Chemspider For Mass Spectrometrists Public Version

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An overview of the types of searches available on ChemSpider for MS Spectrometrists and how MS scientists can derive value from the ChemSpider database

An overview of the types of searches available on ChemSpider for MS Spectrometrists and how MS scientists can derive value from the ChemSpider database

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  • This Powerpoint provides an overview of how MS spectrometrists can derive value from ChemSpider

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  • 1. ChemSpider for Mass Spectrometrists Antony Williams
  • 2. ChemSpider - A Search Engine for Chemists
    • Questions a chemist might ask…
      • What is the melting point of n-butanol?
      • What is the chemical structure of Xanax?
      • Chemically, what is phenolphthalein?
      • What are the stereocenters of cholesterol?
      • Where can I find publications about xylene?
      • What are the different trade names for Ketoconazole?
      • What is the NMR spectrum of Aspirin?
      • What are the safety handling issues for Thymol Blue?
      • ChemSpider can answer all of these questions
  • 3. ChemSpider Data Content
    • Over 21.5 million unique chemical structures from ca. 150 data sources
      • Online Databases –PubChem, Drugbank, HMDB, Wikipedia
      • Chemical Vendors – over 40 different vendors and growing
      • Personal Depositions – individual contributions
      • Journal Publishers
      • Content database vendors
      • Analytical data collections
      • Patents (9 MILLION Structures being deposited now )
      • Web scraping
      • Content is generally linked back to the original data sources
  • 4. ChemSpider for MS Spectrometrists
    • What would an MS spectrometrist want to do?
      • Search the database based on mass (various forms)
      • Search selected subsets of the database based on mass
      • Search based on mass and substructure(s)
      • Search for structure based on name(s) or database IDs
      • Search for structures based on elements/not elements
      • Download the structure/structures in standard format
      • Search literature for information
      • Identify related data sources – chemical vendors, pathway databases, etc
  • 5. Tell me about Aspirin
  • 6. Tell me about Aspirin
  • 7. Link outs
  • 8. Tell me about Aspirin
  • 9. Tell me About Aspirin
  • 10. ChemSpider for MS Spectrometrists
    • What would an MS spectrometrist want to do?
      • Search the database based on mass (various forms)
      • Search selected subsets of the database based on mass
      • Search based on mass and substructure(s)
      • Search for structure based on name(s) or database IDs
      • Search for structures based on elements/not elements
      • Download the structure/structures in standard format
      • Search literature for information
      • Identify related data sources – chemical vendors, pathway databases, etc
  • 11. Search Database Based on Mass
  • 12. Search 309.08+/- 0.001 527 hits out of 21.5 MILLION Structures in 2 seconds
  • 13. Include/Exclude Elements During a Search
  • 14. Search based on Data Sources
  • 15. Combined Searches
    • Search for a particular mass AND
      • Search a series of data sources only AND
      • Search inclusion/exclusion lists of elements AND
      • Search a particular substructure
  • 16. Structure Searching
  • 17. Substructure Searching
  • 18. Outlinks – to vendors and other databases
    • Example databases of interest to MS Spectrometrists:
      • HMDB – Human Metabolome Database
      • KEGG – Kyoto Encyclopedia of Genes and Genomes
      • BioCyc - collection of Pathway/Genome Databases
      • Uni. Minnesota Biodegradation DB - information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds
      • WikiPathways – new initiative to build crowdsourced pathway data management
  • 19. Links out to KEGG Kyoto Encyclopedia of Genes and Genomes
  • 20. WikiPathways Link
  • 21. Download Structure(s)
    • Download individual record – molfile
    • Download SDF file (group of structures)
  • 22. Search Literature
    • Text indexing of >1/2 million Open Access Articles
    • Searching of Pubmed via the NCBI Entrez System
    • Potential directions include extension to focused searching- LCMS only, HPLC only etc. We can index based on Title and Abstracts and on chemical names
  • 23.  
  • 24. MassSpec API Web Services
    • http:// www.chemspider.com/MassSpecAPI.asmx
  • 25. Web Services
  • 26. Test Web Services for MassSpec
    • http:// www.chemspider.com/WebServices/WSMassSpecAPIDemo.aspx
  • 27. Test results
  • 28. Waters Integration
  • 29. Waters Integration
  • 30. Outlinks from Table