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. Agencies 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 the agrochemical industry, such as the US-EPA Environmental Chemistry Methods (https://www.epa.gov/pesticide-analytical-methods/environmental-chemistry-methods-ecm). Instrument vendors 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 4000 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.

1. AMOS: the EPA database of analytical methods
and open mass spectral database supporting
non-targeted analysis
Gregory Janesch1, Erik Carr1, Vicente Samano2, James McCord3,
Jacqueline Bangma3, Jon Sobus4 and Antony Williams4
1. ORAU Student Services Contractor 2. Senior Environmental Employment Program
3. Center for Environmental Measurement and Modeling and 4. Center for Computational Toxicology & Exposure,
ALL at the U.S. Environmental Protection Agency
October 2023: FDA Cheminformatics Workshop
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. Background
• A huge number of openly available sources exist for spectra,
documentation of analytical procedures, etc.
• Search engines can easily find high-traffic sources, but
maybe not niche-but-high-quality ones
– Most are not “structurally-enabled”
• Useful to have complementary types of data alongside each
other, especially with consistent substance identifiers
• Non-targeted analysis can benefit from a broad, high-quality
experimental database as a reference
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3. About AMOS - General
• AMOS is a cheminformatics application integrating spectra
and analytical methods with consistent substance identifiers
• Provides mappings between substances and records (method
documents, experimental spectra, etc.)
• Under development for ~18 months as a “proof-of-concept”;
not yet available publicly
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4. About AMOS - Data
• Three categories of records:
– Spectra (~210,000)
– Methods (~4100)
– Fact Sheets (>3000)
• Most data are open access, some are just external links
– All data links back to the original source, if possible
• Data is being continually updated (new datasets & updates)
• Many chemicals of interest to EPA – PFAS, pesticides, etc.
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5. About AMOS - Curation
• Identifiers vary between different sources so we must curate
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• A single chemical can have dozens
of names
– FTOH 10:1
– 10:1 FTOH
– 10:1 Fluorotelomer alcohol
– 2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,11
-Henicosafluoroundecan-1-ol
– 1-Undecanol, 2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,
10,10,11,11,11-heneicosafluoro-

6. About AMOS – Curation Issue Example
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7. About AMOS – Curating Methods
• Often have a table of
substances
– Can be extracted with scripts
• Sample matrix, limits of
detection, etc. still need to be
manually collected
• Some are old, scanned
documents that require fully
manual work
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8. Spectra
• About 210,000 experimental spectra covering about 21,500
substances (not including externally-linked ones)
• Most are from external sources
– About 90% between MassBank EU, MoNA, & HMDB
• EPA labs now providing spectra (especially PFAS)
• Includes metadata like instrument settings (when possible)
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9. Methods
• Almost 4100 in AMOS so far from an assortment of
vendors, publications, and government agencies
– Agencies including US-EPA, DEA, CDC, FDA, OSHA, USGS, USDA
– Vendors including Agilent, Shimadzu, LECO, Sciex
• Searchable on analytes, matrix, analytical methodology,
source
• Methods can be linked to sets of spectra
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10. • Search by DTXSID,
InChIKey, CAS number,
name
• Can filter on record types or
other information
• InChIKeys and some names
will prompt disambiguation
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General Search

11. General Search – Disambiguation
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InChIKey example search:

12. General Search – Spectra
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13. General Search – Spectra
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14. General Search – Methods & Fact Sheets
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15. General Search – Methods & Fact Sheets
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16. Method with Spectra
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17. Batch Search
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• Search a set of DTXSIDs,
download info on spectra and
methods and links to original data

18. Methods List
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19. Methods List – Filtering
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20. Similar Method Search
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21. Similar Method Search
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22. Spectrum Search
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23. Connections to Other Applications
• Other apps often deal with
focused subsets of
chemicals; AMOS’s data
can augment that
• API endpoints have been
built for an NTA application
– Originally just in silico spectra
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24. Future Work
• Add more data assembled from EPA labs (standards)
• Improvements to spectral searching – in testing
– Structure, substructure, and similarity searching
• Expand spectral and chromatographic metadata
• Additional integration with other EPA applications
– Mostly just simple links to AMOS pages at the moment
• Hoping to release to the public in 2024
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25. Summary
• AMOS combines multiple kinds of analytical chemistry
data
– Primarily mass spectrometry data
– Growing steadily for the foreseeable future
• Data can be queried via a cheminformatically-oriented
application
• Intended to be useful as both an independent application
and a way of augmenting other EPA applications 25

26. Acknowledgements
• Greg Janesch – Database and App Development
• Sakuntala Sivasupramaniam – curation
• Tyler Carr – curation, visualizations
• Joshua Powell, Asif Rashid, Freddie Valone – assorted
technical support
If you want to help, send information regarding analytical
methods and method articles to williams.antony@epa.gov
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