1. PROTEOMICS Tools,Techniques & Application
Kumari Rashmi
Sem-3

2. Introduction
Proteomics is the large-scale study of proteins, particularly their structures and function.
Proteomics is the systematic study of all of the proteins in a cell, tissue, or organism.
The term proteomics was coined in 1994 by Marc Wilkins.
The study of the Proteome.
The proteome is the entire set of proteome expressed by a genome, cell, tissue or organism.

4. Proteomics classification
Expression
Cell map or Interaction
Functional
Structural

5. Steps in Proteomic Research
Sample collection,handling and storage.
Protein seperation
Protein identification and characterization

6. Techniques used in Proteomics study
2-D gel electophoresis
ICAT(isotope coded affinity tags)
Mass spectroscopy
MALDI
PMF(Peptide mass fingerprinting)

7. 2-D gel electophoresis Sample preparation buffer composition
IPG strip rehydration
1st dimension: IEF run
2nd dimension: SDS-PAGE
Gel staining
Imaging

8. ICAT(isotope coded affinity tags)
Using ICAT you can compare relative protein abundance between two samples.
ICAT is particularly useful for comparision between healthy and diseased tissue

9. Mass spectroscopy Used for protein identification.
Mass spectrometer seperates proteins according to their mass-to-charge (m/z) ratio.
used for determining masses of particles, for determining the elemental composition of a sample or molecule.
The molecule is first ionized which results in the formation of charged particles. The ions are separated according to their (m/z)ratio in an analyzer by electromagnetic fields.

10. MALDI Matrix-assisted laser desorption/ionization
 is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules and large organic molecules.

11. PMF(Peptide mass fingerprinting)
technique for protein
identification

12. Database of proteomics
PRIDE-The PRIDE PRoteomics IDEntifications database is a centralised, standards compliant, public data repository for proteomics data.
PROTICdb access- PROTICdb is a tool developed by INRA that we have chosen for storing and processing our proteomic data.
 The PPDB stores experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization.

13. Human Proteome Project
Launched by the Human Proteome Organization (HUPO).
Designed to map the entire human protein set.
the three working pillars for HPP:
mass spectrometry,
antibodycapture,and
bioinformatics tools & knowledge bases.

14. Application of Proteomics
Nutrition Research
diabetes research.
Cardiovascular research.
Autoantibody profiling for the study and treatment of autoimmune disease.
Urological Cancer Research
Fetal and maternal medicine
Neurology
Renal disease diagnosis.
Study of Tumor Metastasis.
Protein Biomarker

15. Research Areas in Proteomics
Quantitative proteomics
Phosphoproteomics
Glycoproteomics
Proteogenomics
Neuroproteomics
Plant proteomics
Toxicoproteomics
Ethnoproteomics

16. Software for Proteomics
Description
Bhageerath
Protein Structure Generation
Persistence Length
Radius of Gyration
Hydrophobicity
ProRegIn
Protein structure optimizer
ProSEE - Scoring Function for Protein Structure Evaluation
Predicts native-like structures for small globular proteins
Structure Generation from given dihedrals
Filters for Globular Protein Evaluation
Protein Regularity Index
Energy minimizer for proteins
Calculates intramolecular energy of a protein in component-wise break up.

18. Thank You