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Tsoukalas D, Sarandi E, Thanasoula M, Docea AO, Tsilimidos G, Calina D, Tsatsakis A. Metabolic Fingerprint of Chronic Obstructive Lung Diseases: A New Diagnostic Perspective. Metabolites 2019; 9:E290. [PMID: 31779131 PMCID: PMC6949962 DOI: 10.3390/metabo9120290] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic obstructive lung disease (COLD) is a group of airway diseases, previously known as emphysema and chronic bronchitis. The heterogeneity of COLD does not allow early diagnosis and leads to increased morbidity and mortality. The increasing number of COLD incidences stresses the need for precision medicine approaches that are specific to the patient. Metabolomics is an emerging technology that allows for the discrimination of metabolic changes in the cell as a result of environmental factors and specific genetic background. Thus, quantification of metabolites in human biofluids can provide insights into the metabolic state of the individual in real time and unravel the presence of, or predisposition to, a disease. In this article, the advantages of and potential barriers to putting metabolomics into clinical practice for COLD are discussed. Today, metabolomics is mostly lab-based, and research studies with novel COLD-specific biomarkers are continuously being published. Several obstacles in the research and the market field hamper the translation of these data into clinical practice. However, technological and computational advances will facilitate the clinical interpretation of data and provide healthcare professionals with the tools to prevent, diagnose, and treat COLD with precision in the coming decades.
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Affiliation(s)
- Dimitris Tsoukalas
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
- Metabolomic Medicine Clinic, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece; (E.S.); (M.T.); (G.T.)
| | - Evangelia Sarandi
- Metabolomic Medicine Clinic, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece; (E.S.); (M.T.); (G.T.)
- Laboratory of Toxicology and Forensic Sciences, Medical School, University of Crete, 71003 Heraklion, Greece;
| | - Maria Thanasoula
- Metabolomic Medicine Clinic, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece; (E.S.); (M.T.); (G.T.)
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Gerasimos Tsilimidos
- Metabolomic Medicine Clinic, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece; (E.S.); (M.T.); (G.T.)
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Aristides Tsatsakis
- Laboratory of Toxicology and Forensic Sciences, Medical School, University of Crete, 71003 Heraklion, Greece;
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Ismail IT, Showalter MR, Fiehn O. Inborn Errors of Metabolism in the Era of Untargeted Metabolomics and Lipidomics. Metabolites 2019; 9:metabo9100242. [PMID: 31640247 PMCID: PMC6835511 DOI: 10.3390/metabo9100242] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022] Open
Abstract
Inborn errors of metabolism (IEMs) are a group of inherited diseases with variable incidences. IEMs are caused by disrupting enzyme activities in specific metabolic pathways by genetic mutations, either directly or indirectly by cofactor deficiencies, causing altered levels of compounds associated with these pathways. While IEMs may present with multiple overlapping symptoms and metabolites, early and accurate diagnosis of IEMs is critical for the long-term health of affected subjects. The prevalence of IEMs differs between countries, likely because different IEM classifications and IEM screening methods are used. Currently, newborn screening programs exclusively use targeted metabolic assays that focus on limited panels of compounds for selected IEM diseases. Such targeted approaches face the problem of false negative and false positive diagnoses that could be overcome if metabolic screening adopted analyses of a broader range of analytes. Hence, we here review the prospects of using untargeted metabolomics for IEM screening. Untargeted metabolomics and lipidomics do not rely on predefined target lists and can detect as many metabolites as possible in a sample, allowing to screen for many metabolic pathways simultaneously. Examples are given for nontargeted analyses of IEMs, and prospects and limitations of different metabolomics methods are discussed. We conclude that dedicated studies are needed to compare accuracy and robustness of targeted and untargeted methods with respect to widening the scope of IEM diagnostics.
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Affiliation(s)
- Israa T Ismail
- National Liver Institute, Menoufia University, Shebeen El Kom 55955, Egypt.
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Megan R Showalter
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
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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: 63] [Impact Index Per Article: 12.6] [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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Mawalagedera SMUP, Callahan DL, Gaskett AC, Rønsted N, Symonds MRE. Combining Evolutionary Inference and Metabolomics to Identify Plants With Medicinal Potential. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Llufrio EM, Cho K, Patti GJ. Systems-level analysis of isotopic labeling in untargeted metabolomic data by X 13CMS. Nat Protoc 2019; 14:1970-1990. [PMID: 31168088 PMCID: PMC7323898 DOI: 10.1038/s41596-019-0167-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 03/15/2019] [Indexed: 12/18/2022]
Abstract
Identification of previously unreported metabolites (so-called 'unknowns') in untargeted metabolomic data has become an increasingly active area of research. Considerably less attention, however, has been dedicated to identifying unknown metabolic pathways. Yet, for each unknown metabolite structure, there is potentially a yet-to-be-discovered chemical transformation. Elucidating these biochemical connections is essential to advancing our knowledge of cellular metabolism and can be achieved by tracking an isotopically labeled precursor to an unexpected product. In addition to their role in mapping metabolic fates, isotopic labels also provide critical insight into pathway dynamics (i.e., metabolic fluxes) that cannot be obtained from conventional label-free metabolomic analyses. When labeling is compared quantitatively between conditions, for example, isotopic tracers can enable relative pathway activities to be inferred. To discover unexpected chemical transformations or unanticipated differences in metabolic pathway activities, we have developed X13CMS, a platform for analyzing liquid chromatography/mass spectrometry (LC/MS) data at the systems level. After providing cells, animals, or patients with an isotopically enriched metabolite (e.g., 13C, 15N, or 2H), X13CMS identifies compounds that have incorporated the isotopic tracer and reports the extent of labeling for each. The analysis can be performed with a single condition, or isotopic fates can be compared between multiple conditions. The choice of which metabolite to enrich and which isotopic label to use is highly context dependent, but 13C-glucose and 13C-glutamine are often applied because they feed a large number of metabolic pathways. X13CMS is freely available.
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Affiliation(s)
- Elizabeth M Llufrio
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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Asami P, Rupasinghe T, Moghaddam L, Njaci I, Roessner U, Mundree S, Williams B. Roots of the Resurrection Plant Tripogon loliiformis Survive Desiccation Without the Activation of Autophagy Pathways by Maintaining Energy Reserves. FRONTIERS IN PLANT SCIENCE 2019; 10:459. [PMID: 31105716 PMCID: PMC6494956 DOI: 10.3389/fpls.2019.00459] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/27/2019] [Indexed: 05/18/2023]
Abstract
Being sessile, plants must regulate energy balance, potentially via source-sink relations, to compromise growth with survival in stressful conditions. Crops are sensitive, possibly because they allocate their energy resources toward growth and yield rather than stress tolerance. In contrast, resurrection plants tightly regulate sugar metabolism and use a series of physiological adaptations to suppress cell death in their vegetative tissue to regain full metabolic capacity from a desiccated state within 72 h of watering. Previously, we showed that shoots of the resurrection plant Tripogon loliiformis, initiate autophagy upon dehydration as one strategy to reinstate homeostasis and suppress cell death. Here, we describe the relationship between energy status, sugar metabolism, trehalose-mediated activation of autophagy pathways and investigate whether shoots and roots utilize similar desiccation tolerance strategies. We show that despite containing high levels of trehalose, dehydrated Tripogon roots do not display elevated activation of autophagy pathways. Using targeted and non-targeted metabolomics, transmission electron microscopy (TEM) and transcriptomics we show that T. loliiformis engages a strategy similar to the long-term drought responses of sensitive plants and continues to use the roots as a sink even during sustained stress. Dehydrating T. loliiformis roots contained more sucrose and trehalose-6-phosphate compared to shoots at an equivalent water content. The increased resources in the roots provides sufficient energy to cope with stress and thus autophagy is not required. These results were confirmed by the absence of autophagosomes in roots by TEM. Upregulation of sweet genes in both shoots and roots show transcriptional regulation of sucrose translocation from leaves to roots and within roots during dehydration. Differences in the cell's metabolic status caused starkly different cell death responses between shoots and roots. These findings show how shoots and roots utilize different stress response strategies and may provide candidate targets that can be used as tools for the improvement of stress tolerance in crops.
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Affiliation(s)
- Pauline Asami
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thusitha Rupasinghe
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Lalehvash Moghaddam
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Isaac Njaci
- Biosciences Eastern and Central Africa-International Livestock Research Institute, Nairobi, Kenya
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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Djoumbou-Feunang Y, Pon A, Karu N, Zheng J, Li C, Arndt D, Gautam M, Allen F, Wishart DS. CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification. Metabolites 2019; 9:metabo9040072. [PMID: 31013937 PMCID: PMC6523630 DOI: 10.3390/metabo9040072] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/31/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM-ID) was developed to accurately predict electrospray ionization-MS/MS (ESI-MS/MS) spectra from chemical structures and to aid in compound identification via MS/MS spectral matching. While earlier versions of CFM-ID performed very well, CFM-ID's performance for predicting the MS/MS spectra of certain classes of compounds, including many lipids, was quite poor. Furthermore, CFM-ID's compound identification capabilities were limited because it did not use experimentally available MS/MS spectra nor did it exploit metadata in its spectral matching algorithm. Here, we describe significant improvements to CFM-ID's performance and speed. These include (1) the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID; (2) the inclusion of experimental MS/MS spectra and other metadata to enhance CFM-ID's compound identification abilities; (3) the development of new scoring functions that improves CFM-ID's accuracy by 21.1%; and (4) the implementation of a chemical classification algorithm that correctly classifies unknown chemicals (based on their MS/MS spectra) in >80% of the cases. This improved version called CFM-ID 3.0 is freely available as a web server. Its source code is also accessible online.
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Affiliation(s)
| | - Allison Pon
- OMx Personal Health Analytics, Edmonton, AB T5J 1B9, Canada.
| | - Naama Karu
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jiamin Zheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Carin Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - David Arndt
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Maheswor Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Felicity Allen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
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Boonchaisri S, Rochfort S, Stevenson T, Dias DA. Recent developments in metabolomics-based research in understanding transgenic grass metabolism. Metabolomics 2019; 15:47. [PMID: 30877485 DOI: 10.1007/s11306-019-1507-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Transgenic herbicide-resistant (HR) turfgrass together with its associated, broad spectrum herbicides promise cheap, selective and efficient weed control by excluding infested weeds resulting in turf lawn with high uniformity and aesthetic value. The concept of this "weeding program" initiated from modern biotechnology has been widely implemented in several principal crops including maize, soybean, canola and cotton as early as the 1990s. Transgenic HR turfgrass classified as a genetically modified organism (GMO) has undoubtedly caused public concern with respect to its biosafety and legalities similar to well-established HR crops. Nevertheless, applying metabolomics-based approaches which focuses on the identification of the global metabolic state of a biological system in response to either internal or external stimuli can also provide a comprehensive characterization of transgenic grass metabolism and its involvement in biosecurity and public perception. AIM OF REVIEW This review summaries the recent applications of metabolomics applied to HR crops to predict the molecular and physiological phenotypes of HR turfgrass species, glyphosate-resistant Kentucky bluegrass (Poa pratensis L.) and glufosinate-resistant creeping bentgrass (Agrotis stonifera L.). Additionally, this review also presents background knowledge with respect to the application of metabolomics, transformation of HR crops and its biosafety concerns, turfgrass botanical knowledge and its economic and aesthetic value. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is to demonstrate the molecular and physiological phenotypes of HR turfgrass based on several lines of evidence primarily derived from metabolomics data applied to HR crops to identify alterations on HR turfgrass metabolism as a result of genetic modification that confers resistant traits.
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Affiliation(s)
| | - Simone Rochfort
- Agriculture Research Victoria, AgriBio, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
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Thomas M, Stuani L, Darii E, Lechaplais C, Pateau E, Tabet JC, Salanoubat M, Saaidi PL, Perret A. De novo structure determination of 3-((3-aminopropyl)amino)-4-hydroxybenzoic acid, a novel and abundant metabolite in Acinetobacter baylyi ADP1. Metabolomics 2019; 15:45. [PMID: 30874951 DOI: 10.1007/s11306-019-1508-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Metabolite identification remains a major bottleneck in the understanding of metabolism. Many metabolomics studies end up with unknown compounds, leaving a landscape of metabolites and metabolic pathways to be unraveled. Therefore, identifying novel compounds within a metabolome is an entry point into the 'dark side' of metabolism. OBJECTIVES This work aimed at elucidating the structure of a novel metabolite that was first detected in the soil bacterium Acinetobacter baylyi ADP1 (ADP1). METHODS We used high resolution multi-stage tandem mass spectrometry for characterizing the metabolite within the metabolome. We purified the molecule for 1D- and 2D-NMR (1H, 13C, 1H-1H-COSY, 1H-13C-HSQC, 1H-13C-HMBC and 1H-15N-HMBC) analyses. Synthetic standards were chemically prepared from MS and NMR data interpretation. RESULTS We determined the de novo structure of a previously unreported metabolite: 3-((3-aminopropyl)amino)-4-hydroxybenzoic acid. The proposed structure was validated by comparison to a synthetic standard. With a concentration in the millimolar range, this compound appears as a major metabolite in ADP1, which we anticipate to participate to an unsuspected metabolic pathway. This novel metabolite was also detected in another γ-proteobacterium. CONCLUSION Structure elucidation of this abundant and novel metabolite in ADP1 urges to decipher its biosynthetic pathway and cellular function.
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Affiliation(s)
- Marion Thomas
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucille Stuani
- INSERM, Institut National de la Santé et de la Recherche Médicale - CNRS - UPS - Centre de Recherche en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Claude Tabet
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
- CEA, iBiTec-S, SPI, LEMM, Gif-sur-Yvette, France
| | - Marcel Salanoubat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Pierre-Loïc Saaidi
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
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Korte AR, Morris NJ, Vertes A. High Throughput Complementary Analysis and Quantitation of Metabolites by MALDI- and Silicon Nanopost Array-Laser Desorption/Ionization-Mass Spectrometry. Anal Chem 2019; 91:3951-3958. [PMID: 30786207 DOI: 10.1021/acs.analchem.8b05074] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Silicon nanopost array (NAPA) structures have been shown to be effective substrates for laser desorption/ionization-mass spectrometry (LDI-MS) and have been used to analyze a variety of samples including peptides, metabolites, drugs, explosives, and intact cells, as well as to image lipids and metabolites in tissue sections. However, no direct comparison has yet been conducted between NAPA-MS and the most commonly used LDI-MS technique, matrix-assisted laser desorption/ionization (MALDI)-MS. In this work, we compare the utility of NAPA-MS to that of MALDI-MS using two common matrices for the analysis of metabolites in cellular extracts and human urine. Considerable complementarity of molecular coverage was observed between the two techniques. Of 178 total metabolites assigned from cellular extracts, 68 were uniquely detected by NAPA-MS and 62 were uniquely detected by MALDI-MS. NAPA-MS was found to provide enhanced coverage of low-molecular weight compounds such as amino acids, whereas MALDI afforded better detection of larger, labile compounds including nucleotides. In the case of urine, a sample largely devoid of higher-mass labile compounds, 88 compounds were uniquely detected by NAPA-MS and 13 by MALDI-MS. NAPA-MS also favored more extensive alkali metal cation adduction relative to MALDI-MS, with the [M + 2Na/K - H]+ species accounting for as much as 97% of the total metabolite ion signal in positive mode. The capability of NAPA-MS for targeted quantitation of endogenous metabolites in urine via addition of isotopically labeled standards was also examined. Both NAPA-MS and MALDI-MS provided quantitative results in good agreement with one another and the concentrations reported in the literature, as well as good sample-to-sample reproducibility (RSD < 10%).
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Affiliation(s)
- Andrew R Korte
- Department of Chemistry , George Washington University , Washington , D.C. 20052 , United States
| | | | - Akos Vertes
- Department of Chemistry , George Washington University , Washington , D.C. 20052 , United States
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Duncan KD, Fyrestam J, Lanekoff I. Advances in mass spectrometry based single-cell metabolomics. Analyst 2019; 144:782-793. [DOI: 10.1039/c8an01581c] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Single cell metabolomics using mass spectrometry can contribute to understanding biological activities in health and disease.
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Zhang XM, Han LW, Zhang SS, Li XB, He QX, Han J, Wang XM, Liu KC. Targeted discovery and identification of novel nucleoside biomarkers in Apostichopus japonicus viscera using metabonomics. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 38:203-217. [PMID: 30588871 DOI: 10.1080/15257770.2018.1514121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this study, we investigated the metabonomic profiles of Apostichopus japonicus using an LC-MS-based method in conjunction with multivariate data analysis. Based on the PLS-DA model, 85 differential metabolites (VIP value >1.0) were obtained from viscera and body wall samples. The MS/MS and NMR experiments were used for the qualitative identification of the characteristic peaks. Sphingoid-based nucleoside analogues were the main components in Chinese A. japonicus viscera. Our findings demonstrate that A. japonicus viscera contain a large number of compounds that may have applications as nutraceuticals or pharmaceuticals.
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Affiliation(s)
- Xuan-Ming Zhang
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Li-Wen Han
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Shan-Shan Zhang
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Xiao-Bin Li
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Qiu-Xia He
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Jian Han
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Xi-Min Wang
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
| | - Ke-Chun Liu
- a Key Laboratory for Drug Screening Technology, Biology Institute , Qilu University of Technology (Shandong Academy of Sciences) , Jinan , Shandong , P.R. China
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Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Anal Chem 2018; 91:704-742. [DOI: 10.1021/acs.analchem.8b05112] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | | | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 44035 Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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Beale DJ, Pinu FR, Kouremenos KA, Poojary MM, Narayana VK, Boughton BA, Kanojia K, Dayalan S, Jones OAH, Dias DA. Review of recent developments in GC-MS approaches to metabolomics-based research. Metabolomics 2018; 14:152. [PMID: 30830421 DOI: 10.1007/s11306-018-1449-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC-MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and 'in house' metabolite databases available. AIM OF REVIEW This review provides an overview of developments in GC-MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC-MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is to both highlight and provide an update on GC-MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC-MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.
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Affiliation(s)
- David J Beale
- Land and Water, Commonwealth Scientific & Industrial Research Organization (CSIRO), P.O. Box 2583, Brisbane, QLD, 4001, Australia.
| | - Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Trajan Scientific and Medical, 7 Argent Pl, Ringwood, 3134, Australia
| | - Mahesha M Poojary
- Chemistry Section, School of Science and Technology, University of Camerino, via S. Agostino 1, 62032, Camerino, Italy
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Vinod K Narayana
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | - Komal Kanojia
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, GPO Box 2476, Melbourne, 3001, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, 3083, Australia.
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Schüler JA, Neumann S, Müller-Hannemann M, Brandt W. ChemFrag: Chemically meaningful annotation of fragment ion mass spectra. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1104-1115. [PMID: 30103269 DOI: 10.1002/jms.4278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 05/26/2023]
Abstract
Identification and structural determination of small molecules by mass spectrometry is an important step in chemistry and biochemistry. However, the chemically realistic annotation of a fragment ion spectrum can be a difficult challenge. We developed ChemFrag, for the detection of fragmentation pathways and the annotation of fragment ions with chemically reasonable structures. ChemFrag combines a quantum chemical with a rule-based approach. For different doping substances as test instances, ChemFrag correctly annotates fragment ions. In most cases, the predicted fragments are chemically more realistic than those from purely combinatorial approaches, or approaches based on machine learning. The annotation generated by ChemFrag often coincides with spectra that have been manually annotated by experts. This is a major advance in peak annotation and allows a more precise automatic interpretation of mass spectra.
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Affiliation(s)
- Jördis-Ann Schüler
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle (Saale), 06120, Germany
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
| | - Steffen Neumann
- Department of Stress and Development Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Matthias Müller-Hannemann
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle (Saale), 06120, Germany
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
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Afshari R, Pillidge CJ, Dias DA, Osborn AM, Gill H. Cheesomics: the future pathway to understanding cheese flavour and quality. Crit Rev Food Sci Nutr 2018; 60:33-47. [DOI: 10.1080/10408398.2018.1512471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Roya Afshari
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | | | - Daniel A. Dias
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - A. Mark Osborn
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Harsharn Gill
- School of Science, RMIT University, Bundoora, Victoria, Australia
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Vanderplanck M, Glauser G. Integration of non-targeted metabolomics and automated determination of elemental compositions for comprehensive alkaloid profiling in plants. PHYTOCHEMISTRY 2018; 154:1-9. [PMID: 29929020 DOI: 10.1016/j.phytochem.2018.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Plants produce a large array of specialized metabolites to protect themselves. Among these allelochemicals, alkaloids display highly diverse and complex structures that are directly related to their biological activities. Plant alkaloid profiling traditionally requires extensive and time-consuming sample preparation and analysis. Herein, we developed a rapid and efficient approach for the comprehensive profiling of alkaloids in plants using ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS)-based metabolomics. Using automated compound extraction and elemental composition assignment, our method achieved >83% correct alkaloid identification and even >90% for medium to high intensity peaks. This represented a significant improvement in identification rate compared to generic methods used for EC determination with no a priori, such as in untargeted metabolomics studies. The developed approach was then applied to identify specific alkaloids of Aconitum lycoctonum L. and A. napellus L. (Ranunculaceae) using different parts of the plant (leaf, perianth and pollen). Significant differences in alkaloid profiles between the two species were highlighted and discussed under taxonomic and evolutionary perspectives. Taken together, the presented approach constitutes a valuable chemotaxonomic tool in the search for known and unknown alkaloids from plants.
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Affiliation(s)
- Maryse Vanderplanck
- Analytical Chemistry, AgroBioChem Department, University of Liège - Gembloux Agro-Bio-Tech, Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, CH-2000 Neuchâtel, Switzerland.
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Klarskov K, Gagnon H, Racine M, Boudreault PL, Normandin C, Marsault E, Gleich GJ, Naylor S. Peak AAA fatty acid homolog contaminants present in the dietary supplement l-Tryptophan associated with the onset of eosinophilia-myalgia syndrome. Toxicol Lett 2018; 294:193-204. [PMID: 29800716 DOI: 10.1016/j.toxlet.2018.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/08/2018] [Accepted: 05/22/2018] [Indexed: 12/17/2022]
Abstract
The eosinophilia-myalgia syndrome (EMS) outbreak that occurred in the USA and elsewhere in 1989 was caused by the ingestion of Showa Denko K.K. (SD) L-tryptophan (L-Trp). "Six compounds" detected in the L-Trp were reported as case-associated contaminants. Recently the final and most statistically significant contaminant, "Peak AAA" was structurally characterized. The "compound" was actually shown to be two structural isomers resulting from condensation reactions of L-Trp with fatty acids derived from the bacterial cell membrane. They were identified as the indole C-2 anteiso (AAA1-343) and linear (AAA2-343) aliphatic chain isomers. Based on those findings, we utilized a combination of on-line HPLC-electrospray ionization mass spectrometry (LC-MS), as well as both precursor and product ion tandem mass spectrometry (MS/MS) to facilitate identification of a homologous family of condensation products related to AAA1-343 and AAA2-343. We structurally characterized eight new AAA1-XXX/AAA2-XXX contaminants, where XXX represents the integer molecular ions of all the related homologs, differing by aliphatic chain length and isomer configuration. The contaminants were derived from the following fatty acids of the bacterial cell membrane, 5-methylheptanoic acid (anteiso-C8:0) for AAA1-315; n-octanoic acid (n-C8:0) for AAA2-315; 6-methyloctanoic acid (anteiso-C9:0) for AAA1-329; n-nonanoic acid (n-C9:0) for AAA2-329; 10-methyldodecanoic acid (anteiso-C13:0) for AAA1-385; n-tridecanoic acid (n-C13:0) for AAA2-385; 11-methyltridecanoic acid (anteiso-C14:0) for AAA1-399; and n-tetradecanoic acid (n-C14:0) for AAA2-399. The concentration levels for these contaminants were estimated to be 0.1-7.9 μg / 500 mg of an individual SD L-Trp tablet or capsule The structural similarity of these homologs to case-related contaminants of Spanish Toxic Oil Syndrome (TOS) is discussed.
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Affiliation(s)
- Klaus Klarskov
- Laboratory of Mass Spectrometry and Xenobiotics, Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Hugo Gagnon
- PhenoSwitch Bioscience, Sherbrooke, Quebec J1H 5N4, Canada
| | - Mathieu Racine
- PhenoSwitch Bioscience, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Chad Normandin
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Eric Marsault
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Gerald J Gleich
- Departments of Dermatology and Medicine, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA
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Chalet C, Hollebrands B, Duchateau GS, Augustijns P. Intestinal phase-II metabolism of quercetin in HT29 cells, 3D human intestinal tissues and in healthy volunteers: a qualitative comparison using LC-IMS-MS and LC-HRMS. Xenobiotica 2018; 49:945-952. [PMID: 30085847 DOI: 10.1080/00498254.2018.1509246] [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: 12/19/2022]
Abstract
Flavonoids are a large class of dietary molecules, among which quercetin is the most ubiquitous, which undergo an extensive intestinal phase-II metabolism. We compared the in vivo metabolism of quercetin in healthy volunteers with two in vitro models, HT29 cells and 3 D human intestinal tissues. Supernatants of the in vitro experiments and the human intestinal fluids (HIF) were analyzed by LC-IMS-MS and LC-HRMS in a qualitative way. Quercetin glucuronides, sulfates and their methyl conjugates were detected in all three systems. The metabolic profiles were found to be different, both in terms of the metabolites produced and their relative proportions. In particular, quercetin sulfates were almost absent in supernatants from HT29 cells incubations while they were a major metabolite in HIF and also found in 3 D intestinal tissues incubations. IMS provided structural information as well as a third dimension of characterization, while HRMS brought increased sensitivity and MS/MS confirmation. HT29 cells are a useful tool to generate phase-II metabolites but do not represent the in vivo situation. 3 D intestinal tissues appear as a more relevant tool to study the intestinal phase-II metabolism of flavonoids.
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Affiliation(s)
- Clément Chalet
- a Unilever R&D , Vlaardingen , The Netherlands.,b Drug Delivery and Disposition , KU Leuven , Leuven , Belgium
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Jones OAH. Illuminating the dark metabolome to advance the molecular characterisation of biological systems. Metabolomics 2018; 14:101. [PMID: 30830382 DOI: 10.1007/s11306-018-1396-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND The latest version of the Human Metabolome Database (v4.0) lists 114,100 individual entries. Typically, however, metabolomics studies identify only around 100 compounds and many features identified in mass spectra are listed only as 'unknown compounds'. The lack of ability to detect all metabolites present, and fully identify all metabolites detected (the dark metabolome) means that, despite the great contribution of metabolomics to a range of areas in the last decade, a significant amount of useful information from publically funded studies is being lost or unused each year. This loss of data limits our potential gain in knowledge and understanding of important research areas such as cell biology, environmental pollution, plant science, food chemistry and health and biomedical research. Metabolomics therefore needs to develop new tools and methods for metabolite identification to advance as a field. AIM OF REVIEW In this critical review, some potential issues with metabolite identification are identified and discussed. New and novel emerging technologies and tools which may contribute to expanding the number of compounds identified in metabolomics studies (thus illuminating the dark metabolome) are reviewed. The aim is to stimulate debate and research in the molecular characterisation of biological systems to drive forward metabolomic research. KEY SCIENTIFIC CONCEPTS OF REVIEW The work specifically discusses dynamic nuclear polarisation nuclear magnetic resonance spectroscopy (DNP-NMR), non-proton NMR active nuclei, two-dimensional liquid chromatography (2DLC) and Raman spectroscopy (RS). It is suggested that developing new methods for metabolomics with these techniques could lead to advances in the field and better characterisation of biological systems.
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Affiliation(s)
- Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3001, Australia.
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Mandal R, Chamot D, Wishart DS. The role of the Human Metabolome Database in inborn errors of metabolism. J Inherit Metab Dis 2018; 41:329-336. [PMID: 29663269 DOI: 10.1007/s10545-018-0137-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/06/2017] [Accepted: 01/04/2018] [Indexed: 12/31/2022]
Abstract
Metabolomics holds considerable promise to advance our understanding of human disease, including our understanding of inborn errors of metabolism (IEM). The application of metabolomics in IEM research has already led to the discovery of several novel IEMs and the identification of novel IEM biomarkers. However, with hundreds of known IEMs and more than 700 associated IEM metabolites, it is becoming increasingly challenging for clinical researchers to keep track of IEMs, their associated metabolites, and their corresponding metabolic mechanisms. Furthermore, when using metabolomics to assist in IEM biomarker discovery or even in IEM diagnosis, it is becoming much more difficult to properly identify metabolites from the complex NMR and MS spectra collected from IEM patients. To that end, comprehensive, open access metabolite databases that provide up-to-date referential information about metabolites, metabolic pathways, normal/abnormal metabolite concentrations, and reference NMR or MS spectra for compound identification are essential. Over the last few years, a number of compound databases, including the Human Metabolome Database (HMDB), have been developed to address these challenges. First described in 2007, the HMDB is now the world's largest and most comprehensive metabolomic resource for human metabolic studies. The latest release of the HMDB contains 114,100 metabolite entries (with 247 being relevant to IEMs), thousands of metabolite concentrations (with 600 being relevant to IEMs), and ~33,000 metabolic and disease-associated pathways (with 202 being relevant to IEMs). Here we provide a summary of the HMDB and offer some guidance on how it can be used in metabolomic studies of IEMs.
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Affiliation(s)
- Rupasri Mandal
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Danuta Chamot
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - David S Wishart
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
- Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada.
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Zhang Q, Ford LA, Evans AM, Toal DR. Identification of an Endogenous Organosulfur Metabolite by Interpretation of Mass Spectrometric Data. Org Lett 2018; 20:2100-2103. [DOI: 10.1021/acs.orglett.8b00664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Qibo Zhang
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, North Carolina 27560, United States
| | - Lisa A. Ford
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, North Carolina 27560, United States
| | - Anne M. Evans
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, North Carolina 27560, United States
| | - Douglas R. Toal
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, North Carolina 27560, United States
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Artyukhin AB, Zhang YK, Akagi AE, Panda O, Sternberg PW, Schroeder FC. Metabolomic "Dark Matter" Dependent on Peroxisomal β-Oxidation in Caenorhabditis elegans. J Am Chem Soc 2018; 140:2841-2852. [PMID: 29401383 PMCID: PMC5890438 DOI: 10.1021/jacs.7b11811] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peroxisomal β-oxidation (pβo) is a highly conserved fat metabolism pathway involved in the biosynthesis of diverse signaling molecules in animals and plants. In Caenorhabditis elegans, pβo is required for the biosynthesis of the ascarosides, signaling molecules that control development, lifespan, and behavior in this model organism. Via comparative mass spectrometric analysis of pβo mutants and wildtype, we show that pβo in C. elegans and the satellite model P. pacificus contributes to life stage-specific biosynthesis of several hundred previously unknown metabolites. The pβo-dependent portion of the metabolome is unexpectedly diverse, e.g., intersecting with nucleoside and neurotransmitter metabolism. Cell type-specific restoration of pβo in pβo-defective mutants further revealed that pβo-dependent submetabolomes differ between tissues. These results suggest that interactions of fat, nucleoside, and other primary metabolism pathways can generate structural diversity reminiscent of that arising from combinatorial strategies in microbial natural product biosynthesis.
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Affiliation(s)
- Alexander B. Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Ying K. Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Allison E. Akagi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
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Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vázquez-Fresno R, Sajed T, Johnson D, Li C, Karu N, Sayeeda Z, Lo E, Assempour N, Berjanskii M, Singhal S, Arndt D, Liang Y, Badran H, Grant J, Serra-Cayuela A, Liu Y, Mandal R, Neveu V, Pon A, Knox C, Wilson M, Manach C, Scalbert A. HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res 2018; 46:D608-D617. [PMID: 29140435 PMCID: PMC5753273 DOI: 10.1093/nar/gkx1089] [Citation(s) in RCA: 2362] [Impact Index Per Article: 393.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/19/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022] Open
Abstract
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC-MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2N8, Canada
| | | | - Ana Marcu
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - An Chi Guo
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Kevin Liang
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Rosa Vázquez-Fresno
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Tanvir Sajed
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Daniel Johnson
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Carin Li
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Naama Karu
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Zinat Sayeeda
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Elvis Lo
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Nazanin Assempour
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mark Berjanskii
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sandeep Singhal
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - David Arndt
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Yonjie Liang
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Hasan Badran
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jason Grant
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Arnau Serra-Cayuela
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Yifeng Liu
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Rupa Mandal
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vanessa Neveu
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
| | - Allison Pon
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
- OMx Personal Health Analytics, Inc., 301-10359 104 St NW, Edmonton, AB T5J 1B9, Canada
| | - Craig Knox
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
- OMx Personal Health Analytics, Inc., 301-10359 104 St NW, Edmonton, AB T5J 1B9, Canada
| | - Michael Wilson
- Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada
- OMx Personal Health Analytics, Inc., 301-10359 104 St NW, Edmonton, AB T5J 1B9, Canada
| | - Claudine Manach
- Institut National de la Recherche Agronomique (INRA) – Human Nutrition Unit, Université Clermont Auvergne, F63000 Clermont-Ferrand, France
| | - Augustin Scalbert
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
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Chaleckis R, Naz S, Meister I, Wheelock CE. LC-MS-Based Metabolomics of Biofluids Using All-Ion Fragmentation (AIF) Acquisition. Methods Mol Biol 2018; 1730:45-58. [PMID: 29363064 DOI: 10.1007/978-1-4939-7592-1_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The field of liquid chromatography-mass spectrometry (LC-MS)-based nontargeted metabolomics has advanced significantly and can provide information on thousands of compounds in biological samples. However, compound identification remains a major challenge, which is crucial in interpreting the biological function of metabolites. Herein, we present a LC-MS method using the all-ion fragmentation (AIF) approach in combination with a data processing method using an in-house spectral library. For the purposes of increasing accuracy in metabolite annotation, up to four criteria are used: (1) accurate mass, (2) retention time, (3) MS/MS fragments, and (4) product/precursor ion ratios. The relative standard deviation between ion ratios of a metabolite in a biofluid vs. its analytical standard is used as an additional metric for confirming metabolite identity. Furthermore, we include a scheme to distinguish co-eluting isobaric compounds. Our method enables database-dependent targeted as well as nontargeted metabolomics analysis from the same data acquisition, while simultaneously improving the accuracy in metabolite identification to increase the quality of the resulting biological information.
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Affiliation(s)
- Romanas Chaleckis
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan
| | - Shama Naz
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Meister
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan.
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76
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Abstract
LC-MS untargeted analysis is a valuable tool in the field of metabolic profiling (metabonomics/metabolomics), and the applications of this technology have grown rapidly over the past decade. LC-MS offers advantages over other analytical platforms such as speed, sensitivity, relative ease of sample preparation, and large dynamic range. As with any analytical approach, there are still drawbacks and challenges to overcome, but advances are constantly being made regarding both column chemistries and instrumentation. There are numerous untargeted LC-MS approaches which can be used in this ever-growing research field; these can be optimized depending on sample type and the nature of the study or biological question. Some of the main LC-MS approaches for the untargeted analysis of biological samples will be described in detail in the following protocol.
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Affiliation(s)
- Elizabeth J Want
- Computational and Systems Medicine, Imperial College London, London, UK.
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77
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Bøgeskov Schmidt F, Heskes AM, Thinagaran D, Lindberg Møller B, Jørgensen K, Boughton BA. Mass Spectrometry Based Imaging of Labile Glucosides in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:892. [PMID: 30002667 PMCID: PMC6031732 DOI: 10.3389/fpls.2018.00892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/07/2018] [Indexed: 05/19/2023]
Abstract
Mass spectrometry based imaging is a powerful tool to investigate the spatial distribution of a broad range of metabolites across a variety of sample types. The recent developments in instrumentation and computing capabilities have increased the mass range, sensitivity and resolution and rendered sample preparation the limiting step for further improvements. Sample preparation involves sectioning and mounting followed by selection and application of matrix. In plant tissues, labile small molecules and specialized metabolites are subject to degradation upon mechanical disruption of plant tissues. In this study, the benefits of cryo-sectioning, stabilization of fragile tissues and optimal application of the matrix to improve the results from MALDI mass spectrometry imaging (MSI) is investigated with hydroxynitrile glucosides as the main experimental system. Denatured albumin proved an excellent agent for stabilizing fragile tissues such as Lotus japonicus leaves. In stem cross sections of Manihot esculenta, maintaining the samples frozen throughout the sectioning process and preparation of the samples by freeze drying enhanced the obtained signal intensity by twofold to fourfold. Deposition of the matrix by sublimation improved the spatial information obtained compared to spray. The imaging demonstrated that the cyanogenic glucosides (CNglcs) were localized in the vascular tissues in old stems of M. esculenta and in the periderm and vascular tissues of tubers. In MALDI mass spectrometry, the imaged compounds are solely identified by their m/z ratio. L. japonicus MG20 and the mutant cyd1 that is devoid of hydroxynitrile glucosides were used as negative controls to verify the assignment of the observed masses to linamarin, lotaustralin, and linamarin acid.
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Affiliation(s)
- Frederik Bøgeskov Schmidt
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
| | - Allison M. Heskes
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dinaiz Thinagaran
- Metabolomics Australia, School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Birger Lindberg Møller,
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
| | - Berin A. Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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78
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Peisl BYL, Schymanski EL, Wilmes P. Dark matter in host-microbiome metabolomics: Tackling the unknowns-A review. Anal Chim Acta 2017; 1037:13-27. [PMID: 30292286 DOI: 10.1016/j.aca.2017.12.034] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
The "dark matter" in metabolomics (unknowns) represents an exciting frontier with significant potential for discovery in relation to biochemistry, yet it also presents one of the largest challenges to overcome. This focussed review takes a close look at the current state-of-the-art and future challenges in tackling the unknowns with specific focus on the human gut microbiome and host-microbe interactions. Metabolomics, like metabolism itself, is a very dynamic discipline, with many workflows and methods under development, both in terms of chemical analysis and post-analysis data processing. Here, we look at developments in the mutli-omic analyses and the use of mass spectrometry to investigate the exchange of metabolites between the host and the microbiome as well as the environment within the microbiome. A case study using HuMiX, a microfluidics-based human-microbial co-culture system that enables the co-culture of human and microbial cells under controlled conditions, is used to highlight opportunities and current limitations. Common definitions, approaches, databases and elucidation techniques from both the environmental and metabolomics fields are covered, with perspectives on how to merge these, as the boundaries blur between the fields. While reflecting on the number of unknowns remaining to be conquered in typical complex samples measured with mass spectrometry (often orders of magnitude above the "knowns"), we provide an outlook on future perspectives and challenges in elucidating the relevant "dark matter".
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Affiliation(s)
- B Y Loulou Peisl
- Environmental Cheminformatics Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; Eco-Systems Biology Group, LCSB, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
| | - Emma L Schymanski
- Environmental Cheminformatics Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
| | - Paul Wilmes
- Eco-Systems Biology Group, LCSB, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
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79
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Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands. Metabolites 2017; 7:metabo7040064. [PMID: 29258276 PMCID: PMC5746744 DOI: 10.3390/metabo7040064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/04/2023] Open
Abstract
Metabolomic techniques are powerful tools for investigating organism-environment interactions. Metabolite profiles have the potential to identify exposure or toxicity before populations are disrupted and can provide useful information for environmental assessment. However, under complex environmental scenarios, metabolomic responses to exposure can be distorted by background and/or organismal variation. In the current study, we use LC-MS (liquid chromatography-mass spectrometry) and GC-MS (gas chromatography-mass spectrometry) to measure metabolites of the midge Procladius villosimanus inhabiting 21 urban wetlands. These metabolites were tested against common sediment contaminants using random forest models and metabolite enrichment analysis. Sediment contaminant concentrations in the field correlated with several P. villosimanus metabolites despite natural environmental and organismal variation. Furthermore, enrichment analysis indicated that metabolite sets implicated in stress responses were enriched, pointing to specific cellular functions affected by exposure. Methionine metabolism, sugar metabolism and glycerolipid metabolism associated with total petroleum hydrocarbon and metal concentrations, while mitochondrial electron transport and urea cycle sets associated only with bifenthrin. These results demonstrate the potential for metabolomics approaches to provide useful information in field-based environmental assessments.
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80
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Scheubert K, Hufsky F, Petras D, Wang M, Nothias LF, Dührkop K, Bandeira N, Dorrestein PC, Böcker S. Significance estimation for large scale metabolomics annotations by spectral matching. Nat Commun 2017; 8:1494. [PMID: 29133785 PMCID: PMC5684233 DOI: 10.1038/s41467-017-01318-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/08/2017] [Indexed: 12/17/2022] Open
Abstract
The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate (FDR) for 70 public metabolomics data sets. We show that the spectral matching settings need to be adjusted for each project. By adjusting the scoring parameters and thresholds, the number of annotations rose, on average, by +139% (ranging from -92 up to +5705%) when compared with a default parameter set available at GNPS. The FDR estimation methods presented will enable a user to assess the scoring criteria for large scale analysis of mass spectrometry based metabolomics data that has been essential in the advancement of proteomics, transcriptomics, and genomics science.
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Affiliation(s)
- Kerstin Scheubert
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Franziska Hufsky
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany.
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81
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Hollender J, Schymanski EL, Singer HP, Ferguson PL. Nontarget Screening with High Resolution Mass Spectrometry in the Environment: Ready to Go? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11505-11512. [PMID: 28877430 DOI: 10.1021/acs.est.7b02184] [Citation(s) in RCA: 348] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The vast, diverse universe of organic pollutants is a formidable challenge for environmental sciences, engineering, and regulation. Nontarget screening (NTS) based on high resolution mass spectrometry (HRMS) has enormous potential to help characterize this universe, but is it ready to go for real world applications? In this Feature article we argue that development of mass spectrometers with increasingly high resolution and novel couplings to both liquid and gas chromatography, combined with the integration of high performance computing, have significantly widened our analytical window and have enabled increasingly sophisticated data processing strategies, indicating a bright future for NTS. NTS has great potential for treatment assessment and pollutant prioritization within regulatory applications, as highlighted here by the case of real-time pollutant monitoring on the River Rhine. We discuss challenges for the future, including the transition from research toward solution-centered and robust, harmonized applications.
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Affiliation(s)
- Juliane Hollender
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich, 8092 Zürich, Switzerland
| | - Emma L Schymanski
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
| | - Heinz P Singer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
| | - P Lee Ferguson
- Department of Civil & Environmental Engineering, Duke University , Box 90287, Durham, North Carolina 27708, United States
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82
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van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. The future of metabolomics in ELIXIR. F1000Res 2017; 6. [PMID: 29043062 PMCID: PMC5627583 DOI: 10.12688/f1000research.12342.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 01/11/2023] Open
Abstract
Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.
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Affiliation(s)
- Merlijn van Rijswijk
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands.,Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
| | - Charlie Beirnaert
- ADReM, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Christophe Caron
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Victoria Dominguez
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
| | - Warwick B Dunn
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy M D Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Franck Giacomoni
- INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont Auvergne University, Clermont-Ferrand, F-63000, France
| | | | - Thomas Hankemeier
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands.,Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2300 RA, Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Jose L Izquierdo-Garcia
- Centro Nacional Investigaciones Cardiovasculares, Madrid, 28029, Spain.,CIBER de Enfermedades Respiratorias, Madrid, 28029 , Spain
| | | | - Fabien Jourdan
- Toxalim, UMR 1331, Université de Toulouse, Toulouse, F-31300, France
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece
| | - Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.,Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany
| | - Kairi Koort
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.,School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia
| | - Kim Kultima
- Department of Medical Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Gildas Le Corguillé
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France.,UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, F-29680, France
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Nicholas K Moschonas
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece.,Department of General Biology, School of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | | | - Philippe Rocca-Serra
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
| | - Antonio Rosato
- Magnetic Resonance Center, Interuniversity Consortium for Magnetic Resonance on MetalloProteins, University of Florence, Florence, 50121, Italy
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
| | - Venkata Satagopam
- Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Daniel Schober
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Ruth Shimmo
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.,School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia
| | - Rachel A Spicer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, MetaboHUB, Gif-sur-Yvette, F-91191, France
| | - Mark R Viant
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, NL-6200, Netherlands
| | - Gianluigi Zanetti
- CRS4, Data Intensive Computing Group, Ed.1 POLARIS, Pula, 09010, Italy
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83
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Havelund JF, Heegaard NHH, Færgeman NJK, Gramsbergen JB. Biomarker Research in Parkinson's Disease Using Metabolite Profiling. Metabolites 2017; 7:E42. [PMID: 28800113 PMCID: PMC5618327 DOI: 10.3390/metabo7030042] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/08/2023] Open
Abstract
Biomarker research in Parkinson's disease (PD) has long been dominated by measuring dopamine metabolites or alpha-synuclein in cerebrospinal fluid. However, these markers do not allow early detection, precise prognosis or monitoring of disease progression. Moreover, PD is now considered a multifactorial disease, which requires a more precise diagnosis and personalized medication to obtain optimal outcome. In recent years, advanced metabolite profiling of body fluids like serum/plasma, CSF or urine, known as "metabolomics", has become a powerful and promising tool to identify novel biomarkers or "metabolic fingerprints" characteristic for PD at various stages of disease. In this review, we discuss metabolite profiling in clinical and experimental PD. We briefly review the use of different analytical platforms and methodologies and discuss the obtained results, the involved metabolic pathways, the potential as a biomarker and the significance of understanding the pathophysiology of PD. Many of the studies report alterations in alanine, branched-chain amino acids and fatty acid metabolism, all pointing to mitochondrial dysfunction in PD. Aromatic amino acids (phenylalanine, tyrosine, tryptophan) and purine metabolism (uric acid) are also altered in most metabolite profiling studies in PD.
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Affiliation(s)
- Jesper F Havelund
- Villum Centre for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institute, DK-2300 Copenhagen, Denmark.
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, DK-5000 Odense, Denmark.
| | - Nils J K Færgeman
- Villum Centre for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.
| | - Jan Bert Gramsbergen
- Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark.
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84
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Abstract
Metabolomics is the newest addition to the "omics" disciplines and has shown rapid growth in its application to human health research because of fundamental advancements in measurement and analysis techniques. Metabolomics has unique and proven advantages in systems biology and biomarker discovery. The next generation of analysis techniques promises even richer and more complete analysis capabilities that will enable earlier clinical diagnosis, drug refinement, and personalized medicine. A review of current advancements in methodologies and statistical analysis that are enhancing and improving the performance of metabolomics is presented along with highlights of some recent successful applications.
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Affiliation(s)
- Eli Riekeberg
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
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85
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Naz S, Gallart-Ayala H, Reinke SN, Mathon C, Blankley R, Chaleckis R, Wheelock CE. Development of a Liquid Chromatography-High Resolution Mass Spectrometry Metabolomics Method with High Specificity for Metabolite Identification Using All Ion Fragmentation Acquisition. Anal Chem 2017. [PMID: 28641411 DOI: 10.1021/acs.analchem.7b00925] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-resolution mass spectrometry (HRMS)-based metabolomics approaches have made significant advances. However, metabolite identification is still a major challenge with significant bottleneck in translating metabolomics data into biological context. In the current study, a liquid chromatography (LC)-HRMS metabolomics method was developed using an all ion fragmentation (AIF) acquisition approach. To increase the specificity in metabolite annotation, four criteria were considered: (i) accurate mass (AM), (ii) retention time (RT), (iii) MS/MS spectrum, and (iv) product/precursor ion intensity ratios. We constructed an in-house mass spectral library of 408 metabolites containing AMRT and MS/MS spectra information at four collision energies. The percent relative standard deviations between ion ratios of a metabolite in an analytical standard vs sample matrix were used as an additional metric for establishing metabolite identity. A data processing method for targeted metabolite screening was then created, merging m/z, RT, MS/MS, and ion ratio information for each of the 413 metabolites. In the data processing method, the precursor ion and product ion were considered as the quantifier and qualifier ion, respectively. We also included a scheme to distinguish coeluting isobaric compounds by selecting a specific product ion as the quantifier ion instead of the precursor ion. An advantage of the current AIF approach is the concurrent collection of full scan data, enabling identification of metabolites not included in the database. Our data acquisition strategy enables a simultaneous mixture of database-dependent targeted and nontargeted metabolomics in combination with improved accuracy in metabolite identification, increasing the quality of the biological information acquired in a metabolomics experiment.
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Affiliation(s)
- Shama Naz
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm SE 17177, Sweden
| | - Hector Gallart-Ayala
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm SE 17177, Sweden
| | - Stacey N Reinke
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm SE 17177, Sweden
| | - Caroline Mathon
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm SE 17177, Sweden
| | | | - Romanas Chaleckis
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm SE 17177, Sweden.,Gunma University Initiative for Advanced Research (GIAR), Gunma University , Gunma, Japan
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm SE 17177, Sweden.,Gunma University Initiative for Advanced Research (GIAR), Gunma University , Gunma, Japan
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Aksenov AA, da Silva R, Knight R, Lopes NP, Dorrestein PC. Global chemical analysis of biology by mass spectrometry. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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87
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Labradorins with Antibacterial Activity Produced by Pseudomonas sp. Molecules 2017; 22:molecules22071072. [PMID: 28654009 PMCID: PMC6151975 DOI: 10.3390/molecules22071072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/11/2017] [Accepted: 06/21/2017] [Indexed: 11/16/2022] Open
Abstract
The urgent need for new antibacterial drugs has led to renewed interest in microorganisms, which historically have been the main source of previously discovered antibiotics. The present study describes the discovery of two new antibacterial oxazolylindole type alkaloids, labradorins 5 (1) and 6 (2), which were isolated and characterized from two isolates of Pseudomonas sp., along with four previously known tryptophane derived alkaloids. The structures of 1 and 2 were determined by NMR spectroscopy and MS, and confirmed by synthesis. During bioassay-guided isolation using several human bacterial pathogens, 1 and 2 displayed activity towards Staphylococcus aureus and Acinetobacter baumannii. The minimal inhibitory concentrations (MIC) of compounds 1 and 2 against S. aureus were 12 μg·mL-1 and 50 μg·mL-1, respectively, whereas the MICs against A. baumannii were >50 μg·mL-1. The CC50 values of compound 1 towards a liver cell line (HEP-G2) and a T-cell line (MT4) were 30 μg·mL-1 and 20 μg·mL-1, respectively, and for compound 2 were >100 μg·mL-1 and 20 μg·mL-1, respectively. Due to the limited potency of compounds 1 and 2, along with their toxicity, the compounds do not warrant further development towards new antibiotics.
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Zhang Q, Ford LA, Evans AM, Toal DR. Structure elucidation of metabolite x17299 by interpretation of mass spectrometric data. Metabolomics 2017; 13:92. [PMID: 28706470 PMCID: PMC5486616 DOI: 10.1007/s11306-017-1231-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/19/2017] [Indexed: 12/11/2022]
Abstract
INTRODUCTION A major bottleneck in metabolomic studies is metabolite identification from accurate mass spectrometric data. Metabolite x17299 was identified in plasma as an unknown in a metabolomic study using a compound-centric approach where the associated ion features of the compound were used to determine the true molecular mass. OBJECTIVES The aim of this work is to elucidate the chemical structure of x17299, a new compound by de novo interpretation of mass spectrometric data. METHODS An Orbitrap Elite mass spectrometer was used for acquisition of mass spectra up to MS4 at high resolution. Synthetic standards of N,N,N-trimethyl-l-alanyl-l-proline betaine (l,l-TMAP), a diastereomer, and an enantiomer were chemically prepared. RESULTS The planar structure of x17299 was successfully proposed by de novo mechanistic interpretation of mass spectrometric data without any laborious purification and nuclear magnetic resonance spectroscopic analysis. The proposed structure was verified by deuterium exchanged mass spectrometric analysis and confirmed by comparison to a synthetic standard. Relative configuration of x17299 was determined by direct chromatographic comparison to a pair of synthetic diastereomers. Absolute configuration was assigned after derivatization of x17299 with a chiral auxiliary group followed by its chromatographic comparison to a pair of synthetic standards. CONCLUSION The chemical structure of metabolite x17299 was determined to be l,l-TMAP.
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Affiliation(s)
- Qibo Zhang
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, NC 27560 USA
| | - Lisa A. Ford
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, NC 27560 USA
| | - Anne M. Evans
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, NC 27560 USA
| | - Douglas R. Toal
- Metabolon, Inc., 617 Davis Drive, Suite 400, Morrisville, NC 27560 USA
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Tolstikov V, Akmaev VR, Sarangarajan R, Narain NR, Kiebish MA. Clinical metabolomics: a pivotal tool for companion diagnostic development and precision medicine. Expert Rev Mol Diagn 2017; 17:411-413. [DOI: 10.1080/14737159.2017.1308827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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90
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Identification of In Vivo Metabolites of Levophencynonate in Human Plasma and Urine by High-Performance Liquid Chromatography Tandem Triple-Time-of-Flight Mass Spectrometry. Chromatographia 2017. [DOI: 10.1007/s10337-017-3264-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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