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Integrating Eawag, LCSB, MetFrag and the CompTox Efforts in ENTACT
Citation:
Schymanski, E., B. Beck, P. Longree, H. Singer, J. Hollender, C. Ruttkies, A. McEachran, A. Chao, C. Grulke, J. Sobus, AND A. Williams. Integrating Eawag, LCSB, MetFrag and the CompTox Efforts in ENTACT. Presented at EPA's Non-Targeted Analysis Collaborative Trial (ENTACT) Workshop, RTP, NC, August 13 - 15, 2018. https://doi.org/10.23645/epacomptox.7754519
Impact/Purpose:
Abstract for presentation at Tools/Demonstration session at the EPA's Non-Targeted Analysis Collaborative Trial (ENTACT) Workshop Aug 2018
Description:
The successful identification of chemicals from non-target screening efforts often depends on the integration of experimental metadata into candidate selection and prioritization. ENTACT provided an ideal opportunity to explore how chemical information, related properties and metadata from the CompTox Chemistry Dashboard could be incorporated into the in silico identification approach MetFrag. The ENTACT challenge involved identifying chemicals in samples formed by combining substances (including mixtures) from the ToxCast library. This included identifying single components as observed in the mass spectrometer and linking these back to the source substances from ToxCast. For instance, (S)-nicotine dicitrate (substance identifier DTXSID20237235) would be observed in samples as nicotine (compound identifier DTXCID9028128) and citric acid (compound identifier DTXCID50332). The “MS-ready” linking of substance and compound identifiers employed in the Dashboard has now been integrated into MetFrag in a variety of ways to provide access to the metadata behind mixtures, yet fragment the structure as the component that is visible in the mass spectrometer. As far as we know, this is the first approach to enable in silico fragmentation and prioritization of mixtures. A MetFrag Beta Export file, including a choice of all relevant metadata fields on the Dashboard, is available via the MS-ready formula batch search option (https://comptox.epa.gov/dashboard/dsstoxdb/batch_search). A download file will allow users to use the entire Dashboard, including selected metadata, as an MS-ready database encapsulating individual components, their corresponding mixtures and metadata. This functionality is available both via the MetFrag web interface (https://msbi.ipb-halle.de/MetFragBeta/) and the command line version (http://c-ruttkies.github.io/MetFrag/projects/metfragcl/). R functions supporting the creation, batching and interpretation of MetFrag files will be public soon. This talk will demonstrate the integration efforts using a few key examples to show how critical the combination of experimental evidence and metadata can be in non-target screening identification efforts. Note: This abstract does not reflect US EPA policy.
URLs/Downloads:
DOI: Integrating Eawag, LCSB, MetFrag and the CompTox Efforts in ENTACT
ENTACT_EAWAGLCSBMETFRAGCOMPTOX_V2_M.PDF (PDF, NA pp, 7926.711 KB, about PDF)