PROTEOMICS FALL ’05 SYLLABUS

Course # BIOL 4340-001 or BIOL 5373-001

Lecturer Dr. Steven Goodman

Office: FO 3.702
Phone: 972-883-4872
E-mail: sgoodmn@utdallas.edu

Days/Time Wednesdays & Fridays 11:00 am – 12:15 pm

Location FO 3.616

Textbook Introduction to Proteomics, Tools for the New Biology, Humana Press; by Daniel C. Liebler

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: 20%
Exam 2: 20%
Exam 3: 20%
Final Paper: 20%
Class Participation: 20%
100%
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) F (graduate students)
50 or above F (undergrads)

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 Lectures / Exams

8-19-05 Organizational Meeting
8-24-05 NO CLASS
8-26-05 NO CLASS
8-31-05 Review of Protein Structure
9-02-05 Proteomics & the New Biology
9-07-05 The Proteome
9-09-05 Overview of Analytical Proteomics
9-14-05 Analytical Protein and Peptide Separations
9-16-05 Protein Digestion Techniques
9-21-05 Study Date
9-23-05 Exam 1
9-28-05 Mass Spectrometers for Protein and Peptide Analysis
9-30-05 Protein Identification by Peptide Mass Fingerprinting
10-05-05 Protein Sequence Analysis by Tandem Mass Spectrometry
10-07-05 Protein Identification with Tandem Mass Spectrometry Data
10-12-05 SALSA: An Algorithm for Mining Specific Features of Tandem MS Data
10-14-05 Mining Proteomes
10-19-05 Study Date
10-21-05 Exam 2
10-26-05 Protein Expression Profiling
10-28-05 Identifying Protein-Protein Interactions and Protein Complexes
11-02-05 Mapping Protein Modifications
11-04-05 New Directions in Proteomics
11-09-05 Protein Chips and Arrays
11-11-05 The Application of Mass Spectrometry to Membrane Proteins
11-16-05 Study Date
11-18-05 Exam 3
11-23-05 Proteomics and Human Disease
11-25-05 THANKSGIVING HOLIDAY – UNIVERSITY CLOSED
12-02-05 PAPERS DUE TODAY
 2005 Proteomics Reading List
Date Articles Liebler
Ch.
9/2/2005 Aebersold and Mann Nature 422: 198-207, 2003 1
9/7/2005 Taylor et al Nature Biotech. 21: 281-286, 2003 2
9/9/2005 Kakhniashvili et al Mol. Cell Prot. 3:501-509, 2004 3
9/14/2005 Low et al. Proteom. 2:1229-1239, 2002 4
9/16/2005 Olsen et al. Mol. Cell Prot. 3:608-614, 2004 5
9/28/2005 Anderson et al Mol. Cell Prot. 3:311-326, 2004 6
9/30/2005 Krokhen et al Mol. Cell Prot. 2: 346-356, 2003 7
Baldwin Mol. Cell Prot. 3:1-9, 2004

10/5/2005 Peng and Gygi J. Mass Spec. 36:1083-1091, 2001 8

Medzihradszky et al Mol Cell Prot. 3:429-440, 2004

10/7/2005 Durr et al Nature Biotech 22:985-992, 2004 9

10/12/2005 Hansen et al Anal. Chem. 73:1676-1683, 2001 10
10/14/2005 Washburn et al Nature Biotech. 19:242-247, 2001 11
10/26/2005 Han et al Nature Biotech 19:946-951, 2001 12
10/28/2005 Blagoev et al Nature Biotech 21:315-318, 2003 13
11/2/2005 Peng et al Nature Biotech 21:921-926, 2003 14
Mann and Jensen Nature Biotech 21:255-261, 2003

11/4/2005 Candas et al Mol. Cell Prot. 2:19-28, 2003 15

11/9/2005 Coleman et al Proteom. 3:2101-2107, 2003 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