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
Thank You