FragPipe is a comprehensive computational platform designed for the analysis of mass spectrometry-based proteomics data. It includes a Graphical User Interface and pipeline wrapper code (FragPipe-GUI), distributed alongside various independent software tools and workflow files. Each component of FragPipe is available under its own license, as detailed in the FRAGPIPE-THIRD-PARTY-LICENSES.txt (in https://github.com/Nesvilab/FragPipe) file. Users must review and comply with the licenses of each component when using FragPipe. FragPipe and its contributors disclaim any liability for damages or issues resulting from the use, misuse, or inability to use the software. Users are responsible for ensuring that FragPipe and its components are suitable for their intended purposes and adhere to all relevant legal and regulatory requirements.