Introduction to Proteomics. What is Proteomics?. Proteomics - A newly emerging field of life science research that uses High Throughput (HT) technologies to display, identify and/or characterize all the proteins in a given cell, tissue or organism (I.e. the proteome). 3 Kinds of Proteomics.
Proteomics - A newly emerging field of life science research that uses High Throughput (HT) technologies to display, identify and/or characterize all the proteins in a given cell, tissue or organism (I.e. the proteome).
2-D Gel QTOF Mass Spectrometry
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Concerned with the display, measurement and analysis of global changes in protein expression
Monitors global changes arising from application of drugs, pathogens or toxins
Monitors changes arising from developmental, environmental or disease perturbations
Applications in medical diagnostics and therapeutic drug monitoring
Jungblut PR et al., “Proteomics in Human Disease: Cancer, Heart and Infectious Disease” Electrophoresis 20:100-110 (1999)
Zhukov TA et al., “Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI”Lung Cancer 40:267-279 (2003)
Ghaemmaghami S, et al., “Global analysis of protein expression in yeast” Nature 425:737-741 (2003).
In silico methods (bioinformatics)
Genome-wide Protein Tagging
Genome-wide Gene Deletion or Knockouts
Random Tagged Mutagenisis or Transposon Insertion
Yeast two-hybrid Methods
Protein (Ligand) Chips
Concerned with the identification and classification of protein functions, activities locations and interactions at a global level
To compare organisms at a global level so as to extract phylogenetic information
To understand the network of interactions that take place in a cell at a molecular level
To predict the phenotypic response of a cell or organism to perturbations or mutations
Organize all known protein sequences into sequence families
Select family representatives as targets
Solve the 3D structures of these targets by X-ray or NMR
Build models for the remaining proteins via comparative (homology) modeling
Organize and recruit interested structural biologists and structure biology centres from around the world
Coordinate target selection
Develop new kinds of high throughput techniques
Solve, solve, solve, solve….
20 registered centres (~30 organisms)
82700 targets have been selected
52705 targets have been cloned
29855 targets have been expressed
12311 targets are soluble
1493 X-ray structures determined
502 NMR structures determined
1743 Structures deposited in PDB
543 structures deposited by Riken
265 structures deposited by Mid-West
187 structures deposited by North-East
179 structures deposited by New York
178 structures deposited by JCSG (UCSD)
52 structures deposited by Berkeley
31 structures deposited by Montreal/Kingston
How to classify proteins into functional classes?
How to compare one proteome with another?
How to include functional/activity/pathway information in databases?
How to extract functional motifs from sequence data?
How to predict phenotype from proteotype?
How to correlate changes in protein expression with disease?
How to distinguish important from unimportant changes in expression?
How to compare, archive, retrieve gel data?
How to rapidly, accurately identify proteins from MS and 2D gel data?
How to include expression info in databases?
How to predict 3D structure from 1D sequence?
How to determine function from structure?
How to classify proteins on basis of structure?
How to recognize 3D motifs and patterns?
How to use bioinformatics databases to help in 3D structure determination?
How to predict which proteins will express well or produce stable, folded molecules?