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Beger RD, Goodacre R, Jones CM, Lippa KA, Mayboroda OA, O'Neill D, Najdekr L, Ntai I, Wilson ID, Dunn WB. Analysis types and quantification methods applied in UHPLC-MS metabolomics research: a tutorial. Metabolomics 2024; 20:95. [PMID: 39110307 PMCID: PMC11306277 DOI: 10.1007/s11306-024-02155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Different types of analytical methods, with different characteristics, are applied in metabolomics and lipidomics research and include untargeted, targeted and semi-targeted methods. Ultra High Performance Liquid Chromatography-Mass Spectrometry is one of the most frequently applied measurement instruments in metabolomics because of its ability to detect a large number of water-soluble and lipid metabolites over a wide range of concentrations in short analysis times. Methods applied for the detection and quantification of metabolites differ and can either report a (normalised) peak area or an absolute concentration. AIM OF REVIEW In this tutorial we aim to (1) define similarities and differences between different analytical approaches applied in metabolomics and (2) define how amounts or absolute concentrations of endogenous metabolites can be determined together with the advantages and limitations of each approach in relation to the accuracy and precision when concentrations are reported. KEY SCIENTIFIC CONCEPTS OF REVIEW The pre-analysis knowledge of metabolites to be targeted, the requirement for (normalised) peak responses or absolute concentrations to be reported and the number of metabolites to be reported define whether an untargeted, targeted or semi-targeted method is applied. Fully untargeted methods can only provide (normalised) peak responses and fold changes which can be reported even when the structural identity of the metabolite is not known. Targeted methods, where the analytes are known prior to the analysis, can also report fold changes. Semi-targeted methods apply a mix of characteristics of both untargeted and targeted assays. For the reporting of absolute concentrations of metabolites, the analytes are not only predefined but optimized analytical methods should be developed and validated for each analyte so that the accuracy and precision of concentration data collected for biological samples can be reported as fit for purpose and be reviewed by the scientific community.
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Affiliation(s)
- Richard D Beger
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Royston Goodacre
- Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Christina M Jones
- Office of Advanced Manufacturing, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Katrice A Lippa
- Office of Weights and Measures, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Donna O'Neill
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
| | - Lukas Najdekr
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University Olomouc, 779 00, Olomouc, Czech Republic
| | - Ioanna Ntai
- BioMarin Pharmaceutical Inc., San Rafael, CA, USA
| | - Ian D Wilson
- Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Warwick B Dunn
- Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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2
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Yin J, Guo W, Li X, Ding H, Han L, Yang X, Zhu L, Li F, Bie S, Song X, Yu H, Li Z. Extensive evaluation of plasma metabolic sample preparation process based on liquid chromatography-mass spectrometry and its application in the in vivo metabolism of Shuang-Huang-Lian powder injection. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123808. [PMID: 37453388 DOI: 10.1016/j.jchromb.2023.123808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Shuang-Huang-Lian powder injection (SHLPI) is a natural drug injection made of honeysuckle, scutellaria baicalensis and forsythia suspensa. It has the characteristics of complex chemical composition and difficult metabolism research in vivo. LC-MS platform has been proven to be an important analytical technology in plasma metabolomics. Unfortunately, the lack of an effective sample preparation strategy before analysis often significantly impacts experimental results. In this work, twenty-one extraction protocols including eight protein precipitation (PPT), eight liquid-liquid extractions (LLE), four solid-phase extractions (SPE), and one ultrafiltration (U) were simultaneously evaluated using plasma metabolism of SHLPI in vivo. In addition, a strategy of "feature ion extraction of the multi-component metabolic platform of traditional Chinese medicine" (FMM strategy) was proposed for the in-depth characterization of metabolites after intravenous injection of SHLPI in rats. The results showed that the LLE-3 protocol (Pentanol:Tetrahydrofuran:H2O, 1:4:35, v:v:v) was the most effective strategy in the in vivo metabolic detection of SHLPI. Furthermore, we used the FMM strategy to elaborate the in vivo metabolic pathways of six representative substances in SHLPI components. This research was completed by ion migration quadrupole time of flight mass spectrometer combined with ultra high performance liquid chromatography (UPLC/Vion™-IMS-QTof-MS) and UNIFI™ metabolic platform. The results showed that 114 metabolites were identified or preliminarily identified in rat plasma. This work provides relevant data and information for further research on the pharmacodynamic substances and in vivo mechanisms of SHLPI. Meanwhile, it also proves that LLE-3 and FMM strategies could achieve the in-depth characterization of complex natural drug metabolites related to Shuang-Huang-Lian in vivo.
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Affiliation(s)
- Jiaxin Yin
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Wen Guo
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Xuejuan Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Hui Ding
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Lifeng Han
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Xiangdong Yang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Limin Zhu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Fangyi Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Songtao Bie
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Xinbo Song
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Heshui Yu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China.
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China.
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3
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Toward building mass spectrometry-based metabolomics and lipidomics atlases for biological and clinical research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Zhang Y, Xie Y, Lv W, Hu C, Xu T, Liu X, Zhang R, Xu G, Xia Y, Zhao X. A high throughput lipidomics method and its application in atrial fibrillation based on 96-well plate pretreatment and liquid chromatography-mass spectrometry. J Chromatogr A 2021; 1651:462271. [PMID: 34102397 DOI: 10.1016/j.chroma.2021.462271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/27/2022]
Abstract
Successful applications of lipidomics in clinic need study large-scale samples, and the bottlenecks are in throughput and robustness of the lipid analytical method. Here, we report an untargeted lipidomics method by combining high throughput pretreatment in the 96-well plate with ultra-high performance liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry. The developed method was validated to have satisfactory analytical characteristics in terms of linearity, repeatability and extraction recovery. It can be used to handle 96 samples simultaneously in 25 min and detect 441 lipids in plasma sample. Storage stability investigation on lipid extracts provided an operable procedure for large-scale sample analysis and demonstrated most lipids were stable in autosampler at 10 °C within 36 h and at -80 °C within 72 h after the pretreatment. To prove the usefulness, the method was employed to investigate abnormal plasma lipidome related to atrial fibrillation. A biomarker panel with the area under the curve (AUC) values of 0.831 and 0.745 was achieved in the discovery and external validation sets, respectively. These results showed that the developed method is applicable for large-scale biological sample handling and lipid analysis of plasma.
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Affiliation(s)
- Yuqing Zhang
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yunpeng Xie
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wangjie Lv
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. 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 116023, P. R. China
| | - Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Rongfeng Zhang
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Guowang Xu
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yunlong Xia
- The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
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5
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A Novel Solid Phase Extraction Sample Preparation Method for Lipidomic Analysis of Human Plasma Using Liquid Chromatography/Mass Spectrometry. Metabolites 2021; 11:metabo11050294. [PMID: 34064397 PMCID: PMC8147762 DOI: 10.3390/metabo11050294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 02/02/2023] Open
Abstract
Lipidomic approaches are widely used to investigate the relationship between lipids, human health, and disease. Conventional sample preparation techniques for the extraction of lipids from biological matrices like human plasma are based on liquid-liquid extraction (LLE). However, these methods are labor-intensive, time-consuming, and can show poor reproducibility and selectivity on lipid extraction. A novel, solid-phase extraction (SPE) approach was demonstrated to extract lipids from human plasma using a lipid extraction SPE in both cartridge and 96-well-plate formats, followed by analysis using a combination of targeted and untargeted liquid chromatography/mass spectrometry. The Lipid Extraction SPE method was compared to traditional LLE methods for lipid class recovery, lipidome coverage, and reproducibility. The novel SPE method used a simplified protocol with significant time and labor savings and provided equivalent or better qualitative and quantitative results than traditional LLE methods with respect to several critical performance metrics; recovery, reproducibility, and lipidome coverage.
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6
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He Y, Rashan EH, Linke V, Shishkova E, Hebert AS, Jochem A, Westphall MS, Pagliarini DJ, Overmyer KA, Coon JJ. Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis. Anal Chem 2021; 93:4217-4222. [PMID: 33617230 PMCID: PMC8028036 DOI: 10.1021/acs.analchem.0c04764] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry (MS) serves as the centerpiece technology for proteome, lipidome, and metabolome analysis. To gain a better understanding of the multifaceted networks of myriad regulatory layers in complex organisms, integration of different multiomic layers is increasingly performed, including joint extraction methods of diverse biomolecular classes and comprehensive data analyses of different omics. Despite the versatility of MS systems, fractured methodology drives nearly all MS laboratories to specialize in analysis of a single ome at the exclusion of the others. Although liquid chromatography-mass spectrometry (LC-MS) analysis is similar for different biomolecular classes, the integration on the instrument level is lagging behind. The recent advancements in high flow proteomics enable us to take a first step towards integration of protein and lipid analysis. Here, we describe a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through multi-omic single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow. MOST achieved great robustness and reproducibility. Its application to a Saccharomyces cerevisiae study consisting of 20 conditions revealed 2842 protein groups and 325 lipids and potential molecular relationships.
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Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Vanessa Linke
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Alexander S. Hebert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - David J. Pagliarini
- Departments of Cell Biology and Physiology; Biochemistry and Molecular Biophysics; and Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
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7
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Amer B, Baidoo EEK. Omics-Driven Biotechnology for Industrial Applications. Front Bioeng Biotechnol 2021; 9:613307. [PMID: 33708762 PMCID: PMC7940536 DOI: 10.3389/fbioe.2021.613307] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.
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Affiliation(s)
- Bashar Amer
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Edward E. K. Baidoo
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- U.S. Department of Energy, Agile BioFoundry, Emeryville, CA, United States
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8
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Tang J, Xiong K, Zhang T, Han Han. Application of Metabolomics in Diagnosis and Treatment of Chronic Liver Diseases. Crit Rev Anal Chem 2020; 52:906-916. [PMID: 33146026 DOI: 10.1080/10408347.2020.1842172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic liver disease represents stepwise destruction of the liver parenchyma after chronic liver injury, which is often difficult to be diagnosed accurately. Thus, the development of specific biomarkers of chronic liver disease is important. Metabolomics is a powerful tool for biomarker exploration, which enables the exploration of disease pathogenesis or drug action mechanisms at the global metabolic level. The metabolomics workflow generally includes collection, preparation, and analysis of samples, and data processing and bioinformatics. A metabolomics study can simultaneously detect the dysfunctions in the glucose, lipid, amino-acid, and nucleotide metabolisms. Hence, it facilitates the obtaining of a better understanding of the pathogenesis of chronic liver disease and its diagnosis. Many effective drugs could reverse the change of comprehensive biochemical phenotypes induced by chronic liver disease. They can even potentially restore the normal metabolic signatures of patients. Increasingly more researchers have begun to apply metabolomics technologies to diagnose chronic liver disease and investigate the mechanism of action of effective drugs or the variations in drug responses. We are convinced that deepening the understanding of the metabolic alterations could extend their use as powerful biomarkers, promoting the more effective clinical diagnosis and treatment of chronic liver disease in the future.
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Affiliation(s)
- Jie Tang
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kai Xiong
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tong Zhang
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Han Han
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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9
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Villaret-Cazadamont J, Poupin N, Tournadre A, Batut A, Gales L, Zalko D, Cabaton NJ, Bellvert F, Bertrand-Michel J. An Optimized Dual Extraction Method for the Simultaneous and Accurate Analysis of Polar Metabolites and Lipids Carried out on Single Biological Samples. Metabolites 2020; 10:E338. [PMID: 32825089 PMCID: PMC7570216 DOI: 10.3390/metabo10090338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022] Open
Abstract
The functional understanding of metabolic changes requires both a significant investigation into metabolic pathways, as enabled by global metabolomics and lipidomics approaches, and the comprehensive and accurate exploration of specific key pathways. To answer this pivotal challenge, we propose an optimized approach, which combines an efficient sample preparation, aiming to reduce the variability, with a biphasic extraction method, where both the aqueous and organic phases of the same sample are used for mass spectrometry analyses. We demonstrated that this double extraction protocol allows working with one single sample without decreasing the metabolome and lipidome coverage. It enables the targeted analysis of 40 polar metabolites and 82 lipids, together with the absolute quantification of 32 polar metabolites, providing comprehensive coverage and quantitative measurement of the metabolites involved in central carbon energy pathways. With this method, we evidenced modulations of several lipids, amino acids, and energy metabolites in HepaRG cells exposed to fenofibrate, a model hepatic toxicant, and metabolic modulator. This new protocol is particularly relevant for experiments involving limited amounts of biological material and for functional metabolic explorations and is thus of particular interest for studies aiming to decipher the effects and modes of action of metabolic disrupting compounds.
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Affiliation(s)
- Joran Villaret-Cazadamont
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Anthony Tournadre
- MetaboHUB-MetaToul-Lipidomics Core Facility, Inserm U1048, 31432 Toulouse, France; (A.T.); (A.B.)
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
| | - Aurélie Batut
- MetaboHUB-MetaToul-Lipidomics Core Facility, Inserm U1048, 31432 Toulouse, France; (A.T.); (A.B.)
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
| | - Lara Gales
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 31400 Toulouse, France
| | - Daniel Zalko
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Nicolas J. Cabaton
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Floriant Bellvert
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 31400 Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB-MetaToul-Lipidomics Core Facility, Inserm U1048, 31432 Toulouse, France; (A.T.); (A.B.)
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
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10
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Liu X, Zhou L, Shi X, Xu G. New advances in analytical methods for mass spectrometry-based large-scale metabolomics study. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115665] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Lankatillake C, Huynh T, Dias DA. Understanding glycaemic control and current approaches for screening antidiabetic natural products from evidence-based medicinal plants. PLANT METHODS 2019; 15:105. [PMID: 31516543 PMCID: PMC6731622 DOI: 10.1186/s13007-019-0487-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/20/2019] [Indexed: 05/15/2023]
Abstract
Type 2 Diabetes Mellitus has reached epidemic proportions as a result of over-nutrition and increasingly sedentary lifestyles. Current therapies, although effective, are not without limitations. These limitations, the alarming increase in the prevalence of diabetes, and the soaring cost of managing diabetes and its complications underscores an urgent need for safer, more efficient and affordable alternative treatments. Over 1200 plant species are reported in ethnomedicine for treating diabetes and these represents an important and promising source for the identification of novel antidiabetic compounds. Evaluating medicinal plants for desirable bioactivity goes hand-in-hand with methods in analytical biochemistry for separating and identifying lead compounds. This review aims to provide a comprehensive summary of current methods used in antidiabetic plant research to form a useful resource for researchers beginning in the field. The review summarises the current understanding of blood glucose regulation and the general mechanisms of action of current antidiabetic medications, and combines knowledge on common experimental approaches for screening plant extracts for antidiabetic activity and currently available analytical methods and technologies for the separation and identification of bioactive natural products. Common in vivo animal models, in vitro models, in silico methods and biochemical assays used for testing the antidiabetic effects of plants are discussed with a particular emphasis on in vitro methods such as cell-based bioassays for screening insulin secretagogues and insulinomimetics. Enzyme inhibition assays and molecular docking are also highlighted. The role of metabolomics, metabolite profiling, and dereplication of data for the high-throughput discovery of novel antidiabetic agents is reviewed. Finally, this review also summarises sample preparation techniques such as liquid-liquid extraction, solid phase extraction, and supercritical fluid extraction, and the critical function of nuclear magnetic resonance and high resolution liquid chromatography-mass spectrometry for the dereplication, putative identification and structure elucidation of natural compounds from evidence-based medicinal plants.
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Affiliation(s)
- Chintha Lankatillake
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, Bundoora, 3083 Australia
| | - Tien Huynh
- School of Science, RMIT University, Bundoora, VIC 3083 Australia
| | - Daniel A. Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, Bundoora, 3083 Australia
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12
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Aristizabal-Henao JJ, Fernandes MF, Duncan RE, Stark KD. Development of a Rapid Ultra High-Performance Liquid Chromatography/Tandem Mass Spectrometry Method for the Analysis of sn-1 and sn-2 Lysophosphatidic Acid Regioisomers in Mouse Plasma. Lipids 2019; 54:479-486. [PMID: 31236951 DOI: 10.1002/lipd.12172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022]
Abstract
Lysophosphatidic acids (lysoPtdOH) are involved in several physiological processes including cell proliferation, inflammation, and glucose metabolism. However, measuring lysoPtdOH is challenging due to inadequate extraction techniques, poor chromatographic resolution, or the inability to discriminate between sn-1 and sn-2 regioisomers. In the present work, we developed a high-throughput (10 min run times) ultra-high-performance liquid chromatography-tandem mass spectrometry method capable of discriminating lysoPtdOH species by their fatty acyl composition and sn-localization on glycerol backbones. We quantitated sn-1/sn-2 regioisomeric pairs of lysoPtdOH with 16:0, 18:0, 18:1, 18:2, 20:4, and 22:6 fatty acyl chains using 50 μL of mouse plasma. The method presented here can be expanded to profile more lysoPtdOH species, and has the potential to be used in clinical settings to quickly screen lysoPtdOH profiles. Finally, the ability to discriminate between sn-1 and sn-2 isomers can provide insights regarding the metabolic origins and fates of specific lysoPtdOH molecules.
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Affiliation(s)
- Juan J Aristizabal-Henao
- Department of Kinesiology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Maria F Fernandes
- Department of Kinesiology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Robin E Duncan
- Department of Kinesiology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Ken D Stark
- Department of Kinesiology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
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13
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Chan W, Zhao Y, Zhang J. Evaluating the performance of sample preparation methods for ultra-performance liquid chromatography/mass spectrometry based serum metabonomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:561-568. [PMID: 30614103 DOI: 10.1002/rcm.8381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Metabonomics investigating perturbation to endogenous metabolism in response to external stimuli is emerging as a powerful tool for clinical diagnosis as well as in many other areas. The ability to retrieve reliable and reproducible information from complex biological fluids such as serum is crucial for its further applications. METHODS In this study, the performance of the commonly used sample preparation methods for ultra-performance liquid chromatography/mass spectrometry (UPLC/MS)-based metabonomics was investigated. Specifically, we compared the extraction efficiencies, the method reproducibility, and the ability to identify potential biomarkers using solvent-based protein precipitation and solid-phase extraction (SPE) for serum metabonomic studies. Differences between extraction methods were explored using principal component analysis (PCA) and orthogonal partial least squares-discrimination analysis (OPLS-DA). RESULTS Among the sample preparation methods tested, solvent-based protein precipitation using methanol has demonstrated the best analytical precision and extraction efficiency. Furthermore, this study revealed, for the first time, gender-specific differences in levels of two lysophosphatidylcholines (lysoPC 18:0 and lysoPC 18:1) in rat serum samples. CONCLUSIONS The performance of sample preparation methods for UPLC/MS-based serum metabonomics was evaluated systematically. Results showed sample preparation by solvent precipitation using methanol provided the best analytical precision and extraction efficiency for UPLC/MS-based serum metabonomics.
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Affiliation(s)
- Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Yao Zhao
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jiayin Zhang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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14
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Wang J, Kano K, Saigusa D, Aoki J. Measurement of the Spatial Distribution of S1P in Small Quantities of Tissues: Development and Application of a Highly Sensitive LC-MS/MS Method Combined with Laser Microdissection. ACTA ACUST UNITED AC 2019; 8:A0072. [PMID: 30805275 PMCID: PMC6372364 DOI: 10.5702/massspectrometry.a0072] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/03/2018] [Indexed: 11/23/2022]
Abstract
Sphingosine-1-phosphate (S1P) acts as an extracellular signaling molecule with diverse biological functions. Tissues appear to have an S1P gradient, which is functionally relevant in the biological significance of S1P, although its existence has not been measured directly. Here, we report a highly sensitive method to determine the distribution of S1P, using a column-switching LC-MS/MS system combined with laser microdissection (LMD). Column switching using narrow core Capcell Pak C18 analytical and trap columns with 0.3 mm inner diameter improved the performance of the LC-MS/MS system. The calibration curve of S1P showed good linearity (r>0.999) over the range of 0.05–10 nM (1–200 fmol/injection). The accuracy of the method was confirmed by measuring S1P-spiked laser microdissected mice tissue sections. To evaluate our S1P analytical method, we quantified S1P extracted from micro-dissected mouse brain and spleen. These results show that this method can measure low S1P concentrations and determine S1P distribution in tissue microenvironments.
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Affiliation(s)
- Jiao Wang
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Kuniyuki Kano
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University.,AMED·LEAP
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University.,Medical Biochemistry, Tohoku University School of Medicine.,AMED·LEAP
| | - Junken Aoki
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University.,AMED·LEAP
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15
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Schwaiger M, Schoeny H, El Abiead Y, Hermann G, Rampler E, Koellensperger G. Merging metabolomics and lipidomics into one analytical run. Analyst 2019; 144:220-229. [PMID: 30411762 DOI: 10.1039/c8an01219a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel integrated metabolomics/lipidomics workflow is introduced enabling high coverage of polar metabolites and non-polar lipids within one analytical run. Dual HILIC and RP chromatography were combined to high-resolution mass spectrometry. As a major advantage, only one data file per sample was obtained by fully automated simultaneous analysis of two extracts per sample. Hence, the unprecedented high coverage without compromise on analytical throughput was not only obtained by the orthogonality of the chromatographic separations, but also by the implementation of dedicated sample preparation procedures resulting in optimum extraction efficiency for both sub-omes. Thus, the method addressed completely hydrophilic sugars and organic acids next to water-insoluble triglycerides. As for the timing of the dual chromatography setup, HILIC and RP separation were performed consecutively. However, re-equilibration of the HILIC column during elution of RP compounds and vice versa reduced the overall analysis time by one third to 32 min. Application to the Standard Reference Material SRM 1950 - Metabolites in Frozen Human Plasma resulted in >100 metabolite and >380 lipid identifications based on accurate mass implementing fast polarity switching and acquiring data dependent MS2 spectra with the use of automated exclusion lists. Targeted quantification based on external calibrations and 13C labeled yeast internal standards was successfully accomplished for 59 metabolites. Moreover, the potential for lipid quantification was shown integrating non-endogenous lipids as internal standards. In human plasma, concentrations ranging over 4 orders of magnitude (low nM to high μM) were assessed.
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Affiliation(s)
- Michaela Schwaiger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and ISOtopic solutions, Waehringerstr. 38, 1090 Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
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16
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Leuthold P, Schwab M, Hofmann U, Winter S, Rausch S, Pollak MN, Hennenlotter J, Bedke J, Schaeffeler E, Haag M. Simultaneous Extraction of RNA and Metabolites from Single Kidney Tissue Specimens for Combined Transcriptomic and Metabolomic Profiling. J Proteome Res 2018; 17:3039-3049. [PMID: 30091608 DOI: 10.1021/acs.jproteome.8b00199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tissue analysis represents a powerful tool for the investigation of disease pathophysiology. However, the heterogeneous nature of tissue samples, in particular of neoplastic, may affect the outcome of such analysis and hence obscure interpretation of results. Thus, comprehensive isolation and extraction of transcripts and metabolites from an identical tissue specimen would minimize variations and enable the economic use of biopsy material which is usually available in limited amounts. Here we demonstrate a fast and simple protocol for combined transcriptomics and metabolomics analysis in homogenates prepared from one single tissue sample. Metabolites were recovered by protein precipitation from lysates originally prepared for RNA isolation and were analyzed by LC-QTOF-MS after HILIC and RPLC separation, respectively. Strikingly, although ion suppression was observed, over 80% of the 2885 detected metabolic features could be extracted and analyzed with high reproducibility (CV ≤ 20%). Moreover fold changes of different tumor and nontumor kidney tissues were correlated to an established metabolomics protocol and revealed a strong correlation ( rp ≥ 0.75). In order to demonstrate the feasibility of the combined analysis of RNA and metabolites, the protocol was applied to kidney tissue of metformin treated mice to investigate drug induced alterations.
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Affiliation(s)
- Patrick Leuthold
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology , University Hospital Tübingen , Tübingen , Germany.,Department of Pharmacy and Biochemistry , University of Tübingen , Tübingen , Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Steffen Rausch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany.,Department of Urology , University Hospital Tübingen , Tübingen , Germany
| | | | - Jörg Hennenlotter
- Department of Urology , University Hospital Tübingen , Tübingen , Germany
| | - Jens Bedke
- Department of Urology , University Hospital Tübingen , Tübingen , Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
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17
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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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18
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Rapid profiling and quantification of phospholipid molecular species in human plasma based on chemical derivatization coupled with electrospray ionization tandem mass spectrometry. Anal Chim Acta 2018; 1024:101-111. [PMID: 29776536 DOI: 10.1016/j.aca.2018.04.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 12/23/2022]
Abstract
In this study, we developed a novel strategy using solid-phase extraction (SPE) coupled with shotgun mass spectrometry (MS) based on trimethylsilyldiazomethane (TMSCHN2) stable-isotope derivatization for rapid profiling and accurate quantification of phospholipids (PLs) in human plasma. HybridSPE-Phospholipid (HybridSPE-PL, zirconia coated silica stationary phase) was used for sample pretreatment via the Lewis acid-base interaction between zirconia and phosphate moiety of PLs. This step allows rapid enrichment and recovery of PLs from human plasma. Afterward, PLs were derivatized with TMSCHN2, which leads to methylation of hydroxyl and amino groups in PLs and allows highly sensitive PL analysis by shotgun MS in positive ionization mode (limit of detection decreased up to 116.67 fold compared to underived PLs). We developed an accuracy quantification method for determination of PL molecular species in biological samples. Two or more PL standards were selected for each PL class and derivatized with TMSCHN2 without stable-isotope coding. They were then used as the internal standards. PLs in biological samples were isotopic derivatized via acid-catalyzed H/D exchange and methanolysis of TMSCHN2. For accurate quantification, a calibration curve for each class of PLs was typically constructed by using the internal standards to normalize the non-uniformity response caused by the differential fragmentation kinetics resulting from the distinct chemical constitution of individual PL species in the biological samples. This newly developed method was used to comprehensively analyze PL molecular species in human plasma samples. It is a promising methodology for rapid profiling and accurate quantification of complex lipid molecules in biological samples.
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19
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Xie J, Dong W, Liu R, Wang Y, Li Y. Research on the hepatotoxicity mechanism of citrate-modified silver nanoparticles based on metabolomics and proteomics. Nanotoxicology 2017; 12:18-31. [DOI: 10.1080/17435390.2017.1415389] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jiabin Xie
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Wenying Dong
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Rui Liu
- School of Chinese Materia Medica, Shanxi University of Traditional Chinese Medicine, Shanxi, PR China
| | - Yuming Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
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20
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Rustam YH, Reid GE. Analytical Challenges and Recent Advances in Mass Spectrometry Based Lipidomics. Anal Chem 2017; 90:374-397. [PMID: 29166560 DOI: 10.1021/acs.analchem.7b04836] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yepy H Rustam
- Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Gavin E Reid
- Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3010, Australia.,School of Chemistry, University of Melbourne , Parkville, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
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21
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Hu T, Zhang JL. Mass-spectrometry-based lipidomics. J Sep Sci 2017; 41:351-372. [PMID: 28859259 DOI: 10.1002/jssc.201700709] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023]
Abstract
Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.
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Affiliation(s)
- Ting Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
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22
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Recent advances in liquid and gas chromatography methodology for extending coverage of the metabolome. Curr Opin Biotechnol 2017; 43:77-85. [DOI: 10.1016/j.copbio.2016.09.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 01/15/2023]
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23
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Zhang Z, Zhang Y, Yin J, Li Y. An integrated strategy for the rapid extraction and screening of phosphatidylcholines and lysophosphatidylcholines using semi-automatic solid phase extraction and data processing technology. J Chromatogr A 2016; 1461:192-7. [PMID: 27475993 DOI: 10.1016/j.chroma.2016.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
Abstract
This study attempts to establish a comprehensive strategy for the rapid extraction and screening of phosphatidylcholines (PCs) and lysophosphatidylcholines (LysoPCs) in biological samples using semi-automatic solid phase extraction (SPE) and data processing technology based on ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF-MS). First, the Ostro sample preparation method (i.e., semi-automatic SPE) was compared with the Bligh-Dyer method in terms of substance coverage, reproducibility and sample preparation time. Meanwhile, the screening method for PCs and LysoPCs was built through mass range screening, mass defect filtering and diagnostic fragments filtering. Then, the Ostro sample preparation method and the aforementioned screening method were combined under optimal conditions to establish a rapid extraction and screening platform. Finally, this developed method was validated and applied to the preparation and data analysis of tissue samples. Through a systematic evaluation, this developed method was shown to provide reliable and high-throughput experimental results and was suitable for the preparation and analysis of tissue samples. Our method provides a novel strategy for the rapid extraction and analysis of functional phospholipids. In addition, this study will promote further study of phospholipids in disease research.
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Affiliation(s)
- Zhenzhu Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan West Road, Tianjin 300193, China
| | - Yani Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan West Road, Tianjin 300193, China
| | - Jia Yin
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan West Road, Tianjin 300193, China
| | - Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan West Road, Tianjin 300193, China.
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24
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Zhang Z, Qin L, Guo M, Gao S, Zhang Q, Wang Q, Lu Z, Zhao H, Liu Y, Wang M, Fu S, Bai X, Gao X. Delipidation-based solid-phase extraction pretreatment technique for plasma broad-coverage metabolomic profiling to reveal the potential pathogenesis of yeast-induced fever in rats. J Sep Sci 2016; 39:2616-25. [DOI: 10.1002/jssc.201600091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/09/2016] [Accepted: 04/28/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Zhixin Zhang
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Lingling Qin
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Mingxing Guo
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Shanshan Gao
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Qingqing Zhang
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Qing Wang
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Zhiwei Lu
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Huizhen Zhao
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Yuehong Liu
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Meiling Wang
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Shuang Fu
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
| | - Xu Bai
- Waters Technologies (Shanghai) Ltd; Shanghai P. R. China
| | - Xiaoyan Gao
- School of Chinese Materia Medica; Beijing University of Chinese Medicine; Beijing P. R. China
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25
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Cajka T, Fiehn O. Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics. Anal Chem 2015; 88:524-45. [PMID: 26637011 DOI: 10.1021/acs.analchem.5b04491] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomas Cajka
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States
| | - Oliver Fiehn
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States.,King Abdulaziz University , Faculty of Science, Biochemistry Department, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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26
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Semenistaya E, Zvereva I, Krotov G, Rodchenkov G. Solid-phase extraction of small biologically active peptides on cartridges and microelution 96-well plates from human urine. Drug Test Anal 2015; 8:940-9. [DOI: 10.1002/dta.1890] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/12/2015] [Accepted: 09/02/2015] [Indexed: 11/12/2022]
Affiliation(s)
| | - Irina Zvereva
- Antidoping Center; Elizavetinsky per., 10/1 Moscow 105005 Russian Federation
| | - Grigory Krotov
- Antidoping Center; Elizavetinsky per., 10/1 Moscow 105005 Russian Federation
| | - Grigory Rodchenkov
- Antidoping Center; Elizavetinsky per., 10/1 Moscow 105005 Russian Federation
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