Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops

Catchpole, Gareth; Beckmann, Manfred; Enot, David; Mondhe, Madhav; Zywicki, Britta; Taylor, Janet A.; Hardy, Nigel; Smith, A. R.; King, Ross D.; Kell, Douglas B.; Fiehn, Oliver; Draper, John

doi:10.1073/pnas.0503955102

Cited by 356 publications

(309 citation statements)

References 26 publications

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“…26 Metabolite changes that are observed in diseased individuals as a primary indicator have been an important part of clinical practice. 27 Metabolomics is the comprehensive assessment of endogenous metabolites and attempts to systematically identify and quantify metabolites from a biological sample.…”

Section: Bringing Metabolomics Into the Forefront Of Hcc Researchmentioning

confidence: 99%

Power of metabolomics in diagnosis and biomarker discovery of hepatocellular carcinoma

2013

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Hepatocellular carcinoma (HCC) is the commonest primary hepatic malignancy and the third most common cause of cancer-related death worldwide. Incidence remains highest in the developing world and is steadily increasing across the developed world. Current diagnostic modalities, of ultrasound and a-fetoprotein, are expensive and lack sensitivity in tumor detection. Because of its asymptomatic nature, HCC is usually diagnosed at late and advanced stages, for which there are no effective therapies. Thus, biomarkers for early detection and molecular targets for treating HCC are urgently needed. Emerging highthroughput metabolomics technologies have been widely applied, aiming at the discovery of candidate biomarkers for cancer staging, prediction of recurrence and prognosis, and treatment selection. Metabolic profiles, which are affected by many physiological and pathological processes, may provide further insight into the metabolic consequences of this severe liver disease. Small-molecule metabolites have an important role in biological systems and represent attractive candidates to understand HCC phenotypes. The power of metabolomics allows an unparalleled opportunity to query the molecular mechanisms of HCC. This technique-driven review aims to demystify the metabolomics pathway, while also illustrating the potential of this technique, with recent examples of its application in

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Section: Bringing Metabolomics Into the Forefront Of Hcc Researchmentioning

confidence: 99%

Power of metabolomics in diagnosis and biomarker discovery of hepatocellular carcinoma

2013

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“…Compounds can be identified which determine the taste of some foods. Metabolomics has shown that genetically modified potatoes and tomatoes differ from normal ones by just a few compounds like fructans and flavonoids respectively [37,38]. Also, verification of labelled ingredients which we believe to be true can be achieved by metabolomics.…”

Section: Metabolomics In Food Industrymentioning

confidence: 88%

Metabolomics: A Tool Ahead for Understanding Molecular Mechanisms of Drugs and Diseases

2014

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To refer to metabolomics as a new field is injustice to ancient doctors who used ants to diagnose the patients of diabetes having glycosuria. Measuring the levels of molecules in biological fluids believing them to be the representatives of biochemical pathways of carbohydrates, fats, proteins, nucleic acids or xenobiotic metabolism and deciphering meaningful data from it is what can be called as metabolomics, just as high glucose in urine suggests diabetes mellitus. Genomics, epigenetics, proteomics, transcriptomics finally converge to metabolomics, which are the signatures of mechanisms of bodily processes which is why understanding this science can have many applications. Just as a heap of stones does not make a house, having data of metabolite levels does not make it a science. Analyzing this data would help us in constructing biochemical pathways and their interactions. Analyzing the changes caused by a drug in the metabolite levels would help us in deriving the mechanisms by which the drug acts. Comparing metabolite levels in diseased with non-diseased, good-responders with poor-responders to a particular drug can help in identifying new markers of a disease or response to a drug respectively. Also, metabolite levels of an endogenous substrate can tell us the status of a person's metabolizing enzymes and help in drug dose titration. Generating hypothesis by identifying the new molecular markers and testing their utility in clinics seems to be the most promising approach in future. This review narrates the modes of quantifying and identifying metabolome, its proposed applications in diagnosis, monitoring and understanding the diseases and drug responses. We also intend to identify hindrances in using metabolomics in clinical studies or experiments.

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“…chromatography combined with mass spectrometry (MS) or nuclear magnetic resonance (NMR) spectroscopy is capable of detecting all metabolites within a given biological sample Hall, 2006;Allwood et al, 2008). Over the past decade many methods for the high-throughput metabolomic analysis of plant derived samples have been established for gas chromatography combined with MS (GC-MS; Fiehn et al, 2000;Fernie et al, 2004;Lisec et al, 2006), direct injection mass spectrometry (DIMS; Goodacre et al, 2003;Catchpole et al, 2005;Allwood et al, 2006), liquid chromatography MS (LC-MS; Tolstikov et al, 2003;Jander et al, 2004;von Roepenack-Lahaye et al, 2004;Vorst et al, 2005;Moco et al, 2006;Rischer et al, 2006;De Vos et al, 2007), capillary electrophoresis MS (CE-MS; Sato et al, 2004), and 1 H-NMR (Ratcliff e and Shachar-Hill, 2001;Le Gall et al, 2003;Ward et al, 2003;Choi et al, 2004Choi et al, , 2006. 1 H-NMR has proven to be an appropriate tool for untargeted plant metabolomics, especially where studies focus upon samples that contain highly abundant bulk metabolite species, for example sugars in fruits (Biais et al, 2009).…”

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confidence: 99%

“…1 H-NMR has the advantage that it produces signals that correlate directly and linearly with compound abundance (Lewis et al, 2007), although for many studies it lacks the sensitivity required to obtain information on low-level metabolites that can alternatively be 34 provided by MS based approaches. DIMS provides a rapid (∼2 min per sample) metabolite fi ngerprint (Goodacre et al, 2003;Allwood et al, 2006), which has proven to be valuable for a fi rstround screen of material (indicating robust sample growth, collection and extraction methods) prior to more expensive and time-consuming chromatography combined with MS approaches (Catchpole et al, 2005). DIMS is also gaining in popularity with the advent of high-resolution and -precision Fourier transform ion cyclotron resonance (FT-ICR)-MS instruments (Aharoni et al, 2002;Hirai et al, 2004;Southam et al, 2007), although without the application of chromatography, DIMS alone cannot resolve isobaric metabolites.…”

mentioning

confidence: 99%

“…Metabolomics has proven to be a valuable tool for the comprehensive profi ling of plant derived samples for the study of plant systems (Fiehn et al, 2000;Ratcliff e and Shachar-Hill, 2001;Catchpole et al, 2005;Krishnan et al, 2005;von RoepenackLahaye et al, 2004;Moco et al, 2006) and natural products research Ketchum et al, 2003;Pauli et al, 2005), especially when combined with chemometric data analysis approaches (Goodacre et al, 2004;Jonsson et al, 2004;van der Greef and Smilde, 2005;Goodacre, 2007). Plants provide a great challenge in metabolomics due to the rich chemical diversity of metabolites that they possess across a huge range of concentrations; estimates of 100000-200000 metabolites have been made for the plant kingdom (Oksman-Caldentey and Inzé, 2004).…”

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confidence: 99%

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An introduction to liquid chromatography–mass spectrometry instrumentation applied in plant metabolomic analyses

Allwood

Goodacre

2009

Phytochemical Analysis

218

143

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Over the past decade the application of non-targeted high-throughput metabolomic analysis within the plant sciences has gained ever increasing interest and has truly established itself as a valuable tool for plant functional genomics and studies of plant biochemical composition. Whilst proton nuclear magnetic resonance ( 1 H-NMR) spectroscopy is particularly appropriate for the analysis of bulk metabolites and gas chromatography mass spectrometry (GC-MS) to the analysis of volatile organic compounds (VOC's) and derivatised primary metabolites, liquid chromatography (LC)-MS is highly applicable to the analysis of a wide range of semi-polar compounds including many secondary metabolites of interest to plant researchers and nutritionists. In view of the recent developments in the separation sciences, leading to the advent of ultra high performance liquid chromatography (UHPLC) and MS based technology showing the ever improving resolution of metabolite species and precision of mass measurements (sub-ppm accuracy now being achievable), this review sets out to introduce the background and update the reader upon LC, high performance (HP)LC and UHPLC, as well as the large range of MS instruments that are being applied in current plant metabolomic studies. As well as covering the theory behind modern day LC-MS, the review also discusses the most relevant metabolomics applications for the wide range of MS instruments that are currently being applied to LC.

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Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops

Cited by 356 publications

References 26 publications

Power of metabolomics in diagnosis and biomarker discovery of hepatocellular carcinoma

Power of metabolomics in diagnosis and biomarker discovery of hepatocellular carcinoma

Metabolomics: A Tool Ahead for Understanding Molecular Mechanisms of Drugs and Diseases

An introduction to liquid chromatography–mass spectrometry instrumentation applied in plant metabolomic analyses

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