Xtractor2D
Copyright Notice
Xtractor2D is copyright (c) 2009- Magnus Palmblad
This work is licensed under a
Creative Commons Attribution-Share Alike 3.0 License.
About Xtractor2D
Xtractor2D is a simple and fast tool for integrating pre-defined regions (peaks or bins) in calibrated mass spectra in two-column ASCII
format using the GD library for generating PNG images of spectra with integrated regions. Xtractor2D runs from the command line and comes with a number of options:
-m the input mzXML file
-r reference list, defining peaks or bins, including retention time windows (see example)
-o the output filename
-nographics do not generate graphical output
In addition to extracting the peak or bin areas (total intensities), Xtractor2D plots the spectra with m/z on the horizontal and intensity on the vertical axis and colors extracted peaks or bins in red. This feature can be disabled with the -nographics option.
Download the Xtractor2D source code here. (Right-click and choose "Save Link As...".)
Compiling Xtractor2D
Compile Xtractor2D with: ./compile.sh
Using Xtractor2D
Usage: Xtractor2D -r<Xtractor2D reference filename>
-m<aligned LC-MS data in mzXML> -e<max. mass error in MS-only data (in ppm)>
[-l <residual deviation in LC retention time in LC-MS data> -R<MS start read scan>,<MS end read scan>
-o<output file> -nographics] (type --help for more information)
with the options described above. The resulting peak lists or bins can be merged into a uniform sample/data array by a simple shell script.
Precompiled binaries
Windows/Cygwin (Right-click and choose "Save Link As...".)
magnus.palmblad@gmail.com