Courses » Introduction to Proteomics

Introduction to Proteomics

About the Course :

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.

Intended Audience :
Core course. All UG and PG students can attend this course. It would be applied to B.Sc., M.Sc. and MS.

Any B.Sc. Or M.Sc.The target audiences of this course are required to have a basic introduction to biology.

About the Instructor :

Dr. Sanjeeva Srivastava is the Group Leader for the Proteomics Laboratory at the Indian Institute of Technology Bombay India (IITB). He obtained his Ph.D. from the University of Alberta and post-doc from the Harvard Medical School in the area of proteomics, stress physiology and has specialized expertise in applications of data enabled sciences in global health, developing country and resource limited settings.

Dr. Srivastava has considerable experience for teaching proteomics courses and conducting hands-on crash-courses on proteomics at IIT Bombay and many other institutes including proteomics workshop at Reliance Life Sciences, Mumbai, and Continuing Education Programme (CEP) on proteomics at IIT Bombay, and three proteomics courses in Cold Spring Harbor Laboratory (CSHL), New York. Apart from the regular research work, Dr. Srivastava has been actively involved in the development of various proteomics e-Learning & Open-Learning curriculums and Virtual Lab initiatives at IIT Bombay generated with an intention to disseminate high-quality educational materials on proteomics at a global scale [Ray et al., PLoS Biol. 2012; Ray et al., J Proteomics. 2012; Srivastava et al., Nature 2013]. These Virtual Lab initiatives have been included as a part (Tutorial- IPTP 14) of the International Proteomics Tutorial Programme (supported by Human Proteome Organization (HUPO) and European Proteomics Association (EuPA)).

At IIT Bombay Dr. Srivastava has established an excellent infrastructure for quantitative and targeted proteomics and metabolomics at IIT Bombay, which includes different instrumentations and software for gel-based proteomics [Two Dimensional gel Electrophoresis (2-DE) and 2D- Differential Gel Electrophoresis (2D-DIGE) [Ettan IPGphore 3 isoelectric focusing unit (GE Healthcare), Ettan DALT six electrophoresis unit (GE Healthcare), LabScan software version 6.0 (GE Healthcare), Image Master,2D Platinum 7.0 software (GE Healthcare), ImageQuant software version 5.0 (GE Healthcare), Typhoon 9400 variable mode imager (GE Healthcare) and DeCyder 2D software, version 7.0 (GE Healthcare)], and MS-based proteomics and metabolomics platforms [MALDI TOF/TOF MS (4800 MALDI-TOF/TOF mass spectrometer (AB Sciex, Framingham, MA), Autoflex Speed (Bruker Daltonics)), 3100 OFFGEL fractionator (Agilent Technologies, Santa Clara, CA), Agilent 6550 iFunnel Q-TOF LC MS/MS instrument (Agilent Technologies, USA), Accu TOF GCv (JMS-T100GCv) system from Jeol Asia equipped with Agilent 7690 GC, Spectrum Mill Protein Identification software (Agilent Technologies, USA), MASCOT version 2.1 (http://www.martixscience.com), Mass Profiler Professional (MPP) software package (version 2.2, Agilent Technologies, Santa Clara, CA, USA) and Surface Plasmon Resonance (SPR): Biacore T200 system (GE Healthcare), Gene Pix Pro Microarray Scanner; Microarrayer printer]. Consequently, we have both expertise and infrastructure for conducting such bilateral training program at IIT Bombay.

Click here to view Faculty Profile: http://www.bio.iitb.ac.in/~sanjeeva/

About the Instructor: https://youtu.be/sb4faypvWwk

Course Plan :

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

ertification Exam :

  • The exam is optional for a fee.Exams will be on 23 April 2017.
  • Time : Shift 1: 9 AM -12 Noon;Shift 2 : 2 PM-5 PM
  • Any one shift can be chosen to write the exam for a course.
  • Registration URL : Announcements will be made when the registration form is open for registrations.
  • The online Registration form has to be filled and the certification exam fee needs to be paid.More details will be made available when the exam registration form is published.
Certificate :
  • Final score will be calculated as : 25% assignment score + 75% final exam score.
  • 25% assignment score is calculated as 25% of average of 8 weeks course : Best 6 out of 8 assignments
  • E-Certificate will be given to those who register and write the exam and score greater than or equal to 40% final score. Certificate will have your name, photograph and the score in the final exam with the breakup. It will have the logos of NPTEL and IIT Bombay. It will be e-verifiable at nptel.ac.in/noc.