FragPipe v16.0

Downloading

• The zip (FragPipe-16.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-16.0.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:

v16.0:

• Require MSFragger 3.3+
• Require Philosopher 4.0.0+
• Upgrade Crystal-C to 1.4.2
• Upgrade IonQuant to 1.7.5
• Upgrade TMT-Integrator to 3.0.0
• Upgrade PTMShepherd to 1.1.0
• Upgrade batmass-io to 1.23.4
• Add Percolator as an alternative to PeptideProphet
• Change how files are passed to ProteinProphet, IonQuant, and EasyPQP to bypass the Windows command length limitation
• Various minor bug fixes and improvements