LipidSearch Getting Started

LipidSearch 4.2 comes with a free 60-day trial license. After the trial period, purchase LipidSearch from your Thermo Fisher Scientific sales representative. The unlicensed software requires activation by sending the inactive license key to ThermoMSLicensing@thermofisher.com. Please follow the licensing directions found in the installation notes.

Note: The unlicensed demo version can read the zipped results files processed using a licensed version and is a fully functional data browser for data review, re-integration of peak areas, and exporting lipid results.

Before registering your license key, please make sure you are logged into an account with Administrator privileges. You can run the LipidSearch launcher by right clicking and selecting "Run as Administrator".

• Software does not run or has missing features.
  • Read the Installation Notes and make sure your PC meets the minimum requirements.
  • Make sure you have installed LipidSearch using the Administrator account or with Admin privileges.
  • Make sure you have a valid license as described in the Installation Notes.
  • If you have a prior installation of LipidSearch 4.0/4.1, purchase an upgrade to version 4.2.
  • In Windows Server 2012, make sure the Java installation process has sufficient memory: Control Panel > System > Advance system settings > Environment variables
• LipidSearch crashes the first time you process a Thermo raw file.
  • Uninstall a prior version of 32-bit MSFileReader that is preventing the use of 64-bit MSFR.
  • Update with the latest version of MSFR 3.1 SP4 (x64) from the Thermo software download website.
  • Make sure System > Configuration settings are setup for 64-bit (x64) data processing.
• LipidSearch does not display the search details (chromatograms, spectra) or alignment details.
  • Uninstall 64-bit Java 8 if it is installed since this prevents running the 32-bit Java 8 applet.
  • Uninstall old versions of Java and download 32-bit Java 8 update 171 or higher.
  • Make sure you are using Internet Explorer 11 (32-bit) and not the Chrome browser.
• LipidSearch crashes the first time you process a non-Thermo raw file.
  • Make sure you have a valid license as described above.
  • You need to have the correct 32-bit vendor DLL installed and properly registered in Windows.
  • You need to change from 64-bit to 32-bit file processing in the System > Configuration settings: \spiceCmd\x64\SpiceCmd.exe > \spiceCmd\x86\SpiceCmd.exe \spiceCmd\x64\SpiceQuantitationCmd.exe > \spiceCmd\x86\SpiceQuantitationCmd.exe

This is possible with the architecture employed in LipidSearch. However, we don’t support this and it’s up to the user to supply the appropriate 32-bit DLL’s. Any file that can be read on the workstation should be available in the LipidSearch data browser (i.e., the raw file type is recognized in Windows).

Yes, if a program such as ProteoWizard (http://proteowizard.sourceforge.net/formats.shtml) is installed that supports and registers the file type in the Windows registry. LipidSearch reads raw file formats that are native to the data processing workstation. With ProteoWizard installed LipidSearch can read mzXML version 2.1 files.

Yes, full text file export is available for the Search and Aligned results.

You can export lipid annotations and m/z using the "CD Format" which is a TraceFinder compound database (csv) file that can be imported into TraceFinder or Compound Discoverer 3.0.