MS Andrea

Documentation ​

MS Andrea is an open modification search engine that is designed to directly identify peptide modifications on the PSM level. MS Andrea uses a sequence tag-based approach for filtering peptide candidates before score based filtering and final scoring using the MS Amanda scoring function.

Installation and Usage ​

Installation on Windows ​

  • Download MS Andrea for Windows here: download
  • Extract the downloaded .zip file.
  • Open a commandline and navigate to the extracted MS Andrea folder.
  • Run MS Andrea by calling:
    bash
    MSAndrea.exe -s spectrumFile -d proteinDatabase -e settings.xml [-o outputfilename]

Installation on Linux ​

  • Download MS Andrea for Linux here: download
  • Extract the MS Andrea archive and navigate to the extracted folder in a terminal.
  • MS Andrea for Linux can be used the same way as on Windows platforms.
  • Run MS Andrea by calling:
    bash
    ./MSAndrea -s spectrumFile -d proteinDatabase -e settings.xml [-o outputfilename]

Installation on macOS ​

  • Download MS Andrea for macOS here: download
  • Extract the MS Andrea archive and navigate to the extracted folder in a terminal.
  • MS Andrea for macOS can be used the same way as on Windows platforms.
  • Run MS Andrea by calling:
    bash
    ./MSAndrea -s spectrumFile -d proteinDatabase -e settings.xml [-o outputfilename]

Limitations ​

Currently, MS Andrea does not provide quantification or support for the associated labeling strategies (TMT, iTRAQ, SILAC)

Getting Help ​

If something is not working or if you need help with MS Andrea, please contact us! You can open an issue here or start a discussion here. We are usually fast to respond on GitHub and other users might be able to help too! Alternatively, you can contact us by e-mail (see Contact).

Citing ​

If you are using MS Andrea please cite:

text
Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches 
Louise M. Buur, Stephan Winkler, Viktoria Dorfer 
Journal of Proteome Research. 2026
DOI: https://doi.org/10.1021/acs.jproteome.6c00296

Copyright © 2026 Louise M. Buur