501
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Showalter MR, Cajka T, Fiehn O. Epimetabolites: discovering metabolism beyond building and burning. Curr Opin Chem Biol 2017; 36:70-76. [PMID: 28213207 PMCID: PMC5850962 DOI: 10.1016/j.cbpa.2017.01.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/30/2016] [Accepted: 01/18/2017] [Indexed: 12/20/2022]
Abstract
Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism. Epimetabolites are discovered by untargeted metabolomics using liquid- or gas chromatography-high resolution mass spectrometry and structurally annotated by in-silico fragmentation prediction tools. Their specific biological functions are subsequently investigated by targeted metabolomics methods.
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Affiliation(s)
- Megan R Showalter
- NIH West Coast Metabolomics Center, University of California Davis, Davis 95616 CA, United States
| | - Tomas Cajka
- NIH West Coast Metabolomics Center, University of California Davis, Davis 95616 CA, United States
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, Davis 95616 CA, United States; Biochemistry Department, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia.
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502
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Tumanov S, Kamphorst JJ. Recent advances in expanding the coverage of the lipidome. Curr Opin Biotechnol 2017; 43:127-133. [PMID: 27915214 PMCID: PMC5312421 DOI: 10.1016/j.copbio.2016.11.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022]
Abstract
The lipidome comprises a large array of molecules with diverse physicochemical properties. Lipids are structural components of cells, act as a source of energy, and function as signaling mediators. Alterations in lipid metabolism are involved in the onset and progression of a variety of diseases, including metabolic syndrome and cancer. Because of this, interest in lipidomics, the comprehensive characterization of the lipidome by mass spectrometry, has intensified in recent years. However, obtaining a truly complete overview of all lipids in a sample has remained very challenging due to their enormous structural diversity. Here, we provide an overview of the collection of analytical approaches used to study various lipid classes, emphasizing innovations in sample preparation and liquid chromatography-mass spectrometry (LC-MS). Additionally, we provide practical suggestions for increasing the coverage of the lipidome.
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Affiliation(s)
- Sergey Tumanov
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Jurre J Kamphorst
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK.
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503
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Guder JC, Schramm T, Sander T, Link H. Time-Optimized Isotope Ratio LC–MS/MS for High-Throughput Quantification of Primary Metabolites. Anal Chem 2017; 89:1624-1631. [DOI: 10.1021/acs.analchem.6b03731] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Christopher Guder
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Timur Sander
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
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504
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Leuthold P, Schaeffeler E, Winter S, Büttner F, Hofmann U, Mürdter TE, Rausch S, Sonntag D, Wahrheit J, Fend F, Hennenlotter J, Bedke J, Schwab M, Haag M. Comprehensive Metabolomic and Lipidomic Profiling of Human Kidney Tissue: A Platform Comparison. J Proteome Res 2017; 16:933-944. [DOI: 10.1021/acs.jproteome.6b00875] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Patrick Leuthold
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Florian Büttner
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Thomas E. Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Steffen Rausch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
- Department
of Urology, University Hospital Tübingen, 72076 Tübingen, Germany
| | | | | | - Falko Fend
- Institute
of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Jörg Hennenlotter
- Department
of Urology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Jens Bedke
- Department
of Urology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
- Department
of Clinical Pharmacology, University Hospital Tübingen, 72076 Tübingen, Germany
- Department
of Pharmacy and Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
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505
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Begou O, Gika HG, Wilson ID, Theodoridis G. Hyphenated MS-based targeted approaches in metabolomics. Analyst 2017; 142:3079-3100. [DOI: 10.1039/c7an00812k] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Review of targeted metabolomics, with a focus on the description of analytical methods.
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Affiliation(s)
- O. Begou
- Department of Chemistry
- Aristotle University
- 54124 Thessaloniki
- Greece
| | - H. G. Gika
- Department of Medicine
- Aristotle University
- 54124 Thessaloniki
- Greece
| | - I. D. Wilson
- Division of Computational and Systems Medicine
- Department of Surgery and Cancer
- Imperial College
- London
- UK
| | - G. Theodoridis
- Department of Chemistry
- Aristotle University
- 54124 Thessaloniki
- Greece
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506
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LC-MS-Based Lipidomics and Automated Identification of Lipids Using the LipidBlast In-Silico MS/MS Library. Methods Mol Biol 2017; 1609:149-170. [PMID: 28660581 DOI: 10.1007/978-1-4939-6996-8_14] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
This protocol describes the analysis, specifically the identification, of blood plasma lipids. Plasma lipids are extracted using methyl tert-butyl ether (MTBE), methanol, and water followed by separation and data acquisition of isolated lipids using reversed-phase liquid chromatography coupled to quadrupole/time-of-flight mass spectrometry (RPLC-QTOFMS) operated in MS/MS mode. For lipid identification, acquired MS/MS spectra are converted to the mascot generic format (MGF) followed by library search using the in-silico MS/MS library LipidBlast. Using this approach, lipid classes, carbon-chain lengths, and degree of unsaturation of fatty-acid components are annotated.
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507
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Liang Q, Zhu Y, Liu H, Li B, Zhang AH. High-throughput lipidomics enables discovery of the mode of action of huaxian capsule impacting the metabolism of sepsis. RSC Adv 2017. [DOI: 10.1039/c7ra07873k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Severe sepsis (SS) is a major cause of mortality and morbidity in the intensive care unit and requires rapid diagnosis and treatment.
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Affiliation(s)
- Qun Liang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Yongzhi Zhu
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Han Liu
- Simon Fraser University (SFU)
- Burnaby
- Canada
| | - Bingbing Li
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Ai-Hua Zhang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
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508
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Sánchez-López E, Happé H, Steenvoorden E, Crego AL, Marina ML, Peters DJM, Mayboroda OA. A cross-platform metabolomics workflow for volume-restricted tissue samples: application to an animal model for polycystic kidney disease. MOLECULAR BIOSYSTEMS 2017; 13:1940-1945. [DOI: 10.1039/c7mb00245a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Metabolic profiling provides an unbiased view of the physiological status of an organism as a “function” of the metabolic composition of a measured sample.
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Affiliation(s)
- E. Sánchez-López
- Department of Analytical Chemistry
- Physical Chemistry and Chemical Engineering
- University of Alcalá
- 28871 Alcalá de Henares
- Spain
| | - H. Happé
- Department of Human Genetics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - E. Steenvoorden
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - A. L. Crego
- Department of Analytical Chemistry
- Physical Chemistry and Chemical Engineering
- University of Alcalá
- 28871 Alcalá de Henares
- Spain
| | - M. L. Marina
- Department of Analytical Chemistry
- Physical Chemistry and Chemical Engineering
- University of Alcalá
- 28871 Alcalá de Henares
- Spain
| | - D. J. M. Peters
- Department of Human Genetics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - O. A. Mayboroda
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
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509
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Fully Automated Trimethylsilyl (TMS) Derivatisation Protocol for Metabolite Profiling by GC-MS. Metabolites 2016; 7:metabo7010001. [PMID: 28036063 PMCID: PMC5372204 DOI: 10.3390/metabo7010001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/22/2016] [Accepted: 12/26/2016] [Indexed: 11/30/2022] Open
Abstract
Gas Chromatography-Mass Spectrometry (GC-MS) has long been used for metabolite profiling of a wide range of biological samples. Many derivatisation protocols are already available and among these, trimethylsilyl (TMS) derivatisation is one of the most widely used in metabolomics. However, most TMS methods rely on off-line derivatisation prior to GC-MS analysis. In the case of manual off-line TMS derivatisation, the derivative created is unstable, so reduction in recoveries occurs over time. Thus, derivatisation is carried out in small batches. Here, we present a fully automated TMS derivatisation protocol using robotic autosamplers and we also evaluate a commercial software, Maestro available from Gerstel GmbH. Because of automation, there was no waiting time of derivatised samples on the autosamplers, thus reducing degradation of unstable metabolites. Moreover, this method allowed us to overlap samples and improved throughputs. We compared data obtained from both manual and automated TMS methods performed on three different matrices, including standard mix, wine, and plasma samples. The automated TMS method showed better reproducibility and higher peak intensity for most of the identified metabolites than the manual derivatisation method. We also validated the automated method using 114 quality control plasma samples. Additionally, we showed that this online method was highly reproducible for most of the metabolites detected and identified (RSD < 20) and specifically achieved excellent results for sugars, sugar alcohols, and some organic acids. To the very best of our knowledge, this is the first time that the automated TMS method has been applied to analyse a large number of complex plasma samples. Furthermore, we found that this method was highly applicable for routine metabolite profiling (both targeted and untargeted) in any metabolomics laboratory.
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510
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Wang X, Han J, Hardie DB, Yang J, Pan J, Borchers CH. Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:755-767. [PMID: 28017863 DOI: 10.1016/j.bbapap.2016.12.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022]
Abstract
In this work, we combined the use of two MALDI matrices (quercetin and 9-aminoacridine), a recently developed new matrix coating technique - matrix coating assisted by an electric field (MCAEF), and matrix-assisted laser desorption/ionization - Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) to detect and image endogenous compounds in the cancerous and non-cancerous regions of three human prostate cancer (stage II) tissue specimens. After three rounds of imaging data acquisitions (i.e., quercetin for positive and negative ion detection and 9-aminoacridine for negative ion detection), and metabolite identification, a total of 1091 metabolites including 1032 lipids and 59 other metabolites were routinely detected and successfully localized. Of these compounds, 250 and 217 were only detected in either the cancerous or the non-cancerous regions respectively, although we cannot rule out the presence of these metabolites at concentrations below the detection limit. In addition, 152 of the other 624 metabolites showed differential distributions (p<0.05, t-test) between the two regions of the tissues. Further studies on a larger number of clinical specimens will need to be carried out to confirm this large number of apparently cancer-related metabolites. The successful determination of the spatial locations and abundances of these endogenous biomolecules indicated significant metabolism abnormalities - e.g., increased energy charge and under-expression of neutral acyl glycerides, in the prostate cancer samples. To our knowledge, this work has resulted in MALDI-MS imaging of the largest group of metabolites in prostate cancer thus far and demonstrated the importance of using complementary matrices for comprehensive metabolomic imaging by MALDI-MS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jingxi Pan
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
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511
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Sitnikov DG, Monnin CS, Vuckovic D. Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS. Sci Rep 2016; 6:38885. [PMID: 28000704 PMCID: PMC5175266 DOI: 10.1038/srep38885] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/10/2016] [Indexed: 12/28/2022] Open
Abstract
The comparison of extraction methods for global metabolomics is usually executed in biofluids only and focuses on metabolite coverage and method repeatability. This limits our detailed understanding of extraction parameters such as recovery and matrix effects and prevents side-by-side comparison of different sample preparation strategies. To address this gap in knowledge, seven solvent-based and solid-phase extraction methods were systematically evaluated using standard analytes spiked into both buffer and human plasma. We compared recovery, coverage, repeatability, matrix effects, selectivity and orthogonality of all methods tested for non-lipid metabolome in combination with reversed-phased and mixed-mode liquid chromatography mass spectrometry analysis (LC-MS). Our results confirmed wide selectivity and excellent precision of solvent precipitations, but revealed their high susceptibility to matrix effects. The use of all seven methods showed high overlap and redundancy which resulted in metabolite coverage increases of 34-80% depending on LC-MS method employed as compared to the best single extraction protocol (methanol/ethanol precipitation) despite 7x increase in MS analysis time and sample consumption. The most orthogonal methods to methanol-based precipitation were ion-exchange solid-phase extraction and liquid-liquid extraction using methyl-tertbutyl ether. Our results help facilitate rational design and selection of sample preparation methods and internal standards for global metabolomics.
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Affiliation(s)
- Dmitri G. Sitnikov
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec, H4B 1R6, Canada
- PERFORM Centre, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec, H4B 1R6, Canada
| | - Cian S. Monnin
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec, H4B 1R6, Canada
| | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec, H4B 1R6, Canada
- PERFORM Centre, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec, H4B 1R6, Canada
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512
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Li Z, Li Y, Chen W, Cao Q, Guo Y, Wan N, Jiang X, Tang YJ, Wang Q, Shui W. Integrating MS1 and MS2 Scans in High-Resolution Parallel Reaction Monitoring Assays for Targeted Metabolite Quantification and Dynamic 13C-Labeling Metabolism Analysis. Anal Chem 2016; 89:877-885. [DOI: 10.1021/acs.analchem.6b03947] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zhucui Li
- Tianjin Institute
of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yujing Li
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wujiu Chen
- Tianjin Institute
of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qichen Cao
- Tianjin Institute
of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yufeng Guo
- Tianjin Institute
of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ni Wan
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Xiaolong Jiang
- Tianjin Institute
of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yinjie J. Tang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Qinhong Wang
- Tianjin Institute
of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
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513
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Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA. Untargeted Metabolomics Strategies-Challenges and Emerging Directions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1897-1905. [PMID: 27624161 PMCID: PMC5110944 DOI: 10.1007/s13361-016-1469-y] [Citation(s) in RCA: 692] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 05/05/2023]
Abstract
Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches. Research focuses have now shifted toward a fundamental understanding of the biology responsible for metabolomic changes. There are several types of metabolomics experiments including both targeted and untargeted analyses. While untargeted, hypothesis generating workflows exhibit many valuable attributes, challenges inherent to the approach remain. This Critical Insight comments on these challenges, focusing on the identification process of LC-MS-based untargeted metabolomics studies-specifically in mammalian systems. Biological interpretation of metabolomics data hinges on the ability to accurately identify metabolites. The range of confidence associated with identifications that is often overlooked is reviewed, and opportunities for advancing the metabolomics field are described. Graphical Abstract ᅟ.
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Affiliation(s)
- Alexandra C Schrimpe-Rutledge
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - Stacy D Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA.
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514
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Kompauer M, Heiles S, Spengler B. Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution. Nat Methods 2016; 14:90-96. [PMID: 27842060 DOI: 10.1038/nmeth.4071] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023]
Abstract
We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of 0.9 at 337 nm and a free working distance of 18 mm in coaxial geometry to an orbitrap mass spectrometer and optimizing the matrix application. We demonstrate improvement in image contrast, lateral resolution, and ion yield per unit area compared with a state-of-the-art commercial MSI source. We show that our setup can be used to detect metabolites, lipids, and small peptides, as well as to perform tandem MS experiments with 1.5-μm2 sampling areas. To showcase these capabilities, we identified subcellular lipid, metabolite, and peptide distributions that differentiate, for example, cilia and oral groove in Paramecium caudatum.
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Affiliation(s)
- Mario Kompauer
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
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515
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Regueiro J, Negreira N, Berntssen MHG. Ion-Mobility-Derived Collision Cross Section as an Additional Identification Point for Multiresidue Screening of Pesticides in Fish Feed. Anal Chem 2016; 88:11169-11177. [PMID: 27779869 DOI: 10.1021/acs.analchem.6b03381] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility spectrometry allows for the measurement of the collision cross section (CCS), which provides information about the shape of an ionic molecule in the gas phase. Although the hyphenation of traveling-wave ion mobility spectrometry (TWIMS) with high-resolution quadrupole time-of-flight mass spectrometry (QTOFMS) has been mainly used for structural elucidation purposes, its potential for fast screening of small molecules in complex samples has not yet been thoroughly evaluated. The current work explores the capabilities of ultrahigh-performance liquid chromatography (UHPLC) coupled to a new design TWIMS-QTOFMS for the screening and identification of a large set of pesticides in complex salmon feed matrices. A database containing TWIMS-derived CCS values for more than 200 pesticides is hereby presented. CCS measurements showed high intra- and interday repeatability (RSD < 1%), and they were not affected by the complexity of the investigated matrices (ΔCCS ≤ 1.8%). The use of TWIMS in combination with QTOFMS was demonstrated to provide an extra-dimension, which resulted in increased peak capacity and selectivity in real samples. Thus, many false-positive detections could be straightforwardly discarded just by applying a maximum ΔCCS tolerance of ±2%. CCS was proposed as a valuable additional identification point in the pesticides screening workflow. Several commercial fish feed samples were finally analyzed to demonstrate the applicability of the proposed approach. Ethoxyquin and pirimiphos-methyl were identified in most of the analyzed samples, whereas tebuconazole and piperonil butoxide were identified for the first time in fish feed samples.
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Affiliation(s)
- Jorge Regueiro
- National Institute of Nutrition and Seafood Research (NIFES), P.O. Box 2029 Nordnes, N-5817 Bergen, Norway
| | - Noelia Negreira
- National Institute of Nutrition and Seafood Research (NIFES), P.O. Box 2029 Nordnes, N-5817 Bergen, Norway
| | - Marc H G Berntssen
- National Institute of Nutrition and Seafood Research (NIFES), P.O. Box 2029 Nordnes, N-5817 Bergen, Norway
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516
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Zhou Z, Shen X, Tu J, Zhu ZJ. Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry. Anal Chem 2016; 88:11084-11091. [DOI: 10.1021/acs.analchem.6b03091] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhiwei Zhou
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
| | - Xiaotao Shen
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
| | - Jia Tu
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
| | - Zheng-Jiang Zhu
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
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517
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Jorge TF, Mata AT, António C. Mass spectrometry as a quantitative tool in plant metabolomics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:20150370. [PMID: 27644967 PMCID: PMC5031636 DOI: 10.1098/rsta.2015.0370] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 05/03/2023]
Abstract
Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Tiago F Jorge
- Plant Metabolomics Laboratory, ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Ana T Mata
- Plant Metabolomics Laboratory, ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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518
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Strategy for non-target ionic analysis by capillary electrophoresis with ultraviolet detection. Anal Bioanal Chem 2016; 409:1067-1077. [DOI: 10.1007/s00216-016-0025-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 01/11/2023]
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519
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Furuhashi T, Nakamura T, Fragner L, Roustan V, Schön V, Weckwerth W. Biodiesel and poly-unsaturated fatty acids production from algae and crop plants - a rapid and comprehensive workflow for lipid analysis. Biotechnol J 2016; 11:1262-1267. [PMID: 27440175 DOI: 10.1002/biot.201400197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/17/2016] [Accepted: 07/07/2016] [Indexed: 11/07/2022]
Abstract
Fatty acid methyl ester analysis (FAME) by gas chromatography coupled to mass spectrometry (GC-MS) is a widely used technique in biodiesel/bioproduct (e.g. poly-unsaturated fatty acids, PUFA) research but typically does not allow distinguishing between bound and free fatty acids. To understand and optimize biosynthetic pathways, however, the origin of the fatty acid is an important information. Furthermore the annotation of PUFAs is compromised in classical GC-EI-MS because the precursor molecular ion is missing. In the present protocol an alkaline methyl esterification step with TMS derivatization enabling the simultaneous analysis of bound and free fatty acids but also further lipids such as sterols in one GC-MS chromatogram is combined. This protocol is applied to different lipid extracts from single cell algae to higher plants: Chlorella vulgaris, Chlamydomonas reinhardtii, Coffea arabica, Pisum sativum and Cuscuta japonica. Further, field ionization (GC-FI-MS) is introduced for a better annotation of fatty acids and exact determination of the number of double bonds in PUFAs. The proposed workflow provides a convenient strategy to analyze algae and other plant crop systems with respect to their capacity for third generation biodiesel and high-quality bioproducts for nutrition such as PUFAs.
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Affiliation(s)
- Takeshi Furuhashi
- Department of Ecogenomics and Systems Biology, Vienna University, Vienna, Austria.
| | - Takemichi Nakamura
- Collaboration Promotion Unit, RIKEN Global Research Cluster, Wako,, Saitama, Japan
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, Vienna University, Vienna, Austria
| | - Valentin Roustan
- Department of Ecogenomics and Systems Biology, Vienna University, Vienna, Austria
| | - Verena Schön
- Department of Ecogenomics and Systems Biology, Vienna University, Vienna, Austria
- Ecoduna Produktions GmbH, Bruck/Leitha, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Vienna University, Vienna, Austria.
- Vienna Metabolomics Center (VIME), Vienna University, Vienna, Austria.
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520
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Albrecht U, Fiehn O, Bowman KD. Metabolic variations in different citrus rootstock cultivars associated with different responses to Huanglongbing. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:33-44. [PMID: 27236226 DOI: 10.1016/j.plaphy.2016.05.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/03/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive bacterial diseases of citrus. No resistant cultivars have been identified, although tolerance has been observed in the genus Poncirus and some of its hybrids with Citrus that are commonly used as rootstocks. In this study we exploited this tolerance by comparing five different tolerant hybrids with a cultivar that shows pronounced HLB sensitivity to discern potential contributing metabolic factors. Whole leaves of infected and non-infected greenhouse-grown seedlings were extracted and subjected to untargeted GC-TOF MS based metabolomics. After BinBase data filtering, 342 (experiment 1) and 650 (experiment 2) unique metabolites were quantified, of which 122 and 195, respectively, were assigned by chemical structures. The number of metabolites found to be differently regulated in the infected state compared with the non-infected state varied between the cultivars and was largest (166) in the susceptible cultivar Cleopatra mandarin (Citrus reticulata) and lowest (3) in the tolerant cultivars US-897 (C. reticulata 'Cleopatra' × Poncirus trifoliata) and US-942 (C. reticulata 'Sunki' × P. trifoliata) from experiment 2. Tolerance to HLB did not appear to be associated with accumulation of higher amounts of protective metabolites in response to infection. Many metabolites were found in higher concentrations in the tolerant cultivars compared with susceptible Cleopatra mandarin and may play important roles in conferring tolerance to HLB. Lower availability of specific sugars necessary for survival of the pathogen may also be a contributing factor in the decreased disease severity observed for these cultivars.
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Affiliation(s)
- Ute Albrecht
- Southwest Florida Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, 2685 SR 29 North, Immokalee, FL 34142, USA; US Horticultural Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 2001 South Rock Rd., Fort Pierce, FL 34945, USA.
| | - Oliver Fiehn
- UC Davis Genome Center - Metabolomics, University of California, 451 Health Drive, Davis, CA 95616, USA; King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
| | - Kim D Bowman
- US Horticultural Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 2001 South Rock Rd., Fort Pierce, FL 34945, USA
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521
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Tebani A, Afonso C, Marret S, Bekri S. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations. Int J Mol Sci 2016; 17:ijms17091555. [PMID: 27649151 PMCID: PMC5037827 DOI: 10.3390/ijms17091555] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM) are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.
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Affiliation(s)
- Abdellah Tebani
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031 Rouen, France.
- Normandie University, UNIROUEN, INSERM, CHU Rouen, Laboratoire NeoVasc ERI28, 76000 Rouen, France.
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Carlos Afonso
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Stéphane Marret
- Normandie University, UNIROUEN, INSERM, CHU Rouen, Laboratoire NeoVasc ERI28, 76000 Rouen, France.
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031 Rouen, France.
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031 Rouen, France.
- Normandie University, UNIROUEN, INSERM, CHU Rouen, Laboratoire NeoVasc ERI28, 76000 Rouen, France.
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522
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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523
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Gorrochategui E, Jaumot J, Lacorte S, Tauler R. Data analysis strategies for targeted and untargeted LC-MS metabolomic studies: Overview and workflow. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.07.004] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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524
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Chemical derivatization-based LC–MS for metabolomics: advantages and challenges. Bioanalysis 2016; 8:1881-3. [DOI: 10.4155/bio-2016-0192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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525
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Li H, Cai Y, Guo Y, Chen F, Zhu ZJ. MetDIA: Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition. Anal Chem 2016; 88:8757-64. [DOI: 10.1021/acs.analchem.6b02122] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hao Li
- Interdisciplinary Research
Center on Biology and Chemistry, and Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
| | - Yuping Cai
- Interdisciplinary Research
Center on Biology and Chemistry, and Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
| | - Yuan Guo
- Interdisciplinary Research
Center on Biology and Chemistry, and Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
| | - Fangfang Chen
- Interdisciplinary Research
Center on Biology and Chemistry, and Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research
Center on Biology and Chemistry, and Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
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526
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Abstract
Aim: Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) has recently emerged as a powerful high resolution mass spectrometric data independent acquisition technique. In the present work, the potential and challenges of an integrated strategy based on LC-SWATH/MS for simultaneous drug metabolism and metabolomics studies was investigated. Methodology: The richness of SWATH data allows numerous data analysis approaches, including: detection of metabolites by prediction; metabolite detection by mass defect filtering; quantification from high-resolution MS precursor chromatograms or fragment chromatograms. Multivariate analysis can be applied to the data from the full scan or SWATH windows and allows changes in endogenous metabolites as well as xenobiotic metabolites, to be detected. Principal component variable grouping detects intersample variable correlation and groups variables with similar profiles which simplifies interpretation and highlights related ions and fragments. Principal component variable grouping can extract product ion spectra from the data collected by fragmenting a wide precursor ion window. Conclusion: It was possible to characterize 28 vinpocetine metabolites in urine, mostly mono- and di-hydroxylated forms, and detect endogenous metabolite expression changes in urine after the administration of a single dose of a model drug (vinpocetine) to rats.
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527
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Darshi M, Van Espen B, Sharma K. Metabolomics in Diabetic Kidney Disease: Unraveling the Biochemistry of a Silent Killer. Am J Nephrol 2016; 44:92-103. [PMID: 27410520 PMCID: PMC6581452 DOI: 10.1159/000447954] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The development of new therapies for chronic diseases, such as diabetic kidney disease (DKD), will continue to be hampered by lack of sufficient biomarkers that will provide insights and will be responsive to treatment interventions. The recent application of metabolomic technologies, such as nuclear magnetic resonance and mass spectroscopy, has allowed large-scale analysis of small molecules to be interrogated in a targeted or untargeted manner. Recent advances from both human and animal studies that have arisen from metabolomic analysis have recognized that mitochondrial function and fatty acid oxidation play key roles in the development and progression of DKD. Although many challenges in the technology for clinical chronic kidney disease (CKD) are yet to be validated, there will very likely be ongoing major contributions of metabolomics to develop new biochemical understanding for diabetic and CKD. The clinical application of metabolomics and accompanying bioinformatic tools will likely be a cornerstone of personalized medicine triumphs for CKD.
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Affiliation(s)
- Manjula Darshi
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Center for Renal Translational Medicine, University of California San Diego, La Jolla, California 92093, USA
- Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, California 92093, USA
| | - Benjamin Van Espen
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Center for Renal Translational Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Kumar Sharma
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Center for Renal Translational Medicine, University of California San Diego, La Jolla, California 92093, USA
- Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, California 92093, USA
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528
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Dona AC, Coffey S, Figtree G. Translational and emerging clinical applications of metabolomics in cardiovascular disease diagnosis and treatment. Eur J Prev Cardiol 2016; 23:1578-89. [DOI: 10.1177/2047487316645469] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/31/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Anthony C Dona
- North Shore Heart Research, Kolling Institute, Sydney Medical School (Northern), University of Sydney, Australia
- Charles Perkins Centre, University of Sydney, Australia
| | - Sean Coffey
- North Shore Heart Research, Kolling Institute, Sydney Medical School (Northern), University of Sydney, Australia
- Department of Cardiology, Royal North Shore Hospital, St Leonards, Australia
| | - Gemma Figtree
- North Shore Heart Research, Kolling Institute, Sydney Medical School (Northern), University of Sydney, Australia
- Charles Perkins Centre, University of Sydney, Australia
- Department of Cardiology, Royal North Shore Hospital, St Leonards, Australia
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529
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Abstract
Metabolomics-based strategies have become an integral part of modern clinical research, allowing for a better understanding of pathophysiological conditions and disease mechanisms, as well as providing innovative tools for more adequate diagnostic and prognosis approaches. Metabolomics is considered an essential tool in precision medicine, which aims for personalized prevention and tailor-made treatments. Nevertheless, multiple pitfalls may be encountered in clinical metabolomics during the entire workflow, hampering the quality of the data and, thus, the biological interpretation. This review describes the challenges underlying metabolomics-based experiments, discussing step by step the potential pitfalls of the analytical process, including study design, sample collection, storage, as well as preparation, chromatographic and electrophoretic separation, detection and data analysis. Moreover, it offers practical solutions and strategies to tackle these challenges, ensuring the generation of high-quality data.
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530
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Collins JR, Edwards BR, Fredricks HF, Van Mooy BAS. LOBSTAHS: An Adduct-Based Lipidomics Strategy for Discovery and Identification of Oxidative Stress Biomarkers. Anal Chem 2016; 88:7154-62. [DOI: 10.1021/acs.analchem.6b01260] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- James R. Collins
- Massachusetts
Institute of Technology/Woods Hole Oceanographic Institution Joint
Program in Oceanography, Woods Hole, Massachusetts 02543, United States
- Department
of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Bethanie R. Edwards
- Massachusetts
Institute of Technology/Woods Hole Oceanographic Institution Joint
Program in Oceanography, Woods Hole, Massachusetts 02543, United States
- Department
of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Helen F. Fredricks
- Department
of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Benjamin A. S. Van Mooy
- Department
of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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531
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Lu N, Chen JH, Wei D, Chen F, Chen G. Global Metabolic Regulation of the Snow Alga Chlamydomonas nivalis in Response to Nitrate or Phosphate Deprivation by a Metabolome Profile Analysis. Int J Mol Sci 2016; 17:ijms17050694. [PMID: 27171077 PMCID: PMC4881520 DOI: 10.3390/ijms17050694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 01/27/2023] Open
Abstract
In the present work, Chlamydomonas nivalis, a model species of snow algae, was used to illustrate the metabolic regulation mechanism of microalgae under nutrient deprivation stress. The seed culture was inoculated into the medium without nitrate or phosphate to reveal the cell responses by a metabolome profile analysis using gas chromatography time-of-flight mass spectrometry (GC/TOF-MS). One hundred and seventy-one of the identified metabolites clustered into five groups by the orthogonal partial least squares discriminant analysis (OPLS-DA) model. Among them, thirty of the metabolites in the nitrate-deprived group and thirty-nine of the metabolites in the phosphate-deprived group were selected and identified as “responding biomarkers” by this metabolomic approach. A significant change in the abundance of biomarkers indicated that the enhanced biosynthesis of carbohydrates and fatty acids coupled with the decreased biosynthesis of amino acids, N-compounds and organic acids in all the stress groups. The up- or down-regulation of these biomarkers in the metabolic network provides new insights into the global metabolic regulation and internal relationships within amino acid and fatty acid synthesis, glycolysis, the tricarboxylic acid cycle (TCA) and the Calvin cycle in the snow alga under nitrate or phosphate deprivation stress.
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Affiliation(s)
- Na Lu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Jun-Hui Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Dong Wei
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Feng Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Gu Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
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532
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Xie T, Zhou X, Wang S, Lu Y, Zhu H, Kang A, Deng H, Xu J, Shen C, Di L, Shan J. Development and application of a comprehensive lipidomic analysis to investigate Tripterygium wilfordii-induced liver injury. Anal Bioanal Chem 2016; 408:4341-55. [PMID: 27086014 DOI: 10.1007/s00216-016-9533-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/30/2016] [Indexed: 12/16/2022]
Abstract
Lipid metabolic pathways play pivotal roles in liver function, and disturbances of these pathways are associated with various diseases. Thus, comprehensive characterization and measurement of lipid metabolites are essential to deciphering the contributions of lipid network metabolism to diseases or its responses to drug intervention. Here, we report an integrated lipidomic analysis for the comprehensive detection of lipid metabolites. To facilitate the characterization of untargeted lipids through fragmentation analysis, nine formulas were proposed to identify the fatty acid composition of lipids from complex MS (n) spectrum information. By these formulas, the co-eluted isomeric compounds could be distinguished. In total, 250 lipids were detected and characterized, including diacylglycerols, triacylglycerols, glycerophosphoethanolamines, glycerophosphocholines, glycerophosphoserines, glycerophosphoglycerols, glycerophosphoinositols, cardiolipins, ceramides, and sphingomyelins. Integrated with the targeted lipidomics, a total of 27 inflammatory oxylipins were also measured. To evaluate the aberrant lipid metabolism involved in liver injury induced by Tripterygium wilfordii, lipid network metabolism was further investigated. Results indicated that energy lipid modification, membrane remodeling, potential signaling lipid alterations, and abnormal inflammation response were associated with injury. Because of the important roles of lipids in liver metabolism, this new method is expected to be useful in analyzing other lipid metabolism diseases.
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Affiliation(s)
- Tong Xie
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China.
| | - Xueping Zhou
- The First Clinical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Shouchuan Wang
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Yan Lu
- The First Clinical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Huaxu Zhu
- Jiangsu Engineering Research Center for Efficient Delivery System of TCM, College of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - An Kang
- Jiangsu Engineering Research Center for Efficient Delivery System of TCM, College of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Haishan Deng
- Jiangsu Engineering Research Center for Efficient Delivery System of TCM, College of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Jianya Xu
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Cunsi Shen
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Liuqing Di
- Jiangsu Engineering Research Center for Efficient Delivery System of TCM, College of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China.
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533
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Tebani A, Schmitz-Afonso I, Rutledge DN, Gonzalez BJ, Bekri S, Afonso C. Optimization of a liquid chromatography ion mobility-mass spectrometry method for untargeted metabolomics using experimental design and multivariate data analysis. Anal Chim Acta 2016; 913:55-62. [DOI: 10.1016/j.aca.2016.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 01/10/2023]
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534
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Liang Q, Liu H, Jiang Y, Xing H, Zhang T, Zhang AH. Discovering lipid phenotypic changes of sepsis-induced lung injury using high-throughput lipidomic analysis. RSC Adv 2016. [DOI: 10.1039/c6ra03979k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The aim of this study was to use lipidomics to identify lipid molecules that could predict patients with sepsis-induced lung injury.
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Affiliation(s)
- Qun Liang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Han Liu
- Simon Fraser University (SFU)
- Burnaby
- Canada
| | - Yan Jiang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Haitao Xing
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Tianyu Zhang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Ai-Hua Zhang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
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535
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Liu J, Xiao HT, Wang HS, Mu HX, Zhao L, Du J, Yang D, Wang D, Bian ZX, Lin SH. Halofuginone reduces the inflammatory responses of DSS-induced colitis through metabolic reprogramming. MOLECULAR BIOSYSTEMS 2016; 12:2296-2303. [DOI: 10.1039/c6mb00154h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Halofuginone inhibits both HIF-1alpha and incomplete FAO to reduce the inflammatory response in DSS-induced colitis.
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Affiliation(s)
- Jing Liu
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
- School of Chinese Medicine
| | - Hai-Tao Xiao
- School of Chinese Medicine
- Hong Kong Baptist University
- China
- School of Pharmacy
- Guizhou Medicial University
| | - Hong-Sheng Wang
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Huai-Xue Mu
- School of Chinese Medicine
- Hong Kong Baptist University
- China
| | - Ling Zhao
- School of Chinese Medicine
- Hong Kong Baptist University
- China
| | - Jun Du
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Depo Yang
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Dongmei Wang
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | | | - Shu-Hai Lin
- School of Chinese Medicine
- Hong Kong Baptist University
- China
- Department of Biochemistry and Molecular Cell Biology
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation
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