The CroCo cross-link converter

CroCo converts multiple data format from cross-linking mass spectrometry software tools to xTable format (in csv format). It is distributed as graphical programme to be run from an executable and as a Python module to be integrated into workflows.

System requirements

For the GUI:

• Windows 7/8/10

For the Python module:

Python==3.6.5
numpy==1.14.2
wxPython==4.0.2a1.dev3717+d4bd2fe
pandas==0.22.0

Usage of the GUI

For the conversion of data of every input program, a slightly different usage is required for gathering all data that are required for xTable. In general, information that is not present in the input files will be asked from the user.

For detailed information how to use the GUI, see The graphical User-Interface.

Supported formats

Currently the following input formats are supported:

• Kojak
• Kojak with Percolator
• StavroX
• Xi
• Xi + XiFDR
• pLink1 (discontinued)
• pLink2
• xQuest
• xTable

Input files can be converted into different formats typically used for analysis of cross-linking data (e.g. visualisation, spectra annotation, …). The following formats are supported:

• DynamXL
• customTable
• pLabel
• xTable
• xVis
• xWalk
• xiNet

CroCo Documentation contents

• Functions documentation for read functions
  • Kojak
  • pLink
  • StavroX
  • Xi
  • xQuest
• Functions documentation for write functions
  • xTable
  • xWalk
  • xVis
  • customTable
  • DynamXL
  • xiNET
  • pLabel
• The graphical User-Interface
• General usage
• Starting the CroCo GUI from Python
• The CroCoWX Class

Indices and tables

• Index
• Module Index
• Search Page