Module: Mass spectrometry for biological systems
CSB 1021H/F, Teaching Section LEC 0137
Coordinator: Professor Michael Phillips
Offered: Fall 2025 session for 6 weeks tentatively scheduled for Monday, September 22nd to Monday, November 3rd, 2025 (course meets once per week on Mondays for six 3 hour sessions). Meeting room on UTM campus will be posted to Quercus.
Weight: One module (0.25 FCE)
Time: 1:10 pm – 4 pm
Location: UTM campus, building/room TBA and remote/hybrid.
Enrollment: limited to 15 students
Description:
This is a mixed lecture and seminar-based course that covers the theory and application of mass spectrometry in biological research. Initial lectures by the instructor will cover principles of mass spectrometry, chromatography, ionization and design of modern mass analyzers (quadrupole, ion trap, orbitrap, and time-of-flight). Course material will focus on the detection of small molecules, although peptide mass spectrometry will also be discussed in the context of proteomic analysis. Students will participate in discussions, give an oral presentation on one application of mass spectrometry, and submit a term paper on another. Students will acquire practical training in data analysis by working with targeted and untargeted sample data sets provided to the students. Free software will be available for analysis of data files, and students will utilize online platforms for statistical analysis of processed data sets.
Textbook
Students will be assigned readings from the primary literature and chapters from Martin Smith’s textbook “Understanding Mass Spectra”, which is available for free online in PDF form. Readings are intended to prepare students for upcoming lectures. It is therefore essential that students complete readings beforehand. The following primary literature readings have been assigned in previous years, and additional readings will be assigned during lecture.
Ricci, Fiorentino, Piccolella, D’Abrosca, Pacifico and Monaco “Structural discrimination of isomeric tetrahydrofuran lignan glucosides by tandem mass spectrometry” (2010) Rapid Comm Mass Spec
Cajka and Fiehn “Toward merging untargeted and targeted methods in mass spectrometry-based metabolomics and lipidomics” 2016 Anal chem
Ma, Li, Van den Heuvel and Claeys “Characterization of Flavone and Flavonol Aglycones by Collision-induced Dissociation Tandem Mass Spectrometry” 1997 Rapid Comm Mass Spec
Es-Safi, Kerhoas and Ducrot “Application of positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry to a study of the fragmentation of 6-hydroxyluteolin 7-O-glucoside and 7-O-glucosyl-(1-3)-glucoside” (2005) Rapid Comm Mass Spec
Schedule:
Six meetings of 3 h (meets every week beginning end of Sep and first week of Nov, 2025). Week 1-3 consist of introductory lectures by instructor and discussion of reading assignments. Week 4-5 will feature students presentations and discussion. Week 6 is a writing workshop to discuss term paper drafts as well as finishing any remaining student presentations. Preliminary dates are listed below (to be confirmed prior to start date in September).
Date Topic Reading
Sep 22 Lecture 1: Mass spec theory and application Smith chs. 1+2
Sep 29 Lecture 2: Mass spec theory and application Smith ch 3
Oct 6 Lecture 3: Mass spec theory and application Smith ch 4
Oct 20 Student presentations 1
Oct 27 Student presentations 2
Nov 3 Student presentations 3 & writing workshop
Evaluation:
Students will deliver an oral presentation on one application of mass spectrometry and submit a term paper on another by end of term. A list of suggested topics will be provided, and presentation dates and papers will be assigned the first day of class. Students are expected to complete all readings assignments before the corresponding lecture and participate in all discussions. Students must attend all lectures and seminars for full participation credit. The term paper is on a different topic than the oral presentation. Students must write and speak on topics not directly related to their thesis work.
Seminar: 20 min oral presentation + 20 min discussion – 40%
Participation during discussion period of oral presentations – 10%
Term paper – 35%
Practice data sets – 10%
Attendance – 5%
Pre-requisites: None. Two semesters of organic chemistry or one semester of quantitative analysis, analytical chemistry or instrumental analysis is strongly recommended.
Course delivery: UTM campus and remote/hybrid
Last updated on August 28th, 2025