ColorizeMSWiki: Difference between revisions

Revision as of 11:33, 23 February 2010

File:ColorizeMSWiki$logo-small.png

ColorizeMS is a Java application that allows to qualitatively compare up to three experimental conditions measured via hyphenated mass spectrometry (MS).

File:ColorizeMSWiki$gui2.png

Single hyphenated MS datasets can be visualized as contour plots. The intensities measured for individual ion channels at individual mass spectral scans can be represented using a color mapping as shown in the following image.

In this example, the retention time of the measurement 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 nominal masses and binning the measured intensities.

File:ColorizeMSWiki$twod.png

ColorizeMS provides functionality to compare measurements from up to three experimental conditions and rapidly visualize qualitative differences. ColorizeMS is realized as web-start application which has been tested on Microsoft Windows, Mac OS X, Linux and Solaris . The project is licensed under the GNU Public License 3.0.

Downloads

The ColorizeMS Java application for different platforms can be downloaded here. A Java Web Start link for ColorizeMS is available here.

Requirements

The software requirements are specified in the JNLP description of ColorizeMS and will be installed upon start of the application using Java Web Start technology. The application relies on Java3D with OpenGL bindings:

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 analyzed.
Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC-, LC-, or GCGC-MS contour plots.
ColorizeMS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences in the measured samples.
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 representing the described experimental data.

Integration with MeltDB

File:ColorizeMSWiki$meltdb.png

We have realized the direct exchange of experimental data form the metabolomics software suite MeltDB to the ColorizeMS Web Start application using on-the-fly generation of JNLP files which describe the input parameters of the software. We are therefore able to directly export 2D representations of chromatograms generated by MeltDB to ColorizeMS.

File:ColorizeMSWiki$meltdb-form.png

Up to three measurements from any given experiment can be directly submitted to the ColorizeMS application.

Further information

User documentation

Sample Data Sets

@@ Line 3: / Line 3: @@
 ColorizeMS is a Java application that allows to qualitatively compare
-up to three experimental conditions from separation experiments.
+up to three experimental conditions measured via hyphenated mass spectrometry (MS).
-Single GC-MS datasets can be visualized as heatmaps. the intensities measured for individual ion channels at
+ [[Image:ColorizeMSWiki$gui2.png]]
-individual scans are represented using a color mapping as shown in the previous image.
- [[Image:ColorizeMSWiki$gui2.png]]
+Single hyphenated MS datasets can be visualized as contour plots. The intensities measured for individual ion channels at
+individual mass spectral scans can be represented using a color mapping as shown in the following image.
-In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is
+In this example, the retention time of the measurement 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 nominal masses and binning the measured intensities.
-Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.
   [[Image:ColorizeMSWiki$twod.png]]