Proteomics Conversion Tool (ProCon)
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Proteomics Conversion Tool (ProCon)

The Proteomics Conversion Tool was prototyped within the EU funded "Coordination Action" ProDaC (grant number LSHG-CT-2006-036814). New features were added within the EU funded "Collaborative Project" ProteomeXchange (grant number 260558). Now it is supported by de.NBI (http://www.denbi.de), a project funded by the German Federal Ministry of Education and 414 Research (BMBF), grant number FKZ 031 A 534A.

ProCon is a Java application for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats.

Current functionality

ProCon allows the conversion of:
- peptide information of Sequest® .out (Thermo Scientific, Waltham, MA, USA) or Comet .out files into mzIdentML 1.1
- Proteome Discoverer® 1.1, 1.2, 1.3 + 1.4 (Thermo Scientific, Waltham, MA, USA) .msf (mass spec format) (and .prot.xml for PD1.1 and PD1.2) file information to mzIdentML 1.1
- ProteinScape® 1.3 (Bruker Daltonik GmbH, Bremen, Germany) results to PRIDE XML
- ProteinScape® 2.1 (Bruker Daltonik GmbH, Bremen, Germany) results to mzIdentML 1.1

For more details about ProCon please download our poster or the ProCon paper (coming soon).

Starting ProCon

ProCon is written in Java 7 and tested with Java (TM) Java 7 Update 80 and Java 8 Update 77. The 64bit version enabling the use of more than 3.2 GB memory is recommended.
Download the current zip package (version 0.9.641, April 6th, 2016), unzip it (e.g.to C:\ProCon_dist-0.9.xyz) and follow the user installation and configuration instructions in .\documentation\ProCon_user_manual.pdf.

Download:

Paper download link:

ProCon - PROteomics CONversion tool

Contact: