This article is part of the supplement: European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

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'Brukin2D': a 2D visualization and comparison tool for LC-MS data

Dimosthenis Tsagkrasoulis12, Panagiotis Zerefos3, George Loudos2, Antonia Vlahou3, Marc Baumann1* and Sophia Kossida2*

Author Affiliations

1 Protein Chemistry/Proteomics Laboratory and the Neuroscience Research Program Biomedicum Helsinki P.O. Box 63 (Haartmaninkatu 8) 00014 University of Helsinki, Finland

2 Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece

3 Biotechnology Division, Proteomics Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece

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BMC Bioinformatics 2009, 10(Suppl 6):S12  doi:10.1186/1471-2105-10-S6-S12

Published: 16 June 2009



Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spectra that correspond to its compounds is the focus of this work.


The in-house developed 'Brukin2D' software, built in Matlab 7.4, which is presented here, uses the compound data that are exported from the Bruker 'DataAnalysis' program, and depicts the mean mass spectra of all the chromatogram compounds from one LC-MS run, in one 2D contour/density plot. Two contour plots from different chromatograph runs can then be viewed in the same window and automatically compared, in order to find their similarities and differences. The results of the comparison can be examined through detailed mass quantification tables, while chromatogram compound statistics are also calculated during the procedure.


'Brukin2D' provides a user-friendly platform for quick, easy and integrated view of complex LC-MS data. The software is available at webcite.