Abstract
Chemical database searching has become a fixture in many non-targeted identification workflows based on high-resolution mass spectrometry (HRMS). However, the form of a chemical structure observed in HRMS does not always match the form stored in a database (e.g., the neutral form versus a salt; one component of a mixture rather than the mixture form used in a consumer product). Linking the form of a structure observed via HRMS to its related form(s) within a database will enable the return of all relevant variants of a structure, as well as the related metadata, in a single query. A Konstanz Information Miner (KNIME) workflow has been developed to produce structural representations observed using HRMS (“MS-Ready structures”) and links them to those stored in a database. These MS-Ready structures, and associated mappings to the full chemical representations, are surfaced via the US EPA’s Chemistry Dashboard (https://comptox.epa.gov/dashboard/). This article describes the workflow for the generation and linking of ~ 700,000 MS-Ready structures (derived from ~ 760,000 original structures) as well as download, search and export capabilities to serve structure identification using HRMS. The importance of this form of structural representation for HRMS is demonstrated with several examples, including integration with the in silico fragmentation software application MetFrag. The structures, search, download and export functionality are all available through the CompTox Chemistry Dashboard, while the MetFrag implementation can be viewed at https://msbi.ipb-halle.de/MetFragBeta/.
Highlights
In recent years the use of high-resolution mass spectrometry (HRMS) instrumentation coupled to gas and liquid chromatography has become increasingly common in environmental, exposure and health sciences for the detection of small molecules such as metabolites, natural products and chemicals of concern [1,2,3,4,5]
Linking metadata via MS‐Ready structures It has been demonstrated that data sources and other metadata linked to chemical structures improve identification of unknowns [7, 15, 55]
Nicarbazin (DTXSID6034762, C19H18N6O6 [58]), a coccidiostat used in poultry production, is a two component chemical whose components would dissociate in the environment, leading to the observation of individual components only via HRMS
Summary
In recent years the use of high-resolution mass spectrometry (HRMS) instrumentation coupled to gas and liquid chromatography has become increasingly common in environmental, exposure and health sciences for the detection of small molecules such as metabolites, natural products and chemicals of concern [1,2,3,4,5]. Common data processing workflows in NTA and SSA often utilize a combination of vendor-specific software, open source platforms, and in-house resources [1, 3, 7]. In NTA the analyst generally uses peak-picking software to identify molecular features to find the (pseudo) molecular ion (m/z) along with associated isotopic peaks and calculate the neutral monoisotopic mass (Fig. 1a, b). Monoisotopic masses can be searched in structure databases to retrieve tentative candidates or can be used in combination with isotopic distributions and/or
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