Mass Spectrometry

6 EC

Semester 1, period 2

5254MASP6Y

Owner Master Chemistry (joint degree)
Coordinator Garry Corthals
Part of Master Chemistry (joint degree), track Analytical Sciences, Master Forensic Science, year 2

Course manual 2021/2022

Course content

The course covers basic **Principles of Mass Spectrometry** (MS) and the application of MS in various fields of life sciences, environmental sciences, forensics and chemistry in general. In this course we will focus on the basic understanding of how mass spectrometers function. Therefore the various segments and parts of a mass spectrometer are explained, as well as how these segments, when connected to each other, operate as a whole. 

We will discuss: 1) commonly used ionisation methods and allied MS applications; 2) mass analysers and mass filters used throughout the field, how they differ, and what these differences entail and enable; 3) different forms of MS data and how this is converted to meaningful digital information; and 4) a selection of applications covering organic and polymer chemistry, biological and clinical sciences, environment and biodiversity, forensics and art sciences. 

Study materials

Literature

  • Edmond de Hoffmann, Jean Charette and Vincent Stroobant, 'Mass Spectrometry Principles and Applications', John Wiley & Sons and lecture notes.

Syllabus

Practical training material

  • Yes, via Canvas announcements

Software

  • Yes, via Canvas announcements

Other

  • Presentations, handouts and possible video recording

Objectives

  • Understand 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
  • how different ionisation methods are used in different applications
  • the 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.
  • hybrid instruments and how combining mass analysers give rise to specific applications, such as quadrupole/time-of-flight, quadrupole/orbitrap, etc
  • structure determination of molecular compounds based on gas-phase dissociation reactions of ions, and the interpretation of resulting mass spectra and tandem MS analysis.
  • 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 how workflows for simple bio- and chemical analysis are employed.
  • how to determine a molecular identity and quantity based on data generated by mass spectrometers.
  • data analysis techniques for mass spectral interpretation, spectral libraries and "omics" based data analysis.

Teaching methods

  • Lecture
  • Self-study
  • Seminar

Lectures and tutorials with problem solving sessions are integrated.

Learning activities

Activity

Number of hours

Lectures

14 x 2

Tutorials / discussion of
selected assignments

6 x 2

Exam

3
Selfstudy

116

Attendance

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

Additional requirements for this course:

None

Assessment

Item and weight Details

Final grade

1 (100%)

Tentamen 1

Open book examination, graphical calculators, laptops and tablets are allowed.

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

Week Day
 Onderwerpen Studiestof
1 Mon Fundamentals of MS: Introduction and Ionisation methods (EI) Book Introduction, Chapter 1 and Chapter 7;
sections 1; 1.1; 7.1; 7.2  pp 275 - 27. 
1 Wed Fundamentals of MS: Ionisation methods (CI, FI, FD, Maldi and ESI) Book Chapter 1, sections: 1,2 - 1.3; 1,5; 1.8; 1,11 
2 Mon Fundamentals of MS: Instrumentation (TOF, reflectron, sector) Book Chapter 2; Introduction; sections 2.4; 2.5 untill p 149
2 Wed Fundamentals of MS: Instrumentation (quadrupole, Ion traps, orbitrap, FT-ICR) Book Chapter 2: sections 2.1, 2.2, 2.3, 2.6
2 Thu Fundamentals of MS: Unimolecular reactions in the gas phase Book Chapter 7; sections 7.1, 7.2, 7.3.
3 Mon Fundamentals of MS: Fragementation reactions of ions ((EI) Book Chapter 7, sections 7.4, 7.7,  presentation and excersises
3 Wed Fundamentals of MS: Fragmentation reactionsof ions (EI, CI) Book Chapter 7, sections 7.4, 7.7,  presentation and excersises
3 Thu Fundamentals of MS: Interpretation of mass spectra (EI, CI) Book Chapter 7, sections 7.4, 7.7,  presentation and excersises
4 Mon Fundamentals of MS: MS-MS principle and instrumentation (CID) Book: Chapter 4
4 Wed Fundamentals of MS: Interpretation of mass spectra (EI, CI, MS-MS) Exercises
4 Thu Fundamentals of MS: Discussion of examination questions in fundamentals of MS Previous examinations
5 Mon (bio)analytical MS  
5 Wed (bio)analytical MS  
5 Thu (bio)analytical MS  
6 Mon (bio)analytical MS  
6 Wed (bio)analytical MS  
6 Thu Ions, sources and analysers for proteomics  
7 Mon Proteome technology: robustness & reproducibility, untargeted vs targeted MS  
7 Wed MS in life Proteome applications: protein ID and quantitation, PTMs, networks, clinicalsciences  
7 Thu Practical: split into group to review applied and relevant MS examples   
8 Mon Examination  

Timetable

The schedule for this course is published on DataNose.

Additional information

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

Contact information

Coordinator

  • Garry Corthals
  • prof. dr. Garry Corthals