ColorizeMSWiki

ColorizeMS

ColorizeMS is a Java Application that allows to qualitatively compare up to three experimental conditions from separation experiments.

Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.

Single GC-MS datasets can be visualized as heatmaps. the intensities measured for individual ion channels at individual scans are represented using a color mapping as shown in the previous image.

In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is represented on the y-axis. In GC- and LC-MS measurements the time axis is discretized by the scan rate of the instrument. Each scan is represented in this visualization by one pixel and the discretization of the mass to charge ratio is done by rounding to integer values.

The ColorimzeMS application provides functionality to map up to three experimental conditions and rapidly visualize qualitative differences between the measurements. ColorizeMS is realized as web-start application and is licensed under the Gnu Public License 3.0.

Currently the program has been tested on Windows, Mac OS X and Linux systems.

Requirements

There are several requirements which are specified in the JNLP description of ColorizeMS and will be installed upon start of the application. - Java3D technology - OpenGL Bindings for Java

Please follow the instructions for installing a current version of Java3D on your Mac OS X machine if you experience any problems with the ColorizeMS application.

Features

- Visualize and compare up to three experimental conditions - Interactively correct drifts in separation (e.g. retention time in GC- or LC-MS experiments) - Adjust the intensity of individual measurements to compensate for e.g. different amounts of sample that were analyze - Apply the visualization methods to various datasources, images from 2D gel electrophoresis measurements, GC- or LC-MS heatmaps - Colorize MS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences of - Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics Processing Unit and allows to interactively visualize High resolution images of the described experimental data.

Integration with MeltDB

We have realized the exchange of experimental data form the Metabolomics software suite MeltDB to the ColorizeMS WebStart application using web services technology and the modular generation of JNLP files which describe the input parameters of the software. We are therefore able to export information on chromatogram alignments generated by the various tools in MeltDB to the ColorizeMS images which renders the linear interpolation of aligned features between thje individual raw data representations.

User documentation

Select your png files representing experimental results and map them to the three color channels in ColorizeMS

Navigate and zoom the visualization using the right mouse button and the scroll wheel. Users may adjust the position of the three different texture layers to compensate drifts using the buttons to the right.

File:ColorizeMSWiki$mover.png

To compensate differences between the amount of sample measured, the intensity of individual channels can be modified. It is also possible to completely remove the influence of individual layers by setting the intensity to zero.

File:ColorizeMSWiki$alpha.png

ColorizeMS allows to rapidly identify common characteristics and features of the experimental dataset.

File:ColorizeMSWiki$main.png

Sample Data

2D representation of GC-MS measurements on Thermo Finnigan IonTra GC-MS measurement of Xanthomonas campestris pv. campestris grown under the three different carbon sources Glucose, Succinate and Mannitol.

File:ColorizeMSWiki$gcred.png

File:ColorizeMSWiki$gcblue.png

File:ColorizeMSWiki$gcgreen.png

Three 2D gel electrophofesis scans of the separated proteome of the organism Xanthomonas campestris pv. campestris. The two dimensional gel electrophoresis allows to separate the proteins by weight and polarity and the coloring of the spots has been achieved by Coomassie Blue.

File:ColorizeMSWiki$gered.png

File:ColorizeMSWiki$geblue.png

File:ColorizeMSWiki$gegreen.png

Java Web Start

File:ColorizeMSWiki$ws.png

- ColorizeMS WebStart (MAC)
- ColorizeMS WebStart

Download jar archive of ColorizeMS

- ColorizeMS Application