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Sarenqimuge S, Wang Y, Alhussein M, Koopmann B, von Tiedemann A. The interplay of suppressive soil bacteria and plant root exudates determines germination of microsclerotia of Verticillium longisporum. Appl Environ Microbiol 2024; 90:e0058924. [PMID: 38814059 DOI: 10.1128/aem.00589-24] [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: 03/27/2024] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Dormant microsclerotia play a vital role in the survival and spread of Verticillium longisporum, as they can stay viable in the soil and maintain their infectivity for many years. In our previous work, we revealed that soil bacterial volatiles are a key inhibitory factor causing microsclerotia dormancy in the soil. In this study, we further demonstrate that root exudates collected from both host and non-host plants can effectively rescue microsclerotia from bacterial suppression and initiate germination. To identify the specific compounds in root exudates responsible for microsclerotia germination, we fractionated the collected root exudates into polar and non-polar compounds. Subsequently, we conducted comprehensive bioassays with each fraction on germination-suppressed microsclerotia. The result revealed a pivotal role of primary metabolites in root exudates, particularly glutamic acid, in triggering microsclerotia germination and overcoming bacterial inhibition. Moreover, our studies revealed a decrease in inhibitory bacterial volatile fatty acids when bacteria were cultured in the presence of root exudates or glutamic acid. This suggests a potential mechanism, by which root exudates set-off bacterial suppression on microsclerotia. Here, we reveal for the first time that plant root exudates, instead of directly inducing the germination of microsclerotia, enact a set-off effect by counteracting the suppressive impact of soil bacteria on the microsclerotia germination process. This nuanced interaction advances our understanding of the multifaceted dynamics governing microsclerotia dormancy and germination in the soil environment. IMPORTANCE Our research provides first-time insights into the crucial interaction between plant root exudates and soil bacteria in regulating the germination of Verticillium longisporum microsclerotia, a significant structure in the survival and proliferation of this soil-borne pathogen. We describe so far unknown mechanisms, which are key to understand how root infections on oilseed rape can occur. By pinpointing primary metabolites in root exudates as key factors in overcoming bacteria-induced dormancy and promote microsclerotia germination, our study highlights the potential for exploiting plant - as well as soil microbe-derived - compounds to control V. longisporum. This work underscores the importance of elucidating the nuanced interactions within the soil ecosystem to devise innovative strategies for managing root infective plant diseases, thereby contributing to the resilience and health of cropping systems.
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Affiliation(s)
- Sarenqimuge Sarenqimuge
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Yao Wang
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Mohammad Alhussein
- Agricultural Entomology Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Birger Koopmann
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Andreas von Tiedemann
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
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Cajka T, Hricko J, Rakusanova S, Brejchova K, Novakova M, Rudl Kulhava L, Hola V, Paucova M, Fiehn O, Kuda O. Hydrophilic Interaction Liquid Chromatography-Hydrogen/Deuterium Exchange-Mass Spectrometry (HILIC-HDX-MS) for Untargeted Metabolomics. Int J Mol Sci 2024; 25:2899. [PMID: 38474147 DOI: 10.3390/ijms25052899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Liquid chromatography with mass spectrometry (LC-MS)-based metabolomics detects thousands of molecular features (retention time-m/z pairs) in biological samples per analysis, yet the metabolite annotation rate remains low, with 90% of signals classified as unknowns. To enhance the metabolite annotation rates, researchers employ tandem mass spectral libraries and challenging in silico fragmentation software. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) may offer an additional layer of structural information in untargeted metabolomics, especially for identifying specific unidentified metabolites that are revealed to be statistically significant. Here, we investigate the potential of hydrophilic interaction liquid chromatography (HILIC)-HDX-MS in untargeted metabolomics. Specifically, we evaluate the effectiveness of two approaches using hypothetical targets: the post-column addition of deuterium oxide (D2O) and the on-column HILIC-HDX-MS method. To illustrate the practical application of HILIC-HDX-MS, we apply this methodology using the in silico fragmentation software MS-FINDER to an unknown compound detected in various biological samples, including plasma, serum, tissues, and feces during HILIC-MS profiling, subsequently identified as N1-acetylspermidine.
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Affiliation(s)
- Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Jiri Hricko
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Stanislava Rakusanova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Kristyna Brejchova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Novakova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Lucie Rudl Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Veronika Hola
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Paucova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
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3
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Bresnahan DR, Catandi GD, Peters SO, Maclellan LJ, Broeckling CD, Carnevale EM. Maturation and culture affect the metabolomic profile of oocytes and follicular cells in young and old mares. Front Cell Dev Biol 2024; 11:1280998. [PMID: 38283993 PMCID: PMC10811030 DOI: 10.3389/fcell.2023.1280998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction: Oocytes and follicular somatic cells within the ovarian follicle are altered during maturation and after exposure to culture in vitro. In the present study, we used a nontargeted metabolomics approach to assess changes in oocytes, cumulus cells, and granulosa cells from dominant, follicular-phase follicles in young and old mares. Methods: Samples were collected at three stages associated with oocyte maturation: (1) GV, germinal vesicle stage, prior to the induction of follicle/oocyte maturation in vivo; (2) MI, metaphase I, maturing, collected 24 h after induction of maturation in vivo; and (3) MIIC, metaphase II, mature with collection 24 h after induction of maturation in vivo plus 18 h of culture in vitro. Samples were analyzed using gas and liquid chromatography coupled to mass spectrometry only when all three stages of a specific cell type were obtained from the same mare. Results and Discussion: Significant differences in metabolite abundance were most often associated with MIIC, with some of the differences appearing to be linked to the final stage of maturation and others to exposure to culture medium. While differences occurred for many metabolite groups, some of the most notable were detected for energy and lipid metabolism and amino acid abundance. The study demonstrated that metabolomics has potential to aid in optimizing culture methods and evaluating cell culture additives to support differences in COCs associated with maternal factors.
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Affiliation(s)
- D R Bresnahan
- Department of Animal Sciences, Berry College, Mount Berry, GA, United States
| | - G D Catandi
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - S O Peters
- Department of Animal Sciences, Berry College, Mount Berry, GA, United States
| | - L J Maclellan
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - C D Broeckling
- Proteomic and Metabolomics Core Facility, Colorado State University, Fort Collins, CO, United States
| | - E M Carnevale
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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Salm F, Znalesniak EB, Laskou A, Harder S, Schlüter H, Hoffmann W. Expression Profiling along the Murine Intestine: Different Mucosal Protection Systems and Alterations in Tff1-Deficient Animals. Int J Mol Sci 2023; 24:12684. [PMID: 37628863 PMCID: PMC10454331 DOI: 10.3390/ijms241612684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Tff1 is a typical gastric peptide secreted together with the mucin, Muc5ac. Tff1-deficient (Tff1KO) mice are well known for their prominent gastric phenotype and represent a recognized model for antral tumorigenesis. Notably, intestinal abnormalities have also been reported in the past in these animals. Here, we have compared the expression of selected genes in Tff1KO mice and their corresponding wild-type littermates (RT-PCR analyses), focusing on different mucosal protection systems along the murine intestine. As hallmarks, genes were identified with maximum expression in the proximal colon and/or the duodenum: Agr2, Muc6/A4gnt/Tff2, Tff1, Fut2, Gkn2, Gkn3, Duox2/Lpo, Nox1. This is indicative of different protection systems such as Tff2/Muc6, Tff1-Fcgbp, gastrokines, fucosylation, and reactive oxygen species (ROS) in the proximal colon and/or duodenum. Few significant transcriptional changes were observed in the intestine of Tff1KO mice when compared with wild-type littermates, Clca1 (Gob5), Gkn1, Gkn2, Nox1, Tff2. We also analyzed the expression of Tff1, Tff2, and Tff3 in the pancreas, liver, and lung of Tff1KO and wild-type animals, indicating a cross-regulation of Tff gene expression. Furthermore, on the protein level, heteromeric Tff1-Fcgbp and various monomeric Tff1 forms were identified in the duodenum and a high-molecular-mass Tff2/Muc6 complex was identified in the proximal colon (FPLC, proteomics).
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Affiliation(s)
- Franz Salm
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Eva B. Znalesniak
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Aikaterini Laskou
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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Farke N, Schramm T, Verhülsdonk A, Rapp J, Link H. Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry. Anal Biochem 2023; 664:115036. [PMID: 36627043 PMCID: PMC9902335 DOI: 10.1016/j.ab.2023.115036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a very high sample-throughput. However, FI-MS is prone to in-source modifications of analytes because samples are directly injected into the electrospray ionization source of a mass spectrometer without prior chromatographic separation. Here, we spiked authentic standards of 160 primary metabolites individually into an Escherichia coli metabolite extract and measured the thus derived 160 spike-in samples by FI-MS. Our results demonstrate that FI-MS can capture a wide range of chemically diverse analytes within 30 s measurement time. However, the data also revealed extensive in-source modifications. Across all 160 spike-in samples, we identified significant increases of 11,013 ion peaks in positive and negative mode combined. To explain these unknown m/z features, we connected them to the m/z feature of the (de-)protonated metabolite using information about mass differences and MS2 spectra. This resulted in networks that explained on average 49 % of all significant features. The networks showed that a single metabolite undergoes compound specific and often sequential in-source modifications like adductions, chemical reactions, and fragmentations. Our results show that FI-MS generates complex MS1 spectra, which leads to an overestimation of significant features, but neutral losses and MS2 spectra explain many of these features.
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Affiliation(s)
| | | | | | | | - Hannes Link
- Bacterial Metabolomics, CMFI, University Tübingen, Auf der Morgenstelle 24, 7206, Tübingen, Germany.
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Toward building mass spectrometry-based metabolomics and lipidomics atlases for biological and clinical research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Metabolomics and modelling approaches for systems metabolic engineering. Metab Eng Commun 2022; 15:e00209. [PMID: 36281261 PMCID: PMC9587336 DOI: 10.1016/j.mec.2022.e00209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering. Constraint-based models, such as genome scale models, have been used successfully to enhance the yield of desired compounds from engineered microbes, however, unlike kinetic or dynamic models, constraint-based models do not incorporate regulatory effects. Nevertheless, the lack of time-series metabolomic data generation has hindered the usefulness of dynamic models till today. In this review, we show that improvements in automation, dynamic real-time analysis and high throughput workflows can drive the generation of more quality data for dynamic models through time-series metabolomics data generation. Spatial metabolomics also has the potential to be used as a complementary approach to conventional metabolomics, as it provides information on the localization of metabolites. However, more effort must be undertaken to identify metabolites from spatial metabolomics data derived through imaging mass spectrometry, where machine learning approaches could prove useful. On the other hand, single-cell metabolomics has also seen rapid growth, where understanding cell-cell heterogeneity can provide more insights into efficient metabolic engineering of microbes. Moving forward, with potential improvements in automation, dynamic real-time analysis, high throughput workflows, and spatial metabolomics, more data can be produced and studied using machine learning algorithms, in conjunction with dynamic models, to generate qualitative and quantitative predictions to advance metabolic engineering efforts.
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Mori A, Masuda T, Ito S, Ohtsuki S. Human Hepatic Transporter Signature Peptides for Quantitative Targeted Absolute Proteomics: Selection, Digestion Efficiency, and Peptide Stability. Pharm Res 2022; 39:2965-2978. [PMID: 36131112 DOI: 10.1007/s11095-022-03387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Quantitative targeted absolute proteomics (QTAP) quantifies proteins by measuring the signature peptides produced from target proteins by trypsin digestion. The selection of signature peptides is critical for reliable peptide quantification. The purpose of this study was to comprehensively assess the digestion efficiency and stability of tryptic peptides and to identify optimal signature peptides for human hepatic transporters and membrane marker proteins. METHODS The plasma membrane fraction of the human liver was digested at different time points and the peptides were comprehensively quantified using quantitative proteomics. Transporters and membrane markers were quantified using the signature peptides by QTAP. RESULTS Tryptic peptides were classified into clusters with low digestion efficiency, low stability, and high digestion efficiency and stability. Using the cluster information, we found that a proline residue next to the digestion site or the peptide position in or close to the transmembrane domains lowers digestion efficiency. A peptide containing cysteine at the N-terminus or arginine-glycine lowers peptide stability. Based on this information and the time course of peptide quantification, optimal signature peptides were identified for human hepatic transporters and membrane markers. The quantification of transporters with multiple signature peptides yielded consistent absolute values with less than 30% of coefficient variants in human liver microsomes and homogenates. CONCLUSIONS The signature peptides selected in the present study enabled the reliable quantification of human hepatic transporters. The QTAP protocol using these optimal signature peptides provides quantitative data on hepatic transporters usable for integrated pharmacokinetic studies.
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Affiliation(s)
- Ayano Mori
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan. .,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
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GC-MS Studies on the Conversion and Derivatization of γ-Glutamyl Peptides to Pyroglutamate (5-Oxo-Proline) Methyl Ester Pentafluoropropione Amide Derivatives. Molecules 2022; 27:molecules27186020. [PMID: 36144754 PMCID: PMC9501402 DOI: 10.3390/molecules27186020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Glutathione (γ-L-glutamyl-L-cysteinyl-glycine, γ-Glu-Cys-Gly) is the most abundant intra-cellular dicarboxylic tripeptide with multiple physiological roles. In biological samples, glutathione exists in its reduced form GSH and in two stable oxidized forms, i.e., in its symmetric disulfide form GSSG and as S-glutathionyl residue in proteins. S-Glutathionylation is a post-translational modification, which is involved in several pathophysiological processes, including oxidative stress. The GSH-to-GSSG molar ratio is widely used as a measure of oxidative stress. γ-Glutamyl is the most characteristic structural moiety of GSH. We performed gas chromatography-mass spectrometry (GC-MS) studies for the development of a highly specific qualitative and quantitative method for γ-glutamyl peptides. We discovered intra-molecular conversion of GSH, GSSG, γ-Glu-Cys and of ophthalmic acid (OPH; γ-glutamyl-α-amino-n-butyryl-glycine) to pyroglutamate (pGlu; 5-oxo-proline, also known as pidolic acid) during their derivatization with 2 M HCl/CH3OH (60 min, 80 °C). For GC-MS analysis, the methyl esters (Me) were further derivatized with pentafluoropropionic (PFP) anhydride in ethyl acetate (1:4, v/v; 30 min, 65 °C) to their PFP derivatives. At longer reaction times, pGlu is hydrolyzed to Glu. Internal standards were prepared by derivatizing GSH, GSSG, γ-Glu-Cys and OPH in 2 M HCl/CD3OD. Quantification of the Me-PFP derivative of pGlu was performed in the electron-capture negative-ion chemical ionization (ECNICI) mode by selected-ion monitoring (SIM) of the mass-to-charge (m/z) ions 269 for unlabeled pGlu (d0Me-PFP-pGlu) and m/z 272 for the in situ prepared deuterium-labeled pGlu (d3Me-PFP-pGlu). Although not inherent to the analysis of small peptides, the present GC-MS method is useful to study several biochemical aspects of GSH. Using pentafluorobenzyl bromide (PFB-Br) as the derivatization reagent, we found that synthetic pGlu is converted in aqueous acetone (60 min, 50 °C) into its pentafluorobenzyl (PFB) ester (PFB-pGlu). This derivatization procedure is useful for the GC-MS analysis of free pGlu in the ECNICI mode. Quantitative analysis of PFB-pGlu by GC-MS requires the use of stable-isotope labeled analogs of pGlu as an internal standard.
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Jiang F, Zhang C, Lu Z, Liu J, Liu P, Huang M, Zhong G. Simultaneous absolute protein quantification of seven cytochrome P450 isoforms in rat liver microsomes by LC-MS/MS-based isotope internal standard method. Front Pharmacol 2022; 13:906027. [PMID: 36059965 PMCID: PMC9428253 DOI: 10.3389/fphar.2022.906027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
The cytochrome P450 (CYP) enzymes play a pivotal role in drug metabolism. LC-MS/MS-based targeting technology has been applied to the analysis of CYP enzymes, promoting drug development and drug-drug interaction studies. Rat is one of the most commonly used models for drug metabolism assessment, but LC-MS/MS assay quantifying the abundance of CYP enzymes in rats is rarely reported. Herein, an accurate and stable LC-MS/MS based method was developed and validated for the simultaneous quantification of seven major rat CYP isoforms (CYP1A2, 2B1, 2C6, 2C11, 2D1, 2E1, and 3A1) in liver microsomes. The careful optimization of trypsin digestion and chromatography combined with isotope-labeled peptide as internal standard improved the efficiency and accuracy of the analysis. Highly specific surrogate peptides were obtained by a procedure including trypsin digestion for six hours and separated on a Hypersil Gold C18 column (100 × 2.1 mm, 3 μm) using gradient elution for 15 min with a mobile phase of water containing 0.1% formic acid and acetonitrile. In the method validation, linearity, matrix effect, recovery, stability, accuracy, and precision all meet the requirements. Subsequently, this method was applied to detect seven enzymes in rat liver microsomes from four different sources, and the correlation between the abundance and activity of CYP enzymes was further analyzed. The high-throughput detection method provided in this study will provide support for pertinent pharmaceutical research based on rat models.
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Affiliation(s)
- Fulin Jiang
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chang Zhang
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zihan Lu
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jingyu Liu
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Min Huang
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Min Huang, ; Guoping Zhong,
| | - Guoping Zhong
- Institute of Clinical Pharmacology, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Min Huang, ; Guoping Zhong,
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Lebart MC, Trousse F, Valette G, Torrent J, Denus M, Mestre-Frances N, Marcilhac A. Reg-1α, a New Substrate of Calpain-2 Depending on Its Glycosylation Status. Int J Mol Sci 2022; 23:ijms23158591. [PMID: 35955718 PMCID: PMC9369050 DOI: 10.3390/ijms23158591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Reg-1α/lithostathine, a protein mainly associated with the digestive system, was previously shown to be overexpressed in the pre-clinical stages of Alzheimer’s disease. In vitro, the glycosylated protein was reported to form fibrils at physiological pH following the proteolytic action of trypsin. However, the nature of the protease able to act in the central nervous system is unknown. In the present study, we showed that Reg-1α can be cleaved in vitro by calpain-2, the calcium activated neutral protease, overexpressed in neurodegenerative diseases. Using chemical crosslinking experiments, we found that the two proteins can interact with each other. Identification of the cleavage site using mass spectrometry, between Gln4 and Thr5, was found in agreement with the in silico prediction of the calpain cleavage site, in a position different from the one reported for trypsin, i.e., Arg11-Ile12 peptide bond. We showed that the cleavage was impeded by the presence of the neighboring glycosylation of Thr5. Moreover, in vitro studies using electron microscopy showed that calpain-cleaved protein does not form fibrils as observed after trypsin cleavage. Collectively, our results show that calpain-2 cleaves Reg-1α in vitro, and that this action is not associated with fibril formation.
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Affiliation(s)
- Marie-Christine Lebart
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
- Correspondence: ; Tel.: +33-4-6714-3889
| | - Françoise Trousse
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
| | | | - Joan Torrent
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- INM, Univ Montpellier, INSERM, 34095 Montpellier, France
| | - Morgane Denus
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
| | - Nadine Mestre-Frances
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
| | - Anne Marcilhac
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
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12
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A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications. J Proteomics 2022; 261:104576. [DOI: 10.1016/j.jprot.2022.104576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/20/2022]
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13
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Chiral secondary amino acids, their importance, and methods of analysis. Amino Acids 2022; 54:687-719. [PMID: 35192062 DOI: 10.1007/s00726-022-03136-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 11/01/2022]
Abstract
Naturally occurring secondary amino acids, with proline as the main representative, contain an alpha-imino group in a cycle that is typically four-, five-, and six-membered. The unique ring structure exhibits exceptional properties-conformational rigidity, chemical stability, and specific roles in protein structure and folding. Many proline analogues have been used as valuable compounds for the study of metabolism of both prokaryotic and eukaryotic cells and for the synthesis of compounds with desired biological, pharmaceutical, or industrial properties. The D-forms of secondary amino acids play different roles in living organisms than the L-forms. They have different metabolic pathways, biological, physiological, and pharmacological effects, they can be indicators of changes and also serve as biomarkers of diseases. In the scientific literature, the number of articles examining D-amino acids in biological samples is increasing. The review summarises information on the occurrence and importance of D- and L-secondary amino acids-azetidic acid, proline, hydroxyprolines, pipecolic, nipecotic, hydroxypipecolic acids and related peptides containing these D-AAs, as well as the main analytical methods (mostly chromatographic) used for their enantiomeric determination in different matrices (biological samples, plants, food, water, and soil).
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14
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Haçariz O, Viau C, Gu X, Xia J. Native Microbiome Members of C. elegans Act Synergistically in Biosynthesis of Pyridoxal 5′-Phosphate. Metabolites 2022; 12:metabo12020172. [PMID: 35208245 PMCID: PMC8879373 DOI: 10.3390/metabo12020172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
The roles of the healthy microbiome on the host and the relationships between members of the microbiome remain to be fully characterized. Due to the complexity of the interactions between the mammalian microbiome and its host, the use of model organisms such as the nematode worm Caenorhabditis elegans is a promising strategy to study host-microbiome interactions in vivo, as well as bacterial crosstalk within the host. Previously it was found that native bacterial isolates of the worm, Chryseobacterium sp. CHNTR56 MYb120 and Comamonas sp. 12022 MYb131, possess genomic diversity in the biosynthesis of the active form of vitamin B6, pyridoxal 5′-phosphate (PLP), and contribute to host fitness and lifespan extension. However, the relative contribution of PLP from each isolate, as well as the existence of interbacterial relationships within the worm gut remain to be characterized. In the present work, we investigated the presence and measured the abundance of PLP in the isolates and in the worms grown with the isolates using ultraperformance liquid chromatography tandem-mass spectrometry (UPLC-MS/MS). Our analyses confirmed the presence of PLP in vitro and in vivo. The elevated abundance of PLP in the isolates (which reached statistically significant levels when the two isolates were combined), and within worms grown with the combination of bacterial isolates, compared to control, indicated synergism between the isolates in the production of PLP. Isotope labeling revealed that Comamonas sp. 12022 MYb131 was the main provider of PLP in worms grown with the combination of bacterial isolates. The dominance of this isolate inside the worm was further confirmed by a colonization assay. An untargeted metabolomics analysis of the bacteria showed that the pathways related to cell growth, protein synthesis and lipid synthesis/energy production were regulated in the combination group in comparison with Comamonas sp. 12022 MYb131 alone. Furthermore, glutamine, involved in the de novo synthesis of purine and pyrimidines, was specifically abundant in this group, indicating the potential role of this metabolite in initiating and sustaining bacterial growth. This bacterial crosstalk is suggested to promote the growth of Comamonas sp. 12022 MYb131 in vivo, and synthesis of bacterial metabolites such as PLP in the worm gut.
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Affiliation(s)
- Orçun Haçariz
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
| | - Charles Viau
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
| | - Xue Gu
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
- Department of Animal Science, McGill University, Montreal, QC H9X 3V9, Canada
- Correspondence:
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15
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da Silva JR, de Cerqueira e Silva MB, Philadelpho BO, de Souza VC, dos Santos JEM, Castilho MS, de Souza Ferreira E, Cilli EM. PyrGF and GSTLN peptides enhance pravastatin's inhibition of 3-hydroxy-3-methyl-glutaryl coenzyme. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
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Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
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17
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Cao M, De Mel N, Wang J, Parthemore C, Jiao Y, Chen W, Lin S, Liu D, Kilby G, Chen X. Characterization of N-Terminal Glutamate Cyclization in Monoclonal Antibody and Bispecific Antibody Using Charge Heterogeneity Assays and Hydrophobic Interaction Chromatography. J Pharm Sci 2021; 111:335-344. [PMID: 34516988 DOI: 10.1016/j.xphs.2021.09.006] [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: 08/09/2021] [Revised: 09/05/2021] [Accepted: 09/05/2021] [Indexed: 11/18/2022]
Abstract
N-terminal glutamate (E) cyclization to form pyroglutamate (pE) generates charge heterogeneities for mAbs and proteins. Thus far, pE formation rate in lyophilized formulation as compared to in liquid formulation has not been reported. Impact of pE on antibody biological activity has only been predicted or assessed using stressed samples that may contain other confounding degradations besides pE. Additionally, application of hydrophobic interaction chromatography (HIC) to separate pE has not been reported. In our study, N-terminal E cyclization was identified as the major degradation pathway in lyophilized formulation at elevated temperature for both monoclonal antibody (mAb-A) and IgG-like bispecific antibody (bsAb-A). pE was enriched in salt-gradient ion exchange chromatography (IEC) as pre-peak and in HIC as post-peak for both mAb-A and bsAb-A. Structure-function studies with pE-enriched IEC and HIC fractions confirmed that pE did not affect binding activities for mAb-A and bsAb-A. In vitro incubation of bsAb-A in serum and PBS revealed that the serum matrix may play a role in pE conversion in human serum, in contrast to the chemical reaction mechanism reported. These techniques can help in characterization of N-terminal E-to-pE cyclization and quality attribute severity assessment during therapeutic protein product development.
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Affiliation(s)
- Mingyan Cao
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878.
| | - Niluka De Mel
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Jihong Wang
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Conner Parthemore
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Yang Jiao
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Weimin Chen
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Shihua Lin
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Dengfeng Liu
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Greg Kilby
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
| | - Xiaoyu Chen
- Analytical Sciences, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD 20878
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18
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An N, Zhu QF, Wang YZ, Xiong CF, Hu YN, Feng YQ. Integration of Chemical Derivatization and in-Source Fragmentation Mass Spectrometry for High-Coverage Profiling of Submetabolomes. Anal Chem 2021; 93:11321-11328. [PMID: 34369157 DOI: 10.1021/acs.analchem.1c02673] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In-source fragmentation-based high-resolution mass spectrometry (ISF-HRMS) is a potential analytical technique, which is usually used to profile some specific compounds that can generate diagnostic neutral loss (NL) or fragment ion (FI) in ion source inherently. However, the ISF-HRMS method does not work for those compounds that cannot inherently produce diagnostic NL or FI in ion source. In this study, a derivatization-based in-source fragmentation-information-dependent acquisition (DISF-IDA) strategy was proposed for profiling the metabolites with easily labeled functional groups (submetabolomes) by liquid chromatography-electrospray ionization-quadrupole time-of-flight mass spectrometry (LC-ESI-Q-TOF MS). As a proof-of-concept study, 36 carboxylated compounds labeled with N,N-dimethylethylenediamine (DMED) were selected as model compounds to examine performance of DISF-IDA strategy in screening the carboxylated metabolites and acquiring their MSn spectra. In ESI source, the DEMD-derived carboxylated compounds were fragmented to produce characteristic neutral losses of 45.0578, 63.0684, and/or 88.1000 Da that were further used as diagnostic features for screening the carboxylated metabolites by DISF-IDA-based LC-Q-TOF MS. Furthermore, high-resolution MSn spectra of the model compounds were also obtained within a single run of DISF-IDA-based LC-Q-TOF MS analysis, which contributed to the improvement of the annotation confidence. To further verify its applicability, DISF-IDA strategy was used for profiling carboxylated submetabolome in mice feces. Using this strategy, a total of 351 carboxylated metabolites were detected from mice feces, of which 178 metabolites (51% of the total) were positively or putatively identified. Moreover, DISF-IDA strategy was also demonstrated to be applicable for profiling other submetabolomes with easily labeled functional groups such as amino, carbonyl, and cis-diol groups. Overall, our proposed DISF-IDA strategy is a promising technique for high-coverage profiling of submetabolomes with easily labeled functional groups in biological samples.
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Affiliation(s)
- Na An
- Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Quan-Fei Zhu
- Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yan-Zhen Wang
- Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Cai-Feng Xiong
- Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu-Ning Hu
- Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, PR China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, PR China.,School of Health Sciences, Wuhan University, Wuhan 430071, PR China
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19
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Bersin LM, Patel SM, Topp EM. Effect of 'pH' on the Rate of Pyroglutamate Formation in Solution and Lyophilized Solids. Mol Pharm 2021; 18:3116-3124. [PMID: 34232660 DOI: 10.1021/acs.molpharmaceut.1c00338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
N-terminal glutamate can cyclize to form pyroglutamate (pGlu) in pharmaceutically relevant peptides and proteins. The reaction occurs nonenzymatically during storage for monoclonal antibodies and shows a strong 'pH' dependence in solution, but the solid-state reaction has not been studied in detail. This work investigates the effect of 'pH' and buffer species on pGlu formation for a model peptide (EVQLVESGGGLVQPGGSLR) in lyophilized solids and in solution. The model peptide was formulated from 'pH' 4 to 'pH' 9 in citrate, citrate-phosphate, phosphate, and carbonate buffers and stored at 50 °C for at least 10 weeks. pGlu formation and loss of the parent peptide were monitored by reversed-phase high-performance liquid chromatography. The apparent 'pH' dependence of the reaction rate in the solid state differed markedly from that in solution. Interestingly, in the 'pH' range often used to formulate mAbs ('pH' 5.5-6), the rate of pGlu formation in the solid state was greater than that in solution. The results have implications for the rational design of stable formulations of peptides and proteins, and for the transition from solid to solution formulations during development.
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Affiliation(s)
- Lia M Bersin
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907-2091, United States
| | - Sajal M Patel
- Dosage Form Design & Development, Biopharmaceutical Development, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907-2091, United States.,National Institute for Bioprocessing Research and Training, Belfield, Blackrock, County Dublin A94 X099, Ireland
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20
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Hikosaka M, Iwahashi F, Yamato S. Metabolomic analysis of Schoenoplectus juncoides reveals common markers of acetolactate synthase inhibition among paddy weeds. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 174:104827. [PMID: 33838720 DOI: 10.1016/j.pestbp.2021.104827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 06/12/2023]
Abstract
Despite the increase in pressure for reducing the use of chemical pesticides in agriculture, herbicides remain one of the efficient tools for augmenting food production. Various herbicide-resistant weeds against most herbicidal modes of action (MoA) are emerging worldwide, and therefore, the necessity of developing herbicides with novel MoA is increasing. Toward this, rigid methods of determining MOA that can be applied for various weeds species are required. Despite the existence of weed species with resistance to acetolactate synthase (ALS) inhibitors, inhibition of ALS remains one of the most widely used herbicidal MoAs containing more than 50 commercial active ingredients. Here, we aimed to identify marker metabolites that are indicative of ALS inhibition. We performed non-targeted and targeted metabolomics using ALS inhibitor-treated Schoenoplectus juncoides. We identified internal metabolite markers for ALS inhibition, with excellent selectivity for ALS inhibitors and herbicides with different MOAs in various weed species. These markers will enable us to evaluate ALS inhibitory activity of chemicals in vivo in a wide variety of weed species.
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Affiliation(s)
- Masashi Hikosaka
- Health & Crop Science Research Laboratory, Sumitomo Chemical Co., Ltd, Takarazuka, Hyogo 665-8555, Japan.
| | - Fukumatsu Iwahashi
- Health & Crop Science Research Laboratory, Sumitomo Chemical Co., Ltd, Takarazuka, Hyogo 665-8555, Japan.
| | - Seiji Yamato
- Health & Crop Science Research Laboratory, Sumitomo Chemical Co., Ltd, Takarazuka, Hyogo 665-8555, Japan.
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21
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de Bie TH, Witkamp RF, Jongsma MA, Balvers MGJ. Development and validation of a UPLC-MS/MS method for the simultaneous determination of gamma-aminobutyric acid and glutamic acid in human plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1164:122519. [PMID: 33454439 DOI: 10.1016/j.jchromb.2020.122519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/02/2020] [Accepted: 12/22/2020] [Indexed: 11/15/2022]
Abstract
Gamma-aminobutyric acid (GABA) and its precursor glutamic acid are important neurotransmitters. Both are also present in peripheral tissues and the circulation, where abnormal plasma concentrations have been linked to specific mental disorders. In addition to endogenous synthesis, GABA and glutamic acid can be obtained from dietary sources. An increasing number of studies suggest beneficial cardio-metabolic effects of GABA intake, and therefore GABA is being marketed as a food supplement. The need for further research into their health effects merits accurate and sensitive methods to analyze GABA and glutamic acid in plasma. To this end, an ultra-pressure liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) method was developed and validated for the quantification of GABA and glutamic acid in human plasma. Samples were prepared by a protein precipitation step and subsequent solid phase extraction using acetonitrile. Chromatographic separation was achieved on an Acquity UPLC HSS reversed phase C18 column using gradient elution. Analytes were detected using electrospray ionization and selective reaction monitoring. Standard curve concentrations for GABA ranged from 3.4 to 2500 ng/mL and for glutamic acid from 30.9 ng/mL to 22,500 ng/mL. Within- and between-day accuracy and precision were <10% in quality control samples at low, medium and high concentrations for both GABA and glutamic acid. GABA and glutamic acid were found to be stable in plasma after freeze-thaw cycles and up to 12 months of storage. The validated method was applied to human plasma from 17 volunteers. The observed concentrations ranged between 11.5 and 20.0 ng/ml and 2269 and 7625 ng/ml for respectively GABA and glutamic acid. The reported method is well suited for the measurement of plasma GABA and glutamic acid in pre-clinical or clinical studies.
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Affiliation(s)
- Tessa H de Bie
- Division of Human Nutrition and Health, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands; Wageningen Plant Research, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, the Netherlands.
| | - Renger F Witkamp
- Division of Human Nutrition and Health, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Maarten A Jongsma
- Wageningen Plant Research, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, the Netherlands
| | - Michiel G J Balvers
- Division of Human Nutrition and Health, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
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22
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Although metabolomics applications span a wide range of disciplines, a majority has focused on understanding, preventing, diagnosing, and managing human diseases. This chapter describes NMR-based methods relevant to the rapidly expanding metabolomics field.
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23
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Typek R, Dawidowicz AL, Stankevič M. Stability of stevioside in food processing conditions: unexpected recombination of stevioside hydrolysis products in ESI source. Food Chem 2020; 331:127262. [PMID: 32563799 DOI: 10.1016/j.foodchem.2020.127262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 11/25/2022]
Abstract
Stevioside is the main and the sweetest glycoside of stevia plant. It is attractive as a natural sweetener to diabetics and others on carbohydrate-controlled diets. This paper discusses the stability of stevioside under food processing conditions. It was found that stevioside was transformed not only to rubusoside, steviolbioside, steviol monoside and steviol but also to previously unknown stevioside α-anomer and rubusoside α-anomer. Those two identified stevioside transformation products are formed not only during the heating of acidic, neutral and alkaline stevioside standard solutions and stevia leaves suspensions in water and ethanol/water solvents but also during the processing of foods containing stevia. Apart from presenting the new compounds, the paper additionally shows that the recombination of sugar moiety with steviolbioside molecule in MS/ESI source can occur. The effect of molecule recombination in the MS source is known from the literature; however, it has not been reported previously in relation to stevioside derivatives.
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Affiliation(s)
- Rafał Typek
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie Sklodowska University in Lublin, 20-031 Lublin, Pl. Maria Curie Sklodowska 3, Poland.
| | - Andrzej L Dawidowicz
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie Sklodowska University in Lublin, 20-031 Lublin, Pl. Maria Curie Sklodowska 3, Poland
| | - Marek Stankevič
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie Sklodowska University in Lublin, 20-031 Lublin, Pl. Maria Curie Sklodowska 3, Poland
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Mamani-Huanca M, de la Fuente AG, Otero A, Gradillas A, Godzien J, Barbas C, López-Gonzálvez Á. Enhancing confidence of metabolite annotation in Capillary Electrophoresis-Mass Spectrometry untargeted metabolomics with relative migration time and in-source fragmentation. J Chromatogr A 2020; 1635:461758. [PMID: 33302137 DOI: 10.1016/j.chroma.2020.461758] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
Capillary electrophoresis coupled to mass spectrometry is a power tool in untargeted metabolomics studies to analyze charged and polar compounds. However, identification is a challenge due to the variability of migration times and the lack of MS/MS spectra in CE-TOF-MS, the type of instruments most frequently employed. We present here a CE-MS search platform incorporated in CEU Mass Mediator to annotate metabolites with a confidence level L2. For its the development we analyzed 226 compounds using two fragmentor voltages: 100 and 200 V. The information obtained, such as relative migration times (RMT) and in-source fragments, were incorporated into the platform. In addition, we validated the CE-MS search functionality using different types of biological samples such as plasma samples (human, rat, and rabbit), mouse macrophages, and human urine. The RMT tolerance percentage for the search of metabolites has been determined, establishing 5% for all compounds, except for the compounds migrating in the electro-osmotic flow, for which the tolerance should be of 10%. It has also been demonstrated the robustness of the in-source fragmentation, which makes possible the annotation of compounds by means of their fragmentation pattern. As an example, 3-methylhistidine and 1-methilhistidine, whose RMT are very close, have been annotated. Studies of the fragmentation mechanisms of acyl-L-carnitines have shown that in-source fragmentation follows the general fragmentation rules and is a suitable alternative to MS/MS.
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Affiliation(s)
- Maricruz Mamani-Huanca
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Alberto Gil de la Fuente
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Department of Information Technology, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Abraham Otero
- Department of Information Technology, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
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Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics. PLANTS 2020; 9:plants9091149. [PMID: 32899727 PMCID: PMC7570186 DOI: 10.3390/plants9091149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 01/15/2023]
Abstract
Global change scenarios in the Mediterranean basin predict a precipitation reduction within the coming hundred years. Therefore, increased drought will affect forests both in terms of adaptive ecology and ecosystemic services. However, how vegetation might adapt to drought is poorly understood. In this report, four years of climate change was simulated by excluding 35% of precipitation above a downy oak forest. RNASeq data allowed us to assemble a genome-guided transcriptome. This led to the identification of differentially expressed features, which was supported by the characterization of target metabolites using a metabolomics approach. We provided 2.5 Tb of RNASeq data and the assembly of the first genome guided transcriptome of Quercus pubescens. Up to 5724 differentially expressed transcripts were obtained; 42 involved in plant response to drought. Transcript set enrichment analysis showed that drought induces an increase in oxidative pressure that is mitigated by the upregulation of ubiquitin-like protein protease, ferrochelatase, oxaloacetate decarboxylase and oxo-acid-lyase activities. Furthermore, the downregulation of auxin biosynthesis and transport, carbohydrate storage metabolism were observed as well as the concomitant accumulation of metabolites, such as oxalic acid, malate and isocitrate. Our data suggest that early metabolic changes in the resistance of Q. pubescens to drought involve a tricarboxylic acid (TCA) cycle shunt through the glyoxylate pathway, galactose metabolism by reducing carbohydrate storage and increased proteolytic activity.
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Mamani-Huanca M, Gradillas A, López-Gonzálvez Á, Barbas C. Unraveling the Cyclization of l-Argininosuccinic Acid in Biological Samples: A Study via Mass Spectrometry and NMR Spectroscopy. Anal Chem 2020; 92:12891-12899. [DOI: 10.1021/acs.analchem.0c01420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Maricruz Mamani-Huanca
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Monteprı́ncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Monteprı́ncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Monteprı́ncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Monteprı́ncipe, 28660 Boadilla del Monte, Madrid, Spain
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27
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Bollenbach A, Tsikas D. Measurement of the tripeptides glutathione and ophthalmic acid by gas chromatography-mass spectrometry. Anal Biochem 2020; 644:113841. [DOI: 10.1016/j.ab.2020.113841] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/29/2020] [Accepted: 06/18/2020] [Indexed: 12/26/2022]
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Johnson SC, Kayser EB, Bornstein R, Stokes J, Bitto A, Park KY, Pan A, Sun G, Raftery D, Kaeberlein M, Sedensky MM, Morgan PG. Regional metabolic signatures in the Ndufs4(KO) mouse brain implicate defective glutamate/α-ketoglutarate metabolism in mitochondrial disease. Mol Genet Metab 2020; 130:118-132. [PMID: 32331968 PMCID: PMC7272141 DOI: 10.1016/j.ymgme.2020.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 03/29/2020] [Indexed: 02/08/2023]
Abstract
Leigh Syndrome (LS) is a mitochondrial disorder defined by progressive focal neurodegenerative lesions in specific regions of the brain. Defects in NDUFS4, a subunit of complex I of the mitochondrial electron transport chain, cause LS in humans; the Ndufs4 knockout mouse (Ndufs4(KO)) closely resembles the human disease. Here, we probed brain region-specific molecular signatures in pre-symptomatic Ndufs4(KO) to identify factors which underlie focal neurodegeneration. Metabolomics revealed that free amino acid concentrations are broadly different by region, and glucose metabolites are increased in a manner dependent on both region and genotype. We then tested the impact of the mTOR inhibitor rapamycin, which dramatically attenuates LS in Ndufs4(KO), on region specific metabolism. Our data revealed that loss of Ndufs4 drives pathogenic changes to CNS glutamine/glutamate/α-ketoglutarate metabolism which are rescued by mTOR inhibition Finally, restriction of the Ndufs4 deletion to pre-synaptic glutamatergic neurons recapitulated the whole-body knockout. Together, our findings are consistent with mTOR inhibition alleviating disease by increasing availability of α-ketoglutarate, which is both an efficient mitochondrial complex I substrate in Ndufs4(KO) and an important metabolite related to neurotransmitter metabolism in glutamatergic neurons.
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Affiliation(s)
- Simon C Johnson
- Department of Neurology, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Ernst-Bernhard Kayser
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Rebecca Bornstein
- Department of Pathology, University of Washington, Seattle, WA 98105, USA
| | - Julia Stokes
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA
| | - Alessandro Bitto
- Department of Pathology, University of Washington, Seattle, WA 98105, USA
| | - Kyung Yeon Park
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Amanda Pan
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Grace Sun
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Department of Chemistry, University of Washington, Seattle, WA 98109, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98105, USA
| | - Margaret M Sedensky
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Philip G Morgan
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
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Wang D, Nowak C, Mason B, Katiyar A, Liu H. Analytical artifacts in characterization of recombinant monoclonal antibody therapeutics. J Pharm Biomed Anal 2020; 183:113131. [DOI: 10.1016/j.jpba.2020.113131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 01/12/2023]
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Xue J, Domingo-Almenara X, Guijas C, Palermo A, Rinschen MM, Isbell J, Benton HP, Siuzdak G. Enhanced in-Source Fragmentation Annotation Enables Novel Data Independent Acquisition and Autonomous METLIN Molecular Identification. Anal Chem 2020; 92:6051-6059. [DOI: 10.1021/acs.analchem.0c00409] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jingchuan Xue
- Scripps Center for Metabolomics and Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Xavier Domingo-Almenara
- Centre for Omic Sciences, EURECAT − Technology Centre of Catalonia and Rovira i Virgili University Joint Unit, Reus, Catalonia, Spain
| | - Carlos Guijas
- Scripps Center for Metabolomics and Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Amelia Palermo
- Scripps Center for Metabolomics and Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Markus M. Rinschen
- Scripps Center for Metabolomics and Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - John Isbell
- Discovery Chemistry, Genomics Institute of the Novartis Research Foundation, Metabolism and Pharmacokinetics, San Diego, California 92121, United States
| | - H. Paul Benton
- Scripps Center for Metabolomics and Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Méndez-Lucas A, Lin W, Driscoll PC, Legrave N, Novellasdemunt L, Xie C, Charles M, Wilson Z, Jones NP, Rayport S, Rodríguez-Justo M, Li V, MacRae JI, Hay N, Chen X, Yuneva M. Identifying strategies to target the metabolic flexibility of tumours. Nat Metab 2020; 2:335-350. [PMID: 32694609 PMCID: PMC7436715 DOI: 10.1038/s42255-020-0195-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/16/2020] [Indexed: 12/13/2022]
Abstract
Plasticity of cancer metabolism can be a major obstacle to efficient targeting of tumour-specific metabolic vulnerabilities. Here, we identify the compensatory mechanisms following the inhibition of major pathways of central carbon metabolism in c-MYC-induced liver tumours. We find that, while inhibition of both glutaminase isoforms (Gls1 and Gls2) in tumours considerably delays tumourigenesis, glutamine catabolism continues, owing to the action of amidotransferases. Synergistic inhibition of both glutaminases and compensatory amidotransferases is required to block glutamine catabolism and proliferation of mouse and human tumour cells in vitro and in vivo. Gls1 deletion is also compensated for by glycolysis. Thus, co-inhibition of Gls1 and hexokinase 2 significantly affects Krebs cycle activity and tumour formation. Finally, the inhibition of biosynthesis of either serine (Psat1-KO) or fatty acid (Fasn-KO) is compensated for by uptake of circulating nutrients, and dietary restriction of both serine and glycine or fatty acids synergistically suppresses tumourigenesis. These results highlight the high flexibility of tumour metabolism and demonstrate that either pharmacological or dietary targeting of metabolic compensatory mechanisms can improve therapeutic outcomes.
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Affiliation(s)
| | - Wei Lin
- The Francis Crick Institute, London, UK
| | | | | | | | - Chencheng Xie
- Department of Internal Medicine, University of South Dakota, Sanford School of Medicine, Vermillion, SD, USA
| | - Mark Charles
- Cancer Research UK, Therapeutic Discovery Laboratories, Cambridge, UK
| | - Zena Wilson
- Bioscience, Discovery, Oncology R&D, AstraZeneca, Macclesfield, UK
| | - Neil P Jones
- Cancer Research UK, Therapeutic Discovery Laboratories, Cambridge, UK
| | - Stephen Rayport
- Department of Psychiatry, Columbia University, New York, NY, USA
- Department of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | | | - Vivian Li
- The Francis Crick Institute, London, UK
| | | | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
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Identifying transglutaminase reaction products via mass spectrometry as exemplified by the MUC2 mucin - Pitfalls and traps. Anal Biochem 2020; 597:113668. [PMID: 32222540 PMCID: PMC7184670 DOI: 10.1016/j.ab.2020.113668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/15/2020] [Accepted: 02/27/2020] [Indexed: 12/26/2022]
Abstract
In order to demonstrate transglutaminase activity in biological samples immunological as well as glutamine- and amine-donor based assays are commonly used. However, the identification of the transglutaminase reaction product, i. e. the isopeptide cross-linked peptides/proteins or the deamidated protein/peptide are often neglected. This article describes a workflow for the detection of the products of transglutaminase-catalyzed reactions. In particular, possible pitfalls and traps that can arise during the mass spectrometry-based identification of isopeptide cross-links are addressed and characterised on actual samples.
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Dai M, Ma T, Niu Y, Zhang M, Zhu Z, Wang S, Liu H. Analysis of low-molecular-weight metabolites in stomach cancer cells by a simplified and inexpensive GC/MS metabolomics method. Anal Bioanal Chem 2020; 412:2981-2991. [PMID: 32185442 DOI: 10.1007/s00216-020-02543-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/01/2020] [Accepted: 02/21/2020] [Indexed: 12/26/2022]
Abstract
GC/MS coupled metabolomics analysis, using a simplified and much less expensive silylation process with trimethylsilyl cyanide (TMSCN), was conducted to investigate metabolic abnormalities in stomach cancer cells. Under optimized conditions for derivatization by TMSCN and methanol extraction, 228 metabolites were detected using GC/MS spectrometry analysis, and 89 metabolites were identified using standard compounds and the NIST database. Ten metabolite levels were found to be lower in stomach cancer cells relative to normal cells. Among those ten metabolites, four metabolites-ribose, proline, pyroglutamic acid, and glucose-were known to be linked to cancers. In particular, pyroglutamic acid level showed a drastic reduction of 22-fold in stomach cancer cells. Since glutamine and glutamic acid are known to undergo cyclization to pyroglutamic acid, the 22-fold reduction might be the actual reduction in the levels of glutamine and/or glutamic acid-both known to be cancer-related. Hence, the marked reduction in pyroglutamic acid level might serve as a biomarker to aid early detection of stomach cancer. Graphical abstract.
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Affiliation(s)
- Min Dai
- College of Chemistry, Zhengzhou University, 75 University Road, Zhengzhou, 450052, Henan, China
| | - Ting Ma
- School of Pharmaceutical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou, 450001, Henan, China
| | - Ying Niu
- College of Chemistry, Zhengzhou University, 75 University Road, Zhengzhou, 450052, Henan, China
| | - Mengmeng Zhang
- College of Chemistry, Zhengzhou University, 75 University Road, Zhengzhou, 450052, Henan, China
| | - Zhiwu Zhu
- College of Chemistry, Zhengzhou University, 75 University Road, Zhengzhou, 450052, Henan, China
| | - Shaomin Wang
- College of Chemistry, Zhengzhou University, 75 University Road, Zhengzhou, 450052, Henan, China.
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou, 450001, Henan, China
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34
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Li J, Wang H, Li J, Liu Y, Ding H. LC-MS analysis of Myrica rubra extract and its hypotensive effects via the inhibition of GLUT 1 and activation of the NO/Akt/eNOS signaling pathway. RSC Adv 2020; 10:5371-5384. [PMID: 35498305 PMCID: PMC9049140 DOI: 10.1039/c9ra05895h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022] Open
Abstract
In the area of medicine food homology, Myrica rubra ((Lour.) Siebold & Zucc.) has been used in medicine as an astringent and anti-diarrheal. However, there are few in-depth studies evaluating the antihypertensive chemical components and antihypertensive mechanisms of Myrica rubra. Thus, the aim in this study was to assess the protective effects of an ethanol extract of bayberry (BE) on spontaneous hypertension in rats. In this study, liquid chromatography-mass spectroscopy (LC-MS) coupled with biochemical assays and western blot have been employed to study the protective effects of BE against hypertension. A total of 28 compounds were identified in BE. According to this study, treatment with BE (2 g kg-1) resulted in the potent and persistent reduction of high blood pressure, even after drug withdrawal. The results indicate that the mechanisms of action might involve protection against damage to the vascular structure. Bayberry extract could enhance the endothelium-independent vascular function, inhibiting the abnormal proliferation of smooth muscle by inhibition of glucose transporter-1 (GLUT 1) and regulation of nitric oxide (NO)/serine/threonine kinases (Akt)/endothelial nitric oxide synthase (eNOS). The results of molecular docking and in vitro research indicated six compounds in BE that might be responsible for the antihypertensive effect attributed to GLUT 1, eNOS and Akt, and further in vivo studies are needed to verify this.
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Affiliation(s)
- Jing Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China+8613007162084
| | - Huiling Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China+8613007162084
| | - Jian Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China+8613007162084
| | - Yonggang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China+8613007162084
| | - Hong Ding
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China+8613007162084
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Lander SS, Chornyy S, Safory H, Gross A, Wolosker H, Gaisler‐Salomon I. Glutamate dehydrogenase deficiency disrupts glutamate homeostasis in hippocampus and prefrontal cortex and impairs recognition memory. GENES BRAIN AND BEHAVIOR 2020; 19:e12636. [DOI: 10.1111/gbb.12636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/11/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sergiy Chornyy
- Department of PsychologyUniversity of Haifa Haifa Israel
| | - Hazem Safory
- Department of Biochemistry, The Ruth and Bruce Rappaport Faculty of MedicineTechnion‐Israel Institute of Technology Haifa Israel
| | - Amit Gross
- Department of PsychologyUniversity of Haifa Haifa Israel
| | - Herman Wolosker
- Department of Biochemistry, The Ruth and Bruce Rappaport Faculty of MedicineTechnion‐Israel Institute of Technology Haifa Israel
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den Ridder M, Daran-Lapujade P, Pabst M. Shot-gun proteomics: why thousands of unidentified signals matter. FEMS Yeast Res 2019; 20:5682490. [DOI: 10.1093/femsyr/foz088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Mass spectrometry-based proteomics has become a constitutional part of the multi-omics toolbox in yeast research, advancing fundamental knowledge of molecular processes and guiding decisions in strain and product developmental pipelines. Nevertheless, post-translational protein modifications (PTMs) continue to challenge the field of proteomics. PTMs are not directly encoded in the genome; therefore, they require a sensitive analysis of the proteome itself. In yeast, the relevance of post-translational regulators has already been established, such as for phosphorylation, which can directly affect the reaction rates of metabolic enzymes. Whereas, the selective analysis of single modifications has become a broadly employed technique, the sensitive analysis of a comprehensive set of modifications still remains a challenge. At the same time, a large number of fragmentation spectra in a typical shot-gun proteomics experiment remain unidentified. It has been estimated that a good proportion of those unidentified spectra originates from unexpected modifications or natural peptide variants. In this review, recent advancements in microbial proteomics for unrestricted protein modification discovery are reviewed, and recent research integrating this additional layer of information to elucidate protein interaction and regulation in yeast is briefly discussed.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Ramotowska S, Zarzeczańska D, Dąbkowska I, Wcisło A, Niedziałkowski P, Czaczyk E, Grobelna B, Ossowski T. Hydrogen bonding and protonation effects in amino acids' anthraquinone derivatives - Spectroscopic and electrochemical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117226. [PMID: 31181504 DOI: 10.1016/j.saa.2019.117226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Six novel amino acid chromophores were synthesized and their spectroscopic, acid-base, and electrochemical properties are discussed in this work. In studied compounds, selected amino acid residues (l-Aspartic acid, l-Glutamic acid, l-Glutamine, l-Histidine, l-Lysine, l-Arginine) are attached to the 1-(piperazine) 9,10-anthraquinone skeleton via the amide bond between the carboxyl group of amino acid and nitrogen atom of the piperazine ring. All derivatives have been characterized using a variety of spectroscopic techniques (mass spectrometry, 1HNMR, UV-Vis, IR spectroscopy), acid-base (electrochemical and UV-Vis) titrations, and cyclic voltammetry methods. Basing on observed experimental effects, supported by quantum chemical simulations, the structure-properties links were established. They are indicative of the specific interactions within and/or in-between amino acid side groups, which are prone to form both, intra- and intermolecular hydrogen bonds as well as electrostatic interactions with the anthraquinone system.
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Affiliation(s)
- Sandra Ramotowska
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Dorota Zarzeczańska
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Iwona Dąbkowska
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Anna Wcisło
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paweł Niedziałkowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Elżbieta Czaczyk
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Beata Grobelna
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Tadeusz Ossowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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Kune C, Delvaux C, Haler JRN, Quinton L, Eppe G, De Pauw E, Far J. A Mechanistic Study of Protonated Aniline to Protonated Phenol Substitution Considering Tautomerization by Ion Mobility Mass Spectrometry and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2238-2249. [PMID: 31520338 DOI: 10.1007/s13361-019-02321-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
We report the use of ion mobility mass spectrometry (IMMS) and energy-resolved collisional activation to investigate gas-phase reactions of protonated aniline and protonated phenol. Protonated aniline prototropic tautomerization and nucleophilic substitution (SN1) to produce phenol with traces of water in the IMMS cell are reported. Tautomerization of protonated phenol and its ability to form protonated aniline in presence of ammonia in the gas phase are also observed. These results are supported by energy landscapes obtained from computational chemistry. These structure modifications in the IMMS cell affected the measured collision cross section (CCS). A thorough understanding of the gas-phase reactions occurring in IMMS appears mandatory before using the experimental CCS as a robust descriptor which is stated by the recent literature.
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Affiliation(s)
- Christopher Kune
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium.
| | - Cédric Delvaux
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Jean R N Haler
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Loïc Quinton
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Gauthier Eppe
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Edwin De Pauw
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Johann Far
- MOLSYS, Mass Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du Six Aout 11, B-4000, Liège, Belgium
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Dong GL, Fang WH, Zhang L, Zhang J. In situ generated pyroglutamate bridged polyoxotitaniums with strong circular dichroism signal. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.01.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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40
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Mello LR, Hamley IW, Miranda A, Alves WA, Silva ER. β
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sheet assembly in amyloidogenic glutamic acid nanostructures: Insights from X‐ray scattering and infrared nanospectroscopy. J Pept Sci 2019; 25:e3170. [DOI: 10.1002/psc.3170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Lucas R. Mello
- Departamento de BiofísicaUniversidade Federal de São Paulo São Paulo Brazil
| | - Ian W. Hamley
- Department of ChemistryUniversity of Reading Reading UK
| | - Antonio Miranda
- Departamento de BiofísicaUniversidade Federal de São Paulo São Paulo Brazil
| | - Wendel A. Alves
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABC Santo André Brazil
| | - Emerson R. Silva
- Departamento de BiofísicaUniversidade Federal de São Paulo São Paulo Brazil
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41
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Lendor S, Hassani SA, Boyaci E, Singh V, Womelsdorf T, Pawliszyn J. Solid Phase Microextraction-Based Miniaturized Probe and Protocol for Extraction of Neurotransmitters from Brains in Vivo. Anal Chem 2019; 91:4896-4905. [DOI: 10.1021/acs.analchem.9b00995] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sofia Lendor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Seyed-Alireza Hassani
- Department of Psychology, Vanderbilt University, PMB 407817, 2301 Vanderbilt Place, Nashville, Tennessee 37240, United States
- Department of Biology, Centre for Vision Research, York University, Toronto, Ontario M6J 1P3, Canada
| | - Ezel Boyaci
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Varoon Singh
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Thilo Womelsdorf
- Department of Psychology, Vanderbilt University, PMB 407817, 2301 Vanderbilt Place, Nashville, Tennessee 37240, United States
- Department of Biology, Centre for Vision Research, York University, Toronto, Ontario M6J 1P3, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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42
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Crooks DR, Fan TWM, Linehan WM. Metabolic Labeling of Cultured Mammalian Cells for Stable Isotope-Resolved Metabolomics: Practical Aspects of Tissue Culture and Sample Extraction. Methods Mol Biol 2019; 1928:1-27. [PMID: 30725447 PMCID: PMC8195444 DOI: 10.1007/978-1-4939-9027-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Stable isotope-resolved metabolomics (SIRM) methods are used increasingly by cancer researchers to probe metabolic pathways and identify vulnerabilities in cancer cells. Analytical and computational advances are being made constantly, but tissue culture and sample extraction procedures are often variable and not elaborated in the literature. This chapter discusses basic aspects of tissue culture practices as they relate to the use of stable isotope tracers and provides a detailed metabolic labeling and metabolite extraction procedure designed to maximize the amount of information that can be obtained from a single tracer experiment.
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Affiliation(s)
- Daniel R Crooks
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Teresa W-M Fan
- Department of Toxicology and Cancer Biology, Center for Environmental and Systems Biochemistry, Markey Cancer Center, and University of Kentucky, Lexington, KY, USA.
| | - W Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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43
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Aguiar NO, Olivares FL, Novotny EH, Canellas LP. Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids. PeerJ 2018; 6:e5445. [PMID: 30202643 PMCID: PMC6129145 DOI: 10.7717/peerj.5445] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) and humic acids (HA) have been used as biostimulants in field conditions. The complete genomic and proteomic transcription of Herbaspirillum seropedicae and Gluconacetobacter diazotrophicus is available but interpreting and utilizing this information in the field to increase crop performance is challenging. The identification and characterization of metabolites that are induced by genomic changes may be used to improve plant responses to inoculation. The objective of this study was to describe changes in sugarcane metabolic profile that occur when HA and PGPB are used as biostimulants. Inoculum was applied to soil containing 45-day old sugarcane stalks. One week after inoculation, the methanolic extracts from leaves were obtained and analyzed by gas chromatography coupled to time-of-flight mass spectrometry; a total of 1,880 compounds were observed and 280 were identified in all samples. The application of HA significantly decreased the concentration of 15 metabolites, which generally included amino acids. HA increased the levels of 40 compounds, and these included metabolites linked to the stress response (shikimic, caffeic, hydroxycinnamic acids, putrescine, behenic acid, quinoline xylulose, galactose, lactose proline, oxyproline and valeric acid) and cellular growth (adenine and adenosine derivatives, ribose, ribonic acid and citric acid). Similarly, PGPB enhanced the level of metabolites identified in HA-treated soils; e.g., 48 metabolites were elevated and included amino acids, nucleic acids, organic acids, and lipids. Co-inoculation (HA+PGPB) boosted the level of 110 metabolites with respect to non-inoculated controls; these included amino acids, lipids and nitrogenous compounds. Changes in the metabolic profile induced by HA+PGPB influenced both glucose and pentose pathways and resulted in the accumulation of heptuloses and riboses, which are substrates in the nucleoside biosynthesis and shikimic acid pathways. The mevalonate pathway was also activated, thus increasing phytosterol synthesis. The improvement in cellular metabolism observed with PGPB+HA was compatible with high levels of vitamins. Glucuronate and amino sugars were stimulated in addition to the products and intermediary compounds of tricarboxylic acid metabolism. Lipids and amino acids were the main compounds induced by co-inoculation in addition to antioxidants, stress-related metabolites, and compounds involved in cellular redox. The primary compounds observed in each treatment were identified, and the effect of co-inoculation (HA+PGPB) on metabolite levels was discussed.
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Affiliation(s)
- Natalia O Aguiar
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense, Campos dos Goytacaes, Rio de Janeiro, Brazil
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense, Campos dos Goytacaes, Rio de Janeiro, Brazil
| | | | - Luciano P Canellas
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense, Campos dos Goytacaes, Rio de Janeiro, Brazil
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44
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Ivleva VB, Schneck NA, Gollapudi D, Arnold F, Cooper JW, Lei QP. Investigation of Sequence Clipping and Structural Heterogeneity of an HIV Broadly Neutralizing Antibody by a Comprehensive LC-MS Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1512-1523. [PMID: 29736600 PMCID: PMC6652184 DOI: 10.1007/s13361-018-1968-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/07/2018] [Accepted: 04/14/2018] [Indexed: 05/11/2023]
Abstract
CAP256 is one of the highly potent, broadly neutralizing monoclonal antibodies (bNAb) designed for HIV-1 therapy. During the process development of one of the constructs, an unexpected product-related impurity was observed via microfluidics gel electrophoresis. A panel of complementary LC-MS analyses was applied for the comprehensive characterization of CAP256 which included the analysis of the intact and reduced protein, the middle-up approach, and a set of complementary peptide mapping techniques and verification of the disulfide bonds. The designed workflow allowed to identify a clip within a protruding acidic loop in the CDR-H3 region of the heavy chain, which can lead to the decrease of bNAb potency. This characterization explained the origin of the additional species reflected by the reducing gel profile. An intra-loop disulfide bond linking the two fragments was identified, which explained why the non-reducing capillary electrophoresis (CE) profile was not affected. The extensive characterization of CAP256 post-translational modifications was performed to investigate a possible cause of CE profile complexity and to illustrate other structural details related to this molecule's biological function. Two sites of the engineered Tyr sulfation were verified in the antigen-binding loop, and pyroglutamate formation was used as a tool for monitoring the extent of antibody clipping. Overall, the comprehensive LC-MS study was crucial to (1) identify the impurity as sequence clipping, (2) pinpoint the clipping location and justify its susceptibility relative to the molecular structure, (3) lead to an upstream process optimization to mitigate product quality risk, and (4) ultimately re-engineer the sequence to be clip-resistant. Graphical Abstract ᅟ.
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Affiliation(s)
- Vera B Ivleva
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA.
| | - Nicole A Schneck
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Deepika Gollapudi
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Frank Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Jonathan W Cooper
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Q Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA.
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45
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Briggs KT, Taraban MB, Yu YB. Water proton NMR detection of amide hydrolysis and diglycine dimerization. Chem Commun (Camb) 2018; 54:7003-7006. [PMID: 29850691 DOI: 10.1039/c8cc03935f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The transverse relaxation rate of water protons R2(1H2O) is found to be sensitive to amide hydrolysis and diglycine dimerization. The results demonstrate the feasibility of using R2(1H2O) as a diagnostic tool to detect chemical changes in aqueous solutions. Potential applications include drug product formulation and inspection.
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Affiliation(s)
- Katharine T Briggs
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21201, USA.
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46
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Trefely S, Mesaros C, Xu P, Doan MT, Jiang H, Altinok O, Orynbayeva Z, Snyder NW. Artefactual formation of pyruvate from in-source conversion of lactate. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:10.1002/rcm.8159. [PMID: 29740888 PMCID: PMC6312753 DOI: 10.1002/rcm.8159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/02/2018] [Accepted: 04/24/2018] [Indexed: 05/05/2023]
Abstract
RATIONALE Lactate and pyruvate are high abundance products of glucose metabolism. Analysis of both molecules as part of metabolomics studies in cellular metabolism and physiology have been aided by advances in liquid chromatography-mass spectrometry (LC-MS). METHODS We used ion pairing-chromatography and negative ion mode ESI on an QExactive HF to perform stable isotope assisted metabolomics profiling of lactate and pyruvate metabolism. RESULTS Using an LC-MS method for polar metabolite analysis we discovered an artefactual formation of pyruvate from in-source fragmentation of lactate. Surprisingly, this in-source fragmentation has not been previously described, thus we report this identification to warn other investigators. This artefact was detected by baseline chromatographic resolution of lactate and pyruvate by LC with confirmation of this artefact by stable isotope labeling of lactate and pyruvate. CONCLUSIONS These findings have immediate implications for metabolomics studies by LC-MS and direct infusion MS, especially in negative ion mode, whereby users should resolve lactate from pyruvate or robustly quantify the potential formation of pyruvate from higher abundance lactate in their assays.
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Affiliation(s)
- Sophie Trefely
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104
| | - Clementina Mesaros
- Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104
| | - Pening Xu
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104
| | - Mary T Doan
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104
| | - Helen Jiang
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104
| | - Oya Altinok
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Zulfiya Orynbayeva
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104
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47
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Heuillet M, Bellvert F, Cahoreau E, Letisse F, Millard P, Portais JC. Methodology for the Validation of Isotopic Analyses by Mass Spectrometry in Stable-Isotope Labeling Experiments. Anal Chem 2018; 90:1852-1860. [PMID: 29260858 DOI: 10.1021/acs.analchem.7b03886] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stable-isotope labeling experiments (ILEs) are widely used to investigate the topology and operation of metabolic networks. The quality of isotopic data collected in ILEs is of utmost importance to ensure reliable biological interpretations, but current evaluation approaches are limited due to a lack of suitable reference material and relevant evaluation criteria. In this work, we present a complete methodology to evaluate mass spectrometry (MS) methods used for quantitative isotopic studies of metabolic systems. This methodology, based on a biological sample containing metabolites with controlled labeling patterns, exploits different quality metrics specific to isotopic analyses (accuracy and precision of isotopologue masses, abundances, and mass shifts and isotopic working range). We applied this methodology to evaluate a novel LC-MS method for the analysis of amino acids, which was tested on high resolution (Orbitrap operating in full scan mode) and low resolution (triple quadrupole operating in multiple reaction monitoring mode) mass spectrometers. Results show excellent accuracy and precision over a large working range and revealed matrix-specific as well as mode-specific characteristics. The proposed methodology can identify reliable (and unreliable) isotopic data in an easy and straightforward way and efficiently supports the identification of sources of systematic biases as well as of the main factors that influence the overall accuracy and precision of measurements. This approach is generic and can be used to validate isotopic analyses on different matrices, analytical platforms, labeled elements, or classes of metabolites. It is expected to strengthen the reliability of isotopic measurements and thereby the biological value of ILEs.
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Affiliation(s)
- Maud Heuillet
- LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse, 31077, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics , Toulouse, 31077, France
| | - Floriant Bellvert
- LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse, 31077, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics , Toulouse, 31077, France
| | - Edern Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse, 31077, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics , Toulouse, 31077, France
| | - Fabien Letisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse, 31077, France.,Université Paul Sabatier, Université de Toulouse , Toulouse, 31062, France
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse, 31077, France
| | - Jean-Charles Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse, 31077, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics , Toulouse, 31077, France.,Université Paul Sabatier, Université de Toulouse , Toulouse, 31062, France
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48
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Nagana Gowda GA, Djukovic D, Bettcher LF, Gu H, Raftery D. NMR-Guided Mass Spectrometry for Absolute Quantitation of Human Blood Metabolites. Anal Chem 2018; 90:2001-2009. [PMID: 29293320 DOI: 10.1021/acs.analchem.7b04089] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Broad-based, targeted metabolite profiling using mass spectrometry (MS) has become a major platform used in the field of metabolomics for a variety of applications. However, quantitative MS analysis is challenging owing to numerous factors including (1) the need for, ideally, isotope-labeled internal standards for each metabolite, (2) the fact that such standards may be unavailable or prohibitively costly, (3) the need to maintain the standards' concentrations close to those of the target metabolites, and (4) the alternative use of time-consuming calibration curves for each target metabolite. Here, we introduce a new method in which metabolites from a single serum specimen are quantified on the basis of a recently developed NMR method [ Nagana Gowda et al. Anal. Chem. 2015 , 87 , 706 ] and then used as references for absolute metabolite quantitation using MS. The MS concentrations of 30 metabolites thus derived for test serum samples exhibited excellent correlations with the NMR ones (R2 > 0.99) with a median CV of 3.2%. This NMR-guided-MS quantitation approach is simple and easy to implement and offers new avenues for the routine quantification of blood metabolites using MS. The demonstration that NMR and MS data can be compared and correlated when using identical sample preparations allows improved opportunities to exploit their combined strengths for biomarker discovery and unknown-metabolite identification. Intriguingly, however, metabolites including glutamine, pyroglutamic acid, glucose, and sarcosine correlated poorly with NMR data because of stability issues in their MS analyses or weak or overlapping signals. Such information is potentially important for improving biomarker discovery and biological interpretations. Further, the new quantitation method demonstrated here for human blood serum can in principle be extended to a variety of biological mixtures.
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Affiliation(s)
| | | | | | | | - Daniel Raftery
- Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
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49
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Hayton S, Maker GL, Mullaney I, Trengove RD. Untargeted metabolomics of neuronal cell culture: A model system for the toxicity testing of insecticide chemical exposure. J Appl Toxicol 2017; 37:1481-1492. [DOI: 10.1002/jat.3498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/03/2017] [Accepted: 05/18/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Sarah Hayton
- Separation Sciences and Metabolomics Laboratories; Murdoch University; Perth WA Australia
- School of Veterinary and Life Sciences; Murdoch University; Perth WA Australia
| | - Garth L. Maker
- Separation Sciences and Metabolomics Laboratories; Murdoch University; Perth WA Australia
- School of Veterinary and Life Sciences; Murdoch University; Perth WA Australia
| | - Ian Mullaney
- School of Veterinary and Life Sciences; Murdoch University; Perth WA Australia
| | - Robert D. Trengove
- Separation Sciences and Metabolomics Laboratories; Murdoch University; Perth WA Australia
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50
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Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem 2017; 86:277-304. [PMID: 28654323 DOI: 10.1146/annurev-biochem-061516-044952] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Matthias S Klein
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, California 95616.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
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