FragPipe v14.0

Downloading

• The zip (FragPipe-14.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-14.0.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:

v14.0:

• Add PTMProphet.
• Upgrade Crystal-C to 1.3.2.
• Upgrade IonQuant to 1.4.4.
• Upgrade TMT-Integrator to 2.1.4.
• Upgrade PTM-Shepherd to 0.4.0.
• Require MSFragger 3.1+.
• Retire MsAdjuster. Using MSFragger's built-in isotope error correction module.
• New button to add contaminants and decoys to a fasta.
• Correct the path in interact-*.pep.xml file.
• Print related references after the job.