MS Amanda

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).

Installation of MS Amanda for Proteome Discoverer

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.

Installation of MS Amanda 3.0 Standalone

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 MSAmanda3.0 folder. For Mac and Linux users this folder is usually created in your home directory, for Windows users it should be created in C:\ProgramData, which is a hidden folder (see How to view hidden files).
• Please download the latest version for Windows, Linux, and Mac here:
  • Latest MS Amanda Standalone version for Windows: download
  • Latest MS Amanda Standalone version for Linux: download
  • Latest MS Amanda Standalone version for macOS: download

Older MS Amanda versions can be found here.

Installation on Windows

• Right click on the downloaded .zip file and select the menu item Properties in the context menu.
• If visible, click Unblock at the bottom right of the Properties window.
• Click OK to close the Properties window.
• Extract the downloaded .zip file.
• Open a commandline and navigate to the extracted MS Amanda folder.
• Run MS Amanda by calling: bash MSAmanda.exe -s spectrumFile -d proteinDatabase -e settings.xml [-f fileformat] [-o outputfilename]

Installation on Linux

• 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: bash ./MSAmanda -s spectrumFile -d proteinDatabase -e settings.xml [-f fileformat] [-o outputfilename]

Installation on macOS

• 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: bash ./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 !

Getting Help

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.

Known Issues

List of known issues

Citing

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

Contact

• [preferred] proteomics@fh-hagenberg.at
• marina.strobl@fh-hagenberg.at
• micha.birklbauer@fh-hagenberg.at
• louise.buur@fh-hagenberg.at
• viktoria.dorfer@fh-hagenberg.at