Introduction
Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used method to detect protein-protein interactions and elucidate complex protein mixtures. Visualization of large data sets produced from LC-MS, specifically the chromatograph and the mass spectra that correspond to its peaks is the focus of this work. The Brukin2d software, developed with Matlab 7.4, uses the compound data that are exported from Bruker 'DataAnalysis' program, and depicts the mean mass spectra of all the chromatograph compounds from one LC-MS run, in one 2D contour plot. Each spot in the plot represents one peptide mass. The spot y-axis position is determined by the time of its compound in the chromatograph, while the x-axis position is the mass to charge ratio (m/z). The darkness of the spots is proportional to the intensity of the mass peaks. Deconvolution data are also supported; to visualize uniquely the main singled-charged isotopes. Two contour plots from different chromatograph runs can then be viewed in the same window and automatically compared, in order to find the similarities and the differences between them. The results of the comparison can be examined through detailed mass quantization tables, while chromatograph compound statistics are also calculated during the procedure.
Details
An in-depth description of the application, as well as an example of visualizing and comparing two chromatograph runs, can be found in the Brukin2d manual. All the files that are necessary for the example are included in the Supplementary files at the Download section.
Installation
If the machine has Matlab r2007a or a later version installed in it, then the only necessary files are the Brukin2d Matlab files. Download and unzip the folder in a directory at your computer. In order to execute the software, open Matlab, change current directory to the one where the software is unzipped and type brukin2d at the command window.
If Matlab is not installed on your machine, or a previous version of it exists, you will have to install Matlab Component Runtime 7.6, in order to be able to run the standalone application, which is built only for Windows 32bit. Download and execute MCRInstaller.exe. The following directory should be added automatically to the system path: mcr_root\version\runtime\win32, but in case of trouble, check if it exists. After installing the component, download and unzip the Brukin2d Standalone files. To start the application run brukin2d.exe.
It is recommended to run Brukin2d from Matlab and with a 64bit operating system, due to memory issues.
Note: All the files that are mentioned here, can be found in the Download section.
