![]() ![]() ![]() Furthermore, rigorous standards are needed for normalization of metabolomics data 28, 29. This renders the establishment of good working practices 13, 15, 23, 24, 25, 26 more difficult than with RNA-seq 27, for example. Consequently, many different extraction techniques and combinations of analytical methods have been developed in an attempt to achieve adequate metabolite coverage. Chemical diversity, rapid turnover times and broad dynamic range in cellular abundance currently prohibit the possibility of using single-extraction and single-analysis procedures to measure all metabolites 9. Currently, combinations of the most comprehensive methods are able to quantify 700 of the 3,700 metabolites predicted to be present in Escherichia coli 17, 18, 500 of the 2,680 metabolites predicted to be present in yeast 19, 20, 8,000 of the 114,100 metabolites predicted to be present in humans 21 and only 14,000 of the over 400,000 metabolites predicted to be present in the plant kingdom 4, 22. Current capabilities for detection and quantification of metabolites fall a long way short of being comprehensive. However, thus far, even the most comprehensive methods cannot provide firm upper limits for metabolite number. We have previously estimated that upwards of 1 million different metabolites occur across the tree of life, with between 1,000 and 40,000 estimated to occur in a single species 4. ![]() Despite these comparative limitations, enormous advances have been made with regard to the number of analytes about which accurate quantitative information can be acquired, and a vast number of studies have yielded important biological information and biologically active metabolites across the kingdoms of life 14. Among the many thousands of studies published in this area over the last 20 years, notable highlights 5, 6, 7, 8, 10, 11, 16 are briefly described in Supplementary Note 1.ĭespite the insight afforded by such studies, the nature of metabolites, particularly their diversity (in both chemical structure and dynamic range of abundance 9, 12), remains a major challenge with regard to the ability to provide adequate coverage of the metabolome that can complement that achieved for the genome, transcriptome and proteome. Indeed, it is now a commonly used experimental systems biology tool with demonstrated utility in both fundamental and applied aspects of plant, microbial and mammalian research 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15. Metabolomics, the large-scale study of the metabolic complement of the cell 1, 2, 3, is a mature science that has been practiced for over 20 years 4. Nature Methods volume 18, pages 747–756 ( 2021) Cite this article Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices ![]()
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