From: web-form@Oswego.EDU
Sent: Friday, October 05, 2007 4:54 PM
To: ucc@oswego.edu; loem@oswego.edu
Subject: Web Form: Course Submission

IP Address: 129.3.16.214
Department Chair: Jefferey Schneider
Department Chair Email: schneidr@oswego.edu
Additional Contact: Kestas Bendinskas (Associate Professor)
Additional Contact Email: bendinsk@oswego.edu
Course Number: CHE 471
Course Type: New Course
Course Title: Proteomics with lab
Catalog Description: Proteomics is the large-scale analysis of the entire set of proteins in a cell, tissue, or organism, allowing a description of the system in terms of its functional components.  This course covers theory and applications dealing with techniques and instrumentation utilized in proteomics.  The laboratory component includes proteome analysis using two dimensional electrophoresis, mass spectrometry, and use of databases.
Prerequisites: CHE 332 or CHE 360, and one of the following: BIO 309, BIO 315,  CHE 461
Fl - irregular basis: Yes
Semester Hours: 3
courseObjectives: Upon successful completion of this course, the students should be able to:
1.	Understand and explain the principles of expression proteomics and mass spectrometry.
2.	Understand and explain the principles of all techniques covered in lab.
3.	Demonstrate a broad overview of the applications of proteomics.
4.	Isolate and purify proteins.
5.	Quantify proteins.
6.	Analyze proteomes via electrophoresis and image analysis.
7.	Identify proteins via digestion, mass spectrometry, and database searches.

Course Description: Course Content:
This course covers theory and applications dealing with proteomics, including sequence and structural proteomics, expression proteomics, interaction proteomics, and functional proteomics.  Theories of appropriate instrumentation and techniques are included.  The course content will change as this is a very new and developing field of science. Topics covered during the first two times the course has been offered included: 
Introduction and overview of proteomics and cells.
Protein structure, expression, and function.
Protein purification and separation .
(Including isoelectric focusing, SDS-PAGE, gel staining, gel imaging, protein labeling and digestion)
Mass spectrometry (ESI, MALDI-TOF, in source decay, post source decay).
Database searching.
NMR in proteomics.
The following are key components of the laboratory:
1. Protein extraction and quantification.
2. MALDI-TOF mass spectrometry (whole proteins and in source decay analysis) of an unknown protein.
3. Proteome analysis via isoelectric focusing, SDS PAGE, and 2D gel image analysis.
4. Identification of proteins via protein digestion, mass spectrometry (peptide mass fingerprints and post source decay) and database searching.
The following may be incorporated into the lab:
1. NMR structural determination of peptides.
2. Group projects.

The methods of instruction will include three semester hour combinations of lectures and laboratory. There are no specific course requirements besides the Prerequisites listed above. The budgetary issues are outlined in the Other Comments. The means of evaluation will include quizzes, laboratory reports, and exams as desired. The number of evaluations could vary from term to term, depending upon the instructor(s).

Resources: At SUNY Oswego, we currently have access to adequate proteomics and mass spectrometry journals.  The book holdings are sufficient.  As proteomics techniques continue to be incorporated into courses and research, we request that the library continue to obtain books in the field of mass spectrometry and proteomics.  A variety of software, which is sufficient for this course, is housed in the Mass Spectrometry and Proteomics Center.
Bibliography: Aebersold, R., and M. Mann. 2003. Mass spectrometry-based proteomics. Nature 422:198-207.
Ainsworth, S. J. 2006. Genomics and Proteomics: Exciting career paths await scientists with specific analytical and technical skills. Chemical and Engineering News 84:45-49.
de Hoffman, E., and V. Stroobant. 2002. Mass Spectrometry: Principles and Applications 2ed. John Wiley & Sons, Hoboken.
Garfin, D., and S. Ahuja (ed.). 2005. Handbook of isoelectric focusing and proteomics vol. 7. Elsevier Academic Press, Boston.
Graves, P. R., and T. A. J. Haystead. 2002. Molecular Biologist's Guide to Proteomics. Microbiol. Mol. Biol. Rev. 66:39-63.
Habermann, B., J. Oegema, S. Sunyaev, and A. Shevchenko. 2004. The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches. Mol Cell Proteomics 3:238-249.
Herbert, C. G., and R. A. A. Johnstone. 2003. Mass Spectrometry Basics. CRC Press, Boca Raton.
Johnson, R. S., M. T. Davis, J. A. Taylor, and S. D. Patterson. 2005. Informatics for protein identification by mass spectrometry. Methods 35:223-236.
Nedelkov, D., and R. W. Nelson. (ed.). 2006. New and emerging proteomic techniques Humana Press, Totowa.
Phillips, C. I., and M. Bogyo. 2005. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cellular Microbiology 7:1061-1076.
Siuzdak, G. 2006. The Expanding Role of Mass Spectrometry in Biotechnology, 2 ed. MCC Press, San Diego.
Sparkman, O. D. 2000. Mass Spec Desk Reference, 1 ed. Global View Publishing, Pitsburg.
Twyman, R. M. 2004. Principles Of Proteomics. BIOS Scientific Publishers, New York.
Westermeier, R., and T. Naven. 2002. Proteomics in Practice, 3 ed. Wiley-VCH, Weinheim.
Wilmes, P., and P. L. Bond. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends in Microbiology 14:92-97.

Other Comments: This has been and will continue to be a cross-listed course that can be taken for elective credit in the biological sciences and chemistry. It has been co-taught by faculty from the Department of Biological Sciences and the Department of Chemistry. The budget is to be provided equally by both departments if that is to be continued. Otherwise, the funds will be drawn from the department of the instructor. It is a relatively expensive course, and from the two times we have delivered this course,  we estimate that IEF strips, SDS-PAGE gradient gels, protein purification kits, and other reagents (such as matrix, stains, and buffers), cost about $1200 for a class of 10 students using the spring 2007 prices. This and the fact that we have a single scanner and a single MALDI-TOF limits the number of students we can possibly serve in this very hi-tech course.  Costs for instrument maintenance and the Nitrogen for running the MALDI-TOF instrument are not figured into these cos