FragPipe v12.1

Windows users

• Download FragPipe.exe and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
  • If you don't have a compatible Java version, you will be redirected to a website where you can download one.
• Or download FragPipe-12.1.zip.
  • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
• Or download the FragPipe-12.1.jar.
  • You can start the jar file with java -jar FragPipe-12.1.jar or start javaw -jar FragPipe-12.1.jar if you prefer to not have the console window open.
    If Java is configured to auto-run .jar files, double clicking might also work.

Linux/MacOS users

• Either download FragPipe-12.1.zip, which contains FragPipe shell script to start the program
• Or download the FragPipe-12.1.jar and run with java -jar FragPipe-12.1.jar.

Changelog:

v12.1:

• IMQuant fixes after initial release.

v12.0:

• Add IMQuant - quantitation for timsTOF.
• PTMShepherd updates - in-depth PTM analysis and reporting.
• Fix running FragPipe without an internet connection.
• Choice of default enzyme specifications in MSFragger config.

v11.0:

• Parallel execution engine. Used only for PeptideProphet now, utilizing all CPU cores.
• DIA-Umpire requires MSConvert from ProteoWizard on Linux.