Workshops

Workshop – LIFS Training session I & II

Date:
October 5th, 2021, 9:00 – 17:00 (CEST)

Educators:
Jacobo Miranda Ackerman, Daniel Krause, Fadi Al Machot, Dominik Kopczynski, Nils Hoffmann (de.NBI, BioInfra.Prot / LIFS)

Deadline for Workshop Registration:
Until capacity is reached.

Location:
On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise)

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. In part four, we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology.

Morning
09:00 – 09:30 Welcome and Introduction
09:30 – 11:30 Targeted Lipidomics with LipidCreator and Skyline
11:30 –12:00 Shotgun Lipidomics with LipidXplorer

Afternoon
13:00 – 14:00 Shotgun Lipidomics with LipidXplorer
14:00 – 15:00 Quantification of Shotgun Lipidomics data with lxPostman
15:00 – 15:30 Break
15:30 – 16:30 Lipidome comparison with LUX Score
16:30 – 17:00 Questions and Discussion

Learning goals:
Participants will be able to understand and explain the shotgun MS and targeted 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.

Keywords:
Lipidomics, Shotgun, Targeted, LC-MS

Tools:
PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score

Registration:
Please select the “LIFS Training session I & II” in the Workshops section of the conference registration. Capacity is limited to 30 participants.

Contact:
Nils Hoffmann – nils.hoffmann@cebitec.uni-bielefeld.de

Workshop – LipiTUM Workshop

Date:
05.10.2021, 9:00 – 12:00 (CEST)

Educators:
Nikolai Köhler, Tim Rose & Josch Pauling (LipiTUM)

Deadline for Workshop Registration:
Until capacity is reached.

Location:
On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise)

Contents:
The course will start with an introductory presentation on the theoretical background. A hands-on application will follow, where we will explain the basic workflow for clustering and sample stratification along with possible options and caveats. Participants will identify sample groups and characterize them based on their lipidomics signatures. The second part will be dedicated to analysing lipid metabolic networks with LINEX. Again, a short theoretical introduction will be followed by a practical example with public lipidomics data. We will go through possible visualisations and how to analyse and interpret quantitative lipid data in the context of lipid reaction networks.

09:00 – 09:45 Welcome and Introduction to clustering and sample stratification
9:45 – 10:30 Sample stratification and signature extraction with MoSBi 
10:30 – 11:00 Introduction to pathway analysis
11:00 – 11:45 Lipid metabolic network analysis with LINEX
11:45 – 12:00 Questions and Discussion

Learning goals:
Participants will learn how to analyse and explore lipidomics data using biclustering and lipid metabolic networks. They will stratify lipidomics samples and draw conclusions based on functional associations between lipids. This will allow them to biologically interpret the results. They will be able utilise the respective software tools for different experimental settings and to choose the appropriate settings based on their research question.

Prerequisites:
Basic knowledge about lipidomics, biochemistry and statistics is recommended, but not required. An introductory lecture will provide you with the necessary information. All hands-on analysis will be performed using web-based tools, which only require a modern internet browser (Chrome or Firefox recommended). We suggest a spreadsheet program (Excel, LibreOffice or OpenOffice) to be able to view the example data. Course materials and example data will be provided at the workshop or shortly before.

Keywords:
Lipidomics, Data integration, Bioinformatics, Clustering, Stratification, Pathway analysis

Tools:
MoSBi, LINEX

Registration:
Please select the “LipiTUM Workshop” in the Workshops section of the conference registration. Capacity is limited to 30 participants.

Contact:
Josch Pauling – josch.pauling@wzw.tum.de

Workshop – ILS Interest Groups Workshop

Date:
05.10.2021, 13:00 – 17:00 (CEST)

Speakers:
Kim Ekroos, Markus Wenk, Michal Holčapek, Robert Ahrends, Xianlin Han  (International Lipidomics Society)

Deadline for Workshop Registration:
No registration required.

Location:
On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise)

Contents:

13:00 – 13:20 ILS – Intro + Current Activities
13:20 – 13:40 Reference materials and biological reference ranges
13:40 – 14:00 Clinical lipidomics
14:00 – 14:20 Applied Bioinformatics
14:20 – 14:40 Instrumental and Methodological Developments
14:40 – 14:50 Lipid Function
14:50 – 15:00 Global Networking
15:00 – 15:30 Break
15:30 – 17:00 Lipidomics Standardization Update – Discussion of Checklist/White Paper

Registration:
There is no dedicated registration necessary for this workshop.

Contact:
Kim Ekroos – kim@lipidomicsconsulting.com

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