Non-targeted and suspect screening studies using high resolution mass spectrometry (HRMS) have revolutionized the detection of chemicals in complex matrices. However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. The US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov) to address challenges related to data processing and analysis in HRMS. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will introduce the tools and combined workflow, including visualization and access via the CompTox Chemicals Dashboard. These tools, data, and visualization approaches within an open chemistry resource provides a publicly available software tool to support structure identification and non-targeted analyses. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

1. Applications of the US EPA’s CompTox
Chemicals Dashboard to support
structure identification and chemical
forensics using mass spectrometry
Antony Williams1 and Andrew D. McEachran2,3
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) Present Address: Agilent Inc., Santa Clara, CA
March 18th 2019
Pittcon, Philadelphia
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

2. CompTox Chemicals Dashboard
• A publicly accessible website delivering access:
– ~875,000 chemicals with related property data
– Searchable by chemical, product use, gene and assay (ToxCast)
– Experimental and predicted physicochemical property data
– “Bioactivity data” for the ToxCast/Tox21 project
– Links to other agency websites and public data resources
– “Literature” searches for chemicals using public resources
– “Batch searching” for thousands of chemicals
– DOWNLOADABLE Open Data for reuse and repurposing
1

3. CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
2

4. BASIC Search
3

5. Detailed Chemical Pages
4

6. Access to Chemical Hazard Data
5

7. In Vitro Bioassay Screening
ToxCast and Tox21
6

8. Sources of Exposure to Chemicals
7

9. Identifiers to Support Searches
8

10. Literature Searches and Links
9

11. Link Access
10

12. NIST WebBook
https://webbook.nist.gov/chemistry/
11

13. MassBank of North America
https://mona.fiehnlab.ucdavis.edu
12

14. m/z CLOUD
https://www.mzcloud.org/
13

15. SIMPLE
APPLICATIONS
FOR MASS SPEC.
14

16. Find me “opioids like Morphine”
Structure Similarity
15

17. Find me “opioids like Morphine”
Structure Similarity
16

18. Find me “opioids like Morphine”
Structure Similarity – sort on mass
17

19. Find me “opioids like Morphine”
Formula-Based Search
18

20. Select Chemicals of Interest
19

21. Prune to list of interest
20

22. Sort for “morphine” by string
21

23. Literature Searching
22

24. Literature Searching
23

25. Literature Searching
24

26. FOCUSED
CHEMICAL LISTS
OF INTEREST
25

27. Chemical Lists
26

28. PFAS lists of Chemicals
27

29. EPAHFR: Hydraulic Fracturing
28

30. Aggregate data for a list of chemicals
29

31. Batch Search Names
30
Excel
Download

32. Add Other Data of Interest
31

33. Batch Search in specific lists
32

34. MASS AND
FORMULA
SEARCHING
33

35. Advanced Searches
Mass and Formula Based Search
34

36. Advanced Searches
Mass and Formula Based Search
35

37. 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?
36

38. Batch Searching Formula/Mass
37

39. DO WE REALLY
NEED ANOTHER
DATABASE?
38

40. Is a bigger database better?
39
• ChemSpider was 26 million chemicals then
• Much BIGGER today
• Is bigger better??

41. Comparing Search Performance
40
• Dashboard content was 720k chemicals
• Only 3% of ChemSpider size
• What was the comparison in performance?

42. SAME dataset for comparison
41

43. How did performance compare?
42

44. Data Quality is important
• Data quality in free web-based databases!
43

45. Will the correct Microcystin LR Stand Up?
ChemSpider Skeleton Search
44

46. Comparing ChemSpider Structures
45

47. Comparing ChemSpider Structures
46

48. Other Searches
47

49. Delivering a Better Database
• An ideal database would provide:
– Curated CAS Number-Name mappings with “correct”
chemical structures
• We have full time curators checking data
48

50. Names to CASRN Mappings
49

51. Subtleties
50
E/Z-stereochemistry E-stereochemistry
“4-Decene”

52. CAS Registry Numbers
51

53. Alternative Synonyms
52

54. SPECIFIC
APPLICATIONS
TO MASS SPEC.
53

55. Mass Spec Focused Applications
54

56. Mass Spec Focused Applications
55

57. “MS-Ready Structures”
https://doi.org/10.1186/s13321-018-0299-2
56

58. Specific Data-Mappings
“MS-Ready Structures”
57

59. 58

60. MS-Ready Mappings
59

61. MS-Ready Mappings Set
60

62. Advanced Searches
Mass Search
61

63. Advanced Searches
Mass Search
62

64. MS-Ready Structures for
Formula Search
63

65. MS-Ready Structures
Batch Searches
64

66. MS-Ready Mappings
• EXACT Formula: C10H16N2O8: 3 Hits
65

67. MS-Ready Mappings
• Same Input Formula: C10H16N2O8
• MS Ready Formula Search: 125 Chemicals
66

68. 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
67

69. Complexity to Simplicity - Use Lists
125 Chemicals – 7 in EPAHFR
68

70. Complexity to Simplicity
125 Chemicals – 7 in the list
69

71. Searching batches using MS-Ready
Formula (or mass) searching
70

72. UVCB
CHEMICAL
SUBSTANCES
71

73. UVCB Chemicals
72

74. Many Hydraulic Fracturing
Chemicals are “Complex”
73

75. “Markush Structures”
https://en.wikipedia.org/wiki/Markush_structure
74

76. UVCB: Complex Surfactants
75

77. UVCB: Complex Surfactants
76

78. UVCB: Complex Surfactants
77

79. WORK IN
PROGRESS
78

80. Work in Progress
• CFM-ID
– Viewing and Downloading pre-predicted spectra
– Search spectra against the database
79

81. 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
80

82. Search Expt. vs. Predicted Spectra

83. Search Expt. vs. Predicted Spectra

84. Spectral Viewer Comparison
83

85. Work in Progress
• CFM-ID
– Viewing and Downloading pre-predicted spectra
– Search spectra against the database
• Retention Time Index Prediction
84

86. Retention Time Prediction for Ranking
85

87. Moving to Relative Retention Times
86

88. Work in Progress
• CFM-ID
– Viewing and Downloading pre-predicted spectra
– Search spectra against the database
• Retention Time Index Prediction
• Structure/substructure/similarity search
87

89. Prototype Development
88

90. Prototype Development
89

91. Work in Progress
• CFM-ID
– Viewing and Downloading pre-predicted spectra
– Search spectra against the database
• Retention Time Index Prediction
• Structure/substructure/similarity search
• Integration of predicted ion mobility data
90

92. Collision Cross Section Prediction
91

93. Work in Progress
• CFM-ID
– Viewing and Downloading pre-predicted spectra
– Search spectra against the database
• Retention Time Index Prediction
• Structure/substructure/similarity search
• Integration of predicted ion mobility data
• Access to API and web services for
programmatic access
92

94. API services and Open Data
• Groups waiting on our API and web services
• Mass Spec companies instrument integration
• Release will be in iterations but for now our
data are available
93

95. SIDE EFFECTS
OF SHARING
OPEN DATA
94

96. NORMAN Suspect List Exchange
https://www.norman-network.com/?q=node/236
95

97. Integration to MetFrag in place
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0299-2
96

98. Conclusion
• Dashboard access to data for ~875,000 chemicals
• MS-Ready data facilitates structure identification
• Related metadata facilitates candidate ranking
97
• Relationship mappings and
chemical lists of great utility
• Dashboard and contents
are one part of the solution
• Future releases will offer
even more utility
• We are committed to open
API development with time..

99. Acknowledgements
• THANK YOU for the invitation!
• IT Development team – especially Jeff
Edwards and Jeremy Dunne
• Chris Grulke for the ChemReg system
• NERL colleagues – Jon Sobus, Elin Ulrich,
Mark Strynar, Seth Newton
• Emma Schymanski, LCSB, Luxembourg
• The NORMAN Network and all contributors
98

100. Contact
Antony Williams
US EPA Office of Research and Development
National Center for Computational Toxicology
EMAIL: Williams.Antony@epa.gov
ORCID: https://orcid.org/0000-0002-2668-4821
99