| BCHM676 & BIOE689B: Biological Mass Spectrometry [ Spring 2006 ] |
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Course Information
Time: Tuesday & Thursday, 12:30-1:45.
Location: BCHM 2507.
Instructor: Dr. Catherine Fenselau (Chemistry & Biochemistry), Biochemistry Building 1504, fenselau @ umail.umd.edu
Instructor: Dr. Nathan Edwards, (CBCB), Biomolecular Sciences Building 3119, nedwards @ umiacs.umd.edu
Credits: 3 credit hours
This course addresses the fundamentals of modern mass spectrometry and its interdigitation with biochemical techniques to provide unrivaled, authoritative analyses of drug metabolites, lipids, carbohydrates and nucleotides. We will focus particularly on the new field of proteomics, where the enabling role of mass spectrometry garnered two Nobel prizes in 2002. The interface with bioinformatics will be explored. One semester of biochemistry is a prerequisite.
Announcements
Lectures
| Date | Topics | Slides/Handouts | Resources |
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| 1/26 | What is Mass Spectrometry? Isotopes | Course Information;
Exercise | Dass, Chapter 1;
Anal. Chem. 55:353-356, 1983;
IsoPro |
| 1/31 | Ionization | Handout | Dass, Chapter 2;
Chem. Rev. 87:501-512, 1987;
Anal. Chem. 69:661A-665A, 1997;
Anal. Chem. 65:972A-986A |
| 2/ 2 | Ion Analyzers | Handout | Dass, Chapters 3 and 6 |
| 2/ 7 | Fragmentation | Handout | |
| 2/ 9 | Tandem Mass Spectrometry | Handout | Dass, Chapter 4 (Recommended) |
| 2/14 | LCMS strategies | Handout | Dass, Chapter 7;
Protein Science 2:183-196, 1993;
JASMS 4:710-717, 1993;
Anal. Chem. 75:3731-3738, 2003;
J. Chromatog. A 591:325-339, 1992 |
| 2/16 | Quantitation | Handout | J. Proteome Research 1:27-33, 2002;
Nature Biotechnology 17:994-999, 1999 |
| 2/21 | Peptide Sequencing | Handout;
Interpretation of the Product Ion Spectra of Tryptic Peptides;
Exercise | Foodborne Pathogens and Disease 1:185-194, 2004;
Nature Medicine 6:215-218, 2000;
Kinter and Sherman, Chapter 4 (Recommended);
Amino-Acid Reference (Matrix Science);
Peptide Fragmentation (Matrix Science) |
| 2/28 | Peptide Modifications | Handout | J. Proteome Research 1:435-442, 2002 |
| 3/ 2 | Peptide Modifications | Handout | J. Am. Soc. Mass Spectrom. 4:710-717;
Current Opinion in Chemical Biology 5:591-602, 2001;
Molecular & Cellular Proteomics 2:138-145, 2003 |
| 3/ 7 | In Class Exam | | |
| 3/ 9 | Proteomics | Handout | |
| 3/16 | Proteomics | Handout | |
| 3/28 | Protein Identification Search Engines | Lecture;
Homework | |
| 3/30 | Lab and Homework | Lab Worksheet | Spectra:
hm270304_bsa100fm_0001a.pkl,
HM424304_4thHF_09.pkl,
DK102403EGFRband3ParentIon1.pkl
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| 4/ 4 | Protein Sequence Databases | Lecture;
Homework | |
| 4/ 6 | Lab and Homework | | |
| 4/11 | Student presentations | Kathy Goodson | J. Proteome Research 3:956-978, 2004 |
| 4/13 | Student presentations | Karen Thomas;
Mike Armani | Proteomics 6:654-666, 2006;
J. Mass. Spec. 39:193-201, 2004 |
| 4/18 | Student presentations | Veka Ohtamaa | Rapid Comm. in Mass Spectrometry 18:609-616, 2004 |
| 4/20 | Student presentations | Adrian Williams;
Ming-Yih Lai | Anal. Chem. 78:1494-1502, 2006;
Biochemistry 42:10024-10033, 2003 |
| 4/25 | Student presentations | Zheng Cao | Protein Science 14:1438-1446, 2005 |
| 4/27 | Student presentations | Huan Wang;
Dan Gowetski | Trends in Biochemical Sciences 30:583-592, 2005;
J. Proteome Research 5:651-658, 2006 |
| 5/ 2 | Homework and Lab discussion | | |
| 5/ 4 | Student presentations | Eli Moore | J. Biological Chemistry 279:15805-15813, 2004 |
| 5/ 9 | Carbohydrates | | |
| 5/11 | Nucleic Acids and SNPS | | |
Grading
Class Participation 10%,
In Class Test 25%,
Final Exam 30%,
Literature Presentation 15%,
Two Take-home Problems 20%.
Good Reference Books
- Chhabil Dass
- Principles and Practice of Biological Mass Spectrometry. Wiley Interscience, New York, 2001
- Fred W. McLafferty and Frantisek Turecek
- Interpretation of Mass Spectra. University Science Books, Mil Valley California, 1993
- Robert J. Cotter
- Time-of-Flight Mass Spectrometry Instrumentation and Applications to Biological Research. American Chemical Society, Washington, DC, 1997
- Michael Kinter and Nicholas E. Sherman
- Protein Sequencing and Identification Using Tandem Mass Spectrometry. Wiley-Interscience, 2000
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