Analytical methods can vary in nature from detailed regulatory methods to more summary in nature. Regulatory method documents can include details of analytes which can be studied, supported matrices, reagents, methodological details, statistical performance, interlaboratory validation and other details. Summary methods provide a general overview of reagents, instrumentation and commonly a short list of analytes. Regulatory bodies including the US Environmental Protection Agency (US-EPA), US Geological Survey (USGS), US Department of Agriculture (USDA) and others provide detailed analytical methods and collections of summary methods from industry. Instrument vendors including Agilent, Shimadzu and others, also provide access to many hundreds of application notes which can be considered as summary methods. We have developed a cheminformatically enabled database of methods whereby chemicals have been extracted from the methods, with the identifiers (names and/or chemical abstracts registry numbers) mapped to chemical structures. The resulting database of almost 3000 methods can be searched by chemical name, CASRN, structure and similarity of chemical structure. The resulting database has been integrated into a web-based application and includes integration to public domain mass spectral data and filtering of the methods based on analyte, chemical class, method source and other related metadata. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

1. Using Cheminformatics Approaches to Develop
a Structure Searchable Database
of Analytical Methods
Antony Williams1, Greg Janesch2, Tyler Carr2,
Sakuntala Sivasupramaniam3, and Nancy Baker4
1. Center for Computational Toxicology and Exposure, US-EPA, RTP, NC
2. ORAU Student Services Contractor
3. Senior Environmental Employment (SEE) Program
4. ParlezChem Inc.
http://www.orcid.org/0000-0002-2668-4821
March 2024: Spring Fall Meeting, New Orleans, LA
The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA

2. Building a Methods Database
• Simple Vision: I want to find the best method(s) associated with a
chemical and/or class of chemicals
• Answer the question “I cannot find a method for my chemical” - HELP
• The Approach:
– Aggregate MS method documents (and adjust the definition of “what is a useful method”)
– Extract chemistry (mostly CASRN and Names)
– Map CASRN and Names to structures
– Deliver a proof-of-concept application to search a database by names, CASRNs, InChIKeys
and ultimately structure
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3. Most people start with Google
• People have many places to search for methods, and
there is no one integration hub, except for search engines
• Search engines can return so many hits – then you filter
by analytes, matrix, analytical methodology, so many
synonyms and abbreviations for so many chemicals
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4. Synonyms, Abbreviations and Chemicals
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• CAS Numbers, Names
and Abbreviations can
limit what’s possible…

5. Might this be a better view?
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6. Might this be a better view?
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7. When methods are mapped to chemistry…
• The advantages of mapping chemicals directly to methods
– When chemicals are mapped it opens access to many other tools
– Chemical structures allow for QSAR modeling
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8. …and what if we could then profile toxicity?
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9. …and what if we could then profile toxicity?
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10. …or simply harvest data from the
CompTox Chemicals Dashboard
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11. What data would you like???
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12. Introducing AMOS
Analytical Methods and Spectra Database
• Three types of data in the database:
– Methods (regulatory, lab manuals and SOPs, publications, tech notes)
– Spectra (from public domain and our own laboratories)
– Monographs (harvested from SWGDRUG and other sites)
• Some methods have associated spectra
• Some data are just externally linked
• Currently contains around 263,000 spectra, 600,000 external
links, 4800 “Fact Sheets” and ~5000 methods
• Spectra – LC-MS, GC-MS, NMR
• ALL data are growing in number
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13. Where are there methods?
• Agency-based methods
– EPA, USGS, USDA, CDC, FDA, OSHA, DEA, ATSDR, NIOSH …
• ASTM and ISO methods
• Vendor application notes – Bruker, Waters, Agilent, Sciex,
Shimadzu, LECO, Thermo
• Peer-reviewed articles
• Laboratory Documents – lab manuals, SOPs
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14. A view of the methods list
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15. Filtering the list for interests…
• Look for pesticides studied in water, by GC/MS, after 1990
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16. Where are there methods?
• 900 method documents from the EPA harvested
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17. Many Scanned Documents!!!
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• Methods generally developed by
the agrochemical companies
• Include parents plus degradation
products
• Lots of scanned, old, documents
but the historical records are still
of significant use
• Electronic document forms of old
documents still of benefit

18. Embedding the old Method PDFs
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19. Embedding New Method PDFs
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20. When Methods are OPEN Access
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21. When Methods are PubMed OPEN Access
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22. Proprietary Methods for INTERNAL Access
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23. If there is no method for your chemical
• Use “Chemical Similarity Searching” so that you can find
chemicals that are similar in structure space
• Use the “Tanimoto Similarity Search
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24. Searching for a chemical – CASRN, Name
Direct structure searching coming
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25. When Methods are Not Enough
• EPA is highly active in the field of non-targeted analysis
• We have been applying lots of cheminformatics approaches
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26. Building a spectrum library to search against
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27. Linking to actual spectra
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28. Linking to actual spectra
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29. There are errors EVERYWHERE: 110-75-8

30. It can be challenging
9/365 chemicals…

31. There are MANY errors in public
spectral databases
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32. There are MANY errors in public
spectral databases
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33. There are MANY errors in public
spectral databases
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34. There are MANY errors in public
spectral databases
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• Chemical structure representations would ideally
be standardized…consider tautomeric forms
• Not all substances are explicit and can be
ambiguous representations

35. Fact Sheets – 4800 of them and growing
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36. >40,000 AnalyticalQC spectra
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37. Conclusions
• We have built the first chemical structure indexed open
database of “methods”.
• Methods are not just “approved methods” but also
standard operating procedures, application notes, lab
manuals, regulatory methods etc.
• Integrating methods to experimental spectral data will
serve our non-targeted analysis efforts
• Work is underway to make it public
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38. If you want to help…
• Send information regarding analytical methods and method
articles to williams.antony@epa.gov
• If you want to add methods or spectral data please contact me
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