51
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Tran TB, Bergen PJ, Creek DJ, Velkov T, Li J. Synergistic Killing of Polymyxin B in Combination With the Antineoplastic Drug Mitotane Against Polymyxin-Susceptible and -Resistant Acinetobacter baumannii: A Metabolomic Study. Front Pharmacol 2018; 9:359. [PMID: 29713282 PMCID: PMC5911485 DOI: 10.3389/fphar.2018.00359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/27/2018] [Indexed: 12/16/2022] Open
Abstract
Polymyxins are currently used as the last-resort antibiotics against multidrug-resistant Acinetobacter baumannii. As resistance to polymyxins emerges in A. baumannii with monotherapy, combination therapy is often the only remaining treatment option. A novel approach is to employ the combination of polymyxin B with non-antibiotic drugs. In the present study, we employed metabolomics to investigate the synergistic mechanism of polymyxin B in combination with the antineoplastic drug mitotane against polymyxin-susceptible and -resistant A. baumannii. The metabolomes of four A. baumannii strains were analyzed following treatment with polymyxin B, mitotane and the combination. Polymyxin B monotherapy induced significant perturbation in glycerophospholipid (GPL) metabolism and histidine degradation pathways in polymyxin-susceptible strains, and minimal perturbation in polymyxin-resistant strains. Mitotane monotherapy induced minimal perturbation in the polymyxin-susceptible strains, but caused significant perturbation in GPL metabolism, pentose phosphate pathway and histidine degradation in the LPS-deficient polymyxin-resistant strain (FADDI-AB065). The polymyxin B – mitotane combination induced significant perturbation in all strains except the lipid A modified polymyxin-resistant FADDI-AB225 strain. For the polymyxin-susceptible strains, the combination therapy significantly perturbed GPL metabolism, pentose phosphate pathway, citric acid cycle, pyrimidine ribonucleotide biogenesis, guanine ribonucleotide biogenesis, and histidine degradation. Against FADDI-AB065, the combination significantly perturbed GPL metabolism, pentose phosphate pathway, citric acid cycle, and pyrimidine ribonucleotide biogenesis. Overall, these novel findings demonstrate that the disruption of the citric acid cycle and inhibition of nucleotide biogenesis are the key metabolic features associated with synergistic bacterial killing by the combination against polymyxin-susceptible and -resistant A. baumannii.
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Affiliation(s)
- Thien B Tran
- Monash Biomedicine Discovery Institute, Department of Microbiology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Phillip J Bergen
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Tony Velkov
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
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52
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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 2018; 29:897-910. [PMID: 29444955 PMCID: PMC5896929 DOI: 10.1091/mbc.e17-11-0666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic dysregulation leading to sugar-phosphate accumulation is toxic in organisms ranging from bacteria to humans. By comparing two models of sugar-phosphate toxicity in Saccharomyces cerevisiae, we demonstrate that toxicity occurs, at least in part, through multiple, isomer-specific mechanisms, rather than a single general mechanism.
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Affiliation(s)
- Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jonathan C Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Maxim Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew Volpe
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Sanford J Silverman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
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53
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Hey JA, Kocis P, Hort J, Abushakra S, Power A, Vyhnálek M, Yu JY, Tolar M. Discovery and Identification of an Endogenous Metabolite of Tramiprosate and Its Prodrug ALZ-801 that Inhibits Beta Amyloid Oligomer Formation in the Human Brain. CNS Drugs 2018; 32:849-861. [PMID: 30076539 PMCID: PMC6153967 DOI: 10.1007/s40263-018-0554-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND ALZ-801 is an oral, small-molecule inhibitor of beta amyloid (Aβ) oligomer formation in clinical development for Alzheimer's disease (AD). ALZ-801 is a prodrug of tramiprosate with improved pharmacokinetic properties and gastrointestinal tolerability. During clinical studies, we discovered that the primary metabolite of tramiprosate and its prodrug ALZ-801, 3-sulfopropanoic acid (3-SPA), is an endogenous molecule in the human brain and present in the cerebrospinal fluid (CSF) of patients with AD and other neurodegenerative brain diseases. OBJECTIVE The objectives of this research were to (1) identify and confirm the presence of 3-SPA in CSF samples from elderly, drug-naïve patients with memory deficits; (2) quantify the levels of 3-SPA in the CSF of patients with AD from tramiprosate phase III North American (NA) trial; (3) evaluate the in vitro anti-Aβ42 oligomer activity of 3-SPA; and (4) characterize the pharmacokinetics and brain-penetration properties of 3-SPA. METHODS Lumbar CSF samples from 64 drug-naïve patients with cognitive deficits (Mini-Mental State Examination [MMSE] score range 15-30) and six patients with AD treated with tramiprosate 150 mg twice daily in the phase III trial, at week 78, were analyzed. We used liquid chromatography-tandem mass spectrometry to confirm the structural molecular identity of endogenous 3-SPA with a 3-SPA reference standard and ion-mobility spectrometry-mass spectrometry with molecular dynamics to characterize interactions of 3-SPA with Aβ42 monomers, and the resultant conformational alterations. Rat studies using oral (30 mg/kg) and intravenous (10 mg/kg) doses were conducted to characterize the pharmacokinetic properties and brain penetration of 3-SPA. RESULTS We confirmed the presence of 3-SPA in the CSF of drug-naïve patients with cognitive deficits (mean concentration 11.7 ± 4.3 nM). The mean concentration of 3-SPA in patients with AD treated with tramiprosate was 135 ± 51 nM. In vitro studies revealed a multi-ligand interaction of 3-SPA with monomeric Aβ42 that inhibits the aggregation of Aβ42 into small oligomers. Comparisons of the molecular interactions of tramiprosate and 3-SPA with Aβ42 are also presented. Furthermore, in rat preclinical studies, 3-SPA displayed 100% oral bioavailability and 25% brain penetration, indicating that the metabolite is well absorbed and crosses the blood-brain barrier. CONCLUSIONS We confirmed the endogenous presence of 3-SPA, the major metabolite of tramiprosate, in the CSF of drug-naïve elderly patients with memory deficits due to AD and a variety of other neurodegenerative disorders. The levels of 3-SPA were up to 12.6-fold greater in patients with AD receiving tramiprosate than in drug-naïve patients. In addition, we showed that 3-SPA has potent anti-Aβ oligomer activity, inhibiting aggregation of Aβ42 into small oligomers with efficacy comparable to that of tramiprosate. 3-SPA displays excellent oral availability and brain penetration in rats, suggesting that the higher CSF concentrations of 3-SPA in the human brain after oral administration of ALZ-801 or tramiprosate (and subsequent conversion to 3-SPA) result from the penetration of the metabolite into the central nervous system. These data suggest that 3-SPA is an endogenous agent with potential activity stabilizing the conformational flexibility of Aβ monomers that, in turn, inhibit Aβ misfolding and formation of soluble toxic Aβ oligomers in humans, thereby preventing the initial pathogenic step in the progression of AD. Clinical improvements observed in patients with AD carrying the ε4 allele of the apolipoprotein E gene in tramiprosate phase III studies may in part be explained by the therapeutic effects of excess levels of the metabolite in the brains of these patients. The potential protective role of 3-SPA in AD pathogenesis, as well as its therapeutic role in AD and other neurodegenerative disorders, warrants further investigation.
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Affiliation(s)
- John A. Hey
- Alzheon, Inc, 111 Speen Street Suite 306, Framingham, MA 01701 USA
| | - Petr Kocis
- Alzheon, Inc, 111 Speen Street Suite 306, Framingham, MA 01701 USA
| | - Jakub Hort
- 0000 0004 0608 7557grid.412752.7International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic ,0000 0004 1937 116Xgrid.4491.8Department of Neurology, Cognitive Center, 2nd Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Susan Abushakra
- Alzheon, Inc, 111 Speen Street Suite 306, Framingham, MA 01701 USA
| | - Aidan Power
- Alzheon, Inc, 111 Speen Street Suite 306, Framingham, MA 01701 USA
| | - Martin Vyhnálek
- 0000 0004 0608 7557grid.412752.7International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic ,0000 0004 1937 116Xgrid.4491.8Department of Neurology, Cognitive Center, 2nd Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Jeremy Y. Yu
- Alzheon, Inc, 111 Speen Street Suite 306, Framingham, MA 01701 USA
| | - Martin Tolar
- Alzheon, Inc, 111 Speen Street Suite 306, Framingham, MA 01701 USA
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54
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Pirok BW, Molenaar SR, van Outersterp RE, Schoenmakers PJ. Applicability of retention modelling in hydrophilic-interaction liquid chromatography for algorithmic optimization programs with gradient-scanning techniques. J Chromatogr A 2017; 1530:104-111. [DOI: 10.1016/j.chroma.2017.11.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 10/18/2022]
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55
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Fenaille F, Barbier Saint-Hilaire P, Rousseau K, Junot C. Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand? J Chromatogr A 2017; 1526:1-12. [PMID: 29074071 DOI: 10.1016/j.chroma.2017.10.043] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/15/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
Abstract
Typical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools.
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Affiliation(s)
- François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Pierre Barbier Saint-Hilaire
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Kathleen Rousseau
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France.
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56
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Hu Y, Zheng Q, Wanek W. Flux Analysis of Free Amino Sugars and Amino Acids in Soils by Isotope Tracing with a Novel Liquid Chromatography/High Resolution Mass Spectrometry Platform. Anal Chem 2017; 89:9192-9200. [PMID: 28776982 PMCID: PMC5605124 DOI: 10.1021/acs.analchem.7b01938] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Soil fluxomics analysis can provide
pivotal information for understanding
soil biochemical pathways and their regulation, but direct measurement
methods are rare. Here, we describe an approach to measure soil extracellular
metabolite (amino sugar and amino acid) concentrations and fluxes
based on a 15N isotope pool dilution technique via liquid
chromatography and high-resolution mass spectrometry. We produced
commercially unavailable 15N and 13C labeled
amino sugars and amino acids by hydrolyzing peptidoglycan isolated
from isotopically labeled bacterial biomass and used them as tracers
(15N) and internal standards (13C). High-resolution
(Orbitrap Exactive) MS with a resolution of 50 000 allowed
us to separate different stable isotope labeled analogues across a
large range of metabolites. The utilization of 13C internal
standards greatly improved the accuracy and reliability of absolute
quantification. We successfully applied this method to two types of
soils and quantified the extracellular gross fluxes of 2 amino sugars,
18 amino acids, and 4 amino acid enantiomers. Compared to the influx
and efflux rates of most amino acids, similar ones were found for
glucosamine, indicating that this amino sugar is released through
peptidoglycan and chitin decomposition and serves as an important
nitrogen source for soil microorganisms. d-Alanine and d-glutamic acid derived from peptidoglycan decomposition exhibited
similar turnover rates as their l-enantiomers. This novel
approach offers new strategies to advance our understanding of the
production and transformation pathways of soil organic N metabolites,
including the unknown contributions of peptidoglycan and chitin decomposition
to soil organic N cycling.
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Affiliation(s)
- Yuntao Hu
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna , Althanstraße 14, 1090 Vienna, Austria
| | - Qing Zheng
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna , Althanstraße 14, 1090 Vienna, Austria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna , Althanstraße 14, 1090 Vienna, Austria
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57
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Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem 2017; 86:277-304. [PMID: 28654323 DOI: 10.1146/annurev-biochem-061516-044952] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Matthias S Klein
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, California 95616.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
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58
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Zenezini Chiozzi R, Capriotti AL, Cavaliere C, Ferraris F, La Barbera G, Piovesana S, Laganà A. Evaluation of column length and particle size effect on the untargeted profiling of a phytochemical mixture by using UHPLC coupled to high-resolution mass spectrometry. J Sep Sci 2017; 40:2541-2557. [DOI: 10.1002/jssc.201700135] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/06/2017] [Accepted: 04/12/2017] [Indexed: 01/21/2023]
Affiliation(s)
| | | | - Chiara Cavaliere
- Department of Chemistry; University of Rome “La Sapienza”; Rome Italy
| | | | | | - Susy Piovesana
- Department of Chemistry; University of Rome “La Sapienza”; Rome Italy
| | - Aldo Laganà
- Department of Chemistry; University of Rome “La Sapienza”; Rome Italy
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59
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Jandera P, Janás P. Recent advances in stationary phases and understanding of retention in hydrophilic interaction chromatography. A review. Anal Chim Acta 2017; 967:12-32. [DOI: 10.1016/j.aca.2017.01.060] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/01/2022]
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60
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Khamis MM, Adamko DJ, El-Aneed A. Mass spectrometric based approaches in urine metabolomics and biomarker discovery. MASS SPECTROMETRY REVIEWS 2017; 36:115-134. [PMID: 25881008 DOI: 10.1002/mas.21455] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 05/25/2023]
Abstract
Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.
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Affiliation(s)
- Mona M Khamis
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
- Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Darryl J Adamko
- Department of Pediatrics, College of Medicine, University of Saskatchewan, 103 Hospital Drive, Saskatoon, SK, Canada
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
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Srivastava A, Evans KJ, Sexton AE, Schofield L, Creek DJ. Metabolomics-Based Elucidation of Active Metabolic Pathways in Erythrocytes and HSC-Derived Reticulocytes. J Proteome Res 2017; 16:1492-1505. [PMID: 28166632 DOI: 10.1021/acs.jproteome.6b00902] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A detailed analysis of the metabolic state of human-stem-cell-derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high-resolution LC-MS-based untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite classes. An untargeted metabolomics analysis using stable-isotope-labeled glucose showed that only glycolysis and the pentose phosphate pathway actively contributed to the biosynthesis of metabolites in erythrocytes, and these pathways were upregulated in reticulocytes. Most metabolite species found to be enriched in reticulocytes were residual pools of metabolites produced by earlier erythropoietic processes, and their systematic depletion in mature erythrocytes aligns with the simplification process, which is also seen at the cellular and the structural level. Our work shows that high-resolution LC-MS-based untargeted metabolomics provides a global coverage of the biochemical species that are present in erythrocytes. However, the incorporation of stable isotope labeling provides a more accurate description of the active metabolic processes that occur in each developmental stage. To our knowledge, this is the first detailed characterization of the active metabolic pathways of the erythroid lineage, and it provides a rich database for understanding the physiology of the maturation of reticulocytes into mature erythrocytes.
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Affiliation(s)
- Anubhav Srivastava
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Krystal J Evans
- Walter and Eliza Hall Institute of Medical Research , Division of Infection and Immunity, Parkville, Victoria 3052, Australia
| | - Anna E Sexton
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Louis Schofield
- Walter and Eliza Hall Institute of Medical Research , Division of Infection and Immunity, Parkville, Victoria 3052, Australia.,Australian Institute of Tropical Health and Medicine, James Cook University , Douglas, Queensland 4814, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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Tailored liquid chromatography–mass spectrometry analysis improves the coverage of the intracellular metabolome of HepaRG cells. J Chromatogr A 2017; 1487:168-178. [DOI: 10.1016/j.chroma.2017.01.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/15/2017] [Accepted: 01/22/2017] [Indexed: 12/12/2022]
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63
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Guder JC, Schramm T, Sander T, Link H. Time-Optimized Isotope Ratio LC–MS/MS for High-Throughput Quantification of Primary Metabolites. Anal Chem 2017; 89:1624-1631. [DOI: 10.1021/acs.analchem.6b03731] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Christopher Guder
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Timur Sander
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
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64
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La Barbera G, Capriotti AL, Cavaliere C, Piovesana S, Samperi R, Zenezini Chiozzi R, Laganà A. Comprehensive polyphenol profiling of a strawberry extract (Fragaria × ananassa) by ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry. Anal Bioanal Chem 2017; 409:2127-2142. [DOI: 10.1007/s00216-016-0159-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/25/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
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65
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Boháčová I, Halko R, Jandera P. The effects of temperature and mobile phase on the retention of aliphatic carboxylic acids in hydrophilic interaction chromatography on zwitterionic stationary phases. J Sep Sci 2016; 39:4732-4739. [DOI: 10.1002/jssc.201601049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Iveta Boháčová
- Faculty of Natural Sciences, Department of Analytical Chemistry; Comenius University in Bratislava; Bratislava Slovakia
| | - Radoslav Halko
- Faculty of Natural Sciences, Department of Analytical Chemistry; Comenius University in Bratislava; Bratislava Slovakia
| | - Pavel Jandera
- Faculty of Chemical Technology; Department of Analytical Chemistry; University of Pardubice; Pardubice Czech Republic
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Najdekr L, Friedecký D, Tautenhahn R, Pluskal T, Wang J, Huang Y, Adam T. Influence of Mass Resolving Power in Orbital Ion-Trap Mass Spectrometry-Based Metabolomics. Anal Chem 2016; 88:11429-11435. [DOI: 10.1021/acs.analchem.6b02319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Lukáš Najdekr
- Laboratory
of Metabolomics, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská
5, 775 15 Olomouc, Czech Republic
- University Hospital Olomouc, I.P.
Pavlova 185/6, 779 00 Olomouc, Czech Republic
| | - David Friedecký
- Laboratory
of Metabolomics, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská
5, 775 15 Olomouc, Czech Republic
- University Hospital Olomouc, I.P.
Pavlova 185/6, 779 00 Olomouc, Czech Republic
| | - Ralf Tautenhahn
- Thermo Fisher Scientific, 355
River Oaks Parkway, San Jose, 95134 California United States
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142-1479, United States
| | - Junhua Wang
- Thermo Fisher Scientific, 355
River Oaks Parkway, San Jose, 95134 California United States
| | - Yingying Huang
- Thermo Fisher Scientific, 355
River Oaks Parkway, San Jose, 95134 California United States
| | - Tomáš Adam
- Laboratory
of Metabolomics, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská
5, 775 15 Olomouc, Czech Republic
- University Hospital Olomouc, I.P.
Pavlova 185/6, 779 00 Olomouc, Czech Republic
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Yao Y, Wang P, Shao G, Del Toro LVA, Codero J, Giese RW. Nontargeted analysis of the urine nonpolar sulfateome: a pathway to the nonpolar xenobiotic exposome. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2341-2350. [PMID: 27557133 PMCID: PMC5070653 DOI: 10.1002/rcm.7726] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/09/2016] [Accepted: 08/20/2016] [Indexed: 05/04/2023]
Abstract
RATIONALE Testing the urine nonpolar sulfateome can enable discovery of xenobiotics that are most likely to be bioactive. This is based on the fact that nonpolar xenobiotics are more likely to enter cells where they tend to undergo metabolism, in part, to sulfates that are then largely excreted into the urine. METHODS The following sequence of steps, with conditions that achieve high reproducibility, was applied to large human urine samples: (1) competitive nonpolar extraction with a porous extraction paddle; (2) weak anion-exchange extraction with strong organic washing; and (3) ultrahigh-performance liquid chromatography (UHPLC)/negative ion matrix-assisted laser desorption ionization tandem time-of-flight mass spectrometery (MALDI-TOF/TOF-MS) with recording of ions with signal-to-noise (S/N) ≥ 20 that yielded M-1-80 (loss of SO3 ) or m/z 97 (HSO4- ) upon fragmentation. RESULTS From a collection of urine samples from six pregnant women, the masses of 1129 putative sulfates were measured. Three lists of candidate compounds (preliminary hits) from these masses were formed by searching METLIN, especially via MATLAB, yielding putative xenobiotic contaminants (35 compounds), steroids (122), and flavonoids (1582). CONCLUSIONS A new way to reveal some of the nonpolar xenobiotic exposome has been developed that applies to urine samples. The value of the method is to suggest xenobiotics for subsequent targeted analysis in the population of people under study, in order to relate the environment to health and disease. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yuanyuan Yao
- Northeastern University, Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, 360, Huntington, Ave., Boston, MA, 02115, USA
| | - Poguang Wang
- Northeastern University, Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, 360, Huntington, Ave., Boston, MA, 02115, USA
| | - Gang Shao
- Northeastern University, Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, 360, Huntington, Ave., Boston, MA, 02115, USA
| | | | - Jose Codero
- University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Roger W Giese
- Northeastern University, Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, 360, Huntington, Ave., Boston, MA, 02115, USA.
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Metabolomics-Based Screening of the Malaria Box Reveals both Novel and Established Mechanisms of Action. Antimicrob Agents Chemother 2016; 60:6650-6663. [PMID: 27572396 DOI: 10.1128/aac.01226-16] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/16/2016] [Indexed: 12/22/2022] Open
Abstract
High-throughput phenotypic screening of chemical libraries has resulted in the identification of thousands of compounds with potent antimalarial activity, although in most cases, the mechanism(s) of action of these compounds remains unknown. Here we have investigated the mode of action of 90 antimalarial compounds derived from the Malaria Box collection using high-coverage, untargeted metabolomics analysis. Approximately half of the tested compounds induced significant metabolic perturbations in in vitro cultures of Plasmodium falciparum In most cases, the metabolic profiles were highly correlated with known antimalarials, in particular artemisinin, the 4-aminoquinolines, or atovaquone. Select Malaria Box compounds also induced changes in intermediates in essential metabolic pathways, such as isoprenoid biosynthesis (i.e., 2-C-methyl-d-erythritol 2,4-cyclodiphosphate) and linolenic acid metabolism (i.e., traumatic acid). This study provides a comprehensive database of the metabolic perturbations induced by chemically diverse inhibitors and highlights the utility of metabolomics for triaging new lead compounds and defining specific modes of action, which will assist with the development and optimization of new antimalarial drugs.
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69
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Tang DQ, Zou L, Yin XX, Ong CN. HILIC-MS for metabolomics: An attractive and complementary approach to RPLC-MS. MASS SPECTROMETRY REVIEWS 2016; 35:574-600. [PMID: 25284160 DOI: 10.1002/mas.21445] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/28/2014] [Indexed: 05/14/2023]
Abstract
Hydrophilic interaction chromatography (HILIC) is an emerging separation mode of liquid chromatography (LC). Using highly hydrophilic stationary phases capable of retaining polar/ionic metabolites, and accompany with high organic content mobile phase that offer readily compatibility with mass spectrometry (MS) has made HILIC an attractive complementary tool to the widely used reverse-phase (RP) chromatographic separations in metabolomic studies. The combination of HILIC and RPLC coupled with an MS detector expands the number of detected analytes and provides more comprehensive metabolite coverage than use of only RP chromatography. This review describes the recent applications of HILIC-MS/MS in metabolomic studies, ranging from amino acids, lipids, nucleotides, organic acids, pharmaceuticals, and metabolites of specific nature. The biological systems investigated include microbials, cultured cell line, plants, herbal medicine, urine, and serum as well as tissues from animals and humans. Owing to its unique capability to measure more-polar biomolecules, the HILIC separation technique would no doubt enhance the comprehensiveness of metabolite detection, and add significant value for metabolomic investigations. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:574-600, 2016.
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Affiliation(s)
- Dao-Quan Tang
- Department of Pharmaceutical Analysis, Xuzhou Medical College, Xuzhou, 221044, China
- Jiangsu Key Lab for the study of New Drug and Clinical Pharmacy, Xuzhou Medical College, Yunlong, China
- NUS Environmental Research Inst., National University of Singapore, 5 A Engineering Srive 1, Singapore, 117411, Singapore
| | - Ll Zou
- Saw Swee Hock School of Public Health, National University of Singapore, 16 Medical Drive, Singapore, 117597, Singapore
| | - Xiao-Xing Yin
- Jiangsu Key Lab for the study of New Drug and Clinical Pharmacy, Xuzhou Medical College, Yunlong, China
| | - Choon Nam Ong
- NUS Environmental Research Inst., National University of Singapore, 5 A Engineering Srive 1, Singapore, 117411, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, 16 Medical Drive, Singapore, 117597, Singapore
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Saigusa D, Okamura Y, Motoike IN, Katoh Y, Kurosawa Y, Saijyo R, Koshiba S, Yasuda J, Motohashi H, Sugawara J, Tanabe O, Kinoshita K, Yamamoto M. Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery. PLoS One 2016; 11:e0160555. [PMID: 27579980 PMCID: PMC5006994 DOI: 10.1371/journal.pone.0160555] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 07/20/2016] [Indexed: 01/04/2023] Open
Abstract
Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens’ pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
- CREST, Japan Agency for Medical Research and Development (AMED), Chiyoda, Tokyo, Japan
- * E-mail: (DS); (MY)
| | - Yasunobu Okamura
- Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Ikuko N. Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yasutake Katoh
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yasuhiro Kurosawa
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Reina Saijyo
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Hozumi Motohashi
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Junichi Sugawara
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Osamu Tanabe
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
- * E-mail: (DS); (MY)
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Acinetobacter baumannii phenylacetic acid metabolism influences infection outcome through a direct effect on neutrophil chemotaxis. Proc Natl Acad Sci U S A 2016; 113:9599-604. [PMID: 27506797 DOI: 10.1073/pnas.1523116113] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Innate cellular immune responses are a critical first-line defense against invading bacterial pathogens. Leukocyte migration from the bloodstream to a site of infection is mediated by chemotactic factors that are often host-derived. More recently, there has been a greater appreciation of the importance of bacterial factors driving neutrophil movement during infection. Here, we describe the development of a zebrafish infection model to study Acinetobacter baumannii pathogenesis. By using isogenic A. baumannii mutants lacking expression of virulence effector proteins, we demonstrated that bacterial drivers of disease severity are conserved between zebrafish and mammals. By using transgenic zebrafish with fluorescent phagocytes, we showed that a mutation of an established A. baumannii global virulence regulator led to marked changes in neutrophil behavior involving rapid neutrophil influx to a localized site of infection, followed by prolonged neutrophil dwelling. This neutrophilic response augmented bacterial clearance and was secondary to an impaired A. baumannii phenylacetic acid catabolism pathway, which led to accumulation of phenylacetate. Purified phenylacetate was confirmed to be a neutrophil chemoattractant. These data identify a previously unknown mechanism of bacterial-guided neutrophil chemotaxis in vivo, providing insight into the role of bacterial metabolism in host innate immune evasion. Furthermore, the work provides a potentially new therapeutic paradigm of targeting a bacterial metabolic pathway to augment host innate immune responses and attenuate disease.
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DEUTERIUM FRACTIONATION DURING AMINO ACID FORMATION BY PHOTOLYSIS OF INTERSTELLAR ICE ANALOGS CONTAINING DEUTERATED METHANOL. ACTA ACUST UNITED AC 2016. [DOI: 10.3847/2041-8205/827/1/l18] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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73
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Christophoridis C, Nika MC, Aalizadeh R, Thomaidis NS. Ozonation of ranitidine: Effect of experimental parameters and identification of transformation products. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 557-558:170-182. [PMID: 27133934 DOI: 10.1016/j.scitotenv.2016.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 02/16/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
This study focuses on the effect of experimental parameters on the removal of ranitidine (RAN) during ozonation and the identification of the formed transformation products (TPs). The influence of pH value, the initial concentrations, the inorganic and the organic matter on RAN's removal were evaluated. Results indicated high reactivity of RAN with molecular aqueous ozone. Initial ozone concentration and pH were proven the major process parameters. Alkaline pH values promoted degradation and overall mineralization. Dissolved organic matter reacts competitively to RAN with the oxidants (ozone and/or radicals), influencing the target compound's removal. The presence of inorganic ions in the matrix did not seem to affect RAN ozonation. A total of eleven TPs were identified and structurally elucidated, with the complementary use of both Reversed Phase (RP) and Hydrophilic Interaction Liquid Chromatography (HILIC) quadrupole time of flight tandem mass spectrometry (Q-ToF-MS/MS). Most of the TPs (TP-304, TP-315b, TP-299b, TP-333, TP-283) were generated by the attack of ozone at the double bond or the adjacent secondary amine, with the abstraction of NO2 moiety, forming TPs with an aldehyde group and an imine bond. Oxidized derivatives with a carboxylic group (TP-315a, TP-331a, TP-331b, TP-299a) were also formed. RAN S-oxide was identified as an ozonation TP (TP-330) and its structure was confirmed through the analysis of a reference standard. TP-214 was also produced during ozonation, through the CN bond rupture adjacent to the NO2 moiety. HILIC was used complementary to RP, either for the separation and identification of TPs with isomeric structures that may have been co-eluted in RPLC or for the detection of new TPs that were not eluted in the RP chromatographic system. Retention time prediction was used as a supporting tool for the identification of TPs and results were in accordance with the experimental ones in both RP and HILIC.
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Affiliation(s)
- Christophoros Christophoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Athens 15771, Greece
| | - Maria-Christina Nika
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Athens 15771, Greece
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Athens 15771, Greece
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Athens 15771, Greece.
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Nielsen NJ, Tomasi G, Christensen JH. Evaluation of chromatographic conditions in reversed phase liquid chromatography-mass spectrometry systems for fingerprinting of polar and amphiphilic plant metabolites. Anal Bioanal Chem 2016; 408:5855-5865. [DOI: 10.1007/s00216-016-9700-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/29/2022]
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75
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Zhang T, Watson DG. Evaluation of the technical variations and the suitability of a hydrophilic interaction liquid chromatography-high resolution mass spectrometry (ZIC-pHILIC-Exactive orbitrap) for clinical urinary metabolomics study. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1022:199-205. [DOI: 10.1016/j.jchromb.2016.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/24/2016] [Accepted: 04/08/2016] [Indexed: 01/09/2023]
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76
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Tang Z, Cao T, Lin S, Fu L, Li S, Guan XY, Cai Z. Characterization of oncogene-induced metabolic alterations in hepatic cells by using ultrahigh performance liquid chromatography-tandem mass spectrometry. Talanta 2016; 152:119-26. [PMID: 26992502 DOI: 10.1016/j.talanta.2016.01.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/16/2016] [Accepted: 01/23/2016] [Indexed: 12/28/2022]
Abstract
Elucidation of altered metabolic pathways by using metabolomics may open new avenues for basic research on disease mechanisms and facilitate the development of novel therapeutic strategies. Here, we report the development of ultrahigh performance liquid chromatography-tandem mass spectrometry-based metabolomics platform with capability of measuring both cationic and anionic intermediates in cellular metabolism. The platform was established based on the hydrophobic ion-pairing interaction chromatography coupled with tandem mass spectrometry in multiple reaction monitoring (MRM) mode. The MRM transitions were created and optimized via energy-resolved collision-induced dissociation experiments, serving as an essential reference point for the quantification and identification. For chromatographic separation, application of hydrophobic ion-pairing interaction led to dramatic enhancement on retention of water-soluble metabolites and provision of good peak shapes. Two volatile ion-pairing reagents, namely heptafluorobutyric acid and tributylamine, were used with dedicated C18 columns as complementary separation systems coupled with the MRM analysis, allowing measurement of the metabolites of interest at nanomolar levels. The developed platform was successfully applied to investigate the altered metabolism in hepatic cells with over-expression of an oncogene, thus can provide important information on the rewired metabolism.
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Affiliation(s)
- Zhi Tang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Tingting Cao
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong SAR, China
| | - Shuhai Lin
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Li Fu
- Shenzhen Key Laboratory of Translational Medicine of Tumor and Cancer Research Centre, School of Medicine, Shenzhen University, Shenzhen, China
| | - Shangfu Li
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China.
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Ramakrishnan P, Nair S, Rangiah K. A method for comparative metabolomics in urine using high resolution mass spectrometry. J Chromatogr A 2016; 1443:83-92. [PMID: 27012786 DOI: 10.1016/j.chroma.2016.02.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/11/2016] [Accepted: 02/29/2016] [Indexed: 01/30/2023]
Abstract
Developing a workflow for metabolite profiling from biological fluids using mass spectrometry is imperative to extract accurate information. In this study, urine samples from smokers (n=10) and nonsmokers (n=10) were analyzed using an ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) system. For the analysis, two different chromatographic methods [Reversed phase chromatography (RPC) and Hydrophilic interaction liquid chromatography (HILIC)], in two ionization modes (positive and negative) were used. Spiked reserpine (positive ion mode) or taurocholate (negative ion mode) were used for data extraction and normalization. Quality controls (QCs), prepared by pooling urine samples from both smokers and non-smokers (each n=10), were used to assess the reproducibility of the method. The final data output from SIEVE 2.2 after applying a cut-off for QC coefficient of variation (CV) <20% and p-value <0.05 showed 165, 83, 177 and 100 unique components in RP positive/negative, HILIC positive/negative modes, respectively. Statistical analysis showed clustering of the two groups and the QCs, while the variable importance in projection (VIP) scores for the top fifteen metabolites in each of the four modes indicated the metabolites most responsible for the differences. Application of the developed workflow for comparative metabolomic analysis of urine in different diseased models will be of great use in the field of clinical metabolomics.
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Affiliation(s)
- Padma Ramakrishnan
- Metabolomics Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560065, India
| | - Sreenath Nair
- Metabolomics Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560065, India
| | - Kannan Rangiah
- Metabolomics Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560065, India.
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Mahamad Maifiah MH, Cheah SE, Johnson MD, Han ML, Boyce JD, Thamlikitkul V, Forrest A, Kaye KS, Hertzog P, Purcell AW, Song J, Velkov T, Creek DJ, Li J. Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii. Sci Rep 2016; 6:22287. [PMID: 26924392 PMCID: PMC4770286 DOI: 10.1038/srep22287] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/11/2016] [Indexed: 02/07/2023] Open
Abstract
Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and polymyxin-resistant A. baumannii using untargeted metabolomics. The metabolome of each A. baumannii strain was measured using liquid chromatography-mass spectrometry. Multivariate and univariate statistics and pathway analyses were employed to elucidate metabolic differences between the polymyxin-susceptible and -resistant A. baumannii strains. Significant differences were identified between the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii strains. The lipopolysaccharide (LPS) deficient, polymyxin-resistant 19606R showed perturbation in specific amino acid and carbohydrate metabolites, particularly pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle intermediates. Levels of nucleotides were lower in the LPS-deficient 19606R. Furthermore, 19606R exhibited a shift in its glycerophospholipid profile towards increased abundance of short-chain lipids compared to the parent polymyxin-susceptible ATCC 19606. In contrast, in a pair of clinical isolates 03-149.1 (polymyxin-susceptible) and 03-149.2 (polymyxin-resistant, due to modification of lipid A), minor metabolic differences were identified. Notably, peptidoglycan biosynthesis metabolites were significantly depleted in both of the aforementioned polymyxin-resistant strains. This is the first comparative untargeted metabolomics study to show substantial differences in the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii.
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Affiliation(s)
- Mohd Hafidz Mahamad Maifiah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Soon-Ee Cheah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Matthew D. Johnson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Mei-Ling Han
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - John D. Boyce
- Department of Microbiology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Visanu Thamlikitkul
- Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Alan Forrest
- UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7569, USA
| | - Keith S. Kaye
- Detroit Medical Centre and Wayne State University, University Health Centre, Detroit, MI, 48201, USA
| | - Paul Hertzog
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Tony Velkov
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Jian Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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Zhang R, Zhang T, Ali AM, Al Washih M, Pickard B, Watson DG. Metabolomic Profiling of Post-Mortem Brain Reveals Changes in Amino Acid and Glucose Metabolism in Mental Illness Compared with Controls. Comput Struct Biotechnol J 2016; 14:106-16. [PMID: 27076878 PMCID: PMC4813093 DOI: 10.1016/j.csbj.2016.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 12/04/2022] Open
Abstract
Metabolomic profiling was carried out on 53 post-mortem brain samples from subjects diagnosed with schizophrenia, depression, bipolar disorder (SDB), diabetes, and controls. Chromatography on a ZICpHILIC column was used with detection by Orbitrap mass spectrometry. Data extraction was carried out with m/z Mine 2.14 with metabolite searching against an in-house database. There was no clear discrimination between the controls and the SDB samples on the basis of a principal components analysis (PCA) model of 755 identified or putatively identified metabolites. Orthogonal partial least square discriminant analysis (OPLSDA) produced clear separation between 17 of the controls and 19 of the SDB samples (R2CUM 0.976, Q2 0.671, p-value of the cross-validated ANOVA score 0.0024). The most important metabolites producing discrimination were the lipophilic amino acids leucine/isoleucine, proline, methionine, phenylalanine, and tyrosine; the neurotransmitters GABA and NAAG and sugar metabolites sorbitol, gluconic acid, xylitol, ribitol, arabinotol, and erythritol. Eight samples from diabetic brains were analysed, six of which grouped with the SDB samples without compromising the model (R2 CUM 0.850, Q2 CUM 0.534, p-value for cross-validated ANOVA score 0.00087). There appears on the basis of this small sample set to be some commonality between metabolic perturbations resulting from diabetes and from SDB.
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Affiliation(s)
- Rong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, Scotland, UK; Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510405, China
| | - Tong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, Scotland, UK
| | - Ali Muhsen Ali
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, Scotland, UK; Department of Clinical Biochemistry/Diabetes and Endocrinology Centre, Thi-Qar Health Office, Thi-Qar, Nassiriya, Iraq
| | - Mohammed Al Washih
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, Scotland, UK; General Directorate of Medical Services, Ministry of Interior, Riyadh 13321, KSA
| | - Benjamin Pickard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, Scotland, UK
| | - David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, Scotland, UK
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80
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West JA, Beqqali A, Ament Z, Elliott P, Pinto YM, Arbustini E, Griffin JL. A targeted metabolomics assay for cardiac metabolism and demonstration using a mouse model of dilated cardiomyopathy. Metabolomics 2016; 12:59. [PMID: 27069442 PMCID: PMC4781888 DOI: 10.1007/s11306-016-0956-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/14/2015] [Indexed: 12/12/2022]
Abstract
Metabolomics can be performed either as an 'open profiling' tool where the aim is to measure, usually in a semi-quantitative manner, as many metabolites as possible or perform 'closed' or 'targeted' analyses where instead a pre-defined set of metabolites are measured. Targeted methods can be designed to be more sensitive and quantitative and so are particularly appropriate to systems biology for quantitative models of systems or when metabolomics is performed in a hypothesis driven manner to test whether a particular pathway is perturbed. We describe a targeted metabolomics assay that quantifies a broad range of over 130 metabolites relevant to cardiac metabolism including the pathways of the citric acid cycle, fatty acid oxidation, glycolysis, the pentose phosphate pathway, amino acid metabolism, the urea cycle, nucleotides and reactive oxygen species using tandem mass spectrometry to produce quantitative, sensitive and robust data. This assay is illustrated by profiling cardiac metabolism in a lamin A/C (Lmna) mouse model of dilated cardiomyopathy (DCM). The model of DCM was characterised by increases in concentrations of proline and methyl-histidine suggestive of increased myofibrillar and collagen degradation, as well as decreases in a number of citric acid cycle intermediates and carnitine derivatives indicating reduced energy metabolism in the dilated heart. These assays could be used for any other cardiac or cardiovascular disease in that they cover central core metabolism and key pathways involved in cardiac metabolism, and may provide a general start for many mammalian systems.
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Affiliation(s)
- James A. West
- The Department of Biochemistry & The Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
- The Elsie Widdowson Laboratory, Medical Research Council Human Nutrition Research, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - Abdelaziz Beqqali
- Department of Experimental Cardiology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Zsuzsanna Ament
- The Department of Biochemistry & The Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
- The Elsie Widdowson Laboratory, Medical Research Council Human Nutrition Research, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - Perry Elliott
- Heart Hospital, University College London, London, W1G 8PH UK
| | - Yigal M. Pinto
- Department of Experimental Cardiology, Academic Medical Centre, Amsterdam, The Netherlands
| | | | - Julian L. Griffin
- The Department of Biochemistry & The Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
- The Elsie Widdowson Laboratory, Medical Research Council Human Nutrition Research, 120 Fulbourn Road, Cambridge, CB1 9NL UK
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81
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Zhang T, Zhang R, Zhang L, Zhang Z, Hou R, Wang H, Loeffler IK, Watson DG, Kennedy MW. Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth--Three Phases in Early Lactation and Progressive Individual Differences. PLoS One 2015; 10:e0143417. [PMID: 26630345 PMCID: PMC4668050 DOI: 10.1371/journal.pone.0143417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/04/2015] [Indexed: 12/24/2022] Open
Abstract
Ursids (bears) in general, and giant pandas in particular, are highly altricial at birth. The components of bear milks and their changes with time may be uniquely adapted to nourish relatively immature neonates, protect them from pathogens, and support the maturation of neonatal digestive physiology. Serial milk samples collected from three giant pandas in early lactation were subjected to untargeted metabolite profiling and multivariate analysis. Changes in milk metabolites with time after birth were analysed by Principal Component Analysis, Hierarchical Cluster Analysis and further supported by Orthogonal Partial Least Square-Discriminant Analysis, revealing three phases of milk maturation: days 1–6 (Phase 1), days 7–20 (Phase 2), and beyond day 20 (Phase 3). While the compositions of Phase 1 milks were essentially indistinguishable among individuals, divergences emerged during the second week of lactation. OPLS regression analysis positioned against the growth rate of one cub tentatively inferred a correlation with changes in the abundance of a trisaccharide, isoglobotriose, previously observed to be a major oligosaccharide in ursid milks. Three artificial milk formulae used to feed giant panda cubs were also analysed, and were found to differ markedly in component content from natural panda milk. These findings have implications for the dependence of the ontogeny of all species of bears, and potentially other members of the Carnivora and beyond, on the complexity and sequential changes in maternal provision of micrometabolites in the immediate period after birth.
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Affiliation(s)
- Tong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
| | - Rong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, Chengdu, Sichuan Province, P.R. China
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, Chengdu, Sichuan Province, P.R. China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, Chengdu, Sichuan Province, P.R. China
| | - Hairui Wang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, Chengdu, Sichuan Province, P.R. China
| | - I. Kati Loeffler
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, Chengdu, Sichuan Province, P.R. China
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
| | - Malcolm W. Kennedy
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow, Scotland, United Kingdom
- * E-mail:
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82
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Diémé B, Mavel S, Blasco H, Tripi G, Bonnet-Brilhault F, Malvy J, Bocca C, Andres CR, Nadal-Desbarats L, Emond P. Metabolomics Study of Urine in Autism Spectrum Disorders Using a Multiplatform Analytical Methodology. J Proteome Res 2015; 14:5273-82. [PMID: 26538324 DOI: 10.1021/acs.jproteome.5b00699] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with no clinical biomarker. The aims of this study were to characterize a metabolic signature of ASD and to evaluate multiplatform analytical methodologies in order to develop predictive tools for diagnosis and disease follow-up. Urine samples were analyzed using (1)H and (1)H-(13)C NMR-based approaches and LC-HRMS-based approaches (ESI+ and ESI- on HILIC and C18 chromatography columns). Data tables obtained from the six analytical modalities on a training set of 46 urine samples (22 autistic children and 24 controls) were processed by multivariate analysis (orthogonal partial least-squares discriminant analysis, OPLS-DA). The predictions from each of these OPLS-DA models were then evaluated using a prediction set of 16 samples (8 autistic children and 8 controls) and receiver operating characteristic curves. Thereafter, a data fusion block-scaling OPLS-DA model was generated from the 6 best models obtained for each modality. This fused OPLS-DA model showed an enhanced performance (R(2)Y(cum) = 0.88, Q(2)(cum) = 0.75) compared to each analytical modality model, as well as a better predictive capacity (AUC = 0.91, p-value = 0.006). Metabolites that are most significantly different between autistic and control children (p < 0.05) are indoxyl sulfate, N-α-acetyl-l-arginine, methyl guanidine, and phenylacetylglutamine. This multimodality approach has the potential to contribute to find robust biomarkers and characterize a metabolic phenotype of the ASD population.
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Affiliation(s)
- Binta Diémé
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France
| | - Sylvie Mavel
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France
| | - Hélène Blasco
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France.,Service de Biochimie Et Biologie Moléculaire, Centre Hospitalier Régional Universitaire (CHRU) de Tours , 37044 Tours, France
| | - Gabriele Tripi
- Service de Pédopsychiatrie, CHRU de Tours , 37044 Tours, France
| | - Frédérique Bonnet-Brilhault
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France.,Service de Pédopsychiatrie, CHRU de Tours , 37044 Tours, France
| | - Joëlle Malvy
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France.,Service de Pédopsychiatrie, CHRU de Tours , 37044 Tours, France
| | - Cinzia Bocca
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France
| | - Christian R Andres
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France.,Service de Biochimie Et Biologie Moléculaire, Centre Hospitalier Régional Universitaire (CHRU) de Tours , 37044 Tours, France
| | - Lydie Nadal-Desbarats
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France
| | - Patrick Emond
- INSERM U930, Imagerie et Cerveau, Université François-Rabelais , 37000 Tours, France.,Service de Biochimie Et Biologie Moléculaire, Centre Hospitalier Régional Universitaire (CHRU) de Tours , 37044 Tours, France.,Service de Médecine Nucléaire In Vitro, CHRU de Tours , 37044 Tours, France
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83
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Westrop GD, Williams RAM, Wang L, Zhang T, Watson DG, Silva AM, Coombs GH. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism. PLoS One 2015; 10:e0136891. [PMID: 26368322 PMCID: PMC4569581 DOI: 10.1371/journal.pone.0136891] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/09/2015] [Indexed: 01/09/2023] Open
Abstract
Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.
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Affiliation(s)
- Gareth D. Westrop
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Roderick A. M. Williams
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, United Kingdom
| | - Lijie Wang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Tong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Ana Marta Silva
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Graham H. Coombs
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail:
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84
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Yan Z, Yan R. Increase the accessibility and scale of targeted metabolomics: Construction of a human urinary metabolome-wide multiple reaction monitoring library using directly-coupled reversed-phase and hydrophilic interaction chromatography. Anal Chim Acta 2015; 894:65-75. [DOI: 10.1016/j.aca.2015.08.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/26/2015] [Accepted: 08/30/2015] [Indexed: 12/31/2022]
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85
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Mackay GM, Zheng L, van den Broek NJF, Gottlieb E. Analysis of Cell Metabolism Using LC-MS and Isotope Tracers. Methods Enzymol 2015; 561:171-96. [PMID: 26358905 DOI: 10.1016/bs.mie.2015.05.016] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Here we discuss our methods to analyze small polar compounds involved in central carbon metabolism using LC-MS. Methods described include sample extraction procedures for cells and medium, as well as for plasma/serum, urine, CSF, and tissue samples. Different extraction solvents are assessed. Our methods for using (13)C stable isotope tracers to examine the kinetics and distributions of mass isotopologues of many metabolites are discussed. Quantification methods are described for (13)C stable isotope tracer experiments as well as for unlabeled experiments. These methods were applied in a fumarate hydratase deficient cell model to show how isotope tracing can demonstrate shifts in metabolic pathways and, together with metabolite exchange rates, can be used to gain insights into changes in cell metabolism.
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Affiliation(s)
| | - Liang Zheng
- Cancer Research UK Beatson Institute, Glasgow, UK
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86
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Computational analysis and ratiometric comparison approaches aimed to assist column selection in hydrophilic interaction liquid chromatography–tandem mass spectrometry targeted metabolomics. J Chromatogr A 2015; 1406:145-55. [DOI: 10.1016/j.chroma.2015.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 12/27/2022]
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87
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Thévenot EA, Roux A, Xu Y, Ezan E, Junot C. Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses. J Proteome Res 2015; 14:3322-35. [PMID: 26088811 DOI: 10.1021/acs.jproteome.5b00354] [Citation(s) in RCA: 744] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Urine metabolomics is widely used for biomarker research in the fields of medicine and toxicology. As a consequence, characterization of the variations of the urine metabolome under basal conditions becomes critical in order to avoid confounding effects in cohort studies. Such physiological information is however very scarce in the literature and in metabolomics databases so far. Here we studied the influence of age, body mass index (BMI), and gender on metabolite concentrations in a large cohort of 183 adults by using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). We implemented a comprehensive statistical workflow for univariate hypothesis testing and modeling by orthogonal partial least-squares (OPLS), which we made available to the metabolomics community within the online Workflow4Metabolomics.org resource. We found 108 urine metabolites displaying concentration variations with either age, BMI, or gender, by integrating the results from univariate p-values and multivariate variable importance in projection (VIP). Several metabolite clusters were further evidenced by correlation analysis, and they allowed stratification of the cohort. In conclusion, our study highlights the impact of gender and age on the urinary metabolome, and thus it indicates that these factors should be taken into account for the design of metabolomics studies.
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Affiliation(s)
- Etienne A Thévenot
- †CEA, LIST, Laboratory for Data Analysis and Smart Systems, MetaboHUB Paris, F-91191 Gif-sur-Yvette, France
| | - Aurélie Roux
- ‡Laboratoire d'Etude du Métabolisme des Médicaments, DSV/iBiTec-S/SPI, MetaboHUB Paris, CEA-Saclay, Gif-Sur-Yvette, France
| | - Ying Xu
- ‡Laboratoire d'Etude du Métabolisme des Médicaments, DSV/iBiTec-S/SPI, MetaboHUB Paris, CEA-Saclay, Gif-Sur-Yvette, France
| | - Eric Ezan
- ‡Laboratoire d'Etude du Métabolisme des Médicaments, DSV/iBiTec-S/SPI, MetaboHUB Paris, CEA-Saclay, Gif-Sur-Yvette, France
| | - Christophe Junot
- ‡Laboratoire d'Etude du Métabolisme des Médicaments, DSV/iBiTec-S/SPI, MetaboHUB Paris, CEA-Saclay, Gif-Sur-Yvette, France
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88
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Munoz G, Vo Duy S, Budzinski H, Labadie P, Liu J, Sauvé S. Quantitative analysis of poly- and perfluoroalkyl compounds in water matrices using high resolution mass spectrometry: Optimization for a laser diode thermal desorption method. Anal Chim Acta 2015; 881:98-106. [DOI: 10.1016/j.aca.2015.04.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/11/2015] [Accepted: 04/03/2015] [Indexed: 11/26/2022]
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89
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Wang J, Guo Z, Shen A, Yu L, Xiao Y, Xue X, Zhang X, Liang X. Hydrophilic-subtraction model for the characterization and comparison of hydrophilic interaction liquid chromatography columns. J Chromatogr A 2015; 1398:29-46. [DOI: 10.1016/j.chroma.2015.03.065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 03/25/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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90
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Pesek JJ, Matyska MT. Ammonium fluoride as a mobile phase additive in aqueous normal phase chromatography. J Chromatogr A 2015; 1401:69-74. [PMID: 26008598 DOI: 10.1016/j.chroma.2015.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/22/2015] [Accepted: 05/06/2015] [Indexed: 11/17/2022]
Abstract
The use of ammonium fluoride as a mobile phase additive in aqueous normal phase chromatography with silica hydride-based stationary phases and mass spectrometry detection is evaluated. Retention times, peak shape, efficiency and peak intensity are compared to the more standard additives formic acid and ammonium formate. The test solutes were NAD, 3-hydroxyglutaric acid, α-ketoglutaric acid, p-aminohippuric acid, AMP, ATP, aconitic acid, threonine, N-acetyl carnitine, and 3-methyladipic acid. The column parameters are assessed in both the positive and negative ion detection modes. Ammonium fluoride is potentially an aggressive mobile phase additive that could have detrimental effects on column lifetime. Column reproducibility is measured and the effects of switching between different additives are also tested.
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Affiliation(s)
- Joseph J Pesek
- Department of Chemistry, San Jose State University, San Jose, CA 95192, USA.
| | - Maria T Matyska
- Department of Chemistry, San Jose State University, San Jose, CA 95192, USA
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91
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Comparison of the performance of different silica hydride particles for the solid-phase extraction of non-volatile analytes from dark chocolate with analysis by gas chromatography–quadrupole mass spectrometry. Food Chem 2015; 174:434-9. [DOI: 10.1016/j.foodchem.2014.10.083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/09/2014] [Accepted: 10/15/2014] [Indexed: 01/10/2023]
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92
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Tomita S, Nemoto T, Matsuo Y, Shoji T, Tanaka F, Nakagawa H, Ono H, Kikuchi J, Ohnishi-Kameyama M, Sekiyama Y. A NMR-based, non-targeted multistep metabolic profiling revealed l-rhamnitol as a metabolite that characterised apples from different geographic origins. Food Chem 2015; 174:163-72. [DOI: 10.1016/j.foodchem.2014.11.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/27/2014] [Accepted: 11/03/2014] [Indexed: 01/27/2023]
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93
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Ebshiana AA, Snowden SG, Thambisetty M, Parsons R, Hye A, Legido-Quigley C. Metabolomic method: UPLC-q-ToF polar and non-polar metabolites in the healthy rat cerebellum using an in-vial dual extraction. PLoS One 2015; 10:e0122883. [PMID: 25853858 PMCID: PMC4390242 DOI: 10.1371/journal.pone.0122883] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/24/2015] [Indexed: 11/19/2022] Open
Abstract
Unbiased metabolomic analysis of biological samples is a powerful and increasingly commonly utilised tool, especially for the analysis of bio-fluids to identify candidate biomarkers. To date however only a small number of metabolomic studies have been applied to studying the metabolite composition of tissue samples, this is due, in part to a number of technical challenges including scarcity of material and difficulty in extracting metabolites. The aim of this study was to develop a method for maximising the biological information obtained from small tissue samples by optimising sample preparation, LC-MS analysis and metabolite identification. Here we describe an in-vial dual extraction (IVDE) method, with reversed phase and hydrophilic liquid interaction chromatography (HILIC) which reproducibly measured over 4,000 metabolite features from as little as 3mg of brain tissue. The aqueous phase was analysed in positive and negative modes following HILIC separation in which 2,838 metabolite features were consistently measured including amino acids, sugars and purine bases. The non-aqueous phase was also analysed in positive and negative modes following reversed phase separation gradients respectively from which 1,183 metabolite features were consistently measured representing metabolites such as phosphatidylcholines, sphingolipids and triacylglycerides. The described metabolomics method includes a database for 200 metabolites, retention time, mass and relative intensity, and presents the basal metabolite composition for brain tissue in the healthy rat cerebellum.
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Affiliation(s)
- Amera A. Ebshiana
- Institute of Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom
| | - Stuart G. Snowden
- Institute of Psychiatry, Department of Old Age Psychiatry, King’s College London, De Crespigny Park, London, SE5 8AF, United Kingdom
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioural Neuroscience, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Richard Parsons
- Institute of Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom
| | - Abdul Hye
- Institute of Psychiatry, Department of Old Age Psychiatry, King’s College London, De Crespigny Park, London, SE5 8AF, United Kingdom
| | - Cristina Legido-Quigley
- Institute of Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom
- * E-mail:
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Contrepois K, Jiang L, Snyder M. Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry. Mol Cell Proteomics 2015; 14:1684-95. [PMID: 25787789 PMCID: PMC4458729 DOI: 10.1074/mcp.m114.046508] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 12/01/2022] Open
Abstract
Profiling of body fluids is crucial for monitoring and discovering metabolic markers of health and disease and for providing insights into human physiology. Since human urine and plasma each contain an extreme diversity of metabolites, a single liquid chromatographic system when coupled to mass spectrometry (MS) is not sufficient to achieve reasonable metabolome coverage. Hydrophilic interaction liquid chromatography (HILIC) offers complementary information to reverse-phase liquid chromatography (RPLC) by retaining polar metabolites. With the objective of finding the optimal combined chromatographic solution to profile urine and plasma, we systematically investigated the performance of five HILIC columns with different chemistries operated at three different pH (acidic, neutral, basic) and five C18-silica RPLC columns. The zwitterionic column ZIC-HILIC operated at neutral pH provided optimal performance on a large set of hydrophilic metabolites. The RPLC columns Hypersil GOLD and Zorbax SB aq were proven to be best suited for the metabolic profiling of urine and plasma, respectively. Importantly, the optimized HILIC-MS method showed excellent intrabatch peak area reproducibility (CV < 12%) and good long-term interbatch (40 days) peak area reproducibility (CV < 22%) that were similar to those of RPLC-MS procedures. Finally, combining the optimal HILIC- and RPLC-MS approaches greatly expanded metabolome coverage with 44% and 108% new metabolic features detected compared with RPLC-MS alone for urine and plasma, respectively. The proposed combined LC-MS approaches improve the comprehensiveness of global metabolic profiling of body fluids and thus are valuable for monitoring and discovering metabolic changes associated with health and disease in clinical research studies.
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Affiliation(s)
- Kévin Contrepois
- From the Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lihua Jiang
- From the Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Snyder
- From the Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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95
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van der Hooft JJJ, Ridder L, Barrett MP, Burgess KEV. Enhanced acylcarnitine annotation in high-resolution mass spectrometry data: fragmentation analysis for the classification and annotation of acylcarnitines. Front Bioeng Biotechnol 2015; 3:26. [PMID: 25806366 PMCID: PMC4353373 DOI: 10.3389/fbioe.2015.00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/19/2015] [Indexed: 11/24/2022] Open
Abstract
Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software1. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context of untargeted metabolomics experiments is a valuable tool to enhance the annotation of small metabolites.
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Affiliation(s)
| | - Lars Ridder
- Laboratory of Biochemistry, Wageningen University and Research Centre , Wageningen , Netherlands
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96
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Yan Z, Yan R. Improved Data-Dependent Acquisition for Untargeted Metabolomics Using Gas-Phase Fractionation with Staggered Mass Range. Anal Chem 2015; 87:2861-8. [DOI: 10.1021/ac504325x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zhixiang Yan
- State Key Laboratory
of Quality
Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao 999078, China
| | - Ru Yan
- State Key Laboratory
of Quality
Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao 999078, China
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97
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Xu YF, Lu W, Rabinowitz JD. Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics. Anal Chem 2015; 87:2273-81. [PMID: 25591916 DOI: 10.1021/ac504118y] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. When analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, and hexose-phosphates generate triose-phosphates. We evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University , Princeton, New Jersey 08544, United States
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98
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Wang Y, Liu S, Hu Y, Li P, Wan JB. Current state of the art of mass spectrometry-based metabolomics studies – a review focusing on wide coverage, high throughput and easy identification. RSC Adv 2015. [DOI: 10.1039/c5ra14058g] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metabolomics aims at the comprehensive assessment of a wide range of endogenous metabolites and attempts to identify and quantify the attractive metabolites in a given biological sample.
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Affiliation(s)
- Yang Wang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Shuying Liu
- Jilin Ginseng Academy
- Changchun University of Chinese Medicine
- Changchun
- China
| | - Yuanjia Hu
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Peng Li
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Jian-Bo Wan
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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99
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Zhang T, Watson DG. A short review of applications of liquid chromatography mass spectrometry based metabolomics techniques to the analysis of human urine. Analyst 2015; 140:2907-15. [DOI: 10.1039/c4an02294g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry based metabolomics profiling.
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Affiliation(s)
- Tong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences
- University of Strathclyde
- Glasgow
- UK
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences
- University of Strathclyde
- Glasgow
- UK
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100
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Alkhaldi AAM, Creek DJ, Ibrahim H, Kim DH, Quashie NB, Burgess KE, Changtam C, Barrett MP, Suksamrarn A, de Koning HP. Potent trypanocidal curcumin analogs bearing a monoenone linker motif act on trypanosoma brucei by forming an adduct with trypanothione. Mol Pharmacol 2014; 87:451-64. [PMID: 25527638 DOI: 10.1124/mol.114.096016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have previously reported that curcumin analogs with a C7 linker bearing a C4-C5 olefinic linker with a single keto group at C3 (enone linker) display midnanomolar activity against the bloodstream form of Trypanosoma brucei. However, no clear indication of their mechanism of action or superior antiparasitic activity relative to analogs with the original di-ketone curcumin linker was apparent. To further investigate their utility as antiparasitic agents, we compare the cellular effects of curcumin and the enone linker lead compound 1,7-bis(4-hydroxy-3-methoxyphenyl)hept-4-en-3-one (AS-HK014) here. An AS-HK014-resitant line, trypanosomes adapted to AS-HK014 (TA014), was developed by in vitro exposure to the drug. Metabolomic analysis revealed that exposure to AS-HK014, but not curcumin, rapidly depleted glutathione and trypanothione in the wild-type line, although almost all other metabolites were unchanged relative to control. In TA014 cells, thiol levels were similar to untreated wild-type cells and not significantly depleted by AS-HK014. Adducts of AS-HK014 with both glutathione and trypanothione were identified in AS-HK014-exposed wild-type cells and reproduced by chemical reaction. However, adduct accumulation in sensitive cells was much lower than in resistant cells. TA014 cells did not exhibit any changes in sequence or protein levels of glutathione synthetase and γ-glutamylcysteine synthetase relative to wild-type cells. We conclude that monoenone curcuminoids have a different mode of action than curcumin, rapidly and specifically depleting thiol levels in trypanosomes by forming an adduct. This adduct may ultimately be responsible for the highly potent trypanocidal and antiparasitic activity of the monoenone curcuminoids.
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Affiliation(s)
- Abdulsalam A M Alkhaldi
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Darren J Creek
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Hasan Ibrahim
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Dong-Hyun Kim
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Neils B Quashie
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Karl E Burgess
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Chatchawan Changtam
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Michael P Barrett
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Apichart Suksamrarn
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (A.A.M.A, D.J.C., H.I., D.-H.K., N.B.Q., K.E.B., M.P.B., H.P.K.); Department of Biology, College of Science, Aljouf University, Skaka, Kingdom of Saudi Arabia (A.A.M.A); Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia (D.J.C.); Faculty of Science, Department of Zoology, Sebha University, Libya (H.I.); Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom (D.-H.K.); Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana (N.B.Q.); Division of Physical Science, Faculty of Science and Technology, Huachiew Chalermprakiet University, Samutprakarn, Thailand (C.C.); Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom (M.P.B.); and Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand (A.S.)
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