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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

Finding same mass peaks and inserting the appropriate shift vectors. Only one shift vector is accepted per chromatogram compound.
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Figure 4: Finding same mass peaks and inserting the appropriate shift vectors. Only one shift vector is accepted per chromatogram compound.

Mentions: We will discuss in more detail the functionality of the dual view window (figures 3 and 4), since it provides a semi-automated way to compare two contour plots, and find the differences between the two chromatograph runs. After clicking the dual view button in the main window, a dialog panel opens in order to select two mixes from the parsed ones. When the selection is made, the dual view window opens. It contains the two contour plots, which are superimposed, as well as the chromatograms of the mixes. A problem in LC-MS is that between different chromatograph runs of even the same peptide mix, there may be slight differences in the compounds' elution times (i.e. same compounds appear at slightly different times in the chromatograms). In order to eliminate these time differences, it is possible to insert shift vectors manually, through the dual view window. The application can then automatically compare the two plots and find the similarities and differences between the mass peaks, as well as the chromatogram compounds. There are parameters that can be set in order to control the leniency of that matching process. The results can be viewed through assimilated quantification tables and bar figures.


'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)

Finding same mass peaks and inserting the appropriate shift vectors. Only one shift vector is accepted per chromatogram compound.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Finding same mass peaks and inserting the appropriate shift vectors. Only one shift vector is accepted per chromatogram compound.
Mentions: We will discuss in more detail the functionality of the dual view window (figures 3 and 4), since it provides a semi-automated way to compare two contour plots, and find the differences between the two chromatograph runs. After clicking the dual view button in the main window, a dialog panel opens in order to select two mixes from the parsed ones. When the selection is made, the dual view window opens. It contains the two contour plots, which are superimposed, as well as the chromatograms of the mixes. A problem in LC-MS is that between different chromatograph runs of even the same peptide mix, there may be slight differences in the compounds' elution times (i.e. same compounds appear at slightly different times in the chromatograms). In order to eliminate these time differences, it is possible to insert shift vectors manually, through the dual view window. The application can then automatically compare the two plots and find the similarities and differences between the mass peaks, as well as the chromatogram compounds. There are parameters that can be set in order to control the leniency of that matching process. The results can be viewed through assimilated quantification tables and bar figures.

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