Xtractor2D

Copyright Notice

Xtractor2D is copyright (c) 2009- Magnus Palmblad

Creative Commons License
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