Kumari Rashmi

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PROTEOMICSTools,Techniques Application

• Kumari Rashmi
• Sem-3

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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 express
  ed by a genome, cell, tissue or organism.

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Proteomics classification

• Expression
• Cell map or Interaction
• Functional
• Structural

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Steps in Proteomic Research

• Sample collection,handling and storage.
• Protein seperation
• Protein identification and characterization

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Techniques used in Proteomics study

• 2-D gel electophoresis
• ICAT(isotope coded affinity tags)
• Mass spectroscopy
• MALDI
• PMF(Peptide mass fingerprinting)

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2-D gel electophoresis

• Sample preparation
• buffer composition
• IPG strip rehydration
• 1st dimension IEF run
• 2nd dimension SDS-PAGE
• Gel staining
• Imaging

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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

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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.

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MALDIMatrix-assisted laser desorption/ionizati
on

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

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PMF(Peptide mass fingerprinting)

• technique for protein
• identification

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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.

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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.

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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

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Research Areas in Proteomics

• Quantitative proteomics
• Phosphoproteomics
• Glycoproteomics
• Proteogenomics
• Neuroproteomics
• Plant proteomics
• Toxicoproteomics
• Ethnoproteomics

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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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Thank You