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Rabti H, Amrane M, Lalaouna A, Flilissa A, Benguerba Y. Optimization and validation of a bioanalytical HPLC-UV technique for simultaneous determination of underivatized phenylalanine and tyrosine in the blood for phenylketonuria diagnosis and monitoring. Biomed Chromatogr 2024; 38:e5758. [PMID: 37795814 DOI: 10.1002/bmc.5758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/10/2023] [Accepted: 09/16/2023] [Indexed: 10/06/2023]
Abstract
This study aimed to develop a fast, accurate, and precise high-performance liquid chromatography with UV detection method for simultaneous analysis of underivatized phenylalanine (Phe) and tyrosine (Tyr) in biological samples. Separation of the analytes was accomplished using a Discovery HS F5-3 column, which offered better retention and peak symmetry for the tested analytes. Chromatographic conditions were optimized using central composite experimental design, and three factors were investigated: the concentration of ammonium acetate (A), the acetonitrile proportion in the mobile phase (B) and the column oven temperature (C). The approach was verified using β-expectation tolerance intervals for total error measurement that did not exceed 15%. Optimal settings were A = 50 mm, B = 24% and C = 28°C. The method applicability was determined using human plasma from 75 volunteers. The limits of detection and quantification of the technique were satisfactory at 9 and 29 μm for Phe and 4 and 13 μm for Tyr. The mean analytical bias in spiking levels was acceptable, ranging from -1.649 to +1.659% for both substances, with RSD <5% in all instances. The suggested approach was successfully used to analyze Phe and Tyr in human blood samples and calculate the Phe/Tyr ratio.
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Affiliation(s)
- Hadjira Rabti
- Laboratory of Cardiovascular Diseases with Genetic and Nutritional Origin (LMCGN), Ferhat Abbas-Setif 1 University, Setif, Algeria
- Department of Pharmaceutical Engineering, Faculty of Process Engineering, Salah Boubnider-Constantine 3 University, Constantine, Algeria
| | - Mounira Amrane
- Laboratory of Cardiovascular Diseases with Genetic and Nutritional Origin (LMCGN), Ferhat Abbas-Setif 1 University, Setif, Algeria
- Mokhtari Abdelghani Cancer Center, Elbez, Setif, Algeria
| | - Abdeldjalil Lalaouna
- Analytical Chemistry Laboratory, Pharmacy Department, Faculty of Medicine, Salah Boubnider-Constantine 3 University, Constantine, Algeria
| | - Abdenacer Flilissa
- Laboratory of Cardiovascular Diseases with Genetic and Nutritional Origin (LMCGN), Ferhat Abbas-Setif 1 University, Setif, Algeria
| | - Yacine Benguerba
- Biopharmacy and Pharmatechnie Laboratory (LBPT), Ferhat ABBAS University- Setif 1, Setif, Algeria
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Sha Y, Guo X, He Y, Li W, Liu X, Zhao S, Hu J, Wang J, Li S, Zhao Z, Hao Z. Synergistic Responses of Tibetan Sheep Rumen Microbiota, Metabolites, and the Host to the Plateau Environment. Int J Mol Sci 2023; 24:14856. [PMID: 37834304 PMCID: PMC10573510 DOI: 10.3390/ijms241914856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Plateau adaptation in animals involves genetic mechanisms as well as coevolutionary mechanisms of the microbiota and metabolome of the animal. Therefore, the characteristics of the rumen microbiome and metabolome, transcriptome, and serum metabolome of Tibetan sheep at different altitudes (4500 m, 3500 m, and 2500 m) were analyzed. The results showed that the rumen differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and carbohydrate metabolism, and there was a significant correlation with microbiota. The differentially expressed genes and metabolites at middle and high altitudes were coenriched in asthma, arachidonic acid metabolism, and butanoate and propanoate metabolism. In addition, the serum differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and metabolism of xenobiotics by cytochrome P450, and they were also related to microbiota. Further analysis revealed that rumen metabolites accounted for 7.65% of serum metabolites. These common metabolites were mainly enriched in metabolic pathways and were significantly correlated with host genes (p < 0.05). This study found that microbiota, metabolites, and epithelial genes were coenriched in pathways related to lipid metabolism, energy metabolism, and immune metabolism, which may be involved in the regulation of Tibetan sheep adaptation to plateau environmental changes.
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Affiliation(s)
- Yuzhu Sha
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Xinyu Guo
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand;
| | - Wenhao Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China;
| | - Xiu Liu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Shengguo Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Jiang Hu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Jiqing Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Shaobin Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Zhidong Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
| | - Zhiyun Hao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.S.); (X.G.); (S.Z.); (J.H.); (J.W.); (S.L.); (Z.Z.); (Z.H.)
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3
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Giacomello G, Otto C, Priller J, Ruprecht K, Böttcher C, Parr MK. 1,2- 13C 2-Glucose Tracing Approach to Assess Metabolic Alterations of Human Monocytes under Neuroinflammatory Conditions. Curr Issues Mol Biol 2023; 45:765-781. [PMID: 36661537 PMCID: PMC9857935 DOI: 10.3390/cimb45010051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/17/2023] Open
Abstract
Neuroinflammation is one of the common features in most neurological diseases including multiple sclerosis (MScl) and neurodegenerative diseases such as Alzheimer's disease (AD). It is associated with local brain inflammation, microglial activation, and infiltration of peripheral immune cells into cerebrospinal fluid (CSF) and the central nervous system (CNS). It has been shown that the diversity of phenotypic changes in monocytes in CSF relates to neuroinflammation. It remains to be investigated whether these phenotypic changes are associated with functional or metabolic alteration, which may give a hint to their function or changes in cell states, e.g., cell activation. In this article, we investigate whether major metabolic pathways of blood monocytes alter after exposure to CSF of healthy individuals or patients with AD or MScl. Our findings show a significant alteration of the metabolism of monocytes treated with CSF from patients and healthy donors, including higher production of citric acid and glutamine, suggesting a more active glycolysis and tricarboxylic acid (TCA) cycle and reduced production of glycine and serine. These alterations suggest metabolic reprogramming of monocytes, possibly related to the change of compartment (from blood to CSF) and/or disease-related. Moreover, the levels of serine differ between AD and MScl, suggesting different phenotypic alterations between diseases.
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Affiliation(s)
- Ginevra Giacomello
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2 + 4, 14195 Berlin, Germany
| | - Carolin Otto
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University Munich, 81675 Munich, Germany
- UK Dementia Research Institute (UK DRI), University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Klemens Ruprecht
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Chotima Böttcher
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maria Kristina Parr
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2 + 4, 14195 Berlin, Germany
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Fan S, Wilson CM, Fridley BL, Li Q. Statistics and Machine Learning in Mass Spectrometry-Based Metabolomics Analysis. Methods Mol Biol 2023; 2629:247-269. [PMID: 36929081 DOI: 10.1007/978-1-0716-2986-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
In this chapter, we review the cutting-edge statistical and machine learning methods for missing value imputation, normalization, and downstream analyses in mass spectrometry metabolomics studies, with illustration by example datasets. The missing peak recovery includes simple imputation by zero or limit of detection, regression-based or distribution-based imputation, and prediction by random forest. The batch effect can be removed by data-driven methods, internal standard-based, and quality control sample-based normalization. We also summarize different types of statistical analysis for metabolomics and clinical outcomes, such as inference on metabolic biomarkers, clustering of metabolomic profiles, metabolite module building, and integrative analysis with transcriptome.
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Affiliation(s)
- Sili Fan
- Graduate Group of Biostatistics, University of California, Davis, CA, USA
| | - Christopher M Wilson
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Qian Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Han W, Li L. Evaluating and minimizing batch effects in metabolomics. MASS SPECTROMETRY REVIEWS 2022; 41:421-442. [PMID: 33238061 DOI: 10.1002/mas.21672] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Determining metabolomic differences among samples of different phenotypes is a critical component of metabolomics research. With the rapid advances in analytical tools such as ultrahigh-resolution chromatography and mass spectrometry, an increasing number of metabolites can now be profiled with high quantification accuracy. The increased detectability and accuracy raise the level of stringiness required to reduce or control any experimental artifacts that can interfere with the measurement of phenotype-related metabolome changes. One of the artifacts is the batch effect that can be caused by multiple sources. In this review, we discuss the origins of batch effects, approaches to detect interbatch variations, and methods to correct unwanted data variability due to batch effects. We recognize that minimizing batch effects is currently an active research area, yet a very challenging task from both experimental and data processing perspectives. Thus, we try to be critical in describing the performance of a reported method with the hope of stimulating further studies for improving existing methods or developing new methods.
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Affiliation(s)
- Wei Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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6
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Peng KW, Klotz A, Guven A, Gray K, Friss T, Ravipaty S, Sarangarajan R, Tolstikov V, Kellogg MD, Narain NR, Kiebish MA. Multiplexed LC-MS/MS analysis of methylsuccinic acid, ethylmalonic acid, and glutaric acid in plasma and urine. Anal Biochem 2022; 645:114604. [PMID: 35217005 DOI: 10.1016/j.ab.2022.114604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/01/2022]
Abstract
Low molecular-mass aliphatic carboxylic acids are critically important for intermediate metabolism and may serve as important biomarkers for metabolic homeostasis. Here in, we focused on multiplexed method development of aliphatic carboxylic analytes, including methylsuccinic acid (MSA), ethylmalonic acid (EMA), and glutaric acid (GA). Also assessed was their utility in a population's health as well as metabolic disease screening in both plasma and urine matrices. MSA, EMA, and GA are constitutional isomers of dicarboxylic acid with high polarity and poor ionization efficiency, resulting in such challenges as poor signal intensity and retention, particularly in reversed-phase liquid chromatography with electrospray mass spectrometry (RP-LC-ESI-MS/MS). Derivatization using n-butanol was performed in the sample preparation to enhance the signal intensity accompanied with a positive charge from ionization in complicated biomatrices as well as to improve the separation of these isomers with optimal retention. Fit-for-purpose method validation results demonstrated quantitative ranges for MSA/EMA/GA from 5/10/20 ng/mL to 400 ng/mL in plasma analysis, and 100/200/100 ng/mL to 5000/10000/5000 ng/mL in urine analysis. This validated method demonstrates future utility when exploring population health analysis and biomarker development in metabolic diseases.
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Affiliation(s)
- Kuan-Wei Peng
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA
| | - Allison Klotz
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA
| | - Arcan Guven
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA
| | - Kayleigh Gray
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA
| | - Tracey Friss
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA
| | | | | | | | - Mark D Kellogg
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; Department of Laboratory Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Niven R Narain
- BERG, 500 Old Connecticut Path, Framingham, MA, 01701, USA
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7
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Analytical Platforms for Mass Spectrometry-Based Metabolomics of Polar and Ionizable Metabolites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:215-242. [PMID: 34628634 DOI: 10.1007/978-3-030-77252-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Metabolomics studies rely on the availability of suitable analytical platforms to determine a vast collection of chemically diverse metabolites in complex biospecimens. Liquid chromatography-mass spectrometry operated under reversed-phase conditions is the most commonly used platform in metabolomics, which offers extensive coverage for nonpolar and moderately polar compounds. However, complementary techniques are required to obtain adequate separation of polar and ionic metabolites, which are involved in several fundamental metabolic pathways. This chapter focuses on the main mass-spectrometry-based analytical platforms used to determine polar and/or ionizable compounds in metabolomics (GC-MS, HILIC-MS, CE-MS, IPC-MS, and IC-MS). Rather than comprehensively describing recent applications related to GC-MS, HILIC-MS, and CE-MS, which have been covered in a regular basis in the literature, a brief discussion focused on basic principles, main strengths, limitations, as well as future trends is presented in this chapter, and only key applications with the purpose of illustrating important analytical aspects of each platform are highlighted. On the other hand, due to the relative novelty of IPC-MS and IC-MS in the metabolomics field, a thorough compilation of applications for these two techniques is presented here.
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8
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Cummings DA, Snelling AI, Puri AW. Methylotroph Quorum Sensing Signal Identification by Inverse Stable Isotopic Labeling. ACS Chem Biol 2021; 16:1332-1338. [PMID: 34328722 DOI: 10.1021/acschembio.1c00329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a 13C-carbon source and then identifying 12C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate that this method identifies N-acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously detect five previously unidentified signals produced by a methylotroph and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive 13C-carbon sources.
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Affiliation(s)
- Dale A. Cummings
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Alice I. Snelling
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
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Asare SO, Dean KR, Lynn BC. The study of the chromatographic behavior and a mass spectrometric approach to differentiating the diastereomer pair of the β-O-4 lignin dimer series. Anal Bioanal Chem 2021; 413:4037-4048. [PMID: 33934193 DOI: 10.1007/s00216-021-03358-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/29/2022]
Abstract
Lignin and lignans are natural products found in plant cell walls. Lignin research has historically focused on lignin degradation techniques in the hope of converting lignin into useful aromatic carbon feedstocks. In contrast, investigations of lignans existing as natural product dimers, have been focused on thier interesting biological activities. Many lignan compounds are chemically identical to dimers derived from lignin, and both lignin and lignan dimers can possess multiple chiral centers leading to observations of diastereomer pairs where one diastereomer exhibits the bulk of the activity. For example, the G-(β-O-4')-G dimer was reported to have a pro-angiogenic activity with one diastereomer of the pair showing enhanced pro-angiogenic activity. Traditional analytical techniques such as nuclear magnetic resonance (NMR) can differentiate the diastereomer pairs of β-O-4 compounds; however, isolation of a pure sample is often required for analysis. This work was aimed at exploring the potential use of tandem mass spectrometry to differentiate diastereomer pairs in the β-O-4 dimer series. Each diastereomer pair in the nine-dimer series was separated by HPLC and interrogated by tandem mass spectrometry. To understand the chromatographic behavior of the diastereomer pair in the β-O-4 dimer series, three commercially available reverse phase HPLC columns were evaluated. A temperature programming experiment using water/acetonitrile isocratic elution showed that the chromatographic retention mechanism of these diastereomers was hydrophobically driven with analytes having more methoxy groups exhibiting larger ΔH0 and higher octanol-water partition coefficient values. Tandem mass spectrometry performed on each of the diastereomers produced fragment ions having different ion abundances. A mechanistic study based on the ion abundance of "sequence-specific ions" and "-48 ions" was used to assign a configuration to each of the pairs of diastereomers in the nine-dimer series.
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Affiliation(s)
- Shardrack O Asare
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA.,Abbvie Inc., 1 N. Waukegan Rd., North Chicago, IL, 60064, USA
| | - Kimberly R Dean
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
| | - Bert C Lynn
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA.
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10
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Ma ZX, Zhang M, Zhang CT, Zhang H, Mo XH, Xing XH, Yang S. Metabolomic analysis improves bioconversion of methanol to isobutanol in Methylorubrum extorquens AM1. Biotechnol J 2021; 16:e2000413. [PMID: 33595188 DOI: 10.1002/biot.202000413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Methylorubrum extorquens AM1 can be engineered to convert methanol to value-added chemicals. Most of these chemicals derive from acetyl-CoA involved in the serine cycle. However, recent studies on methylotrophic metabolism have suggested that C3 pyruvate is a good potential precursor for broadening the types of synthesized products. METHODS AND RESULTS In the present study, we found that isobutanol was a model chemical that could be generated from pyruvate through a 2-keto acid pathway. Initially, the engineered M. extorquens AM1 could only produce a trace amount of isobutanol at 0.62 mgL-1 after introducing the heterologous 2-ketoisovalerate decarboxylase and alcohol dehydrogenase. Furthermore, the metabolomic analysis revealed that insufficient carbon fluxes through 2-ketoisovalerate and pyruvate were the key limitation steps for efficient biosynthesis of isobutanol. Based on this analysis, the titer of isobutanol was improved by over 20-fold after overexpressing alsS gene encoding acetolactate synthase and deleting ldhA gene for lactate dehydrogenase. Moreover, substituting the cell chassis with the isobutanol-tolerant strain isolated from adaptive evolution of M. extorquens AM1 further increased the production of isobutanol by 1.7-fold, resulting in the final titer of 19 mgL-1 in flask cultivation. CONCLUSION Our current findings provided promising insights into engineering methylotrophic cell factories capable of converting methanol to isobutanol or value-added chemicals using pyruvate as the precursor.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Shandong Longkete Enzyme Co., Ltd., Linyi, Shandong, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, and Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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Ikegami T, Taniguchi A, Okada T, Horie K, Arase S, Ikegami Y. Functionalization using polymer or silane? A practical test method to characterize hydrophilic interaction chromatography phases in terms of their functionalization method. J Chromatogr A 2020; 1638:461850. [PMID: 33482613 DOI: 10.1016/j.chroma.2020.461850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/28/2022]
Abstract
Herein, commercially available columns employed in hydrophilic interaction chromatography (HILIC) were characterized by determining their ability to selectively distinguish the minute structural differences between small molecules such as nucleosides and xanthines in complex sample matrices. Principal component analysis (PCA) was applied to the data obtained from structurally similar analytes, and the results showed that HILIC columns could generally be classified into two groups: (i) silane-modified columns that were prepared from either native silica particles or silica particles modified with low-molecular-weight silanes and (ii) polymer-modified columns obtained from silica particles functionalized with organic polymers. These two groups could be further subdivided based on the functionalities attached to the respective stationary phases. These results were confirmed via cluster analysis by preparing a dendrogram using the morphology-based selectivity parameters associated with the respective columns. We were able to determine the selectivity of columns for the OH groups, i.e., α(OH) and the prevailing pH conditions (cation- and anion-exchanging natures) on the surface of the respective stationary phases; α(theobromine/theophylline) was employed to obtain a similar two-dimensional plot. This test scheme, in which five compounds were analyze for each column, was helpful for understanding the impact of factors such as the hydrophilicity, degree of hydration, acidity/basicity, or the weak ion-exchange nature of the respective stationary phases on the separation characteristics of new HILIC stationary phases. The selectivity of columns for the CH2 group was also examined. The cation-exchange nature of the HILIC columns significantly influenced native silica columns and some polymer-modified columns. Herein, 45 commercially available HILIC columns were classified according to this method, and the results proved useful for understanding distinct separation characteristics of each HILIC column, enabling improved column selection.
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Affiliation(s)
- Tohru Ikegami
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Ashin Taniguchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tomoyuki Okada
- YMC Co., Ltd., Miwa, Miwa-cho, Fukuchiyama, Kyoto, 620-1445, Japan
| | - Kanta Horie
- Translational Science, Neurology Business Group, Eisai Co., Ltd. Tsukuba, Ibaraki, 300-2635, Japan; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Syuntaro Arase
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan; Formulation Research, Pharmaceutical Science & Technology Core Function Unit, Medicine Development Center, Eisai Co., Ltd., Kagamigahara, Gifu, 501-6195, Japan
| | - Yuka Ikegami
- Okami Chemical Industry Co., Ltd., Makishima, Enba 78, Uji, Kyoto, 611-0041, Japan
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12
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Li H, Yu Q, Li T, Shao L, Su M, Zhou H, Qu J. Rumen Microbiome and Metabolome of Tibetan Sheep ( Ovis aries) Reflect Animal Age and Nutritional Requirement. Front Vet Sci 2020; 7:609. [PMID: 32984417 PMCID: PMC7492597 DOI: 10.3389/fvets.2020.00609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 07/28/2020] [Indexed: 01/26/2023] Open
Abstract
The rumen microbiota plays an important role in animal functional attributes. These microbes are indispensable for the normal physiological development of the rumen, and may also convert the plant polysaccharides from grass into available milk and meat, making it highly valuable to humans. Exploring the microbial composition and metabolites of rumen across developmental stages is important for understanding ruminant nutrition and metabolism. However, relatively few reports have investigated the microbiome and metabolites across developmental stages in ruminants. Using 16S rRNA gene sequnecing, metabolomics and high-performance liquid chromatography techniques, we compared the rumen microbiota, metabolites and short chain fatty acids (SCFAs) between lambs and sub-adult Tibetan sheep (Ovis aries) from Qinghai-Tibetan Plateau. Bacteroidetes and Spirochaetae were enriched in sub-adult sheep, while Firmicutes and Tenericutes were more abundant in young individuals. The sub-adult individuals had higher alpha diversity values than those in young sheep. Metabolomics analysis showed that the content of essential amino acids and related gene functional pathways in rumen were different between the lambs and sub-adult population. L-Leucine that participates in valine, leucine and isoleucine biosynthesis was more abundant in the lambs, while phenylethylamine that takes part in phenylalanine metabolism was more enriched in the sub-adults. Both rumen microbial community structures and metabolite profiles were impacted by age, but rumen SCFA concentration was relatively stable between different age stages. Some specific microbes (e.g., Clostridium and Ruminococcaceae) were positively associated with L-Leucine but negatively correlated with phenylethylamine, implying that rumen microbes may play different roles for metabolite production at different ages. Mantel test analysis showed that rumen microbiota was significantly correlated with metabolomics and SCFA profiles. Our results indicates the close relationship between microbial composition and metabolites, and also reveal different nutritional requirement for different ages in ruminants, thus having important significance for regulating animal nutrition and metabolism by microbiome intervention.
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Affiliation(s)
- Huan Li
- School of Public Health, Lanzhou University, Lanzhou, China.,Key Laboratory of Restoration Ecology for Cold Regions in Qinghai, Xining, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Liye Shao
- Key Laboratory of Health Aquaculture and Product Processing in Dongting Lake Area of Hunan Province, Zoology Key Laboratory of Hunan Higher Education, Hunan University of Arts and Science, Changde, China
| | - Ming Su
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, Changsha, China
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology for Cold Regions in Qinghai, Xining, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Jiapeng Qu
- Key Laboratory of Restoration Ecology for Cold Regions in Qinghai, Xining, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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13
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A preliminary study of rapid-fire high-throughput metabolite analysis using nano-flow injection/Q-TOFMS. Anal Bioanal Chem 2020; 412:4127-4134. [DOI: 10.1007/s00216-020-02645-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/17/2020] [Accepted: 04/04/2020] [Indexed: 12/25/2022]
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14
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Challenges in Analysis of Hydrophilic Metabolites Using Chromatography Coupled with Mass Spectrometry. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00126-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Røst LM, Shafaei A, Fuchino K, Bruheim P. Zwitterionic HILIC tandem mass spectrometry with isotope dilution for rapid, sensitive and robust quantification of pyridine nucleotides in biological extracts. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1144:122078. [PMID: 32222674 DOI: 10.1016/j.jchromb.2020.122078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
The pyridine nucleotides nicotineamide adenine dinucleotide (NAD) and nicotineamide adenine dinucleotide phosphate (NADP) are conserved coenzymes across all domains of life, and are involved in more than 200 different hydride transfer reactions supporting essential catabolic and anabolic functions. The intracellular levels of these metabolites, and the ratio of their oxidized to reduced forms regulate an extensive network of reactions ranging beyond metabolism. Hence, monitoring their intracellular levels provides information about, but not limited to, the metabolic state of a cell or tissue. Interconversion between oxidized and reduced forms, varying pH liability and varying intracellular concentrations of the different species leaves absolute quantification of the pyridine nucleotides analytically challenging. These polar metabolites are poorly retained on conventional reverseed-phase stationary phases without ion-pair reagents that contaminates the LC-system. Herein we demonstrate that zwitterionic HILIC-tandem mass spectroemtry can be applied to successfully resolve the pyridine nucleotides in biological extracts in a fast, robust and highly sensitive way. The presented method applies isotope dilution to compensate potential loss of these labile metabolites and is validated for low, medium and high biomass samples of two popular biological model systems; Escherichia coli and the human cell line JJN-3. High stability and rapid sample preparation without solvent removal allows for long sequence runs, making this method ideal for high-throughput analysis of biological extracts.
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Affiliation(s)
- Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Armaghan Shafaei
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Katsuya Fuchino
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway.
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16
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Fan S, Kind T, Cajka T, Hazen SL, Tang WHW, Kaddurah-Daouk R, Irvin MR, Arnett DK, Barupal DK, Fiehn O. Systematic Error Removal Using Random Forest for Normalizing Large-Scale Untargeted Lipidomics Data. Anal Chem 2019; 91:3590-3596. [DOI: 10.1021/acs.analchem.8b05592] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sili Fan
- West Coast Metabolomics
Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
| | - Tobias Kind
- West Coast Metabolomics
Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
| | - Tomas Cajka
- West Coast Metabolomics
Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
- Department of Metabolomics, Institute of Physiology CAS, Videnska 1083, 14220 Prague, Czech Republic
| | | | | | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Department of Medicine and the Duke Institute for Brain Sciences, Duke University, Durham, North Carolina 27708, United States
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, 1720 Second Avenue South, Birmingham, Alabama 35294, United States
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, 121 Washington Avenue, Lexington, Kentucky 40508, United States
| | - Dinesh K. Barupal
- West Coast Metabolomics
Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics
Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
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17
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Chen X, Lee J, Wu H, Tsang AW, Furdui CM. Mass Spectrometry in Advancement of Redox Precision Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:327-358. [PMID: 31347057 PMCID: PMC9236553 DOI: 10.1007/978-3-030-15950-4_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Redox (portmanteau of reduction-oxidation) reactions involve the transfer of electrons between chemical species in biological processes fundamental to life. It is of outmost importance that cells maintain a healthy redox state by balancing the action of oxidants and antioxidants; failure to do so leads to a multitude of diseases including cancer, diabetes, fibrosis, autoimmune diseases, and cardiovascular and neurodegenerative diseases. From the perspective of precision medicine, it is therefore beneficial to interrogate the redox phenotype of the individual-similar to the use of genomic sequencing-in order to design tailored strategies for disease prevention and treatment. This chapter provides an overview of redox metabolism and focuses on how mass spectrometry (MS) can be applied to advance our knowledge in redox biology and precision medicine.
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Affiliation(s)
- Xiaofei Chen
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jingyun Lee
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Allen W Tsang
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
- Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.
- Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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18
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Lu W, Wang L, Chen L, Hui S, Rabinowitz JD. Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors. Antioxid Redox Signal 2018; 28:167-179. [PMID: 28497978 PMCID: PMC5737638 DOI: 10.1089/ars.2017.7014] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AIMS Accurate analysis of dinucleotide redox cofactors nicotinamide adenine dinucleotide phosphate reduced (NADPH), nicotinamide adenine dinucleotide phosphate (NADP+), nicotinamide adenine dinucleotide reduced (NADH), and nicotinamide adenine dinucleotide (NAD+) from biological samples is important to understanding cellular redox homeostasis. In this study, we aimed to develop a simple protocol for quenching metabolism and extracting NADPH that avoids interconversion among the reduced forms and the oxidized forms. RESULTS We compared seven different solvents for quenching and extraction of cultured mammalian cells and mouse tissues: a cold aqueous buffer commonly used in enzyme assays with and without detergent, hot aqueous buffer, and cold organic mixtures (80% methanol, buffered 75% acetonitrile, and acidic 40:40:20 acetonitrile:methanol:water with either 0.02 M or 0.1 M formic acid). Extracts were analyzed by liquid chromatography-mass spectrometry (LC-MS). To monitor the metabolite interconversion, cells were grown in 13C6-glucose medium, and unlabeled standards were spiked into the extraction solvents. Interconversion between the oxidized and reduced forms was substantial except for the enzyme assay buffer with detergent, 80% methanol and 40:40:20 acetonitrile:methanol:water, with the 0.1 M formic acid mix giving the least interconversion and best recoveries. Absolute NAD+, NADH, NADP+, and NADPH concentrations in cells and mouse tissues were measured with this approach. INNOVATION We found that the interconversion between the reduced and oxidized forms during extraction is a major barrier to accurately measuring NADPH/NADP+ and NADH/NAD+ ratios. Such interconversion can be monitored by isotope labeling cells and spiking NAD(P)(H) standards. CONCLUSION Extraction with 40:40:20 acetonitrile:methanol:water with 0.1 M formic acid decreases interconversion and, therefore, is suitable for measurement of redox cofactor ratios using LC-MS. This solvent is also useful for general metabolomics. Samples should be neutralized immediately after extraction to avoid acid-catalyzed degradation. When LC-MS is not available and enzyme assays are accordingly used, inclusion of detergent in the aqueous extraction buffer reduces interconversion. Antioxid. Redox Signal. 28, 167-179.
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Affiliation(s)
- Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Lin Wang
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Li Chen
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Sheng Hui
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
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19
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Thongsomboon W, Serra DO, Possling A, Hadjineophytou C, Hengge R, Cegelski L. Phosphoethanolamine cellulose: A naturally produced chemically modified cellulose. Science 2018; 359:334-338. [DOI: 10.1126/science.aao4096] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/13/2017] [Indexed: 12/22/2022]
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20
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Xu XY, Shen XT, Yuan XJ, Zhou YM, Fan H, Zhu LP, Du FY, Sadilek M, Yang J, Qiao B, Yang S. Metabolomics Investigation of an Association of Induced Features and Corresponding Fungus during the Co-culture of Trametes versicolor and Ganoderma applanatum. Front Microbiol 2018; 8:2647. [PMID: 29375514 PMCID: PMC5767234 DOI: 10.3389/fmicb.2017.02647] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/19/2017] [Indexed: 11/26/2022] Open
Abstract
The co-culture of Trametes versicolor and Ganoderma applanatum is a model of intense basidiomycete interaction, which induces many newly synthesized or highly produced features. Currently, one of the major challenges is an identification of the origin of induced features during the co-culture. Herein, we report a 13C-dynamic labeling analysis used to determine an association of induced features and corresponding fungus even if the identities of metabolites were not available or almost nothing was known of biochemical aspects. After the co-culture of T. versicolor and G. applanatum for 10 days, the mycelium pellets of T. versicolor and G. applanatum were sterilely harvested and then mono-cultured in the liquid medium containing half fresh medium with 13C-labeled glucose as carbon source and half co-cultured supernatants collected on day 10. 13C-labeled metabolome analyzed by LC-MS revealed that 31 induced features including 3-phenyllactic acid and orsellinic acid were isotopically labeled in the mono-culture after the co-culture stimulation. Twenty features were derived from T. versicolor, 6 from G. applanatum, and 5 features were synthesized by both T. versicolor and G. applanatum. 13C-labeling further suggested that 12 features such as previously identified novel xyloside [N-(4-methoxyphenyl)formamide 2-O-beta-D-xyloside] were likely induced through the direct physical interaction of mycelia. Use of molecular network analysis combined with 13C-labeling provided an insight into the link between the generation of structural analogs and producing fungus. Compound 1 with m/z 309.0757, increased 15.4-fold in the co-culture and observed 13C incorporation in the mono-culture of both T. versicolor and G. applanatum, was purified and identified as a phenyl polyketide, 2,5,6-trihydroxy-4, 6-diphenylcyclohex-4-ene-1,3-dione. The biological activity study indicated that this compound has a potential to inhibit cell viability of leukemic cell line U937. The current work sets an important basis for further investigations including novel metabolites discovery and biosynthetic capacity improvement.
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Affiliation(s)
- Xiao-Yan Xu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Ting Shen
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Jie Yuan
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Yuan-Ming Zhou
- Central Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Huan Fan
- Tianjin Animal Science and Veterinary Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Li-Ping Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Feng-Yu Du
- School of Chemistry and Pharmacy, Qingdao Agricultural University, Qingdao, China
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Song Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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21
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Mathon C, Barding GA, Larive CK. Separation of ten phosphorylated mono-and disaccharides using HILIC and ion-pairing interactions. Anal Chim Acta 2017; 972:102-110. [DOI: 10.1016/j.aca.2017.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/05/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
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22
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Yong YS, Chong ETJ, Chen HC, Lee PC, Ling YS. A Comparative Study of Pentafluorophenyl and Octadecylsilane Columns in High-throughput Profiling of Biological Fluids. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201600873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yoong-Soon Yong
- Biotechnology Research Institute; Universiti Malaysia Sabah; Kota Kinabalu Sabah 88400 Malaysia
| | - Eric Tzyy Jiann Chong
- Faculty of Science & Natural Resources; Universiti Malaysia Sabah; Kota Kinabalu Sabah 88400 Malaysia
| | - Hsin-Chang Chen
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health; National Taiwan University; Taipei 100 Taiwan
| | - Ping-Chin Lee
- Faculty of Science & Natural Resources; Universiti Malaysia Sabah; Kota Kinabalu Sabah 88400 Malaysia
| | - Yee Soon Ling
- Biotechnology Research Institute; Universiti Malaysia Sabah; Kota Kinabalu Sabah 88400 Malaysia
- Water Research Unit; Universiti Malaysia Sabah; Kota Kinabalu Sabah 88400 Malaysia
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23
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Qin Q, Wang B, Chang M, Zhou Z, Shi X, Xu G. Highly efficient solid-phase derivatization of sugar phosphates with titanium-immobilized hydrophilic polydopamine-coated silica. J Chromatogr A 2016; 1457:125-33. [PMID: 27371021 DOI: 10.1016/j.chroma.2016.06.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
Sugar phosphates are a type of key metabolic intermediates of glycolysis, gluconeogenesis and pentose phosphate pathway, which can regulate tumor energetic metabolism. Due to their low endogenous concentrations, poor chromatographic retention properties as well as ionization suppression from complex matrix interference, the determination of sugar phosphates in biological samples is very difficult. In this study, titanium-immobilized hydrophilic polydopamine-coated silica microspheres (SiO2@PD-Ti(4+)) were synthesized for highly efficient solid-phase derivatization of sugar phosphates. Sugar phosphates were selectively captured onto the surface of the SiO2@PD-Ti(4+) microspheres by chelating with phosphate groups, and then reacted with 3-amino-9-ethylcarbazole via reductive amination based on solid-phase derivatization, which could not only increase the retention and resolution of sugar phosphates on reversed-phase liquid chromatography (RPLC), but also improve the mass spectrometry (MS) sensitivity of sugar phosphates. The adsorption capacity of SiO2@PD-Ti(4+) microspheres towards glucose-6-phosphate is 0.76mg/g, which is much larger than that of commercial TiO2. Compared with the traditional liquid-phase derivatization, the solid-phase derivatization based on the SiO2@PD-Ti(4+) microspheres displayed several superiorities including shorter derivatization time (within 10min), higher product purity and much lower limit of detection (up to 38pmol/L). In addition, good linearity (R(2)≥0.99), excellent recovery (80.6-118%) and high precision (RSDs with 2.8-7.8%) were obtained when the developed method was used for quantitative analysis of sugar phosphates. Finally, the SiO2@PD-Ti(4+) microspheres combined with RPLC-MS were successfully applied to the determination of sugar phosphates from hepatocarcinoma cell lines and could even detect the trace sugar phosphates in thousands of cells.
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Affiliation(s)
- Qian Qin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bohong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Chang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Zhou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianzhe Shi
- 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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24
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Reaser BC, Yang S, Fitz BD, Parsons BA, Lidstrom ME, Synovec RE. Non-targeted determination of 13C-labeling in the Methylobacterium extorquens AM1 metabolome using the two-dimensional mass cluster method and principal component analysis. J Chromatogr A 2016; 1432:111-21. [DOI: 10.1016/j.chroma.2015.12.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/04/2015] [Accepted: 12/20/2015] [Indexed: 11/15/2022]
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25
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Hu B, Yang YM, Beck DAC, Wang QW, Chen WJ, Yang J, Lidstrom ME, Yang S. Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:84. [PMID: 27069508 PMCID: PMC4827201 DOI: 10.1186/s13068-016-0497-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/25/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND The toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. However, M. extorquens AM1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. Only a few studies have reported the general stress response of M. extorquens AM1 to solvent stress. Therefore, it is highly desirable to obtain a strain with ameliorated 1-butanol tolerance and elucidate the molecular mechanism of 1-butnaol tolerance in M. extorquens AM1 for future strain improvement. RESULTS In this work, adaptive laboratory evolution was used as a tool to isolate mutants with 1-butanol tolerance up to 0.5 %. The evolved strains, BHBT3 and BHBT5, demonstrated increased growth rates and higher survival rates with the existence of 1-butanol. Whole genome sequencing revealed a SNP mutation at kefB in BHBT5, which was confirmed to be responsible for increasing 1-butanol tolerance through an allelic exchange experiment. Global metabolomic analysis further discovered that the pools of multiple key metabolites, including fatty acids, amino acids, and disaccharides, were increased in BHBT5 in response to 1-butanol stress. Additionally, the carotenoid synthesis pathway was significantly down-regulated in BHBT5. CONCLUSIONS We successfully screened mutants resistant to 1-butanol and provided insights into the molecular mechanism of 1-butanol tolerance in M. extorquens AM1. This research will be useful for uncovering the mechanism of cellular response of M. extorquens AM1 to solvent stress, and will provide the genetic blueprint for the rational design of a strain of M. extorquens AM1 with increased 1-butanol tolerance in the future.
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Affiliation(s)
- Bo Hu
- />Department of Chemical Engineering, University of Washington, Seattle, WA USA
- />Industrial Product Division, Intrexon Corporation, South San Francisco, CA 94080 USA
| | - Yi-Ming Yang
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - David A. C. Beck
- />Department of Chemical Engineering, University of Washington, Seattle, WA USA
- />eScience Institute, University of Washington, Seattle, WA USA
| | - Qian-Wen Wang
- />Central Laboratory, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - Wen-Jing Chen
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - Jing Yang
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - Mary E. Lidstrom
- />Department of Chemical Engineering, University of Washington, Seattle, WA USA
- />Department of Microbiology, University of Washington, Seattle, WA 98195-1750 USA
| | - Song Yang
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
- />Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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26
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Ortmayr K, Hann S, Koellensperger G. Complementing reversed-phase selectivity with porous graphitized carbon to increase the metabolome coverage in an on-line two-dimensional LC-MS setup for metabolomics. Analyst 2015; 140:3465-73. [PMID: 25824707 PMCID: PMC4719141 DOI: 10.1039/c5an00206k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Efficient and robust separation methods are indispensable in modern LC-MS based metabolomics, where high-resolution mass spectrometers are challenged by isomeric and isobaric metabolites. The optimization of chromatographic separation hence remains an invaluable tool in the comprehensive analysis of the chemically diverse intracellular metabolome. While it is widely accepted that a single method with comprehensive metabolome coverage does not exist, the potential of combining different chromatographic selectivities in two-dimensional liquid chromatography is underestimated in the field. Here, we introduce a novel separation system combining reversed-phase and porous graphitized carbon liquid chromatography in a heart-cut on-line two-dimensional setup for mass spectrometry. The proposed experimental setup can be readily implemented using standard HPLC equipment with only one additional HPLC pump and a two-position six-port valve. The method proved to be robust with excellent retention time stability (average 0.4%) even in the presence of biological matrix. Testing the presented approach on a test mixture of 82 relevant intracellular metabolites, the number of metabolites that are retained could be doubled as compared to reversed-phase liquid chromatography alone. The presented work further demonstrates how the distinct selectivity of porous graphitized carbon complements reversed-phase liquid chromatography and extends the metabolome coverage of conventional LC-MS based methods in metabolomics to biologically important, but analytically challenging compound groups such as sugar phosphates. Both metabolic profiling and metabolic fingerprinting benefit from this method's increased separation capabilities that enhance sample throughput and the biological information content of LC-MS data. An inter-platform comparison with GC- and LC-tandem MS analyses confirmed the validity of the presented two-dimensional approach in the analysis of yeast cell extracts from P. pastoris.
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Affiliation(s)
- Karin Ortmayr
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
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27
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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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28
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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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29
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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: 115] [Impact Index Per Article: 11.5] [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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30
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Adaway JE, Keevil BG, Owen LJ. Liquid chromatography tandem mass spectrometry in the clinical laboratory. Ann Clin Biochem 2014; 52:18-38. [DOI: 10.1177/0004563214557678] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clinical laboratory medicine has seen the introduction and evolution of liquid chromatography tandem mass spectrometry in routine clinical laboratories over the last 10–15 years. There still exists a wide diversity of assays from very esoteric and highly specialist manual assays to more simplified kit-based assays. The technology is not static as manufacturers are continually making improvements. Mass spectrometry is now commonly used in several areas of diagnostics including therapeutic drug monitoring, toxicology, endocrinology, paediatrics and microbiology. Some of the most high throughput analyses or common analytes include vitamin D, immunosuppressant monitoring, androgen measurement and newborn screening. It also offers flexibility for the measurement of analytes in a variety of different matrices which would prove difficult with immunoassays. Unlike immunoassays or high-pressure liquid chromatography assays using ultraviolet or fluorescence detection, mass spectrometry offers better specificity and reduced interferences if attention is paid to potential isobaric compounds. Furthermore, multiplexing, which enables multiple analytes to be measured with the same volume of serum is advantageous, and the requirement for large sample volumes is decreasing as instrument sensitivity increases. There are many emerging applications in the literature. Using mass spectrometry to identify novel isoforms or modified peptides is possible as is quantification of proteins and peptides, with or without protein digests. Future developments by the manufacturers may also include mechanisms to improve the throughput of samples and strategies to decrease the level of skill required by the operators.
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Affiliation(s)
- Joanne E Adaway
- Biochemistry Department, University Hospital of South Manchester, Manchester, UK
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Brian G Keevil
- Biochemistry Department, University Hospital of South Manchester, Manchester, UK
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Laura J Owen
- Biochemistry Department, University Hospital of South Manchester, Manchester, UK
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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31
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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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32
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Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun 2014; 4:2785. [PMID: 24302011 DOI: 10.1038/ncomms3785] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 10/16/2013] [Indexed: 11/08/2022] Open
Abstract
Methane is an essential component of the global carbon cycle and one of the most powerful greenhouse gases, yet it is also a promising alternative source of carbon for the biological production of value-added chemicals. Aerobic methane-consuming bacteria (methanotrophs) represent a potential biological platform for methane-based biocatalysis. Here we use a multi-pronged systems-level approach to reassess the metabolic functions for methane utilization in a promising bacterial biocatalyst. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under oxygen limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock.
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33
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Gertsman I, Gangoiti JA, Barshop BA. Validation of a dual LC-HRMS platform for clinical metabolic diagnosis in serum, bridging quantitative analysis and untargeted metabolomics. Metabolomics 2014; 10:312-323. [PMID: 25411574 PMCID: PMC4234038 DOI: 10.1007/s11306-013-0582-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mass spectrometry-based metabolomics is a rapidly growing field in both research and diagnosis. Generally, the methodologies and types of instruments used for clinical and other absolute quantification experiments are different from those used for biomarkers discovery and untargeted analysis, as the former requires optimal sensitivity and dynamic range, while the latter requires high resolution and high mass accuracy. We used a Q-TOF mass spectrometer with two different types of pentafluorophenyl (PFP) stationary phases, employing both positive and negative ionization, to develop and validate a hybrid quantification and discovery platform using LC-HRMS. This dual-PFP LC-MS platform quantifies over 50 clinically relevant metabolites in serum (using both MS and MS/MS acquisitions) while simultaneously collecting high resolution and high mass accuracy full scans to monitor all other co-eluting non-targeted analytes. We demonstrate that the linearity, accuracy, and precision results for the quantification of a number of metabolites, including amino acids, organic acids, acylcarnitines and purines/pyrimidines, meets or exceeds normal bioanalytical standards over their respective physiological ranges. The chromatography resolved highly polar as well as hydrophobic analytes under reverse-phase conditions, enabling analysis of a wide range of chemicals, necessary for untargeted metabolomics experiments. Though previous LC-HRMS methods have demonstrated quantification capabilities for various drug and small molecule compounds, the present study provides an HRMS quant/qual platform tailored to metabolic disease; and covers a multitude of different metabolites including compounds normally quantified by a combination of separate instrumentation.
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Affiliation(s)
- Ilya Gertsman
- Corresponding author. Contact info: Address: 9500 Gilman Dr. La Jolla CA, 92093-0830, Phone: 619-543-5260,
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34
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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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35
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Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun 2014; 5:3233. [DOI: 10.1038/ncomms4233] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/10/2014] [Indexed: 01/21/2023] Open
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36
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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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37
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Comprehensive discovery of 13C labeled metabolites in the bacterium Methylobacterium extorquens AM1 using gas chromatography–mass spectrometry. J Chromatogr A 2013; 1317:175-85. [DOI: 10.1016/j.chroma.2013.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/12/2013] [Accepted: 08/16/2013] [Indexed: 01/31/2023]
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38
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Liquid chromatography–mass spectrometry for metabolic footprinting of co-cultures of lactic and propionic acid bacteria. Anal Bioanal Chem 2013; 405:8151-70. [DOI: 10.1007/s00216-013-7269-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 12/28/2022]
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39
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Yao L, Zheng S, Guan Y, Yang J, Liu B, Wang W, Zhu X. Development of a rapid method for the simultaneous separation and determination of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol and its N- and O-glucuronides in human urine by liquid chromatography–tandem mass spectrometry. Anal Chim Acta 2013; 788:61-7. [DOI: 10.1016/j.aca.2013.06.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/15/2013] [Accepted: 06/21/2013] [Indexed: 01/12/2023]
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40
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Han J, Tschernutter V, Yang J, Eckle T, Borchers CH. Analysis of selected sugars and sugar phosphates in mouse heart tissue by reductive amination and liquid chromatography-electrospray ionization mass spectrometry. Anal Chem 2013; 85:5965-73. [PMID: 23682691 PMCID: PMC3989532 DOI: 10.1021/ac400769g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sensitive and reliable analysis of sugars and sugar phosphates in tissues and cells is essential for many biological and cell engineering studies. However, the successful analysis of these endogenous compounds in biological samples by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) is often difficult because of their poor chromatographic retention properties in reversed-phase LC, the complex biological matrices, and the ionization suppression in ESI. This situation is further complicated by the existence of their multiple structural isomers in vivo. This work describes the combination of reductive amination using 3-amino-9-ethylcarbazole, with a new LC approach using a pentafluorophenyl core-shell ultrahigh performance (UP) LC column and methylphosphonic acid as an efficient tail-sweeping reagent for improved chromatographic separation. This new method was used for selected detection and accurate quantitation of the major free and phosphorylated reducing sugars in mouse heart tissue. Among the detected compounds, accurate quantitation of glyceraldehyde, ribose, glucose, glycerylaldehyde-3-phosphate, ribose-5-phosphate, glucose-6-phosphate, and mannose-6-phosphate was achieved by UPLC/multiple-reaction monitoring (MRM)-MS, with analytical accuracies ranging from 87.4% to 109.4% and CVs of ≤8.5% (n = 6). To demonstrate isotope-resolved metabolic profiling, we used UPLC/quadrupole time-of-flight (QTOF)-MS to analyze the isotope distribution patterns of C3 to C6 free and phosphorylated reducing sugars in heart tissues from (13)C-labeled wild type and knockout mice. In conclusion, the preanalytical derivatization-LC/ESI-MS method has resulted in selective determination of free and phosphorylated reducing sugars without the interferences from their nonreducing structural isomers in mouse heart tissue, with analytical sensitivities in the femtomole to low picomole range.
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Affiliation(s)
- Jun Han
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Vera Tschernutter
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Tobias Eckle
- Mucosal Inflammation Program, Department of Anesthesiology, University of Colorado, Denver, Colorado, United States
| | - Christoph H. Borchers
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
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41
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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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42
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Zhao S, Huang D, Qi H, Wen J, Jia X. Comparative metabolic profiling-based improvement of rapamycin production by Streptomyces hygroscopicus. Appl Microbiol Biotechnol 2013; 97:5329-41. [PMID: 23604534 DOI: 10.1007/s00253-013-4852-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 01/07/2023]
Abstract
Rapamycin is a clinically important macrocyclic polyketide with immunosuppressive activity produced by Streptomyces hygroscopicus. To rationally guide the improvement of rapamycin production, comparative metabolic profiling analysis was performed in this work to investigate the intracellular metabolic changes in S. hygroscopicus U1-6E7 fermentation in medium M1 and derived medium M2. A correlation between the metabolic profiles and rapamycin accumulation was revealed by partial least-squares to latent structures analysis, and 16 key metabolites that most contributed to the metabolism differences and rapamycin production were identified. Most of these metabolites were involved in tricarboxylic acid cycle, fatty acids, and shikimic acid and amino acids metabolism. Based on the analysis of key metabolites changes in the above pathways, corresponding exogenous addition strategies were proposed as follows: 1.0 g/L methyl oleate was added at 0 h; 1.0 g/L lysine was added at 12 h; 0.5 g/L shikimic acid was added at 24 h; 0.5 g/L sodium succinate, 0.1 g/L phenylalanine, 0.1 g/L tryptophan, and 0.1 g/L tyrosine were added at 36 h, successively, and a redesigned fermentation medium (M3) was obtained finally on the basis of M2. The production of rapamycin in M3 was increased by 56.6 % compared with it in M2, reaching 307 mg/L at the end of fermentation (120 h). These results demonstrated that metabolic profiling analysis was a successful method applied in the rational guidance of the production improvement of rapamycin, as well as other industrially or clinically important compounds.
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Affiliation(s)
- Sumin Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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43
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Yang S, Matsen JB, Konopka M, Green-Saxena A, Clubb J, Sadilek M, Orphan VJ, Beck D, Kalyuzhnaya MG. Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-Labeling Study. Front Microbiol 2013; 4:70. [PMID: 23565113 PMCID: PMC3615224 DOI: 10.3389/fmicb.2013.00070] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 03/12/2013] [Indexed: 11/27/2022] Open
Abstract
In this work we use metabolomics and 13C-labeling data to refine central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is represented by several tightly connected metabolic cycles, such as the serine pathway, the ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle. Both in silico estimations and stable isotope labeling experiments combined with single cell (NanoSIMS) and bulk biomass analyses indicate that a significantly larger portion of the cell carbon (over 60%) is derived from CO2 in this methanotroph. Our13 C-labeling studies revealed an unusual topology of the assimilatory network in which phosph(enol) pyruvate/pyruvate interconversions are key metabolic switches. A set of additional pathways for carbon fixation are identified and discussed.
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Affiliation(s)
- Song Yang
- Department of Chemical Engineering, University of Washington Seattle, WA, USA
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44
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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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45
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Antoniewicz MR. Tandem mass spectrometry for measuring stable-isotope labeling. Curr Opin Biotechnol 2013; 24:48-53. [DOI: 10.1016/j.copbio.2012.10.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 10/02/2012] [Accepted: 10/16/2012] [Indexed: 12/31/2022]
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46
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Gika HG, Theodoridis GA, Vrhovsek U, Mattivi F. Quantitative profiling of polar primary metabolites using hydrophilic interaction ultrahigh performance liquid chromatography–tandem mass spectrometry. J Chromatogr A 2012; 1259:121-7. [DOI: 10.1016/j.chroma.2012.02.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/27/2012] [Accepted: 02/05/2012] [Indexed: 01/10/2023]
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47
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Li S, Hao Q, Gounarides J, Wang YK. Full utilization of a mass spectrometer using on-demand sharing with multiple LC units. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1074-1082. [PMID: 22899517 DOI: 10.1002/jms.3061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The applicability of liquid chromatography-mass spectrometry (LC/MS) is often limited by throughput. The sharing of a mass spectrometer with multiple LCs significantly improves throughput; however, the reported systems have not been designed to fully utilize the MS duty cycle, and as a result to achieve maximum throughput. To fully utilize the mass spectrometer, the number of LC units that a MS will need to recruit is application dependent and could be significantly larger than the current commercial or published implementations. For the example of a single analyte, the number may approach the peak capacity to a first degree approximation. Here, the construction of a MS system that flexibly recruits any number of LC units demanded by the application is discussed, followed by the method to port a previously developed LC/MS method to the system to fully utilize a mass spectrometer. To demonstrate the performance and operation, a prototypical MS system of eight LC units was constructed. When 1-min chromatographic separations were performed in parallel on the eight LCs of the system, the average LC/MS analysis time per sample was 10.5 s when applied to the analysis of samples in 384-well plate format. This system has been successfully used to conduct large-volume biochemical assays with the analysis of a variety of molecular entities in support of drug discovery efforts. Allowing the recruitment of the number of LC units appropriate for a given application, this system has the potential to be a plug-and-play system to fully utilize a mass spectrometer.
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Affiliation(s)
- Shu Li
- Analytical Sciences, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Kolwicz SC, Olson DP, Marney LC, Garcia-Menendez L, Synovec RE, Tian R. Cardiac-specific deletion of acetyl CoA carboxylase 2 prevents metabolic remodeling during pressure-overload hypertrophy. Circ Res 2012; 111:728-38. [PMID: 22730442 DOI: 10.1161/circresaha.112.268128] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RATIONALE Decreased fatty acid oxidation (FAO) with increased reliance on glucose are hallmarks of metabolic remodeling that occurs in pathological cardiac hypertrophy and is associated with decreased myocardial energetics and impaired cardiac function. To date, it has not been tested whether prevention of the metabolic switch that occurs during the development of cardiac hypertrophy has unequivocal benefits on cardiac function and energetics. OBJECTIVE Because malonyl CoA production via acetyl CoA carboxylase 2 (ACC2) inhibits the entry of long chain fatty acids into the mitochondria, we hypothesized that mice with a cardiac-specific deletion of ACC2 (ACC2H-/-) would maintain cardiac FAO and improve function and energetics during the development of pressure-overload hypertrophy. METHODS AND RESULTS ACC2 deletion led to a significant reduction in cardiac malonyl CoA levels. In isolated perfused heart experiments, left ventricular function and oxygen consumption were similar in ACC2H-/- mice despite an ≈60% increase in FAO compared with controls (CON). After 8 weeks of pressure overload via transverse aortic constriction (TAC), ACC2H-/- mice exhibited a substrate utilization profile similar to sham animals, whereas CON-TAC hearts had decreased FAO with increased glycolysis and anaplerosis. Myocardial energetics, assessed by 31P nuclear magnetic resonance spectroscopy, and cardiac function were maintained in ACC2H-/- after 8 weeks of TAC. Furthermore, ACC2H-/--TAC demonstrated an attenuation of cardiac hypertrophy with a significant reduction in fibrosis relative to CON-TAC. CONCLUSIONS These data suggest that reversion to the fetal metabolic profile in chronic pathological hypertrophy is associated with impaired myocardial function and energetics and maintenance of the inherent cardiac metabolic profile and mitochondrial oxidative capacity is a viable therapeutic strategy.
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Affiliation(s)
- Stephen C Kolwicz
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, 850 Republican St, Seattle, WA 98109, USA
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Yang S, Nadeau JS, Humston-Fulmer EM, Hoggard JC, Lidstrom ME, Synovec RE. Gas chromatography–mass spectrometry with chemometric analysis for determining 12C and 13C labeled contributions in metabolomics and 13C flux analysis. J Chromatogr A 2012; 1240:156-64. [DOI: 10.1016/j.chroma.2012.03.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 03/17/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
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Abstract
The metabolome is the complete set of small molecules coming from protein activity (anabolism and catabolism) in living systems. They have a broad range of chemical structures and physicochemical properties and therefore different analytical methodologies are necessary. Highly polar metabolites, such as sugars and most amino acids are not retained by conventional reversed-phase LC columns. Without sufficient retention, coelution may result in identification problems while the detection of compounds by MS at low concentrations may also be problematic due to ion suppression. In order to retain compounds based on their hydrophilicity, polar stationary phases and hydrophilic-interaction LC provide a complementary tool to reversed-phase LC for untargeted comprehensive metabolite fingerprinting. However, robustness of the methods is still limiting their applications. This review focuses on sample pretreatment, stationary phases, analytical methods and applications for polar compound analysis in biological matrices.
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