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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 (, 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.

ProCon is also available on our pre-configured Proteomics Toolbox and can be executed on out high-performance compute environment offering enough memory and disk storage space. For using the Proteomics ToolBox please contact us.

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 0.9.804 needs Java 13 or higher.
Download the proper zip package, unzip it ( C:\ and follow the user installation and configuration instructions in .\documentation\ProCon_user_manual.pdf.


Paper download link:

ProCon - PROteomics CONversion tool



Link to de.NBI
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Link to BioInfra.Prot
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