101
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Challenges of analyzing different classes of metabolites by a single analytical method. Bioanalysis 2014; 6:3393-416. [DOI: 10.4155/bio.14.236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Complex biological samples include thousands of metabolites that range widely in both physiochemical properties and concentration. Simultaneously analyzing metabolites with different properties using a single analytical method is very challenging. The analytical process for metabolites comprises multiple steps including sampling, quenching, sample preparation, separation and detection. Each step can have a significant effect on the reliability and precision of ultimate analytic results. The aim of review is a discussion of considerations and challenges for the simultaneous analysis of metabolites using LC– and GC–MS systems. The review discusses available methodology for each analytical step, and presents the limitations and advantages of each method for the large-scale targeted metabolomics analysis of human and animal biological samples.
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102
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Yin P, Xu G. Current state-of-the-art of nontargeted metabolomics based on liquid chromatography-mass spectrometry with special emphasis in clinical applications. J Chromatogr A 2014; 1374:1-13. [PMID: 25444251 DOI: 10.1016/j.chroma.2014.11.050] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 11/16/2014] [Accepted: 11/17/2014] [Indexed: 12/21/2022]
Abstract
Metabolomics, as a part of systems biology, has been widely applied in different fields of life science by studying the endogenous metabolites. The development and applications of liquid chromatography (LC) coupled with high resolution mass spectrometry (MS) greatly improve the achievable data quality in non-targeted metabolic profiling. However, there are still some emerging challenges to be covered in LC-MS based metabolomics. Here, recent approaches about sample collection and preparation, instrumental analysis, and data handling of LC-MS based metabolomics are summarized, especially in the analysis of clinical samples. Emphasis is put on the improvement of analytical techniques including the combination of different LC columns, isotope coded derivatization methods, pseudo-targeted LC-MS method, new data analysis algorithms and structural identification of important metabolites.
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Affiliation(s)
- Peiyuan Yin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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103
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Junot C, Fenaille F, Colsch B, Bécher F. High resolution mass spectrometry based techniques at the crossroads of metabolic pathways. MASS SPECTROMETRY REVIEWS 2014; 33:471-500. [PMID: 24288070 DOI: 10.1002/mas.21401] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
The metabolome is the set of small molecular mass compounds found in biological media, and metabolomics, which refers to as the analysis of metabolome in a given biological condition, deals with the large scale detection and quantification of metabolites in biological media. It is a data driven and multidisciplinary approach combining analytical chemistry for data acquisition, and biostatistics, informatics and biochemistry for mining and interpretation of these data. Since the middle of the 2000s, high resolution mass spectrometry is widely used in metabolomics, mainly because the detection and identification of metabolites are improved compared to low resolution instruments. As the field of HRMS is quickly and permanently evolving, the aim of this work is to review its use in different aspects of metabolomics, including data acquisition, metabolite annotation, identification and quantification. At last, we would like to show that, thanks to their versatility, HRMS instruments are the most appropriate to achieve optimal metabolome coverage, at the border of other omics fields such as lipidomics and glycomics.
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Affiliation(s)
- Christophe Junot
- Commissariat à l'Energie Atomique, Centre de Saclay, DSV/iBiTec-S/SPI, Laboratoire d'Etude du Métabolisme des Médicaments, 91191, Gif-sur-Yvette Cedex, France
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104
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Hirayama A, Igarashi K, Tomita M, Soga T. Development of quantitative method for determination of γ-glutamyl peptides by capillary electrophoresis tandem mass spectrometry: an efficient approach avoiding matrix effect. J Chromatogr A 2014; 1369:161-9. [PMID: 25441083 DOI: 10.1016/j.chroma.2014.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 11/15/2022]
Abstract
Serum γ-glutamyl di- and tripeptides have proven to be useful biomarkers to accurately predict nine different forms of liver disease. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM), serum and liver samples spiked with γ-glutamyl peptide standards were analyzed to estimate accuracy. Unexpectedly, the recovery rates for several γ-glutamyl peptides in the serum samples were quite low, whereas values for some γ-glutamyl peptides in the liver samples were highly elevated. Most of these peptides were barely retained on the reverse-phase column, resulting in significant ion suppression or enhancement. In contrast, a capillary electrophoresis tandem mass spectrometry (CE-MS/MS) method with MRM was minimally affected by matrix effects. Of the 39 tested compounds, most of γ-glutamyl peptides that did not contain a thiol substituent in its structure gave acceptable recoveries (70-120%), and limits of detection for the analytes were between 3.6 and 800 nmol/l with pressure injection at 5 kPa for 10 s (ca. 10 nl). The CE-MS/MS method provided high resolution and proved to be highly selective and sensitive, its utility being demonstrated by the determination of γ-glutamyl di- and tripeptides in serum and liver samples.
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Affiliation(s)
- Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Kaori Igarashi
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
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105
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Rainville PD, Theodoridis G, Plumb RS, Wilson ID. Advances in liquid chromatography coupled to mass spectrometry for metabolic phenotyping. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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106
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Zhang R, Watson DG, Wang L, Westrop GD, Coombs GH, Zhang T. Evaluation of mobile phase characteristics on three zwitterionic columns in hydrophilic interaction liquid chromatography mode for liquid chromatography-high resolution mass spectrometry based untargeted metabolite profiling of Leishmania parasites. J Chromatogr A 2014; 1362:168-79. [DOI: 10.1016/j.chroma.2014.08.039] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 11/30/2022]
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107
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Liu Z, Rochfort S. Recent progress in polar metabolite quantification in plants using liquid chromatography–mass spectrometry. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:816-825. [PMID: 25340205 DOI: 10.1111/jipb.12181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metabolite analysis or metabolomics is an important component of systems biology in the post-genomic era. Although separate liquid chromatography (LC) methods for quantification of the major classes of polar metabolites of plants have been available for decades, a single method that enables simultaneous determination of hundreds of polar metabolites is possible only with gas chromatography–mass spectrometry (GC–MS) techniques. The rapid expansion of new LC stationary phases in the market and the ready access of mass spectrometry in many laboratories provides an excellent opportunity for developing LC–MS based methods for multi-target quantification of polar metabolites. Although various LC–MS methods have been developed over the last 10 years with the aim to quantify one or more classes of polar compounds in different matrices, currently there is no consensus LC–MS method that is widely used in plant metabolomics studies. The most promising methods applicable to plant metabolite analysis will be reviewed in this paper and the major problems encountered highlighted. The aim of this review is to provide plant scientists, with limited to moderate experience in analytical chemistry, with up-to-date and simplified information regarding the current status of polar metabolite analysis using LC–MS techniques.
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108
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Wang J, Kong S, Yan J, Jin G, Guo Z, Shen A, Xu J, Zhang X, Zou L, Liang X. Hydrophilic interaction liquid chromatography-solid phase extraction directly combined with protein precipitation for the determination of triptorelin in plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 960:214-21. [DOI: 10.1016/j.jchromb.2014.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/15/2014] [Accepted: 04/19/2014] [Indexed: 02/08/2023]
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109
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Wu Q, Wang Y, Gu X, Zhou J, Zhang H, Lv W, Chen Z, Yan C. Urinary metabolomic study of non-small cell lung carcinoma based on ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. J Sep Sci 2014; 37:1728-35. [PMID: 24771673 DOI: 10.1002/jssc.201400222] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/14/2014] [Accepted: 04/14/2014] [Indexed: 01/06/2023]
Affiliation(s)
- Qian Wu
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai China
| | - Yan Wang
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai China
| | - Xue Gu
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai China
| | - Junyi Zhou
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai China
| | - Huiping Zhang
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai China
| | - Wang Lv
- Zhejiang Hospital of Traditional Chinese Medicine; Zhejiang Chinese Medical University; Hangzhou China
| | - Zhe Chen
- Zhejiang Hospital of Traditional Chinese Medicine; Zhejiang Chinese Medical University; Hangzhou China
| | - Chao Yan
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai China
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110
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Benznidazole biotransformation and multiple targets in Trypanosoma cruzi revealed by metabolomics. PLoS Negl Trop Dis 2014; 8:e2844. [PMID: 24853684 PMCID: PMC4031082 DOI: 10.1371/journal.pntd.0002844] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/24/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The first line treatment for Chagas disease, a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, involves administration of benznidazole (Bzn). Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active, although its mode of action is not fully understood. In the present work we used a non-targeted MS-based metabolomics approach to study the metabolic response of T. cruzi to Bzn. METHODOLOGY/PRINCIPAL FINDINGS Parasites treated with Bzn were minimally altered compared to untreated trypanosomes, although the redox active thiols trypanothione, homotrypanothione and cysteine were significantly diminished in abundance post-treatment. In addition, multiple Bzn-derived metabolites were detected after treatment. These metabolites included reduction products, fragments and covalent adducts of reduced Bzn linked to each of the major low molecular weight thiols: trypanothione, glutathione, γ-glutamylcysteine, glutathionylspermidine, cysteine and ovothiol A. Bzn products known to be generated in vitro by the unusual trypanosomal nitroreductase, TcNTRI, were found within the parasites, but low molecular weight adducts of glyoxal, a proposed toxic end-product of NTRI Bzn metabolism, were not detected. CONCLUSIONS/SIGNIFICANCE Our data is indicative of a major role of the thiol binding capacity of Bzn reduction products in the mechanism of Bzn toxicity against T. cruzi.
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111
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Boudah S, Olivier MF, Aros-Calt S, Oliveira L, Fenaille F, Tabet JC, Junot C. Annotation of the human serum metabolome by coupling three liquid chromatography methods to high-resolution mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:34-47. [PMID: 24815365 DOI: 10.1016/j.jchromb.2014.04.025] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 11/15/2022]
Abstract
This work aims at evaluating the relevance and versatility of liquid chromatography coupled to high resolution mass spectrometry (LC/HRMS) for performing a qualitative and comprehensive study of the human serum metabolome. To this end, three different chromatographic systems based on a reversed phase (RP), hydrophilic interaction chromatography (HILIC) and a pentafluorophenylpropyl (PFPP) stationary phase were used, with detection in both positive and negative electrospray modes. LC/HRMS platforms were first assessed for their ability to detect, retain and separate 657 metabolite standards representative of the chemical families occurring in biological fluids. More than 75% were efficiently retained in either one LC-condition and less than 5% were exclusively retained by the RP column. These three LC/HRMS systems were then evaluated for their coverage of serum metabolome. The combination of RP, HILIC and PFPP based LC/HRMS methods resulted in the annotation of about 1328 features in the negative ionization mode, and 1358 in the positive ionization mode on the basis of their accurate mass and precise retention time in at least one chromatographic condition. Less than 12% of these annotations were shared by the three LC systems, which highlights their complementarity. HILIC column ensured the greatest metabolome coverage in the negative ionization mode, whereas PFPP column was the most effective in the positive ionization mode. Altogether, 192 annotations were confirmed using our spectral database and 74 others by performing MS/MS experiments. This resulted in the formal or putative identification of 266 metabolites, among which 59 are reported for the first time in human serum.
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Affiliation(s)
- Samia Boudah
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France; GlaxoSmithKline - Centre de recherche F.Hyafil, 25 Avenue du Québec, Villebon-sur-Yvette, France
| | - Marie-Françoise Olivier
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France
| | - Sandrine Aros-Calt
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France; bioMérieux S.A, Chemin de l'Orme, 69280 Marcy l'Etoile, France
| | - Lydie Oliveira
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Radiobiologie Cellulaire et Moléculaire/Laboratoire de Recherche sur la Transcription et la Réparation des Cellules Souches, 92260 Fontenay-aux-Roses, France
| | - François Fenaille
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France
| | - Jean-Claude Tabet
- Laboratoire de Chimie Structurale Organique et Biologique, IPCM/CNRS UMR 7201, Université Pierre et Marie Curie, 75252 Paris, France
| | - Christophe Junot
- Commissariat à l'Energie Atomique et aux Energies Alternatives/Direction des Sciences du Vivant/Institut de Biologie et de Technologie de Saclay/Service de Pharmacologie et d'Immunoanalyse/Laboratoire d'Etude du Métabolisme des Médicaments, CEA-Saclay, 91191 Gif-Sur-Yvette, France.
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112
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Recent developments in liquid-phase separation techniques for metabolomics. Bioanalysis 2014; 6:1011-26. [DOI: 10.4155/bio.14.51] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Metabolomics is the comprehensive analysis of low molecular weight compounds in biological samples such as cells, body fluids and tissues. Comprehensive profiling of metabolites in complex sample matrices with the current analytical toolbox remains a huge challenge. Over the past few years, liquid chromatography–mass spectrometry (LC–MS) and capillary electrophoresis–mass spectrometry (CE–MS) have emerged as powerful complementary analytical techniques in the field of metabolomics. This Review provides an update of the most recent developments in LC–MS and CE–MS for metabolomics. Concerning LC–MS, attention is paid to developments in column technology and miniaturized systems, while strategies are discussed to improve the reproducibility and the concentration sensitivity of CE–MS for metabolomics studies. Novel interfacing techniques for coupling CE to MS are also considered. Representative examples illustrate the potential of the recent developments in LC–MS and CE–MS for metabolomics. Finally, some conclusions and perspectives are provided.
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113
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Chromatographic analysis with different detectors in the chemical characterisation and dereplication of African propolis. Talanta 2014; 120:181-90. [DOI: 10.1016/j.talanta.2013.11.094] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 11/26/2013] [Accepted: 11/30/2013] [Indexed: 11/19/2022]
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114
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Isokawa M, Funatsu T, Tsunoda M. Fast and simultaneous analysis of biothiols by high-performance liquid chromatography with fluorescence detection under hydrophilic interaction chromatography conditions. Analyst 2013; 138:3802-8. [PMID: 23702918 DOI: 10.1039/c3an00527e] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A method for analyzing biothiols based on high-performance liquid chromatography (HPLC)-fluorescence detection under hydrophilic interaction chromatography (HILIC) conditions has been developed. Thiols were derivatized with nonfluorescent ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate (SBD-F), which selectively reacts with the thiol groups to furnish the corresponding fluorescent SBD-thiols. Among the six different kinds of HILIC columns examined, the ZIC-HILIC column with sulfobetaine groups in the stationary phase proved to be the best for the separation of SBD-thiols. Eight thiols-N-acetylcysteine, cysteamine, homocysteine, cysteine, cysteinylglycine, glutathione, γ-glutamylcysteine, and internal standard N-(2-mercaptopropionyl)glycine-were baseline-separated within 10 min. The detection sensitivity was improved partly due to the increase in the SBD-thiol fluorescence owing to the acetonitrile-rich mobile phase used. The detection limits at a signal-to-noise ratio of 3 were 0.02-3.4 nmol l(-1). The method could successfully quantify six thiols in a human plasma sample, while cysteamine could not be detected. Both the intra- and interday precisions were below 4% for homocysteine, cysteine, cysteinylglycine, glutathione, and γ-glutamylcysteine except for N-acetylcysteine. This method should be a useful tool for investigating the relationship between sulfur metabolism and related diseases, since a multicomponent system consisting of different thiol compounds could be analyzed simultaneously with high sensitivity within a short time.
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Affiliation(s)
- Muneki Isokawa
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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115
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Castro-Puyana M, Mendiola JA, Ibañez E. Strategies for a cleaner new scientific discipline of green foodomics. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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116
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Tears as a source of biomarkers for ocular and systemic diseases. Exp Eye Res 2013; 117:126-37. [DOI: 10.1016/j.exer.2013.07.015] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/05/2013] [Accepted: 07/12/2013] [Indexed: 12/23/2022]
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117
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Siegel D, Permentier H, Reijngoud DJ, Bischoff R. Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 966:21-33. [PMID: 24326023 DOI: 10.1016/j.jchromb.2013.11.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/10/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022]
Abstract
This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.
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Affiliation(s)
- David Siegel
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar Permentier
- University of Groningen, Department of Pharmacy, Mass Spectrometry Core Facility, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- University Medical Center Groningen, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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118
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Fischer R, Bowness P, Kessler BM. Two birds with one stone: doing metabolomics with your proteomics kit. Proteomics 2013; 13:3371-86. [PMID: 24155035 PMCID: PMC4265265 DOI: 10.1002/pmic.201300192] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/13/2013] [Accepted: 09/30/2013] [Indexed: 12/31/2022]
Abstract
Proteomic research facilities and laboratories are facing increasing demands for the integration of biological data from multiple ‘-OMICS’ approaches. The aim to fully understand biological processes requires the integrated study of genomes, proteomes and metabolomes. While genomic and proteomic workflows are different, the study of the metabolome overlaps significantly with the latter, both in instrumentation and methodology. However, chemical diversity complicates an easy and direct access to the metabolome by mass spectrometry (MS). The present review provides an introduction into metabolomics workflows from the viewpoint of proteomic researchers. We compare the physicochemical properties of proteins and peptides with metabolites/small molecules to establish principle differences between these analyte classes based on human data. We highlight the implications this may have on sample preparation, separation, ionisation, detection and data analysis. We argue that a typical proteomic workflow (nLC-MS) can be exploited for the detection of a number of aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids and vitamins, thereby providing a straightforward entry point for metabolomics-based studies. Limitations and requirements are discussed as well as extensions to the LC-MS workflow to expand the range of detectable molecular classes without investing in dedicated instrumentation such as GC-MS, CE-MS or NMR.
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Affiliation(s)
- Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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119
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Shen A, Li X, Dong X, Wei J, Guo Z, Liang X. Glutathione-based zwitterionic stationary phase for hydrophilic interaction/cation-exchange mixed-mode chromatography. J Chromatogr A 2013; 1314:63-9. [DOI: 10.1016/j.chroma.2013.09.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/29/2013] [Accepted: 09/01/2013] [Indexed: 10/26/2022]
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120
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Lesiak AD, Adams KJ, Domin MA, Henck C, Shepard JRE. DART-MS for rapid, preliminary screening of urine for DMAA. Drug Test Anal 2013; 6:788-96. [DOI: 10.1002/dta.1540] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/24/2013] [Accepted: 08/18/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Ashton D. Lesiak
- Department of Chemistry; University at Albany, State University of New York (SUNY); 1400 Washington Ave Albany NY 12222 USA
| | - Kendra J. Adams
- Department of Chemistry; University at Albany, State University of New York (SUNY); 1400 Washington Ave Albany NY 12222 USA
| | - Marek A. Domin
- Mass Spectrometry Center, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467-3808 USA
| | - Colin Henck
- Department of Chemistry; University at Albany, State University of New York (SUNY); 1400 Washington Ave Albany NY 12222 USA
| | - Jason R. E. Shepard
- Department of Chemistry; University at Albany, State University of New York (SUNY); 1400 Washington Ave Albany NY 12222 USA
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121
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Marrubini G, Pedrali A, Hemström P, Jonsson T, Appelblad P, Massolini G. Column comparison and method development for the analysis of short-chain carboxylic acids by zwitterionic hydrophilic interaction liquid chromatography with UV detection. J Sep Sci 2013; 36:3493-502. [DOI: 10.1002/jssc.201300551] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 12/25/2022]
Affiliation(s)
| | - Alice Pedrali
- Department of Drug Sciences; University of Pavia; Pavia Italy
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122
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Theodoridis GA, Michopoulos F, Gika HG, Plumb RS, Wilson ID. Liquid Chromatographic Techniques in Metabolomics. CHROMATOGRAPHIC METHODS IN METABOLOMICS 2013. [DOI: 10.1039/9781849737272-00064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In the past decade, LC‐MS‐based metabolomic/metabonomic profiling has become a major analytical focus for biomarker research. Chromatographic resolution is continually improving with the development of more advanced separation platforms based on smaller particle sizes, new types of stationary phase and miniaturized systems allowing the profiling of biological samples for metabolites in ways that were simply not possible before. Chromatographic advances, combined with increased mass resolution instruments that provide sub‐2 ppm mass accuracy and high sensitivity, have greatly facilitated the detection and identification of potential biomarkers. In this chapter, the most common LC(‐MS) methods utilized in metabolic analyses are presented, with emphasis on novel high‐efficiency and high‐throughput analyses and their suitability for metabolic analyses. Guidelines for the selection of the appropriate method for different applications are given, with emphasis on the use of LC‐MS.
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Affiliation(s)
| | - Filippos Michopoulos
- Department of Chemistry Aristotle University Thessaloniki, 541 24 Thessaloniki Greece
- Oncology IM, AstraZeneca Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG UK
| | - Helen G. Gika
- Department of Chemical Engineering Aristotle University Thessaloniki, 541 24 Thessaloniki Greece
| | - Robert S. Plumb
- Department of Surgery and Oncology Sir Alexander Fleming Building, Imperial College, Exhibition Road, South Kensington, London SW7 2AZ UK
| | - Ian D. Wilson
- Department of Surgery and Oncology Sir Alexander Fleming Building, Imperial College, Exhibition Road, South Kensington, London SW7 2AZ UK
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123
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Ivanisevic J, Zhu ZJ, Plate L, Tautenhahn R, Chen S, O'Brien PJ, Johnson CH, Marletta MA, Patti GJ, Siuzdak G. Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Anal Chem 2013; 85:6876-84. [PMID: 23781873 PMCID: PMC3761963 DOI: 10.1021/ac401140h] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the objective of any 'omic science is broad measurement of its constituents, such coverage has been challenging in metabolomics because the metabolome is comprised of a chemically diverse set of small molecules with variable physical properties. While extensive studies have been performed to identify metabolite isolation and separation methods, these strategies introduce bias toward lipophilic or water-soluble metabolites depending on whether reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) is used, respectively. Here we extend our consideration of metabolome isolation and separation procedures to integrate RPLC/MS and HILIC/MS profiling. An aminopropyl-based HILIC/MS method was optimized on the basis of mobile-phase additives and pH, followed by evaluation of reproducibility. When applied to the untargeted study of perturbed bacterial metabolomes, the HILIC method enabled the accurate assessment of key, dysregulated metabolites in central carbon pathways (e.g., amino acids, organic acids, phosphorylated sugars, energy currency metabolites), which could not be retained by RPLC. To demonstrate the value of the integrative approach, bacterial cells, human plasma, and cancer cells were analyzed by combined RPLC/HILIC separation coupled to ESI positive/negative MS detection. The combined approach resulted in the observation of metabolites associated with lipid and central carbon metabolism from a single biological extract, using 80% organic solvent (ACN:MeOH:H2O 2:2:1). It enabled the detection of more than 30,000 features from each sample type, with the highest number of uniquely detected features by RPLC in ESI positive mode and by HILIC in ESI negative mode. Therefore, we conclude that when time and sample are limited, the maximum amount of biological information related to lipid and central carbon metabolism can be acquired by combining RPLC ESI positive and HILIC ESI negative mode analysis.
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Affiliation(s)
- Julijana Ivanisevic
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California 92037, United States
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124
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Zhang T, Watson DG, Wang L, Abbas M, Murdoch L, Bashford L, Ahmad I, Lam NY, Ng ACF, Leung HY. Application of Holistic Liquid Chromatography-High Resolution Mass Spectrometry Based Urinary Metabolomics for Prostate Cancer Detection and Biomarker Discovery. PLoS One 2013; 8:e65880. [PMID: 23823321 PMCID: PMC3688815 DOI: 10.1371/journal.pone.0065880] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/29/2013] [Indexed: 11/23/2022] Open
Abstract
Human exhibit wide variations in their metabolic profiles because of differences in genetic factors, diet and lifestyle. Therefore in order to detect metabolic differences between individuals robust analytical methods are required. A protocol was produced based on the use of Liquid Chromatography- High Resolution Mass Spectrometry (LC-HRMS) in combination with orthogonal Hydrophilic Interaction (HILIC) and Reversed Phase (RP) liquid chromatography methods for the analysis of the urinary metabolome, which was then evaluated as a diagnostic tool for prostate cancer (a common but highly heterogeneous condition). The LC-HRMS method was found to be robust and exhibited excellent repeatability for retention times (<±1%), and mass accuracy (<±1 ppm). Based on normalised data (against creatinine levels, osmolality or MS total useful signals/MSTUS) coupled with supervised multivariate analysis using Orthogonal Partial Least Square-Discriminant Analysis (OPLS-DA), we were able to discriminate urine samples from men with or without prostate cancer with R2Y(cum) >0.9. In addition, using the receiver operator characteristics (ROC) test, the area under curve (AUC) for the combination of the four best characterised biomarker compounds was 0.896. The four biomarker compounds were also found to differ significantly (P<0.05) between an independent patient cohort and controls. This is the first time such a rigorous test has been applied to this type of model. If validated, the established protocol provides a robust approach with a potentially wide application to metabolite profiling of human biofluids in health and disease.
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Affiliation(s)
- Tong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
- * E-mail:
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
| | - Lijie Wang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
| | - Muhammad Abbas
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, Scotland, United Kingdom
| | - Laura Murdoch
- Glasgow Clinical Research Facility, Glasgow, Scotland, United Kingdom
| | - Lisa Bashford
- The Beatson Institute for Cancer Research, Glasgow, Scotland, United Kingdom
| | - Imran Ahmad
- Department of Urology, Gartnavel General Hospital, Glasgow, Scotland, United Kingdom
- The Beatson Institute for Cancer Research, Glasgow, Scotland, United Kingdom
| | - Nga-Yee Lam
- Department of Urology, Chinese University of Hong Kong, Hong Kong
| | - Anthony C. F. Ng
- Department of Urology, Chinese University of Hong Kong, Hong Kong
| | - Hing Y. Leung
- Department of Urology, Gartnavel General Hospital, Glasgow, Scotland, United Kingdom
- The Beatson Institute for Cancer Research, Glasgow, Scotland, United Kingdom
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125
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Abstract
The discovery, development and optimal utilization of pharmaceuticals can be greatly enhanced by knowledge of their modes of action. However, many drugs currently on the market act by unknown mechanisms. Untargeted metabolomics offers the potential to discover modes of action for drugs that perturb cellular metabolism. Development of high resolution LC-MS methods and improved data analysis software now allows rapid detection of drug-induced changes to cellular metabolism in an untargeted manner. Several studies have demonstrated the ability of untargeted metabolomics to provide unbiased target discovery for antimicrobial drugs, in particular for antiprotozoal agents. Furthermore, the utilization of targeted metabolomics techniques has enabled validation of existing hypotheses regarding antiprotozoal drug mechanisms. Metabolomics approaches are likely to assist with optimization of new drug candidates by identification of drug targets, and by allowing detailed characterization of modes of action and resistance of existing and novel antiprotozoal drugs.
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126
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Kloos DP, Lingeman H, Niessen WM, Deelder AM, Giera M, Mayboroda OA. Evaluation of different column chemistries for fast urinary metabolic profiling. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 927:90-6. [DOI: 10.1016/j.jchromb.2013.02.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 11/15/2022]
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127
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Numerous protein-bound solutes are cleared by the kidney with high efficiency. Kidney Int 2013; 84:585-90. [PMID: 23636170 PMCID: PMC3758437 DOI: 10.1038/ki.2013.154] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 11/21/2022]
Abstract
The kidney clears numerous solutes from the plasma; however, retention of these solutes
causes uremic illness when the kidneys fail. We know remarkably little about which retained solutes
are toxic and this limits our ability to improve dialysis therapies. To explore this we employed
untargeted mass spectrometry to identify solutes that are efficiently cleared by the kidney. High
resolution mass spectrometry detected 1808 features in the urine and plasma ultrafiltrate of 5
individuals with normal renal function. The estimated clearance rates of 1082 peaks were greater
than the creatinine clearance indicating tubular secretion. Further analysis identified 90 features
representing solutes with estimated clearance rates greater than the renal plasma flow. Quantitative
mass spectrometry with stable isotope dilution confirmed that efficient clearance of these solutes
is made possible by the combination of binding to plasma proteins and tubular secretion. Tandem mass
spectrometry established the chemical identity of 13 solutes including hippuric acid, indoxyl
sulfate, and p-cresol sulfate. These 13 efficiently cleared solutes were found to accumulate in the
plasma of hemodialysis patients, with free levels rising to more than 20-fold normal for all but two
of them. Thus, further analysis of solutes efficiently cleared by secretion in the native kidney may
provide a potential route to the identification of uremic toxins.
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128
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Metabolomics guides rational development of a simplified cell culture medium for drug screening against Trypanosoma brucei. Antimicrob Agents Chemother 2013; 57:2768-79. [PMID: 23571546 DOI: 10.1128/aac.00044-13] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In vitro culture methods underpin many experimental approaches to biology and drug discovery. The modification of established cell culture methods to make them more biologically relevant or to optimize growth is traditionally a laborious task. Emerging metabolomic technology enables the rapid evaluation of intra- and extracellular metabolites and can be applied to the rational development of cell culture media. In this study, untargeted semiquantitative and targeted quantitative metabolomic analyses of fresh and spent media revealed the major nutritional requirements for the growth of bloodstream form Trypanosoma brucei. The standard culture medium (HMI11) contained unnecessarily high concentrations of 32 nutrients that were subsequently removed to make the concentrations more closely resemble those normally found in blood. Our new medium, Creek's minimal medium (CMM), supports in vitro growth equivalent to that in HMI11 and causes no significant perturbation of metabolite levels for 94% of the detected metabolome (<3-fold change; α = 0.05). Importantly, improved sensitivity was observed for drug activity studies in whole-cell phenotypic screenings and in the metabolomic mode of action assays. Four-hundred-fold 50% inhibitory concentration decreases were observed for pentamidine and methotrexate, suggesting inhibition of activity by nutrients present in HMI11. CMM is suitable for routine cell culture and offers important advantages for metabolomic studies and drug activity screening.
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129
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Watson DG, Tonelli F, Osaimi MA, Williamson L, Chan E, Gorshkova I, Berdyshev E, Bittman R, Pyne NJ, Pyne S. The roles of sphingosine kinases 1 and 2 in regulating the Warburg effect in prostate cancer cells. Cell Signal 2013; 25:1011-7. [PMID: 23314175 PMCID: PMC3595369 DOI: 10.1016/j.cellsig.2013.01.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/06/2013] [Indexed: 12/30/2022]
Abstract
Two isoforms of sphingosine kinase, SK1 and SK2, catalyze the formation of the bioactive lipid sphingosine 1-phosphate (S1P) in mammalian cells. We have previously shown that treatment of androgen-sensitive LNCaP prostate cancer cells with a non-selective SK isoform inhibitor, 2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole (SKi), induces the proteasomal degradation of SK1. This is concomitant with a significant increase in C22:0-ceramide and sphingosine levels and a reduction in S1P levels, resulting in the apoptosis of LNCaP cells. In contrast, we show here that a SK2-selective inhibitor, (R)-FTY720 methyl ether (ROME), increases sphingosine and decreases S1P levels but has no effect on ceramide levels and does not induce apoptosis in LNCaP cells. We also show that several glycolytic metabolites and (R)-S-lactoylglutathione are increased upon treatment of LNCaP cells with SKi, which induces the proteasomal degradation of c-Myc. These changes reflect an indirect antagonism of the Warburg effect. LNCaP cells also respond to SKi by diverting glucose 6-phosphate into the pentose phosphate pathway to provide NADPH, which serves as an antioxidant to counter an oxidative stress response. SKi also promotes the formation of a novel pro-apoptotic molecule called diadenosine 5',5'''-P(1),P(3)-triphosphate (Ap3A), which binds to the tumor suppressor fragile histidine triad protein (FHIT). In contrast, the SK2-selective inhibitor, ROME, induces a reduction in some glycolytic metabolites and does not affect oxidative stress. We conclude that SK1 functions to increase the stability of c-Myc and suppresses Ap3A formation, which might maintain the Warburg effect and cell survival, while SK2 exhibits a non-overlapping function.
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Affiliation(s)
| | | | | | | | | | - Irina Gorshkova
- The University of Illinois at Chicago Section of Pulmonary, Critical Care, Sleep, and Allergy, 909 S. Wolcott Ave., Chicago, IL 60612, USA
| | - Evgeny Berdyshev
- The University of Illinois at Chicago Section of Pulmonary, Critical Care, Sleep, and Allergy, 909 S. Wolcott Ave., Chicago, IL 60612, USA
| | - Robert Bittman
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, Flushing, New York 11367-1597, USA
| | | | - Susan Pyne
- To whom correspondence should be addressed (Tel: 441415482012; Fax: 441415522562; )
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130
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Kuehnbaum NL, Britz-McKibbin P. New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era. Chem Rev 2013; 113:2437-68. [DOI: 10.1021/cr300484s] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Naomi L. Kuehnbaum
- Department of Chemistry
and Chemical Biology, McMaster University, Hamilton, Canada
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131
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Yang Y, Matyska MT, Boysen RI, Pesek JJ, Hearn MTW. Simultaneous separation of hydrophobic and polar bases using a silica hydride stationary phase. J Sep Sci 2013; 36:1209-16. [DOI: 10.1002/jssc.201201113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/06/2013] [Accepted: 01/07/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Yuanzhong Yang
- Australian Research Council Special Research Centre for Green Chemistry; Monash University; Melbourne Victoria Australia
| | - Maria T. Matyska
- Department of Chemistry; San Jose State University; San Jose CA USA
| | - Reinhard I. Boysen
- Australian Research Council Special Research Centre for Green Chemistry; Monash University; Melbourne Victoria Australia
| | - Joseph J. Pesek
- Department of Chemistry; San Jose State University; San Jose CA USA
| | - Milton T. W. Hearn
- Australian Research Council Special Research Centre for Green Chemistry; Monash University; Melbourne Victoria Australia
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132
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Watson DG. A rough guide to metabolite identification using high resolution liquid chromatography mass spectrometry in metabolomic profiling in metazoans. Comput Struct Biotechnol J 2013; 4:e201301005. [PMID: 24688687 PMCID: PMC3962115 DOI: 10.5936/csbj.201301005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/28/2013] [Accepted: 02/08/2013] [Indexed: 12/15/2022] Open
Abstract
Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.
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Affiliation(s)
- David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, United Kingdom
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133
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Limenitakis J, Oppenheim RD, Creek DJ, Foth BJ, Barrett MP, Soldati-Favre D. The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Mol Microbiol 2013; 87:894-908. [PMID: 23279335 PMCID: PMC3593168 DOI: 10.1111/mmi.12139] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2012] [Indexed: 12/22/2022]
Abstract
Toxoplasma gondii belongs to the coccidian subgroup of the Apicomplexa phylum. The Coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. These parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (BCAA) as a possible pathway to generate acetyl-CoA. Importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-CoA, a toxic metabolite that inhibits cell growth. Like fungi and bacteria, the Coccidia possess the complete set of enzymes necessary to metabolize and detoxify propionate by oxidation to pyruvate via the 2-methylcitrate cycle (2-MCC). Phylogenetic analysis provides evidence that the 2-MCC was acquired via horizontal gene transfer. In T. gondii tachyzoites, this pathway is split between the cytosol and the mitochondrion. Although the rate-limiting enzyme 2-methylisocitrate lyase is dispensable for parasite survival, its substrates accumulate in parasites deficient in the enzyme and its absence confers increased sensitivity to propionic acid. BCAA is also dispensable in tachyzoites, leaving unresolved the source of mitochondrial acetyl-CoA.
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Affiliation(s)
- Julien Limenitakis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU 1 Rue Michel Servet, 1211 Geneva, Switzerland
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134
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Schuster G, Lindner W. Comparative characterization of hydrophilic interaction liquid chromatography columns by linear solvation energy relationships. J Chromatogr A 2013; 1273:73-94. [DOI: 10.1016/j.chroma.2012.11.075] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/23/2012] [Accepted: 11/26/2012] [Indexed: 11/30/2022]
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135
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Ali JAM, Creek DJ, Burgess K, Allison HC, Field MC, Mäser P, De Koning HP. Pyrimidine salvage in Trypanosoma brucei bloodstream forms and the trypanocidal action of halogenated pyrimidines. Mol Pharmacol 2012. [PMID: 23188714 DOI: 10.1124/mol.112.082321] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
African trypanosomes are capable of both pyrimidine biosynthesis and salvage of preformed pyrimidines from the host. However, uptake of pyrimidines in bloodstream form trypanosomes has not been investigated, making it difficult to judge the relative importance of salvage and synthesis or to design a pyrimidine-based chemotherapy. Detailed characterization of pyrimidine transport activities in bloodstream form Trypanosoma brucei brucei found that these cells express a high-affinity uracil transporter (designated TbU3) that is clearly distinct from the procyclic pyrimidine transporters. This transporter had low affinity for uridine and 2'deoxyuridine and was the sole pyrimidine transporter expressed in these cells. In addition, thymidine was taken up inefficiently through a P1-type nucleoside transporter. Of importance, the anticancer drug 5-fluorouracil was an excellent substrate for TbU3, and several 5-fluoropyrimidine analogs were investigated for uptake and trypanocidal activity; 5F-orotic acid, 5F-2'deoxyuridine displayed activity in the low micromolar range. The metabolism and mode of action of these analogs was determined using metabolomic assessments of T. brucei clonal lines adapted to high levels of these pyrimidine analogs, and of the sensitive parental strains. The analysis showed that 5-fluorouracil is incorporated into a large number of metabolites but likely exerts toxicity through incorporation into RNA. 5F-2'dUrd and 5F-2'dCtd are not incorporated into nucleic acids but act as prodrugs by inhibiting thymidylate synthase as 5F-dUMP. We present the most complete model of pyrimidine salvage in T. brucei to date, supported by genome-wide profiling of the predicted pyrimidine biosynthesis and conversion enzymes.
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Affiliation(s)
- Juma A M Ali
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
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136
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Bawazeer S, Sutcliffe OB, Euerby MR, Bawazeer S, Watson DG. A comparison of the chromatographic properties of silica gel and silicon hydride modified silica gels. J Chromatogr A 2012; 1263:61-7. [PMID: 23040975 DOI: 10.1016/j.chroma.2012.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/01/2012] [Accepted: 09/03/2012] [Indexed: 11/26/2022]
Abstract
The retention properties of a silica gel column and a type C silica (silicon hydride) column for bases, sugars and polar acids were compared in hydrophilic interaction chromatography (HILIC) mode with formic acid or ammonium acetate as aqueous phase modifiers. The type C silica column was much more retentive for a series of model bases than the silica gel column and, surprisingly, retention of bases increased on the type C silica column when, the higher pH, ammonium acetate containing mobile phase was used. The retention of sugars was greater on the type C silica column than on the silica gel column and also increased on the type C silica column with increased pH suggesting either a silanophilic mechanism of retention or some unknown mechanism. Three type C silica based columns, type C silica, cogent diamond hydride and a β-pinene modified column, which it was hoped might exert some additional stereochemical discrimination, were tested for metabolomic profiling of urine. In general the unmodified type C silica column gave the strongest retention of the many polar metabolites in urine and could provide a useful complement to established HILIC methods for metabolomic profiling.
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Affiliation(s)
- Saud Bawazeer
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, UK
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137
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Peironcely JE, Rojas-Chertó M, Fichera D, Reijmers T, Coulier L, Faulon JL, Hankemeier T. OMG: Open Molecule Generator. J Cheminform 2012; 4:21. [PMID: 22985496 PMCID: PMC3558358 DOI: 10.1186/1758-2946-4-21] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/03/2012] [Indexed: 12/31/2022] Open
Abstract
Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.
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Affiliation(s)
- Julio E Peironcely
- Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands.
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138
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Moco S, Martin FPJ, Rezzi S. Metabolomics view on gut microbiome modulation by polyphenol-rich foods. J Proteome Res 2012; 11:4781-90. [PMID: 22905879 DOI: 10.1021/pr300581s] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Health is influenced by genetic, lifestyle, and diet determinants; therefore, nutrition plays an essential role in health management. Still, the substantiation of nutritional health benefits is challenged by the intrinsic macro- and micronutrient complexity of foods and individual responses. Evidence of healthy effects of food requires new strategies not only to stratify populations according to their metabolic requirements but also to predict and measure individual responses to dietary intakes. The influence of the gut microbiome and its interaction with the host is pivotal to understand nutrition and metabolism. Thus, the modulation of the gut microbiome composition by alteration of food habits has potentialities in health improvement or even disease prevention. Dietary polyphenols are naturally occurring constituents in vegetables and fruits, including coffee and cocoa. They are commonly associated to health benefits, although mechanistic evidence in vivo is not yet fully understood. Polyphenols are extensively metabolized by gut bacteria into a complex series of end-products that support a significant effect on the functional ecology of symbiotic partners that can affect the host physiology. This review reports recent nutritional metabolomics inspections of gut microbiota-host metabolic interactions with a particular focus on the cometabolism of cocoa and coffee polyphenols.
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Affiliation(s)
- Sofia Moco
- BioAnalytical Science, Nestle Research Center, Vers-chez-les-Blanc, PO Box 44, 1000 Lausanne 26, Switzerland.
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139
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Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C. Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem 2012; 84:6429-37. [PMID: 22770225 DOI: 10.1021/ac300829f] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolic profiles of biofluids obtained by atmospheric pressure ionization mass spectrometry-based technologies contain hundreds to thousands of features, most of them remaining unknown or at least not characterized in analytical systems. We report here on the annotation of the human adult urinary metabolome and metabolite identification from electrospray ionization mass spectrometry (ESI-MS)-based metabolomics data sets. Features of biological interest were first of all annotated using the ESI-MS database of the laboratory. They were also grouped, thanks to software tools, and annotated using public databases. Metabolite identification was achieved using two complementary approaches: (i) formal identification by matching chromatographic retention times, mass spectra, and also product ion spectra (if required) of metabolites to be characterized in biological data sets to those of reference compounds and (ii) putative identification from biological data thanks to MS/MS experiments for metabolites not available in our chemical library. By these means, 384 metabolites corresponding to 1484 annotated features (659 in negative ion mode and 825 in positive ion mode) were characterized in human urine samples. Of these metabolites, 192 and 66 were formally and putatively identified, respectively, and 54 are reported in human urine for the first time. These lists of features could be used by other laboratories to annotate their ESI-MS metabolomics data sets.
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Affiliation(s)
- Aurelie Roux
- CEA-Centre d'Etude de Saclay, Gif-sur-Yvette, France
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