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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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Results of the matching process – 50000 intensity minimum cutoff. Same as in figure 5 but with a 50000 intensity minimum cutoff.
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Figure 7: Results of the matching process – 50000 intensity minimum cutoff. Same as in figure 5 but with a 50000 intensity minimum cutoff.

Mentions: In this example, the peak matching procedure was repeated two more times by setting two different mass intensity minimums in the contour plots, in order to take into consideration only mass peaks with high intensity. This was done by returning to the main program window and refreshing the contour plots, in order to exclude mass peaks that had intensity lower than 10000 and 50000 each time. In the first case, the peaks that were left in the two mixes were 140 and 376, and in the second case, only 17 and 42 peaks had intensity above 50000. After creating the new contours, the same shift vectors were used and the peak matching process was repeated. The results can be seen in figure 6 and figure 7 respectively. The black columns in the compound percentage plots represent compounds that had no mass peaks with intensity greater than the minimum. It can be noticed that by keeping only high intensity peaks, the matching results are better, meaning that the percentage of the matched peaks is raised. Some slight differences in the compound correspondence between the first comparison and the other two are due to mass intensity differences that exist between same peaks of the two mixes (peaks from one mix may have intensity lower than the boundary, while their matched peaks from the other mix have higher).


'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)

Results of the matching process – 50000 intensity minimum cutoff. Same as in figure 5 but with a 50000 intensity minimum cutoff.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Results of the matching process – 50000 intensity minimum cutoff. Same as in figure 5 but with a 50000 intensity minimum cutoff.
Mentions: In this example, the peak matching procedure was repeated two more times by setting two different mass intensity minimums in the contour plots, in order to take into consideration only mass peaks with high intensity. This was done by returning to the main program window and refreshing the contour plots, in order to exclude mass peaks that had intensity lower than 10000 and 50000 each time. In the first case, the peaks that were left in the two mixes were 140 and 376, and in the second case, only 17 and 42 peaks had intensity above 50000. After creating the new contours, the same shift vectors were used and the peak matching process was repeated. The results can be seen in figure 6 and figure 7 respectively. The black columns in the compound percentage plots represent compounds that had no mass peaks with intensity greater than the minimum. It can be noticed that by keeping only high intensity peaks, the matching results are better, meaning that the percentage of the matched peaks is raised. Some slight differences in the compound correspondence between the first comparison and the other two are due to mass intensity differences that exist between same peaks of the two mixes (peaks from one mix may have intensity lower than the boundary, while their matched peaks from the other mix have higher).

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