Mass Spectrometry

6 EC

Semester 1, period 2

5254MASP6Y

Owner Master Chemistry (joint degree)
Coordinator dr. Steen Ingemann Jorgensen
Part of Master Chemistry (joint degree), track Analytical Sciences, year 1

Course manual 2018/2019

Course content

The course covers basic principles of mass spectrometry (MS) and the application of the method in chemistry and life sciences. The following topics are treated:

  • The principles of the Ionization methods: Electron Ionisation (EI), Chemical Ionisation (CI), Electrospray Ionisation (ESI) and Matrix Assisted Laser Desorption Ionisation (MALDI).
  • Basic principle and analytical features of common mass spectrometers, such as Sector, Time-of-flight, quadrupoles and Ion trap instruments. 
  • Structure determination of (bio)organic compounds based on dissociation reactions of ions in the gas phase, interpretation of mass spectra and MS-MS analysis.
  • (Bio)analytical Mass Spectrometry and in particular the role of hyphenated methods, GC-MS, LC-MS and LC-MS-MS in (bio)chemical analysis and drug development and quantitative analysis of (bio)organic compounds.
  • Proteomics covering the application of mass spectrometry in identification of proteins, peptide mass fingerprinting, sequence tag analysis, analysis of post translational modifications quantitative proteomics, interpretation of peptide MS/MS spectra.

Study materials

Literature

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

Syllabus

Other

  • Presentations and handouts

Objectives

  • Know the basic principles of common mass spectrometric Instrumentation;
  • Know the principle of common ionisation methods;
  • Know the common dissociation reactions of molecular ions and protonated molecules;
  • Be able to interpret mass spectra of simple (bio)organic compounds;
  • Know the combinations between chromatographic methods and mass spectrometry;
  • Be able to devise a procedure for quantitative analysis of compounds with the use of the combination of a chromatographic method and mass spectrometry;
  • Know the basics of the application of mass spectrometry in proteomics.

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

The programme does not have requirements concerning attendance (OER-B).

Additional requirements for this course:

None

Assessment

Item and weight Details

Final grade

1 (100%)

Tentamen

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: organic chemistry, biochemistry and physics at the level of a BSc Chemistry.

Contact information

Coordinator

  • dr. Steen Ingemann Jorgensen
  • prof. dr. Garry Cothals
  • prof. dr. Zoltan Takats