Metabolomics: current state and evolving methodologies and tools

Oldiges, Marco; Lütz, Stephan; Pflug, Simon; Schroer, Kirsten; Stein, Nadine; Wiendahl, C.

doi:10.1007/s00253-007-1029-2

Cited by 208 publications

(135 citation statements)

References 199 publications

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“…Genetical metabolomics aims at identifying genomic loci that regulate the level of secondary metabolites of interest using comprehensive metabolomics approaches coupled to large-scale genetic marker analyses. Genetical metabolomics metabolite profi ling combined with quantitative trait locus (QTL) analysis has been proposed as a new tool to identify loci that control metabolite abundance [Oldiges et al, 2007].…”

Section: Metabolomics Engineering Of Bioactive Compoundsmentioning

confidence: 99%

Current Approaches for Enhanced Expression of Secondary Metabolites as Bioactive Compounds in Plants for Agronomic and Human Health Purposes

Jiménez-García¹,

Vazquez-Cruz²,

Guevara-González³

et al. 2013

Pol. J. Food Nutr. Sci.

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The study of secondary metabolism in plants is an important source for the discovery of bioactive compounds with a wide range of applications. Today these bioactive compounds derived from plants are important drugs such as antibiotics, and agrochemicals substitutes, they also have been economically important as fl avors and fragrances, dyes and pigments, and food preservatives. Many of the drugs sold today are synthetic modifi cations of naturally obtained substances. There is no rigid scheme for classifying secondary metabolites, but they can be divided into different groups based on their chemical components, function and biosynthesis: terpenoids and steroids, fatty acid-derived substances and polyketides, alkaloids, phenolic compounds, non-ribosomal polypeptides and enzyme cofactors. The increasing commercial importance of these chemical compounds has resulted in a great interest in secondary metabolism, particularly the possibility of altering the production of bioactive plant metabolites by means of tissue culture technology and metabolomics. In today's world the use of bioactive compounds derived from plants plays an important role in pharmaceutical applications. This review presents information about these metabolites and their applications as well as their importance in agronomy and bioactive effects on human health as nutraceuticals. This review includes also the new tendencies to produce these bioactive compounds under different stresses conditions such as biotic and abiotic stress that could be included in production systems.

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Section: Metabolomics Engineering Of Bioactive Compoundsmentioning

confidence: 99%

Current Approaches for Enhanced Expression of Secondary Metabolites as Bioactive Compounds in Plants for Agronomic and Human Health Purposes

Jiménez-García¹,

Vazquez-Cruz²,

Guevara-González³

et al. 2013

Pol. J. Food Nutr. Sci.

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“…Additional cell-wide studies, such as metabolomics [ 35] and flux analysis [ 36], are fast growing into well-established workflows that provide a truly orthologous measurement of the cellular response to stress and manipulation. Advances in the field of metabolomics have made it possible to identify thousands of metabolites [ 37] and quantify tens to hundreds of metabolites in targeted sets [ 38].…”

Section: Methods In Systems Biologymentioning

confidence: 99%

Importance of systems biology in engineering microbes for biofuel production

Mukhopadhyay

Redding

Rutherford

et al. 2008

Current Opinion in Biotechnology

121

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Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systemslevel studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.

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“…Examples are structural characterization and identification, 25,26 quantitation, 27 high-throughput screening, 28,29 proteomics, 30,31 metabonomics, 32-34 metabolomics, [35][36][37][38][39][40][41] and dereplication of natural products. In the area of dereplication, MS delivers the molecular mass information that can be used as a search query in almost all databases of small molecules.…”

Section: Introductionmentioning

confidence: 99%

Automated molecular formula determination by tandem mass spectrometry (MS/MS)

Jarussophon

Acoca

Gao

et al. 2009

Analyst

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Automated software was developed to analyze the molecular formula of organic molecules and peptides based on high-resolution MS/MS spectroscopic data. The software was validated with 96 compounds including a few small peptides in the mass range of 138-1569 Da containing the elements carbon, hydrogen, nitrogen and oxygen. A Micromass Waters Q-TOF Ultima Global mass spectrometer was used to measure the molecular masses of precursor and fragment ions. Our software assigned correct molecular formulas for 91 compounds, incorrect molecular formulas for 3 compounds, and no molecular formula for 2 compounds. The obtained 95% success rate indicates high reliability of the software. The mass accuracy of the precursor ion and the fragment ions, which is critical for the success of the analysis, was high, i.e. the accuracy and the precision of 850 data were 0.0012 Da and 0.0016 Da, respectively. For the precursor and fragment ions below 500 Da, 60% and 90% of the data showed accuracy within #0.001 Da and #0.002 Da, respectively. The precursor and fragment ions above 500 Da showed slightly lower accuracy, i.e. 40% and 70% of them showed accuracy within #0.001 Da and #0.002 Da, respectively. The molecular formulas of the precursor and the fragments were further used to analyze possible mass spectrometric fragmentation pathways, which would be a powerful tool in structural analysis and identification of small molecules. The method is valuable in the rapid screening and identification of small molecules such as the dereplication of natural products, characterization of drug metabolites, and identification of small peptide fragments in proteomics. The analysis was also extended to compounds that contain a chlorine or bromine atom.

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Metabolomics: current state and evolving methodologies and tools

Cited by 208 publications

References 199 publications

Current Approaches for Enhanced Expression of Secondary Metabolites as Bioactive Compounds in Plants for Agronomic and Human Health Purposes

Current Approaches for Enhanced Expression of Secondary Metabolites as Bioactive Compounds in Plants for Agronomic and Human Health Purposes

Importance of systems biology in engineering microbes for biofuel production

Automated molecular formula determination by tandem mass spectrometry (MS/MS)

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