Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics

Metabolite identification is one of the biggest bottlenecks in metabolomics. Identifying human metabolites poses experimental, analytical, and computational challenges. Here we present a pipeline of previously developed cheminformatic tools and demonstrate how it facilitates metabolite identification using solely LC/MSn data. These tools process...

How do metabolites differ from their parent molecules and how are they excreted?

Understanding which physicochemical properties, or property distributions, are favorable for successful design and development of drugs, nutritional supplements, cosmetics, and agrochemicals is of great importance. In this study we have analyzed molecules from three distinct chemical spaces (i) approved drugs, (ii) human metabolites, and (iii)...

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees

Multistage mass spectrometry (MS n) generating so-called spectral trees is a powerful tool in the annotation and structural elucidation of metabolites and is increasingly used in the area of accurate mass LC/MS-based metabolomics to identify unknown, but biologically relevant, compounds. As a consequence, there is a growing need for...

OMG: Open molecule generator

Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental...

MetiTree: A web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data

Identification of metabolites using high-resolution multi-stage mass spectrometry (MSn) data is a significant challenge demanding access to all sorts of computational infrastructures. MetiTree is a user-friendly, web application dedicated to organize, process, share, visualize and compare MS n data. It integrates several features to export and...

Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space

Chemogenomic approaches, which link ligand chemistry to bioactivity against targets (and, by extension, to phenotypes) are becoming more and more important due to the increasing number of bioactivity data available both in proprietary databases as well as in the public domain. In this article we review chemogenomics approaches applied in four...

Understanding and classifying metabolite space and Metabolite-Likeness

While the entirety of 'Chemical Space' is huge (and assumed to contain between 1063 and 10200 'small molecules'), distinct subsets of this space can nonetheless be defined according to certain structural parameters. An example of such a subspace is the chemical space spanned by endogenous metabolites, defined as 'naturally occurring' products of...