/rkmd

Automatically exported from code.google.com/p/rkmd

Primary LanguageJava

Overview/Announcements

rae-Lipid/RKMD (rae: Roger, Ankit, Elna) is a basic console and GUI-based screening tool which calculates the Reference Kendrick Mass Defect and the total number of carbon atoms (NCT) from a raw, experimental array of observed m/z values in order to identify m/z values which may represent compounds of a known lipid species. Input consists of the raw array of m/z ions as well as literature-derived RKMDs and NCTs through which to iterate and match with experimental data.

2014 Dec 16: A user manual has been released! (View) or (Download). This version guides users through technical operation of raeLipID. The theory and background of the software is omitted but is planned to be incorporated into the user guide.

Release Notes

2016 May 24: Excel Tool for RKMD Calculation (Direct Download)

    This is an excel tool developed by Roger and Elna to calculate KMD and cross check against nominal values as well. Click on "view raw" to use and download.

2015 Dec 13: RKMD v.0.6, commit 205ecbc (View and Download)

  • new back-end and front-end update with oxidized lipid screening support
  • bug fixes and code restructuring for accurate ppm calculations
  • please note that an updated user manual to reflect a few GUI changes is a work in progress

2015 Mar 21: RKMD Revision 29, v.0.5.4 (rae-LipID GUI) (Direct Download)

  • formatting changes to output files for easier import into spreadsheet programs
  • changed default referenceKMD.csv file for fixes and to add more compounds

2015 Feb 21: RKMD Revision 28, v.0.5.3 (rae-LipID GUI) (Direct Download)

  • fixed bug in rae-LipID GUI that caused match results window to print ppm error instead of match name
  • added functionality for plasmalogen-class species: "Plasmalogen" can now be specified under the "FA_type" field of the referenceKMD.csv value. Additionally, any number of carbonyl chains "Ncc" can be specified as any integer value greater than 0 since the following equation is now used: http://tinyurl.com/eqnrkmd.


    Where N_ch represents the number of chains attached to the headgroup, N_TC represents the total number of carbon atoms in the fatty acid chains, and m_X are atomic masses for each element X.

    • Further revisions are underway in which different degrees of oxidation for the fatty acid chains can be taken into account.

    2014 Dec 14: RKMD Revision 22, v.0.5.2 (rae-lipID GUI) (Direct Download)

    • output files now contain an additional field specifying the ppm error between a theoretically calculated mass and the observed mass; this gives a broad idea of the quality of the result being returned
    • retention time filtering has been added; two optional columns "TLOW" and "THIGH" can be specified in the referenceKMD.csv file for compounds, and a retention time filtering checkbox has been added to the GUI as an option for the user
    • to adjust the look and feel of the GUI for your platform, use the following launchers available in this download. For Windows users, double-click on WindowsLaunch.exe to run raeLipid; for Linux users, execute LinuxLaunch.sh. Manually adjust the look and feel (including font rendering fixes for Linux users) by running:

    For Linux:

    java -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel -Dswing.aatext=TRUE -Dawt.useSystemAAFontSettings=on -jar raeLipidGUI.jar

    For Windows:

    java -Dswing.defaultlaf=com.sun.java.swing.plaf.windows.WindowsLookAndFeel -jar raeLipidGUI.jar

    2014 Oct 20: RKMD Revision 20, v.0.5.1 (rae-lipID GUI) (Direct Download)

    • Revised the RKMD back-end to include the functionality of specifying aliphatic or carbonyl fatty acid chains in the referenceKMD.csv file, as their carbon number calculations slightly differ. A new column in the referenceKMD.csv file named "FA_type" is mandatory and must specify either "aliphatic" or "carbonyl" as the FA_type for all species.
    • no GUI changes in this revision

    2014 Oct 18: RKMD Revision 18, v.0.5 (rae-lipID GUI) (Direct Download)

    • This revision updates the GUI to the new rae-lipID front end. The GUI has been overhauled to be more user-friendly and to optimize workflow for repetitive calculations. The user-interface should be self-explanatory for the most part but a user manual will be published for more nuanced details (specific formatting requirements, etc.)
    • A sample .csv file for input has been provided in this download.
    • Special thanks to Hawskmont for the artwork brushes that were used in the rae-lipID's logo's design

    See the Release_History wiki page for previous release notes

    Implementation Notes

    Full implementation notes are available in the project's google drive folder (downloads for google-code hosted projects have now been deprecated). The following UML diagram is a rough outline as implemented since revision 2:

    Google Drive End-User Downloads