Educators:
Ballal Hossen (FZ Borstel), Dominik Schwudke (FZ Borstel), Dominik Kopczynski (Uni Vienna), Nina Troppmair (Uni Vienna), Robert Ahrends (Uni Vienna), Sanjay Kumar Srikakulam (FZ Jülich), Nils Hoffmann (FZ Jülich)

Date & Time:
Monday, September 7th, 2026
10:00 - 16:30

Agenda:

Morning
10:00 – 10:20 Part 1: Welcome and Introduction (Dominik Schwudke)
10:20 – 12:00 Part 2: Shotgun Lipidomics with LipidXplorer & lxPostman (Ballal Hossen & Dominik Schwudke)

12:00 – 13:00 Lunch Break

Afternoon
13:00 – 14:00 Part 3: LipidCreator & Skyline (Nina Troppmair & Dominik Kopczynski)
14:00 – 16:00 Part 4: FAIR Lipidomics & LipidCompass (Sanjay Kumar Srikakulam & Nils Hoffmann)
16:00 – 16:30 Questions, Discussion and Feedback

Location:
On-Site training as part of 11th Lipidomics Forum 2026 in Borstel.

Contents:
In the first part of the course, we will provide insights into using LipidXplorer to identify and quantify lipids from shotgun lipidomics and will inspect, check, and normalize the data and calculate absolute quantities using internal class-specific standards with lxPostman. In part two, we will work through an example of targeted LC-MS lipidomics with LipidCreator and Skyline. Part three will cover FAIR aspects for lipidomics data and different lipidomics tools for comparison, visualization, and enrichtment, like MapToGo, LipidSpace and LipidCompass. The course will consist of a short theory and background overview of the employed programs complemented by applying the tools to provided data sets. 

Learning goals:
Participants will be able to understand and explain the targeted shotgun MS and LC-MS workflows for lipidomics. They will learn the fundamentals of the FAIR principles with respect to lipidomics data, they will learn to apply lipidomics software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each pipeline step.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics, and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises requiring proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. The workshop will be held in person on site.

Keywords:
Lipidomics, Shotgun, Targeted Analysis, LC-MSn, Reporting, Visualization, Enrichment

Tools:
LipidXplorer, LipidCreator, Skyline, Goslin, lxPostman, LipidSpace, Reporting Checklist, MapToGo, LipidCompass

Registration:
Please register for the course by ticking the LIFS Workshop option on the Lipidomics Forum registration page. (Fee: 20 €)
We will contact you prior to the course with instructions to access the Moodle course material.

Contact:
Please use our contact form if you have any questions!

This workshop is kindly supported by the German Network for Bioinformatics Infrastructure (de.NBI) and Elixir Germany:

Date & Time:
March 24-28, 2025

Registration Deadline:
February 10, 2025

Topic: Bioinformatics for Lipidomics, with a focus on mass spectrometry data analysis and workflows

Contents: The de.NBI Spring School 2025 will provide in-depth knowledge and practical experience in lipidomics bioinformatics. Participants will explore state-of-the-art bioinformatics tools essential for lipidomics research, comprehensive lipidomics workflows, and the challenges and limitations of lipidomics from multiple perspectives.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics, and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises requiring proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshops.

Learning goals: Gain understanding of bioinformatics for lipidomics, possibilities,
challenges, and limitations

Keywords:
Lipidomics, Pre-Analytics, Research Data Management, Mass Spectrometry, Data Analysis, Visualization

Tools:
LipidCreator & Skyline, LipidXplorer & lxPostman, mzmine, LipidSpace, Lipidomics Checklist, Goslin, LipidCompass, MetaboLights

Organizers:

• Nils Hoffmann, Helena Schnitzer, Daniel Wibberg (CAU, Forschungszentrum Jülich GmbH)
• Dominik Schwudke (BioInfra.Prot, Research Center Borstel)
• Dominik Kopczynski, Robert Ahrends (University of Vienna, Austria)

Trainers:

• Daniel Wibberg, Sebastian Beier, Sara Beier, Nils Hoffmann (all FZ Jülich)
• Dominik Kopczynski (University of Vienna)
• Lisa Hahnefeld (Goethe-Universität Frankfurt und Fraunhofer ITMP)
• Dominik Schwudke, Ballal Hossen (FZ Borstel)
• Ansgar Korf (mzmine)
• Noemi Tejera Hernandez (EMBL-EBI, MetaboLights)
• Lisa Hahnefeld (Goethe-Universität Frankfurt und Fraunhofer ITMP)
• Cristina Coman & Nina Troppmair (Skyline & LipidCreator Tutorial Material, University of Vienna)

Keynote Speakers:

• Sebastian Beier & Sara Beier (Forschungszentrum Jülich)
• Andrej Shevchenko / Vannuruswamy Garikapati (MPI-CBG, Dresden)
• Robert Ahrends (University of Vienna)
  
• Hanna Bednarz (Bielefeld University)

Location:
On-Site, Center for Biotechnology, Bielefeld University, Bielefeld, Germany

Accommodation: For accepted participants, accommodation costs will be covered by the
organizers.

More information and application:
https://www.denbi.de/training-courses-2025/1847-de-nbi-spring-school-2025-
bioinformatics-for-lipidomics

Contact:
Please use our contact form if you have any questions!

This workshop is kindly supported by the German Network for Bioinformatics Infrastructure (de.NBI) and Elixir Germany: