MS Ana

MS Ana is a scoring system to identify peptides in tandem mass spectrometry data using a library of previously identified spectra. Furthermore, MS Ana can create decoy spectral libraries that are to allow for validation of results using the target-decoy approach.


This software is especially designed to work with high accuracy tandem mass spectra and modern spectral libraries build from high accuracy tandem mass spectra. By using a suitable library you can achieve higher sensitivity and increased processing speed compared to traditional database search. Identifications from MS Ana are also highly accurate, as we observe a strong overlap with identifications from database search algorithms like SEQUEST, as well as gold-standard spectral library search algorithm SpectraST.
Manuscript in preparation.

Installation of MS Ana for Proteome Discoverer 2.1 or 2.2

The Proteome Discoverer Node of MS Ana can be used with Thermo Scientific Proteome Discoverer 2.1 or Thermo Scientific Proteome Discoverer 2.2. To install MS Ana for Proteome Discoverer please perform the following steps:

  1. Download the latest installer for your Proteome Discoverer version here:
  2. Make sure that Proteome Discoverer is closed
  3. Extract the contents of the .zip archive and run the setup .exe
  4. Follow the installation instructions and carefully read the license agreement
  5. Restart Proteome Discoverer

MS Ana is now ready for use in Proteome Discoverer! For detailed documentation please refer to the MS Ana user manual and example workflow which are included with the download.

Please note: If you are experiencing problems during the installation because of Windows security services you need to use the provided certificate to add FHOÖ & IMP as a trusted software source. Double-click the FHOOE_IMP_CERT.cer, then choose ‘Install Certificate...’ and follow the instructions on screen.

Adding Spectral Libraries to Proteome Discoverer

To run a workflow with MS Ana you must first add a spectral library using the Spectral Library interface in Proteome Discoverer. Suitable libraries for different standard organisms can be downloaded from the NIST website. In Proteome Discoverer go to Administration, Maintain Spectral Libraries, (+) Add. Then select the .msp file to start importing the spectral library.

Please note: The latest spectral libraries from NIST cannot be imported in Proteome Discoverer version 2.2 or earlier. We provide a quick fix for this in the form of a Windows PowerShell Script. Copy the fix_msp.ps1 from the MS Ana download into the directory with the spectral libraries. Right-click the fix_msp.ps1 and select 'Run with PowerShell' to execute the script. A dialog will ask for confirmation before the script creates fixed copies of the libraries. Progress is displayed in the PowerShell window and a notification appears once the process is finished. You can then add the newly created *_fix.msp libraries file to Proteome Discoverer.


This research project is a collaboration of the Protein Chemistry Group at the IMP, Vienna and the Bioinformatics Research Group at the FH Upper Austria, Hagenberg Campus. For any further questions, bug reports, or ideas please contact: Sebastian Dorl, Viktoria Dorfer, Stephan Winkler, Karl Mechtler, or post your comment in the IMP Nodes for Proteome Discoverer Google Group.