Course content

• An introduction to proteomics: Basics of protein structure and function, An overview of systems biology, Evolution from protein chemistry to proteomics
• Abundance-based proteomics: Sample preparation and pre-fractionation steps, Gel-based proteomics - two-dimensional gel electrophoresis (2-DE), two-dimensional fluorescence difference in-gel electrophoresis (DIGE), Staining techniques
• Central role of mass spectrometry: ionization sources, mass analyzers, different types of mass spectrometers; Quantitative proteomics - stable isotope labelling by amino acids in cell culture (SILAC), isotope-coded affinity tag (ICAT), isobaric tagging for relative and absolute quantitation (iTRAQ)
• Functional proteomics: Recombinational cloning, Interactomics techniques to study protein-protein interactions, yeast two-hybrid, immunoprecipitation, protein microarrays, Nucleic Acid Programmable Protein Array (NAPPA)
• Label-free nanotechnologies in proteomics, Surface Plasmon Resonance (SPR); Modificomics: understanding post-translational modifications; Structural proteomics; Bioinformatics in proteomics; Challenges and future prospects of proteomics research
• Proteomics course will cover several basic concepts of various technologies but emphasis will be more on software's and hands-on sessions/ data analysis. 

References

• Introduction to Proteomics: Tools for the New Biology, D.C. Liebler, Humana Press, 2002. 
• Principles of Proteomics, R.M. Twyman, Bios Scientific Pub., 2004.
• Proteomics for Biological Discovery, T.D. Veenstra, J.R. Yates III, John-Wiley & Sons, Hoboken, New Jersey, USA; 2006.
• Protein Biochemistry and Proteomics (The Experimenter Series), R. Hubert, Academic Press, 2006. 
• Proteomics in Practice: A Guide to Successful Experimental Design, R. Westermeier, T. Naven, H-R. Hopker, Wiley-VCH, 2008. 
• Proteomics: A Cold Spring Harbor Laboratory Course Manual, A.J. Link and J. LaBaer, Cold Spring Harbor Laboratory Press, 2009. 
• Selected papers from scientific journals.