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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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Related in: MedlinePlus

Contour plot window. Screenshot of a zoomed in region, with overlapping information for some of the mass peaks. This information can be viewed in an undocked plot window, by clicking on a spot of interest.
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Figure 2: Contour plot window. Screenshot of a zoomed in region, with overlapping information for some of the mass peaks. This information can be viewed in an undocked plot window, by clicking on a spot of interest.

Mentions: In addition, the main window incorporates three plot windows, which show the contour plot (figure 2), the chromatogram of the selected analysis and the compound mass spectrum of the selected compound. The quantification table includes detailed information for each mass peak in the plot and the dual view window allows the comparison of two mixes. Both can be accessed through the appropriate buttons in the main window.


'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)

Contour plot window. Screenshot of a zoomed in region, with overlapping information for some of the mass peaks. This information can be viewed in an undocked plot window, by clicking on a spot of interest.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Contour plot window. Screenshot of a zoomed in region, with overlapping information for some of the mass peaks. This information can be viewed in an undocked plot window, by clicking on a spot of interest.
Mentions: In addition, the main window incorporates three plot windows, which show the contour plot (figure 2), the chromatogram of the selected analysis and the compound mass spectrum of the selected compound. The quantification table includes detailed information for each mass peak in the plot and the dual view window allows the comparison of two mixes. Both can be accessed through the appropriate buttons in the main window.

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
Related in: MedlinePlus