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The EPA CompTox Chemicals Dashboard to support structure identification and chemical forensics using mass spectrometry Fal...
Overview • The CompTox Chemicals Dashboard - web- based database of 875k substances • Associated data including: – Experim...
CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 2
BASIC Search 3
Detailed Chemical Pages 4
Sources of Exposure to Chemicals 5
Identifiers to Support Searches 6
Link Access 7
NIST WebBook https://webbook.nist.gov/chemistry/ 8
MassBank of North America https://mona.fiehnlab.ucdavis.edu 9
Batch Searching 10
Aggregate data for a list of chemicals 11
Batch Search Names 12 Excel Download
Add Other Data of Interest 13
Chemical Lists of Interest… 14
Chemical Lists 15
PFAS lists of Chemicals 16
Batch Search in specific lists 17
“MS-ready” Structures 18
19
“MS-Ready Structures” https://doi.org/10.1186/s13321-018-0299-2 20
MS-Ready Mappings 21
MS-Ready Mappings Set 22
Mass and Formula Searching 23
Advanced Searches Mass Search 24
Advanced Searches Mass Search 25
MS-Ready Structures for Formula Search 26
MS-Ready Structures Batch Searches 27
MS-Ready Mappings • EXACT Formula: C10H16N2O8: 3 Hits 28
MS-Ready Mappings • Same Input Formula: C10H16N2O8 • MS Ready Formula Search: 125 Chemicals 29
MS-Ready Mappings • 125 chemicals returned in total – 8 of the 125 are single component chemicals – 3 of the 8 are isotope...
Batch Searching • Singleton searches are useful but we work with thousands of masses and formulae! • Typical questions – W...
Batch Searching Formula/Mass 32
Searching batches using MS-Ready Formula (or mass) searching 33
Additional Mass-Spec Functionality 34
Formula-Based Search 35
Select Chemicals of Interest 36
Prune to list of interest 37
Literature Searching 38
Literature Searching 39
Literature Searching 40
Work in Progress 41
List Registration Activities • Registering and curating numerous lists – NIST library of chemicals – United States Geologi...
Work in Progress • CFM-ID – Viewing and Downloading pre-predicted spectra – Search spectra against the database • Structur...
Predicted Mass Spectra http://cfmid.wishartlab.com/ • MS/MS spectra prediction for ESI+, ESI-, and EI • Predictions genera...
Search Expt. vs. Predicted Spectra
Search Expt. vs. Predicted Spectra
Spectral Viewer Comparison 47
Presented at this meeting 48
Example match 49
Predicted Data Already Public Publication and Data Files 50 https://epa.figshare.com/articles/CFM-ID_Paper_Data/7776212/1
Prototype Development 51
Prototype Development 52
API services and Open Data • Web Services https://actorws.epa.gov/actorws/ • Data sets also available for download.. 53
Web Services https://actorws.epa.gov/actorws/ • Data in UI, JSON and XML format 54
InChIKey to DTXCIDs 55 https://actorws.epa.gov/actorws/dsstox/v02/msready?identifier =UVOFGKIRTCCNKG-UHFFFAOYSA-N
MassBank mapping to Dashboard 56
When data is openly shared… 57
NORMAN Suspect List Exchange https://www.norman-network.com/?q=node/236 58
Conclusion • Dashboard access to data for ~875,000 chemicals • MS-Ready data facilitates structure identification • Relate...
Acknowledgements • An enormous team of contributors from NCCT, especially the IT software development team • Our curation ...
Contact Antony Williams NCCT, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/...
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Applications of the US EPA’s CompTox Chemistry Dashboard to support structure identification and chemical forensics using mass spectrometry

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High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. At the US Environmental Protection Agency, our research using HRMS for non-targeted and suspect screening analyses utilizes databases and cheminformatics approaches that are applicable to chemical forensics. The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. Basic functionality for searching through the data is provided through identifier searches, such as systematic name, trade names and CAS Registry Numbers. Advanced Search capabilities supporting mass spectrometry include mass and formula-based searches, combined substructure-mass searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how the CompTox Chemicals Dashboard supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

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Applications of the US EPA’s CompTox Chemistry Dashboard to support structure identification and chemical forensics using mass spectrometry

  1. 1. The EPA CompTox Chemicals Dashboard to support structure identification and chemical forensics using mass spectrometry Fall 2019 ACS Fall Meeting, San Diego http://www.orcid.org/0000-0002-2668-4821 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 Antony Williams1, Alex Chao2, Tom Transue3, Tommy Cathey3, Elin Ulrich4 and Jon Sobus4 1) National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC 2) Oak Ridge Institute of Science and Education (ORISE) Research Participant, RTP, NC 3) General Dynamics Information Technology, RTP, NC 4) National Exposure Research Laboratory, U.S. Environmental Protection Agency, RTP, NC
  2. 2. Overview • The CompTox Chemicals Dashboard - web- based database of 875k substances • Associated data including: – Experimental and predicted physicochemical data – In vivo hazard data – In vitro bioactivity screening data – Link farm to tens of public resources • Integrated modules – read-across, lit search • Data mappings and searches supporting Mass Spectrometry & structure identification 1
  3. 3. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 2
  4. 4. BASIC Search 3
  5. 5. Detailed Chemical Pages 4
  6. 6. Sources of Exposure to Chemicals 5
  7. 7. Identifiers to Support Searches 6
  8. 8. Link Access 7
  9. 9. NIST WebBook https://webbook.nist.gov/chemistry/ 8
  10. 10. MassBank of North America https://mona.fiehnlab.ucdavis.edu 9
  11. 11. Batch Searching 10
  12. 12. Aggregate data for a list of chemicals 11
  13. 13. Batch Search Names 12 Excel Download
  14. 14. Add Other Data of Interest 13
  15. 15. Chemical Lists of Interest… 14
  16. 16. Chemical Lists 15
  17. 17. PFAS lists of Chemicals 16
  18. 18. Batch Search in specific lists 17
  19. 19. “MS-ready” Structures 18
  20. 20. 19
  21. 21. “MS-Ready Structures” https://doi.org/10.1186/s13321-018-0299-2 20
  22. 22. MS-Ready Mappings 21
  23. 23. MS-Ready Mappings Set 22
  24. 24. Mass and Formula Searching 23
  25. 25. Advanced Searches Mass Search 24
  26. 26. Advanced Searches Mass Search 25
  27. 27. MS-Ready Structures for Formula Search 26
  28. 28. MS-Ready Structures Batch Searches 27
  29. 29. MS-Ready Mappings • EXACT Formula: C10H16N2O8: 3 Hits 28
  30. 30. MS-Ready Mappings • Same Input Formula: C10H16N2O8 • MS Ready Formula Search: 125 Chemicals 29
  31. 31. MS-Ready Mappings • 125 chemicals returned in total – 8 of the 125 are single component chemicals – 3 of the 8 are isotope-labeled – 3 are neutral compounds and 2 are charged 30
  32. 32. Batch Searching • Singleton searches are useful but we work with thousands of masses and formulae! • Typical questions – What is the list of chemicals for the formula CxHyOz – What is the list of chemicals for a mass +/- error – Can I get chemical lists in Excel files? In SDF files? – Can I include properties in the download file? 31
  33. 33. Batch Searching Formula/Mass 32
  34. 34. Searching batches using MS-Ready Formula (or mass) searching 33
  35. 35. Additional Mass-Spec Functionality 34
  36. 36. Formula-Based Search 35
  37. 37. Select Chemicals of Interest 36
  38. 38. Prune to list of interest 37
  39. 39. Literature Searching 38
  40. 40. Literature Searching 39
  41. 41. Literature Searching 40
  42. 42. Work in Progress 41
  43. 43. List Registration Activities • Registering and curating numerous lists – NIST library of chemicals – United States Geological Survey chemicals in water – Scientific Working Group for the Analysis of Seized Drugs – Synthetic Cannabinoids – Mycotoxins 42
  44. 44. Work in Progress • CFM-ID – Viewing and Downloading pre-predicted spectra – Search spectra against the database • Structure/substructure/similarity search • Access to API and web services 43
  45. 45. Predicted Mass Spectra http://cfmid.wishartlab.com/ • MS/MS spectra prediction for ESI+, ESI-, and EI • Predictions generated and stored for >800,000 structures, to be accessible via Dashboard 44
  46. 46. Search Expt. vs. Predicted Spectra
  47. 47. Search Expt. vs. Predicted Spectra
  48. 48. Spectral Viewer Comparison 47
  49. 49. Presented at this meeting 48
  50. 50. Example match 49
  51. 51. Predicted Data Already Public Publication and Data Files 50 https://epa.figshare.com/articles/CFM-ID_Paper_Data/7776212/1
  52. 52. Prototype Development 51
  53. 53. Prototype Development 52
  54. 54. API services and Open Data • Web Services https://actorws.epa.gov/actorws/ • Data sets also available for download.. 53
  55. 55. Web Services https://actorws.epa.gov/actorws/ • Data in UI, JSON and XML format 54
  56. 56. InChIKey to DTXCIDs 55 https://actorws.epa.gov/actorws/dsstox/v02/msready?identifier =UVOFGKIRTCCNKG-UHFFFAOYSA-N
  57. 57. MassBank mapping to Dashboard 56
  58. 58. When data is openly shared… 57
  59. 59. NORMAN Suspect List Exchange https://www.norman-network.com/?q=node/236 58
  60. 60. Conclusion • Dashboard access to data for ~875,000 chemicals • MS-Ready data facilitates structure identification • Related metadata facilitates candidate ranking 59 • Relationship mappings and chemical lists of great utility • Curation and mutual sharing of chemical lists is important (e.g. NORMAN)
  61. 61. Acknowledgements • An enormous team of contributors from NCCT, especially the IT software development team • Our curation team for their care and focus on data quality • Many public domain databases and open data contributors • Emma Schymanski, University of Luxembourg for coordinating curation of NORMAN lists • Jerry Zweigenbaum and Andrew McEachran, Agilent Inc., for example spectra to test CFM-ID matching
  62. 62. Contact Antony Williams NCCT, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 61 https://doi.org/10.1186/s13321-017-0247-6

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