FragPipe

Overview

FragPipe is a comprehensive and popular platform for the analysis of mass spectrometry based proteomics data. It can be used to generate and export spectral libraries suitable for OpenSWATH.

Contact and Support

FragPipe is supported by a very active community via their github issues tracker.

For TargetedFileConverter, we provide support via the OpenMS support channels.

Tutorial

The FragPipe team provides extensive documentation and tutorials on their website. Please follow their instructions to generate spectral libraries. The resulting spectral library will be in a tab delimited format that can be directly converted to TraML/PQP using the TargetedFileConverter tool in OpenMS ( follow the remaining steps in the Generic Transition Lists section).