Separation and mass spectrometry in microbial metabolomics

Garcia, David E.; Baidoo, Edward E. K.; Benke, Peter I.; Pingitore, Francesco; Tang, Yinjie J.; Villa, Sandra Irina Villa; Keasling, Jay D.

doi:10.1016/j.mib.2008.04.002

Cited by 95 publications

(66 citation statements)

References 67 publications

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“…Though it should be noted that Fourier transform ion cyclotron resonance mass spectrometry (FTICR/MS) can often resolve complex mixtures of metabolites without chromatography [15]. The wide range of chromatography (LC) options allow physical separation of most molecules to reduce signal suppression [16]. While reversephase methods tend to utilize C18 columns, a wide range of normal phase materials are utilized [16,17] e.g., popular new materials, including hydrophilic interaction chromatography (HILIC) and aqueous normal phase (ANP) have recently been developed for improved separation of polar metabolites [18].…”

Section: Lc/ms Based Metabolomicsmentioning

confidence: 99%

Dealing with the unknown: Metabolomics and Metabolite Atlases

Bowen

Northen

2010

J. Am. Soc. Mass Spectrom.

178

158

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Metabolomics is the comprehensive profiling of the small molecule composition of a biological sample. Since metabolites are often the indirect products of gene expression, this approach is being used to provide new insights into a variety of biological systems (clinical, bioenergy, etc.). A grand challenge for metabolomics is the complexity of the data, which often include many experimental artifacts. This is compounded by the tremendous chemical diversity of metabolites. Identification of each uncharacterized metabolite is in many ways its own puzzle (compared with proteomics, which is based on predictable fragmentation patterns of polypeptides). Therefore, effective data reduction/prioritization strategies are critical for this rapidly developing field. Here we review liquid chromatography electrospray ionization mass spectrometry (LC/MS)-based metabolomics, methods for feature finding/prioritization, approaches for identifying unknown metabolites, and construction of method specific 'Metabolite Atlases'.(J Am Soc Mass Spectrom 2010, 21, 1471-1476) © 2010 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry N ature utilizes a tremendous diversity of metabolites, and it is estimated that there are Ͼ200,000 plant metabolites alone [1]. Metabolomics is a rapidly growing field for studying the small molecule composition of a biological system. Liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) is becoming a method of choice for profiling metabolites in complex biological samples. This is due to its ability to effectively ionize a breath of metabolites with minimal fragmentation (versus gas chromatography-mass spectroscopy (GC/MS), robustness, and ability to scale-up to support tandem mass spectrometry based structural studies (versus capillary electrophoresis-mass spectrometry (CE-MS)) [2]. However, known metabolites are typically a small portion of the data obtained in a LC/MS metabolomics experiment (ϳ10%) [3] where the bulk are MS-artifacts and uncharacterized metabolites.Identification of unknown metabolites is cost and effort intensive, often requiring preparative scale isolation for nuclear magnetic resonance (NMR) studies or extensive chemical synthesis to enable structural comparisons using tandem mass spectrometry (MS/MS) [4]. Therefore, it is not surprising that the majority of reports focus on changes in metabolites that have authentic standards or at a minimum are found in metabolite databases. Yet, there are only a few thousand commercially available analytical standards due to lack of demand and the inherent instability of many metabolites. These standards and the endogenous metabolites contained in databases represent only a portion of endogenous metabolites. Therefore, effective methods for prioritizing, studying, and ultimately identifying uncharacterized metabolites is a critical development for LC/MS based metabolomics [5][6][7][8][9][10]. Here we discuss current LC/MS metabolomic approaches (detailed elsewhere [2,4,11,12]) and their inte...

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Section: Lc/ms Based Metabolomicsmentioning

confidence: 99%

Dealing with the unknown: Metabolomics and Metabolite Atlases

Bowen

Northen

2010

J. Am. Soc. Mass Spectrom.

178

158

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“…In context to microbiology, metabolomics can be regarded as "microbial metabolomics" which involves identifying the complete set of metabolites produced within a microbe that in turn reflects the enzymatic pathways and other network processes involved in the functioning of the cell [95][96][97]. Metabolomics assesses the interaction between cell's genome and its environment thereby understanding the novel biosynthetic and degradative pathways exploited by the microbe in utilizing the organic content present in a particular soil ecosystem [98,99].…”

Section: Metabolomicsmentioning

confidence: 99%

Decoding Complex Soil Microbial Communities through New Age "Omics"

Nair¹,

Raja²

2017

J Microb Biochem Technol

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“…Sampling of metabolite levels. For some metabolites in the system, measurements specific to the experimental system or estimates from experiments under similar physiological conditions might be available [11][12][13][14]; these estimates can provide the bounds for the computational sampling of the metabolites. In addition, the information from Step 2 will determine the direction that reversible reactions will operate and, combined with the information from Step 3, will be used for sampling the metabolite levels without violating thermodynamic and directionality constraints [57][58][59].…”

Section: Optimization and Risk Analysis Of Complex Living Entities (Omentioning

confidence: 99%

“…However, one of the limitations of these methods is that they provide only a snapshot of the fluxes and do not quantify the responses of metabolic networks to the changes in the metabolic parameters or the process parameters, such as oxygen and carbon substrate limitation, or stress agents, such as organic acids and pH. Similar to flux analysis, metabolite profiling, although provides information about the redox state of the cells, it is only a quantitative snapshot of the metabolite levels and, currently, only represents a partial set of the metabolites in pathways of interest [11][12][13][14].Mathematical modeling and computational analyses have been used successfully for metabolic engineering [15][16][17][18][19][20]. Constrained-based flux balance analysis has been one of the most widely used approaches.…”

mentioning

confidence: 99%

Production of biofuels and biochemicals: in need of an ORACLE

Mišković

Hatzimanikatis

2010

Trends in Biotechnology

101

110

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The engineering of cells for the production of fuels and chemicals involves simultaneous optimization of multiple objectives, such as specific productivity, extended substrate range and improved tolerance -all under a great degree of uncertainty. The achievement of these objectives under physiological and process constraints will be impossible without the use of mathematical modeling. However, the limited information and the uncertainty in the available information require new methods for modeling and simulation that will characterize the uncertainty and will quantify, in a statistical sense, the expectations of success of alternative metabolic engineering strategies. We discuss these considerations toward developing a framework for the Optimization and Risk Analysis of Complex Living Entities (ORACLE) -a computational method that integrates available information into a mathematical structure to calculate control coefficients. Biofuels and biochemicals: a multi-objective optimization problem Nearly 20 years ago, Tong and Cameron classified the applications of metabolic engineering into five main areas: (i) improved production and utilization of chemicals already produced/used by the host; (ii) extended substrate range for growth and production; (iii) addition of new catabolic activities for the degradation of toxic chemicals; (iv) production of chemicals new to the host; and (v) modification of the cell [1]. In the development of microorganisms for fuels and chemicals, one must consider and optimize almost all of these objectives simultaneously. For example, the economics of the fuels and commodity chemicals will require a host that is able to overproduce a fuel or chemical (native or new to the organism) from a broad range of carbon substrates, some of them not used previously by this organism, with high specific rates and with near-theoretical yields [2]. All of these issues become more challenging when we consider the use of new hosts for engineering [3,4], where there is not enough genomic information, the genetic tools for metabolic engineering are limited, and extensive knowledge about their physiology is lacking.The development of microorganisms for fuels and chemicals will also require the fine-tuning of carbon flows and redox balance. All of the biofuels currently considered require delicate manipulation of the carbon flows in the central metabolism, and any intervention in these pathways can have significant implications for the cellular physiology. Redox balance, energy charge and cofactor levels are also important because they are involved in many of the pathways for the production of biofuels and acids. For example, these pathways involve reactions that produce and consume redox potential, and their directionality is determined by the NAD + /NADH ratio. Metabolic engineering of these pathways could alter the balance of redox and coenzyme cofactors, thereby reducing the productivity and the yield, leading to the production of byproducts that could increase the cost of downstream processing [2,[5][6][...

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Separation and mass spectrometry in microbial metabolomics

Cited by 95 publications

References 67 publications

Dealing with the unknown: Metabolomics and Metabolite Atlases

Dealing with the unknown: Metabolomics and Metabolite Atlases

Decoding Complex Soil Microbial Communities through New Age "Omics"

Production of biofuels and biochemicals: in need of an ORACLE

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