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Bioinformatics on Proteomics

Bioinformatics on Proteomics. Hsueh-Fen Juan April 24, 2003 NTNU. Bioinformatics. ?. Outline. Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites. Introduction

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Bioinformatics on Proteomics

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  1. Bioinformatics on Proteomics Hsueh-Fen Juan April 24, 2003 NTNU

  2. Bioinformatics ?

  3. Outline • Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  4. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  5. Introduction • ExPaSy: Expert Protein Analysis System • SWISS-PROT: Protein knowledgebase • TrEMBL: Computer-annotated supplement to Swiss-Prot

  6. Proteomics

  7. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Useful Bio-websites

  8. Primary Structure Analysis • Object: To compute the characters of proteins. -Amino acid composition -Atomic composition -pI -Molecular weight

  9. Amino Acid & Atomic Composition ProtParam

  10. http://www.expasy.ch/tools/ protparam.html

  11. Amino Acid Composition Atomic Composition

  12. Computing pI and MW

  13. MW pI

  14. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  15. P02571

  16. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  17. Similarity is very low No similarity

  18. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  19. The Information Stored in Genes Is Expressed by a Multistage Process Eur J Nucl Med 2002, 29, 115-32

  20. http://www.expasy.ch/tools/

  21. Protein DNA

  22. Two-dimensional Gel Approach Nature 2000, 405, 837-846

  23. Image Matching kDa 150 Increase of 50% 70 Decrease of 50% 60 42 Unmatched spots Matched spots 10 3.5 10 pH

  24. http://www.expasy.ch/melanie/

  25. Standard Proteome Analysis by 2DE-MS Mass Fingerprint Searching in http://www.expasych/tools/peptident.html Current Opinion in Chemical Biology 2000, 4:489–494

  26. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  27. Gel Control Treated sample

  28. - gel membrane + Transfer proteins from gel to PVDF membrane Sequencing (Very time-Consuming)

  29. Mass spectrometry

  30. For peptide mass fingerprint data

  31. pI and MW Species

  32. Introduction • Primary Structure Analysis • Protein Sequence Searching • Protein Sequence Alignment • Proteomics Tools • Protein Identification • Useful Bio-websites

  33. Useful Bio Websites • PROSITE http://tw.expasy.org/prosite/ • Amos' WWW links page http://tw.expasy.org/alinks.html • Phosphoprotein Database (PPDB) http://www-lmmb.ncifcrf.gov/phosphoDB/

  34. PROSITE is a database of protein families and domains. http://tw.expasy.org/prosite/

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