Module: Mass spectrometry for biological systems

CSB 1021H/F, Teaching Section LEC 0137

Coordinator: Professor Michael Phillips

Offered: Fall 2023 session for 6 weeks from late September to November, 2023 (course meets once per week for six 3 hour sessions). Meeting room on UTM campus will be posted to Quercus.

Weight: One module (0.25 FCE)

Time: 10 am – 1 pm, on Thursdays from September 28th to November 2nd.

Location: UTM campus, room TBA.

Enrollment: limited to 15 students


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). Although peptide mass spectrometry will be discussed in the context of proteomic analysis, course theory will focus on the detection of small molecules. 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.


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


Six meetings of 3 hours (meets every week beginning end of October and first week of December, 2023). Weeks 1-3 consist of introductory lectures by instructor and discussion of reading assignments. Weeks 4-5 will feature students presentations and discussion. Week 6 is the writing workshop to discuss term paper drafts as well as finishing any remaining student presentations.

Date                 Topic                                                                           Reading

tbd                   Lecture 1: Mass spec theory and application             Smith chs. 1+2

tbd                   Lecture 2: Mass spec theory and application             Smith ch 3

tbd                   Lecture 3: Mass spec theory and application             Smith ch 4

tbd                   Student presentations 1

tbd                   Student presentations 2

tbd                   Student presentations 3 & writing workshop


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 normally on the same topic as the oral presentation, but students may choose to write on a different mass spectrometry subject if desired. 

Seminar: 20 min + 60 min for discussion of the paper – 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: This course is delivered exclusively in person on the UTM campus. Attendance at all meetings is mandatory.

Last updated on August 15th, 2023