Available courses

9th Lipidomics Forum 2024 - LIFS Workshop

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

Date:
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 for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the 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. 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 as well as 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 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 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 ensure that the Zoom client software is installed on your computer.

Keywords:
Lipidomics, Shotgun, Targeted, LC-MS

Tools:
PeakStrainer and LipidXplorer, LipidCreator, Skyline, Goslin, lxPostman, LipidSpace


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