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, especially with MS Amanda 2.0. 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.


Elutator is a new tool to validate PSMs identified with MS Amanda. It is based on the principles of Percolator but uses an extended set of features, especially suitable for MS Amanda search results. These features include, for example, additional ion series and mass recalibrations for precursor and fragment ions. Elutator can be used with both, a combined target and decoy database or a forward and an automatically generated decoy database. FDR threshold calculation can be applied either on PSM or on peptide level.

Installation of MS Amanda 2.0 & Elutator for Proteome Discoverer 2.1

We have developed a new, significantly faster version of our MS Amanda algorithm: MS Amanda 2.0.

The Proteome Discoverer Nodes of MS Amanda 2.0 and Elutator can be used with Thermo Scientific Proteome Discoverer 2.1. To install MS Amanda 2.0 and Elutator, please perform the following steps:

MS Amanda 2.0 and Elutator should now be successfully installed on your computer. Attention: this is the new version of MS Amanda, your old MS Amanda workflows will not work with this version! If you want to use your old workflows, please install MS Amanda 1.0 available within the PD Nodes Collection.

Installation of MS Amanda 1.0 for Proteome Discoverer 1.3, 1.4, and 2.1

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.

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!


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.