| Biological Mass Spectrometry [ Spring 2007 ] |
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Course Information
Time: Tuesday & Thursday, 12:30-1:45.
Location: CHM 0115.
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 recommended.
Announcements
| 1/31 |
Dass is available on reserve in the library. |
Lectures
| Date | Topics | Slides/Handouts | Resources |
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| 1/23 | What is
Mass Spectrometry? Isotopes | Handout 1 (Course Information);
Handout 2 (Books);
Handout 3 (Description);
Lecture 1 | Dass, Chapter 1;
Anal. Chem. 55:353-356, 1983;
IsoPro |
| 1/30 | Ionization | Handout | Dass, Chapter 2;
Anal. Chem. 69:661A-665A, 1997;
Anal. Chem. 65:972A-986A, 1993 |
| 2/ 1 | Ion Analyzers | Handout | Dass, Chapter 3 |
| 2/ 8 | Fragmentation | Handout | |
| 2/13 | Tandem Mass Spectrometry | Handout | Dass, Chapter 4 |
| 2/15 | 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 |
| 2/20 | Quantitation | Handout | Dass, Chapter 6;
J. Proteome Research 1:27-33, 2002;
Nature Biotechnology 17:994-999, 1999 |
| 2/22 | Peptide Sequencing | Handout;
Interpretation of the Product Ion Spectra of Tryptic Peptides;
| Dass, Chapter 9;
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) |
| 3/ 1 | Peptide Modifications | Handout | J. Proteome Research 1:435-442, 2002;
Current Opinion in Chemical Biology 5:591-602, 2001;
Molecular & Cellular Proteomics 2:138-145, 2003 |
| 3/ 8 | Peptide Sequence Databases | Lecture | |
| 3/13 | In Class Exam | | |
| 3/15 | Proteomics | Handout | |
| 3/29 | Proteomics | Handout | |
| 4/ 3 | Protein Identification Search Engines | Lecture;
Homework | |
| 4/ 5 | Lab and Homework | Lab Worksheet | Spectra:
hm270304_bsa100fm_0001a.pkl,
HM424304_4thHF_09.pkl
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| 4/10 | Statistical Significance for Peptide Identification | Lecture;
Homework | |
| 4/12 | Lab and Homework | | |
| 4/17 | Student presentations | Sebastian Engelmann;
Karen Lohnes | J. Mass Spectreometry 42:1-10, 2007;
J. Proteome Research 6:337-347, 2007 |
| 4/19 | Student presentations | Jamie Boehmer;
Colin Wynne | Mol. & Cell Proteomics 5:573-588, 2006;
Anal. Chem. 78:8549-8555, 2006 |
| 4/24 | Student presentations | Jinxi Li;
Seth Thomas | Rapid Comm. in Mass Spec. 21:1485-1496, 2007;
Mol. & Cell. Proteomics 5:1045-1053, 2006 |
| 5/ 1 | Student presentations | Chris Keller;
Kathleen Sanders-Winters | Anal. Chem. 79:2296-2302, 2007;
J. Proteome Research 6:133, 2007 |
| 5/ 3 | Student presentations | Sofia Herrero;
Derick Lucas | Anal. Chem. 78:1494, 2006;
Science 316:277-280, 2007 |
| 5/ 8 | Carbohydrates | Handout | Mass Spec. Reviews 23:161, 2004;
Rapid Comm. Mass Spec. 11:1635, 1997;
JASMS 11:900, 2000;
Glycoconjugates 5:397, 1988;
Biochemistry 40:3109, 2001;
Anal. Chem. 69:2919, 1997;
Anal. Chem. 70:4441, 1998;
Mass Spec. Reviews 18:349, 1999;
Anal. Chem. 73:19, 2001;
Anal. Chem. 71:4431, 1999;
J. Chromatography A 978:141, 2002;
Prot. Sci. 2:183, 1993;
J. Proteome Res. 3:556, 2004 |
| 5/10 | Nucleic Acids and SNPS | Handout | Nucleic Acids Res. 21:3191, 1993;
Anal. Chem. 75:5944, 2003;
Rapid Comm. Mass Spec. 8:184, 1994;
Science 281:260, 1998;
JASMS 3:60, 1992;
Anal. Chem. 68:1989, 1996;
Anal. Chem. 68:941, 1996;
Nature Biotech. 14:1123, 1996;
Nature Reviews Genetics 4:1001, 2003;
Anal. Chem. 69:4540, 1997 |
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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