CHEM 720/7200 - Mass Spectrometry

Semester: Winter 2019

Professor: W. Gabryelski | Discipline: Inorganic | Campus: Guelph


Background Info: CHEM 7200/720 is a graduate course in Mass Spectrometry (MS). During the three decades, mass spectrometry has evolved to a powerful technique for analyzing a variety of materials ranging from small molecules to large biopolymers. Mass spectrometry has been used in many areas of research including chemistry, biochemistry, environmental science, pharmacology, medicine and forensics. This course provides an opportunity for you to learn about this exciting technique.

Learning Objectives: Little prior knowledge of mass spectrometry is assumed and required with respect to participating students. General principles of mass spectrometry will be described at a level appropriate to graduate students in chemistry and biochemistry. The first part of the course deals with instrumental aspects of mass spectrometry, whereas the second part involves general methodology important applications of this technique in research. Students will leave the course with sufficient knowledge to effectively design and execute mass spectrometry experiments in their research.  Students will be trained to become experts in the interpretation of mass spectral data.


There is no single textbook that would adequately cover the material for this course.   A good introductory reference to mass spectrometry is the book by Edmond De Hoffmann and Vincent Stroobant, “Mass Spectrometry: Principles and Applications”, 2nd ed., John Wiley, 2002 (translated from French).  If you decide to purchase this book, buy the less expensive paper-bound version (e.g. from   Remember that even newest mass spectrometry textbooks will become obsolete in few years. Various textbooks, journal articles and review papers are used as a source of information for my lectures. Lecture notes and course materials will be available on the course website.


The course grade will be based on the following criteria:

  • Written assignment I (20% of course grade), Deadline: March 1st, 2019
  • Written assignment II (40% of course grade) Deadline: March 21st, 2019
  • Written assignment III (max. 5 % that will be added to your course grade). Assignment III will be distributed together with the final exam.
  • Final exam (40 % of course grade), TAKE HOME April 4th-April 17th. The completed final exam has to be e-mailed to me by April 17, 2019.

Written Assignment I: The first written assignment will be a short take-home exam. The exam will be posted on the course website at the beginning of the term. Each student will have to answer (independently) a few questions related to instrumental aspects of mass spectrometry. Reference articles will be posted together with the assignment. You will simply use a provided PDF template to write your answers. You must e-mail your assignment to me before the deadline (March 1st, 2019).

Written Assignment II: During the course, each student will work on preparing a paper in a form of a NSERC Discovery Grant Proposal. NSERC supports research in science and chemists from different fields write NSERC proposals describing mass spectrometry related research. Your proposal should describe an important research project that can be accomplished using mass spectrometry.

Merits of a good NSERC proposal:
• Clearly defined scope and objectives of proposed research
• Its significance and expected contributions to research (science); potential for technological impact
• Originality and innovation (extent to which the proposal explores novel scientific concepts and methods).
• Feasibility, clarity and appropriateness of methodology including the need for varied expertise and justification for the budget
• Appropriateness of the proposal for training highly qualified personnel (e.g., postdoctoral fellows, graduate and undergraduate students)
• Clear, comprehensive and convincing for a non-expert reader

Although there is no strict format of NSERC Discovery Grant Proposals, your paper should include:
• Clearly defined scope and objectives of proposed research
• Background information justifying your research
• Outline and discussion of proposed experimental methods
• Description of the proposed research program to achieve its short and long term objectives
• Discussion of significance of proposed research

Your proposal will be based mainly on information from your independent literature research. You should be able to show deep understanding of proposed work and point out advantages, improvements, limitations, or problems that you may identify in the proposed research. In your discussion, express your own opinions and do not hesitate to point out the strength of your ideas. Your proposal will be limited to 5 pages (including text, figures and tables) and two extra pages for references only. Your proposal is expected to be of professional content and quality. It will be evaluated based on the following criteria (the maximum mark for merit):
• Clearly defined scope and objectives of proposed research (10)
• Background information justifying your research (10)
• Appropriateness of proposed experimental methods (10)
• Evaluation of proposed research to achieve its short and long term objectives (10)
• Evaluation of significance of proposed research (10)
• Student’s depth of knowledge shown in her/his proposal (10)

You will have to hand in your proposal before March 21st, 2019.

Supplementary Written Assignment III: This assignment will test your ability to interpret experimental data from mass (MS) and tandem mass (M/MS) spectrometry. At the end of the course, I will give you a problem set related to the structural identification of chemical compounds using recently acquired MS and MS/MS data. You will analyze the data and try to use the relevant information from the course to determine chemical structures of investigated species. You will be able to score up to 5% of the total course weight and this contribution will be added to your course grade. It means that you will have an opportunity to improve your final mark in the course by submitting this supplementary assignment. Assignment III will be distributed together with the final exam and should be submitted by April 17th, 2019.
Final Exam: The final written exam will be a take home exam. Waterloo campus students will not have to come to Guelph. The final exam will address the material from the entire course. The final exam will be posted on the course web site not later than on April 4th, 2019. The completed final exam should be e-mailed to me by April 17, 2019.


The CHEM 7200/720 Mass Spectrometry course site: In order to login to the course site ( under CHEM 7200/720 Mass Spectrometry, you will use your id and password If you are a Guelph student, you will have to use your central login account username (id) and password to view the lecture materials.  If you are a Waterloo student, your id and your password will be provided for you by e-mail.

Mass Spectrometry lab sessions: The course will provide an opportunity for students to become acquainted with recent mass spectrometry technology.  I will organize a MS facility session to look at several unique mass spectrometry systems.

Evaluation of the Course: As part of the faculty evaluation process in the Department of Chemistry, students are reminded that written comments on the teaching performance of the lecturer may be sent to the Chair, Department of Chemistry, at any time. Such letters must be signed; a copy will be made available to the instructor after submission of final grades. You will also have the opportunity near the end of the term to evaluate the course.


  • Wed: 7:00 pm - 9:20 pm in MacN-203/C2-278

Office Hours

There are no scheduled office hours. If you need help I will be available for consultation almost anytime; drop by my office (1248 SSC), send e-mail ([email protected]) or call to make an appointment (519-824-4120 ext. 53850).