MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra

Abstract

Despite the increasing importance of metabolomics approaches, the structural elucidation of metabolites from mass spectral data remains a challenge.Although several reliable tools to identify known metabolites exist, identifying compounds that have not been previously seen is a challenging task that still eludes modern bioinformatics tools. Here, we describe an automated method for substructure recommendation from mass spectra using pattern mining techniques. Based on previously seen recurring substructures our approach succeeds in identifying parts of unknown metabolites. An important advantage of this approach is that it does not require any prior informationNC 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/134189 doi: bioRxiv preprint first posted online May. 4, 2017; concerning the metabolites to be identified, and therefore it can be used for the (partial) identification of unknown unknowns. Using association rule mining we are able to recommend valid substructures even for those metabolites for which no match can be found in spectral libraries or structural databases. We further demonstrate how this approach is complementary to existing metabolite identification tools, achieving improved identification results. The method is called MESSAR (MEtabolite SubStructure AutoRecommender) and is implemented as a free online web service available at

Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

“…To further support the in silico -predicted optimal enzyme-catalyzed path towards a particular product, the intermediates can be searched for in the metabolome network. Recent progress in the annotation of metabolite substructure based on CID spectra might help in annotating unknown peaks as pathway intermediates [192] . However, retrosynthesis, performed on a multitude of precursor–product metabolite pairs, might boost the metabolic network complexity.…”