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Bioinformatics Advance Access originally published online on April 3, 2008
Bioinformatics 2008 24(10):1310-1312; doi:10.1093/bioinformatics/btn116
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins

Janosch Hennig 1,*, Klaus D. M. Hennig 2 and Maria Sunnerhagen 1

1Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden and 2Department of Informatics, Gabriele-von-Bülow Gymnasium, DE-13509 Berlin, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: In structural biology and -genomics, nuclear magnetic resonance (NMR) spectroscopy and crystallography are the methods of choice, but sample requirements can be hard to fulfil. Valuable structural information can also be obtained by using a combination of limited proteolysis and mass spectrometry, providing not only knowledge of how to improve sample conditions for crystallization trials or NMR spectrosopy by gaining insight into subdomain identities but also probing tertiary and quaternary structure, folding and stability, ligand binding, protein interactions and the location of post-translational modifications. For high-throughput studies and larger proteins, however, this experimentally fast and easy approach produces considerable amounts of data, which until now has made the evaluation exceedingly laborious if at all manually possible. MTMDAT, equipped with a browser-like graphical user interface, accelerates this evaluation manifold by automated peak picking, assignment, data processing and visualization.

Availability: MTMDAT can be downloaded from the following page: http://www.cms.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat by clicking on the corresponding links (windows- or unix-based) together with the manual and example files. The program is free for academic/non-commercial purposes only.

Contact: janhe{at}ifm.liu.se

Associate Editor: Anna Tramontano

Received on February 19, 2008; revised on March 14, 2008; accepted on March 29, 2008

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