FragPipe
=========

Overview
--------

`FragPipe
<https://fragpipe.nesvilab.org/>`_ 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
<https://github.com/Nesvilab/FragPipe/issues>`_.

For ``TargetedFileConverter``, we provide support via the `OpenMS
<http://www.openms.de/support/>`_ support channels.

Tutorial
--------

The FragPipe team provides extensive documentation and `tutorials
<https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html>`_ 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 :doc:`generic` section).