Using online chemistry databases to facilitate structure identification in mass spectral data
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The document discusses the use of ChemSpider, an online chemistry database, for structure identification in mass spectral data, providing free access to over 34 million chemicals. It highlights the database's capabilities in searching by mass, linking structure-based data, and offering programming interfaces for integration. Future developments aim to expand spectral data availability, including the transformation of text and figures into spectral formats.
Using online chemistry databases to facilitate structure identification in mass spectral data
- 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/
- 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?
- 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
- 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?
- 22. What can I find on ChemSpider?
- 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?
- 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?
- 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