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The great challenge facing metabolomics today is the expansion of metabolome coverage from a lower percentage of the cell's metabolic complement to the level of coverage offered by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the great diversity of chemicals that make up the metabolome, and the number of metabolites in the plant kingdom is considered to exceed 200,000. In this review, we focus on web resources that can be exploited in order to improve the identification and quantification of analytes and, ultimately, metabolites.

There is a wide range of software available that not only helps in this, but also in the related area of ​​peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software, as well as comments on the level of programming skills required to effectively exploit its core functions.

Furthermore, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up more valuable resources for the identification of metabolites. Ultimately, we postulate that only through ongoing community sharing of information, such as that deposited in the databases described in the article, is it likely that we can make significant progress toward improving our coverage of the plant metabolome. .


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