MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.
The MS Amanda 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 since 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), Dorfer et al. Rapid Commun Mass Spectrom. 2021, 35(11) and Buur et al. J Proteome Res. 2024, 23(8).
The Proteome Discoverer Node of MS Amanda can be used with Thermo Scientific's Proteome Discoverer. To install MS Amanda, please perform the following steps:
- Close Proteome Discoverer
- Download the latest MS Amanda installer:
- Latest MS Amanda 3.0 version for Proteome Discoverer 3.1: download
- Latest MS Amanda 2.0 version for Proteome Discoverer 3.0: download
- Latest MS Amanda 2.0 version for Proteome Discoverer 2.5: download
- Latest MS Amanda 2.0 version for Proteome Discoverer 2.4: download
- Latest MS Amanda 2.0 version for Proteome Discoverer 2.3: download
- Latest MS Amanda 2.0 version for Proteome Discoverer 2.2: download
- Latest MS Amanda 2.0 version for Proteome Discoverer 2.1: download
- Follow the installation instructions and carefully read the license agreement
- Restart Proteome Discoverer
MS Amanda 2.0/3.0 should now be successfully installed on your computer!
Older MS Amanda versions for Proteome Discoverer can be found here.
MS Amanda 3.0 Standalone can be used from the command line or called from any already established proteomics pipelines.
To install MS Amanda 3.0 please perform the following steps:
- Carefully read the license agreement and proceed only if you agree to the terms and conditions.
- Attention: Please delete all subfolders in the
MSAmanda3.0folder. For Mac and Linux users this folder is usually created in your home directory, for Windows users it should be created inC:\ProgramData, which is a hidden folder (see How to view hidden files). - Please download the latest version for Windows, Linux, and Mac here:
Older MS Amanda versions can be found here.
- Right click on the downloaded
.zipfile and select the menu itemPropertiesin the context menu. - If visible, click
Unblockat the bottom right of thePropertieswindow. - Click
OKto close thePropertieswindow. - Extract the downloaded
.zipfile. - Open a commandline and navigate to the extracted MS Amanda folder.
- Run MS Amanda by calling:
MSAmanda.exe -s spectrumFile -d proteinDatabase -e settings.xml [-f fileformat] [-o outputfilename]
- The new version of MS Amanda no longer requires
mono. - Extract the MS Amanda archive and navigate to the extracted folder in a terminal.
- MS Amanda for linux can be used the same way as on windows platforms.
- To run MS Amanda please call:
./MSAmanda -s spectrumFile -d proteinDatabase -e settings.xml [-f fileformat] [-o outputfilename]
- The new version of MS Amanda no longer requires
mono. - Extract the MS Amanda archive and navigate to the extracted folder in a terminal.
- MS Amanda for Mac can be used the same way as on windows platforms.
- To run MS Amanda please call:
./MSAmanda -s spectrumFile -d proteinDatabase -e settings.xml [-f fileformat] [-o outputfilename]
MS Amanda 3.0 Standalone is now ready for use!.
In addition, MS Amanda Standalone is also integrated in SearchGUI and PeptideShaker !
In case something isn't working or if you need any help with MS Amanda, please don't hesitate to reach out to us! Please check out the MS Amanda Google Group! Alternatively, you can open up an issue here or start a discussion there. We are usually fast to respond on GitHub and other users might be able to help too! Alternatively, you can always drop us an email at the addresses below.
If you are using MS Amanda please cite:
MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra
Viktoria Dorfer, Peter Pichler, Thomas Stranzl, Johannes Stadlmann, Thomas Taus, Stephan Winkler, and Karl Mechtler
Journal of Proteome Research 2014 13 (8), 3679-3684
DOI: 10.1021/pr500202e
and/or
MS Amanda 2.0: Advancements in the standalone implementation
Viktoria Dorfer, Marina Strobl, Stephan Winkler, and Karl Mechtler
Rapid Communications in Mass Spectrometry 2021 35 (e9088)
DOI: 10.1002/rcm.9088
and/or
MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0
Louise M. Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, and Ralf Gabriels
Journal of Proteome Research 2024 23 (8), 3200-3207
DOI: 10.1021/acs.jproteome.3c00785