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Di Minno A, Gelzo M, Caterino M, Costanzo M, Ruoppolo M, Castaldo G. Challenges in Metabolomics-Based Tests, Biomarkers Revealed by Metabolomic Analysis, and the Promise of the Application of Metabolomics in Precision Medicine. Int J Mol Sci 2022; 23:5213. [PMID: 35563604 PMCID: PMC9103094 DOI: 10.3390/ijms23095213] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolomics helps identify metabolites to characterize/refine perturbations of biological pathways in living organisms. Pre-analytical, analytical, and post-analytical limitations that have hampered a wide implementation of metabolomics have been addressed. Several potential biomarkers originating from current targeted metabolomics-based approaches have been discovered. Precision medicine argues for algorithms to classify individuals based on susceptibility to disease, and/or by response to specific treatments. It also argues for a prevention-based health system. Because of its ability to explore gene-environment interactions, metabolomics is expected to be critical to personalize diagnosis and treatment. Stringent guidelines have been applied from the very beginning to design studies to acquire the information currently employed in precision medicine and precision prevention approaches. Large, prospective, expensive and time-consuming studies are now mandatory to validate old, and discover new, metabolomics-based biomarkers with high chances of translation into precision medicine. Metabolites from studies on saliva, sweat, breath, semen, feces, amniotic, cerebrospinal, and broncho-alveolar fluid are predicted to be needed to refine information from plasma and serum metabolome. In addition, a multi-omics data analysis system is predicted to be needed for omics-based precision medicine approaches. Omics-based approaches for the progress of precision medicine and prevention are expected to raise ethical issues.
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Affiliation(s)
- Alessandro Di Minno
- Dipartimento di Farmacia, University of Naples Federico II, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
| | - Monica Gelzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Marianna Caterino
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Michele Costanzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Margherita Ruoppolo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
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Sumabe BK, Ræder SB, Røst LM, Sharma A, Donkor ES, Mosi L, Duodu S, Bruheim P, Otterlei M. Nucleoside Analogues Are Potent Inducers of Pol V-mediated Mutagenesis. Biomolecules 2021; 11:843. [PMID: 34198819 PMCID: PMC8227612 DOI: 10.3390/biom11060843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/18/2022] Open
Abstract
Drugs targeting DNA and RNA in mammalian cells or viruses can also affect bacteria present in the host and thereby induce the bacterial SOS system. This has the potential to increase mutagenesis and the development of antimicrobial resistance (AMR). Here, we have examined nucleoside analogues (NAs) commonly used in anti-viral and anti-cancer therapies for potential effects on mutagenesis in Escherichia coli, using the rifampicin mutagenicity assay. To further explore the mode of action of the NAs, we applied E. coli deletion mutants, a peptide inhibiting Pol V (APIM-peptide) and metabolome and proteome analyses. Five out of the thirteen NAs examined, including three nucleoside reverse transcriptase inhibitors (NRTIs) and two anti-cancer drugs, increased the mutation frequency in E. coli by more than 25-fold at doses that were within reported plasma concentration range (Pl.CR), but that did not affect bacterial growth. We show that the SOS response is induced and that the increase in mutation frequency is mediated by the TLS polymerase Pol V. Quantitative mass spectrometry-based metabolite profiling did not reveal large changes in nucleoside phosphate or other central carbon metabolite pools, which suggests that the SOS induction is an effect of increased replicative stress. Our results suggest that NAs/NRTIs can contribute to the development of AMR and that drugs inhibiting Pol V can reverse this mutagenesis.
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Affiliation(s)
- Balagra Kasim Sumabe
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway; (B.K.S.); (S.B.R.)
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. BOX LG 54 Accra, Ghana; (L.M.); (S.D.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. BOX LG 54 Accra, Ghana
| | - Synnøve Brandt Ræder
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway; (B.K.S.); (S.B.R.)
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway; (L.M.R.); (P.B.)
| | - Animesh Sharma
- Proteomics and Modomics Experimental Core Facility (PROMEC), NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway;
| | - Eric S. Donkor
- Department of Medical Microbiology, University of Ghana Medical School, P.O. Box 4236 Accra, Ghana;
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. BOX LG 54 Accra, Ghana; (L.M.); (S.D.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. BOX LG 54 Accra, Ghana
| | - Samuel Duodu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. BOX LG 54 Accra, Ghana; (L.M.); (S.D.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. BOX LG 54 Accra, Ghana
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway; (L.M.R.); (P.B.)
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway; (B.K.S.); (S.B.R.)
- Clinic of Laboratory medicine, St. Olav University Hospital, NO-7006 Trondheim, Norway
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Kollmeier AS, de la Torre X, Müller C, Botrè F, Parr MK. In-depth gas chromatography/tandem mass spectrometry fragmentation analysis of formestane and evaluation of mass spectral discrimination of isomeric 3-keto-4-ene hydroxy steroids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8937. [PMID: 32876355 DOI: 10.1002/rcm.8937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The aromatase inhibitor formestane (4-hydroxyandrost-4-ene-3,17-dione) is included in the World Anti-Doping Agency's List of Prohibited Substances in Sport. However, it also occurs endogenously as do its 2-, 6- and 11-hydroxy isomers. The aim of this study is to distinguish the different isomers using gas chromatography/electron ionization mass spectrometry (GC/EI-MS) for enhanced confidence in detection and selectivity for determination. METHODS Established derivatization protocols to introduce [2 H9 ]TMS were followed to generate perdeuterotrimethylsilylated and mixed deuterated derivatives for nine different hydroxy steroids, all with 3-keto-4-ene structure. Formestane was additionally labelled with H2 18 O to obtain derivatives doubly labelled with [2 H9 ]TMS and 18 O. GC/EI-MS spectra of labelled and unlabelled TMS derivatives were compared. Proposals for the generation of fragment ions were substantiated by high-resolution MS (GC/QTOFMS) and tandem mass spectrometry (MS/MS) experiments. RESULTS Subclass-specific fragment ions include m/z 319 for the 6-hydroxy and m/z 219 for the 11-hydroxy compounds. Ions at m/z 415, 356, 341, 313, 269 and 267 were indicative for the 2- and 4-hydroxy compounds. For their discrimination the transition m/z 503 → 269 was selective for formestane. In 2-, 4- and 6-hydroxy steroids loss of a TMSO radical takes place as cleavage of a TMS-derived methyl radical and a neutral loss of (CH3 )2 SiO. Further common fragments were also elucidated. CONCLUSIONS With the help of stable isotope labelling, the structures of postulated diagnostic fragment ions for the different steroidal subclasses were elucidated. 18 O-labelling of the other compounds will be addressed in future studies to substantiate the obtained findings. To increase method sensitivity MS3 may be suitable in future bioanalytical applications requiring discrimination of the 2- and 4-hydroxy compounds.
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Affiliation(s)
| | | | - Christian Müller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 34-36, Berlin, 14195, Germany
| | - Francesco Botrè
- Laboratorio Antidoping FSMI, Largo Giulio Onesti 1, Rome, 00197, Italy
| | - Maria Kristina Parr
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin, 14195, Germany
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Khodadadi M, Pourfarzam M. A review of strategies for untargeted urinary metabolomic analysis using gas chromatography-mass spectrometry. Metabolomics 2020; 16:66. [PMID: 32419109 DOI: 10.1007/s11306-020-01687-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Human urine gives evidence of the metabolism in the body and contains different metabolites at various concentrations. A number of analytical techniques including mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been used to obtain metabolites levels in urine samples. However, gas chromatography-mass spectrometry (GC-MS) is one of the most widely used techniques for urinary metabolomics studies due to its higher sensitivity, resolution, reproducibility, reliability, relatively low cost and ease of operation compared to liquid chromatography-mass spectrometry and NMR. AIM OF REVIEW This review looks at various aspects of urine preparation prior to analysis by GC-MS including sample storage, urease pretreatment, derivatization, use of internal standard and quality control samples for data correction. In addition, most common types of inlet liners, ionization techniques and columns are discussed and a summary of mass analyzers are also highlighted. Lastly, the role of retention index in metabolite identification and data normalization methods are presented. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is summarizing methods of sample storage, pretreatment, and GC-MS analysis that are mostly used in urine metabolomics studies. Specific emphasis is given to the critical steps within the GC-MS urine metabolomics that those new to this field need to be aware of and the remaining challenges that require further attention and studies.
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Affiliation(s)
- Mohammad Khodadadi
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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Pinu FR, Goldansaz SA, Jaine J. Translational Metabolomics: Current Challenges and Future Opportunities. Metabolites 2019; 9:E108. [PMID: 31174372 PMCID: PMC6631405 DOI: 10.3390/metabo9060108] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand.
| | - Seyed Ali Goldansaz
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jacob Jaine
- Analytica Laboratories Ltd., Ruakura Research Centre, Hamilton 3216, New Zealand.
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Assaf J, Kollmeier AS, Müller C, Parr MK. Reconsidering mass spectrometric fragmentation in electron ionization mass spectrometry - new insights from recent instrumentation and isotopic labelling exemplified by ketoprofen and related compounds. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:215-228. [PMID: 30334294 DOI: 10.1002/rcm.8313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/12/2018] [Accepted: 10/13/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE In various fields of chemical analyses, structurally unknown analytes are considered. Proper structure confirmation may be challenged by the low amounts of analytes that are available, e.g. in early stage drug development, in metabolism studies, in toxicology or in environmental analyses. In these cases, mass spectrometric techniques are often used to build up structure proposals for these unknowns. Fragmentation reactions in mass spectrometry are known to follow definite pathways that may help to assign structural elements by fragment ion recognition. This work illustrates an investigation of fragmentation reactions for gas chromatography/electron ionization mass spectrometric characterization of benzophenone derivatives using the analgesic drug ketoprofen and seven of its related compounds as model compounds. METHODS Deuteration and 18 O-labelling experiments along with high-resolution accurate mass and tandem mass spectrometry (MS/MS) were used to further elucidate fragmentation pathways and to substantiate rationales for structure assignments. Low-energy ionization was investigated to increase confidence in the identity of the molecular ion. RESULTS The high-resolution mass analyses yielded unexpected differences that led to reconsideration of the proposals. Site-specific isotopic labelling helped to directly trace back fragment ions to their respective structural elements. The proposed fragmentation pathways were substantiated by MS/MS experiments. CONCLUSIONS The described method may offer a perspective to increase the level of confidence in unknown analyses, where reference material is not (yet) available.
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Affiliation(s)
- Jaber Assaf
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | | | - Christian Müller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 34-36, 14195, Berlin, Germany
| | - Maria Kristina Parr
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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A Simultaneous Metabolic Profiling and Quantitative Multimetabolite Metabolomic Method for Human Plasma Using Gas-Chromatography Tandem Mass Spectrometry. J Proteome Res 2015; 15:259-65. [PMID: 26615962 DOI: 10.1021/acs.jproteome.5b00790] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
For the first time it is possible to simultaneously collect targeted and nontargeted metabolomics data from plasma based on GC with high scan speed tandem mass spectrometry (GC-MS/MS). To address the challenge of getting broad metabolome coverage while quantifying known biomarker compounds in high-throughput GC-MS metabolomics, we developed a novel GC-MS/MS metabolomics method using a high scan speed (20 000 Da/second) GC-MS/MS that enables simultaneous data acquisition of both nontargeted full scan and targeted quantitative tandem mass spectrometry data. The combination of these two approaches has hitherto not been demonstrated in metabolomics. This method allows reproducible quantification of at least 37 metabolites using multiple reaction monitoring (MRM) and full mass spectral scan-based detection of 601 reproducible metabolic features from human plasma. The method showed good linearity over normal concentrations in plasma (0.06-343 to 0.86-4800 μM depending on the metabolite) and good intra- and interbatch precision (0.9-16.6 and 2.6-29.6% relative standard deviation). Based on the parameters determined for this method, targeted quantification using MRM can be expanded to cover at least 508 metabolites while still collecting full scan data. The new simultaneous targeted and nontargeted metabolomics method enables more sensitive and accurate detection of predetermined metabolites and biomarkers of interest, while still allowing detection and identification of unknown metabolites. This is the first validated GC-MS/MS metabolomics method with simultaneous full scan and MRM data collection, and clearly demonstrates the utility of GC-MS/MS with high scanning rates for complex analyses.
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Assessment of capillary anion exchange ion chromatography tandem mass spectrometry for the quantitative profiling of the phosphometabolome and organic acids in biological extracts. J Chromatogr A 2014; 1370:70-9. [PMID: 25454131 DOI: 10.1016/j.chroma.2014.10.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/01/2014] [Accepted: 10/09/2014] [Indexed: 11/24/2022]
Abstract
Metabolic profiling has become an important tool in biological research, and the chromatographic separation of metabolites coupled with mass spectrometric detection is the most frequently used approach for such studies. The establishment of robust chromatographic methods for comprehensive coverage of the anionic metabolite pool is especially challenging. In this study, the development of a capillary ion exchange chromatography (capIC) - negative ESI tandem mass spectrometry (MS/MS) workflow for the quantitative profiling of the phosphometabolome (e.g., sugar phosphates and nucleotides) is presented. The chromatographic separation and MS/MS conditions were optimized, and the precision of repetitive injections and accuracy in terms of error percentage to true concentration were assessed. The precision is excellent for a capillary flow system with an average CV% of 8.5% for a 50-fmol standard injection and in the lower 2.4-4.4% range for higher concentrations (500-7,500 fmol). The limit of detection (LOD) ranges from 1 to 100 nM (5-500 fmol injected on column), and the limit of quantitation (LOQ) ranges from 1 to 500 nM (5-2,500 fmol injected on column). A fast gradient method with the injection of 50% methanol in water between analytical samples is needed to eliminate carry-over and ensure optimal re-equilibration of the column. Finally, the quantitative applicability of the system was tested on real biological matrices using the constant-volume standard addition method (SAM). Extracts of the human kidney Hek293 cell line were spiked with increasing concentrations of standards to determine the concentration of each metabolite in the sample. Forty-four metabolites were detected with an average uncertainty of 4.1%. Thus, the capIC-MS/MS method exhibits excellent selectivity, sensitivity and precision for the quantitative profiling of the phosphometabolome.
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Chen R, Han S, Dong D, Wang Y, Liu Q, Xie W, Li M, Yao M. Serum fatty acid profiles and potential biomarkers of ankylosing spondylitis determined by gas chromatography-mass spectrometry and multivariate statistical analysis. Biomed Chromatogr 2014; 29:604-11. [PMID: 25223299 DOI: 10.1002/bmc.3321] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/03/2014] [Accepted: 07/30/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Rui Chen
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
| | - Su Han
- Department of Parasitology; Harbin Medical University; Harbin People's Republic of China
| | - Daming Dong
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
| | - Yansong Wang
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
| | - Qingpeng Liu
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
| | - Wei Xie
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
| | - Mi Li
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
| | - Meng Yao
- Department of Spine Surgery; The Second Affiliated Hospital of Harbin Medical University; Harbin People's Republic of China
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Kell DB, Goodacre R. Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. Drug Discov Today 2014; 19:171-82. [PMID: 23892182 PMCID: PMC3989035 DOI: 10.1016/j.drudis.2013.07.014] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/03/2013] [Accepted: 07/16/2013] [Indexed: 02/06/2023]
Abstract
Metabolism represents the 'sharp end' of systems biology, because changes in metabolite concentrations are necessarily amplified relative to changes in the transcriptome, proteome and enzyme activities, which can be modulated by drugs. To understand such behaviour, we therefore need (and increasingly have) reliable consensus (community) models of the human metabolic network that include the important transporters. Small molecule 'drug' transporters are in fact metabolite transporters, because drugs bear structural similarities to metabolites known from the network reconstructions and from measurements of the metabolome. Recon2 represents the present state-of-the-art human metabolic network reconstruction; it can predict inter alia: (i) the effects of inborn errors of metabolism; (ii) which metabolites are exometabolites, and (iii) how metabolism varies between tissues and cellular compartments. However, even these qualitative network models are not yet complete. As our understanding improves so do we recognise more clearly the need for a systems (poly)pharmacology.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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13
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Kvitvang HFN, Kristiansen KA, Lien SK, Bruheim P. Quantitative analysis of amino and organic acids by methyl chloroformate derivatization and GC-MS/MS analysis. Methods Mol Biol 2014; 1198:137-145. [PMID: 25270928 DOI: 10.1007/978-1-4939-1258-2_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Alkyl chloroformates are known for their ability to produce mixed anhydrides, and they have found use as versatile derivatization reagents for gas chromatographic (GC) separation of amino- and organic acids. Triple-quadrupole mass spectrometers are excellent detectors for high sensitive and selective analysis. Here, we describe a methyl chloroformate (MCF) GC-MS/MS method for the quantitative analysis of metabolites containing amino- and/or carboxylic groups. The method covers over 60 metabolites with quantitation limits down to the low picomole range injected on column, and any metabolite with amino- and/or carboxylic acid functional groups that yield a stable and volatile MCF derivative can be included in the method. Absolute quantitation can be achieved by including a stable isotope-coded derivatization agent (d3-MCF) and deuterated alcohol solvent (e.g., d4-methanol). As the carboxylic and amino groups are differently labeled, the former from the solvent methanol while the latter from MCF, this approach can also be used to identify a number of amino and carboxylic groups in unknown analytes in an extract.
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Affiliation(s)
- Hans Fredrik Nyvold Kvitvang
- NTNU Department of Biotechnology, Norwegian University of Science and Technology, Sem Selands vei 6/8, 7491, Trondheim, Norway
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Laulhé S, Geers TE, Shi X, Zhang X, Nantz MH. Electron Ionization-Induced Release of Coded Isotopic Reporter Ions in an m/z Zone of Minimal Interference for Quantifiable, Multiplexed GC-MS Analyses. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2013; 5:10.1039/C3AY41124A. [PMID: 24235976 PMCID: PMC3822575 DOI: 10.1039/c3ay41124a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We describe an isotope coding strategy that enables simultaneous GC-MS analysis of multiple samples for substrate identification and quantification. The method relies on direct measurement of isotopic ethyl carbenium ions serving as mass spectral tags in a zone of minimal interference (ZMI) at m/z 31-37. Sample aldehyde and ketone mixtures were reacted with isotopic 2-aminooxyethyl propionates to illustrate the method, which determined the relative abundance of the mixed compounds with an average 95% accuracy. ZMI reporter ion detection also enables chemoselective substrate profiling and absolute quantification, as demonstrated using a biologically derived sample.
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Wachsmuth CJ, Vogl FC, Oefner PJ, Dettmer K. Gas Chromatographic Techniques in Metabolomics. CHROMATOGRAPHIC METHODS IN METABOLOMICS 2013. [DOI: 10.1039/9781849737272-00087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
High chemical diversity and abundances ranging from trace to millimolar levels still constitute at times insurmountable challenges in the comprehensive analysis of metabolites in biomedical specimens. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) hyphenated with separation techniques such as liquid chromatography (LC), gas chromatography (GC) and capillary electrophoresis (CE) are the most frequently used techniques for both targeted and discovery‐driven metabolomics. Of the separation techniques, comprehensive two‐dimensional gas chromatography (GC×GC) offers the highest peak resolution and capacity, and in combination with MS lower quantification limits in the submicromolar concentration range are realized. Moreover, electron ionization (EI), the most prominent ionization technique for GC‐MS, is highly reproducible, facilitating the generation of mass spectral libraries for routine metabolite identification. However, GC analysis often requires a derivatization prior to analysis and not all metabolite derivatives are recorded in the libraries available. Consequently, metabolite identification is still a major challenge. To identify unknown metabolite signals, soft ionization techniques in combination with high‐resolution MS are employed to determine the accurate mass of the quasi‐molecular ion. The latter is used to calculate elemental formulae that can be fed into metabolite databases for a putative identification or used for the interpretation of EI spectra.
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Affiliation(s)
- Christian J. Wachsmuth
- Institute of Functional Genomics University of Regensburg, Josef‐Engert‐Strasse 9, 93053 Regensburg Germany ‐regensburg.de
| | - Franziska C. Vogl
- Institute of Functional Genomics University of Regensburg, Josef‐Engert‐Strasse 9, 93053 Regensburg Germany ‐regensburg.de
| | - Peter J. Oefner
- Institute of Functional Genomics University of Regensburg, Josef‐Engert‐Strasse 9, 93053 Regensburg Germany ‐regensburg.de
| | - Katja Dettmer
- Institute of Functional Genomics University of Regensburg, Josef‐Engert‐Strasse 9, 93053 Regensburg Germany ‐regensburg.de
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Bruheim P, Kvitvang HFN, Villas-Boas SG. Stable isotope coded derivatizing reagents as internal standards in metabolite profiling. J Chromatogr A 2013; 1296:196-203. [DOI: 10.1016/j.chroma.2013.03.072] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 12/26/2022]
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17
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Kuehnbaum NL, Britz-McKibbin P. New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era. Chem Rev 2013; 113:2437-68. [DOI: 10.1021/cr300484s] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Naomi L. Kuehnbaum
- Department of Chemistry
and Chemical Biology, McMaster University, Hamilton, Canada
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