I ran some metabolomics results through MetaboAnalyst 5.0 a few months ago and the pathway analysis results included aminoacyl-tRNA biosynthesis. I ran them again after the update to 6.0, and aminoacyl-tRNA biosynthesis was not among the results. When I downloaded the databases from MetaboAnalyst, and searched for the Pathway-related library for the string “aminoacyl-tRNA” in the Ontology field and in the Biological library, my searches did not return any results.
Is accurate with respect to the underlying databases that support the current version of MSEA, and if so, is there a reason why aminoacyl-tRNA biosynthesis has been removed from these databases?
In MSEA, we mainly use the metabolic pathways. Aminoacyl-tRNA biosynthesis is categorized to Genetic Information Processing. It has contain two types of metabolites, either basic amino acids or their related aminoacyl-tRNA without exact molecular weight. The basic amino acids are quite common in the metabolic datasets. It would be more meaningful to use this pathway for gene/protein enrichment as the extensive existing amino acids could result in false positives.
Just to make sure I understand - this pathway, and possibly other pathways, that exist in the underlying database at its source (eg, KEGG), have been curated out of the database for purposes of MSEA? The rationale in this case is that this particular pathway has been deemed not appropriate to identify as an enriched pathway within a metabolomics dataset?
Thanks again!