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


RESULTS
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.


CONCLUSIONS
'Brukin2D' provides a user-friendly platform for quick, easy and integrated view of complex LC-MS data. The software is available at http://www.bioacademy.gr/bioinformatics/Brukin2d/index.html.
Tsagkrasoulis
Dimosthenis
D
Protein Chemistry/Proteomics Laboratory, Neuroscience Research Program, Biomedicum Helsinki, P.O. Box 63 (Haartmaninkatu 8) 00014 University of Helsinki, Finland. piv07010@di.uoa.gr
Zerefos
Panagiotis
P
Loudos
George
G
Vlahou
Antonia
A
Baumann
Marc
M
Kossida
Sophia
S
D002853:Chromatography, Liquid; D030562:Databases, Protein; D013058:Mass Spectrometry; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D014584:User-Computer Interface
D011506:Proteins