CHEM 720/7200-02 - Mass Spectrometry

Semester: Fall 2025

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

Description

CHEM 720(0) 02 [0.5] is a graduate course in Mass Spectrometry (MS) with prior average enrolments of 20 students in the class.

During the three decades, mass spectrometry has evolved as 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 and indispensable technique.

Learning Objectives: No prior knowledge of mass spectrometry is required for students participating in the course. 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.

Course Content:

  1. Introduction, History and Unique Capabilities of Mass Spectrometry
  2. Instruments and Instrumental Techniques in Mass Spectrometry

2.1.      Ion Separation and Mass Measurement for Different Types of Mass Analyzers
2.1.1.   Quadrupole MS
2.1.2.   Ion Trap MS
2.1.3.   Time-of-Flight (TOF) MS
2.1.4.   Fourier Transform-Ion Cyclotron Resonance (FT-ICR) MS
2.1.5.   Sector Instruments
2.2.      Tandem Mass Spectrometry (MS-MS)
2.2.1.   Ion Activation Techniques
2.2.2.   Collision Induced Dissociation (CID)
2.2.3.   Laser Induced Dissociation (LID)
2.2.4.   Tandem Mass Spectrometry in Space
2.2.5.   Tandem Mass Spectrometry in Time
2.2.6.   Electron Induced Ionization Methods
2.2.7.   Recent Instrumental Development in MS (Hybrid Instruments)

  1. Ionization Methods in Mass Spectrometry

3.1.      Electron-Impact Ionization (EI)
3.2.      Chemical Ionization (CI)
3.3.      Matrix-Assisted Laser Desorption Ionization (MALDI)
3.3.1.   Laser Desorption Ionization from a Porous Silicon/Metal Surface
3.3.2.   Imaging MALDI Mass Spectrometry
3.4.      Spray, Electrospray and Nano-electrospray Ionization
3.5.      Ambient Ionization Methods (DART, DESI ….)
3.6.      Interpretation of MS Spectra from Different Ionization Methods

  1. General Principles of Gas-Phase Ion Chemistry

4.1       Reactions of Odd Electron Radical Molecular Ions
4.2       Reactions of Even Electron Positive Ions
4.3       Reactions of Even Electron Negative Ions

  1. Sample Introduction (Inlet Systems in MS)

5.1.      Combination of Chemical Separation Methods and Mass Spectrometry
5.1.2.   Gas Chromatography-Mass Spectrometry (GC-MS)
5.1.2.   Liquid Chromatography-Mass Spectrometry (LC-MS)
5.1.3.   Capillary Electrophoresis-Mass Spectrometry (CE-MS)
5.1.4.   Ion Mobility Spectroscopy-Mass Spectrometry (IMS-MS)

  1. Overview of Biological Applications of Mass Spectrometry

6.1.      MS Strategies for Characterization of Proteins and Peptides (Dr. Diane Brewer)
6.2.      MS Strategies for Characterization of Lipids and Metabolites
6.3.      MS Strategies for Characterization of Carbohydrates
6.4.      MS Strategies for Characterization of DNA

7          Overview of MS Applications in Environmental and Drug Analysis

  1. Quantitative Mass Spectrometry

8.1.      Selected/Multiple Reaction Monitoring (SRM)
8.2.      Selectivity, Sensitivity, and Limits of Detection
8.3.      Standards and Calibration Methods

  1. De Novo Identification Techniques in Mass Spectrometry

9.1.      Spectral Databases
9.2       Principles of Gas-Phase Ion Chemistry

Materials

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 amazon.com).   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 CHEM 720(0) 02 Mass Spectrometry course site: In order to login to the course site (https://courselink.uoguelph.ca/shared/login/login.html) 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.

Evaluation

  • Written assignment I (20% of course grade),
  • Written assignment II (40% of course grade)
  • Written assignment III (max. 5 % that will be added to your course grade). Supplementary Assignment III will be distributed together with the final exam.
  • Final TAKE HOME exam (40 % of course grade),

Lab/Project

Written Assignment I: The first written assignment will be a short take-home exam. The PDF template of this exam will be posted on the course website at the beginning of the term.  Each student will have to answer (independently) questions related to instrumental aspects of mass spectrometry.  Reference articles will be posted together with the assignment. You should e-mail your assignment to me before the submission deadline on October 30th, 2025.

Written Assignment II: During the course, each student will work on preparing a.

Nomination Letter for Darwin Award in Mass Spectrometry                            

The main purpose of Assignment II is to develop your capabilities for searching, organizing, processing, understanding, interpreting, and evaluating the information available in the literature on mass spectrometry You will write a short paper related to any research involving mass spectrometry in a form of a nomination letter for Darwin Award (Prize). In contrast to Nobel Prize, which is often given to a great scientist whose outstandingly good work has provided enormous benefit to the society, Darwin Prize should be given to a scientist whose outstandingly bad work has provided significant damage to the society and science community.

Assignment II involves your initial search for the worst (in your opinion) scientific article and subsequent write up of your nomination letter for Darwin Award for work presented in this paper. Your task should not be difficult because there are many very weak articles published in the past. Your selected research paper should be published in the last 30 years in any peer-reviewed journal and should contain a significant mass spectrometry component

Although there is no strict format of the Darwin Price nomination letter, you should consider several components and focus on:

  • Clearly defining the scope, objectives, and goals of research in the article
  • Providing background information justifying described research
  • Describing and critically discussing proposed experimental methods and their execution
  • Explaining and critically evaluating results of described studies
  • Discussing deficiencies and impact of the selected paper
  • Clear, comprehensive, and convincing writing with good judgement

Your nomination letter should be limited to 4 pages (including text, figures, tables, etc.) and one extra page for references only. The content of your nomination letter will be evaluated based on the following criteria (the maximum mark for merit):

  • The most appropriate choice of the article (journal impact and publication time) (10)
  • Background information justifying described research (10)
  • Clearly defined scope and objective of presented research (10)
  • Appropriateness of proposed experimental methods, focusing on mass spectrometry and its role in published studies (10)
  • Critical evaluation of the quality of the paper including its significance and impact (10)
  • Student’s depth of knowledge shown in writing her/his nomination letter (10)

Assignment II is worth 40% of your total course grade and will be graded out of 60 points. Assignment II is due on December 2nd, 2025. You will have to e-mail the PDF file of your nomination letter to me before the deadline.

Supplementary Written Assignment III: This assignment will test your ability to interpret spectral data from mass (MS) and tandem mass (M/MS) spectrometry. You will work on the structural identification of chemical compounds using spectral MS and MS/MS data acquired in my laboratory. You will use spectral databases and the relevant information from the course to determine chemical structures of investigated species. By submitting this supplementary assignment, you will be able to score up to 5% of the total course weight and this contribution will be added to your course grade from mandatory assignments. It means that you will have an opportunity to improve your final mark by submitting the supplementary assignment. Assignment III will be posted on the course web site on December 2nd, 2025 together with the final exam.

Final Exam: The final written exam will be a take home exam. The final exam will address the material from the entire course. The final exam will be posted on the course web site on December 2nd, 2025. The completed final exam and Assignment III should be e-mailed to me no later than 10 days after their posting on the course web site.

Schedule

  • Thu: 7:00 pm - 9:20 pm in MacN 203

Office Hours

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