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

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

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

10. Amino Acid & Atomic Composition ProtParam

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

12. Amino Acid Composition Atomic Composition

13. Computing pI and MW

15. MW pIpI

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

17. P02571

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

25. Similarity is very low No similarity

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

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

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

29. DNA Protein

33. Nature 2000, 405, 837-846

34. 3.510 42 60 70 150 kDa pH Increase of 50% Decrease of 50% Unmatched spots Matched spots

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

39. Standard Proteome Analysis by 2DE-MS Current Opinion in Chemical Biology 2000, 4:489–494 Mass Fingerprint Searching in http://www.expas ych/tools/peptide nt.html

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

41. ControlTreated sample Gel

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

43. Mass spectrometry

44. For peptide mass fingerprint data

45. Species pI and MW

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

48. 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/

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

51. http://tw.expasy.org/alinks.html

52. http://tw.expasy.org/alinks.html#PTM

53. http://www.cbs.dtu.dk/databases/PhosphoBase/