Setting up FragPipe


Install or update OpenJDK

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



Note: During installation, remember to enable Set JAVA_HOME variable and JavsSOFT (Oracle) register keys.


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

Bruker .d reader and DIA-NN need Visual C++ Redistributable in Windows. If you see an error related to timsTOF data or DIA-NN, 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. You will be prompted to fill out a short form before proceeding with the download.


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.

FragPipe requires Python 3.8, 3.9, or 3.10

If you already have Python 3.8, 3.9, or 3.10, specify the python executable file path in the Config tab, click Install/Upgrade EasyPQP, and wait for a few minutes.

If Python 3.8, 3.9, or 3.10 is not already installed: 1) Download and install Python 3.9

Windows: download the installer from here

Linux: different Linux distributions have different commands to install Python. Please figure it out by yourself. If you are not familiar with the command line interface, please switching to Windows.

2) To enable spectral library building with EasyPQP (which also works for timsTOF data), click Install/Upgrade EasyPQP at the bottom of the Config tab and wait for a few minutes. FragPipe will froze during the installation.

3) 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.