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.
Pre-requisites Any B.Sc. Or M.Sc.The target audiences of this course are required to have a basic introduction to biology.
951 students have enrolled already!!
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.
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 Certification 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.
