From European Proteomics Academy
Jump to navigation Jump to search
Original author(s) V Dorfer, P Pichler, T Stranzl, J Stadlmann, T Taus, S Winkler, K Mechtler
Citation Dorfer et al., J Proteome Res. 2014, 13(8):3679-84
Usage Details
Input format MGF
Output format text, mzIdentML
Software Details
Operating system Windows, Linux, Mac OSX
License special license
Initial release 01.01.2000
Development status active

MSAmanda is a free search engine developed at the IMP[1]. Most importantly it is directly integrated into ThermoFisher's ProteomeDiscoverer and SearchGUI.


MSAmanda was originally developed to replace Mascot in Karl Mechtler's lab at IMP. It is optimized to work with high-resolution data.

Supported Operating Systems

MSAmanda is available in ProteomeDiscoverer which runs on windows. Additionally, a command line version running natively on Windows and using mono on linux and OS X is available as well.


Installing MS Amanda

To install MSAmanda as a stand-alone search engine.

Running a search

To run a search simply navigate to the folder where MSAmanda is installed

mono MSAmanda.exe /path/to/my/species.fasta /path/to/my/search.mgf /path/to/my/settings.xml


  1. Dorfer et al. J Proteome Res. 2014, 13(8):3679-84 pubmed