Mass Spectrometry

Course manual 2024/2025

Course content

The course covers basic Principles of Mass Spectrometry (MS) and a selection of applications of MS in various fields including life sciences, environmental sciences, forensics and organic chemistry.

By doing the course you will be able to understanding and identify various functions of a mass spectrometer, including with concepts of weighing molecules, charge and charge states, isotopes, resolution and generation and interpretation of spectra. Furthermore, you will learn and be able to explain different modes of molecular ionization (e.g. ESI and MALDI), as well as several methods for ion fragmentation (e.g. CID). Important information on mass analysers and mass filters are explained and examples are discussed for you to demonstrate how these give rise to various scanning modes and hybrid instruments.

Scanning modes will be discussed in the context of key applications in MS that should be understood and so the student repeat by designing experiments. You will also demonstrate via several assignments how data analysis is converted to meaningful information, via new MS specific data science methods.

Finally, a selection of applications will be covered throughout the course, covering organic and polymer chemistry, biological and clinical sciences, environment and biodiversity, forensic and art sciences. The student should be able to explain which instrumental MS setup is correct for specific applications.

Study materials

Literature

• The primary source of literature will be via lectures in the class. Additionally, by completing assignments (in tutorials) students will acquire a broader level of understanding. 

   

  Online, there are many websites and we encourage to review publicly available information in addition to the lectures and assignments. More information can also be found in one of the many available book on MS, such as Edmond de Hoffmann, Jean Charette and Vincent Stroobant, 'Mass Spectrometry Principles and Applications', John Wiley & Sons. 

Syllabus

• No Syllabus, all learning material via lectures, notes, tutorials.

Practical training material

• Yes, via Canvas announcements.

Software

• Yes, via Canvas announcements.

Other

• Presentations, handouts and possible video recording.

Objectives

• Understand and explain the basic principles and definitions used in mass spectrometry, such as molecular weight determination, quantification, structure and chemical composition. What they are how they are measured, and the theories behind these topics.
• Learn and describe various forms of MS data, mass calibration and instrument tuning methods etc.
• Explain what charge is and how it is obtained, and relates to ionisation. Understand and explain the principles of various ionisation methods: including but not limited to Electron Ionisation (EI), Chemical Ionisation (CI), Electrospray Ionisation (ESI) and Matrix Assisted Laser Desorption/Ionisation (MALDI), and selected ambient ionisation methods.
• List, describe and evaluate how different ionisation methods are used in different applications.
• Describe and demonstrate principles and features of mass analysers and mass filters, including but not limited to quadrupole, time-of-flight, ion trapping analysers (3D, linear, orbitrap) instruments.
• Describe and compare hybrid instruments and how specific combinations of mass analysers allow various applications, such as quadrupole/time-of-flight (qToF), quadrupole/orbitrap (Q Exactive), etc.
• Determine the structure, charge and masses of molecular compounds based on gas-phase dissociation reactions of ions, and the interpretation of resulting mass spectra and tandem MS analysis.
• Explain what the integration of MS systems with separation systems such as gas and liquid separation (GC-MS, LC/LC-MS and MS/MS) brings, and describe how workflows for simple bio- and chemical analysis are employed.
• Describe how one determines molecular identity and quantity based on MS data.
• Explain different data analysis techniques for mass spectral interpretation, such as spectral libraries and "omics" based data analysis.
• Understand and explain the use numerous MS instruments and various configurations for instruments.

Teaching methods

• Lecture
• Self-study
• Seminar
• Working independently on e.g. a project or thesis
• Computer lab session/practical training

Lectures and tutorials with problem solving sessions are integrated in the course.

Learning activities

Attendance

This programme does not have requirements concerning attendance (TER part B).

Additional requirements for this course:

Attendance is required for all Tutorials. 

Absence must be agreed upon. 

Assessment

The written exam counts for 60% of the grade. The other 40% is taken from the assignments. 

Assignments

 Information about Assignments will be communicated via the digitial learning environment.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Additional information

Recommended prior knowledge in analytical science and technology, chemistry, biochemistry and physics at the level of a BSc Chemistry. Data science enthusiasm is a welcome benefit. 

Contact information

Coordinator

• prof. dr. Garry Corthals

Staff

• dr. J.M. Bärenfänger
• dr. A. Chojnacka
• dr. A. Gargano
• Viktoriia Turkina MSc
• Maria Hayder MSc
• dr. Steen Ingemann Jorgensen
• dr. S. Samanipour
• Ziran Zhai MSc