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Introduction to Proteomics

Indian Institute of Technology Bombay via NPTEL

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Overview

This course introduces to the basic biology of proteins and the new advanced science called as proteomics which aims to look into the protein properties from a global perspective, i.e., not undertaking one protein at a time, but an entire set of proteins in the milieu. The course will cover in detail the two major aspects of proteomics i.e., Gel-based proteomics and Mass spectrometry-based proteomics. The gel-based module will cover different techniques like SDS-PAGE, 2-DE, 2D-DIGE etc. These techniques had a major contribution in transition from protein chemistry to proteomics. Mass spectrometry, on the other hand, is an advanced analytical technique for accurate mass measurement. In this module, we will discuss the basics of mass spectrometry, sample preparations, liquid chromatography, hybrid mass spectrometers and quantitative proteomics techniques such as iTRAQ, SILAC and TMT using mass spectrometry. The course will also provide the basic knowledge about sample preparation, mass spectrometry workflow, different chromatography technologies and quantitative proteomics.

Syllabus

Module 1 : Gel based Proteomics

Week 1 : Basics of proteins and proteomics
Lecture 1 : Introduction to amino acids
Lecture 2 : Introduction to proteins
Lecture 3 : Protein folding & misfolding
Lecture 4:  Introduction to proteomics
Lecture 5 : Lab session – Protein-protein interaction using label-free biosensors
Assignment 1

Week 2 : Gel-based proteomics
Lecture 6 : Sample preparation and pre-analytical factors
Lecture 7 : Sample preparation: Pre-analytical factors (contd.)
Lecture 8 : Sample preparation: Protein extraction and quantification
Lecture 9 : One-dimensional electrophoresis
Lecture 10 : Introduction to 2-DE
Assignment 2

Week 3 : Two-dimensional gel electrophoresis (2-DE)

Lecture 11 : 2-DE: Second dimension, staining & destaining
Lecture 12 : 2-DE: Gel analysis
Lecture 13 : 2-DE Applications
Lecture 14 : 2-DE Applications (contd.) & Challenges
Lecture 15 : Lab session - Protein/peptide pre-fractionation using OFFGEL FRACTIONATOR & data analysis
Assignment 3

Week 4 : Difference in gel electrophoresis (DIGE) & Systems Biology
Lecture 16 : 2D-DIGE: Basics
Lecture 17 : 2D-DIGE: Data analysis
Lecture 18 : 2D-DIGE: Applications
Lecture 19 : Systems biology and proteomics - I
Lecture 20 : Systems biology and proteomics - II
Assignment 4

Module 2 : Gel based Proteomics

Week 5 : Basics of mass spectrometry
Lecture 21 : Fundamentals of mass spectrometry
Lecture 22 : Chromatography technologies
Lecture 23 : Liquid chromatography
Lecture 24 : Mass spectrometry: Ionization sources
Lecture 25 : Mass spectrometry: Mass analyzers
Assignment 5

Week 6 : Basics of mass spectrometry and sample preparation
Lecture 26 : MALDI sample preparation and analysis
Lecture 27 : Hybrid mass spectrometry configurations
Lecture 28 : Lab session - Demonstration of Q-TOF MS technology
Lecture 29 : In-gel & in-solution digestion
Lecture 30 : Lab session - Sample preparation: tissue sample preservation technology
Assignment 6

Week 7 : Quantitative proteomics
Lecture 31 : Introduction to quantitative proteomics
Lecture 32 : SILAC: In vivo labeling
Lecture 33 : iTRAQ: In vitro labeling
Lecture 34 : TMT: In vitro labeling
Lecture 35 : Quantitative proteomics data analysis
Assignment 7

Week 8 : Advancement in Proteomics
Lecture 36 : Proteomics applications
Lecture 37 : Challenges in proteomics
Lecture 38 : OMICS and translational research
Lecture 39 : Lab session – Targeted proteomics using triple quadrupole mass spectrometry
Lecture 40 : Lab session – Targeted proteomics: multiple reaction monitoring
Assignment 8

Taught by

Sanjeeva Srivastava

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