Mass spectrometry based environmental metabolomics: a primer and review

Viant, Mark R.; Sommer, Ulf

doi:10.1007/s11306-012-0412-x

Cited by 133 publications

(73 citation statements)

References 109 publications

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“…Metabolomics use analytical techniques such as nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry to identify metabolites in pathways or classes of compounds (Viant and Sommer, 2013). The capacity to detect subtle molecular changes, and the comprehensive nature of metabolite measurements, have resulted in the increased popularity of metabolomics in aquatic toxicology (Lankadurai et al, 2013;Tuffnail et al, 2009).…”

Section: Toxicogenomics In Aquatic Toxicology Studiesmentioning

confidence: 99%

Toxicogenomic applications of Chinese rare minnow (Gobiocypris rarus) in aquatic toxicology

Liang

Zha

2016

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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Rare minnow (Gobiocypris rarus), a Chinese native species, are an excellent emerging model organism for aquatic toxicity testing and chemical safety assessment. "Big data" omics approaches (i.e., genomics, proteomics, and metabolomics) to inform mechanistic toxicology are now applied to studies in rare minnows to better understand toxicity and molecular pathways perturbed by chemicals. This review highlights recent applications of toxicogenomics to study changes in the gene and protein expression profiles in rare minnows in response to chemicals. Here we briefly describe studies that utilized cDNA microarrays in characterization of the cellular effects of rare minnows in single and mixed chemical exposures. Then we compare gel-based proteomics studies in liver of rare minnows following treatment with endocrine disrupting chemicals including 17β-estradiol, 17α-methyltestosterone, pentachlorophenol, and perfluorooctanoic acid. A total of 90 proteins identified in these studies were functionally annotated and categorized. These responsive proteins have roles in biological processes that include metabolism (37.8%), response to oxidation/chemicals (16.7%), signal transduction (11.1%), transport (10%), cytoskeleton (6.7%) and others (17.8%). In addition, recent investigations of endocrine disrupting effects and neurotoxicity of benzotriazole, an emerging contaminant, are summarized. The objective is to continue to enrich genome and protein databases for this species and to integrate molecular datasets to consider temporal effects and complex regulation at the level of the genome and proteome.

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Section: Toxicogenomics In Aquatic Toxicology Studiesmentioning

confidence: 99%

Toxicogenomic applications of Chinese rare minnow (Gobiocypris rarus) in aquatic toxicology

Liang

Zha

2016

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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“…This enables structural annotations, which provide molecular level identification, through database comparison of tandem MS spectra and/or retention times (Vinaixa et al, 2016). Such an approach is common in metabolomic studies and has been extensively reviewed (Liesenfeld et al, 2013;Viant and Sommer, 2013;Gika et al, 2014;Rubert et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

et al. 2017

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Dissolved organic matter (DOM) is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 10 15 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS). To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI) MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS) and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC), molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the annotation rate and should be broadly encouraged. Our analysis also identifies shortcomings of the current Petras et al. LC-MS/MS Analysis of DOMdata analysis workflow that need to be addressed by the community in the future. This work will lay the foundation for an integrative, non-targeted molecular analysis of DOM which, together with next generation sequencing, meta-proteomics and physical data, will pave the way to a more comprehensive understanding of the role of DOM in structuring marine ecosystems.

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“…61 A metabolômica ambiental envolve o estudo das repostas metabólicas de organismos a fatores bióticos (competição, mutualismo, relação parasita-hospedeiro, planta-herbívoro, entre outros), e abióticos (temperatura, umidade, disponibilidade de nutrientes, exposição a poluentes, etc.). [62][63][64][65][66][67] A aplicação da metabolômica na área ambiental é muito ampla e envolve o estudo de organismos aquáticos, [67][68][69][70] de plantas, 71 e como estes respondem ao estresse oxidativo, 72 estresse abiótico, [73][74][75] fatores bióticos, 76 ou fatores bióticos e abióticos simultaneamente. 77 Também são encontrados trabalhos de exposição de organismos a poluentes, 78 18,86 entre outros.…”

Section: Ambientalunclassified

Metabolômica: Definições, Estado-Da-Arte E Aplicações Representativas

Canuto¹,

Costa²,

Cruz³

et al. 2017

Quim. Nova

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METABOLOMICS: DEFINITIONS, STATE-OF-THE-ART AND REPRESENTATIVE APPLICATIONS.Metabolomics is an emerging and promising omics approach used to understand biological mechanisms. By untargeted and targeted metabolomics analyses, metabolites are determined in biological samples (fluids, cells, tissues, etc.) by comparison of control groups with altered groups, undergoing different therapies, submitted to differing stress levels, dietary modulation, or promoted by a disease, or specific condition, etc., using sophisticated analytical techniques, and advanced data treatment and statistical analyses. In this review, the concepts involved in metabolomics studies were presented, describing in details all steps involved in the metabolomics workflow, for untargeted and targeted strategies. Finally, the potential of metabolomics is illustrated by applications in representative areas: clinical, environmental, food and nutrition, forensic toxicology, microbiology, parasitology, plants, and sports. Relevant reviews were compiled to characterize each of these areas, and a corresponding application of untargeted and targeted metabolomics were described.Keywords: metabolomics; untargeted metabolomics; targeted metabolomics; metabolomics workflow. INTRODUÇÃOAs ciências ômicas buscam o entendimento do funcionamento celular dos organismos e suas alterações biológicas. Fazem parte deste conjunto de ciências, a genômica (estudo da alteração dos genes), a transcriptômica (estudo das alterações dos transcritos), a proteômica (estudo das alterações das proteínas), e a metabolômica (estudo das alterações dos metabólitos). Metabólitos são produtos intermediários ou finais do metabolismo em uma amostra biológica.1 O conjunto de todos os metabólitos de baixa massa molecular (até 1500 Da), presentes ou alterados em um sistema biológico, é chamado de metaboloma (do inglês, metabolome).2 A pesquisa relacionada a metabólitos vem sendo desenvolvida há décadas, mas em 1999, Nicholson et al. definiram a metabonômica (do inglês, metabonomics), como sendo a medida quantitativa da resposta metabólica de um sistema biológico após estímulos fisiopatológicos ou modificações genéticas.3 Já o termo metabolômica (do inglês, metabolomics) foi introduzido em 2001, por Oliver Fiehn, como sendo a análise abrangente e quantitativa do metaboloma de um sistema biológico. 4 Além disso, a literatura nos apresenta outras denominações envolvendo esse campo da ciência, tais como: perfil metabólico (do inglês, metabolic profiling), descrito como sendo a análise de metabólitos previamente selecionados de rotas bioquímicas específicas, 5 a impressão digital metabólica (do inglês, metabolic fingerprinting), que é definida como sendo "uma classificação de amostras de acordo com sua origem ou sua relevância biológica", 3 e, por último, análise footprinting (ainda sem tradução para o português), para se referir aos metabólitos excretados por uma célula em condições controladas. Observa-se, portanto, uma divergência em relação às terminologias aplicadas às análises metabolômic...

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Mass spectrometry based environmental metabolomics: a primer and review

Cited by 133 publications

References 109 publications

Toxicogenomic applications of Chinese rare minnow (Gobiocypris rarus) in aquatic toxicology

Toxicogenomic applications of Chinese rare minnow (Gobiocypris rarus) in aquatic toxicology

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

Metabolômica: Definições, Estado-Da-Arte E Aplicações Representativas

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