Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)
November 10th, 2019
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)
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 inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards. We will then perform a qualitative 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.
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
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.
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.
Lipidomics, Statistical Analysis, Visualization
R, RStudio, LUX Score, ClovR.