PROTEOMICS Tools,Techniques & Application

1. PROTEOMICSTools,Techniques & Application KumariRashmi 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. MALDIMatrix-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 PRoteomicsIDEntifications database is a centralised, standards compliant, public data repository for proteomics data. PROTICdbaccess-PROTICdbis 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 Software 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 Filters for Globular Protein Evaluation Filters for Globular Protein Evaluation Protein Regularity Index Energy minimizer for proteins Calculates intramolecular energy of a protein in component-wise break up.

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