Chem204: Introduction to Proteomics

Winter Quarter 2011

Starting with a review of protein chemistry, emphasizing chemical modification and separation technologies, the course will review current approaches to the study of proteomics and predict what is likely to be realized in the next several years.

In addition to the lectures, each student will present a review of a published paper selected by the instructors (see below) and write a paper on a topic of current interest to the field (from a list provided, or select their own topic after instructor approval).

Lecture Series

All lectures will take place from 9:00am - 10:30am in room GH-S202.
(*except on 1/20/11, when class will be held in Rock Hall 102)

	Date	Topic	Lecturer	Materials
1.	Tue. 1/4	Overview / Protein Chemistry	RAB	lecture notes
2.	Thu. 1/6	Protein Purification and Separation/Gels	RJC	lecture notes
3.	Tue. 1/11	Peptide Purification and Separation	JCT	lecture notes
4.	Thu. 1/13	Introduction to Mass Spectrometry	RJC	lecture notes
5.	Tue. 1/18	Protein ID 1 – Non-MS	RAB	lecture notes
6.	Thu. 1/20 *	Protein ID 2 – MS	RJC	lecture notes
7.	Tue. 1/25	Biophysical Methods (Fluorescence / Hydrodynamics)	KFM	lecture notes
8.	Thu. 1/27	Bioinformatics	PCB	lecture notes
9.	Tue. 2/1	Quantification	JCT	lecture notes
10.	Thu. 2/3	Protein – Protein Interactions: Non-MS (Y2H; IP)	RAB	lecture notes
11.	Tue. 2/8	Protein – Protein Interactions: TAP Tag; Cross-linking	KFM	lecture notes
12.	Thu. 2/10	PTMs – Overview	KFM	lecture notes
13.	Tue. 2/15	PTMs – Complex / Crosstalk	RJC	lecture notes
14.	Thu. 2/17	Signaling	JCT	lecture notes
15.	Tue. 2/22	Network Analysis and Clustering	JCT	lecture notes
16.	Thu. 2/24	Protein Machines / Sociology	AS	lecture notes
17.	Tue. 3/1	Arrays	RAB	lecture notes
18.	Thu. 3/3	Translational / Biomarkers	RAB	lecture notes
19.	Tue. 3/8	Micro-fluidics / Robotics / Nanotech	JCT	lecture notes
20.	Thu. 3/10	Interaction with other OMICS	RJC	lecture notes

Lecturers

RAB	-	Ralph Bradshaw
RJC	-	Robert Chalkley
JCT	-	Jonathan Trinidad
PCB	-	Patricia Babbitt
KFM	-	Katalin Medzihradszky
AS	-	Andrej Sali

Student Presentations

Students taking this course for credit are required to select and present two papers to the class. Topics for the first paper will be drawn from lectures 2-10 and topics for the second paper will be drawn from lectures 11-20. For each set of lectures, the instructors will select an assorment of papers and students will need to select a paper and email the course organizer the paper selected and the day for the presentation. Assignments are done on a first-come basis.

Section 1

Papers drawn from lectures 2-10.

1.	Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
2.	sensitive multiplexed analysis of kinase activities and activity-based kinase identification
3.	Comprehensive Mapping of Post-Translational Modiﬁcations on Synaptic, Nuclear, and Histone Proteins in the Adult Mouse Brain
4.	A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae
5.	Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes
6.	A Tissue-Speciﬁc Atlas of Mouse Protein Phosphorylation and Expression
7.	Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

Course Organizer

For more details contact course organizer: Robert Chalkley or Ralph Bradshaw.