, U.K.,∥MRC-NIHR National Phenome Centre, IRDB Building, Imperial College London, Hammersmith Hospital, London W12 0NN, U.K
| | - Elaine Holmes
- †Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, U.K.,∥MRC-NIHR National Phenome Centre, IRDB Building, Imperial College London, Hammersmith Hospital, London W12 0NN, U.K
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19
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Tufi S, Lamoree MH, De Boer J, Leonards PEG. Cross-platform metabolic profiling: application to the aquatic model organism Lymnaea stagnalis. Anal Bioanal Chem 2015; 407:1901-12. [DOI: 10.1007/s00216-014-8431-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
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20
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Comparison of capillary electrophoresis–mass spectrometry and hydrophilic interaction chromatography–mass spectrometry for anionic metabolic profiling of urine. Talanta 2015; 132:1-7. [DOI: 10.1016/j.talanta.2014.08.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 08/13/2014] [Accepted: 08/18/2014] [Indexed: 01/24/2023]
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21
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Junot C, Fenaille F, Colsch B, Bécher F. High resolution mass spectrometry based techniques at the crossroads of metabolic pathways. MASS SPECTROMETRY REVIEWS 2014; 33:471-500. [PMID: 24288070 DOI: 10.1002/mas.21401] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
The metabolome is the set of small molecular mass compounds found in biological media, and metabolomics, which refers to as the analysis of metabolome in a given biological condition, deals with the large scale detection and quantification of metabolites in biological media. It is a data driven and multidisciplinary approach combining analytical chemistry for data acquisition, and biostatistics, informatics and biochemistry for mining and interpretation of these data. Since the middle of the 2000s, high resolution mass spectrometry is widely used in metabolomics, mainly because the detection and identification of metabolites are improved compared to low resolution instruments. As the field of HRMS is quickly and permanently evolving, the aim of this work is to review its use in different aspects of metabolomics, including data acquisition, metabolite annotation, identification and quantification. At last, we would like to show that, thanks to their versatility, HRMS instruments are the most appropriate to achieve optimal metabolome coverage, at the border of other omics fields such as lipidomics and glycomics.
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Affiliation(s)
- Christophe Junot
- Commissariat à l'Energie Atomique, Centre de Saclay, DSV/iBiTec-S/SPI, Laboratoire d'Etude du Métabolisme des Médicaments, 91191, Gif-sur-Yvette Cedex, France
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22
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Kok MG, Somsen GW, de Jong GJ. The role of capillary electrophoresis in metabolic profiling studies employing multiple analytical techniques. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Raterink RJ, Lindenburg PW, Vreeken RJ, Ramautar R, Hankemeier T. Recent developments in sample-pretreatment techniques for mass spectrometry-based metabolomics. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.06.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Naz S, Vallejo M, García A, Barbas C. Method validation strategies involved in non-targeted metabolomics. J Chromatogr A 2014; 1353:99-105. [DOI: 10.1016/j.chroma.2014.04.071] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
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25
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Boudah S, Olivier MF, Aros-Calt S, Oliveira L, Fenaille F, Tabet JC, Junot C. Annotation of the human serum metabolome by coupling three liquid chromatography methods to high-resolution mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:34-47. [PMID: 24815365 DOI: 10.1016/j.jchromb.2014.04.025] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 11/15/2022]
Abstract
This work aims at evaluating the relevance and versatility of liquid chromatography coupled to high resolution mass spectrometry (LC/HRMS) for performing a qualitative and comprehensive study of the human serum metabolome. To this end, three different chromatographic systems based on a reversed phase (RP), hydrophilic interaction chromatography (HILIC) and a pentafluorophenylpropyl (PFPP) stationary phase were used, with detection in both positive and negative electrospray modes. LC/HRMS platforms were first assessed for their ability to detect, retain and separate 657 metabolite standards representative of the chemical families occurring in biological fluids. More than 75% were efficiently retained in either one LC-condition and less than 5% were exclusively retained by the RP column. These three LC/HRMS systems were then evaluated for their coverage of serum metabolome. The combination of RP, HILIC and PFPP based LC/HRMS methods resulted in the annotation of about 1328 features in the negative ionization mode, and 1358 in the positive ionization mode on the basis of their accurate mass and precise retention time in at least one chromatographic condition. Less than 12% of these annotations were shared by the three LC systems, which highlights their complementarity. HILIC column ensured the greatest metabolome coverage in the negative ionization mode, whereas PFPP column was the most effective in the positive ionization mode. Altogether, 192 annotations were confirmed using our spectral database and 74 others by performing MS/MS experiments. This resulted in the formal or putative identification of 266 metabolites, among which 59 are reported for the first time in human serum.
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Affiliation(s)
- Samia Boudah
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France; GlaxoSmithKline - Centre de recherche F.Hyafil, 25 Avenue du Québec, Villebon-sur-Yvette, France
| | - Marie-Françoise Olivier
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France
| | - Sandrine Aros-Calt
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France; bioMérieux S.A, Chemin de l'Orme, 69280 Marcy l'Etoile, France
| | - Lydie Oliveira
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Radiobiologie Cellulaire et Moléculaire/Laboratoire de Recherche sur la Transcription et la Réparation des Cellules Souches, 92260 Fontenay-aux-Roses, France
| | - François Fenaille
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France
| | - Jean-Claude Tabet
- Laboratoire de Chimie Structurale Organique et Biologique, IPCM/CNRS UMR 7201, Université Pierre et Marie Curie, 75252 Paris, France
| | - Christophe Junot
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France.
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26
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Kok MGM, Swann JR, Wilson ID, Somsen GW, de Jong GJ. Hydrophilic interaction chromatography-mass spectrometry for anionic metabolic profiling of urine from antibiotic-treated rats. J Pharm Biomed Anal 2014; 92:98-104. [PMID: 24503197 DOI: 10.1016/j.jpba.2014.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/09/2014] [Indexed: 11/26/2022]
Abstract
Hydrophilic interaction chromatography-mass spectrometry (HILIC-MS) was used for anionic metabolic profiling of urine from antibiotic-treated rats to study microbial-host co-metabolism. Rats were treated with the antibiotics penicillin G and streptomycin sulfate for four or eight days and compared to a control group. Urine samples were collected at day zero, four and eight, and analyzed by HILIC-MS. Multivariate data analysis was applied to the urinary metabolic profiles to identify biochemical variation between the treatment groups. Principal component analysis found a clear distinction between those animals receiving antibiotics and the control animals, with twenty-nine discriminatory compounds of which twenty were down-regulated and nine up-regulated upon treatment. In the treatment group receiving antibiotics for four days, a recovery effect was observed for seven compounds after cessation of antibiotic administration. Thirteen discriminatory compounds could be putatively identified based on their accurate mass, including aconitic acid, benzenediol sulfate, ferulic acid sulfate, hippuric acid, indoxyl sulfate, penicillin G, phenol and vanillin 4-sulfate. The rat urine samples had previously been analyzed by capillary electrophoresis (CE) with MS detection and proton nuclear magnetic resonance ((1)H NMR) spectroscopy. Using CE-MS and (1)H NMR spectroscopy seventeen and twenty-five discriminatory compounds were found, respectively. Both hippuric acid and indoxyl sulfate were detected across all three platforms. Additionally, eight compounds were observed with both HILIC-MS and CE-MS. Overall, HILIC-MS appears to be highly complementary to CE-MS and (1)H NMR spectroscopy, identifying additional compounds that discriminate the urine samples from antibiotic-treated and control rats.
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Affiliation(s)
- Miranda G M Kok
- Biomolecular Analysis, Department of Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands; Research group Analysis Techniques in Life Sciences, Avans Hogeschool, P.O. Box 90116, 4800 RA Breda, The Netherlands.
| | - Jonathan R Swann
- Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Ian D Wilson
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Govert W Somsen
- AIMSS Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, VU University, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Gerhardus J de Jong
- Biomolecular Analysis, Department of Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands; Research group Analysis Techniques in Life Sciences, Avans Hogeschool, P.O. Box 90116, 4800 RA Breda, The Netherlands
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27
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Martin AC, Pawlus AD, Jewett EM, Wyse DL, Angerhofer CK, Hegeman AD. Evaluating solvent extraction systems using metabolomics approaches. RSC Adv 2014. [DOI: 10.1039/c4ra02731k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Metabolomics generated features were used as unbiased metrics to identify solvents that produce botanical extracts with the greatest chemical diversity.
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Affiliation(s)
- Amanda C. Martin
- Department of Horticultural Science
- Plant Biological Sciences Graduate Program
- Department of Plant Biology, and Microbial and Plant Genomics Institute
- University of Minnesota
- St Paul, USA
| | - Alison D. Pawlus
- Department of Horticultural Science
- Plant Biological Sciences Graduate Program
- Department of Plant Biology, and Microbial and Plant Genomics Institute
- University of Minnesota
- St Paul, USA
| | - Erin M. Jewett
- Department of Horticultural Science
- Plant Biological Sciences Graduate Program
- Department of Plant Biology, and Microbial and Plant Genomics Institute
- University of Minnesota
- St Paul, USA
| | - Donald L. Wyse
- Department of Agronomy and Plant Genetics
- University of Minnesota
- St. Paul, USA
| | | | - Adrian D. Hegeman
- Department of Horticultural Science
- Plant Biological Sciences Graduate Program
- Department of Plant Biology, and Microbial and Plant Genomics Institute
- University of Minnesota
- St Paul, USA
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28
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Moniruzzaman M, Sulaiman SA, Azlan SAM, Gan SH. Two-year variations of phenolics, flavonoids and antioxidant contents in acacia honey. Molecules 2013; 18:14694-710. [PMID: 24287998 PMCID: PMC6270151 DOI: 10.3390/molecules181214694] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 12/20/2022] Open
Abstract
Honey is a good source of several important chemical compounds and antioxidants and is harvested throughout the year. However, no study has determined how their contents change over the years. The aim of the present research was to investigate the changes in the phenolics, flavonoids and antioxidant properties, as well as other physicochemical properties, of Malaysian acacia honey collected during different months during a two year period. The DPPH (1,1-diphenyl-2-picrylhydrazyl) and FRAP (ferric reducing antioxidant power) methods were used to determine the total antioxidant activity of the honey samples. Generally, honey samples collected in the beginning and the middle of the year tended to have higher sugar content, which may be attributed to its high acidic nature and low moisture content. There was a gradual increase in the phenolic content of the acacia honey samples collected between September 2010 and December 2010. The honey sample collected at the beginning of the year (January) showed the highest color intensity and was dark amber in color. It also contained the highest concentration of phenolic compounds (341.67 ± 2.94 mg(gallic acid)/kg), the highest flavonoid content (113.06 ± 6.18 mg(catechin)/kg) and the highest percentage of DPPH inhibition and the highest FRAP value, confirming its high antioxidant potential. There was a positive correlation between DPPH and total phenolic content, suggesting that phenolic compounds are the strongest contributing factor to the radical scavenging activity of Malaysian acacia honeys. Overall, our results indicated that there were significant seasonal variations in the antioxidant potentials of honey over the two year period and the time of honey collection affects its physicochemical properties. Therefore, acacia honey from Malaysia should ideally be collected during the dry season, particularly in the months of January, May and June.
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Affiliation(s)
- Mohammed Moniruzzaman
- Department of Pharmacology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; E-Mails: (M.M.); (S.A.M.A.)
| | - Siti Amrah Sulaiman
- Department of Pharmacology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; E-Mails: (M.M.); (S.A.M.A.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +609-7676-124; Fax: +609-7653-370
| | - Siti Amirah Mohd Azlan
- Department of Pharmacology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; E-Mails: (M.M.); (S.A.M.A.)
| | - Siew Hua Gan
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; E-Mail:
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29
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Naz S, García A, Barbas C. Multiplatform Analytical Methodology for Metabolic Fingerprinting of Lung Tissue. Anal Chem 2013; 85:10941-8. [DOI: 10.1021/ac402411n] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shama Naz
- CEMBIO (Center for Metabolomics and Bioanalysis),
Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, Spain
| | - Antonia García
- CEMBIO (Center for Metabolomics and Bioanalysis),
Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, Spain
| | - Coral Barbas
- CEMBIO (Center for Metabolomics and Bioanalysis),
Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, Spain
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30
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Kuehnbaum NL, Kormendi A, Britz-McKibbin P. Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry: A High-Throughput Platform for Metabolomics with High Data Fidelity. Anal Chem 2013; 85:10664-9. [DOI: 10.1021/ac403171u] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Naomi L. Kuehnbaum
- Department of Chemistry and
Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4M1, Canada
| | - Aleshia Kormendi
- Department of Chemistry and
Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4M1, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and
Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4M1, Canada
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31
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Ivanisevic J, Zhu ZJ, Plate L, Tautenhahn R, Chen S, O'Brien PJ, Johnson CH, Marletta MA, Patti GJ, Siuzdak G. Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Anal Chem 2013; 85:6876-84. [PMID: 23781873 PMCID: PMC3761963 DOI: 10.1021/ac401140h] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the objective of any 'omic science is broad measurement of its constituents, such coverage has been challenging in metabolomics because the metabolome is comprised of a chemically diverse set of small molecules with variable physical properties. While extensive studies have been performed to identify metabolite isolation and separation methods, these strategies introduce bias toward lipophilic or water-soluble metabolites depending on whether reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) is used, respectively. Here we extend our consideration of metabolome isolation and separation procedures to integrate RPLC/MS and HILIC/MS profiling. An aminopropyl-based HILIC/MS method was optimized on the basis of mobile-phase additives and pH, followed by evaluation of reproducibility. When applied to the untargeted study of perturbed bacterial metabolomes, the HILIC method enabled the accurate assessment of key, dysregulated metabolites in central carbon pathways (e.g., amino acids, organic acids, phosphorylated sugars, energy currency metabolites), which could not be retained by RPLC. To demonstrate the value of the integrative approach, bacterial cells, human plasma, and cancer cells were analyzed by combined RPLC/HILIC separation coupled to ESI positive/negative MS detection. The combined approach resulted in the observation of metabolites associated with lipid and central carbon metabolism from a single biological extract, using 80% organic solvent (ACN:MeOH:H2O 2:2:1). It enabled the detection of more than 30,000 features from each sample type, with the highest number of uniquely detected features by RPLC in ESI positive mode and by HILIC in ESI negative mode. Therefore, we conclude that when time and sample are limited, the maximum amount of biological information related to lipid and central carbon metabolism can be acquired by combining RPLC ESI positive and HILIC ESI negative mode analysis.
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Affiliation(s)
- Julijana Ivanisevic
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California 92037, United States
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32
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Kuehnbaum NL, Britz-McKibbin P. New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era. Chem Rev 2013; 113:2437-68. [DOI: 10.1021/cr300484s] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Naomi L. Kuehnbaum
- Department of Chemistry
and Chemical Biology, McMaster University, Hamilton, Canada
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