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

  1. Download MZmine-2.1.zip and PaDEL-AIMA.zip
  2. Unzip MZmine-2.1.zip to a folder and unzip PaDEL-AIMA.zip to the same folder as MZmine.
  3. 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.
  4. 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

  1. Download PaDEL-AIMA.zip
  2. Unzip PaDEL-AIMA.zip, into a directory where MZmine2.jar is located.
  3. 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.
  4. 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>

  5. 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

  1. Version 1.0 [25 Sep 2010]: First release.

Last modified on 3 February, 2012 by Yap Chun Wei