Genome 490 – Undergraduate Seminar (Intro to Proteomics)

Instructor: Michael J. MacCoss, Ph.D.

Office: K328A (after Oct 26th I will be located in Foege S113)

Phone: 206-616-7451



Meets 2:30-4:20pm in Foege 040

Course Description:
This seminar course will introduce the student to a broad range of proteomics technologies and applications.  The focus will be on providing a historical perspective leading to the most recent discoveries.  Original papers will be assigned and students will be expected to discuss the papers and ask relevant questions regarding the significance, technical soundness, and methodological validation of the work.  Students will be asked to read the papers and submit a total of 4 questions each week relating to the papers assigned.

Class Schedule:

Oct 3, 2006: Introduction. Class overview and expectations.  What is proteomics?  Why measure proteins on a global level?  Why is it such a challenge?  What types of technologies do we need?  Presentation

                        The basics of reading the primary literature; examples from the primary literature. 

Introduction to 2D-gel electrophoresis

Background Reading  (O'Farrell,P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021 (1975).)

Background Reading (Görg,A., Postel,W., Günther,S., Two-dimensional electrophoresis. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9, 531-546 (1988).)

Background Reading (Ünlü,M., Morgan,M.E., Minden,J.S., Difference electrophoresis. A single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077 (1997).)

** Reading assignment (Gygi,S.P., Rochon,Y., Franza,B.R., Aebersold,R. Correlation between protein and mRNA abundance in yeast. Molecular and Cellular Biology 19, 1720-1730 (1999))

** Reading assignment (Shin,B.K. et al. Global profiling of the cell surface proteome of cancer cells uncovers an abundance of protein with chaperone function. J. Bio. Chem. 278, 7607-7616 (2003))

Oct 10, 2006: Discussion of 2D-gel papers. Presentation

Introduction to mass spectrometry basics.  How and why is mass spectrometry used to characterize proteins?

Background Reading (Steen,H., Mann M., The ABC's (and XYZ's) of peptide sequencing. Nature Reviews, 5, 699-711 (2004))

** Reading assignment (Wilm,M., Shevchenko,A., Houthaeve,T., Breit,S., Schweigerer,L., Fotsis,T., Mann,M., Femtomole sequencing of proteins from polyacrylamide gels by nanoelectrospray mass spectrometry. Nature 379, 466-469(1996)).

** Reading assignment (Washburn,M.P., Wolters,D., Yates III,J.R. Large scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotech. 19 242-247 (2001)).

** Reading assignment (Anderson,L. & Hunter,C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell Proteomics. 5, 573-588 (2006).)


Oct 17, 2006: Discussion of mass spectrometry papers.  Presentation

Introduction to protein biomarker detection.

Discussion of writing a manuscript review.

** Written review assignment. (Petricoin et al. Use of proteomics patterns in serum to identify ovarian cancer. The Lancet 359 572-577 (2002))


Oct 24, 2006: Discussion of assignment and review.

Alternative applications of proteomics:

Profiling, detection of protein-protein interactions, mapping post-translational modifications, gene annotation, etc…

** Reading assignment (Rigaut et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotech. 17 1030-1032 (1999))

** Reading assignment (Hazbun,T.R. et al., Assigning function to yeast proteins by integration of technologies. Mol. Cell. 12 1353-1365 (2003))

** Reading assignment (MacCoss,M.J. et al., Shotgun identification of protein modifications from protein complexes and lens tissue. PNAS 99 7900-7905 (2002))


Oct 31, 2006: I'm out of town this week.  Class will be handled by Greg Finney and Mike Hoopmann

Discussion of assigned papers.

Discussion of Affinity Based Proteomics and Protein Arrays

** Reading assignment (Michaud et al., Analyzing antibody specificity with whole proteome microarrays. Nat. Biotech., 21, 1509-1513 (2003))

** Reading assignment (Huang et al., Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. PNAS, 101, (2004))

** Reading assignment (Jessani et al., Enzyme activity profiles of the secreted and membrane proteome that depict cancer and cell invasiveness, PNAS, 99, (2002))

Nov 7, 2006: Discussion of assigned papers. Presentation

How to present a journal article.   

The Remaining Class will be focused on student presentations of papers of their own interest.  Some suggested papers.

Nov 14th
James Austill Wu et al Nature Biotech 2003
Lani Chun
Oda et al PNAS 1999
Isaac Frye
LaCount et al. Nature 2005

Nov 21th
Amy Chen
Wan et al. Amino Acids 2006
Nicole Day-Bazhaw
Jassani et al. Nat Methods 2005
Margo Haney
Kalume et al. Proteomics 2006

Nov 28th
Paul Biswajit
Novikova et al. Neurobiology of Disease 2006
Sahar Manavi
Beausoleil et al. PNAS 2004
Katherine Reinhart

Dec 5th
Wenyu Zhou Kratchmarova et al. Science 2005
Lisa Ven