TOPP, The OpenMS Proteomics Pipeline provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and then be used in proteomics workflows. These applications range from useful utilities file format conversion, peak picking) over wrapper applications for known applications (e.g. Mascot) to completely new algorithmic techniques for data reduction and data analysis. TOPP is based on the OpenMS library and as more functionality is added to new OpenMS releases, TOPP will naturally contain new or updated tools.

In addition to offering a toolbox, TOPP contains TOPPView - the central graphical user interface - which allows the user to view, inspect and manipulate proteomics data. TOPPView reads standard formats and allows the user not only to view the data, but also to interactively call TOPP tools and display the results. As such it is a powerful tool for interactive data manipulation.

In this tutorial we will now in detail explain the capabilities of TOPPView and the TOPP tools using real data sets and standard analysis tasks.