Increasingly online databases are being used for the purpose of structure identification. In many cases an unknown to an investigator is known in the chemical literature or online database and these “known unknowns” are commonly available in these aggregated internet resources. The identification of these types of compounds in commercial, environmental, forensic, and natural product samples can be identified by searching against these large aggregated databases querying by either elemental composition or monoisotopic mass. We will report on the search approaches that we offer on aggregated compound databases hosted by the Royal Society of Chemistry and how these resources can be used for the purpose of structure identification.

1. Using online chemistry databases
to facilitate structure identification
in mass spectral data
Antony Williams,
Valery Tkachenko, Alexey Pshenichnov
ACS Denver, March 2015

2. Free and Easy
• Everything I will show in terms of ChemSpider
is available for free online today
• To make it easy to “take notes” these slides
will be available at:
www.slideshare.net/AntonyWilliams/

3. www.ChemSpider.com

4. ChemSpider

5. What will ChemSpider give us?

6. What will ChemSpider give us?

7. For Mass Spectrometrists
• Valuable searches for Mass Spec would be:
• Search the database by mass or formula for
structure identification
• Search subsets of data – e.g. “metabolism”,
pesticides etc
• Link structure-based data across the internet
• Provide “programming interfaces” to integrate
• Does ChemSpider provide value to Mass
Spectrometrists?

8. Pre-calculated data

9. Data Source Selection
• >34 million chemicals include
• Vendor collections
• Government databases
• Individual/Lab data
• Publication data
• All segregated allowing for data source
selection

10. Data Source Selection - Type

11. Data Source Selection -
Individual

12. Mass Spec Analysis
Jim Little, Eastman Chemical

13. ChemSpider Interface

14. 1287 Hits Ranked by Defect

15. 1287 Hits Ranked by # of
References

16. Top Ranked Hit

17. Tinuvin 328

18. What can I find on ChemSpider?

19. What can I find?

20. What can I find?

21. Source and Purchase…

22. What can I find on ChemSpider?

23. External Calculation Engines

24. What can I find on ChemSpider?

25. …and in the RSC Databases..

26. Linked to the Publisher

27. What can I find?

28. And out to Google Patents

29. What About the Entire Web?

30. The InChI Identifier

31. InChIStrings Hash to InChIKeys

32. Searching Internet by Structure

33. Extended Study
Sorting by references

34. Position sorted by references

35. Position 1 only

36. Web Services For Collaboration
• Many instrument vendors are using or
investigating our web-based services for
compound lookup
• Many academic sites integrating directly –
metabonomics, name lookup, mass-based
searching

37. Results of the ChemSpider Search
in the MarkerLynx Worksheet

38. Hit Details in ChemSpider

39. “REAL Spectral Data”
• Masses on ChemSpider are clearly valuable!
• We’d like to host “spectral curves”
• But we’re a publisher so what can we do?

40. Spectra: Cholesterol

41. ChemSpider ID 24528095 H1 NMR

42. ChemSpider ID 24528095 HHCOSY

43. Publications & “Real Spectra”
• We are turning text into spectra
• We are turning figures into spectra

44. ESI – Text Spectra

45. 1H NMR (CDCl3, 400 MHz):
δ = 2.57 (m, 4H, Me, C(5a)H), 4.24 (d, 1H, J = 4.8 Hz, C(11b)H), 4.35 (t,
1H, Jb = 10.8 Hz, C(6)H), 4.47 (m, 2H, C(5)H), 4.57 (dd, 1H, J = 2.8 Hz,
C(6)H), 6.95 (d, 1H, J = 8.4 Hz, ArH), 7.18–7.94 (m, 11H, ArH)

46. “Where is the real data please?”
FIGURE
DATA

47. Future Developments
• We have extracted 100s of 1000s of text strings
from patents – next we go into our archive
• We estimate many 1000s of figures with spectral
data in our ESI and articles
• We are aiming for a million spectra online…
• But YOU can submit your data today and share it

48. We want this…we need YOU!

49. Data Mining – it’s mine, mine!

50. New Repository Architecture
doi: 10.1007/s10822-014-9784-5

51. Acknowledgments
• Jim Little, Eastman Chemical Company
• Daniel Lowe – NextMove Software
• Bill Brouwer – Plot2Txt Development
• Carlos Cobas and Stan Sykora– MestreLabs
• Patrick Wheeler - ACD/Labs

52. Thank you
Email: williamsa@rsc.org
ORCID: 0000-0002-2668-4821
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams