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Welcome to the ProteinClusterQuant wiki!

• Executing ProteinClusterQuant:

ProteinClusterQuant software is a Java command line tool that can be run in two different modes: analysis mode or comparison mode. * Analysis mode: this mode is the main execution mode of ProteinClusterQuant. It takes an input parameters file as input and performs the analysis. In order to run this mode, provide with the option -f the setup.properties file with the appropriate content:
java -jar pcq.jar -f setup.properties

* **[[Comparison mode|Comparison mode]]**: the purpose of this mode is just to compare up to 3 protein-peptide networks generated with the `analysis mode`. In order to run this mode, add the option `-c` and change the setup.parameters file by a [[comparison_file.txt|Comparison mode#input parameters file]]:   
`java -jar pcq.jar -c -f comparison_file.txt`

• Input parameters files:

  Depending on the execution mode a different input parameter file is needed:

  • analysis mode: Input file for analysis mode
  • comparison mode: Input file for comparison mode

• Classification schema

• XGMML output files

• Setting up SanXot with PCQ

• Comparison of surface accessibility in multiple samples