1. Comparing the
Protein expression profiles from
healthy and disease states
Cell / tissue / organ
Or
Biological fluids

2. Today
1. Understanding Proteomics
2. How is it different from protein analytical chemistry?
3. Why not genomics?
4. Approaches in Proteomics
5. Tools in Proteomics
6. Applications

3. General scheme of proteomic analysis

4. Approaches in Proteomics
1. Mining
2. Expression proteomics
3. Network mapping
4. Structural proteomics

5. Genomics and Proteomics
Term coined by Marc Wilkins and co-workers 1990 to complement genome and genomics
DNA - RNA - Protein
Allows study of actual functional units of the cell
Limitations of genomics
Levels of RNA do not correlate with protein
Differing stabilities of mRNA and different translational
efficiencies
No information about the regulatory state of the proteins

6. Proteomics
Can be defined as the total protein complement of a system
(be that an organelle/cell/tissue/organism).
This includes:-
all proteins
all states of proteins
The genome is for the most part static (within a generation)
whereas the proteome is more dynamic cell cycle,
development, response to environment, etc

7. • Defined as “the analysis of the entire protein
complement in a given cell, tissue, or organism.”
• Proteomics “also assesses activities, modifications,
localization, and interactions of proteins in complexes.”
• Proteomes of organisms share intrinsic differences
across species and growth conditions.

8. The virtue of proteomics
• Proteome= Protein complement of the genome
• Proteomics= Study of the proteome
• Proteome world= Study of less abundant protein
• Transcriptomic= often insufficient study to study most
functional aspect of genomics

9. Challenges in proteomics
The number of different proteins is much larger than the number of genes or
mRNAs:
– Alternative splicing
– Post-translational modifications
– Proteolytic cleavage
• Changes in protein “states” (e.g. phosphorylation) occur typically much faster
than changes in transcriptional regulation
• DNA/RNA has four different building blocks and a (mainly) uniform
hydrophilic negatively charged structure – proteins have 20 building blocks,
highly variable structure, hydrophobicity, and charge
• Proteins need to be kept in a functional correctly folded state for most
proteomics applications

10. Number of proteins in one cell
1. High expression: 105-106
2. Moderate expression: 103-104
3. Low expression: 101-102

11. Challenges facing Proteomic Technologies
• Limited/variable sample material
• Sample degradation (occurs rapidly, even during sample preparation)
• Vast dynamic range required
• Post-translational modifications (often skew results)
• Specificity among tissue, developmental and temporal stages
• Perturbations by environmental (disease/drugs) conditions
• Researchers have deemed sequencing the genome “easy,” as PCR was able
to assist in overcoming many of these issues in genomics.

12. Different from Protein chemistry?
Protein Chemistry Proteomics
Individual protein Complex mixtrure
Complete sequence Partial sequence
Structure and Function Identification
Structural Biology Systems Biology

13. Types of proteomics
• Protein Expression
– Quantitative study of protein expression between samples that differ by
some variable
• Structural Proteomics
– Goal is to map out the 3-D structure of proteins and protein complexes
• Functional Proteomics
- Protein Networks

14. Applications of Proteomics
• Characterization of Protein Complexes
• Protein Expression Profiling
• Yeast Genomics and Proteomics
• Proteome Mining
• Protein Arrays

15. Tools in Proteomics
1. Databases
2. Mass spectrometry
3. Softwares
4. Protein resolution methods

16. Experimental platform

17. Approaches in Proteomics
1. Mining
2. Expression proteomics
3. Network mapping
4. Structural proteomics

18. Studying the proteome
Cell culture
extraction method separation
(i.e. lipid solubilisation) methods
(2D gels)
protein protein extraction from comparison methods
fragmentation and gels (spot cutting) to identify changed
mass spec. proteins in gels
matching spectrum to
virtual spectrum for
protein identification

19. Two dimensional gel electrophoresis
Comparison of complete protein profiles or
proteomes under different conditions.
e.g. healthy and disease samples
Mass spectrometry
Identification of specific proteins.
-biomarkers for diagnosis, drug targets for
therapeutics

20. Two dimensional gel electrophoresis
1) Sample preparation
Source: Biological source (tissue, cell, body fluid)
Removal of the interfering components (Extra- cellular matrix, salts, oils)
Isolation of the fraction of interest (whole cells or sub cellular fraction)
Lysis or homogenization of the isolated fraction in homogenization buffer
(With protease inhibitor or any other specific inhibitors)
Precipitation of proteins from the lysate using plus one 2D cleanup kit.
2) Rehydration (overnight) of the IPG Dry strips (of desired pH range)
with the 2 D lysis buffer containing proteins.
Solubilization of precipitated proteins in 2D lysis buffer.
3)
IEF of the rehydrated gel strips using Ettan IPGphore.
4) Equilibration of the strips in SDS equilibration buffer and second
dimension on the SDS PAGE.
5) Staining of the SDS PAGE gels using coomassie
Brilliant blue.
6) Scanning of the stained gels using Umax scanner.
Image analysis and gels comparison using Ettan progenesis software.

21. Proteomics Overview
Normal cell Diseased cell
Cell Lysates
Two dimentional gel-electrophoresis
2-D Results analysed and compared
using software.
Warped image
The spot of interest is
picked by spot-picker.
In-gel digestion of the desired spot
is performed
Peptide-mapping by mass
spectrometry.

22. Detection technologies in proteome analysis
 General detection methods.
 Differential display proteomics.
 Specific detection methods for
post-translational modifications.

23. Different strategies for proteome purification and protein
separation for identification by MS
 A. Separation of individual
proteins by 2-DE.
 B. Separation of protein
complexes by non-denaturing
2-DE (BN-PAGE)
 C. Purification of protein
complexes by immuno-
affinity chromatography and
SDS-PAGE.
 D. Multidimensional
chromatography.
 E. Organic solvent
fractionation for separation
of complex protein mixtures
of hydrobhobic membrane
proteins.

24. Differential display proteomics
 Detection techniques:
 Difference gel electrophoresis (DIGE).
 Multiplexed proteomics (MP)
 Isotope-coded affinity tagging (ICAT)
 Differential gel exposure.

25. Summary of protein expression profile analysis

26. Difference gel electrophoresis (DIGE)
(Unlu, 1997, electrophoresis 18, 2071)

27. Differential gel exposure
(Monribot-Espagne, 2002, Proteomics 2, 229-240)
 Coelectrophoresis on 2DE of two protein samples.
 In vivo labelling, using 14C and 3H -isotopes.
 2DE separation.
 Transfer on a PVDF membrane.
 3H /14C ratio by exposure to two types of imaging
plates.
 Investigate changes in the rate of synthesis of
individual proteins.

28. Multiplexed proteomics (MP) technology platform

29. • Proteomics is undoubtedly a critical component of systems biology,
however:
– The lack of hypothesis-driven experiments isn’t necessarily “good” for science.
Discovery-based science should be guided by hypotheses, IMO.
– Along these lines, as with the HGP, when it comes to literature, what do you do,
just publish the whole thing?
• This is another stumbling block of what to do with all of this information.
– Proteomics needs its “own PCR,” or “miracle” tool, to increase the throughput.
• A new technology, or instrument that combines other approaches, would be useful,
esp. in structural proteomics, quantification, and sample reproduction.