Advanced Mass Spectrometry

Rapid development of mass spectrometry allowed to apply it in countless fields. This course describes some of these applications - investigation of chemical reactions using mass spectrometry, hyphenated methods, in particular Ion Mobility Spectrometry (IMS), the use of photofragmentation and spectroscopy in combination with Mass Spectrometry, application of mass spectrometry to diagnose diseases, detection of explosives and drugs.

Lecture 1: Recap of the basics

Created with Sketch.

Lecture 2: Tandem Mass Spectrometry

Created with Sketch.

This lecture is about tandem mass spectrometry techniques and about their applications. After the lesson you should be able to give answers to questions such as:


  • Which molecule in your reaction mixture binds strongest to your catalyst?
  • What is the energy required for a C-H activation reaction?
  • Can we compare basicity of molecules and how do we determine proton affinities?


  • What is the primary structure of your protein?

The lecture is divided to several video clips.

  • 2. Tandem mass spectrometry experiments in beam-type instruments (clip 2)

Lecture 3: Reaction Monitoring

Created with Sketch.

This lecture should give you guidelines how to investigate chemical reactions using mass spectrometry. After this lesson you should have this knowledge:

  • You should be aware what type of reactions could be investigated by mass spectrometry
  • You will know what differences you can expect between gas-phase reactions and condensed-phase reactions
  • You will know how you can investigate reaction kinetics and reaction dynamics in the gas phase
  • You will be able to evaluate what information you obtained when you monitored progress of your reaction with an ESI-MS method

The parts of the lecture are:

  • 2. Reaction kinetics in the gas phase (clip 2)

Lecture 4: Ion Mobility

Created with Sketch.

Courtesy of Prof. Anouk M. Rijs (Vrije Univ. Amsterdam)

Introduction (clip 01):  This clip discusses the goal of this lecture, why and when we would like to use hyphenated methods, and of course in particular Ion Mobility Spectrometry (IMS).

First Principles of Ion Mobility (clip 02): Here we see a schematic layout of a typical set-up, focusing first on drift tube ion mobility, as this is the easiest form of IM to understand both qualitatively and quantitively. The first important definition in IM: the arrival time distribution is discussed.

Ion Mobility History (clip 03): A short overview of the origin of IM and its development is shown.

Theory of Ion Mobility (clip 04): In this section the theory behind drift tube ion mobility is presented, discussing key parameters such as mobility, collision cross section, how to measure mobilities etc.

Resolution of Ion Mobility (clip 05): This short clip discusses the resolution of ion mobility and how to improve this. This will also be discussed by you in more detail in the tutorial.

Drift Tube Ion Mobility (clip 06): Drift Tube Ion Mobility Set-ups are discussed with various resolutions. How can the resolution increased even more?

TWIMS and TIMS Ion Mobility (clip 07): Two other types of IM are shown, both developed by commercial companies; i.e. Traveling Wave (Waters) and Trapped (Bruker) IM. We discuss the working principle and the lay-out of the set-up.

Other Types of Ion Mobility (clip 08): Other types of ion mobility will be discussed such as SLIM and FAIMS. In the tutorial, you will classify these different types, which ones belong to temporally dispersive, spatially dispersive or confinement with selective release type of IM.

Possible Experiments using Ion Mobility (clip 09): Finally, we will discuss various types of experiments using Ion Mobility and which parameter to focus on. This will be studied more in-depth in the tutorials.

Lecture 5: Ion Spectroscopy

Created with Sketch.

Courtesy of Prof. Anouk M. Rijs (Vrije Univ. Amsterdam)
Multilaser spectroscopy (pptx, 8,4 MB)

This lecture discusses the use of photofragmentation and spectroscopy in combination with Mass Spectrometry.

Introduction (clip 01): This clip discusses the goal of this lecture, introduction into spectroscopy, why and when we would like to use spectroscopy in combination with MS.

Direct vs indirect absorption (clip 02): Here we discuss how spectroscopy is different when performed in a mass spectrometer compared to what you are used to studying solution phase or solid samples. The second part of this clips shows typical laser integrated MS set-ups.

IRMPD and IR ion spectroscopy (clip 03): What are the different kind of experiments we can do with IR lasers? What is the difference between CID and IRMPD? How do we obtain an IR spectrum?

IR Sources and experimental steps (clip 04): In this section a brief overview of commonly used IR sources is shown. The experimental steps towards recording an IRMPD or IR ion spectrum are discussed.

Examples of IR Spectroscopy (clip 05): The use of IR-MS is very wide. Examples from astrochemistry and analytical/medical chemistry are discussed. What is the additional information obtained by integrating IR-MS. In the third example: cryogenic MS is discussed, what is the advantage for IR-MS?

UVPD and UV spectroscopy (clip 06): UV excitation and absorption is discussed. What are the processes that can occur? How is UV excitation different from IR excitation? How can UV spectroscopy be fragment dependent?

Examples of UV-MS (clip 07): The example shows the possibilities of UV-MS

Lecture 6: Bioanalytical Mass Spectrometry

Created with Sketch.

Courtesy of Prof. Anouk M. Rijs (Vrije Univ. Amsterdam)
UVPD applications (pptx, 4 MB)

This lecture is about use of mass spectrometry for Structural Biology and Biophysics. We will discuss the use of mass spectrometry techniques to understand the structure of biomolecules.

Introduction (clip 01): In this video the topic of structural biology is introduced showing that MS can be used to obtain structural information of all major cellular components. I revisit the topic of bottom-up and top-down mass spectrometry.

Weighing proteins
(clip 02): Here we discuss how we can actually determine the mass of a protein or any other large molecular system with unknown charge state using mass spectrometry. And they key steps in all MS experiments to do this, thereby mainly focusing on which MS are key for precise mass determination.

Cross-Linking (clip 03): A key method to determine the structure of a protein or protein complex is the use of chemical cross linkers. What are they and how can they help you to determine structure?

FPOP (clip 04): In this video, I explain the concept of FPOP as applied to proteins to measure structure and the change of structure of proteins. How does this technique work, what can you learn? Think how FPOP relates to HDX?

Mass Spectrometry Imaging (clip 05): In this last video, I briefly introduce imaging mass spectrometry. Here MS is used to obtain molecular spatial information. This is a huge field within MS resulting from MALDI techniques. We will have a brief introduction in this novel application.

Lecture 7: Mass spectrometry in praxis

Created with Sketch.

Handout1 (pptx, 17 MB)
Handout2 (pptx, 17 MB)
Handout3 (pptx, 589 kB)

This lecture will show you applications of mass spectrometry in selected fields.

Medicine (clip 01): In this video we demonstrate the application of mass spectrometry to diagnose Parkinson's disease.

Surgery (clip 02): Application of MS during operations.

Forensic science (clip 03): Here is an example of IMS for the detection of explosives and drugs.

Teaching Materials

Created with Sketch.

Materials for Advanced Mass Spectrometry.