LipidSearch™ 5.1 Software UPGRADE from LIPIDSEARCH 4.0/4.1/4.2 - FAQs

Triacylglycerol species form NH4 adducts under ESI conditions and species with varying numbers of double bonds typically have different response factors. One way to compensate for this is to model using lipid standards and then apply an average response factor for TG species with varying numbers of double bonds. See reference: Han, X. and R.W. Gross, Anal. Biochem. 2001, 295, 88-100.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

LipidSearch Software only includes basic statistic calculations including mean, standard deviation, % RSD and p-values. To do more sophisticated statistics, use the export function to create a data table in Microsoft Excel format.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Identification in direct infusion is the same for dd-MS2 spectra. However, mixtures of different precursor ions or isomers co-isolated at the same m/z gives rise to mixture MS2 spectra. As a result, ID may be less accurate and the number of species identified is typically lower. We don't recommend LipidSearch Software for the infusion analysis of complex lipid mixtures.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

As long as the experiment is full scan and dd-MS2, the spectra can either be summed together (infusion) or treated as a chromatogram (LC-MS), and the data can be processed by LipidSearch Software.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

TraceFinder Software requires chromatographic peaks for integration, but LipidSearch Software does not. LipidSearch Software can provide some limited relative quantitation from infusion data. TraceFinder Software is required for targeted LC-MS/MS methods.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

The mass tolerance for the precursor ion is ± 5 ppm. In TOP N dd-MS2 experiments, the accurate mass of the precursor ion triggering the MS2 is stored in the spectrum file header.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Full or micro flow rates are typically used for lipid separations, whereas nano-ESI (electrospray ionization) is preferred for infusion. One practical reason is that lipid carryover can be much worse at nanoliter/min flow rates.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

LipidSearch Software looks for fragments of the intact lipid precursor ions which is best achieved using ESI. LipidSearch supports identification of lipids that give intact molecular adduct ions. For example, negative ion APCI of fatty acids gives Cl (chemical ionization) adducts, and these adducts are included in the LipidSearch database.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

The method of identification is the same from dd-MS2 data. However, since several overlapping precursor ions may be co-isolated, infusion typically results in a lower number of lipid species identified.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

At the MS-MS level, this is not possible. However, lipid retention time can be modeled with lipid standards to determine the likely candidates. Right now, double bond position needs to be determined by a separate method such as hydrolysis followed by GC/MS, by ion-molecule reactions (ozone) or UVPD (photodissociation).

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Depending on acquisition parameters, 5,000 to 10,000 or more MS2 spectra may obtained in a Top N experiment during a 30 min run. The number of sum composition lipids detected and integrated corresponds to the number of lipid groups. The number of lipid ions corresponds to the number of lipid species identified from the MS2 spectra.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

It depends on the sample type and extraction conditions. We have seen between 100 to 1000 lipids depending on the sample type/volume (e.g., 1 x 10E6 yeast vs. 80 µL human plasma extract) and the ion mode (positive vs. negative).

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Yes, this is possible 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 Software reads raw file formats that are native to the data processing workstation. With ProteoWizard installed, LipidSearch Software can read mzXML version 2.1 files.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

This is possible with the architecture employed in LipidSearch Software. However, we don't support this and it is 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 Software data browser (i.e., the raw file type is recognized in Windows).

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

LipidSearch 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 Software 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 Software 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 Software crashes the first time you process a Thermo Fisher Scientific 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 Fisher Scientific Mass Spectrometry Software Download site > Demo Software: https://thermo.flexnetoperations.com/control/thmo/RegisterMemberToAccount
- Make sure System > Configuration settings are setup for 64-bit (x64) data processing.

LipidSearch Software 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 Software crashes the first time you process a non-Thermo Fisher Scientific 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

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

LipidSearch Software 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.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

LipidSearch Software 4.2 is available for download from the Thermo Fisher Scientific Mass Spectrometry Software Download site > Demo Software: https://thermo.flexnetoperations.com/control/thmo/RegisterMemberToAccount

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.