FragPipe v17.0

FragPipe v17.0

Downloading

• The zip (FragPipe-17.0.zip) doesn't contain Java, you will need Java 1.8+ to run.

• The other zip with -jre- in its name (FragPipe-jre-17.0.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:

v17.0:

• Require MSFragger 3.4+
• Require Philosopher 4.1.0+
• Add MSBooster 1.0 for deep learning based rescoring (Validation)
• Add glycan assignment with FDR control (PTM)
• Add DIA quantification with DIA-NN 1.8 (DIA Quant tab)
• Support two enzymes and N-terminal cutting enzyme (MSFragger tab)
• Support DDA, DIA, GPF-DIA, and DIA-Quant data types
• Upgrade PTM-Shepherd to 1.2.5
• Upgrade DIA-Umpire to 2.2.3
• Upgrade IonQuant to 1.7.16
• Upgrade TMT-Integrator to 3.2.0
• Various minor bug fixes and improvements