Advanced Mass Spectrometry

Course manual 2025/2026

Course content

The Advanced MS course contains four different topics within the field of Mass Spectrometry. We have chosen to divide the course into two major areas of application, one being the use of MS instrumentation, and the other being MS data science and data workflow strategies. Both are an important part of everyday MS, where initially one requires appropriate instrumentation to acquire a type of data, such as structure or quantitative information. On the other hand, it is also imperative to understand the data generated by MS, and how this can be used in downstream data analytical techniques.

The topics and applications we have selected this year are as follows:

1. Hyphenated Mass Spectrometry using Ion mobility MS and spectroscopic techniques for protein aggregation analysis (Life sciences)
2. A Metabolomics and/or exposomics MS data pipeline (Environmental)
3. Quantitative MS analysis of clinical samples on large cohorts (Clinical)
4. Advanced data analysis of EI-MS spectra from GC-MS (Forensics)

The subjects and format differ from week to week and will be explained during the first lecture each week, as well as an overview in the first lecture.

Grading is done weekly by topic assignments, and follows the course structure to highlight different aspects of MS.

Teamwork, collaboration and critical assessment and thinking are essential during the course, where new information will be discussed collectively and in groups. Students will also discover new MS techniques and approaches through active learning.

Presentations by students take place each week. Specific instructions will be given in due time.

Study materials

Literature

• Provided during course. 

Syllabus

• Provided during course. 

Practical training material

• Provided during course. 

Software

• Provided during course. 

Other

• Provided during course. 

Objectives

• 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.
• Describe single-particle approaches to perform analysis of large molecular structures.
• Discuss the implementation and advantages of charge detection mass spectrometry.
• Discuss the differences between DIA and standard MS/MS approaches and their use in quantitative analysis of complex samples and life science studies.
• Discuss the analytical workflow of DIA approaches and they differ from discovery and targeted MS approaches.
• Describe various forms of data provided by MS instruments, calculate and compare data conversion and visualisation methods.
• Explain the difference in data structure and application of DIA compared to existing sequencing techniques.
• Explain the workflow for single compound library searching, analogue searching, AMDIS and other NIST software.

Teaching methods

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

Learning activities

Attendance

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

Additional requirements for this course:

Absence needs to be communicated and agreed by the course coordinator, and weekly tutor. 

Assessment

Final grade is:

• Average over all 4 assignments
• All assignments count for 25%
• All should be 6 or up (pass for all)
• Random groups are made and online

Inspection of assessed work

Possible upon request.

Assignments

The course has weekly assignments which all need to be passed (> and = to 6). Each weekly assessment is based on evaluation of written assignments. Assignments are completed weekly and the final score is the weighted average of all four (4) grades.

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

Contact information

Coordinator

• prof. dr. Garry Corthals

Staff

• prof. dr. Arian van Asten
• prof. dr. A.M. Rijs
• dr. S. Samanipour