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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.

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what is 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
3 Kinds of Proteomics
  • Expressional Proteomics
    • Electrophoresis, Protein Chips, DNA Chips, SAGE
    • Mass Spectrometry, Microsequencing
  • Functional Proteomics
    • HT Functional Assays, Ligand Chips
    • Yeast 2-hybrid, Deletion Analysis, Motif Analysis
  • Structural Proteomics
    • High throughput X-ray Crystallography/Modelling
    • High throughput NMR Spectroscopy/Modelling
expressional proteomics
Expressional Proteomics

2-D Gel QTOF Mass Spectrometry

expressional proteomics1
Expressional Proteomics

Prostate tumor Normal

why expressional proteomics
Why Expressional Proteomics?

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).

functional proteomics in vitro
Functional Proteomics (in vitro)
  • Multi-well plate readers
  • Full automation/robotics
  • Fluorescent and/or chemi-luminescent detection
  • Small volumes (mL)
  • Up to 1536 wells/plate
  • Up to 200,000 tests/day
  • Mbytes of data/day
functional proteomics2
Functional Proteomics

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

why functional proteomics
Why Functional Proteomics?

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

  • Uetz P et al.,“A Comprehensive Analysis of Protein-Protein Interactions in Saccharomyces cerevisiae” Nature 403:623-627 (2000)
  • First example of whole proteome analysis
  • 957 putative interactions
  • 1004 of 6100 predicted proteins involved
  • Huh, K et al.,“Global analysis of protein localization in budding yeast” Nature, 425:686-691(2003)
  • Used a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein (GFP) fusion proteins
  • Localized 75% of the yeast proteome, into 22 distinct subcellular localization categories
  • Provided localization information for 70% of previously unlocalized proteins
  • Edwards JS & Palsson BO“Systems properties of the H. influenzae Rd metabolic genotype” J. Biol. Chem. 274:17410-17416 (1999)
  • First example of metabolic/phenotypic prediction using proteome-wide information
  • Converting sequence data to differential equations so as to predict biology/behavior
structural proteomics
Structural Proteomics
  • High Throughput protein structure determination via X-ray crystallography, NMR spectroscopy or comparative molecular modeling
structural proteomics the motivation
Structural Proteomics: The Motivation














the protein fold universe
The Protein Fold Universe










protein structure initiative
Protein Structure Initiative

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

protein structure initiative1
Protein Structure Initiative

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….

why structural proteomics
Why Structural Proteomics?
  • Structure Function
  • Structure Mechanism
  • Structure-based Drug Design
  • Solving the Protein Folding Problem
  • Keeps Structural Biologists Employed
structural proteomics status
Structural Proteomics - Status

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

structural proteomics status1
Structural Proteomics - Status

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

bioinformatics proteomics
Bioinformatics & Proteomics






bioinformatics functional proteomics
Bioinformatics & Functional Proteomics

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?

bioinformatics expressional proteomics
Bioinformatics & Expressional Proteomics

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?

bioinformatics structural proteomics
Bioinformatics & Structural Proteomics

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?

  • Download RASMOL
  • Download PDB file from Protein Data Bank
  • Provide functional protein information/characteristics from the PDB file as opened using RASMOL
  • Characteristics
    • Protein name
    • Sequence
    • Number of:
      • Chains
      • Bonds
      • Amino acids
      • Alpha helices
      • Beta strands