PROTEOMICS FALL ’05 SYLLABUS

Course # Lecturer BIOL 4340-001 or BIOL 5373-001 Dr. Steven Goodman Office: FO 3.702 Phone: 972-883-4872 E-mail: sgoodmn@utdallas.edu Wednesdays & Fridays FO 3.616 Introduction to Proteomics, Tools for the New Biology, Humana Press; by Daniel C. Liebler 11:00 am – 12:15 pm

Days/Time Location Textbook

Student Responsibilities Come to class on time. Read the assigned textbook chapters prior to class. Carefully read the assigned scientific literature and be ready to discuss the content in class. Grades There will be three exams (of equal weight) and a final paper (will be described in the organizational meeting). Your numerical grade will be calculated as follows: Exam 1: Exam 2: Exam 3: Final Paper: Class Participation: Your letter grade will be determined as follows: 90 or above A 80 or above B 70 or above C 60 or above D (undergrads) 50 or above F (undergrads) 20% 20% 20% 20% 20% 100%

F (graduate students)

My responsibility Proteomics is one of the most exciting fields in the post human genome world. It is my responsibility to impart that excitement to you and help you to understand the power of modern proteomic technology.

PROTEOMICS BIOL 5373-001 / BIOL 4340-001 Class Dates 8-19-05 8-24-05 8-26-05 8-31-05 9-02-05 9-07-05 9-09-05 9-14-05 9-16-05 9-21-05 9-23-05 9-28-05 9-30-05 10-05-05 10-07-05 10-12-05 10-14-05 10-19-05 10-21-05 10-26-05 10-28-05 11-02-05 11-04-05 11-09-05 11-11-05 11-16-05 11-18-05 11-23-05 11-25-05 12-02-05 Lectures / Exams Organizational Meeting NO CLASS NO CLASS Review of Protein Structure Proteomics & the New Biology The Proteome Overview of Analytical Proteomics Analytical Protein and Peptide Separations Protein Digestion Techniques Study Date Exam 1 Mass Spectrometers for Protein and Peptide Analysis Protein Identification by Peptide Mass Fingerprinting Protein Sequence Analysis by Tandem Mass Spectrometry Protein Identification with Tandem Mass Spectrometry Data SALSA: An Algorithm for Mining Specific Features of Tandem MS Data Mining Proteomes Study Date Exam 2 Protein Expression Profiling Identifying Protein-Protein Interactions and Protein Complexes Mapping Protein Modifications New Directions in Proteomics Protein Chips and Arrays The Application of Mass Spectrometry to Membrane Proteins Study Date Exam 3 Proteomics and Human Disease THANKSGIVING HOLIDAY – UNIVERSITY CLOSED PAPERS DUE TODAY

2005 Proteomics Reading List
Date 9/2/2005 9/7/2005 9/9/2005 9/14/2005 9/16/2005 9/28/2005 9/30/2005 Articles Aebersold and Mann Nature 422: 198-207, 2003 Taylor et al Nature Biotech. 21: 281-286, 2003 Kakhniashvili et al Mol. Cell Prot. 3:501-509, 2004 Low et al. Proteom. 2:1229-1239, 2002 Olsen et al. Mol. Cell Prot. 3:608-614, 2004 Anderson et al Mol. Cell Prot. 3:311-326, 2004 Krokhen et al Mol. Cell Prot. 2: 346-356, 2003 Baldwin Mol. Cell Prot. 3:1-9, 2004 Peng and Gygi J. Mass Spec. 36:1083-1091, 2001 Medzihradszky et al Mol Cell Prot. 3:429-440, 2004 Durr et al Nature Biotech 22:985-992, 2004 Liebler Ch. 1 2 3 4 5 6 7

10/5/2005

8

10/7/2005

9 10 11 12 13 14

10/12/2005 Hansen et al Anal. Chem. 73:1676-1683, 2001 10/14/2005 Washburn et al Nature Biotech. 19:242-247, 2001 10/26/2005 Han et al Nature Biotech 19:946-951, 2001 10/28/2005 Blagoev et al Nature Biotech 21:315-318, 2003 11/2/2005 Peng et al Nature Biotech 21:921-926, 2003 Mann and Jensen Nature Biotech 21:255-261, 2003 Candas et al Mol. Cell Prot. 2:19-28, 2003 Coleman et al Proteom. 3:2101-2107, 2003

11/4/2005 11/9/2005

15 15

11/11/2005 Luche et al Proteom. 3:249-253, 2003 Wu and Yates Nature Biotech. 21:262-267, 2003 11/23/2005 Kakhniashvili et al Exp. Bio. and Med. In Press. 15

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