“MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies

McEachran, Andrew D.; Mansouri, Kamel; Grulke, Chris; Schymanski, Emma L.; Ruttkies, Christoph; Williams, Antony J.

doi:10.1186/s13321-018-0299-2

Title: “MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies

Abstract

Chemical database searching has become a fxture in many non-targeted identifcation workfows based on highresolution 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) workfow 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 workfow 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 identifcation using HRMS. The importance of this form of structural representation for HRMS is demonstrated with several examples, including integration with the in silico fragmentation softwaremore »« less

Authors:

McEachran, Andrew D. ^[1]; Mansouri, Kamel ^[1]; Grulke, Chris ^[2]; Schymanski, Emma L. ^[3]; Ruttkies, Christoph ^[4]; Williams, Antony J. ^[2]

Oak Ridge Inst. for Science and Education (ORISE), Research Triangle Park, NC (United States). Research Participation Program, US Environmental Protection Agency (EPA); US Environmental Protection Agency (EPA), Research Triangle Park, NC (United States). Office of Research and Development. National Center for Computational Toxicology
US Environmental Protection Agency (EPA), Research Triangle Park, NC (United States). Office of Research and Development. National Center for Computational Toxicology
Univ. of Luxembourg, Belvaux, (Luxembourg). Luxembourg Centre for Systems Biomedicine (LCSB)
Leibniz Inst. of Plant Biochemistry (IPB), Halle (Germany). Dept. of Stress and Development Biology

Publication Date:: Thu Aug 30 00:00:00 EDT 2018

Research Org.:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1627027

Grant/Contract Number:: AC05-06OR23100

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Cheminformatics

Additional Journal Information:: Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1758-2946

Publisher:: Chemistry Central Ltd.

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS AND COMPUTING; Chemistry; Computer Science; High-resolution mass spectrometry (HRMS); Structure identification; Structure curation; Database searching

Citation Formats


                    McEachran, Andrew D., Mansouri, Kamel, Grulke, Chris, Schymanski, Emma L., Ruttkies, Christoph, and Williams, Antony J. “MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies.  United States: N. p., 2018. 
Web.  doi:10.1186/s13321-018-0299-2.

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                    McEachran, Andrew D., Mansouri, Kamel, Grulke, Chris, Schymanski, Emma L., Ruttkies, Christoph, & Williams, Antony J. “MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies.  United States.  https://doi.org/10.1186/s13321-018-0299-2

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                    McEachran, Andrew D., Mansouri, Kamel, Grulke, Chris, Schymanski, Emma L., Ruttkies, Christoph, and Williams, Antony J. Thu .  
"“MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies".  United States.  https://doi.org/10.1186/s13321-018-0299-2.  https://www.osti.gov/servlets/purl/1627027.

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@article{osti_1627027,

  title        = {“MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies},

  author       = {McEachran, Andrew D. and Mansouri, Kamel and Grulke, Chris and Schymanski, Emma L. and Ruttkies, Christoph and Williams, Antony J.},

  abstractNote = {Chemical database searching has become a fxture in many non-targeted identifcation workfows based on highresolution 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) workfow 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 workfow 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 identifcation 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/.},

  doi          = {10.1186/s13321-018-0299-2},

  journal      = {Journal of Cheminformatics},

  number       = 1,

  volume       = 10,

  place        = {United States},

  year         = {Thu Aug 30 00:00:00 EDT 2018},

  month        = {Thu Aug 30 00:00:00 EDT 2018}

}

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Aalizadeh, Reza; Thomaidis, Nikolaos S.; Bletsou, Anna A.
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Fourches, Denis; Muratov, Eugene; Tropsha, Alexander
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Journal of Chemical Education, Vol. 87, Issue 11
DOI: 10.1021/ed100697w

The Chemical and Products Database, a resource for exposure-relevant data on chemicals in consumer products
journal, July 2018

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DOI: 10.1038/sdata.2018.125

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Oberacher, Herbert; Sasse, Michael; Antignac, Jean-Philippe
Environmental Sciences Europe, Vol. 32, Issue 1
DOI: 10.1186/s12302-020-00314-9

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity
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Mansouri, Kamel; Kleinstreuer, Nicole; Abdelaziz, Ahmed M.
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DOI: 10.1289/ehp5580

CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification
journal, April 2019

Djoumbou-Feunang, Yannick; Pon, Allison; Karu, Naama
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DOI: 10.3390/metabo9040072

Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag
text, January 2019

Ruttkies, Christoph; Schymanski, Emma L.; Strehmel, Nadine
ETH Zurich
DOI: 10.3929/ethz-b-000354203

Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag
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Ruttkies, Christoph; Schymanski, Emma L.; Strehmel, Nadine
Analytical and Bioanalytical Chemistry, Vol. 411, Issue 19
DOI: 10.1007/s00216-019-01885-0

Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns
journal, August 2019

McEachran, Andrew D.; Balabin, Ilya; Cathey, Tommy
Scientific Data, Vol. 6, Issue 1
DOI: 10.1038/s41597-019-0145-z

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity
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Mansouri, Kamel; Kleinstreuer, Nicole; Abdelaziz, Ahmed M.
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