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 with 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 demonstrate procesing of lipidome data using absolute quantification approaches, the LUX Score lipidome homology and visualize quantitative lipidome data 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.

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