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Automated analysis and visualisation of mass spectrometry data for tertiary and quaternary structure probing of proteins and protein complex structure modeling

This software has been developed by Klaus Hennig (Berlin, Germany) and Janosch Hennig. It facilitates fast and detailed evaluation of mass spectrometry data of limited proteolysis experiments to probe the tertiary structure of proteins and even complex formation with other proteins, ligands, and surfaces. Domain arrangements can be probed as well as stability on residue level.

The results can be plotted as time-course profiles, where degradation of unstable or accumulation of stable peptide fragments can be visualised, or as a 3D view (see figure) where the relative cleavage propensities of each cleavage site are displayed. For more information on the theoretical background you can check the publications and references therein.


As of July 2012, the new MTMDAT-HADDOCK is available, where you can get from limited protelysis/mass spectrometry data of two proteins and their complex, a complete parameter file to be used on the file-upload interface of the HADDOCK web server. This enables high-throughput protein complex structure modelling. Furthermore, the usage has been improved.

The program is free (for academic/non-commercial purposes only) and can be downloaded by clicking on the link below (two links, one for windows and one fur unix-based machines), including a manual and example files. Please read the license agreement below and send it back signed to the address given below, especially if you want to have help.

However, if you intend to you use MTMDAT-HADDOCK for commercial purposes you are welcome to contact Janosch Hennig (see below) to discuss details of usage (e.g. an evaluation license agreement etc.).

Send it to: janhe@ifm.liu.se
or fax to: 004613-281399 (please notify by e-mail that you sent a fax)
snailmail: Janosch Hennig
               IFM/Kemi - Linköping University
               Campus Valla, Hus B
               SE-581 83

If you used MTMDAT-HADDOCK in your research, please cite the following:

Hennig, J., Hennig, K.D., and Sunnerhagen, M., (2008), MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins. Bioinformatics, 24(10):1310-312.

Hennig, J., de Vries, S.J., Hennig, K.D.M., Randles, L., Walters, K.J., Sunnerhagen, M. and Bonvin, A.M.J.J., (2012), MTMDAT-HADDOCK: high-throughput, data-driven protein complex structure modelling. Submitted.

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3D view of limited proteolysis data, analysed with mass spectrometry and evaluated by MTMDAT

Responsible for this page: Maria Sunnerhagen

Last updated: 06/19/13