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Lekka P, Fragopoulou E, Terpou A, Dasenaki M. Exploring Human Metabolome after Wine Intake-A Review. Molecules 2023; 28:7616. [PMID: 38005338 PMCID: PMC10673339 DOI: 10.3390/molecules28227616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Wine has a rich history dating back to 2200 BC, originally recognized for its medicinal properties. Today, with the aid of advanced technologies like metabolomics and sophisticated analytical techniques, we have gained remarkable insights into the molecular-level changes induced by wine consumption in the human organism. This review embarks on a comprehensive exploration of the alterations in human metabolome associated with wine consumption. A great number of 51 studies from the last 25 years were reviewed; these studies systematically investigated shifts in metabolic profiles within blood, urine, and feces samples, encompassing both short-term and long-term studies of the consumption of wine and wine derivatives. Significant metabolic alterations were observed in a wide variety of metabolites belonging to different compound classes, such as phenolic compounds, lipids, organic acids, and amino acids, among others. Within these classes, both endogenous metabolites as well as diet-related metabolites that exhibited up-regulation or down-regulation following wine consumption were included. The up-regulation of short-chain fatty acids and the down-regulation of sphingomyelins after wine intake, as well as the up-regulation of gut microbial fermentation metabolites like vanillic and syringic acid are some of the most important findings reported in the reviewed literature. Our results confirm the intact passage of certain wine compounds, such as tartaric acid and other wine acids, to the human organism. In an era where the health effects of wine consumption are of growing interest, this review offers a holistic perspective on the metabolic underpinnings of this centuries-old tradition.
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Affiliation(s)
- Pelagia Lekka
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
| | - Elizabeth Fragopoulou
- School of Health Science and Education, Department of Nutrition and Dietetics, Harokopio University, 17671 Athens, Greece;
| | - Antonia Terpou
- Department of Agricultural Development, Agrofood and Management of Natural Resources, School of Agricultural Development, Nutrition & Sustainability, National and Kapodistrian University of Athens, 34400 Psachna, Greece;
| | - Marilena Dasenaki
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
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2
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Orzoł A, Cruzado-Tafur E, Gołębiowski A, Rogowska A, Pomastowski P, Górecki RJ, Buszewski B, Szultka-Młyńska M, Głowacka K. Comprehensive Study of Si-Based Compounds in Selected Plants ( Pisum sativum L., Medicago sativa L., Triticum aestivum L.). Molecules 2023; 28:4311. [PMID: 37298792 PMCID: PMC10254194 DOI: 10.3390/molecules28114311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
This review describes the role of silicon (Si) in plants. Methods of silicon determination and speciation are also reported. The mechanisms of Si uptake by plants, silicon fractions in the soil, and the participation of flora and fauna in the Si cycle in terrestrial ecosystems have been overviewed. Plants of Fabaceae (especially Pisum sativum L. and Medicago sativa L.) and Poaceae (particularly Triticum aestivum L.) families with different Si accumulation capabilities were taken into consideration to describe the role of Si in the alleviation of the negative effects of biotic and abiotic stresses. The article focuses on sample preparation, which includes extraction methods and analytical techniques. The methods of isolation and the characterization of the Si-based biologically active compounds from plants have been overviewed. The antimicrobial properties and cytotoxic effects of known bioactive compounds obtained from pea, alfalfa, and wheat were also described.
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Affiliation(s)
- Aleksandra Orzoł
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland; (A.O.); (A.G.); (B.B.)
| | - Edith Cruzado-Tafur
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-720 Olsztyn, Poland; (E.C.-T.); (R.J.G.)
| | - Adrian Gołębiowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland; (A.O.); (A.G.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wilenska 4, 87-100 Torun, Poland; (A.R.); (P.P.)
| | - Agnieszka Rogowska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wilenska 4, 87-100 Torun, Poland; (A.R.); (P.P.)
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wilenska 4, 87-100 Torun, Poland; (A.R.); (P.P.)
| | - Ryszard J. Górecki
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-720 Olsztyn, Poland; (E.C.-T.); (R.J.G.)
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland; (A.O.); (A.G.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wilenska 4, 87-100 Torun, Poland; (A.R.); (P.P.)
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland; (A.O.); (A.G.); (B.B.)
| | - Katarzyna Głowacka
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-720 Olsztyn, Poland; (E.C.-T.); (R.J.G.)
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3
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Theodoridis G, Gika H, Raftery D, Goodacre R, Plumb RS, Wilson ID. Ensuring Fact-Based Metabolite Identification in Liquid Chromatography-Mass Spectrometry-Based Metabolomics. Anal Chem 2023; 95:3909-3916. [PMID: 36791228 PMCID: PMC9979140 DOI: 10.1021/acs.analchem.2c05192] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Metabolite identification represents a major bottleneck in contemporary metabolomics research and a step where critical errors may occur and pass unnoticed. This is especially the case for studies employing liquid chromatography-mass spectrometry technology, where there is increased concern on the validity of the proposed identities. In the present perspective article, we describe the issue and categorize the errors into two types: identities that show poor biological plausibility and identities that do not comply with chromatographic data and thus to physicochemical properties (usually hydrophobicity/hydrophilicity) of the proposed molecule. We discuss the problem, present characteristic examples, and propose measures to improve the situation.
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Affiliation(s)
- Georgios Theodoridis
- Department
of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece,Biomic
AUTh, Center for Interdisciplinary Research
and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd., P.O. Box 8318, Thessaloniki 57001Greece,FoodOmicsGR,
AUTh node, Center for Interdisciplinary
Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, Thessaloniki 57001, Greece,
| | - Helen Gika
- Biomic
AUTh, Center for Interdisciplinary Research
and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd., P.O. Box 8318, Thessaloniki 57001Greece,FoodOmicsGR,
AUTh node, Center for Interdisciplinary
Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, Thessaloniki 57001, Greece,Laboratory
of Forensic Medicine and Toxicology, Department of Medicine, Aristotle University,
Thessaloniki 54124, Greece
| | - Daniel Raftery
- Northwest
Metabolomics Research Center, 850 Republican St., Seattle, Washington 98109, United States,Mitochondria
Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Royston Goodacre
- Centre
for Metabolomics Research, Department of Biochemistry and Systems
Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom
| | - Robert S. Plumb
- Scientific
Operations, IMMERSE, Waters Corporation, Cambridge 02142, Massachusetts United States
| | - Ian D. Wilson
- Centre
for Metabolomics Research, Department of Biochemistry and Systems
Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom,Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom,
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Untargeted Metabolomics Pilot Study Using UHPLC-qTOF MS Profile in Sows' Urine Reveals Metabolites of Bladder Inflammation. Metabolites 2022; 12:metabo12121186. [PMID: 36557224 PMCID: PMC9784506 DOI: 10.3390/metabo12121186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/07/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI) of sows (characterized by ascending infections of the urinary bladder (cyst), ureters, and renal pelvis), are major health issues with a significant economic impact to the swine industry. The current detection of UTI incidents lacks sensitivity; thus, UTIs remain largely under-diagnosed. The value of metabolomics in unraveling the mechanisms of sow UTI has not yet been established. This study aims to investigate the urine metabolome of sows for UTI biomarkers. Urine samples were collected from 58 culled sows from a farrow-to-finish herd in Greece. Urine metabolomic profiles in 31 healthy controls and in 27 inflammatory ones were evaluated. UHPLC-qTOF MS/MS was applied for the analysis with a combination of multivariate and univariate statistical analysis. Eighteen potential markers were found. The changes in several urine metabolites classes (nucleosides, indoles, isoflavones, and dipeptides), as well as amino-acids allowed for an adequate discrimination between the study groups. Identified metabolites were involved in purine metabolism; phenylalanine; tyrosine and tryptophan biosynthesis; and phenylalanine metabolism. Through ROC analysis it was shown that the 18 identified metabolite biomarkers exhibited good predictive accuracy. In summary, our study provided new information on the potential targets for predicting early and accurate diagnosis of UTI. Further, this information also sheds light on how it could be applied in live animals.
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Abdulhafiz F, Reduan MFH, Hisam AH, Mohammad I, Abdul Wahab IR, Abdul Hamid FF, Mohammed A, Nordin ML, Shaari R, Bakar LA, Kari ZA, Wei LS, Goh KW, Ahmad Mohd Zain MR. LC-TOF-MS/MS and GC-MS based phytochemical profiling and evaluation of wound healing activity of Oroxylum Indicum (L.) Kurz (Beka). Front Pharmacol 2022; 13:1050453. [PMID: 36483735 PMCID: PMC9723245 DOI: 10.3389/fphar.2022.1050453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
Background: Beka (Oroxylum indicum (L.) Kurz) has been used as a culinary herb and natural remedy by the local communities in Malaysia. The leaf of O. indicum is traditionally used for the treatment of diarrhea, high blood pressure, and improving digestive health. Objectives: The present study was conducted to evaluate the phytochemical constituents and wound healing properties (in vitro and in vivo models) of aqueous and ethanol extracts of O. indicum leaves. Methods: The total phenolic (TPC) and total flavonoid (TFC) contents in the plant extracts were determined by the spectrophotometric methods. Further, the extract was characterized by Liquid Chromatography Time-of-Flight Mass Spectrometry (LC-TOF-MS/MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The wound healing activity was assessed using the in vitro scratch wound-healing assay and in vivo excisional wound model. Results: The results show the ethanol leaves extract had the higher TPC (164 mg GAE/g) when compared with the aqueous leaves extract (30 mg gallic acid equivalents/g). The ethanol leaves extract was also found to have higher TFC (101 mg Catechin equivalents/g) than the aqueous leaves extract (76 mg Catechin equivalents/g). The ethanol leaves extract was then used for further chemical analysis. The LC-TOF-MS/MS analysis showed that the leaves extracts of O. indicum contains many important compounds such as Orientin, Chrysin, Pinoquercetin, Cupressuflavone, Puerarin xyloside, Forsythiaside and Paederoside. In GC-MS analysis, 19 compounds were identified in ethanolic leaves extract. The wound healing studies shows that O. indicum has promising wound healing activity by increasing the rate of wound contraction significantly (p < 0.05). Conclusion: In conclusion, the present study showed that O. indicum leaf contains important phytochemicals and the wound healing potential of the O. indicum extract may probably be as a result of the presence of various phytoconstituents.
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Affiliation(s)
- Ferid Abdulhafiz
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | | | - Anwar Hazim Hisam
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | - Ibtihal Mohammad
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | | | | | - Arifullah Mohammed
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | | | - Rumaizi Shaari
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | - Luqman Abu Bakar
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | - Zulhisyam Abdul Kari
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | - Lee Seong Wei
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai, Malaysia
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6
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Wu M, Zuo S, Maiorano G, Kosobucki P, Stadnicka K. How to employ metabolomic analysis to research on functions of prebiotics and probiotics in poultry gut health? Front Microbiol 2022; 13:1040434. [PMID: 36452931 PMCID: PMC9701725 DOI: 10.3389/fmicb.2022.1040434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 10/21/2023] Open
Abstract
Gut health can be considered one of the major, manageable constituents of the animal immunity and performance. The fast spread of intestinal diseases, and increase of antimicrobial resistance have been observed, therefore the intestinal health has become not only economically relevant, but also highly important subject addressing the interest of public health. It is expected, that the strategies to control infections should be based on development of natural immunity in animals and producing resilient flocks using natural solutions, whilst eliminating antibiotics and veterinary medicinal products from action. Probiotics and prebiotics have been favored, because they have potential to directly or indirectly optimize intestinal health by manipulating the metabolism of the intestinal tract, including the microbiota. Studying the metabolome of probiotics and gut environment, both in vivo, or using the in vitro models, is required to attain the scientific understanding about the functions of bioactive compounds in development of gut health and life lasting immunity. There is a practical need to identify new metabolites being the key bioactive agents regulating biochemical pathways of systems associated with gut (gut-associated axes). Technological advancement in metabolomics studies, and increasing access to the powerful analytical platforms have paved a way to implement metabolomics in exploration of the effects of prebiotics and probiotics on the intestinal health of poultry. In this article, the basic principles of metabolomics in research involving probiotics and probiotics are introduced, together with the overview of existing strategies and suggestions of their use to study metabolome in poultry.
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Affiliation(s)
- Mengjun Wu
- Department of Animal Biotechnology and Genetics, Faculty of Animal Breeding and Biology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Sanling Zuo
- Department of Animal Biotechnology and Genetics, Faculty of Animal Breeding and Biology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Giuseppe Maiorano
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Przemysław Kosobucki
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Katarzyna Stadnicka
- Department of Animal Biotechnology and Genetics, Faculty of Animal Breeding and Biology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
- Department of Geriatrics, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University, Torun, Poland
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7
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Advanced Microsamples: Current Applications and Considerations for Mass Spectrometry-Based Metabolic Phenotyping Pipelines. SEPARATIONS 2022. [DOI: 10.3390/separations9070175] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Microsamples are collections usually less than 50 µL, although all devices that we have captured as part of this review do not fit within this definition (as some can perform collections of up to 600 µL); however, they are considered microsamples that can be self-administered. These microsamples have been introduced in pre-clinical, clinical, and research settings to overcome obstacles in sampling via traditional venepuncture. However, venepuncture remains the sampling gold standard for the metabolic phenotyping of blood. This presents several challenges in metabolic phenotyping workflows: accessibility for individuals in rural and remote areas (due to the need for trained personnel), the unamenable nature to frequent sampling protocols in longitudinal research (for its invasive nature), and sample collection difficulty in the young and elderly. Furthermore, venous sample stability may be compromised when the temperate conditions necessary for cold-chain transport are beyond control. Alternatively, research utilising microsamples extends phenotyping possibilities to inborn errors of metabolism, therapeutic drug monitoring, nutrition, as well as sport and anti-doping. Although the application of microsamples in metabolic phenotyping exists, it is still in its infancy, with whole blood being overwhelmingly the primary biofluid collected through the collection method of dried blood spots. Research into the metabolic phenotyping of microsamples is limited; however, with advances in commercially available microsampling devices, common barriers such as volumetric inaccuracies and the ‘haematocrit effect’ in dried blood spot microsampling can be overcome. In this review, we provide an overview of the common uses and workflows for microsampling in metabolic phenotyping research. We discuss the advancements in technologies, highlighting key considerations and remaining knowledge gaps for the employment of microsamples in metabolic phenotyping research. This review supports the translation of research from the ‘bench to the community’.
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8
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Impact of Metabolomics Technologies on the Assessment of Peritoneal Membrane Profiles in Peritoneal Dialysis Patients: A Systematic Review. Metabolites 2022; 12:metabo12020145. [PMID: 35208219 PMCID: PMC8879920 DOI: 10.3390/metabo12020145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/31/2022] [Indexed: 02/07/2023] Open
Abstract
Peritoneal dialysis (PD) is an effective and frequent dialysis modality in adults, particularly preferred in infants and young children with end-stage renal disease (ESRD). Long-term exposure of the peritoneal membrane to dialysis solutions results in severe morphologic and functional alterations. Peritoneal dialysis effluent biomarkers are based on omics technologies, which could predict the onset or confirm the diagnosis of peritoneal membrane dysfunction, would allow the development of accurate early prognostic tools and, potentially, the identification of future therapeutic targets. The purpose of our study was to critically review the literature on the impact and the effectiveness of metabolomics technologies in peritoneal health. The main search was performed in electronic databases (PubMed/MEDLINE, Embase and Cochrane Central Register of Controlled Trials) from inception to December 2020, using various combinations of Medical Subject Headings (MeSH). The main search highlighted nine studies, of which seven were evaluated in detail. Metabolomics technologies may provide significant input in the recognition of peritoneal membrane dysfunction in PD patients and provide evidence of early intervention strategies that could protect peritoneum health and function.
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Sponge-associated sp . RM66 metabolome induction with N-acetylglucosamine: Antibacterial, antifungal and anti-trypanosomal activities. Saudi J Biol Sci 2021; 28:4691-4698. [PMID: 34354456 PMCID: PMC8324951 DOI: 10.1016/j.sjbs.2021.04.082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/22/2022] Open
Abstract
The marine sponge Amphimedon sp., collected from Hurghada (Egypt) was investigated for its sponge-derived actinomycetes diversity. Nineteen actinomycetes were cultivated and phylogenetically identified using 16S rDNA gene sequencing were carried out. The strains belong to genera Kocuria, Dietzia, Micrococcus, Microbacterium and Streptomyces. Many silent biosynthetic genes clusters were investigated using genome sequencing of actinomycete strains and has revealed in particular the genus Streptomyces that has indicated their exceptional capacity for the secondary metabolites production that not observed under classical cultivation conditions. In this study, the effect of N-acetylglucosamine on the metabolome of Streptomyces sp. RM66 was investigated using three actinomycetes media (ISP2, M1 and MA). In total, twelve extracts were produced using solid and liquid fermentation approaches. Liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) data were analysed using metabolomics tools to compare natural product production across all crude extracts. Our study highlighted the elicitation effect of N-acetylglucosamine on the secondary metabolite profiles of Streptomyces sp. RM66. These results highlight the of N-acetylglucosamine application as an elicitor to induce the cryptic metabolites and for increasing the chemical diversity. All the twelve extracts were tested for their antibacterial activity was tested against Staphylococcus aureus NCTC 8325, antifungal activity against Candida albicans 5314 (ATCC 90028) and anti-trypanosomal activity against Trypanosoma brucei brucei. Extract St1 showed the most potent one with activities 2.3, 3.2 and 4.7 ug/ml as antibacterial, antifungal and anti-trypanosomal, respectively.
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10
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Wilson ID, Theodoridis G, Virgiliou C. A perspective on the standards describing mass spectrometry-based metabolic phenotyping (metabolomics/metabonomics) studies in publications. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1164:122515. [PMID: 33460910 DOI: 10.1016/j.jchromb.2020.122515] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022]
Abstract
As metabolic phenotyping (metabolomics, metabonomics and also lipidomics) gains in popularity and new investigators enter the field, the need to maintain and improve standards in publication is ever more pressing. In this perspective the requirements for information that should be included in manuscripts published in the Journal of Chromatography B, to ensure that the work is both credible and repeatable, are discussed. These include aspects such as study design, ethics, quality assurance (QA), quality control (QC) and data processing. In addition, aspects such as the level of confidence required for reporting metabolite identification (to a level where they could be subsequently used to develop hypotheses) are discussed.
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Affiliation(s)
- Ian D Wilson
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK.
| | - Georgios Theodoridis
- Department of Chemistry, Aristotle University, Thessaloniki 54124, Greece; Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001, Greece; FoodOmicsGR, Research Infrastructure, Aristotle University Node, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001, Greece
| | - Christina Virgiliou
- Department of Chemistry, Aristotle University, Thessaloniki 54124, Greece; Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001, Greece; FoodOmicsGR, Research Infrastructure, Aristotle University Node, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001, Greece.
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11
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Mass spectrometry-based metabolomics for an in-depth questioning of human health. Adv Clin Chem 2020; 99:147-191. [PMID: 32951636 DOI: 10.1016/bs.acc.2020.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Today, metabolomics is becoming an indispensable tool to get a more comprehensive analysis of complex living systems, providing insights on multiple aspects of physiology. Although its application in large scale population-based studies is very challenging due to the processing of large sample sets as well as the complexity of data information, its potential to characterize human health is well recognized. Technological advances in metabolomics pave the way for the efficient biomarker discovery of disease etiology, diagnosis and prognosis. Here, different steps of the metabolomics workflow, particularly mass spectrometry-based approaches, are discussed to demonstrate the potential of metabolomics to address biological questioning in human health. First an overview of metabolomics is provided with its interest in human health studies. Analytical development and advances in mass spectrometry instrumentation and computational tools are discussed regarding their application limits. Advancing metabolomics for applicability in human health and large-scale studies is presented and discussed in conclusion.
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12
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Pavlaki A, Begou O, Deda O, Farmaki E, Dotis J, Gika H, Taparkou A, Raikos N, Papachristou F, Theodoridis G, Printza N. Serum-Targeted HILIC-MS Metabolomics-Based Analysis in Infants with Ureteropelvic Junction Obstruction. J Proteome Res 2020; 19:2294-2303. [PMID: 32351114 DOI: 10.1021/acs.jproteome.9b00855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ureteropelvic junction obstruction (UPJO) constitutes the predominant cause of obstructive nephropathy in both neonates and infants. Fundamental questions regarding UPJO's mechanism, assessment, and treatment still remain unanswered. The aim of the present study was to elucidate potential differences through serum metabolic profiling of surgical cases of infants with UPJO compared to both nonsurgical cases and healthy age-matched controls. Early diagnosis of renal dysfunction in this cohort based on highlighted biomarkers was the ultimate goal. Thus, serum samples were collected from 20 patients preoperatively, 19 patients with mild stenosis treated conservatively, and 17 healthy controls. All samples were subjected to targeted metabolomics analysis by hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC LC-MS/MS). Both univariate and multivariate statistical analyses were performed. Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) score plots showed that the studied groups differed significantly, with a panel of metabolites, including creatinine, tryptophan, choline, and aspartate, distinguishing patients who required surgery from those followed by systematical monitoring as well as from healthy controls, showing high performance as indicators of UPJO disease.
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Affiliation(s)
- Antigoni Pavlaki
- Paediatric Nephrology Unit, First Department of Paediatrics, Hippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Olga Begou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.,Biomic_Auth, Bioanalysis and Omics Lab, Centre for Interdisciplinary Research of Aristotle University of Thessaloniki, Innovation Area of Thessaloniki, Thermi 57001, Greece
| | - Olga Deda
- Biomic_Auth, Bioanalysis and Omics Lab, Centre for Interdisciplinary Research of Aristotle University of Thessaloniki, Innovation Area of Thessaloniki, Thermi 57001, Greece.,Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Evangelia Farmaki
- Paediatric Immunology and Rheumatology Referral Center, First Department of Paediatrics, Hippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - John Dotis
- Paediatric Nephrology Unit, First Department of Paediatrics, Hippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Helen Gika
- Biomic_Auth, Bioanalysis and Omics Lab, Centre for Interdisciplinary Research of Aristotle University of Thessaloniki, Innovation Area of Thessaloniki, Thermi 57001, Greece.,Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Anna Taparkou
- Paediatric Immunology and Rheumatology Referral Center, First Department of Paediatrics, Hippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Nikolaos Raikos
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Fotios Papachristou
- Paediatric Nephrology Unit, First Department of Paediatrics, Hippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.,Biomic_Auth, Bioanalysis and Omics Lab, Centre for Interdisciplinary Research of Aristotle University of Thessaloniki, Innovation Area of Thessaloniki, Thermi 57001, Greece
| | - Nikoleta Printza
- Paediatric Nephrology Unit, First Department of Paediatrics, Hippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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13
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Zhang XW, Li QH, Xu ZD, Dou JJ. Mass spectrometry-based metabolomics in health and medical science: a systematic review. RSC Adv 2020; 10:3092-3104. [PMID: 35497733 PMCID: PMC9048967 DOI: 10.1039/c9ra08985c] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/14/2019] [Indexed: 01/15/2023] Open
Abstract
Metabolomics is the study of the investigation of small molecules derived from cellular and organism metabolism, which reflects the outcomes of the complex network of biochemical reactions in living systems. As the most recent member of the omics family, there has been notable progress in metabolomics in the last decade, mainly driven by the improvement in mass spectrometry (MS). MS-based metabolomic strategies in modern health and medical science studies provide innovative tools for novel diagnostic and prognostic approaches, as well as an augmented role in drug development, nutrition science, toxicology, and forensic science. In the present review, we not only introduce the application of MS-based metabolomics in the above fields, but also discuss the MS analysis technologies commonly used in metabolomics and the application of metabolomics in precision medicine, and further explore the challenges and perspectives of metabolomics in the field of health and medical science, which are expected to make a little contribution to the better development of metabolomics.
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Affiliation(s)
- Xi-Wu Zhang
- Institute of Chinese Medicine, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin 150040 China +86-451-87266827 +86-451-87266827
| | - Qiu-Han Li
- Institute of Chinese Medicine, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin 150040 China +86-451-87266827 +86-451-87266827
| | - Zuo-di Xu
- Institute of Chinese Medicine, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin 150040 China +86-451-87266827 +86-451-87266827
| | - Jin-Jin Dou
- Institute of Chinese Medicine, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin 150040 China +86-451-87266827 +86-451-87266827
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14
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Johnson AE, Sidwick KL, Pirgozliev VR, Edge A, Thompson DF. The use of metabonomics to uncover differences between the small molecule profiles of eggs from cage and barn housing systems. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Gika H, Virgiliou C, Theodoridis G, Plumb RS, Wilson ID. Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1117:136-147. [PMID: 31009899 DOI: 10.1016/j.jchromb.2019.04.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/25/2022]
Abstract
Liquid chromatography (LC) hyphenated to mass spectrometry is currently the most widely used means of determining metabolic phenotypes via both untargeted and targeted analysis. At present a range of analytical separations, including reversed-phase, hydrophilic interaction and ion-pair LC are employed to maximise metabolome coverage with ultra (high) performance liquid chromatography (UHPLC) increasingly displacing conventional high performance liquid chromatography because of the need for short analysis times and high peak capacity in such applications. However, it is widely recognized that these methodologies do not entirely solve the problems facing researchers trying to perform comprehensive metabolic phenotyping and in addition to these "routine" approaches there are continuing investigations of alternative separation methods including 2-dimensional/multi column approaches. These involve either new stationary phases or multidimensional combinations of the more conventional materials currently used, as well as application of miniaturization or "new" approaches such as supercritical HP and UHP- chromatographic separations. There is also a considerable amount of interest in the combination of chromatographic and ion mobility separations, with the latter providing both an increase in resolution and the potential to provide additional structural information via the determination of molecular collision cross section data. However, key problems remain to be solved including ensuring quality, comparability across different laboratories and the ever present difficulty of identifying unknowns.
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Affiliation(s)
- Helen Gika
- Department of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece
| | - Christina Virgiliou
- Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Georgios Theodoridis
- Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | | | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College, Exhibition Road, South Kensington, London SW7 2AZ, UK.
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16
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Tůma P. The Control of Glucose and Lactate Levels in Nutrient Medium After Cell Incubation and in Microdialysates of Human Adipose Tissue by Capillary Electrophoresis with Contactless Conductivity Detection. Methods Mol Biol 2019; 1972:95-108. [PMID: 30847786 DOI: 10.1007/978-1-4939-9213-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Two methods of capillary electrophoresis with contactless conductivity detection have been developed for monitoring the levels of glucose and lactate in clinical samples. The separations are performed in uncoated fused silica capillaries with inner diameter 10 or 20 μm, total length 31.5 cm, length to detector 18 cm, using an Agilent electrophoretic instrument with an integrated contactless conductivity detector. Glucose is determined in optimized background electrolyte, 50 mM NaOH with pH 12.6 and 2-deoxyglucose is used as an internal standard; the determination of lactate is performed in 40 mM CHES/NaOH with pH 9.4 and lithium cations as an internal standard. Both substances are determined in minimal volumes of (1) nutrient media after cell incubation, and (2) microdialysates of human adipose tissue; after dilution and filtration as the only treatment of the sample. The migration time of glucose is 2.5 min and that of lactate is 1.5 min with detection limits at the micromolar concentration level. The developed techniques are suitable for sequential monitoring of glucose and lactate over time during metabolic experiments.
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Affiliation(s)
- Petr Tůma
- Department of Hygiene, Third Faculty of Medicine, Charles University, Prague, Czech Republic.
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17
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Diamantidou D, Zotou A, Theodoridis G. Wine and grape marc spirits metabolomics. Metabolomics 2018; 14:159. [PMID: 30830493 DOI: 10.1007/s11306-018-1458-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/04/2018] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Mass spectrometry (MS)-based and nuclear magnetic resonance (NMR) spectroscopic analyses play a key role in the field of metabolomics due to their important advantages. The use of metabolomics in wine and grape marc spirits allows a more holistic perspective in monitoring and gaining information on the making processes and thus it can assist on the improvement of their quality. OBJECTIVES This review surveys the latest metabolomics approaches for wine and grape marc spirits with a focus on the description of MS-based and NMR spectroscopic analytical techniques. METHODS We reviewed the literature to identify metabolomic studies of wine and grape marc spirits that were published until the end of 2017, with the key term combinations of 'metabolomics', 'wine' and 'grape marc spirits'. Through the reference lists from these studies, additional articles were identified. RESULTS The results of this review showed that the application of different metabolomics approaches has significantly increased the knowledge of wine metabolome and grape marc spirits; however there is not yet a single analytical platform that can completely separate, detect and identify all metabolites in one analysis. CONCLUSIONS The authentication and quality control of wines and grape marc spirits has to be taken with caution, since the product's chemical composition could be affected by many factors. Despite intrinsic limitations, NMR spectroscopy and MS based strategies remain the key analytical methods in metabolomics studies. Authenticity, traceability and health issues related to their consumption are the major research initiatives in wine and grape marc spirits metabolomics analysis.
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Affiliation(s)
- Dimitra Diamantidou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia Zotou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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18
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Bruderer T, Varesio E, Hidasi AO, Duchoslav E, Burton L, Bonner R, Hopfgartner G. Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition. Anal Bioanal Chem 2018; 410:1873-1884. [PMID: 29411086 DOI: 10.1007/s00216-018-0860-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/12/2017] [Accepted: 01/08/2018] [Indexed: 11/27/2022]
Abstract
High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H]+ and 483 in negative mode [M-H]-. MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously were reported in HMDB to be found in plasma. Graphical abstract Library generation workflow for LC-SWATH MS, using collision energy spread, accurate mass, and fragment annotation.
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Affiliation(s)
- Tobias Bruderer
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24, Quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Emmanuel Varesio
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland
| | - Anita O Hidasi
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24, Quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Eva Duchoslav
- Sciex, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
| | - Lyle Burton
- Sciex, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
| | - Ron Bonner
- Ron Bonner Consulting, Newmarket, ON, L3Y 3C7, Canada
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24, Quai Ernest Ansermet, 1211, Geneva 4, Switzerland.
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19
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Abstract
Metabolic profiling has advanced greatly in the past decade and evolved from the status of a research topic of a small number of highly specialized laboratories to the status of a major field applied by several hundreds of laboratories, numerous national centers, and core facilities. The present chapter provides our view on the status of the remaining challenges and a perspective of this fascinating research area.
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Affiliation(s)
- Helen G Gika
- School of Medicine, Aristotle University, Thessaloniki, Greece.
| | | | - Ian D Wilson
- Department of Surgery and Cancer, Imperial College London, London, UK
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20
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Begou O, Gika HG, Theodoridis GA, Wilson ID. Quality Control and Validation Issues in LC-MS Metabolomics. Methods Mol Biol 2018; 1738:15-26. [PMID: 29654580 DOI: 10.1007/978-1-4939-7643-0_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Global metabolic profiling (untargeted metabolomics) of different and complex biological matrices aims to implement an holistic, hypothesis-free analysis of (potentially) all the metabolites present in the analyzed sample. However, such an approach, although it has been the focus of great interest over the past few years, still faces many limitations and challenges, particularly with regard to the validation and the quality of the obtained results. The present protocol describes a quality control (QC) procedure for monitoring the precision of the analytical process involving untargeted metabolic phenotyping of urine and plasma/serum. The described/suggested methodology can be applied to different biological matrices, such as biological biofluids, cell, and tissue extracts.
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Affiliation(s)
- Olga Begou
- Department of Chemistry, Aristotle University, Thessaloniki, Greece
| | - Helen G Gika
- School of Medicine, Aristotle University, Thessaloniki, Greece.
| | | | - Ian D Wilson
- Department of Surgery and Cancer, Imperial College London, London, UK
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21
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Nothias LF, Boutet-Mercey S, Cachet X, De La Torre E, Laboureur L, Gallard JF, Retailleau P, Brunelle A, Dorrestein PC, Costa J, Bedoya LM, Roussi F, Leyssen P, Alcami J, Paolini J, Litaudon M, Touboul D. Environmentally Friendly Procedure Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking for the Discovery of Potent Antiviral Compounds from Euphorbia semiperfoliata. JOURNAL OF NATURAL PRODUCTS 2017; 80:2620-2629. [PMID: 28925702 DOI: 10.1021/acs.jnatprod.7b00113] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A supercritical fluid chromatography-based targeted purification procedure using tandem mass spectrometry and molecular networking was developed to analyze, annotate, and isolate secondary metabolites from complex plant extract mixture. This approach was applied for the targeted isolation of new antiviral diterpene esters from Euphorbia semiperfoliata whole plant extract. The analysis of bioactive fractions revealed that unknown diterpene esters, including jatrophane esters and phorbol esters, were present in the samples. The purification procedure using semipreparative supercritical fluid chromatography led to the isolation and identification of two new jatrophane esters (13 and 14) and one known (15) and three new 4-deoxyphorbol esters (16-18). The structure and absolute configuration of compound 16 were confirmed by X-ray crystallography. This compound was found to display antiviral activity against Chikungunya virus (EC50 = 0.45 μM), while compound 15 proved to be a potent and selective inhibitor of HIV-1 replication in a recombinant virus assay (EC50 = 13 nM). This study showed that a supercritical fluid chromatography-based protocol and molecular networking can facilitate and accelerate the discovery of bioactive small molecules by targeting molecules of interest, while minimizing the use of toxic solvents.
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Affiliation(s)
- Louis-Félix Nothias
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
- Laboratoire de Chimie des Produits Naturels, CNRS, UMR SPE 6134, University of Corsica , 20250 Corte, France
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Stéphanie Boutet-Mercey
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - Xavier Cachet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
- Laboratoire de Pharmacognosie, UMR 8638 COMETE CNRS, Faculté de Pharmacie, University of Paris Descartes , Sorbonne Paris Cité, 75270 Paris, France
| | - Erick De La Torre
- Departamento de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III , Ctra. Pozuelo Km.2, 28220, Majadahonda, Madrid, Spain
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid . Pz. Ramon y Cajal s/n, 28040 Madrid, Spain
| | - Laurent Laboureur
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Jean Costa
- Laboratoire de Chimie des Produits Naturels, CNRS, UMR SPE 6134, University of Corsica , 20250 Corte, France
| | - Luis M Bedoya
- Departamento de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III , Ctra. Pozuelo Km.2, 28220, Majadahonda, Madrid, Spain
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid . Pz. Ramon y Cajal s/n, 28040 Madrid, Spain
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - Pieter Leyssen
- Laboratory for Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven , B-3000 Leuven, Belgium
| | - José Alcami
- Departamento de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III , Ctra. Pozuelo Km.2, 28220, Majadahonda, Madrid, Spain
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid . Pz. Ramon y Cajal s/n, 28040 Madrid, Spain
| | - Julien Paolini
- Laboratoire de Chimie des Produits Naturels, CNRS, UMR SPE 6134, University of Corsica , 20250 Corte, France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, University of Paris-Saclay , 91198 Gif-sur-Yvette, France
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22
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Gray N, Zia R, King A, Patel VC, Wendon J, McPhail MJW, Coen M, Plumb RS, Wilson ID, Nicholson JK. High-Speed Quantitative UPLC-MS Analysis of Multiple Amines in Human Plasma and Serum via Precolumn Derivatization with 6-Aminoquinolyl-N-hydroxysuccinimidyl Carbamate: Application to Acetaminophen-Induced Liver Failure. Anal Chem 2017; 89:2478-2487. [PMID: 28194962 DOI: 10.1021/acs.analchem.6b04623] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A targeted reversed-phase gradient UPLC-MS/MS assay has been developed for the quantification /monitoring of 66 amino acids and amino-containing compounds in human plasma and serum using precolumn derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AccQTag Ultra). Derivatization of the target amines required minimal sample preparation and resulted in analytes with excellent chromatographic and mass spectrometric detection properties. The resulting method, which requires only 10 μL of sample, provides the reproducible and robust separation of 66 analytes in 7.5 min, including baseline resolution of isomers such as leucine and isoleucine. The assay has been validated for the quantification of 33 amino compounds (predominantly amino acids) over a concentration range from 2 to 20 and 800 μM. Intra- and interday accuracy of between 0.05 and 15.6 and 0.78-13.7% and precision between 0.91 and 16.9% and 2.12-15.9% were obtained. A further 33 biogenic amines can be monitored in samples for relative changes in concentration rather than quantification. Application of the assay to samples derived from healthy controls and patients suffering from acetaminophen (APAP, paracetamol)-induced acute liver failure (ALF) showed significant differences in the amounts of aromatic and branched chain amino acids between the groups as well as a number of other analytes, including the novel observation of increased concentrations of sarcosine in ALF patients. The properties of the developed assay, including short analysis time, make it suitable for high-throughput targeted UPLC-ESI-MS/MS metabonomic analysis in clinical and epidemiological environments.
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Affiliation(s)
- Nicola Gray
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Rabiya Zia
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Adam King
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Vishal C Patel
- Institute of Liver Studies and Transplantation, Kings College Hospital , Denmark Hill, London SE5 9RS, United Kingdom
| | - Julia Wendon
- Institute of Liver Studies and Transplantation, Kings College Hospital , Denmark Hill, London SE5 9RS, United Kingdom
| | - Mark J W McPhail
- Institute of Liver Studies and Transplantation, Kings College Hospital , Denmark Hill, London SE5 9RS, United Kingdom
| | - Muireann Coen
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Robert S Plumb
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Ian D Wilson
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Jeremy K Nicholson
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.,MRC-NIHR National Phenome Centre, Division of Computational and Systems Medicine, Department of Surgery and Cancer, IRDB Building, Imperial College London, Hammersmith Hospital , London W12 0NN, United Kingdom
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23
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Investigation of the derivatization conditions for GC-MS metabolomics of biological samples. Bioanalysis 2017; 9:53-65. [PMID: 27921459 DOI: 10.4155/bio-2016-0224] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AIM Metabolomics applications represent an emerging field where significant efforts are directed. Derivatization consists prerequisite for GC-MS metabolomics analysis. METHODS Common silylation agents were tested for the derivatization of blood plasma. Optimization of methoxyamination and silylation reactions was performed on a mixture of reference standards, consisting of 46 different metabolites. Stability of derivatized metabolites was tested at 4°C. RESULTS Optimum results were achieved using N-methyl-N-(trimethylsilyl)trifluoroacetamide. Methoxyamination at room temperature for 24 h followed by 2-h silylation at high temperature lead to efficient derivatization. CONCLUSION Formation and stability of derivatives among metabolites differ greatly, so derivatization should be studied before application in metabolomics studies.
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24
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Impact of exercise on fecal and cecal metabolome over aging: a longitudinal study in rats. Bioanalysis 2017; 9:21-36. [DOI: 10.4155/bio-2016-0222] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: Physical exercise can reduce adverse conditions during aging, while both exercise and aging act as metabolism modifiers. The present study investigates rat fecal and cecal metabolome alterations derived from exercise during rats’ lifespan. Methods & results: Groups of rats trained life-long or for a specific period of time were under study. The training protocol consisted of swimming, 15–18 min per day, 3–5 days per week, with load of 4–0% of rat's weight. Fecal samples and cecal extracts were analyzed by targeted and untargeted metabolic profiling methods (GC–MS and LC–MS/MS). Effects of exercise and aging on the rats’ fecal and cecal metabolome were observed. Conclusion: Fecal and cecal metabolomics are a promising field to investigate exercise biochemistry and age-related alterations.
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Metabolomic Strategies Involving Mass Spectrometry Combined with Liquid and Gas Chromatography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:77-98. [DOI: 10.1007/978-3-319-47656-8_4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Cai X, Li R. Concurrent profiling of polar metabolites and lipids in human plasma using HILIC-FTMS. Sci Rep 2016; 6:36490. [PMID: 27819279 PMCID: PMC5098236 DOI: 10.1038/srep36490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/17/2016] [Indexed: 12/22/2022] Open
Abstract
Blood plasma is the most popularly used sample matrix for metabolite profiling studies, which aim to achieve global metabolite profiling and biomarker discovery. However, most of the current studies on plasma metabolite profiling focused on either the polar metabolites or lipids. In this study, a comprehensive analysis approach based on HILIC-FTMS was developed to concurrently examine polar metabolites and lipids. The HILIC-FTMS method was developed using mixed standards of polar metabolites and lipids, the separation efficiency of which is better in HILIC mode than in C5 and C18 reversed phase (RP) chromatography. This method exhibits good reproducibility in retention times (CVs < 3.43%) and high mass accuracy (<3.5 ppm). In addition, we found MeOH/ACN/Acetone (1:1:1, v/v/v) as extraction cocktail could achieve desirable gathering of demanded extracts from plasma samples. We further integrated the MeOH/ACN/Acetone extraction with the HILIC-FTMS method for metabolite profiling and smoking-related biomarker discovery in human plasma samples. Heavy smokers could be successfully distinguished from non smokers by univariate and multivariate statistical analysis of the profiling data, and 62 biomarkers for cigarette smoke were found. These results indicate that our concurrent analysis approach could be potentially used for clinical biomarker discovery, metabolite-based diagnosis, etc.
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Affiliation(s)
- Xiaoming Cai
- School of Public Health, Soochow University, Suzhou 215123, China.,Department of Pharmacology, University of California, Irvine, Irvine, CA 92697, United States
| | - Ruibin Li
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.,Division of NanoMedicine, Department of Medicine, University of California, Los Angeles, CA 90095, United States
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27
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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28
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Ortmayr K, Causon TJ, Hann S, Koellensperger G. Increasing selectivity and coverage in LC-MS based metabolome analysis. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Fu HY, Guo JW, Yu YJ, Li HD, Cui HP, Liu PP, Wang B, Wang S, Lu P. A simple multi-scale Gaussian smoothing-based strategy for automatic chromatographic peak extraction. J Chromatogr A 2016; 1452:1-9. [PMID: 27207578 DOI: 10.1016/j.chroma.2016.05.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/23/2022]
Abstract
Peak detection is a critical step in chromatographic data analysis. In the present work, we developed a multi-scale Gaussian smoothing-based strategy for accurate peak extraction. The strategy consisted of three stages: background drift correction, peak detection, and peak filtration. Background drift correction was implemented using a moving window strategy. The new peak detection method is a variant of the system used by the well-known MassSpecWavelet, i.e., chromatographic peaks are found at local maximum values under various smoothing window scales. Therefore, peaks can be detected through the ridge lines of maximum values under these window scales, and signals that are monotonously increased/decreased around the peak position could be treated as part of the peak. Instrumental noise was estimated after peak elimination, and a peak filtration strategy was performed to remove peaks with signal-to-noise ratios smaller than 3. The performance of our method was evaluated using two complex datasets. These datasets include essential oil samples for quality control obtained from gas chromatography and tobacco plant samples for metabolic profiling analysis obtained from gas chromatography coupled with mass spectrometry. Results confirmed the reasonability of the developed method.
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Affiliation(s)
- Hai-Yan Fu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China.
| | - Jun-Wei Guo
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Yong-Jie Yu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China; School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Key Laboratory of Hui Medicine Modernization, Ministry of Education, Yinchuan 750004, China.
| | - He-Dong Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Hua-Peng Cui
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Ping-Ping Liu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Bing Wang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Sheng Wang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peng Lu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
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31
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Zhang T, Watson DG. Evaluation of the technical variations and the suitability of a hydrophilic interaction liquid chromatography-high resolution mass spectrometry (ZIC-pHILIC-Exactive orbitrap) for clinical urinary metabolomics study. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1022:199-205. [DOI: 10.1016/j.jchromb.2016.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/24/2016] [Accepted: 04/08/2016] [Indexed: 01/09/2023]
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32
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Gray N, Adesina-Georgiadis K, Chekmeneva E, Plumb RS, Wilson ID, Nicholson JK. Development of a Rapid Microbore Metabolic Profiling Ultraperformance Liquid Chromatography-Mass Spectrometry Approach for High-Throughput Phenotyping Studies. Anal Chem 2016; 88:5742-51. [PMID: 27116471 DOI: 10.1021/acs.analchem.6b00038] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A rapid gradient microbore ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) method has been developed to provide a high-throughput analytical platform for the metabolic phenotyping of urine from large sample cohorts. The rapid microbore metabolic profiling (RAMMP) approach was based on scaling a conventional reversed-phase UPLC-MS method for urinary profiling from 2.1 mm × 100 mm columns to 1 mm × 50 mm columns, increasing the linear velocity of the solvent, and decreasing the gradient time to provide an analysis time of 2.5 min/sample. Comparison showed that conventional UPLC-MS and rapid gradient approaches provided peak capacities of 150 and 50, respectively, with the conventional method detecting approximately 19 000 features compared to the ∼6 000 found using the rapid gradient method. Similar levels of repeatability were seen for both methods. Despite the reduced peak capacity and the reduction in ions detected, the RAMMP method was able to achieve similar levels of group discrimination as conventional UPLC-MS when applied to rat urine samples obtained from investigative studies on the effects of acute 2-bromophenol and chronic acetaminophen administration. When compared to a direct infusion MS method of similar analysis time the RAMMP method provided superior selectivity. The RAMMP approach provides a robust and sensitive method that is well suited to high-throughput metabonomic analysis of complex mixtures such as urine combined with a 5-fold reduction in analysis time compared with the conventional UPLC-MS method.
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Affiliation(s)
- Nicola Gray
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Kyrillos Adesina-Georgiadis
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Elena Chekmeneva
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Robert S Plumb
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Jeremy K Nicholson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom.,MRC-NIHR National Phenome Centre, Division of Computational and Systems Medicine, Department of Surgery and Cancer, IRDB Building, Imperial College London, Hammersmith Hospital , London, W12 0NN, United Kingdom
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33
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Serum Metabolomic Characterization of Liver Fibrosis in Rats and Anti-Fibrotic Effects of Yin-Chen-Hao-Tang. Molecules 2016; 21:E126. [PMID: 26805802 PMCID: PMC6273494 DOI: 10.3390/molecules21010126] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/31/2015] [Accepted: 01/14/2016] [Indexed: 02/06/2023] Open
Abstract
Yin-Chen-Hao-Tang (YCHT) is a famous Chinese medicine formula which has long been used in clinical practice for treating various liver diseases, such as liver fibrosis. However, to date, the mechanism for its anti-fibrotic effects remains unclear. In this paper, an ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOF-MS)-based metabolomic study was performed to characterize dimethylnitrosamine (DMN)-induced liver fibrosis in rats and evaluate the therapeutic effects of YCHT. Partial least squares-discriminant analysis (PLS-DA) showed that the model group was well separated from the control group, whereas the YCHT-treated group exhibited a tendency to restore to the controls. Seven significantly changed fibrosis-related metabolites, including unsaturated fatty acids and lysophosphatidylcholines (Lyso-PCs), were identified. Moreover, statistical analysis demonstrated that YCHT treatment could reverse the levels of most metabolites close to the normal levels. These results, along with histological and biochemical examinations, indicate that YCHT has anti-fibrotic effects, which may be due to the suppression of oxidative stress and resulting lipid peroxidation involved in hepatic fibrogenesis. This study offers new opportunities to improve our understanding of liver fibrosis and the anti-fibrotic mechanisms of YCHT.
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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: 544] [Impact Index Per Article: 60.4] [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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35
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Wu Y, Li L. Sample normalization methods in quantitative metabolomics. J Chromatogr A 2015; 1430:80-95. [PMID: 26763302 DOI: 10.1016/j.chroma.2015.12.007] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 12/31/2022]
Abstract
To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts.
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Affiliation(s)
- Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada.
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36
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Li Z, Tatlay J, Li L. Nanoflow LC–MS for High-Performance Chemical Isotope Labeling Quantitative Metabolomics. Anal Chem 2015; 87:11468-74. [DOI: 10.1021/acs.analchem.5b03209] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhendong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
| | - Jaspaul Tatlay
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
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37
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Integration of microfluidic LC with HRMS for the analysis of analytes in biofluids: past, present and future. Bioanalysis 2015; 7:1397-411. [DOI: 10.4155/bio.15.68] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Capillary LC (cLC) coupled to MS has the potential to improve detection limits, address limited sample volumes and allow multiple analyses from one sample. This is particularly attractive in areas where ultrahigh assay sensitivity, low limits of detection and small sample volumes are becoming commonplace. However, implementation of cLC–MS in the bioanalytical–drug metabolism area had been hampered by the lack of commercial instrumentation and the need for experts to operate the system. Recent advances in microfabricated devices such as chip-cube and ion-key technologies offer the potential for true implementation of cLC in the modern laboratory including the benefits of the combination of this type of separation with high-resolution MS.
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38
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Rainville PD, Murphy JP, Tomany M, Wilson ID, Smith NW, Evans C, Kheler J, Bowen C, Plumb RS, Nicholson JK. An integrated ceramic, micro-fluidic device for the LC/MS/MS analysis of pharmaceuticals in plasma. Analyst 2015; 140:5546-56. [DOI: 10.1039/c5an00646e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A capillary scale ceramic microfluidic LC/MS/MS system was successfully employed for the analysis of pharmaceutical compounds in plasma.
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Affiliation(s)
| | | | | | - Ian D. Wilson
- Imperial College
- Department of Surgery and Cancer
- South Kensington, London
- UK
| | | | | | | | | | - Robert S. Plumb
- Imperial College
- Department of Surgery and Cancer
- South Kensington, London
- UK
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39
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Miao H, Li MH, Zhang X, Yuan SJ, Ho CC, Zhao YY. The antihyperlipidemic effect of Fu-Ling-Pi is associated with abnormal fatty acid metabolism as assessed by UPLC-HDMS-based lipidomics. RSC Adv 2015. [DOI: 10.1039/c5ra09766e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The surface layer of Poria cocos (SLPC), a traditional Chinese medicine, has been commonly used for diuretic and antihyperlipidemia in Asia.
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Affiliation(s)
- Hua Miao
- Key Laboratory of Resource Biology and Biotechnology in Western China
- Ministry of Education
- Northwest University
- Xi'an
- China
| | - Ming-Hua Li
- National Institutes for Food and Drug Control
- State Food and Drug Administration
- Beijing
- China
| | - Xu Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China
- Ministry of Education
- Northwest University
- Xi'an
- China
| | - Sheng-Jun Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western China
- Ministry of Education
- Northwest University
- Xi'an
- China
| | - Charlene C. Ho
- Department of Biochemistry
- Li Ka Shing Faculty of Medicine
- The University of Hong Kong
- Hong Kong
- China
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China
- Ministry of Education
- Northwest University
- Xi'an
- China
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40
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Shyti R, Kohler I, Schoenmaker B, Derks RJE, Ferrari MD, Tolner EA, Mayboroda OA, van den Maagdenberg AMJM. Plasma metabolic profiling after cortical spreading depression in a transgenic mouse model of hemiplegic migraine by capillary electrophoresis – mass spectrometry. MOLECULAR BIOSYSTEMS 2015; 11:1462-71. [DOI: 10.1039/c5mb00049a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cortical spreading depression-induced brain metabolic changes have been captured in the plasma of a transgenic migraine mouse model using CE-MS.
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Affiliation(s)
- Reinald Shyti
- Department of Human Genetics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Isabelle Kohler
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Bart Schoenmaker
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Rico J. E. Derks
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Michel D. Ferrari
- Department of Neurology
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Else A. Tolner
- Department of Neurology
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
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