CroCo

CroCo converts multiple data format from cross-linking mass spectrometry software tools to xTable format (in csv format).

Important links

You can find the latest release including compiled versions at https://github.com/cschmidtlab/CroCo/releases/latest/.

The full documentation for Croco is available at https://cschmidtlab.github.io/CroCo/.

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 is distributed as graphical program to be run from an executable and as a Python module to be integrated into workflows.

System requirements

For the GUI:

• Windows 10

For the Python module:

• Python3 with the following modules installed
  • pandas
  • numpy
  • re

Usage

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.

Input formats

Kojak

• Load file(s): e.g. FILENAME.kojak.txt
• Provide: Rawfile title (e.g. FILENAME.raw)

Kojak & Percolator

For this script to work, the unpercolated Kojak file (e.g. FILENAME.kojak.txt) has to be in the same directory as the percolated file.

• Load file(s): e.g. FILENAME.validated.txt
• Provide: Rawfile title (e.g. FILENAME.raw)

StavroX

• Load file(s): StavroX results file (e.g. FILENAME.csv)
• Provide: Path to SSF-file

Xi

• Load file(s): Path to Xi results file (e.g. FILENAME_XiVersion1.6.739.csv)

Xi & XiFDR

• Load file(s): Path to xiFDR file (e.g. FILENAME_5_FDR_PSM_xiFDR1.0.22.csv)
• Provide: Path to corresponding Xi results file (e.g. FILENAME_XiVersion1.6.739.csv)

pLink1

• Load file(s) (folder): sample folder within the pLink results dir (e.g. 2.report\sample1)

pLink2

• Load file(s) (folder): reports folder within the pLink results (e.g. pLink_task_2018.06.12.09.33.10\reports)

xQuest

• Load file(s): xQuest results file exported as csv (e.g. FILENAME_xquest.csv)

Output formats

DynamXL

• Write to: Directory in which to save the DynamXL file

customTable

• Write to: Directory in which to save the customTable csv file
• Provide: customTable template file

customTable Format

[header]
Protein 1, Protein 2
[data]
[prot1], [prot2]
[footer]
This is the footer of the file

• Everything between [header] and [data] is considered the header and is printed once on top of the output file
• In the [data] block columns identified by their xTable header are written in substitution of the header name.
  • E.g. instead of [prot1], [prot2] a line like SPA_STAAU, IgG4_heavy is written for every line in the xTable file
  • Everything not enclosed in brackets will be written as is
  • If an invalid header name is given in brackets, the program will stop

pLabel

• Write to: Directory in which to save the pLabel file
• Provide: Directory containing the corresponding mgf-files
  • The mgf filenames must match the rawfile names given in the xTable

xTable

• Write to: Directory in which to save xTable file

xVis

• Write to: Directory in which to save xVis file

xWalk

• Write to: Directory in which to save xWalk file
• Provide:
  • PDB to map xlinks: Name of a PDB file that should be analysed by xWalk
  • PDB Atom code (Text): A PDB atom code (e.g. CB) that should be used for distance calculation

xiNet

• Write to: Directory in which to save xiNez file

Version History

0.5

• customTable support

0.4

• Added pLabel support
• Options Window on GUI