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Ahmad S, Mohammed M, Mekala LP, Anusha R, Sasikala C, Ramana CV. Stable isotope-assisted metabolite profiling reveals new insights into L-tryptophan chemotrophic metabolism of Rubrivivax benzoatilyticus. World J Microbiol Biotechnol 2023; 39:98. [PMID: 36781830 DOI: 10.1007/s11274-023-03537-z] [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: 07/13/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Anoxygenic photosynthetic bacteria (APB) are metabolically versatile, capable of surviving with an extended range of carbon and nitrogen sources. This group of phototrophic bacteria have remarkable metabolic plasticity in utilizing an array of organic compounds as carbon source/electron donors and nitrogen sources with sophisticated growth modes. Rubrivivax benzoatilyticus JA2 is one such photosynthetic bacterium utilizes L-tryptophan as nitrogen source under phototrophic growth mode and produces an array of indolic compounds of biotechnological significance. However, chemotrophic L-tryptophan metabolism is largely unexplored and studying L-tryptophan metabolism under chemotrophic mode would provide new insights into metabolic potential of strain JA2. In the present study, we employed stable-isotopes assisted metabolite profiling to unravel the L-tryptophan catabolism in Rubrivivax benzoatilyticus strain JA2 under chemotrophic (dark aerobic) conditions. Utilization of L-tryptophan as a nitrogen source for growth and simultaneous production of indole derivatives was observed in strain JA2. Liquid chromatography mass spectrometry (LC-MS) analysis of exo-metabolite profiling of carbon labeled L-tryptophan (13C11) fed cultures of strain JA2 revealed at least seventy labeled metabolites. Of these, only fourteen metabolites were confirmed using standards, while sixteen were putative and forty metabolites remained unidentified. L-tryptophan chemotrophic catabolism revealed multiple catabolic pathways and distinct differential catabolism of L-tryptophan under chemotropic state as compared to photo-catabolism of L-tryptophan in strain JA2.
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Affiliation(s)
- Shabbir Ahmad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Mujahid Mohammed
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.,Department of Botany, Bharathidasan Government College for Women, Muthialpet, Puducherry U.T., 605003, India
| | - Lakshmi Prasuna Mekala
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.,Department of Plant Science, Avvaiyar Government College for Women, Karaikal, Puducherry- U.T., 609 602, India
| | - Rai Anusha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | | | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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An accurate and efficient method for simultaneous determination of 16 trichothecenes in maize and wheat by UHPLC-Q-Orbitrap-HRMS combined one-step pretreatment with a novel isotope multipoint calibration strategy. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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3
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A novel method combining stable isotopic labeling and high-resolution mass spectrometry to trace the quinone reaction products in wines. Food Chem 2022; 383:132448. [DOI: 10.1016/j.foodchem.2022.132448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022]
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Butin N, Bergès C, Portais JC, Bellvert F. An optimization method for untargeted MS-based isotopic tracing investigations of metabolism. Metabolomics 2022; 18:41. [PMID: 35713733 PMCID: PMC9205802 DOI: 10.1007/s11306-022-01897-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Stable isotope tracer studies are increasingly applied to explore metabolism from the detailed analysis of tracer incorporation into metabolites. Untargeted LC/MS approaches have recently emerged and provide potent methods for expanding the dimension and complexity of the metabolic networks that can be investigated. A number of software tools have been developed to process the highly complex MS data collected in such studies; however, a method to optimize the extraction of valuable isotopic data is lacking. OBJECTIVES To develop and validate a method to optimize automated data processing for untargeted MS-based isotopic tracing investigations of metabolism. METHODS The method is based on the application of a suitable reference material to rationally perform parameter optimization throughout the complete data processing workflow. It was applied in the context of 13C-labelling experiments and with two different software, namely geoRge and X13CMS. It was illustrated with the study of a E. coli mutant impaired for central metabolism. RESULTS The optimization methodology provided significant gain in the number and quality of extracted isotopic data, independently of the software considered. Pascal triangle samples are well suited for such purpose since they allow both the identification of analytical issues and optimization of data processing at the same time. CONCLUSION The proposed method maximizes the biological value of untargeted MS-based isotopic tracing investigations by revealing the full metabolic information that is encoded in the labelling patterns of metabolites.
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Affiliation(s)
- Noémie Butin
- RESTORE, CNRS ERL5311, EFS, ENVT, Inserm U1031, UPS, Université de Toulouse, Toulouse, France
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Cécilia Bergès
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Jean-Charles Portais
- RESTORE, CNRS ERL5311, EFS, ENVT, Inserm U1031, UPS, Université de Toulouse, Toulouse, France
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Floriant Bellvert
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France.
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.
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Hilgers R, Bijlsma J, Malacaria L, Vincken JP, Furia E, de Bruijn WJC. Transition metal cations catalyze 16O/ 18O exchange of catechol motifs with H 218O. Org Biomol Chem 2022; 20:9093-9097. [DOI: 10.1039/d2ob01884e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the presence of Fe(iii) and several other cations, catechol motifs undergo rapid 16O/18O exchange with H218O under mild conditions. This opens up synthetic possibilities and may have implications for studies using H218O as a mechanistic probe.
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Affiliation(s)
- Roelant Hilgers
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Judith Bijlsma
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Luana Malacaria
- Dipartimento di Chimica e Tecnologie Chimiche, Via P. Bucci, Cubo 12/D, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Emilia Furia
- Dipartimento di Chimica e Tecnologie Chimiche, Via P. Bucci, Cubo 12/D, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Wouter J. C. de Bruijn
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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Flasch M, Bueschl C, Del Favero G, Adam G, Schuhmacher R, Marko D, Warth B. Elucidation of xenoestrogen metabolism by non-targeted, stable isotope-assisted mass spectrometry in breast cancer cells. ENVIRONMENT INTERNATIONAL 2022; 158:106940. [PMID: 34673318 DOI: 10.1016/j.envint.2021.106940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Environmental exposure to xenoestrogens, i.e., chemicals that imitate the hormone 17β-estradiol, has the potential to influence hormone homeostasis and action. Detailed knowledge of xenobiotic biotransformation processes in cell models is key when transferring knowledge learned from in vitro models to in vivo relevance. This study elucidated the metabolism of two naturally-occurring phyto- and mycoestrogens; namely genistein and zearalenone, in an estrogen receptor positive breast cancer cell line (MCF-7) with the aid of stable isotope-assisted metabolomics and the bioinformatic tool MetExtract II. Metabolism was studied in a time course experiment after 2 h, 6 h and 24 h incubation. Twelve and six biotransformation products of zearalenone and genistein were detected, respectively, clearly demonstrating the abundant xenobiotic biotransformation capability of the cells. Zearalenone underwent extensive phase-I metabolism resulting in α-zearalenol (α-ZEL), a molecule known to possess a significantly higher estrogenicity, and several phase-II metabolites (sulfo- and glycoconjugates) of the native compound and the major phase I metabolite α-ZEL. Moreover, potential adducts of zearalenone with a vitamin and several hydroxylated metabolites were annotated. Genistein metabolism resulted in sulfation, combined sulfation and hydroxylation, acetylation, glucuronidation and unexpectedly adduct formation with pentose- and hexose sugars. Kinetics of metabolite formation and subsequent excretion into the extracellular medium revealed a time-dependent increase in most biotransformation products. The untargeted elucidation of biotransformation products formed during cell culture experiments enables an improved and more meaningful interpretation of toxicological assays and has the potential to identify unexpected or unknown metabolites.
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Affiliation(s)
- Mira Flasch
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria
| | - Christoph Bueschl
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Str. 20, 3430 Tulln, Austria; University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Giorgia Del Favero
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria
| | - Gerhard Adam
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad-Lorenz-Str. 24, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Doris Marko
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria.
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7
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Dong Y, Feldberg L, Rogachev I, Aharoni A. Characterization of the PRODUCTION of ANTHOCYANIN PIGMENT 1 Arabidopsis dominant mutant using DLEMMA dual isotope labeling approach. PHYTOCHEMISTRY 2021; 186:112740. [PMID: 33770716 DOI: 10.1016/j.phytochem.2021.112740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Stable isotope labeling has emerged as a valuable tool for metabolite identification and quantification. In this study, we employed DLEMMA, a dual stable isotope labeling approach to identify and track phenylpropanoid pathway in Arabidopsis thaliana. Three forms of phenylalanine (Phe), including unlabeled, Phe13C6 and Phe13C62H5, were used as feeding precursors. The unique isotopic pattern obtained from MS spectra significantly simplified data processing and facilitated global mining of Phe-derived metabolites. Following this approach, we have identified 35 phenylalanine-derived metabolites with high confidence. We next compared phenylpropanoids contents between leaves of wild type (WT) and the dominant PRODUCTION OF ANTHOCYANIN PIGMENT 1 (pap1-D) Arabidopsis thaliana mutant using a combined sample matrices and label-swap approach. This approach was designed to correct any unequal matrix effects between the two divergent samples, and any possible uneven label incorporation efficiency between the two differently labeled Phe precursors. Thirty of the 35 identified metabolites were found differential between WT and pap1-D leaves. Our results shown that the ectopic PAP1 expression led to significant accumulation of cyanidin-type anthocyanins, quercetin-type flavonols and hydroxycinnamic acids and their glycosylated derivatives. While levels of kaempferol glycosides and a hydroxycinnamic acid amide were reduced in the pap1-D leaves.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, 7410001, Israel
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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Metabolic Profiling by UPLC-Orbitrap-MS/MS of Liver from C57BL/6 Mice with DSS-Induced Inflammatory Bowel Disease. Mediators Inflamm 2020; 2020:6020247. [PMID: 33029104 PMCID: PMC7530511 DOI: 10.1155/2020/6020247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Liver disorder often occurs in patients with inflammatory bowel disease (IBD); however, the changes in IBD-induced liver disorder at the intrinsic molecular level (chiefly metabolites) and therapeutic targets are still poorly characterized. First, a refined and translationally relevant model of DSS chronic colitis in C57BL/6 mice was established, and cecropin A and antibiotics were used as interventions. We found that the levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6 in the liver tissues of mice were highly increased in the context of DSS treatment but were lowered by cecropin A and antibiotics. Subsequently, an untargeted metabolomics analysis was performed by UPLC–Orbitrap–MS/MS to reveal the metabolic profile and attempt to find the potential therapeutic targets of the liver disorders that occur in IBD. Notably, 133 metabolites were identified by an integrated database. Metabolism network and pathway analyses demonstrated that the metabolic disturbance of the liver in IBD mice was mainly enriched in bile acid metabolism, arachidonic acid metabolism, amino acid metabolism, and steroid hormone biosynthesis, while those disturbances were regulated or reversed through cecropin A and antibiotic treatment. Furthermore, the top 20 metabolites, such as glutathione, maltose, arachidonic acid, and thiamine, were screened as biomarkers via one-way analysis of variance (one-way ANOVA, p < 0.05) coupled with variable importance for project values (VIP >1) of orthogonal partial least-squares discriminant analysis (OPLS-DA), which could be upregulated or downregulated with the cecropin A and antibiotics treatment. Spearman correlation analysis showed that the majority of the biomarkers have a significant correlation with cytokines (TNF-α, IL-1β, IL-6, and IL-10), indicating that those biomarkers may act as potential targets to interact directly or indirectly with cecropin A and antibiotics to affect liver inflammation. Collectively, our results extend the understanding of the molecular alteration of liver disorders occurring in IBD and offer an opportunity for discovering potential therapeutic targets in the IBD process.
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Otaru S, Niemikoski H, Sarparanta M, Airaksinen AJ. Metabolism of a Bioorthogonal PET Tracer Candidate [ 19F/ 18F]SiFA-Tetrazine in Mouse Liver Microsomes: Biotransformation Pathways and Defluorination Investigated by UHPLC-HRMS. Mol Pharm 2020; 17:3106-3115. [PMID: 32539414 PMCID: PMC7497667 DOI: 10.1021/acs.molpharmaceut.0c00523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Organofluorosilicon based 18F-radiolabeling is an efficient
method for incorporating fluorine-18 into 18F-radiopharmaceuticals
for positron emission tomography (PET) by 19F/18F isotopic exchange (IE). The first PET radiopharmaceutical, 18F-SiFAlin-TATE, radiolabeled with a silicon-based
[18F]fluoride acceptor (SiFA), namely, a para-substituted
di-tert-butyl[18F]fluorosilylbenzene,
has entered clinical trials, and is paving the way for other potential
[18F]SiFA-labeled radiopharmaceuticals for diagnostic use.
In this study, we report the in vitro metabolism
of an oxime-linked SiFA tetrazine (SiFA–Tz), a new PET-radiotracer
candidate, recently evaluated for pretargeted PET imaging and macromolecule
labeling. Metabolism of SiFA–Tz was studied in mouse liver
microsomes (MLM) for elucidating its major biotransformation pathways.
Nontargeted screening by ultrahigh performance liquid chromatography
high-resolution mass spectrometry (UHPLC-HRMS) was utilized for detection
of unknown metabolites. The oxime bond between the SiFA and Tz groups
forms two geometric (E/Z) isomers,
which underwent the same biotransformations, but unexpectedly with
different kinetics. In total, nine proposed metabolites of SiFA–Tz
from phase I and II reactions were detected, five of which were defluorinated
in MLMs, elucidating the metabolic pathway leading to previously reported
defluorination of [18F]SiFA–Tz in vivo. Based on the HRMS studies a biotransformation pathway is proposed:
hydroxylation (+O) to tert-butyl group adjacent to
the silicon, followed by oxidative defluorination (+OH/-F) cleaving
the fluorine off the silicon. Interestingly, eight proposed metabolites
of a reduced dihydrotetrazine analogue, SiFA–H2Tz,
from phase I and II reactions were additionally detected. To the best
of our knowledge, this is the first reported comprehensive investigation
of enzyme mediated metabolic pathway of tetrazines and para-substituted
di-tert-butylfluorosilylbenzene fluoride acceptors,
providing novel structural information on the biotransformation and
fragmentation patterns of radiotracers bearing these structural motifs.
By investigating the metabolism preceding defluorination, structurally
optimized new SiFA compounds can be designed for expanding the portfolio
of efficient 19F/18F isotopic exchange labeling
probes for PET imaging.
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Affiliation(s)
- Sofia Otaru
- Radiochemistry, Department of Chemistry, University of Helsinki, 00014 Helsinki, Finland
| | - Hanna Niemikoski
- Finnish Institute for Verification of the Chemical Weapons Convention (VERIFIN), Department of Chemistry, University of Helsinki, 00014 Helsinki, Finland
| | - Mirkka Sarparanta
- Radiochemistry, Department of Chemistry, University of Helsinki, 00014 Helsinki, Finland
| | - Anu J Airaksinen
- Radiochemistry, Department of Chemistry, University of Helsinki, 00014 Helsinki, Finland.,Turku PET Centre, Department of Chemistry, University of Turku, 20500 Turku, Finland
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Stadler D, Berthiller F, Suman M, Schuhmacher R, Krska R. Novel analytical methods to study the fate of mycotoxins during thermal food processing. Anal Bioanal Chem 2020; 412:9-16. [PMID: 31637463 PMCID: PMC6989622 DOI: 10.1007/s00216-019-02101-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/07/2019] [Accepted: 08/23/2019] [Indexed: 11/25/2022]
Abstract
Food processing can lead to a reduction of contaminants, such as mycotoxins. However, for food processing operations where thermal energy is employed, it is often not clear whether a reduction of mycotoxins also results in a mitigation of the toxicological impact. This is often due to the reason that the formed degradation products are not characterized and data on their toxicity is scarce. From the perspective of an analytical chemist, the elucidation of the fate of a contaminant in a complex food matrix is extremely challenging. An overview of the analytical approaches is given here, and the application and limitations are exemplified based on cases that can be found in recent literature. As most studies rely on targeted analysis, it is not clear whether the predetermined set of compounds differs from the degradation products that are actually formed during food processing. Although untargeted analysis allows for the elucidation of the complete spectrum of degradation products, only one such study is available so far. Further pitfalls include insufficient precision, natural contamination with masked forms of mycotoxins and interferences that are caused by the food matrix. One topic that is of paramount importance for both targeted and untargeted approaches is the availability of reference standards to identity and quantity the formed degradation products. Our vision is that more studies need to be published that characterize the formed degradation products, collect data on their toxicity and thereby complete the knowledge about the mycotoxin mitigating effect during food processing.
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Affiliation(s)
- David Stadler
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Franz Berthiller
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Michele Suman
- Barilla G. R. F.lli SpA, Advanced Laboratory Research, Via Mantova 166, 43122, Parma, Italy
| | - Rainer Schuhmacher
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Rudolf Krska
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, University Road, Belfast, Northern Ireland, BT7 1NN, UK.
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11
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Doppler M, Kluger B, Bueschl C, Steiner B, Buerstmayr H, Lemmens M, Krska R, Adam G, Schuhmacher R. Stable Isotope-Assisted Plant Metabolomics: Investigation of Phenylalanine-Related Metabolic Response in Wheat Upon Treatment With the Fusarium Virulence Factor Deoxynivalenol. FRONTIERS IN PLANT SCIENCE 2019; 10:1137. [PMID: 31736983 PMCID: PMC6831647 DOI: 10.3389/fpls.2019.01137] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/20/2019] [Indexed: 05/03/2023]
Abstract
The major Fusarium mycotoxin deoxynivalenol (DON) is a virulence factor in wheat and has also been shown to induce defense responses in host plant tissue. In this study, global and tracer labeling with 13C were combined to annotate the overall metabolome of wheat spikes and to evaluate the response of phenylalanine-related pathways upon treatment with DON. At anthesis, spikes of resistant and susceptible cultivars as well as two related near isogenic wheat lines (NILs) differing in the presence/absence of the major resistance QTL Fhb1 were treated with 1 mg DON or water (control), and samples were collected at 0, 12, 24, 48, and 96 h after treatment (hat). A total of 172 Phe-derived wheat constituents were detected with our untargeted approach employing 13C-labeled phenylalanine and subsequently annotated as flavonoids, lignans, coumarins, benzoic acid derivatives, hydroxycinnamic acid amides (HCAAs), as well as peptides. Ninety-six hours after the DON treatment, up to 30% of the metabolites biosynthesized from Phe showed significantly increased levels compared to the control samples. Major metabolic changes included the formation of precursors of compounds implicated in cell wall reinforcement and presumed antifungal compounds. In addition, also dipeptides, which presumably are products of proteolytic degradation of truncated proteins generated in the presence of the toxin, were significantly more abundant upon DON treatment. An in-depth comparison of the two NILs with correlation clustering of time course profiles revealed some 70 DON-responsive Phe derivatives. While several flavonoids had constitutively different abundance levels between the two NILs differing in resistance, other Phe-derived metabolites such as HCAAs and hydroxycinnamoyl quinates were affected differently in the two NILs after treatment with DON. Our results suggest a strong activation of the general phenylpropanoid pathway and that coumaroyl-CoA is mainly diverted towards HCAAs in the presence of Fhb1, whereas the metabolic route to monolignol(-conjugates), lignans, and lignin seems to be favored in the absence of the Fhb1 resistance quantitative trait loci.
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Affiliation(s)
- Maria Doppler
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Christoph Bueschl
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Barbara Steiner
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Marc Lemmens
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rudolf Krska
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
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12
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Doppler M, Bueschl C, Kluger B, Koutnik A, Lemmens M, Buerstmayr H, Rechthaler J, Krska R, Adam G, Schuhmacher R. Stable Isotope-Assisted Plant Metabolomics: Combination of Global and Tracer-Based Labeling for Enhanced Untargeted Profiling and Compound Annotation. FRONTIERS IN PLANT SCIENCE 2019; 10:1366. [PMID: 31708958 PMCID: PMC6824187 DOI: 10.3389/fpls.2019.01366] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/04/2019] [Indexed: 05/10/2023]
Abstract
Untargeted approaches and thus biological interpretation of metabolomics results are still hampered by the reliable assignment of the global metabolome as well as classification and (putative) identification of metabolites. In this work we present an liquid chromatography-mass spectrometry (LC-MS)-based stable isotope assisted approach that combines global metabolome and tracer based isotope labeling for improved characterization of (unknown) metabolites and their classification into tracer derived submetabolomes. To this end, wheat plants were cultivated in a customized growth chamber, which was kept at 400 ± 50 ppm 13CO2 to produce highly enriched uniformly 13C-labeled sample material. Additionally, native plants were grown in the greenhouse and treated with either 13C9-labeled phenylalanine (Phe) or 13C11-labeled tryptophan (Trp) to study their metabolism and biochemical pathways. After sample preparation, liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis and automated data evaluation, the results of the global metabolome- and tracer-labeling approaches were combined. A total of 1,729 plant metabolites were detected out of which 122 respective 58 metabolites account for the Phe- and Trp-derived submetabolomes. Besides m/z and retention time, also the total number of carbon atoms as well as those of the incorporated tracer moieties were obtained for the detected metabolite ions. With this information at hand characterization of unknown compounds was improved as the additional knowledge from the tracer approaches considerably reduced the number of plausible sum formulas and structures of the detected metabolites. Finally, the number of putative structure formulas was further reduced by isotope-assisted annotation tandem mass spectrometry (MS/MS) derived product ion spectra of the detected metabolites. A major innovation of this paper is the classification of the metabolites into submetabolomes which turned out to be valuable information for effective filtering of database hits based on characteristic structural subparts. This allows the generation of a final list of true plant metabolites, which can be characterized at different levels of specificity.
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Affiliation(s)
- Maria Doppler
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Christoph Bueschl
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Andrea Koutnik
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Marc Lemmens
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Justyna Rechthaler
- University of Applied Sciences Wr. Neustadt, Degree Programme Biotechnical Processes (FHWN-Tulln), Tulln, Austria
| | - Rudolf Krska
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
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13
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Slobodchikova I, Sivakumar R, Rahman MS, Vuckovic D. Characterization of Phase I and Glucuronide Phase II Metabolites of 17 Mycotoxins Using Liquid Chromatography-High-Resolution Mass Spectrometry. Toxins (Basel) 2019; 11:E433. [PMID: 31344861 PMCID: PMC6723440 DOI: 10.3390/toxins11080433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Routine mycotoxin biomonitoring methods do not include many mycotoxin phase I and phase II metabolites, which may significantly underestimate mycotoxin exposure especially for heavily metabolized mycotoxins. Additional research efforts are also needed to measure metabolites in vivo after exposure and to establish which mycotoxin metabolites should be prioritized for the inclusion during large-scale biomonitoring efforts. The objective of this study was to perform human in vitro microsomal incubations of 17 mycotoxins and systematically characterize all resulting metabolites using liquid chromatography-high-resolution mass spectrometry (LC-HRMS). The results obtained were then used to build a comprehensive LC-MS library and expand a validated 17-mycotoxin method for exposure monitoring to screening of additional 188 metabolites, including 100 metabolites reported for the first time. The final method represents one of the most comprehensive LC-HRMS methods for mycotoxin biomonitoring or metabolism/fate studies.
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Affiliation(s)
- Irina Slobodchikova
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
- Centre for Biological Applications of Mass Spectrometry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
| | - Reajean Sivakumar
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
| | - Md Samiur Rahman
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
| | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada.
- Centre for Biological Applications of Mass Spectrometry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada.
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14
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Tracing oxidation reaction pathways in wine using 13C isotopolog patterns and a putative compound database. Anal Chim Acta 2019; 1054:74-83. [DOI: 10.1016/j.aca.2018.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 11/21/2022]
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15
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Grankvist N, Watrous JD, Lagerborg KA, Lyutvinskiy Y, Jain M, Nilsson R. Profiling the Metabolism of Human Cells by Deep 13C Labeling. Cell Chem Biol 2018; 25:1419-1427.e4. [PMID: 30270114 DOI: 10.1016/j.chembiol.2018.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/15/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022]
Abstract
Studying metabolic activities in living cells is crucial for understanding human metabolism, but facile methods for profiling metabolic activities in an unbiased, hypothesis-free manner are still lacking. To address this need, we here introduce the deep-labeling method, which combines a custom 13C medium with high-resolution mass spectrometry. A proof-of-principle study on human cancer cells demonstrates that deep labeling can identify hundreds of endogenous metabolites as well as active and inactive pathways. For example, protein and nucleic acids were almost exclusively de novo synthesized, while lipids were partly derived from serum; synthesis of cysteine, carnitine, and creatine was absent, suggesting metabolic dependencies; and branched-chain keto acids (BCKAs) were formed and metabolized to short-chain acylcarnitines, but did not enter the tricarboxylic acid cycle. Remarkably, BCKAs could substitute for essential amino acids to support growth. The deep-labeling method may prove useful to map metabolic phenotypes across a range of cell types and conditions.
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Affiliation(s)
- Nina Grankvist
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm 171 76, Sweden; Karolinska University Hospital, Stockholm 171 76, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Jeramie D Watrous
- Departments of Medicine and Pharmacology, University of California, San Diego; 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kim A Lagerborg
- Departments of Medicine and Pharmacology, University of California, San Diego; 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yaroslav Lyutvinskiy
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm 171 76, Sweden; Karolinska University Hospital, Stockholm 171 76, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California, San Diego; 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Roland Nilsson
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm 171 76, Sweden; Karolinska University Hospital, Stockholm 171 76, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 76, Sweden.
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16
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Takahashi M, Izumi Y, Iwahashi F, Nakayama Y, Iwakoshi M, Nakao M, Yamato S, Fukusaki E, Bamba T. Highly Accurate Detection and Identification Methodology of Xenobiotic Metabolites Using Stable Isotope Labeling, Data Mining Techniques, and Time-Dependent Profiling Based on LC/HRMS/MS. Anal Chem 2018; 90:9068-9076. [DOI: 10.1021/acs.analchem.8b01388] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Masatomo Takahashi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Izumi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Fukumatsu Iwahashi
- Health & Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 4-2-1 Takatsukasa, Takarazuka, Hyogo 665-8555, Japan
| | - Yasumune Nakayama
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Mitsuhiko Iwakoshi
- Health & Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 4-2-1 Takatsukasa, Takarazuka, Hyogo 665-8555, Japan
| | - Motonao Nakao
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Seiji Yamato
- Health & Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 4-2-1 Takatsukasa, Takarazuka, Hyogo 665-8555, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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17
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HPLC-high-resolution mass spectrometry with polarity switching for increasing throughput of human in vitro cocktail drug-drug interaction assay. Bioanalysis 2018; 10:659-671. [PMID: 29749249 DOI: 10.4155/bio-2018-0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
AIM Evaluation of HPLC-high-resolution mass spectrometry (HPLC-HRMS) full scan with polarity switching for increasing throughput of human in vitro cocktail drug-drug interaction assay. MATERIALS & METHODS Microsomal incubates were analyzed using a high resolution and high mass accuracy Q-Exactive mass spectrometer to collect integrated qualitative and quantitative (qual/quant) data. RESULTS Within assay, positive-to-negative polarity switching HPLC-HRMS method allowed quantification of eight and two probe compounds in the positive and negative ionization modes, respectively, while monitoring for LOR and its metabolites. CONCLUSION LOR-inhibited CYP2C19 and showed higher activity for CYP2D6, CYP2E1 and CYP3A4. Overall, LC-HRMS-based nontargeted full scan quantitation allowed to improve the throughput of the in vitro cocktail drug-drug interaction assay.
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18
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Tian Z, Vila J, Yu M, Bodnar W, Aitken MD. Tracing the Biotransformation of Polycyclic Aromatic Hydrocarbons in Contaminated Soil Using Stable Isotope-Assisted Metabolomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2018; 5:103-109. [PMID: 31572742 PMCID: PMC6767928 DOI: 10.1021/acs.estlett.7b00554] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Biotransformation of organic pollutants may result in the formation of oxidation products more toxic than the parent contaminants. However, to trace and identify those products, and the metabolic pathways involved in their formation, is still challenging within complex environmental samples. We applied stable isotope-assisted metabolomics (SIAM) to PAH-contaminated soil collected from a wood treatment facility. Soil samples were separately spiked with uniformly 13C-labeled fluoranthene, pyrene, or benzo[a]anthracene at a level below that of the native contaminant, and incubated for 1 or 2 weeks under aerobic biostimulated conditions. Combining high-resolution mass spectrometry and automated SIAM workflows, chemical structures of metabolites and metabolic pathways in the soil were proposed. Ring-cleavage products, including previously unreported intermediates such as C11H10O6 and C15H12O5, were detected originating from fluoranthene and benzo[a]anthracene, respectively. Sulfate conjugates of dihydroxy compounds were found as major metabolites of pyrene and benzo[a]anthracene, suggesting the potential role of fungi in their biotransformation in soils. A series of unknown N-containing metabolites were identified from pyrene, but their structural elucidation requires further investigation. Our results suggest that SIAM can be successfully applied to understand the fate of organic pollutants in environmental samples, opening lines of evidence for novel mechanisms of microbial transformation within such complex matrices.
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Affiliation(s)
- Zhenyu Tian
- Department of Environmental Sciences and
Engineering, Gillings School of Global Public Health, University of North Carolina
at Chapel Hill, CB 7431, Chapel Hill, NC 27599-7431 USA
| | - Joaquim Vila
- Department of Environmental Sciences and
Engineering, Gillings School of Global Public Health, University of North Carolina
at Chapel Hill, CB 7431, Chapel Hill, NC 27599-7431 USA
| | - Miao Yu
- Department of Chemistry, University of Waterloo,
Waterloo, Ontario, Canada N2L 3G1
| | - Wanda Bodnar
- Department of Environmental Sciences and
Engineering, Gillings School of Global Public Health, University of North Carolina
at Chapel Hill, CB 7431, Chapel Hill, NC 27599-7431 USA
| | - Michael D. Aitken
- Department of Environmental Sciences and
Engineering, Gillings School of Global Public Health, University of North Carolina
at Chapel Hill, CB 7431, Chapel Hill, NC 27599-7431 USA
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19
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Mekala LP, Mohammed M, Chintalapati S, Chintalapati VR. Stable Isotope-Assisted Metabolic Profiling Reveals Growth Mode Dependent Differential Metabolism and Multiple Catabolic Pathways of l-Phenylalanine in Rubrivivax benzoatilyticus JA2. J Proteome Res 2017; 17:189-202. [PMID: 29043820 DOI: 10.1021/acs.jproteome.7b00500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anoxygenic phototrophic bacteria are metabolically versatile and survive under different growth modes using diverse organic compounds, yet their metabolic diversity is largely unexplored. In the present study, we employed stable-isotope-assisted metabolic profiling to unravel the l-phenylalanine catabolism in Rubrivivax benzoatilyticus JA2 under varying growth modes. Strain JA2 grows under anaerobic and aerobic conditions by utilizing l-phenylalanine as a nitrogen source. Furthermore, ring-labeled 13C6-phenylalanine feeding followed by liquid chromatography-mass spectrometry exometabolite profiling revealed 60 labeled metabolic features (M + 6, M + 12, and M + 18) derived solely from l-phenylalanine, of which 11 were identified, 7 putatively identified, and 42 unidentified under anaerobic and aerobic conditions. However, labeled metabolites were significantly higher in aerobic compared to anaerobic conditions. Furthermore, detected metabolites and enzyme activities indicated multiple l-phenylalanine catabolic routes mainly Ehrlich, homogentisate-dependent melanin, benzenoid, and unidentified pathways operating under anaerobic and aerobic conditions in strain JA2. Interestingly, the study indicated l-phenylalanine-dependent and independent benzenoid biosynthesis in strain JA2 and a differential flux of l-phenylalanine to Ehrlich and benzenoid pathways under anaerobic and aerobic conditions. Additionally, unidentified labeled metabolites strongly suggest the presence of unknown phenylalanine catabolic routes in strain JA2. Overall, the study uncovered the l-phenylalanine catabolic diversity in strain JA2 and demonstrated the potential of stable isotope-assisted metabolomics in unraveling the hidden metabolic repertoire.
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Affiliation(s)
- Lakshmi Prasuna Mekala
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad , P.O. Central University, Hyderabad 500 046, India
| | - Mujahid Mohammed
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad , P.O. Central University, Hyderabad 500 046, India
| | - Sasikala Chintalapati
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science & Technology, Jawaharlal Nehru Technological University , Kukatpally, Hyderabad 500 085, Telangana, India
| | - Venkata Ramana Chintalapati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad , P.O. Central University, Hyderabad 500 046, India
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20
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Bueschl C, Kluger B, Neumann NKN, Doppler M, Maschietto V, Thallinger GG, Meng-Reiterer J, Krska R, Schuhmacher R. MetExtract II: A Software Suite for Stable Isotope-Assisted Untargeted Metabolomics. Anal Chem 2017; 89:9518-9526. [PMID: 28787149 PMCID: PMC5588095 DOI: 10.1021/acs.analchem.7b02518] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Stable
isotope labeling (SIL) techniques have the potential to
enhance different aspects of liquid chromatography–high-resolution
mass spectrometry (LC-HRMS)-based untargeted metabolomics methods
including metabolite detection, annotation of unknown metabolites,
and comparative quantification. In this work, we present MetExtract
II, a software toolbox for detection of biologically derived compounds.
It exploits SIL-specific isotope patterns and elution profiles in
LC-HRMS(/MS) data. The toolbox consists of three complementary modules:
M1 (AllExtract) uses mixtures of uniformly highly isotope-enriched
and native biological samples for selective detection of the entire
accessible metabolome. M2 (TracExtract) is particularly suited to
probe the metabolism of endogenous or exogenous secondary metabolites
and facilitates the untargeted screening of tracer derivatives from
concurrently metabolized native and uniformly labeled tracer substances.
With M3 (FragExtract), tandem mass spectrometry (MS/MS) fragments
of corresponding native and uniformly labeled ions are evaluated and
automatically assigned with putative sum formulas. Generated results
can be graphically illustrated and exported as a comprehensive data
matrix that contains all detected pairs of native and labeled metabolite
ions that can be used for database queries, metabolome-wide internal
standardization, and statistical analysis. The software, associated
documentation, and sample data sets are freely available for noncommercial
use at http://metabolomics-ifa.boku.ac.at/metextractII.
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Affiliation(s)
- Christoph Bueschl
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
| | - Bernhard Kluger
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
| | - Nora K N Neumann
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
| | - Maria Doppler
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
| | - Valentina Maschietto
- Department of Sustainable Crop Production, School of Agriculture, Università Cattolica del Sacro Cuore , 29100 Piacenza, Italy
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology , 8010 Graz, Austria.,Omics Center Graz, BioTechMed Graz , 8010 Graz, Austria
| | - Jacqueline Meng-Reiterer
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria.,Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
| | - Rudolf Krska
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna , 1180 Vienna, Austria
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21
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Chen Y, Zhou Z, Yang W, Bi N, Xu J, He J, Zhang R, Wang L, Abliz Z. Development of a Data-Independent Targeted Metabolomics Method for Relative Quantification Using Liquid Chromatography Coupled with Tandem Mass Spectrometry. Anal Chem 2017; 89:6954-6962. [PMID: 28574715 DOI: 10.1021/acs.analchem.6b04727] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quantitative metabolomics approaches can significantly improve the repeatability and reliability of metabolomics investigations but face critical technical challenges, owing to the vast number of unknown endogenous metabolites and the lack of authentic standards. The present study contributes to the development of a novel method known as "data-independent targeted quantitative metabolomics" (DITQM), which was used to investigate the label-free quantitative metabolomics of multiple known and unknown metabolites in biofluid samples. This approach initially involved the acquisition of MS/MS data for all metabolites in biosamples using a sequentially stepped targeted MS/MS (sst-MS/MS) method, in which multiple product ion scans were performed by selecting all ions in the targeted mass ranges as the precursor ions. Subsequently, scheduled multiple reaction monitoring (MRM) by LC-MS/MS of the metabolome was established for 1658 characteristic ion pairs of 1324 metabolites. For sensitive and accurate quantification of these metabolites, mixed calibration curves were generated using sequentially diluted standard reference plasma samples using established MRM methods. Relative concentrations of all metabolites in each sample were calculated without using individual authentic standards. To evaluate the reliability and applicability of this new method, the performance of DITQM was validated by comparison to absolute quantification of 12 acylcarnitines using authentic standards and traditional metabolomics analysis for lung cancer. The results proved that the DITQM protocol is more reliable and can significantly improve clustering effects and repeatability in biomarker discovery. In this study, we established a novel methodology to standardize and quantify large-scale metabolome, providing a new choice for metabolomics research and its clinical applications.
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Affiliation(s)
- Yanhua Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China
| | - Zhi Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China
| | - Wei Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China.,Center for DMPK Research of Herbal Medicines, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing 100700, P. R. China
| | - Nan Bi
- Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100021, P. R. China
| | - Jing Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China
| | - Lvhua Wang
- Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100021, P. R. China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, P. R. China.,Centre for Bioimaging & Systems Biology, Minzu University of China , Beijing 100081, P. R. China
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22
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Amaral ACF, Ramos ADS, Ferreira JLP, Santos ARD, Cruz JDD, Luna AVMD, Nery VVC, Lima ICD, Chaves MHDC, Silva JRDA. LC‐HRMS for the Identification of β‐Carboline and Canthinone Alkaloids Isolated from Natural Sources. Mass Spectrom (Tokyo) 2017. [DOI: 10.5772/68075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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23
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Leeming MG, Donald WA, O'Hair RAJ. Nontargeted Identification of Reactive Metabolite Protein Adducts. Anal Chem 2017; 89:5748-5756. [PMID: 28481086 DOI: 10.1021/acs.analchem.6b04604] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metabolic bioactivation of many different chemicals results in the formation of highly reactive compounds (chemically reactive metabolites, CRMs) that can lead to toxicity via binding to macromolecular targets (e.g., proteins or DNA). There is a need to develop robust, rapid, and nontargeted analytical techniques to determine the identity of the protein targets of CRMs and their sites of modification. Here, we introduce a nontargeted methodology capable of determining both the identity of a CRM formed from an administered compound as well as the protein targets modified by the reactive metabolite in a single experiment without prior information. Acetaminophen (N-acetyl-p-aminophenol, APAP) and 13C6-APAP were incubated with rat liver microsomes, which are known to bioactivate APAP to the reactive metabolite N-acetyl-p-benzoquinone imine (NAPQI). Global tryptic digestion followed by liquid chromatographic/mass spectrometric (LC/MS) analysis was used to locate "twin" ion peaks of peptides adducted by NAPQI and for shotgun proteomics via tandem mass spectrometry (MS/MS). By the development of blended data analytics software called Xenophile, the identity of the amino acid residue that was adducted can be established, which eliminates the need for specific parametrization of protein database search algorithms. This combination of experimental design and data analysis software allows the identity of a CRM, the protein target, and the amino acid residues that are modified to be rapidly established directly from experimental data. Xenophile is freely available from https://github.com/mgleeming/Xenophile .
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Affiliation(s)
- Michael G Leeming
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne , Melbourne, Victoria 3010, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne , Melbourne, Victoria 3010, Australia
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Vrobel I, Friedecký D, Faber E, Najdekr L, Mičová K, Karlíková R, Adam T. Novel sulphur-containing imatinib metabolites found by untargeted LC-HRMS analysis. Eur J Pharm Sci 2017; 104:335-343. [PMID: 28433749 DOI: 10.1016/j.ejps.2017.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 01/28/2023]
Abstract
Untargeted metabolite profiling using high-resolution mass spectrometry coupled with liquid chromatography (LC-HRMS), followed by data analysis with the Compound Discoverer 2.0™ software, was used to study the metabolism of imatinib in humans with chronic myeloid leukemia. Plasma samples from control (drug-free) and patient (treated with imatinib) groups were analyzed in full-scan mode and the unknown ions occurring only in the patient group were then, as potential imatinib metabolites, subjected to multi-stage fragmentation in order to elucidate their structure. The application of an untargeted approach, as described in this study, enabled the detection of 24 novel structurally unexpected metabolites. Several sulphur-containing compounds, probably originating after the reaction of reactive intermediates of imatinib with endogenous glutathione, were found and annotated as cysteine and cystine adducts. In the proposed mechanism, the cysteine adducts were formed after the rearrangement of piperazine moiety to imidazoline. On the contrary, in vivo S-N exchange occurred in the case of the cystine adducts. In addition, N-O exchange was observed in the collision cell in the course of the fragmentation of the cystine adducts. The presence of sulphur in the cysteine and cystine conjugates was proved by means of ultra-high resolution measurements using Orbitrap Elite. The detection of metabolites derived from glutathione might improve knowledge about the disposition of imatinib towards bioactivation and help to improve understanding of the mechanism of its hepatotoxicity or nephrotoxicity in humans.
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Affiliation(s)
- Ivo Vrobel
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; Department of Clinical Biochemistry, University Hospital Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic
| | - David Friedecký
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; Laboratory for Inherited Metabolic Disorders, Faculty of Medicine and Dentistry, Palacký University Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic; Department of Clinical Biochemistry, University Hospital Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic.
| | - Edgar Faber
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacký University Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic
| | - Lukáš Najdekr
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; Department of Clinical Biochemistry, University Hospital Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic
| | - Kateřina Mičová
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; Department of Clinical Biochemistry, University Hospital Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic
| | - Radana Karlíková
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; Department of Clinical Biochemistry, University Hospital Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic
| | - Tomáš Adam
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; Laboratory for Inherited Metabolic Disorders, Faculty of Medicine and Dentistry, Palacký University Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic; Department of Clinical Biochemistry, University Hospital Olomouc, I. P. Pavlova 6, 775 20 Olomouc, Czech Republic
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25
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Breitkopf SB, Ricoult SJH, Yuan M, Xu Y, Peake DA, Manning BD, Asara JM. A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source. Metabolomics 2017; 13:30. [PMID: 28496395 PMCID: PMC5421409 DOI: 10.1007/s11306-016-1157-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/21/2016] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Advances in high-resolution mass spectrometry have created renewed interest for studying global lipid biochemistry in disease and biological systems. OBJECTIVES Here, we present an untargeted 30 min. LC-MS/MS platform that utilizes positive/negative polarity switching to perform unbiased data dependent acquisitions (DDA) via higher energy collisional dissociation (HCD) fragmentation to profile more than 1000-1500 lipid ions mainly from methyl-tert-butyl ether (MTBE) or chloroform:methanol extractions. METHODS The platform uses C18 reversed-phase chromatography coupled to a hybrid QExactive Plus/HF Orbitrap mass spectrometer and the entire procedure takes ~10 h from lipid extraction to identification/quantification for a data set containing 12 samples (~4 h for a single sample). Lipids are identified by both accurate precursor ion mass and fragmentation features and quantified using Lipid-Search and Elements software. RESULTS Using this approach, we are able to profile intact lipid ions from up to 18 different main lipid classes and 66 subclasses. We show several studies from different biological sources, including cultured cancer cells, resected tissues from mice such as lung and breast tumors and biological fluids such as plasma and urine. CONCLUSIONS Using mouse embryonic fibroblasts, we showed that TSC2-/- KD significantly abrogates lipid biosynthesis and that rapamycin can rescue triglyceride (TG) lipids and we show that SREBP-/- shuts down lipid biosynthesis significantly via mTORC1 signaling pathways. We show that in mouse EGFR driven lung tumors, a large number of TGs and phosphatidylmethanol (PMe) lipids are elevated while some phospholipids (PLs) show some of the largest decrease in lipid levels from ~ 2000 identified lipid ions. In addition, we identified more than 1500 unique lipid species from human blood plasma.
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Affiliation(s)
- Susanne B Breitkopf
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Stéphane J H Ricoult
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Min Yuan
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ying Xu
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - David A Peake
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA 95134, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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26
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Metabolism of HT-2 Toxin and T-2 Toxin in Oats. Toxins (Basel) 2016; 8:toxins8120364. [PMID: 27929394 PMCID: PMC5198558 DOI: 10.3390/toxins8120364] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/17/2016] [Accepted: 11/24/2016] [Indexed: 12/31/2022] Open
Abstract
The Fusarium mycotoxins HT-2 toxin (HT2) and T-2 toxin (T2) are frequent contaminants in oats. These toxins, but also their plant metabolites, may contribute to toxicological effects. This work describes the use of 13C-assisted liquid chromatography-high-resolution mass spectrometry for the first comprehensive study on the biotransformation of HT2 and T2 in oats. Using this approach, 16 HT2 and 17 T2 metabolites were annotated including novel glycosylated and hydroxylated forms of the toxins, hydrolysis products, and conjugates with acetic acid, putative malic acid, malonic acid, and ferulic acid. Further targeted quantitative analysis was performed to study toxin metabolism over time, as well as toxin and conjugate mobility within non-treated plant tissues. As a result, HT2-3-O-β-d-glucoside was identified as the major detoxification product of both parent toxins, which was rapidly formed (to an extent of 74% in HT2-treated and 48% in T2-treated oats within one day after treatment) and further metabolised. Mobility of the parent toxins appeared to be negligible, while HT2-3-O-β-d-glucoside was partly transported (up to approximately 4%) through panicle side branches and stem. Our findings demonstrate that the presented combination of untargeted and targeted analysis is well suited for the comprehensive elucidation of mycotoxin metabolism in plants.
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27
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Koch S, Bueschl C, Doppler M, Simader A, Meng-Reiterer J, Lemmens M, Schuhmacher R. MetMatch: A Semi-Automated Software Tool for the Comparison and Alignment of LC-HRMS Data from Different Metabolomics Experiments. Metabolites 2016; 6:metabo6040039. [PMID: 27827849 PMCID: PMC5192445 DOI: 10.3390/metabo6040039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/27/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022] Open
Abstract
Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented. The tool is implemented in the Java programming language, it features an intuitive user interface and its main goal is to facilitate the comparison of data obtained from different metabolomics experiments. Based on a feature list (i.e., processed LC-HRMS chromatograms with mass-to-charge ratio (m/z) values and retention times) that serves as a reference, the tool recognizes both m/z and retention time shifts of single or multiple analytical datafiles/batches of interest. MetMatch is also designed to account for differently formed ion species of detected metabolites. Corresponding ions and metabolites are matched and chromatographic peak areas, m/z values and retention times are combined into a single data matrix. The convenient user interface allows for easy manipulation of processing results and graphical illustration of the raw data as well as the automatically matched ions and metabolites. The software tool is exemplified with LC-HRMS data from untargeted metabolomics experiments investigating phenylalanine-derived metabolites in wheat and T-2 toxin/HT-2 toxin detoxification products in barley.
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Affiliation(s)
- Stefan Koch
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
| | - Christoph Bueschl
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
| | - Maria Doppler
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
| | - Alexandra Simader
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
| | - Jacqueline Meng-Reiterer
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
| | - Marc Lemmens
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau 3430, Austria.
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28
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Rhoades SD, Sengupta A, Weljie AM. Time is ripe: maturation of metabolomics in chronobiology. Curr Opin Biotechnol 2016; 43:70-76. [PMID: 27701007 DOI: 10.1016/j.copbio.2016.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 12/14/2022]
Abstract
Sleep and circadian rhythms studies have recently benefited from metabolomics analyses, uncovering new connections between chronobiology and metabolism. From untargeted mass spectrometry to quantitative nuclear magnetic resonance spectroscopy, a diversity of analytical approaches has been applied for biomarker discovery in the field. In this review we consider advances in the application of metabolomics technologies which have uncovered significant effects of sleep and circadian cycles on several metabolites, namely phosphatidylcholine species, medium-chain carnitines, and aromatic amino acids. Study design and data processing measures essential for detecting rhythmicity in metabolomics data are also discussed. Future developments in these technologies are anticipated vis-à-vis validating early findings, given metabolomics has only recently entered the ring with other systems biology assessments in chronometabolism studies.
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Affiliation(s)
- Seth D Rhoades
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Arjun Sengupta
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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29
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Metabolomics: Bridging the Gap between Pharmaceutical Development and Population Health. Metabolites 2016; 6:metabo6030020. [PMID: 27399792 PMCID: PMC5041119 DOI: 10.3390/metabo6030020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/06/2016] [Accepted: 07/01/2016] [Indexed: 12/28/2022] Open
Abstract
Metabolomics has emerged as an essential tool for studying metabolic processes, stratification of patients, as well as illuminating the fundamental metabolic alterations in disease onset, progression, or response to therapeutic intervention. Metabolomics materialized within the pharmaceutical industry as a standalone assay in toxicology and disease pathology and eventually evolved towards aiding in drug discovery and pre-clinical studies via supporting pharmacokinetic and pharmacodynamic characterization of a drug or a candidate. Recent progress in the field is illustrated by coining of the new term—Pharmacometabolomics. Integration of data from metabolomics with large-scale omics along with clinical, molecular, environmental and behavioral analysis has demonstrated the enhanced utility of deconstructing the complexity of health, disease, and pharmaceutical intervention(s), which further highlight it as an essential component of systems medicine. This review presents the current state and trend of metabolomics applications in pharmaceutical development, and highlights the importance and potential of clinical metabolomics as an essential part of multi-omics protocols that are directed towards shaping precision medicine and population health.
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30
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Ghaste M, Mistrik R, Shulaev V. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. Int J Mol Sci 2016; 17:ijms17060816. [PMID: 27231903 PMCID: PMC4926350 DOI: 10.3390/ijms17060816] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
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Affiliation(s)
- Manoj Ghaste
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
| | | | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
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31
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Jiang S, Liang Z, Hao L, Li L. Investigation of signaling molecules and metabolites found in crustacean hemolymph via in vivo microdialysis using a multifaceted mass spectrometric platform. Electrophoresis 2016; 37:1031-8. [PMID: 26691021 DOI: 10.1002/elps.201500497] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/06/2015] [Accepted: 12/08/2015] [Indexed: 12/24/2022]
Abstract
Neurotransmitters (NTs) are endogenous signaling molecules that play an important role in regulating various physiological processes in animals. Detection of these chemical messengers is often challenging due to their low concentration levels and fast degradation rate in vitro. In order to address these challenges, herein we employed in vivo microdialysis (MD) sampling to study NTs in the crustacean model Cancer borealis. Multifaceted separation tools, such as CE and ion mobility mass spectrometry (MS) were utilized in this work. Small molecules were separated by different mechanisms and detected by MALDI mass spectrometric imaging (MALDI-MSI). Performance of this separation-based MSI platform was also compared to LC-ESI-MS. By utilizing both MALDI and ESI-MS, a total of 208 small molecule NTs and metabolites were identified, of which 39 were identified as signaling molecules secreted in vivo. In addition, the inherent property of sub microscale sample consumption using CE enables shorter time of MD sample collection. Temporal resolution of MD was improved by approximately tenfold compared to LC-ESI-MS, indicating the significant advantage of applying separation-assisted MALDI-MS imaging platform.
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Affiliation(s)
- Shan Jiang
- School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Zhidan Liang
- School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, WI, USA.,Department of Chemistry, University of Wisconsin, Madison, WI, USA.,School of Life Sciences, Tianjin University, Nankai District, Tianjin, P. R. China
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32
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Berthiller F, Brera C, Crews C, Iha M, Krska R, Lattanzio V, MacDonald S, Malone R, Maragos C, Solfrizzo M, Stroka J, Whitaker T. Developments in mycotoxin analysis: an update for 2014-2015. WORLD MYCOTOXIN J 2016. [DOI: 10.3920/wmj2015.1998] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This review summarises developments in the determination of mycotoxins over a period between mid-2014 and mid-2015. In tradition with previous articles of this series, analytical methods to determine aflatoxins, Alternaria toxins, ergot alkaloids, fumonisins, ochratoxins, patulin, trichothecenes and zearalenone are covered in individual sections. Advances in proper sampling strategies are discussed in a dedicated section, as are new methods used to analyse botanicals and spices and newly developed LC-MS based multi-mycotoxin methods. The critical review aims to briefly discuss the most important developments and trends in mycotoxin determination as well as to address shortcomings of current methodologies.
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Affiliation(s)
- F. Berthiller
- Christian Doppler Laboratory for Mycotoxin Metabolism and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad Lorenz Str. 20, 3430 Vienna, Austria
| | - C. Brera
- Department of Veterinary Public Health and Food Safety – GMO and mycotoxins unit, ISS, Viale Regina Elena 299, 00161 Rome, Italy
| | - C. Crews
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK
| | - M.H. Iha
- Laboratorio I de Ribeiro Preto, Instituto Adolfo Lutz, Rua Minas 877, CEP 14085-410 Ribeiro Preto-SP, Brazil
| | - R. Krska
- Christian Doppler Laboratory for Mycotoxin Metabolism and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad Lorenz Str. 20, 3430 Vienna, Austria
| | | | - S. MacDonald
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK
| | - R.J. Malone
- Trilogy Analytical Laboratory, 870 Vossbrink Dr., Washington, MO 63090, USA
| | - C. Maragos
- USDA-ARS NCAUR, 1815 N. University St., Peoria, IL 61604, USA
| | | | - J. Stroka
- IRMM, European Commission Joint Research Centre, Retieseweg 111, 2440 Geel, Belgium
| | - T.B. Whitaker
- Biological and Agricultural Engineering Department, North Carolina State University, P.O. Box 7625, Raleigh, NC 27695-7625, USA
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33
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Cajka T, Fiehn O. Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics. Anal Chem 2015; 88:524-45. [PMID: 26637011 DOI: 10.1021/acs.analchem.5b04491] [Citation(s) in RCA: 514] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomas Cajka
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States
| | - Oliver Fiehn
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States.,King Abdulaziz University , Faculty of Science, Biochemistry Department, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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34
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Liu Y, Zhang C, Liao X, Luo Y, Wu S, Wang J. Hydrolysis mechanism of methyl parathion evidenced by Q-Exactive mass spectrometry. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:19747-19755. [PMID: 26278904 DOI: 10.1007/s11356-015-5169-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/06/2015] [Indexed: 06/04/2023]
Abstract
Organophosphorus pesticides (OPPs), a kind of widely used pesticides, are currently attracting great attention due to their adverse effects on human central nervous systems, particularly in children. Although the hydrolysis behavior of OPPs has been studied well, its hydrolysis mechanism remained controversial, especially at various pH conditions, partly due to their relatively complex structures and abundant moieties that were prone to be attacked by nucleophiles. The Q-Exactive mass spectrometer, part of those hybrid high-resolution mass spectrometers (HRMS), was used to determine hydrolysis products of methyl parathion (MP), a kind of OPPs in situ buffer aqueous solution with pH ranging from 1 to 13 in this study. Most of the complex hydrolysis products of MP were identified due to the high sensitivity and accuracy of HRMS. The results demonstrated that the hydrolysis rate and pathway of MP were strong pH dependent. With the increase of pH, the hydrolysis rate of MP increased, and two different reaction mechanisms were identified: SN (2)@P pathway dominated the hydrolysis process at high pH (e.g., pH ≥ 11) while SN (2)@C was the main behavior at low pH (e.g., pH ≤ 9). This study helps understand the hydrolysis mechanism of OPPs at various pH and extends the use of Q-Exactive mass spectrometry in identifying organic pollutants and their degradation products in environmental matrices.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Caixiang Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China.
| | - Xiaoping Liao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Yinwen Luo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Sisi Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Jianwei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
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35
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Meng-Reiterer J, Varga E, Nathanail AV, Bueschl C, Rechthaler J, McCormick SP, Michlmayr H, Malachová A, Fruhmann P, Adam G, Berthiller F, Lemmens M, Schuhmacher R. Tracing the metabolism of HT-2 toxin and T-2 toxin in barley by isotope-assisted untargeted screening and quantitative LC-HRMS analysis. Anal Bioanal Chem 2015; 407:8019-33. [PMID: 26335000 PMCID: PMC4595538 DOI: 10.1007/s00216-015-8975-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 12/02/2022]
Abstract
An extensive study of the metabolism of the type A trichothecene mycotoxins HT-2 toxin and T-2 toxin in barley using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) is reported. A recently developed untargeted approach based on stable isotopic labelling, LC-Orbitrap-MS analysis with fast polarity switching and data processing by MetExtract software was combined with targeted LC-Q-TOF-MS(/MS) analysis for metabolite structure elucidation and quantification. In total, 9 HT-2 toxin and 13 T-2 toxin metabolites plus tentative isomers were detected, which were successfully annotated by calculation of elemental formulas and further LC-HRMS/MS measurements as well as partly identified with authentic standards. As a result, glucosylated forms of the toxins, malonylglucosides, and acetyl and feruloyl conjugates were elucidated. Additionally, time courses of metabolite formation and mass balances were established. For absolute quantification of those compounds for which standards were available, the method was validated by determining apparent recovery, signal suppression, or enhancement and extraction recovery. Most importantly, T-2 toxin was rapidly metabolised to HT-2 toxin and for both parent toxins HT-2 toxin-3-O-β-glucoside was identified (confirmed by authentic standard) as the main metabolite, which reached its maximum already 1 day after toxin treatment. Graphical Abstract Isotope-assisted untargeted screening of HT-2 toxin and T-2 toxin metabolites in barley.
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Affiliation(s)
- Jacqueline Meng-Reiterer
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Institute for Biotechnology in Plant Production, IFA-Tulln, BOKU, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Elisabeth Varga
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Christian Doppler Laboratory for Mycotoxin Metabolism, IFA-Tulln, BOKU, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Alexis V Nathanail
- Chemistry and Toxicology Unit, Research and Laboratory Department, Finnish Food Safety Authority (Evira), Mustialankatu 3, 00790, Helsinki, Finland
| | - Christoph Bueschl
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Justyna Rechthaler
- University of Applied Sciences Wr. Neustadt, Degree Programme Biotechnical Processes (FHWN-Tulln), Konrad-Lorenz-Str. 10, 3430, Tulln, Austria
| | - Susan P McCormick
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL, 61604, USA
| | - Herbert Michlmayr
- Department of Applied Genetics and Cell Biology, BOKU, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
| | - Alexandra Malachová
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Christian Doppler Laboratory for Mycotoxin Metabolism, IFA-Tulln, BOKU, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Philipp Fruhmann
- Department of Applied Genetics and Cell Biology, BOKU, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163, 1060, Vienna, Austria
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology, BOKU, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
| | - Franz Berthiller
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Christian Doppler Laboratory for Mycotoxin Metabolism, IFA-Tulln, BOKU, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Marc Lemmens
- Institute for Biotechnology in Plant Production, IFA-Tulln, BOKU, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
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36
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Nathanail A, Varga E, Meng-Reiterer J, Bueschl C, Michlmayr H, Malachova A, Fruhmann P, Jestoi M, Peltonen K, Adam G, Lemmens M, Schuhmacher R, Berthiller F. Metabolism of the Fusarium Mycotoxins T-2 Toxin and HT-2 Toxin in Wheat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7862-72. [PMID: 26278508 PMCID: PMC4570218 DOI: 10.1021/acs.jafc.5b02697] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/12/2015] [Accepted: 08/15/2015] [Indexed: 05/23/2023]
Abstract
To investigate the metabolic fate of HT-2 toxin (HT2) and T-2 toxin (T2) in wheat (Triticum aestivum L.), an untargeted metabolomics study utilizing stable isotopic labeling and liquid chromatography-high resolution mass spectrometry was performed. In total, 11 HT2 and 12 T2 derived in planta biotransformation products were annotated putatively. In addition to previously reported mono- and diglucosylated forms of HT2, evidence for the formation of HT2-malonyl-glucoside and feruloyl-T2, as well as acetylation and deacetylation products in wheat was obtained for the first time. To monitor the kinetics of metabolite formation, a time course experiment was conducted involving the Fusarium head blight susceptible variety Remus and the resistant cultivar CM-82036. Biotransformation reactions were observed already at the earliest tested time point (6 h after treatment), and formed metabolites showed different kinetic profiles. After ripening, less than 15% of the toxins added to the plants were determined to be unmetabolized.
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Affiliation(s)
- Alexis
V. Nathanail
- Chemistry
and Toxicology Unit, Research
and Laboratory Department, Finnish Food
Safety Authority (Evira), Mustialankatu 3, 00790 Helsinki, Finland
| | - Elisabeth Varga
- Christian
Doppler Laboratory for Mycotoxin Metabolism
and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences,
Vienna (BOKU), Konrad
Lorenz Str. 20, 3430 Tulln, Austria
| | - Jacqueline Meng-Reiterer
- Christian
Doppler Laboratory for Mycotoxin Metabolism
and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences,
Vienna (BOKU), Konrad
Lorenz Str. 20, 3430 Tulln, Austria
- Institute
for Biotechnology in Plant Production, IFA-Tulln,
BOKU, Konrad Lorenz Str.
20, 3430 Tulln, Austria
| | - Christoph Bueschl
- Christian
Doppler Laboratory for Mycotoxin Metabolism
and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences,
Vienna (BOKU), Konrad
Lorenz Str. 20, 3430 Tulln, Austria
| | - Herbert Michlmayr
- Department
of Applied Genetics and Cell Biology, BOKU, Konrad Lorenz Str. 24, 3430 Tulln, Austria
| | - Alexandra Malachova
- Christian
Doppler Laboratory for Mycotoxin Metabolism
and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences,
Vienna (BOKU), Konrad
Lorenz Str. 20, 3430 Tulln, Austria
| | - Philipp Fruhmann
- Institute
of Applied Synthetic Chemistry, Vienna University
of Technology, Getreidemarkt
9/163, 1060 Vienna, Austria
| | - Marika Jestoi
- Product Safety Unit, Control Department, Finnish Food Safety
Authority (Evira), Mustialankatu
3, 00790 Helsinki, Finland
| | - Kimmo Peltonen
- Finnish
Safety and Chemicals Agency (Tukes), Opastinsilta 12 B, 00521 Helsinki, Finland
| | - Gerhard Adam
- Department
of Applied Genetics and Cell Biology, BOKU, Konrad Lorenz Str. 24, 3430 Tulln, Austria
| | - Marc Lemmens
- Institute
for Biotechnology in Plant Production, IFA-Tulln,
BOKU, Konrad Lorenz Str.
20, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Christian
Doppler Laboratory for Mycotoxin Metabolism
and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences,
Vienna (BOKU), Konrad
Lorenz Str. 20, 3430 Tulln, Austria
| | - Franz Berthiller
- Christian
Doppler Laboratory for Mycotoxin Metabolism
and Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences,
Vienna (BOKU), Konrad
Lorenz Str. 20, 3430 Tulln, Austria
- E-mail: . Phone: +43 2272/66280-413. Fax: +43 2272/66280-403
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37
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Leeming MG, Isaac AP, Pope BJ, Cranswick N, Wright CE, Ziogas J, O'Hair RAJ, Donald WA. High-resolution twin-ion metabolite extraction (HiTIME) mass spectrometry: nontargeted detection of unknown drug metabolites by isotope labeling, liquid chromatography mass spectrometry, and automated high-performance computing. Anal Chem 2015; 87:4104-9. [PMID: 25818563 DOI: 10.1021/ac504767d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The metabolic fate of a compound can often determine the success of a new drug lead. Thus, significant effort is directed toward identifying the metabolites formed from a given molecule. Here, an automated and nontargeted procedure is introduced for detecting drug metabolites without authentic metabolite standards via the use of stable isotope labeling, liquid chromatography mass spectrometry (LC/MS), and high-performance computing. LC/MS of blood plasma extracts from rats that were administered a 1:1 mixture of acetaminophen (APAP) and (13)C6-APAP resulted in mass spectra that contained "twin" ions for drug metabolites that were not detected in control spectra (i.e., no APAP administered). Because of the development of a program (high-resolution twin-ion metabolite extraction; HiTIME) that can identify twin-ions in high-resolution mass spectra without centroiding (i.e., reduction of mass spectral peaks to single data points), 9 doublets corresponding to APAP metabolites were identified. This is nearly twice that obtained by use of existing programs that make use of centroiding to reduce computational cost under these conditions with a quadrupole time-of-flight mass spectrometer. By a manual search for all reported APAP metabolite ions, no additional twin-ion signals were assigned. These data indicate that all the major metabolites of APAP and multiple low-abundance metabolites (e.g., acetaminophen hydroxy- and methoxysulfate) that are rarely reported were detected. This methodology can be used to detect drug metabolites without prior knowledge of their identity. HiTIME is freely available from https://github.com/bjpop/HiTIME .
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Affiliation(s)
- Michael G Leeming
- †School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, 30 Flemington Road, Melbourne, Victoria 3010, Australia
| | - Andrew P Isaac
- ‡Victorian Life Sciences Computation Initiative, University of Melbourne, 187 Grattan Street, Carlton, Victoria 3010, Australia
| | - Bernard J Pope
- ‡Victorian Life Sciences Computation Initiative, University of Melbourne, 187 Grattan Street, Carlton, Victoria 3010, Australia.,§Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Noel Cranswick
- ∥Department of Pharmacology and Therapeutics, University of Melbourne, Victoria 3010, Australia.,¶Royal Children's Hospital Melbourne, 50 Flemington Road, Victoria 3052, Australia
| | - Christine E Wright
- ∥Department of Pharmacology and Therapeutics, University of Melbourne, Victoria 3010, Australia.,⊥ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - James Ziogas
- ∥Department of Pharmacology and Therapeutics, University of Melbourne, Victoria 3010, Australia.,⊥ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Richard A J O'Hair
- †School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, 30 Flemington Road, Melbourne, Victoria 3010, Australia.,⊥ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - William A Donald
- #School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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