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.