Available courses

de.NBI Spring School Bioinformatics for Lipidomics 2025

Organizers:
de.NBI Service Center BioInfra.Prot, Lipidomics Informatics for Life Science
Nils Hoffmann, Helena Schnitzer, Daniel Wibberg (FZ Jülich)
Dominik Schwudke (Research Center Borstel)
Dominik Kopczynski, Robert Ahrends (University of Vienna, Austria)

Educators:
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)

Keynotes:
Sebastian Beier & Sara Beier
Andrej Shevchenko / Vannuruswamy Garikapati
Robert Ahrends
Hanna Bednarz

Date & Time:
Monday, March 24th - Friday, March 28th 2025

Contents:
The LIFS de.NBI partner project has pioneered innovative software solutions in the field of mass spectrometry for lipidomics data analysis. Building on this expertise, the de.NBI Spring School 2025 will concentrate specifically on Lipidomics bioinformatics, providing participants with in-depth knowledge and practical experience in this dynamic field. 

Throughout the training, attendees will explore state-of-the-art bioinformatics tools essential for Lipidomics research. They will be introduced to comprehensive lipidomics workflows, offering a clear understanding of the capabilities, challenges and limitations inherent in Lipidomics from multiple perspectives. This knowledge is crucial for effectively analyzing lipid data and integrating it with other biological data types.

The de.NBI Spring School 2025 will feature a mix of engaging lectures and interactive hands-on sessions led by experts from the de.NBI and ELIXIR networks and beyond. The program is designed for PhD students, postdoctoral fellows, and other scientists who have a foundation in bioinformatics and molecular biology, and who are eager to expand their expertise in Lipidomics bioinformatics. 

Participants will leave equipped with the skills and insights necessary to advance their research and contribute to the growing field of Lipidomics, helping to unlock biological insights that can drive innovative solutions in health and disease management and other application areas.

Learning goals:
Participants will be instructed in Lipidomics workflows and gain understanding about the possibilities, challenges and limitations of Lipidomics. 

Prerequisites:
The Spring School is targeted towards early career scientists like PhD students and Postdocs, but also experienced scientists, who want to learn more about Bioinformatics for Lipidomics. Participants should have 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 their workshop sessions. 

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

Tools:
Alister, LipidXplorer, mzmine, LipidCreator, Skyline, Goslin, lxPostman, LipidSpace, Reporting Checklist, LipidCompass, MetaboLights

9th Lipidomics Forum 2024 - LIFS Workshop

Educators:
Robert Ahrends (Uni Vienna, LIFS), Dominik Kopczynski (Uni Vienna, LIFS), Nils Hoffmann (FZ Jülich, LIFS), Dominik Schwudke (FZ Borstel, LIFS)

Date & Time:
Sunday, September 1st 2024
10:00 - 16:30

Location:
On-Site training as part of 9th Lipidomics Forum 2024 in Borstel.

Contents:
In the first part of the course, we will work through an example of targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will provide insights into using LipidXplorer to identify and quantify lipids from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by applying the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check, and normalize the data and calculate absolute quantities using internal class-specific standards with lxPostman. We will then perform a qualitative and quantitative comparison of the lipidomes using LipidSpace.

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 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. We will use Zoom to host the workshop. To participate, please install the Zoom client software on your computer.

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

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


Overview and challenges in lipidomics data analysis

In this workshop, we will give participants a brief overview of some of the challenges that exist in lipidomics identification and quantification from mass spectrometry data and how they should best be tackled. We will present the recommendations provided by the Lipidomics Standards Initiative and will discuss why and when they make sense to be applied. Further, we will give an overview of existing resources and tools for lipidomics researchers, to make data analysis, integration and interpretation easier, also in relation to multi-omics integration efforts. The workshop will include hands-on exercises that walk participants through a typical analysis of a lipidomics MS experiment using a mix of local and web-based software.

Educators:
Nils Hoffmann (FZ Jülich, Uni WIen, LIFS)

Location:
On-Site training.

Contents:

The first part of the course will give a short overview of Lipidomics and its challenges to participants. In the second part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will introduce the Lipidomics Checklist. Part 4 will present LipidSpace, a UI tool to compare and cluster quantitative lipidomics results using the shorthand lipid nomenclature and graph-based similarity and lipid structural space embedding. Finally, we will check out mzQC, not only in the context of lipidomics, and why it may be a really versatile file format for MS-derived QC metrics.

Learning goals:
Participants will be able to understand and explain the targeted and DIA LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline, have a basic understanding on how to report their results and how to ensure good quality.

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 which may require the 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.

Keywords:
Lipidomics, Targeted, LC-MS, DIA

Tools:
LipidCreator, Skyline, Goslin, LipidSpace, Lipidomics Minimal Reporting Checklist, mzQC


LIFS LipidXplorer Training

Educators:
Jacobo Miranda Ackerman

Location:
Online, virtual workshop / training.

Contents:
In this course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets.

Learning goals:
Participants will be able to understand and explain the targeted shotgun MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline.

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 which may require the proper rights. The workshop is a mix of small lecture segments and hands-on exercises.

Keywords:
Lipidomics, Shotgun

Tools:
PeakStrainer and LipidXplorer