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Metabolites, Volume 1, Issue 1 (December 2011), Pages 1-78

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Editorial

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Open AccessEditorial Metabolites: A Novel Platform for Converging Research on Metabolism and Metabolomics
Metabolites 2011, 1(1), 1-2; doi:10.3390/metabo1010001
Received: 3 December 2010 / Accepted: 3 December 2010 / Published: 7 December 2010
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Abstract
Technological advances in analytical instrumentation and advances in data modeling are working in synergy to open up new perspectives and research agendas in metabolic research. Thanks to the legacy of the Human Genome Project and its continued impact in the post-genomic era, metabolism
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Technological advances in analytical instrumentation and advances in data modeling are working in synergy to open up new perspectives and research agendas in metabolic research. Thanks to the legacy of the Human Genome Project and its continued impact in the post-genomic era, metabolism is now thought of in a whole-genome context, even when the focus is on a single metabolite and individual metabolic reactions. For a few model organisms we now have extensive, and in some cases complete, information about components that perform integrated metabolic functions. This promises a true paradigm shift in our understanding of the processes of metabolism, but also poses new challenges. As complex and coordinated global behaviors are observed in what were thought to be "simple" organisms, many challenges remain in the experimental domain, as well as in the integration of data generated by increasingly high-throughput analytical techniques. Indeed, in the new era of metabolic research, mathematical and computational modeling is expected to play an increasingly important role. For many complex biochemical phenomena, use of mathematical models may be the best way to build a consistent picture and generate testable hypotheses based on complex yet inevitably incomplete data sets.[...] Full article

Research

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Open AccessArticle Alkylation or Silylation for Analysis of Amino and Non-Amino Organic Acids by GC-MS?
Metabolites 2011, 1(1), 3-20; doi:10.3390/metabo1010003
Received: 14 December 2010 / Revised: 11 January 2011 / Accepted: 14 January 2011 / Published: 17 January 2011
Cited by 35 | PDF Full-text (507 KB) | HTML Full-text | XML Full-text
Abstract
Gas chromatography–mass spectrometry (GC-MS) is a widely used analytical technique in metabolomics. GC provides the highest resolution of any standard chromatographic separation method, and with modern instrumentation, retention times are very consistent between analyses. Electron impact ionization and fragmentation is generally reproducible between
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Gas chromatography–mass spectrometry (GC-MS) is a widely used analytical technique in metabolomics. GC provides the highest resolution of any standard chromatographic separation method, and with modern instrumentation, retention times are very consistent between analyses. Electron impact ionization and fragmentation is generally reproducible between instruments and extensive libraries of spectra are available that enhance the identification of analytes. The major limitation is the restriction to volatile analytes, and hence the requirement to convert many metabolites to volatile derivatives through chemical derivatization. Here we compared the analytical performance of two derivatization techniques, silylation (TMS) and alkylation (MCF), used for the analysis of amino and non-amino organic acids as well as nucleotides in microbial-derived samples. The widely used TMS derivatization method showed poorer reproducibility and instability during chromatographic runs while the MCF derivatives presented better analytical performance. Therefore, alkylation (MCF) derivatization seems to be preferable for the analysis of polyfunctional amines, nucleotides and organic acids in microbial metabolomics studies. Full article
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Review

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Open AccessReview Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics
Metabolites 2011, 1(1), 21-40; doi:10.3390/metabo1010021
Received: 8 October 2011 / Revised: 2 November 2011 / Accepted: 4 November 2011 / Published: 11 November 2011
Cited by 37 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges of
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Electrospray ionization mass spectrometry (ESI-MS) has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges of lipidomics. Herein, we discuss the principles, advantages, and possible limitations of different mass spectrometry-based methodologies for lipid quantification, as well as a few practical issues important for accurate quantification of individual lipid species. Accordingly, accurate quantification of individual lipid species, one of the key challenges in lipidomics, can be practically met. Full article
(This article belongs to the Special Issue Lipidomics)
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Open AccessReview Volatile Metabolites
Metabolites 2011, 1(1), 41-63; doi:10.3390/metabo1010041
Received: 21 October 2011 / Revised: 16 November 2011 / Accepted: 17 November 2011 / Published: 25 November 2011
Cited by 12 | PDF Full-text (247 KB) | HTML Full-text | XML Full-text
Abstract
Volatile organic compounds (volatiles) comprise a chemically diverse class of low molecular weight organic compounds having an appreciable vapor pressure under ambient conditions. Volatiles produced by plants attract pollinators and seed dispersers, and provide defense against pests and pathogens. For insects, volatiles may
[...] Read more.
Volatile organic compounds (volatiles) comprise a chemically diverse class of low molecular weight organic compounds having an appreciable vapor pressure under ambient conditions. Volatiles produced by plants attract pollinators and seed dispersers, and provide defense against pests and pathogens. For insects, volatiles may act as pheromones directing social behavior or as cues for finding hosts or prey. For humans, volatiles are important as flavorants and as possible disease biomarkers. The marine environment is also a major source of halogenated and sulfur-containing volatiles which participate in the global cycling of these elements. While volatile analysis commonly measures a rather restricted set of analytes, the diverse and extreme physical properties of volatiles provide unique analytical challenges. Volatiles constitute only a small proportion of the total number of metabolites produced by living organisms, however, because of their roles as signaling molecules (semiochemicals) both within and between organisms, accurately measuring and determining the roles of these compounds is crucial to an integrated understanding of living systems. This review summarizes recent developments in volatile research from a metabolomics perspective with a focus on the role of recent technical innovation in developing new areas of volatile research and expanding the range of ecological interactions which may be mediated by volatile organic metabolites. Full article
(This article belongs to the Special Issue Secondary Metabolites and Metabolism)
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Open AccessReview Role of Cereal Secondary Metabolites Involved in Mediating the Outcome of Plant-Pathogen Interactions
Metabolites 2011, 1(1), 64-78; doi:10.3390/metabo1010064
Received: 4 November 2011 / Revised: 21 November 2011 / Accepted: 29 November 2011 / Published: 15 December 2011
Cited by 11 | PDF Full-text (602 KB) | HTML Full-text | XML Full-text
Abstract
Cereal crops such as wheat, rice and barley underpin the staple diet for human consumption globally. A multitude of threats to stable and secure yields of these crops exist including from losses caused by pathogens, particularly fungal. Plants have evolved complex mechanisms to
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Cereal crops such as wheat, rice and barley underpin the staple diet for human consumption globally. A multitude of threats to stable and secure yields of these crops exist including from losses caused by pathogens, particularly fungal. Plants have evolved complex mechanisms to resist pathogens including programmed cell death responses, the release of pathogenicity-related proteins and oxidative bursts. Another such mechanism is the synthesis and release of secondary metabolites toxic to potential pathogens. Several classes of these compounds have been identified and their anti-fungal properties demonstrated. However the lack of suitable analytical techniques has hampered the progress of identifying and exploiting more of these novel metabolites. In this review, we summarise the role of the secondary metabolites in cereal crop diseases and briefly touch on the analytical techniques that hold the key to unlocking their potential in reducing yield losses. Full article
(This article belongs to the Special Issue Secondary Metabolites and Metabolism)

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