PhD Courses in Denmark

To give the students an overview of the fundamental analytical techniques used to analyze small organic molecules and proteins and how they can be extracted, prepared, and processed for chemical analysis. The major objective of the course is to give the students a solid understanding of chromatographic based analytical methods with special emphasis on analysis and detection of both known and unknown compounds by interpretation of mass spectrometric data. The course aims broadly at PhD students studying biotechnology and health sciences, and industry participants who want to strengthen their analytical chemical knowledge. Both discovery and targeted methods will be presented, covering experimental design, acquisition strategies, sample preparation techniques, and applications in complex biological systems.

A student who has met the objectives of the course will be able to:

• Describe the general principles of sample preparation of small organic molecules and proteins, e.g. using solid phase extraction (SPE).
• Explain the general principle of chromatography (LC, GC) including the use of different relevant types of columns.
• Explain the general principles of diode array detection (DAD) and mass spectrometry (e.g. QTOF) coupled to liquid chromatography (LC-DAD-MS).
• Demonstrate the principles of dereplication and accurate mass spectrometry.
• Perform data analysis using standard instrumental software and databases for LC-DAD-MS analysis.
• Compare analytical results to information in commercial and open source databases.
• Explain the basic principles behind quantitative analysis of small organic molecules.
• Describe the fundamental concepts and instrumentation used in high-resolution mass spectrometry for proteomics (e.g. Orbitrap).
• Gain insight into data processing and explain principles of peptide identification in MS-based proteomics.
• Understand the various ways of conducting quantitative proteomics and multiplexed proteomics, e.g. label-free vs. labeled.
• Describe common methodologies for protein-protein interaction analysis and post-translational modification mapping in proteomics workflows.

Industrial production of small organic biomolecules (metabolites or natural products) as well as proteins using microbial cell factories is estimated to increase dramatically in the coming years. This includes important products such as antibiotics, anticancer agents, smaller proteins, and food ingredients like aroma compounds, pigments, antioxidants and vitamins. Other metabolites are toxic to humans and are therefore to be avoided in fermented foods and feeds. Proteomics is becoming indispensable across both industry and basic research, enabling detailed analysis of host cell proteins, verification of cell line integrity, and monitoring of pathway activity in bioprocessing. Proteomics also offer powerful tools to characterize cellular dynamics, elucidate molecular mechanisms, and explore protein-level regulation in health and disease. This course will teach the basic principles behind modern methods for analysis of small organic molecules, as well as proteins, especially based on liquid chromatography coupled to mass spectrometry. Through lectures, exercises, and hands-on data analysis, students will gain practical insights into designing and interpreting metabolomics and proteomics experiments relevant to both academic research and industrial applications.