PreWorkshop
This will take place on 17th June before the official registration. All three workshops run in parallel, so this means after acceptance you may choose one. There will be the principle of 'first come - first served' as we have a limit on the number of participants for each course.
The session will consist of a short presentation from our lab followed by general discussions. This workshop is aimed at experimentally based participants.
Workshop I: Sample preparation methods: advantages, disadvantages and which method to choose
Responsible: Christian Eberl, Dirk Walther, Paul Boersema, Kirti Sharma
Although the focus in this summer school is mainly on instrument performance and downstream bioinformatics, a crucial step in any proteomics project is the sample preparation before analysis by mass spectrometry.
In this seminar we will present and discuss with you sample preparation techniques which are commonly used in our lab. This includes different digestion methods such as in gel digestion, in solution digestion and FASP. Moreover, we will cover enrichment strategies for posttranslational modifications and peptide fractionation methods like ion exchange chromatography methods and isoelectric focusing an emphasis will be on the suitability of these methods for different types of proteomics experiments such as full proteome, interaction and PTM analyses. Furthermore, we will cover the crucial point of in vitro modifications.
The session will consist of short presentation from members of our lab followed by a discussion. This workshop is aimed at participants with a focus on experimental work.
Workshop II: Advanced LC-MS/MS Methods in Xcalibur
Responsible: Annette Michalski, Eugen Damoc (Thermo Scientific), Nagaraj Nagarjuna
Setting up an appropriate LC-MS/MS method in Xcalibur (Thermo Scientific) can be challenging due to the large number of parameters that the software allows to influence, and any optimization procedure will need a good understanding of the different settings and values. Pre-workshop III will cover selected features that are of crucial importance to Orbitrap instrumentation and point out differences between the different platforms such as LTQ Orbitrap Velos, Orbitrap Elite and QExactive. We will discuss the best strategies to set up methods for your applications by giving some hands-on experience with the Tune window and Xcalibur and have a round table discussion about participants’ problems or questions. A brief introduction on how to make best use of the QualBrowser features to evaluate your data quality will complete the pre-workshop. Both beginners and advanced Xcalibur users are welcome!
Coffee & cookies will be served.
Workshop III: Plugin programming in Perseus
Responsible: Jürgen Cox, Marco Hein
The workshop introduces to the programming of customized activities in the Perseus software. It makes use of the plugin architecture of Perseus which allows integrating self-written components into the computational framework. Any type of activity can be implemented as a plugin, from simple matrix processing activities to complex visualizations. Plugins are written in the C# programming language and follow a simple and straightforward interface structure. The inner workings of plugins are studied by examining several examples of standard Perseus plugins in detail. Furthermore, it will be demonstrated how new plugins are generated within the Visual Studio integrated development environment. This is an advanced course. A basic knowledge of the Perseus software is assumed. C# programming skills are not required but familiarity with any programming language is a plus.
