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Swayam Central

Introduction To Proteomics

By Prof. Sanjeeva Srivastava   |   IIT Bombay

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:It would be applied to B.Sc., M.Sc. and MS.
PREREQUISITES: Any B.Sc. Or M.Sc.The target audiences of this course are required to have a basic introduction to biology.

SUMMARY

Course Status : Upcoming
Course Type : Elective
Duration : 8 weeks
Start Date : 26 Aug 2019
End Date : 18 Oct 2019
Exam Date : 16 Nov 2019
Category :
  • Biological Sciences & Bioengineering
  • Level : Postgraduate
    This is an AICTE approved FDP course

    COURSE LAYOUT

    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

    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

    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

    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

    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

    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

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

    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 

    BOOKS AND REFERENCES

    Nil

    INSTRUCTOR BIO


    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 CERTIFICATE

    • The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
    • The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
    • Date and Time of Exams: 16 November 2019: Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
    • 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. If there are any changes, it will be mentioned then.
    • Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

    CRITERIA TO GET A CERTIFICATE
    • Average assignment score = 25% of average of best 6 assignments out of the total 8 assignments given in the course. 
    • Exam score = 75% of the proctored certification exam score out of 100
    • Final score = Average assignment score + Exam score

    YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75
    • If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.
    • 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.
    • Only the e-certificate will be made available. Hard copies are being discontinued from July 2019 semester and will not be dispatched

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