MS Amanda & Elutator

MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.

About

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. (see bibtex)

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 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 for PD 2.1, please perform the following steps:

  1. Close Proteome Discoverer 2.1
  2. Please download the latest installer here: Installer for MSAmanda 2.0 and Elutator
  3. Follow the installation instructions and carefully read the license agreement
  4. Restart Proteome Discoverer 2.1

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 and MS Amanda 2.0 for Proteome Discoverer 2.2

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:

  1. Carefully read the license agreement and proceed only if you agree to the terms and conditions.
  2. Please download the stable version here (as .zip file):
  3. See the MS Amanda google group for information on latest changes.
  4. Right click on the downloaded .zip file and select the menu item Properties in the context menu.
  5. Click "Unblock" at the bottom right of the Properties window.

  6. Click "OK" and close the Properties window.
  7. Extract the downloaded .zip file.
  8. Shutdown Proteome Discoverer
  9. Copy all extracted files to the "System\Release" folder of your Proteome Discoverer Installation.
  10. For a standard installation of Proteome Discoverer 1.4 this is for instance C:\Program Files\Thermo\Discoverer 1.4\System\Release. If you cannot find the installation path, right click on the Proteome Discoverer shortcut on your Desktop or in your start menu and select the menu item "Properties". The location of your installation can be found in the "Target" definition:

  11. Run "AmandaInst.exe" or "UpdateMSAmandaInstallation.exe", respectively, in the folder System\Release.
  12. Restart Proteome Discoverer
  13. MS Amanda should now be successfully installed and appear as a node in the category "Sequence Database Search":

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:

  1. Carefully read the license agreement and proceed only if you agree to the terms and conditions.
  2. Please download the latest version here:

    • MS Amanda Standalone for Windows (MS Amanda v. 2.0.0.9695)
    • MS Amanda Standalone for Linux/Mac (MS Amanda v. 2.0.0.9706)
  3. Please check our google group for further information about latest changes.
  4. 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: "MSAmanda.exe myFile.mgf myDatabase.fasta settings.xml"
  5. Linux:
    • The mono runtime environment version 3.2.1 or higher and the libmono-system-core4.0-cil have to be installed. Some linux distributions already come with an installed mono. To check which version you have installed please run "mono -V" on a terminal.
    • You can install mono by running: "sudo apt-get install mono-runtime"
      and - if neccessary -
      "sudo apt-get install libmono-system-core4.0-cil"
    • 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, except that a preceding "mono" keyword is required before the MS Amanda call.
      To run MS Amanda please call: "mono MSAmanda.exe myFile.mgf myDatabase.fasta settings.xml"
  6. Mac:
    • The mono runtime environment version 3.10 or higher has to be installed and can be downloaded here as a Mac Package (.pkg).
    • 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, except that a preceding "mono" keyword is required before the MS Amanda call. To run MS Amanda please call: "mono MSAmanda.exe myFile.mgf myDatabase.fasta settings.xml"

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!

Contact

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.

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