FragPipe v15.0

Downloading

• The zip (FragPipe-15.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-15.0.zip) contains a Java runtime for Windows only.

Running

• Unzip the file
• In /bin subdirectory you will find a shell script for Linux, bat file for Windows and an exe file for Windows### Note to Windows users
  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.

Changelog:

v15.0:

• Require MSFragger 3.2+.
• Upgrade IonQuant to 1.5.5.
• Upgrade TMT-Integrator to 2.4.0.
• Upgrade PTM-Shepherd to 1.0.0.
• Upgrade DIA-Umpire-SE to 2.2.1, which now supports mzML, mzXML, and raw formats natively.
• Automated MSFragger download.
• Add a button to install/upgrade EasyPQP.
• Automatically detect data types for .d and .raw.
• Additional options added for EasyPQP
• Cosmetic changes for DIA-Umpire, IonQuant, TMT-Integrator tabs
• Remove 'process each experiment separately' checkbox.
• Do not allow space in the path of MSFragger and Philosopher.
• Follow XDG specification for Unix.
• Upgrade the bundled JRE to 11.