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.
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.
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).
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 0.9.642, June 20th, 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.