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"MS-Ready" structures for non-targeted high-resolution mass spectrometry screening studies.
Andrew D McEachran1,2, Kamel Mansouri3,4,5, Chris Grulke4
1Oak 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.
Journal of Cheminformatics
|September 1, 2018
Summary
A new workflow generates "MS-Ready structures" from chemical databases, improving chemical identification in high-resolution mass spectrometry (HRMS) by linking observed forms to database entries. This enhances non-targeted identification workflows.
Area of Science:
- Analytical Chemistry
- Computational Chemistry
- Environmental Science
Background:
- High-resolution mass spectrometry (HRMS) is crucial for non-targeted chemical identification.
- Discrepancies between observed chemical forms in HRMS and database entries hinder accurate identification.
- Linking diverse structural forms is essential for comprehensive data retrieval.
Purpose of the Study:
- To develop a method for generating and linking "MS-Ready structures" to database entries.
- To improve the accuracy and completeness of chemical identification in HRMS workflows.
- To provide accessible tools for searching and utilizing these linked structures.
Main Methods:
- A Konstanz Information Miner (KNIME) workflow was developed to create "MS-Ready structures" from existing chemical databases.
- These MS-Ready structures were linked to their corresponding full chemical representations.
- The generated structures and linking information were integrated into the US EPA's Chemistry Dashboard.
Main Results:
- Approximately 700,000 MS-Ready structures were generated and linked from over 760,000 original structures.
- The US EPA's Chemistry Dashboard now offers download, search, and export functionalities for these structures.
- Demonstrated utility through integration with MetFrag for in silico fragmentation analysis.
Conclusions:
- The developed workflow effectively links HRMS-observed chemical structures to database entries, enhancing identification.
- The MS-Ready structures and associated tools on the CompTox Chemistry Dashboard facilitate HRMS-based chemical identification.
- This approach significantly improves the retrieval of relevant chemical variants and metadata in complex analytical workflows.