SwathWizard is an assistant for Swath analysis.

The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, i.e. the TOPP Documentation: OpenSwathWorkflow tool, including downstream tools such as GitHub:PyProphet/pyProphet and the GitHub:msproteomicstools/TRIC alignment tool.

Since the downstream tools require Python and the respective modules, the Wizard will check their proper installation status and warn the user if a component is missing.

Users can enter the required input data (mzML MS/MS data, configuration files) in dedicated fields, usually by drag and droping files from the operating systems’ file explorer (Explorer, Nautilus, Finder…). The output of the Wizard is both the intermediate files from OpenSWATH (e.g. the XIC data in .sqMass format) and the tab-separated table format (.tsv) from pyProphet and TRIC.

This is how the wizard looks like:


A schematic of the internal data flow (all tools are called by SwathWizard in the background) can be found in the TOPP Documentation: SwathWizard.

A recommended test data for the Wizard is the PASS00779 dataset.