Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows

Bioinformatics. 2011 Apr 15;27(8):1183-4. doi: 10.1093/bioinformatics/btr081. Epub 2011 Feb 16.


We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily.

Availability and implementation: Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Proteomics / methods*
  • Software*
  • Tandem Mass Spectrometry / methods*
  • User-Computer Interface
  • Workflow