Genome 555 – Protein Technologies

Instructor: Michael J. MacCoss, Ph.D.

Office: Foege S113B

Phone: 206-616-7451

E-Mail: maccoss@u.washington.edu

http://proteome.gs.washington.edu/classes/Genome555/

 

Class Schedule:

March 29, 2011: Introduction, protein basics, protein properties, domains, protein modifications, complexity of the proteome

March 31, 2011: Protein separations, 2-dimensional gels, Western blots, Co-immunoprecipitation

            Readings: O’Farrell J. Biological Chemistry 1975 and Rigaut et al. Nat Biotech. 1999

April 5, 2011: Intro to Mass Spectrometry

            Readings: Steen and Mann Nat. Reviews

April 7, 2011: 1) Protein Mass Spectrometry Basics

2) Automated analysis of MS/MS spectra

-       Assignment 1: Problem set handed out (due 4/12)

April 12, 2011: 1) Multiple Testing Statistics in Proteomics

2) Comparative and Quantitative Proteomics

3) Intro to Writing a Manuscript Review

            Readings: MacCoss and Matthews Anal Chem 2005

April 14, 2011: Critical Evaluation of Proteomics Papers

-       Assignment 2: Manuscript Review Due

Paper to Review:

Petricoin et al. The Lancet 359 572-577 (2002)

Papers to Discuss:

Wu, MacCoss, et al. Anal Chem 2004

April 19, 2011: 1) Activity based methods and protein arrays

2) Measurement of protein dynamics. 

3) Fluorescence based technologies

-     Specific Aims for proposal due.

April 21, 2011: 1) Two-hybrid methods

2) Proteomics current status and challenges

            Readings: Fields and Song, Nature 1989 and Vidal and Legrain NAR 1999

April 26, 2011: Proposal Presentations 1

April 28, 2011: Proposal Presentations 2

 

Class Grades:

Class Participation:       30%

Problem Set:                 15%

Manuscript Review:       15%

Proposal and Presentation:  40%

·         Problem set will be a collection of peptide spectra that will need to be interpreted.  The problem set will be due in class April 12th.

·         Each student will propose a novel technology for characterizing proteins.  Any technology that relates to proteins, their structure, and/or their function is acceptable.  The technology does not necessarily have to be related to any of the technologies presented during the class.  The assignment consists of a one page write-up containing a brief background of the problem and two specific aims in addition to a 15 minute presentation (10 minute presentation and 5 minutes for questions).  The first specific aim should describe the proposed technology to be developed and the second aim should describe a biological question that the technology will be applied to. Due April 19th.