Configuration settings

This chapter covers the manual adaption of LDA setting parameters. General settings can be found in the .settings file, and machine specific ones in the LipidDataAnalyzer.properties file. For each machine such a properties file is present in the propterties folder in the installation directory. It is recommended to change the settings for the machine in the corresponding file in the properties folder and, after saving this file, to select the machine and click on “Save as default” (see Settings). If the settings are changed directly in the LipidDataAnalyzer.properties, these settings are overwritten the next time somebody clicks on “Save as default”. The .settings file can be edited directly. In the LipidDataAnalyzer.properties file, not only algorithmic parameters are stored, but default settings for the display as well. The changes take effect after the properties file had been stored and the LDA is restarted.

Path settings (.settings)

This part contains path settings to executables or required files.

- ReadWPath: path to ReadW executable that is required if Thermo Finnegan RAW files are used directly.
 
- MassWolfPath: path to the MassWolf executable if the Waters .raw directories should be used directly.
 
- ElementConfig: path to the required elementconfig.xml file that contains the used chemical elements and the occurrence of their isotopes in nature.

Look & feel settings (.settings)

- LookAndFeel: This value is by default “system”, which corresponds to your system specific look & feel (e.g. Windows). If you prefer Java look & feel change this value to “java”, then you have the same look & feel like in this manual.

Default quantitation settings (.properties)

This stores default settings for the quantitation input page.

- basePeakCutoff: The default value for the “Rel. base-peak cutoff” (see Quantitation).

Excel result file settings (.settings)

- OverviewExcelWorkbook: If “true”, an overview tab is created in the Excel file.

3D viewer default settings (.properties)

For the resolution of the 3D viewer, default settings can be entered.

- hreeDViewerDefaultTimeResolution: The default time resolution of the viewer.
 
- threeDViewerDefaultMZResolution: The default m/z resolution of the viewer.

Standards prefix settings (.settings)

The field for the prefixes of the standard can be set by default (see Results selection settings).

- ISDefaultInput: Default prefix for the internal standard
 
- ESDefaultInput: Default prefix for the external standard

mzXML chrom settings (.properties)

These are settings for the translation from the mzXML to the chrom format.

- maxFileSizeForChromTranslationAtOnce: An approximate value how many MB can be read at once into the memory. The mzXML is translated into the chrom in several rounds. If there is e.g. a mzXML file with 200MB and an m/z range from 600-1400, then this file will be translated in two rounds if this parameter is 100: first round: masses from 600-1000; second round masses from 1000-1400. Thus this parameter does not directly correspond to the required memory, the required memory is normally more. If this parameter would have been 200, the whole file would have been translated in one round. The reason for this parameter is to permit the translation of huge files on machines with low RAM. If this parameter is increased, the translation time is decreased. If this parameter is too high a java.lang.OutOfMemoryException will be thrown and the file cannot be translated.
 
- chromMultiplicationFactorForInt and chromMultiplicationFactorForInt: This parameter define the highest resolution of the chrom file (e.g. chromMultiplicationFactorForInt=1000 and chromMultiplicationFactorForInt=1 would mean a max resolution of 0.001Da; chromMultiplicationFactorForInt=1000 and chromMultiplicationFactorForInt=5 would mean a max resolution of 0.005Da; chromMultiplicationFactorForInt=100 and chromMultiplicationFactorForInt=1 would mean a max resolution of 0.01Da).

General algorithm settings (.properties)

This section contains the most general settings of the algorithm. A detailed description of the parameters of the 3D algorithm is beyond the scope of a user manual. The parameters are described in the LipidDataAnalyzer.properties file.

- coarseChromMzTolerance: the +/-m/z range that is used for the extraction of the first chromatogram of the algorithm which is displayed in the 2D viewer (see chapter Chromatogram viewer).
 
- chromSmoothRange: the smooth range in seconds for Savitzky-Golay filter of the first chromatogram.
 
- chromSmoothRepeats: the smooth repeats for Savitzky-Golay filter of the first chromatogram.
 
- use3D: If yes, the 3D algorithm is used by default for the quantitation, else the 2D algorithm.

Memory settings (.bat, .sh, or. vmoptions)

The memory settings for the executables can be changed in the Lipid Data Analyzer.vmoptions, and for the console in the .bat or .sh, respectively. The Xmx parameter corresponds to the maximally reservable memory, and Xms the immediately reserved memory. The Xms value should be approximately half of the Xmx value.