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J Cheminform. 2018 Aug 30;10(1):45. doi: 10.1186/s13321-018-0299-2.

"MS-Ready" structures for non-targeted high-resolution mass spectrometry screening studies.

Author information

1
Oak Ridge Institute for Science and Education (ORISE) Research Participation Program, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC, 27711, USA. mceachran.andrew@epa.gov.
2
National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Mail Drop D143-02, 109 T.W. Alexander Dr., Research Triangle Park, NC, 27711, USA. mceachran.andrew@epa.gov.
3
Oak Ridge Institute for Science and Education (ORISE) Research Participation Program, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC, 27711, USA.
4
National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Mail Drop D143-02, 109 T.W. Alexander Dr., Research Triangle Park, NC, 27711, USA.
5
Integrated Laboratory Systems, Inc., 601 Keystone Dr., Morrisville, NC, 27650, USA.
6
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, 4367, Belvaux, Luxembourg.
7
Department of Stress and Development Biology, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany.
8
National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Mail Drop D143-02, 109 T.W. Alexander Dr., Research Triangle Park, NC, 27711, USA. williams.antony@epa.gov.

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/ .

KEYWORDS:

Database searching; High-resolution mass spectrometry (HRMS); Structure curation; Structure identification

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