PaDEL-AIMA
Description
A MZmine plugin for a fully automated iterative moving averaging (AIMA) technique for base-line correction.
AIMA was based on the idea of a moving average smoothing. For more information on the AIMA algorithm, please refer to the paper "Prakash BD and Yap CW (2011). A fully Automated Iterative Moving Averaging (AIMA) technique for baseline correction. Analyst. 136 (15):3130-3135".
Installation
Scenario 1: MZmine is not installed
- Download MZmine-2.1.zip and PaDEL-AIMA.zip
- Unzip MZmine-2.1.zip to a folder and unzip PaDEL-AIMA.zip to the same folder as MZmine.
- Type the following in a command line (without the double quotes): "jar uf MZmine2.jar net\*" (Note: jar is a tool from the Java Development Kit).
- Alternatively, you can open MZmine2.jar using an archive software like 7-zip and add the contents of PaDEL-AIMA.zip to MZmine2.jar.
- Start MZmine using either startMZmine_Windows.bat (on Windows),
startMZmine_MacOSX.command (on Mac OS X), or
startMZmine_Linux.sh (on Linux/Unix systems).
Scenario 2: MZmine is already installed
- Download PaDEL-AIMA.zip
- Unzip PaDEL-AIMA.zip, into a directory where MZmine2.jar is located.
- Type the following in a command line (without the double quotes): "jar uf MZmine2.jar net\*" (Note: jar is a tool from the Java Development Kit).
- Alternatively, you can open MZmine2.jar using an archive software like 7-zip and add the contents of PaDEL-AIMA.zip to MZmine2.jar.
- In the conf/config.xml, after
<module class="net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.Deconvolution" />
<parameters>
add the following
<peakbuilder name="AIMA baseline cut-off" /> <parameter name="Min peak height" type="DOUBLE" >0.0</parameter> <parameter name="Min peak duration" type="DOUBLE" >0.0</parameter> <parameter name="AIMA option" type="STRING" >AIMA step 1 and 2</parameter> </peakbuilder>
- Start MZmine using either startMZmine_Windows.bat (on Windows),
startMZmine_MacOSX.command (on Mac OS X), or
startMZmine_Linux.sh (on Linux/Unix systems).
Licence
This software is free for all (e.g. personal, academic, non-profit, non-commercial, government, commercial, etc) to use.
Citation
Please cite using: Prakash BD and Yap CW (2011). A fully Automated Iterative Moving Averaging (AIMA) technique for baseline correction. Analyst. 136 (15):3130-3135
History
- Version 1.0 [25 Sep 2010]: First release.
Last modified on 3 February, 2012 by Yap Chun Wei