8:30-9:45 AM Tuesdays & Thursdays, Angell B203, January 19 - May 4, 2010.
Material to be covered in CHEM 223:
The purpose of CHEM 223 is to look "under the hood" of the mass spectrometer.
The majority of the CHEM 223 course will address how various types of mass spectrometers work and what are the components that make up a mass spectrometer. The primary areas to be covered in detail are
Methods to "ionize" or add a charge to a molecule
Analyzer types that separate charged molecules
Fragmentation of charged molecules
Fundamentals of charged molecules (exact mass and isotopic distribution)
Tandem mass spectrometry
Collisionally-induced dissociation and fragmentation of charged molecules
Other areas that will be covered are
vacuum systems
detector systems
Focus will be primarily on organic compounds and biologically relevant and important molecules.
Proteomics and protein and peptide analysis by mass spectrometry will be discussed specifically
Text:
No single text has been written that really covers mass spectrometry, but some texts are better than others. One problem is that published material becomes old within about 5 years of publication. Another problem is that most books are shallow in key areas. They are good surveys, but do not cover the details of the field in adequate depth for this course.
One book that is a reasonable introductory source I have found and is the book that is useful to have is Edmond De Hoffmann & Vincent Stroobant, Mass Spectrometry: Principles and Applications,, 3rd ed., John Wiley, 2007
De Hoffmann is available on-line in paperback from a variety of sources including Amazon.Com
De Hoffmann is in Bailey-Howe (QD96.M3 H6413 2007) and is also supposed to be on reserve.
Other good sources are
J.Throck Watson & O. David Sparkman, Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation, 4th ed., John Wiley, 2007.
Watson & Sparkman is in Bailey-Howe (QC454.M3 W38 2007) and is also supposed to be on reserve.
C. Dass, Fundamentals of Contemporary Mass Spectrometry, Wiley-Interscience, 2007. New, but shallow and expensive. Available from Amazon.Com
G. Siuzdak, The Expanding Role of Mass Spectrometry in Biotechnology, MCC Press, 2003. Available in paperback from Amazon.Com
Other sources of lecture information during the semester:
Joseph B. Lambert, H.F. Shurvell, D.A. Lightner, & R. G. Cooks, Organic Structural Spectroscopy, Prentice Hall, 1998. Part IV: Mass Spectrometry. In the Cook Library (QD272.S6 O74 1998).
Methods in Enzymology: Mass Spectrometry, edited by James McCloskey, Academic Press. vol. 193, 1990. In the Dana Library under periodicals (shelved by title) and in Bailey/Howe (QP601.M49). Although an older book, it contains a range of basic material by different authors.
See the link on the left to books on mass spectrometry at UVM.
See the link on the left to the journal club for a current list of journals publishing articles on mass spectrometry that are on-line at UVM.
Instructor:
Dwight Matthews 656-8114 dwight.matthews@uvm.edu
Cook Building - Room A204 Office hours:
Available almost anytime; drop by or call first and/or make an appointment.
How the course grade is determined:
Test 1
25%
Test 2
25%
Student journal club presentation
20%
Journal club participation
5%
Final (covers material from journal club)
25%
Course format:
The 1st part of the course covers introductory basic material about different types of mass spectrometers and their components. There is no such thing as a single mass spectrometer to do mass spectrometry. There is a wide range of different instruments with different methods of producing ions, separating ions, and measuring ions. The hope is that every student taking the course will have a good working knowledge of the fundamentals of mass spectrometry instrumentation when these lectures are complete. This portion of the course is directed towards satisfying analytical chemistry graduate student requirements.
Lectures in the 2nd part of the course are directed towards proteomics and biological applications of mass spectrometry. This part of the course is directed towards graduate students in the biomedical sciences. However, because the biomedical applications of mass spectrometry are probably the most important applications, this information is also important to analytical chemistry students.
Each day's lecture notes will be available on line as a PDF file via the link shown on the left.
The 3rd part of the course is a journal club on mass spectrometry (see link on left).
The purpose of the journal club is to cover the most recent mass spectrometry literature relevant to problems and topics of the students in the class. Each of you will select a recent article from the literature concerning mass spectrometry and present the article to the class.
The presentation should provide background as to why the article is important and what problem it addresses. You will walk the class through the methods used, provide any supplementary information needed to understand the article, discuss the results, and provide your opinion of the strength/weaknesses of the article.
It is assumed that all members of the class will participate in the discussion.
Journal club articles will be approved by me before presentation.
We will have two presentations per 75 min class period (30 min per presentation).
Although the final exam is scheduled by UVM for 11:45 am 5/11/10, the final (like the other exams) will be a take-home exam addressing material from the journal club presentations.
Each student may submit to me 2 written questions as a Word Doc file based upon their journal club presentation as exam questions.
Each question needs to be accompanied by a worked answer.
I will select from these questions the material that will go on the final.
The final will be handed out by the afternoon of 5/6/10 and is due back by 5 pm 5/10/10.
See the "Mass spec links" on the left for useful web site links about mass spectrometry.
Any student who finds either a web site that I do not have listed that is useful (and is not a commercial site pushing the benefits of a commercial product) or a relevant book at UVM that I don't have listed will receive 5 exam points added to their grade as a bonus for each web site or book that they turn in and is approved.
