Setting up FragPipe


Install or update Java

FragPipe and MSFragger both require a 64-bit Java to run. Windows users can choose to download the -jre- version of FragPipe (see below) or install 64-bit Java here by selecting the Windows x64 Installer. Launch the installer and follow the prompts. You may need to restart FragPipe after updating Java.


Install or update FragPipe

FragPipe can be downloaded here. Follow the instructions on that same Releases page to launch the program. When FragPipe launches, the first tab in the window (‘Config’) will be used to configure the program.


Install Visual C++ Redistributable for Visual Studio 2017

Bruker’s native library needs Visual C++ Redistributable for Visual Studio 2017 in Windows. If you see an error that the Bruker native library cannot be found, please try to install the Visual C++ redistibutable.


Install Mono (required for Thermo .raw file reading on Linux)

Linux users need to have Mono installed to read Thermo .raw files.


Install, update, or use an already downloaded version of MSFragger

Use an existing MSFragger .jar file: If you already have the latest MSFragger release downloaded, use the ‘Browse’ button on the Config tab in FragPipe to select the .jar file.

Download MSFragger: In FragPipe, use the ‘Download/Update’ button to get the latest version of MSFragger.


Install, update, or use an already downloaded version of Philosopher

If you have already downloaded the latest Philosopher release, use the ‘Browse’ button in FragPipe to select the Philosopher executable file. To upgrade to the most recent release or to download for the first time, use the ‘Download/Update’ button.


Optional: install, update, or use an already installed version of Python

Database splitting (to reduce the size of the in-memory fragment ion index– helpful for workstations with limited memory or for complex searches) and/or spectral library generation will require Python 3 or above.

If you already have Python 3 or above, make sure the following packages are installed: numpy, pandas, matplotlib, cython, and msproteomicstools. The easypqp package is also required to build spectral libraries from timsTOF data. Please note: if Python was installed through Anaconda, you will already have all of these packages except for msproteomicstools (version 0.8.0) and easypqp. In most cases, you can run pip install [package name] in the Anaconda prompt to install a missing package.

If Python 3 is not already installed: 1) Click ‘Download’ in the Python section of the Config tab in FragPipe or click here to go to the Anaconda site, click ‘Download’, then select the latest Python version (3.7 or higher) and launch the installer.

2) Follow the prompts in the graphical installer. Note the install location that you choose and complete the installation. We do not recommend adding Anaconda to your PATH environment variable, but you can choose to register Anaconda as your default Python.

3) From the start menu, search for “Anaconda Prompt” and launch it.

4) To enable spectral library building with EasyPQP (which also works for timsTOF data), type pip install easypqp into the Anaconda prompt window and hit enter to install the easypqp package. To enable spectral library building with SpectraST: type pip install msproteomicstools==0.8.0 into the Anaconda prompt window and hit enter to install the msproteomicstools package. Other packages required for these tools (pandas, cython, matplotlib, and numpy) are included in the Anaconda installation.

5) In FragPipe -> Config -> Python, use the ‘Browse’ button to navigate to the installation location and select python.exe. When FragPipe refreshes, DB Splitting and Spectral Library Generation should now be enabled.


Next: see the FragPipe usage tutorial.