INTRODUCTION GENERAL CONCEPT WHY PROTEIOMIC NECESERY? WHAT PROTEOMIC CAN ANSWER? PRTEOMICS- ANALYSIS AND IDENTIFICATION OF PROTEIN TWO-DIMENSIONAL SDS-PAGE MASS SPECTROMETERS SIGNIFICANCE OF STUDY AN ITS IMPORTANCE APPLICATIONS CHALLENGES CONCLUSIONS REFERENCES

1. PROTEOMICS
GENERAL CONCEPT, SIGNFICANCE OF STUDY AN ITS
IMPORTANCS
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. SYNOPSIS
 INTRODUCTION
 GENERAL CONCEPT
 WHY PROTEIOMIC NECESERY?
 WHAT PROTEOMIC CAN ANSWER?
 PRTEOMICS- ANALYSIS AND IDENTIFICATION OF
PROTEIN
TWO-DIMENSIONAL SDS-PAGE
MASS SPECTROMETERS
 SIGNIFICANCE OF STUDY AN ITS IMPORTANCE
 APPLICATIONS
 CHALLENGES
 CONCLUSIONS
 REFERENCES

3. INTRODUCTION-The term “proteome”
originates from the words protein and genome.
PROTEINS expressed by a GENOME tissue
secreted into physiological fluid .
Definition-The term “omics” is of recent origin
but Is now used by biologists to refer to the study
of a type of molecule or compound in its totality
(or at least on a large scale)

4. ROLE OF PROTEIN
TYPE FUNCTION EXAMPLE
Structural proteins Support Collagen, Elastin,
Keratin
Storage proteins Storage of amino acid Ovalbumin,
Casein
Transport proteins Transport of other
substrate
Hemoglobin
Hormonal proteins Coordination of and
organism’s activities
Insulin
Receptors proteins Response of cell to
chemical stimuli
Receptor in nerve
transmit route
Contractile proteins Movement Actin, Myosin
Defensive proteins Protecton against
disease
Antibodys
Enzymatic proteins Selective acceleraton
of chemical reactions
Trypsin, ATPase,
GAPDH

5. General Concept
Why is proteomics necessary?

6.  1 gene = 1protein?
The concept was proposed by George Beadle and Edward Tatum in
an influential 1941 paper.
1 gene is no longer equal to one protein.
A gene is debatable .(ORF, promoter, pseudo gene, gene product,
etc).
 One gene many protein

7.  If We Can Measure Gene Expression, Why
Bother With Proteomics?

8. What proteomics can answer?
 Protein identification
 Protein Expression Studies
 Protein Function
 Protein Post-Translational Modification
 Protein Localization and Compartmentalization
 Protein-Protein Interactions

9. Co translational modification-The process of covalently
altering one or more amino acids in a protein after
translation has begun but before the protein has been
released from the ribosome.

10. Post translational modification-Protein post-translational
modification (PTM) increases the functional diversity of
the proteome by the covalent addition of functional
groups or proteins, proteolytic cleavage of regulatory
subunits or degradation of entire proteins.

11. General classification of proteomics -

12. PRTEOMICS- ANALYSIS AND IDENTIFICATION OF
PROTEIN
GENERALLY WE USE TWO METHOD-
1 Two-Dimensional SDS-PAGE- Two-dimensional SDS-
PAGE is actually a combination of two different types of
separations. In the first, the proteins are resolved on the
basis of isoelectric point by IEF. In the second, focused
proteins then are further resolved by electrophoresis on a
polyacrylamide gel . Thus 2D-SDS-PAGE resolves
proteins in the first dimension by isoelectric point and in
the second dimension by molecular weight.

13. Fig. Schematic representation of 2D-SDS-PAGE.

14. 2. Mass spectrometers - Mass spectrometers have
three essential parts . The first is the source, which
produces ions from the sample. The second is the
mass analyzer, which resolves ions based on their
mass/charge (m/z) ratio. The third part is the
detector, which detects the ions resolved by the
mass analyzer. In short, the mass spectrometer
converts components of a mixture to ions and then
analyzes them on the basis of their m/z.

15. Fig. Schematic representation of a mass spectrometer

16. SIGNFICANCE OF STUDY AN ITS IMPORTANCE
1. Substantial audits of protein expression, from gel-
based studies coupled with mass spectrometry to
those based on shotgun proteomics and tandem
mass spectrometry, have given and will continue to
give insight into which proteins are present in a
particular cell or tissue.
2. The ‘higher order’ of the proteome, obtained from
large-scale studies of protein–protein interactions in
the cell using proteomic techniques, is just starting
to be revealed .
3. Metaproteomics, a new term used to describe the
shotgun proteomics analysis of mixtures of
microbial species, is providing insights into
microbial diversity and interactions that would
otherwise be impossible to achieve.

17. 4. Proteomics is providing a major new avenue for the discovery
of medical biomarker proteins of diagnostic and/or
prognostic significance. As proteomic technology is
supremely well suited to the analysis of soluble proteins, the
analysis of proteins from body fluids has been and will
continue to be a fruitful Endeavour.
5. Proteomics is providing high-resolution data to supplement
existing biomedical techniques. Toxicology, which has
traditionally relied on histopathology and the evaluation of a
small number of blood-associated proteins and metabolites, is
using proteomics to better understand the effects and side
effects of drugs.

18. Applications of proteomics
1.Application of Proteomics in the Study of Tumor
Metastasis
2.Application of proteomics in renal disease
diagnosis
3.The Application of Proteomics in Neurology
4. Application of Proteomics in Autoantibody
profiling for the study and treatment of
autoimmune disease

19. 5. Toxico proteomics
6. Role of Proteomics in Nutrition Research
7. Proteomic analyses of early-stage cancers

20. What Still Eludes Us?
1. The separation and detection of all proteins in the
proteome remains a challenge. Low-abundance
proteins are particularly elusive, owing to the large
differences in concentration of proteins in many
samples.
2. It is not possible to compare one interactome with
another. The incredible complexity of the
interactome, and the fact that interaction networks
are built from the results of thousands of
individual experiments, makes it impossible to
currently compare one interaction network with
another.

21. 3. We cannot monitor changes in the
proteome in real time. The need to destroy
cells for proteomic analysis, and a lack of
alternative technology to mass
spectrometry, makes it impossible to
understand the myriad of changes that
continuously occur in the cell.
4. Proteomics is currently semi quantitative,
not quantitative. A capacity to undertake
absolute rather than relative quantitation is
desirable.

22. 5. Our capacity to generate proteomic data of a
common type and standard, and thus to have truly
large, collaborative projects, is limited.
6.The field remains slow to embrace advanced
statistics for experimental design and data
analysis.

23. Conclusions
Proteomics provides a powerful set of tools for the
large-scale study of gene function directly at the
protein level. In particular, the mass spectrometric
study of gel-separated proteins is leading to a
renaissance in biochemical approaches to protein
function. Protein characterization will continue to
improve in throughput, sensitivity and
completeness. Post-translational modifications
cannot currently be studied at high throughput
but certain categories such as phosphorylation are
beginning to be amenable to generic Approaches.

24. References
 Introduction to proteomics-
Principles and Applications--
Nawin Mishra
 Proteome Research Concepts,
Technology and Application
Second Edition- M.R. Wilkins R.D.
Appel K.L. Williams D.F.
Hochstrasser (Eds.)