Advanced Mass Spectrometry

On completion of both MS courses, Analytical Chemistry students should be able to:

  • use their knowledge in mass spectrometry to solve analytical questions in all areas of analytical sciences, including bio, life and health sciences, art sciences, environment and biodiversity science, forensics, and polymer chemistry.
  • describe how various Analytical Chemsitry track courses connect with MS and explain which combinations of separation techniques and MS detection are required to solve analytical problems.
  • using MS data apply data analysis and computational approaches to make the data interpretable.
  • explain the roles MS instruments ranging from discovery, to targeted to imaging analysis.


The Mass Spectrometry market size exceeds 4 billion dollars annually. MS instruments are the most complex analytical tool in a laboratory, and are globally used in pharmaceutical R&D, governmental organisations and research institutes. Applications are ubiquitous and still growing.


MS instruments integrate and connect numerous smaller technologies that manipulate and exploit the flight path of ions, under vacuum, to eventually convert liquid or solid samples into molecular and ultimately digital information. Mass spectrometers are readily connected in-line with other analytical techniques, most commonly with separations systems.


The Advanced MS course provides a deeper overview and understanding of different aspects of Mass Spectrometry. Students will learn about data structure, conversion, and visualisation, as well as specific scanning features and which data is obtained. The course also focuses on GC-MS use and applications and highlighting strategies for data(base) searching. In this context we will review database resources and their utility.


We also pay special attention to a number of mass analysers including quadrupoles, iontraps and orbitraps, where from a technical perspective we look at the wealth of applications these analysers enable, and how they differ.


Furthermore, we will look at some of our most challenging analyses including analysis of MDa size molecules and hugely complex biosystems, paying special attention to new trends in the field. Amongst these new areas is MS imaging in that it provides spatial information. Applications will be given for life and health sciences, single molecule characterisation, art sciences, forensics and environmental and sustainability topics.



Study Credits



Elective course




University of Amsterdam




Semester 1, Period 3


prof. dr. Garry Corthals




prof. dr. Garry Corthals, prof. dr. Anouk Rijs, prof. dr. Arian van Asten, dr. Saer Samanipour


Students are required to have completed Mass Spectrometry. If this is not possible, they should contact the coordinator for pre-course learning material.


Education Desk FNWI
Science Park 904
020 5257100

Intended Learning Outcomes

  • describe various forms of data provided by MS instruments, calculate and compare data conversion and visualisation methods
  • generate and report XICs, TICs, spectra and chromatogram in 3D space
  • explain the workflow for single compound library searching, analogue searching, AMDIS and other NIST software
  • describe and explain the operation of quadrupoles and ion trapping mass analysers and discuss how their use stand alone or in combination with other mass analysers, and provide examples
  • explain ion mobility mass spectrometry (IMS) and provide examples of how this provides both structural and high-resolution mass information. Discuss the use and advantages of IMS over other MS techniques
  • discuss the differences between DIA and standard MS/MS approaches and their use in quantitative analysis of complex biosystems
  • explain the difference in data structure and application of DIA compared to existing sequencing techniques
  • discuss the analytical workflow of DIA approaches and they differ from discovery and tar-geted MS approaches
  • describe single-particle approaches to perform analysis of large molecular structures
  • discuss the implementation and advantages of charge detection mass spectrometry
  • describe and discuss the various ionisation techniques, instruments and data generated in MS imaging experiments, and how this differs from most other forms of MS
  • discuss how MS imaging can de used to provide spatial information and how to incorporate this into clinical practice.

Chemometrics & Statistics teaches you how to distill useful information generated by analytical methods.

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