KUMARI RASHMI SEM-3

PROTEOMICSTools,Techniques & Application

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.

Proteomics classification

ExpressionCell map or InteractionFunctionalStructural

Steps in Proteomic Research

Sample collection,handling and storage.Protein seperationProtein identification and characterization

Techniques used in Proteomics study

2-D gel electophoresisICAT(isotope coded affinity tags)Mass spectroscopyMALDIPMF(Peptide mass fingerprinting)

2-D gel electophoresis

Sample preparation buffer composition IPG strip

rehydration 1st dimension: IEF

run 2nd dimension:

SDS-PAGE Gel staining Imaging

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

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.

MALDIMatrix-assisted laser desorption/ionization

 is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules and large organic molecules.

PMF(Peptide mass fingerprinting)

technique for protein identification

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.

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.

Application of Proteomics

Nutrition Researchdiabetes research. Cardiovascular research. Autoantibody profiling for the study and treatment

of autoimmune disease. Urological Cancer ResearchFetal and maternal medicine Neurology Renal disease diagnosis. Study of Tumor Metastasis.Protein Biomarker

Research Areas in Proteomics

Quantitative proteomicsPhosphoproteomicsGlycoproteomicsProteogenomicsNeuroproteomicsPlant proteomicsToxicoproteomicsEthnoproteomics

Software Description

BhageerathProtein Structure Gen

erationPersistence LengthRadius of GyrationHydrophobicityProRegInProtein structure opti

mizerProSEE

- 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.

Software for Proteomics

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