MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
BackgroundIn spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases.DescriptionHere we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC–MS accurate mass data enabled the identity of an unknown peak to be confidently predicted.ConclusionsMINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. Furthermore, MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures.Graphical abstractMINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0087-1) contains supplementary material, which is available to authorized users.
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<p>Metabolomics, the study of the population of small molecules in a cell, has drawn intense interest in fields from medicine to synthetic biology because it can provide a fine-grain representation of cellular state and activity [1–4]. Of particular interest is untargeted metabolomics, which seeks to measure as much of the metabolome as possible by limiting methodological detection bias. The dominant analysis technique for untargeted metabolomics is chromatography coupled with mass spectrometry (MS) but this method is hindered by a large number of unknown peaks [5] and the limited number of reference spectra available to identify the peaks [6]. A number of tools have been developed to propose structural matches for unannotated peaks [7–11] but in practice these tools either return too many candidates when drawing from large chemical databases such as PubChem [12] or miss compounds not yet present in curated biochemical database [13, 14].This has the effect of locking untargeted metabolomics in a unfortunate paradox: compounds that are not present in biochemical databases are not identified and in the absence of experimental identification, new compounds cannot be added to databases [15].</p><p>There is a growing consensus that many enzymes mediate undocumented side-reactions (known as promiscuous activities) as a result of exposure to diverse cellular metabolites [16, 17]. These activities may explain unannotated peaks in metabolomics datasets [18, 19] but are difficult to detect as they may be overshadowed by a known function [20] or be dependent on intracellular conditions [21]. Predicting novel chemical reactions based on broad enzyme specificity has been utilized by a number of tools for the prediction of new biochemical pathways [22–24]. Recently, this technique has also been used to expand structure databases for metabolomics by the MyCompoundID tool [25] the In Vivo/In Silico Metabolites Database (IIMDB) [15], LipidHome [26] and others [27, 28].</p><p>Here we present Metabolic In silico Network Expansions (MINEs) that utilize the Biochemical Network Integrated Network Explorer (BNICE) [29, 30] to expand on general biochemical databases as well as organism-specific databases for Escherichia coli and yeast. The focus on endogenously present and organism-specific metabolites has been cited as critical to improving the confidence of compound matches [5] and thus we complement existing resources that focus on human metabolism. In principle, these predictions could also be made using Reaction Difference Matching (RDM) [23], machine learning methods [31, 32], or other rule-based methods such as ChemAxon's Metabolizer. Each of these approaches has their benefits; the output really depends on the quality and coverage of the reaction rules used in the analysis. We selected BNICE because we have a set of BNICE reaction rules that have been demonstrated to reproduce a large fraction of known biochemical reactions [24], as well as to predict enzyme reactions that were subsequently verified experimentally [33]. Importantly, we also have the right to re-distribute BNICE output. No license is required for academic users to access the website or APIs and all BNICE predicted compounds are available for download in SDF format from the website.</p><!><p>MINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.</p><!><p>Compound information was obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (Release 68.0) [36], the Yeast Metabolome Database (YMDB) (Version 1.0) [37] and EcoCyc (Version 17.0) [38]. Generalized (containing R groups), inorganic compounds, and disconnected fragments were removed using the Pybel toolkit [39]. Generalized structures are of very limited utility, as they cannot be assigned an accurate mass or represented in a canonical form. Where possible, we encourage developers to avoid ambiguity by enumerating all possible structures in their databases. Additionally, biochemical databases often contain numerous duplicate compounds [40] and these were identified by Standard InChIKey [41] comparison and removed for computational efficiency.</p><!><p>Generalizing a BNICE reaction rule from known biochemical reactions. The common motif of the hydrolysis of the 1,3-diketone is shaded for emphasis.</p><!><p>BNICE products may take a variety of tautomeric forms depending on the source structure and the nature of the operator applied. Therefore, products were processed with ChemAxon's Standardizer & Structure Checker (JChem 6.0.4, 2013) to ensure canonical valences and placement of charge. Natural Product Likeness scores [42] and estimated logP values were calculated with a standalone Java ARchive (JAR) package and ChemAxon's Calculator Plugins (JChem 6.0.4, 2013) respectively. Estimated Kováts Retention Indices were calculated using the NIST RI algorithm [43].</p><p>Compounds were matched to PubChem [44] and KEGG COMPOUND databases with the connectivity block of InChIKeys for annotation. Generated compounds are assigned identifiers based on hash of the canonical SMILES [45] for internal use and a numeric MINE ID for human readability. Finally, the exact mass and chemical fingerprints of structures were calculated with Pybel.</p><p>Compound and reaction data is stored as collections in a Mongo Database (v2.6.2). A compound entry contains the chemical formula, exact mass, InChIKey canonical SMILES [45], FP2 and FP4 fingerprints and lists of reactions in which the compound is predicted to participate as a reactant or product. A compound may also be annotated with additional information such as common names or database links if it matches a KEGG or PubChem entry. Reactions are uniquely identified by an 'R' followed by the SHA1 hash of the sorted chemical reaction. Reactions entries contain arrays of reactants and products as tuples of the stoichiometric coefficient and the compound ID as well as a list of the operators that predicted the reaction.</p><!><p>Comparison of MINEs generated from various source databases and other databases containing computationally predicted metabolites</p><p>Histogram of Natural Product Likeness. This plot shows the distribution of Natural Product Likeness Scores for the KEGG Database (mean score 0.77), the KEGG MINE (mean score 0.98) and a random sample of 500,000 PubChem compounds (mean score −0.52). A more positive score indicates more natural atomic features.</p><p>Screenshot of Metabolomics search results. This screenshot displays features of the metabolomics results including filtering by attributes and highlighting (blue) of compound present in a specified KEGG genome reconstruction.</p><p>Annotation of MassBank data</p><!><p>Finally, to demonstrate the practical utility of MINE databases, we utilized the EcoCyc MINE to annotate untargeted metabolomics data from an E. coli knockout study analyzed by LC–MS. The protocols for sample extraction, data acquisition and post processing are available in the supplementary information. 493 distinct exact MS features were extracted, 30 of which were identified following a traditional annotation workflow using NIST MSPepsearch (see Additional file 2); in contrast, the EcoCyc MINE database proposed candidates for 132 of the accurate masses when searching with 5 mDa precision and with [M+]+, [M+H]+, [M+Na]+ adducts. The resulting MINE candidates were consistent with 93% of the NIST MSPepsearch results.</p><!><p>Positive MS spectrum (a), positive MS/MS spectrum (b) and negative MS/MS spectrum (c). The positive MS spectrum provides the mass of the precursor ion [M+H]+ = 690.5099 Da and its isotopic abundance pattern. The prominent ion in the positive MS/MS spectrum corresponds to the neutral loss of the phosphoethanolamine head group. The negative MS/MS spectrum shows the molecular ion [M−H]− as well as a pair of ions corresponding to the (16:0) and (16:1) side chains.</p><!><p>In addition to the existing web tools, the underlying MINE databases are accessible through free, developer-friendly APIs. Clients are available for integration into Python, Perl and JavaScript frameworks at https://github.com/JamesJeffryes/MINE-API. This API allows the databases to be integrated into existing candidate ranking algorithms and pipelines. Future versions of these databases will incorporate transformation rules for spontaneous chemical reactions of metabolites, and improved filtering and prioritization of candidate structures.</p><p>In addition to expanding the scope for the metabolome, the MINE framework also offers a pipeline for illuminating the synthesis and degradation of poorly annotated secondary metabolites. While applied very broadly to nearly all of metabolism in this study, BNICE expansions may be focused on a region of interest in the metabolic network by adjusting the starting compounds and permissible transformations in a manner similar to that recently demonstrated by Ridder et al. [27]. These targeted MINEs will integrate the generation of plausible pathways by BNICE with the tools to detect the presence of predicted pathway intermediates with accurate mass spectrometry thereby accelerating the process of proposing and evaluating hypothetical enzymatic synthesis routes for a number of compounds of interest.</p><!><p>Here we have presented Metabolic In silico Network Expansions (MINEs) that utilizes generalized biochemical transformations to propose structures for use in untargeted metabolomics. The resulting compounds are rarely found in PubChem but are structurally similar to natural products. We have demonstrated the utility of these databases for proposing correct metabolite structures that stymied a standard annotation workflow. MINE data are accessible without licensing restrictions for non-commercial users through a user-friendly web interface and API for developers in several common scripting languages.</p><!><p>MINE databases are freely accessible at: http://minedatabase.mcs.anl.gov and API clients are available at https://github.com/JamesJeffryes/MINE-API. There are no restrictions for Academic Use. Commercial users must obtain a license from Pathway Solutions Inc. (www.pathway.jp) and explicit permission from the authors.</p><!><p>Transformations of High and low Natural Product Likeness compounds.</p><p>Sample extraction, LC–MS data collection and processing protocols and repository access.</p><p>Metabolic In Silico Network Expansions</p><p>natural products</p><p>liquid chromatography–mass spectrometry</p><p>Biochemical Network Integrated Computational Explorer</p><p>Kyoto Encyclopedia of Genes and Genomes</p><p>International Union of Pure and Applied Chemistry</p><p>IUPAC International Chemical Identifier</p><p>Application Programing Interface</p>