Mass spectrometry, Protein Chemistry Facility
Research Institute of Molecular Pathology (IMP)
Institute of molecular biotechnology of the Austrian Academy of Sciences (IMBA)
Gregor Mendel Institute of Molecular Plant Biology (GMI)

PD-Nodes SimpatiQCo Software Tools Publications

MS Amanda

MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins. This algorithm is especially designed for high resolution and high accuracy tandem mass spectra. One advantage of MS Amanda is the high speed of spectrum identification, as it can achieve on average 1.5 ms per spectrum on well-resourced workstations. In addition, MS Amanda is also very accurate, as we observe a high overlap of identified spectra with gold-standard algorithms Mascot and SEQUEST.
To cite MS Amanda and for more detailed information on the algorithm please refer to Dorfer et al. J Proteome Res. 2014, 13(8):3679-84. You can find the bibtex entry here.

Installation of MS Amanda Standalone

MS Amanda Standalone can be used from the command line or called from any already established proteomics pipelines.

To install MS Amanda please perform the following steps:

MS Amanda Standalone is now ready for use! For detailed documentation please refer to the user manual for MS Amanda Standalone.

In addition, MS Amanda Standalone is also integrated in SearchGUI and PeptideShaker!

Installation of MS Amanda for Proteome Discoverer

The Proteome Discoverer Node of MS Amanda can be used with Thermo Scientific Proteome Discoverer v. 1.3, 1.4, or 2.X. To install MS Amanda, please perform the following steps:

A detailed description on how to use MS Amanda for Proteome Discoverer, on the parameters provided by MS Amanda, and how to filter results obtained with MS Amanda can be found in the MS Amanda Manual for PD.

A typical MS Amanda PD workflow can be found here.


This research project is a collaboration of the Protein Chemistry Group at IMP and the Bioinformatics Research Group at FH OÖ, Campus Hagenberg.
For any further questions, bug reports, ideas,... please contact Viktoria Dorfer, Sergey Maltsev, Stephan Winkler, or Karl Mechtler or post your comment in the MS Amanda Google Group.