ChemSpider: Connecting Chemistry & Mass Spectrometry on the Internet


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The internet provides access to unprecedented amounts of data. In the domain of online chemistry resources RSC’s ChemSpider has achieved a role of prominence in providing access to high quality chemistry data. By providing access to a database of almost 25 million unique chemical compounds linked out to over 400 data sources on the internet, ChemSpider provides a platform to source detailed information about chemicals. The website is a crowdsourcing platform allowing members of the community to deposit new data and to annotate and curate the existing data. By providing computationally accessible interfaces into the database third parties can utilize the information on the database to support their software applications. One such application is the identification of metabolites in a field known as metabolomics, metabolic profiling at a cellular or organ level and primarily concerned with normal endogenous metabolism.

High resolution mass spectrometry is an analytical technique used for determining the accurate mass and the elemental composition of a molecule, and aiding in elucidating the chemical structures of molecules. It can be used to identify and quantify metabolites from a complex mixture after separation by GC or HPLC (LC-MS). The integration of mass spectrometric data with ChemSpider can, in many cases, allow for the rapid identification of metabolites.

This presentation will provide an overview of the ChemSpider database and developments in modern mass spectrometry and its application to metabolomics.

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ChemSpider: Connecting Chemistry & Mass Spectrometry on the Internet

  1. 1. ChemSpider: Connecting Chemistry and Mass Spectrometry on the Internet Antony Williams and John Shockcor
  2. 2. A Vision for Our Time <ul><li>Analysis of body fluids can lead to earlier diagnosis </li></ul><ul><li>Analysing the “Metabolome” improves the opportunities for personalized medicine </li></ul><ul><li>Coupled analytical instrumentation with chemical and bio informatics… </li></ul>
  3. 6. It’s about structures… <ul><li>Drugs, metabolites, pesticides – it’s all about chemical structures </li></ul><ul><li>RSC hosts a community resource for chemistry to support chemists </li></ul><ul><li>Chemical compounds, properties, syntheses, analytical data, publications.. </li></ul>
  4. 7. Public Domain Chemistry Databases <ul><li>Online databases can be messy and inconsistent </li></ul><ul><li>Non-curated databases proliferate errors </li></ul><ul><li>Original sources of errors hard to determine </li></ul><ul><li>Data validation is time-consuming, challenging and exacting </li></ul>
  5. 8. The structure of Vitamin K1 is ???
  6. 9. Vitamin K1
  7. 10. ChemSpider <ul><li>A free internet database </li></ul><ul><li>25 million chemicals from 400 data sources </li></ul><ul><li>Data includes: </li></ul><ul><ul><li>Chemical identifiers </li></ul></ul><ul><ul><li>Links to publications </li></ul></ul><ul><ul><li>Links to patents </li></ul></ul><ul><ul><li>Experimental and predicted properties </li></ul></ul><ul><ul><li>Spectral data </li></ul></ul>
  8. 13. For Synthetic Chemists
  9. 14. For NMR Spectroscopists
  10. 15. Community Contribution <ul><li>Community-based deposition of data </li></ul><ul><ul><li>Structures, spectra, links, properties </li></ul></ul><ul><li>Community crowdsourced curation </li></ul><ul><ul><li>Validating and curation data </li></ul></ul><ul><li>>130 people have contributed data, skills and experience </li></ul><ul><ul><li>Synthesis procedures </li></ul></ul><ul><ul><li>Spectral data </li></ul></ul>
  11. 16. A flexible platform for... <ul><li>Searching – many tens of thousands of searches per day </li></ul><ul><li>Teaching - providing data and resources to help teach chemistry </li></ul><ul><li>Integration - available for third parties to take value from the data </li></ul>
  12. 17. For Mass Spectrometrists <ul><li>Valuable searches for Mass Spec would be: </li></ul><ul><ul><li>Search the database by mass or formula for structure identification </li></ul></ul><ul><ul><li>Search subsets of data – “metabolism” </li></ul></ul><ul><ul><li>Link structure-based data across the internet </li></ul></ul><ul><ul><li>Provide “programming interfaces” </li></ul></ul>
  13. 18. What is Metabonomics? <ul><li>Metabonomics “ …measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification…” Nicholson et al., 1999 </li></ul>
  14. 19. Full Metabolic Pathway Chart
  15. 20. Kreb’s Cycle
  16. 21. What is Metabonomics or Metabolomics? <ul><li>Analytical data on two groups of samples which we suspect may be different, can we determine the following information? </li></ul><ul><ul><li>Are the groups different? </li></ul></ul><ul><ul><li>Detect those compounds which have increased or decreased in concentration in each group. </li></ul></ul><ul><ul><li>Detect those compounds which are missing from or unique to each group. </li></ul></ul>
  17. 22. Direct Infusion of Urine into a Mass Spectrometer
  18. 23. UPLC Lipid Class Separation PC, SM, PG, PE, DG ChoE & TG lyso-PC, lyso-PE
  19. 24. Hybrid High Resolution QTof MS
  20. 25. High Resolution MS of a TAG
  21. 26. Extracted Ion Chromatogram of m/z 874.7898
  22. 27. MarkerLynx PCA Analysis of Data Transgenic Mice Study <ul><li>PCA Loadings </li></ul><ul><li>PCA Scores </li></ul>
  23. 28. m/z_RT Pairs Which Describe the Variance Between Transgenic and Wild Type Mice
  24. 29. Trend Plot of Those m/z_RT Pairs Y-axis is the Area of the XIC
  25. 30. Calculation of Elemental Composition & ChemSpider Search of Lipid Maps Database Performed via MarkerLynx
  26. 31. Results of the ChemSpider Search in the MarkerLynx Worksheet
  27. 32. Hit Details in ChemSpider
  28. 33. Hybrid High Resolution QTof MS
  29. 34. Lipid at RT 4.41 with m/z 806.5695 PC 16:0/22:6 16:0 22:6
  30. 35. Phospholipids Elevated in Transgenic Mice
  31. 36. What Have We Done? <ul><li>Turned “Data into Information” </li></ul><ul><li>Now to turn information into knowledge </li></ul><ul><li>We want to visualize our metabolite information and information from other “omics” techniques using modern “pathway” tools. (Systems Biology) </li></ul>
  32. 37. Why Do I Like ChemSpider? <ul><li>It is open to all the scientific community not just a select few. </li></ul><ul><li>It relies on expertise from the scientific community for expansion, curation and improved functionality. Let us work together! </li></ul><ul><li>It is always with me… </li></ul>
  33. 38. Linking and Enabling <ul><li>Clearly mass spectrometry facilitates deeper understanding of metabolomics </li></ul><ul><li>The ChemSpider database is a rich foundation for structure-based analysis </li></ul><ul><li>Community support through data deposition and curation is very enabling </li></ul>
  34. 39. Ideas for Future Work <ul><li>Extend search capabilities </li></ul><ul><li>Expand existing databases </li></ul><ul><li>Integrate to metabolic pathways tools </li></ul>
  35. 40. Thank You!!!