Environmental metabolomics : databases and tools for data analysis
Kido Soule, Melissa C.
Kujawinski, Elizabeth B.
MetadataShow full item record
Metabolomics is the study of small molecules, or ‘metabolites’, that are the end products of biological processes. While -omics technologies such as genomics, transcriptomics, and proteomics measure the metabolic potential of organisms, metabolomics provides detailed information on the organic compounds produced during metabolism and found within cells and in the environment. Improvements in analytical techniques have expanded our understanding of metabolomics and developments in computational tools have made metabolomics data accessible to a broad segment of the scientific community. Yet, metabolomics methods have only been applied to a limited number of projects in the marine environment. Here, we review analysis techniques for mass spectrometry data and summarize the current state of metabolomics databases. We then describe a boutique database developed in our laboratory for efficient data analysis and selection of mass spectral targets for metabolite identification. The code to implement the database is freely available on GitHub (https://github.com/joefutrelle/domdb). Data organization and analysis are critical, but often under-appreciated, components of metabolomics research. Future advances in environmental metabolomics will take advantage of continued development of new tools that facilitate analysis of large metabolomics datasets.
© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marine Chemistry 177 (2015): 366–373, doi:10.1016/j.marchem.2015.06.012.
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International
Showing items related by title, author, creator and subject.
Longnecker, Krista; Kido Soule, Melissa C.; Kujawinski, Elizabeth B. (2014-10)Phytoplankton are significant producers of dissolved organic matter (DOM) in marine ecosystems but the identity and dynamics of this DOM remain poorly constrained. Knowledge on the identity and dynamics of DOM are crucial ...
Kujawinski, Elizabeth B. (2010-05)Microbes mediate global biogeochemical cycles through their metabolism, and all metabolic processes begin with the interaction between the microbial cell wall or membrane and the external environment. For all heterotrophs ...