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Course Detail

Course Name Proteomes in Diseases
Course Code 24MMD211
Program B. Sc. Honors (with Research) in Molecular Medicine
Semester 4
Credits 2
Campus Kochi

Syllabus

Preamble

Despite having the same number of chromosomes in all cells, there are different types of cells and different functions they elicit. This is due to differential gene expression. As a result, the protein expression pattern and proteome of the tissue or cell type is going to be very different. Understanding the cellular proteins by proteome analysis is essential for deciphering the importance of cell/tissue specific proteins role in homeostasis and related functions

Unit 1

Maintenance of cellular protein complexity; what is proteome and proteomics, and its significance; proteomics versus genomics; significance of proteome research in health and disease; different types of proteomics.

Unit 2

How proteins of a cell can be identified; significance of different methods for studying proteomics; principles of mass spectrometry; ionization and its importance; MALDI and ESI; mass analyzers; Time of Flight; MS and MS/MS analyses; peptide fragmentation, deconvulation of mass spectra and peptide sequencing.

Unit 3

Mass spectrometry-based proteomics for protein identification; gel-free and gel-based proteomic approaches; significance of sample preparation in proteomics; protein extraction, protein fractionation; enzymatic digestion; peptide fractionation; database search for protein identification using software and search engines.

Unit 4

Peptide enrichment strategies for glycoproteomics and phosphoproteomics; quantitative proteomics; 2D and 2D-DIGE quantitative proteomics; labelled quantitative proteomics; metabolic (SILAC) and chemical labelling (iTRAQ, TMT) for quantitative proteomics; label-free quantitative proteomics.

Unit 5

Clinical proteomics and significance of mass spectrometry in clinics with respect to cancer and neurodegenerative diseases; application of mass spectrometry-based proteomics for biomarker discovery, drug target discovery, understanding disease pathogenesis, drug response.

Objectives and Outcomes

Course outcome (CO)

CO1: Basic understanding of the proteome and its complexity

CO2: Understand the principles and instrumentation of mass spectrometry

CO3: Understand how proteins are identified and quantified using mass spectrometry-based proteomics

CO4: A deeper understanding of differential expression of cellular proteins using quantitative proteomics

CO5: Significance and application of proteomics in clinical setting

Program Outcome

PO1: Bioscience Knowledge

PO2: Problem Analysis

PO3: Design/Development of Solutions

PO4: Conduct Investigations of complex problems

PO5: Modern tools usage

PO6: Bioscientist and Society

PO7: Environment and Sustainability

PO8: Ethics

PO9: Individual & Team work

PO10: Communication

PO11: Project management & Finance

PO12: Lifelong learning

3 = High Affinity, 2 = Medium Affinity, 1 = Low Affinity, – = No Affinity

PO1

PO2

PO3

PO4

PO5

PO6

PO7

PO8

PO9

PO10

PO11

PO12

CO 1

3

–

–

–

–

–

–

–

–

–

–

1

CO 2

3

–

–

–

3

–

–

–

–

–

–

1

CO 3

3

2

–

2

3

–

–

–

–

–

–

1

CO 4

3

2

–

2

2

–

–

–

–

–

–

1

CO 5

3

2

3

3

2

2

–

–

–

–

–

1

 

Program Specific Outcomes (PSO)

PSO 1 – Chemical and physical basis of biology

PSO 2 – Computational science in biology and medicine

PSO 3 – Biochemical and physiological complexity in biology and medicine

PSO 4 – Molecular technology in biology and medicine

PSO 5 – Cell based approaches in diagnosis and therapy

PSO 6 – Microorganisms in medicine

PSO 7 – Nanoscale entities and its significance in medicine

PSO 8 – Tissue architecture engineering in medicine

PSO 9 – Compounds as drugs and its efficacy

PSO 10 – Bioinformatics and artificial intelligence in medicine

PSO 11 –Technology in personalizing medicine

PSO 12 – Protein structural complexity in medicine

PSO 13 – Projecting science and medicine to public

PSO1

PSO2

PSO3

PSO4

PSO5

PSO6

PSO7

PSO8

PSO9

PSO10

PSO11

PSO12

PSO13

CO 1

3

–

3

–

–

–

–

–

–

–

–

–

–

CO 2

–

–

–

–

–

–

–

–

–

–

–

–

–

CO 3

–

3

–

–

–

–

–

–

–

3

–

–

1

CO 4

–

3

2

–

–

–

–

–

–

3

2

1

2

CO 5

–

–

3

–

–

–

–

–

2

3

3

3

3

Evaluation Pattern

Internal Assessment – 50% 

Periodical 1 

Exam 

20% 

Periodical 2 

Exam 

20% 

Continuous Assessment 

Assignment/Test/Quiz

10% 

50%

End Semester Examination- 50% 

Theory Exam 

50% 

50%

Total

100%

Text Books / References

  1. Nawin C. Mishra, “Introduction to Proteomics: Principles and Applications” Wiley, 2010, ISBN: 0471754021
  2. Proteomics for Biological Discovery: Timothy Veenstra and John Yates

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