Faculty of Science

Advanced Mass Spectrometry
Provider: Faculty of Science

Activity no.: 5842-25-00-00
	Enrollment deadline: 04/12/2025

Place	Department of Plant and Environmental Sciences
Date and time	December 2025 - January 2026
Regular seats	15
Activity Prices:
- 1 Participant fee (all participants in add. to course fee)	4,000.00 kr.
- 2 Course fee PhD student enrolled at UCPH SCIENCE	0.00 kr.
- 3 Course fee PhD student at Danish Universities (except CBS)	0.00 kr.
- 4 Course fee PhD student at Copenhagen Business School	3,000.00 kr.
- 5 Course fee PhD student at foreign university	3,000.00 kr.
- 6 Course fee Master's student at Danish university	0.00 kr.
- 7 Course fee Master's student at foreign university	3,000.00 kr.
- 8 Course fee Employee at university (e.g., postdocs)	3,000.00 kr.
- 9 Course fee Others (e.g., from a private company)	8,400.00 kr.
Lecturers	Nikoline Juul Nielsen
ECTS credits	2.50

Contact person	Nikoline Juul Nielsen E-mail address: njn@plen.ku.dk

Enrolment Handling/Course Organiser	PhD Administration SCIENCE E-mail address: phdcourses@science.ku.dk

Enrolment guidelines This is a toolbox course where 80% of the seats are reserved to PhD students enrolled at the Faculty of SCIENCE at UCPH and 20% and the seats are reserved to PhD students from other Danish Universities/faculties (except CBS). Anyone can apply for the course, but if you are not a PhD student at a Danish university (except CBS), you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. The course is free of charge for PhD students at Danish universities (except CBS). All other participants must pay the course fee (except if you are a master’s student from a Danish University). Aim and Content Today, mass spectrometry is by far the most commonly used detection technique for sensitive and selective analyses. A thorough understanding of the mass spectrometry theory, including the operating mechanism of ionization techniques and mass analyzers, is essential for method selection, development and optimization. This is an Advanced course in mass spectrometry for chemical analysis of organic compounds. The course is a natural extension of any basic course in analytical chemistry for everybody who is going to use modern hyphenated techniques such as GC- and LC-MS, including quadrupole, triple-quadrupole, time-of-flight, quadrupole-time-of-flight, ion traps and orbitraps for the analysis of complex mixtures. The course covers the theory of ionization, mass-to-charge separation, fragmentation, exact mass measurements, ion detection and data interpretation for all common mass spectrometers and ionization techniques. The theory is supplemented with theoretical exercises and laboratory exercises, and lectures from visiting researchers on selected topics e.g. mass spectrometry imaging. Learning outcomes Intended learning outcome for the students who complete the course: Knowledge • A solid theoretical understanding of mass spectrometry at an advanced level. • Some experience in addressing complex analytical problems, and acquaintance with tools to solve them. • Hands-on experience with advanced and diverse mass spectrometers. Skills • Describe, compare and contrast, operate and optimize common ionization techniques and mass analysers • Describe, perform and evaluate exact mass measurements and fragmentation experiments using mass spectrometers. • Asses, quantify and compensate for matrix effects in ionization processes. • Use mass spectrometry and fragmentation theory to annotate mass spectra. • Critically assess reported mass spectrometric research. • Select a suitable analytical platform for the separation, detection and quantification of small molecule organic analytes from complex matrices including selection and assessment of inlet parameters, ionisation source and mode, mass analyser and its parameterisation. Competences • This course enables the student to plan and perform analysis of complex mixtures using modern chromatographic techniques and high-end detectors, including the selection of method, columns and mode of detection, as well as optimization of chromatographic and mass spectrometric conditions for all common instrumental analytical separation methods. Target Group PhD students who need to use mass spectrometry techniques or handle these types of data during or after their PhD study. Recommended Academic Qualifications As prerequisite a course in instrumental analysis, like the BSc/MSc course “Analytical Chemistry” or the PhD course “Analytical Chemistry for Non-Analytical Chemists”, is strongly recommended, since all basic theory of mass spectrometry instruments and common inlets is assumed to be known. Please contact me (njn@plen.ku.dk) directly before registering online and if you have any questions. Research Area Analytical chemistry and applied analytical chemistry (food science, environmental science, biotechnology, natural products research, bioanalysis) Teaching and Learning Methods Lectures, student presentations of curriculum, expert lectures, hands-on laboratory experiments and reporting, theoretical exercises. Type of Assessment Oral exam graded by pass/non-pass. In order to be allowed at the exam active participation in student colloquia (1 out of 1); laboratory exercises (1 out of 2) and approved laboratory reports (1 out of 2) is required, individually or group-wise. Internal censor. The examination format is a 20 min oral exam without preparation. The question will be on ionization techniques or mass analysers; mass spectrometry experiments and acquisition; detectors for mass spectrometry; ions and fragments generated in mass spectrometry; or rules for interpretation of mass spectra. Literature 1) "Mass Spectrometry. Principles and Applications", by Edmond de Hoffmann and Vincent Stroobant, 3rd Ed., Wiley 2007. 2) “Interpretation of Mass Spectra”, by Fred W. McLafferty and Frantisek Turecek, University Science Books 1993 will be used to some extent. 3) We are considering including sections from “Analytical Separation Science”, by B. Pirok and P. Schoenmakers, RSC 2025. 4) Furthermore, selected articles will be included. The course curriculum is revisited on a regular basis. Course coordinator Nikoline Juul Nielsen, Associate Professor, njn@plen.ku.dk Guest Lecturers Associate professor Christian Janfelt (Dept. Pharmacy, HEALTH) gives a 2-hour lecture about MS imaging. Dates Start date Monday 15th December 2025. End date Friday 16th January 2026. NB: No teaching 22nd December to 2nd January around Christmas holiday. Oral exam in the week 19th – 23rd January 2026. Expected frequency The course takes place every year. Course location Frederiksberg Campus Registration Requirements for signing up The PhD-student should contact me directly (njn@plen.ku.dk) before signing up, so that I can evaluate if prerequisites are meet. Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the deadline for registration. Cancellation policy • Cancellations made up to two weeks before the course starts are free of charge. • Cancellations made less than two weeks before the course starts will be charged a fee of DKK 3.000 • Participants with less than 80% attendance cannot pass the course and will be charged a fee of DKK 5.000 • No-show will result in a fee of DKK 5.000 • Participants who fail to hand in any mandatory exams or assignments cannot pass the course and will be charged a fee of DKK 5.000 Course fee and participant fee PhD courses offered at the Faculty of SCIENCE have course fees corresponding to different participant types. In addition to the course fee, there might also be a participant fee. If the course has a participant fee, this will apply to all participants regardless of participant type - and in addition to the course fee.

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