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OpenSwathAssayGenerator

Generates filtered and optimized assays using TraML files.

potential predecessor tools → OpenSwathAssayGenerator → potential successor tools
OpenSwathDecoyGenerator

This module generates assays for targeted proteomics using a set of rules that was found to improve the sensitivity and selectivity for detection of typical peptides (Schubert et al., 2015). The tool operates on TraML files, which can come from TargetedFileConverter or any other tool. In a first step, the tool will annotate all transitions according to the predefined criteria. In a second step, the transitions will be filtered to improve sensitivity for detection of peptides.

Optionally, theoretical identification transitions can be generated when the TraML will be used for IPF scoring in OpenSWATH, see MRMAssay for more information on the algorithm. This is recommended if post-translational modifications are scored with OpenSWATH.

The command line parameters of this tool are:

INI file documentation of this tool: