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

Tsagkrasoulis D, Zerefos P, Loudos G, Vlahou A, Baumann M, Kossida S - BMC Bioinformatics (2009)

Bottom Line: Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Protein Chemistry/Proteomics Laboratory, Neuroscience Research Program, Biomedicum Helsinki, P.O. Box 63 (Haartmaninkatu 8) 00014 University of Helsinki, Finland. piv07010@di.uoa.gr

ABSTRACT

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.

Conclusion: '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.

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'Brukin2D' main application window. Parse XML, Export and Contour Parameters panels can be seen in the upper left corner. The main window at the right shows the contour plot. The red and cyan diagrams correspond to the chromatogram and the mass spectrum respectively.
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Figure 1: 'Brukin2D' main application window. Parse XML, Export and Contour Parameters panels can be seen in the upper left corner. The main window at the right shows the contour plot. The red and cyan diagrams correspond to the chromatogram and the mass spectrum respectively.

Mentions: The main window consists of different panels (figure 1). A short description of the functionality of these panels follows:


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

Tsagkrasoulis D, Zerefos P, Loudos G, Vlahou A, Baumann M, Kossida S - BMC Bioinformatics (2009)

'Brukin2D' main application window. Parse XML, Export and Contour Parameters panels can be seen in the upper left corner. The main window at the right shows the contour plot. The red and cyan diagrams correspond to the chromatogram and the mass spectrum respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697635&req=5

Figure 1: 'Brukin2D' main application window. Parse XML, Export and Contour Parameters panels can be seen in the upper left corner. The main window at the right shows the contour plot. The red and cyan diagrams correspond to the chromatogram and the mass spectrum respectively.
Mentions: The main window consists of different panels (figure 1). A short description of the functionality of these panels follows:

Bottom Line: Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Protein Chemistry/Proteomics Laboratory, Neuroscience Research Program, Biomedicum Helsinki, P.O. Box 63 (Haartmaninkatu 8) 00014 University of Helsinki, Finland. piv07010@di.uoa.gr

ABSTRACT

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.

Conclusion: '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.

Show MeSH