1. Introduction to Proteomics

2. First issue of Proteomics- Jan. 1, 2001

3. abcNEWS.com- April 27 — Genes may be the stuff of life, but they're not the whole story. Scientists wrapping up the mammoth task of decoding the human genome say the next step will be understanding the "proteome" — the proteins that genes help make.

16. Search the Database for a ‘protein match’? How? Explain.

18. Peptide Mass Fingerprinting Developed 1993 Today- automated (including Database Searches)  500 proteins/day analyzed (one lab) Goal- annotated 2D gel map.

24. MS-MS Peptide fingerprints are sufficient ot identify proteins only in cases where the sequence of a protein is already in a database. MS-MS can obtain partial sequence info. from each peptide in the fingerprint. Within the mass spectrometer, each peptide can then be further broken down in to ionized fragments. The goals is to produce a ladder of fragments each differing in length by one aa. Because each aa has different MW, the sequence of each peptide can be deduced.

27. What is DiGE? labeling two protein samples to be compared with different fluorescent dyes, and then mixing the samples before application onto the same 2D gel. The same isoform of a given protein from each sample will thus migrate to same position on the 2D gel. The relative abundance of each protein in each sample can then be obtained by scanning the gel using excitation and emission wavelengths unique to each dye used. This technique known as DiGE or differential gel electrophoresis has been pioneered by the Minden group at Carnegie Mellon University in Pittsburg and relies on the use of the NHS esters of Cy3 and Cy5 binding to a small fraction of lysine residues within a protein sample.

30. ExPASy Molecular Biology Server

31. The primary objective of KEGG is to computerize the current knowledge of molecular interactions; namely, metabolic pathways, regulatory pathways, and molecular assemblies.

33. Current Questions? Are pathways identical across species? Do some speciez have alternative pathways to generic ones? Are certain enzymes in pathway more important than other ones?

34. Kyoto Encyclopedia of Genes and Genomes

35. The Future is Looking Very Small

36. BIOCHEMISTRY: Protein Arrays Step Out of DNA's Shadow

38. Protein arrays Early progress has been slow; proteins are harder to synthesize than DNA, and plunking them down on solid surfaces tends to cause them to unfold and thereby lose their activity. Now, however, those barriers appear to be crumbling. On page 1760 of this issue, researchers at Harvard University report creating arrays of over 10,000 proteins on a piece of glass just half the size of a microscope slide. They then used their arrays to study a variety of protein functions, work that included identifying members of the array that bind to other free-floating proteins and to small, druglike molecules.1760

39. Once protein microarrays are perfected, researchers will be able to measure the functions of thousands upon thousands of proteins simultaneously, and rapidly screening them all for new drug targets. It also will be (relatively) easy to take a potential drug candidate and screen all the metabolic pathways to check for unwanted reactions. But that's the future -- and it's barely begun.

41. The End