LIFS Training Workshops @ Lipidomics Forum 2019
Before this year's Lipidomics Forum 2019 in Borstel, Germany kicks off on the evening of Sunday, November 10th, 2019, LIFS will host two lipidomics tool and workflow workshops. Based on the participant surveys of previous trainings, we will offer two separate courses this year to allow for more hands-on time with the tools and data.
Please go to the Lipidomics Forum registration to sign up for one of the courses (they will be taught in parallel).
Workshop 1 - Lipidomics MS Data processing, identification & quantification
"What is it and how much?"
10:00 - 10:45 Common Introduction
10:45 - 12:30 LipidXplorer Shotgun Lipidomics
12:30 - 13:30 Lunch break
13:30 - 16:30 LipidCreator & Skyline Targeted LC-MS lipidomics
Educators:
Jacobo Miranda Ackermann, Nils Hoffmann (BioInfra.Prot / LIFS)
Date:
November 10th, 2019
Location:
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)
Contents:
In this course, we will work through a typical use-case for bioinformatics processing lipidomics data following MS acquisition. The first part of the course will start with PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The second part of the course 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 a provided data set.
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. Participants are required to bring their own laptop in order to work on the hands-on exercises.
Keywords:
Lipidomics, Shotgun, Targeted, LC-MS
Tools:
PeakStrainer and LipidXplorer, LipidCreator and Skyline.
Workshop 2 - Statistical analysis & qualitative and quantitative comparison of lipidomics data
"How do I compare? Fancy graphics & convincing plots"
10:00 - 10:45 Common Introduction
10:45 - 12:30 R Scripting for LipidXplorer data quantification
Quantitative lipidome comparison wiht ClovR
12:30 - 13:30 Lunch break
13:30 - 16:30 Qualitative lipidome with LUX Score
Machine learning, clustering and classification for lipidomics data
Educators:
Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)
Date:
November 10th, 2019
Location:
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)
Contents:
In this course, we will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will absolute quantification against internal class-specific standards comparison of the lipidomes using the LUX Score lipidome homology, before finally comparing and visualizing our quantitative lipidome results with ClovR. 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 shotgun lipidomics data analysis workflow. 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 applications. Basic knowledge of R and RStudio is a plus to understand the quantitation workflow. Participants are required to bring their own laptop in order to work on the hands-on exercises.
Keywords:
Lipidomics, Statistical Analysis, Visualization
Tools:
R and RStudio, LUX Score, ClovR.
Contact
If you have any questions about the training workshops, please use our Service & Support form.
Acknowlegements
We thank de.NBI - the German Network for Bioinformatics Infrastructure and Elixir for their support.
