FragPipe v19.1

Downloading

• The zip (FragPipe-19.1.zip) doesn't contain Java, you will need Java 9+ to run.

• The other zip with -jre- in its name (FragPipe-jre-19.1.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:

v19.1:

• Require MSFragger 3.7+
• Require Philosopher 4.8.0+
• Require IonQuant 1.8.10+
• Require EasyPQP 0.1.34+
• Add 'write uncalibrated mgf' checkbox
• Add Add iTRAQ4-phospho workflow
• Update iTRAQ4 workflow
• Rename 'combined_annotation.tsv' to 'experiment_annotation.tsv'
• Update the format of experiment_annotation.tsv
• Allow MSBooster for mass-offset search
• In GUI mode, do not load the tools' config paths from the workflow file
• Upgrade Crystal-C to 1.5.1
• Upgrade MSBooster to 1.1.11
• Upgrade DIA-Umpire to 2.3.2
• Various minor bug fixes and improvements