Educators:
Dominik Schwudke (Research Center Borstel – Leibniz Lung Center, Borstel, Germany, BioInfra.Prot, LIFS)
Lisa Hahnefeld (Goethe University & Fraunhofer ITMP, Frankfurt, Germany)
Nils Hoffmann (Forschungszentrum Jülich GmbH, Outbranch Office Bielefeld, Germany & University of Vienna, Austria, BioInfra.Prot, LIFS)
Location:
On-Site training as part of 65th ICBL Conference in Innsbruck, Austria
Date & Time:
Sunday, September 21th 2025
11:00 - 17:00
Content:
Workshop 1: Lipidomics analyses and its specific challenges
Dominik Schwudke, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
Lipidomics results, in terms of identification and quantitation of lipid components require some specific considerations to be able to further our knowledge on membrane organization and lipid metabolism. I will discuss some basic rules for interpreting membrane and storage lipid profiles in context of analytical limits but also redundancy in biological systems. While certain conserved compositional patterns are formed in eukaryotic systems based on known chemical building blocks, the causes of perturbed lipid homeostasis are often hard to assign to a specific biochemical process and might require further kinetic and spatial information. In this regard, I will discuss importance of experimental design of lipidomics studies to reach a level of functional interpretation in lipid metabolism research and give some insights how we adapted our experimental strategies accordingly.
Workshop 2: Experimental designs and its consequences for preanalytics in lipidomics studies
Lisa Hahnefeld, Goethe University Frankfurt & Fraunhofer ITMP, Frankfurt, Germany
Lipidomics has emerged as a powerful tool for understanding physiological and pathophysiological processes, yet the reliability of lipidomic data is profoundly influenced by experimental design and preanalytical variables. Researchers focusing on lipid biology, even if not directly involved in mass spectrometry, need to be aware of how factors such as nutritional status, fasting, and exercise can impact the lipidomic profile. Moreover, sample collection and preparation steps, often considered routine, can introduce significant variability and bias into analytical results.
In this workshop, we will review a range of preanalytical studies addressing both human and animal lipidomics experiments. Through case studies and examples from previous research, we will highlight common challenges encountered in the handling of blood, tissue, and cellular samples. Specific attention will be given to how variations in donor conditions, sample processing, and storage influence lipid measurements. We will further discuss methodological considerations crucial for minimizing artifacts and ensuring robustness in experimental workflows. By examining the consequences of these preanalytical factors, participants will gain practical insights into optimizing their own study designs.
Ultimately, this workshop will underscore the fundamental importance of thoughtful experimental planning and rigorous preanalytical practices in lipidomics research. Attendees will learn how to identify and mitigate preanalytical pitfalls, thereby enhancing the reproducibility and interpretability of their studies. This knowledge is essential for generating meaningful and reliable data.
Workshop 3: LIFS Bioinformatics Tools, Nomenclature, Evidence and Reporting
Nils Hoffmann, Forschungszentrum Jülich GmbH, Germany & University of Vienna, Austria
Compared to more established fields like proteomics, mass spectrometry-based lipidomics still faces significant challenges in terms of availability and quality. To address this, a suite of open-source tools and FAIR (Findable, Accessible, Interoperable, Reusable) data standards have been developed by the Lipidomics Informatics for Life Science (LIFS) consortium, which is part of the German Network for Bioinformatics Infrastructure (de.NBI). Close collaboration has been established with the International Lipidomics Society and the HUPO-PSI to advance lipidomics tools and data standards. The tools are available as libraries and as standalone and web-based applications. They enable the processing and analysis of targeted and untargeted lipidomics data and provide functionality for statistical analysis, comparison and visualization, as well as fort he harmonization of study details reporting and lipid nomenclature, while promoting collaboration through liberal licensing.
In this workshop, we will provide an overview of the current bioinformatics challenges involved in analysing lipids using mass spectrometry, both qualitatively and quantitatively, and explain how adhering to FAIR data principles ultimately simplifies analysis and research for both humans and machines. We will discuss and demonstrate how tools such as LipidCreator, LipidXplorer, Goslin and the Lipidomics Checklist can help to better handle the complexity and ambiguity of lipid identification, and how results should be reported to enable others to understand, interpret and, ideally, reproduce them correctly. Finally, we will discuss the options and benefits of depositing lipidomics data to improve both findability and reusability.
Learning goals:
The workshops aim to enhance understanding of lipidomics challenges, including interpreting lipid profiles, designing robust experiments, and addressing analytical limitations. They emphasize the critical role of preanalytical factors and experimental planning in ensuring reliable lipidomic data. Finally, they promote the use of standardized bioinformatics tools, FAIR data principles, and reproducible reporting to advance lipidomics research.
Prerequisites:
The workshop is targeted towards early career scientists like PhD students and Postdocs, but also experienced scientists, who want to learn more about Lipidomics, Pre-Analytics and Bioinformatics for Lipidomics.
Participants are asked to bring a laptop running MS Windows if they wish to follow the examples or try out the software.
Keywords:
Pre-Analytics, Lipidomics, Shotgun, Targeted Analysis, LC-MSn, Bioinformatics, Reporting
Tools:
LipidXplorer, LipidCreator, Skyline, Goslin, lxPostman, LipidSpace, Reporting Checklist, LipidCompass
Registration:
Please register for the workshops during the ICBL conference registration process. The participation is free of charge and included in the overall conference registration fee.