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Abstract
BackgroundLiquid 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.ResultsThe 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 .
Highlights
Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures
Protein identification is commonly being performed by the so called "bottom-up" approach: Proteins are converted to peptides, the sequences of which are determined by tandem mass spectrometry (MS-MS), combined with the use of search engines and protein databases that are available in the
'Brukin2D' is a Matlab based program, which was developed in order to visualize, evaluate, process and compare LC-MS data. It uses as input 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 plot
Summary
Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Proteomics is the large scale analysis of proteins in a biological system. It is a continuously and rapidly growing scientific area evolving together with the emergence of new methodologies and technologies. Protein identification is commonly being performed by the so called "bottom-up" approach: Proteins are converted to peptides, the sequences of which are determined by tandem mass spectrometry (MS-MS), combined with the use of search engines and protein databases that are available in the (page number not for citation purposes). BMC Bioinformatics 2009, 10(Suppl 6):S12 http://www.biomedcentral.com/1471-2105/10/S6/S12 internet [1]. This analysis is widely performed by the use of Liquid Chromatography-Mass Spectrometry (LC-MS). It should be noted that many diverse chromatographic separations can be serially applied (multi-dimensional chromatography) and connected to the mass spectrometer, providing the ability to identify and quantify hundreds to thousands of proteins in a single experiment [4]
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