FragPipe v23.1

Downloading

• The FragPipe-23.1-installer.exe is for Windows. You will need to install it. Java runtime is bundled and Python will be installed automatically.
• The FragPipe-23.1-linux.zip is for Linux. You will need Java 11+ to run.
• The docker image is available at https://hub.docker.com/r/fcyucn/fragpipe
• NOTE: Non-academic users (including those with an existing commercial license from the University of Michigan) must visit Fragmatics at www.fragmatics.com or email info@fragmatics.com to purchase or confirm their license and access the tools.

Running

• In Windows, install FragPipe using the installer. Then double-click the FragPipe-23.1.exe file.
• In Linux, unzip the file. In bin subdirectory you will find a shell script for Linux

Changelog:

v23.1:

• FragPipe GUI:
  • New metaproteomics database generation module (beta)
  • Add Prosit MultiFrag model to the MSBosoter's dropdown menu
  • Do not run Abacus when IonQuant is used in the TMT intensity extraction
  • Add intensity mode to IonQuant panel
  • Add the 'export log' back
  • Optimize the memory footprint
• MSFragger version 4.3 full changelog can be found in https://msfragger.nesvilab.org/CHANGELOG.html
• IonQuant version 1.11.11 full changelog can be found in https://ionquant.nesvilab.org/CHANGELOG.html
• diaTracer version 1.3.3 changelog can be found in https://diatracer.nesvilab.org/CHANGELOG.html
• Various bug fixes and performance improvements
• Miscellaneous:
  • Require Java 11+
  • Require MSFragger 4.3+
  • Require IonQuant 1.11.11+
  • Require diaTracer 1.3.3+
  • Require Python 3.9, 3.10, or 3.11
  • Require EasyPQP 0.1.52+
  • Upgrade Crystal-C to 1.5.9
  • Upgrade MSBooster to 1.3.17
  • Upgrade Philosopher to 5.1.2
  • Upgrade PTM-Shepherd to 3.0.2