Chem204: Introduction to Proteomics

Winter Quarter 2010

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 two reviews of published papers 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-S261.

	Date	Topic	Lecturer	Student	Materials
1.	Tue. 1/5	Overview / Protein Chemistry	RAB	---	lecture notes and reading
2.	Thu. 1/7	2D Gels	RJC	---	lecture notes and reading
3.	Tue. 1/12	Introduction to Mass Spectrometry	RJC	---	lecture notes
4.	Thu. 1/14	Sample Preparation	JCT	---	lecture notes
5.	Tue. 1/19	Protein ID 1 – Non-MS	RAB	SM - 12	lecture notes
6.	Thu. 1/21	Protein ID 2 – MS	RJC	DB - 2	lecture notes and reading
7.	Tue. 1/26	Bioinformatics	PCB	---	lecture notes and reading1 and reading2
8.	Thu. 1/28	PTMs – Overview	KFM	XW - 7	lecture notes
9.	Tue. 2/2	PTMs – Complex / Crosstalk	RJC	BT - 6 DG - 5	lecture notes
10.	Thu. 2/4	Quantitation	JCT	JG - 3	lecture notes and reading
11.	Tue. 2/9	Signaling	JCT	DG - 19	lecture notes
12.	Thu. 2/11	Biophysical Methods (Fluorescence / Hydrodynamics)	KFM	DB - 17	lecture notes
13.	Tue. 2/16	Structural (X-Ray / NMR)	RMS	---
14.	Thu. 2/18	Protein – Protein Interactions: Non-MS (Y2H; IP)	RAB	XW - 20	lecture notes
15.	Tue. 2/23	Protein – Protein Interactions: TAP Tag; Cross-linking	KFM	SM - 25	lecture notes
16.	Thu. 2/25	Protein Machines / Sociology	AS	---	lecture notes
17.	Tue. 3/2	Arrays	RAB	JG - 24	lecture notes
18.	Thu. 3/4	Translational / Biomarkers	RAB	BT - 16	lecture notes
19.	Tue. 3/9	Micro-fluidics / Robotics / HT	JCT	---
20.	Thu. 3/11	Interaction with other OMICS	RJC	---

Lecturers

RAB	-	Ralph Bradshaw
RJC	-	Robert Chalkley
JCT	-	Jonathan Trinidad
PCB	-	Patricia Babbitt
KFM	-	Katalin Medzihradszky
RMS	-	Robert Stroud
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.	Activity-Based Proteome Profiling of Hepatoma Cells during Hepatitis C Virus Replication Using Protease Substrate Probes
2.	Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
3.	Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins
4.	Proteomic analysis of doxorubicin induced changes in the proteome of HepG2cells combining 2D-DIGE and LC-MS/MS approaches
5.	Dissection of the insulin signaling pathway via quantitative phosphoproteomics
6.	Differential protein expression on the cell surface of colorectal cancer cells associated to tumor metastasis
7.	Simultaneous Characterization of Glyco- and Phospho-proteomes of Mouse Brain Membrane Proteome with Electrostatic Repulsion Hydrophilic Interaction Chromatography (ERLIC)
8.	Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response
9.	Analysis of human C1q by combined bottom-up and top-down mass spectrometry: detailed mapping of post-translational modifications and insights into the C1r/C1s binding sites
10.	Detection of Differentially Expressed Basal Cell Proteins by Mass Spectrometry
11.	Glycation Isotopic Labelling (GIL) with ¹³C-reducing Sugars for Quantitative Analysis of Glycated Proteins in Human Plasma
12.	Comprehensive Mapping of Post-Translational Modifications on Synaptic, Nuclear, and Histone Proteins in the Adult Mouse Brain

Section 2

Papers drawn from lectures 11-20.

13.	Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution
14.	Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
15.	Integrated microfluidic device for mass spectrometry-based proteomics and its application to biomarker discovery programs
16.	A quantitative atlas of mitotic phosphorylation
17.	Pyruvate kinase M2 is a phosphotyrosine-binding protein
18.	Utility of formaldehyde crosslinking and mass spectrometry in the study of protein–protein interactions
19.	BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals
20.	Proteomic Studies of a Single CNS Synapse Type: The Parallel Fiber/Purkinje Cell Synapse
21.	Progress in analytical imaging of the cell by dynamic secondary ion mass spectrometry (SIMS microscopy)
22.	Monoclonal antibody proteomics: Discovery and prevalidation of chronic obstructive pulmonary disease biomarkers in a single step
23.	Targeted Proteomic Analysis of 14-3-3σ, a p53 Effector Commonly Silenced in Cancer
24.	Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes
25.	Direct Interaction of Tumor Suppressor CEACAM1 with Beta Catenin: Identification of Key Residues in the Long Cytoplasmic Domain

Term Papers

The following topics for the term paper are available on a first come, first serve basis and should not be duplicated. Anyone who wishes to write on a topic not listed should get approval from one of the teaching staff (Chalkley, Bradshaw, Trinidad, or Medzihradszky). Email your selection to Ralph Bradshaw.

	Student	Topic
1.	SM	Discuss the strengths and weaknesses of intact protein analysis. Talk about the limitations that need to be surmounted in order to conduct these experiments on a wide variety of proteins and discuss the feasibility of overcoming the limitations.
2.		Discuss the bottlenecks with protein cross linking experiments and approaches that could be taken to make these techniques widely applicable to a variety of complex biological samples.
3.		Compare and contrast the various search algorithm approaches to interpret MS/MS spectra. Is there significant room for improvement, and in general, how might these algorithms be improved upon?
4.		Proteomic techniques are increasingly effective at generating large scale quantitative datasets of specific biological phenotypes. How are these datasets being analyzed using available bioinformatic techniques? In what way do we really want to understand biological systems and what needs to be done to get there?
5.	DG	Discuss the varied ways in which the TAP-tag approach has been applied and their respective strengths and weaknesses. What role, if any, will TAP approaches have in the future of mass spectrometry-based proteomics?
6.		Give an overview of the “progress” made in the biomarker discovery field. (This does not have to be limited to human disease). Why is this such a complex problem, and what future approaches are likely to be required to realize its potential.
7.		What approaches can be used for identification of a drug target and characterizing the interaction? Discuss strengths and weaknesses of different approaches.
8.	WX	What means are available for identifying interaction partners of integral membrane proteins? What different challenges do these present in comparison to cytoplasmic protein studies?
9.		What techniques are used for characterizing a recombinant protein pharmaceutical? What are the specific concerns compared to characterizing a natively expressed protein?
10.		Outline proteomic approaches available for characterizing a signal transduction pathway, discussing their strengths and weaknesses. What do you see as the future of such studies?
11.		Contrast the utility to cellular regulation of reversible vs non-reversible PTMs. What differing challenges do they present for proteomic analyses.
12.		Give an example of a proteomic experiment where 2D gel electrophoresis is the most effective analytical method. What other approaches could be used to address the same question, and why do you think 2D gels are the method of choice in this example?
13.	DB	Outline the different options available for characterizing the binding interface between two proteins, discussing their strengths and weaknesses.
14.		Many proteomic experiments now involve global quantitative analysis. What level of accuracy is required in these measurements in order to answer biological questions? Does this differ for protein level vs PTM level studies?
15.		The proteomics of proteolysis. What are the questions that need answers and how can proteomics address them? Why does this type of post-translational modification have issues unique to it?
16.		Stem cells are a particularly interesting (and important) challenge because of their therapeutic potential. What are the issues in characterizing these cells, what is known (or needs to be known) and how can proteomics advance this field?

Course Organizer

For more details contact course organizer: Robert Chalkley (currently on holiday until March) or Ralph Bradshaw.