LipidCreator is a lipid building block-based workbench and knowledge base for the automated generation of targeted lipidomics mass spectrometry assays and in-silico spectral libraries. Assay generation can be conducted with a generic user interface (GUI) or on the command line, covering lipids of the following categories: sphingolipids (SL), glycerolipids (GL), glycerophospholipids (PL), sterol and sterol derivates (ST, SE), e.g. Cholesterol and Cholesterol esters, as well as fatty acids, including mediators (LM). LipidCreator can calculate masses for lipid species and their derived fragment ions, covering over 60 lipid classes and a lipid array of 10^12 lipid molecules with the consensus nomenclature recommended by the lipidomics standards initiative. Using the batch-processing mode, LipidCreator computes precursor-product ion pairs at a rate of 60,000 pairs per second on a standard notebook (i5-4310M CPU @ 2.70GHz with 8GB main memory). Besides the computation of fragment ions, another critical feature to generate an in-silico spectral library is the ability to determine the relative intensities of fragment ions at different defined collision energies (CE). We therefore trained non-linear regression models on empirical data from standard measurements of lipid mediators on Thermo QExactive HF and Agilent QTof instruments.
LipidCreator further contains a visual inspection level for fragments and a lipid nomenclature translator supporting LIPID MAPS formulations.It can be integrated into KNIME and Galaxy workflows as a native node via its command line interface on Linux and Windows. LipidCreator can work standalone but it is also fully integrable into Skyline and its small molecule support, allowing vendor-independent assay usage, data visualization and quality control of MS and MS/MS data.
In combination with Skyline, LipidCreator provides an integrated and user-friendly targeted workflow development environment for comprehensive lipidomics analyses.
Changelog
Changes up to 1.2.1 - 787
Changes up to 1.2.0 - 772
- Added a list of contributors
- Added information for GM1 sphingo lipids (using experimental data provided by Dr. Andreas Hülsmeier)
- Added session saving dialog request when closing LipidCreator #8
- Updated the logging framework #13
- Adjusted lipid grammar to recognize all phospho lipids containing a plasmalogen ecbecb7, da1215d
Changes up to 1.1.1 - 747
- Added 'version' option to command line #1
- Fixed issue #2 SLs were not showing +heavy isotopes
- Fixed issue #3 Missing FA chain for GP Plasmalogens
- Fixed an issue with create lipid list button
- Fixed FA creation issue when switching between even / odd / all
- Fixed some typos
Changes in 1.1.0 - 736
- Updated analytics server connection to TLS 1.2. To further support the development of LipidCreator through funding, we need to provide anonymized usage statistics. Please help us achieve this by agreeing to submit data on the number of starts of LipidCreator, and how often you create transition lists!
Changes in 1.1.0 - 734
- Removed BOM in info.properties which prevented Skyline and the Tool Store from installation.
- Fixed build to update build number correctly in info.properties.
Changes in 1.1.0 - 731
- Added new wizard for simplified, guided transition list generation.
- Added sterols and sterol esters.
- Updated multi-select behavior for head group lists.
- Added CTRL+A to select all items in head group lists.
- Updated manual pdf.
Installation
System Requirements:
- either Windows Vista / 7 / 8 / 10 (only 64 bit) with .NET framwork 4.5.1 or higher
- or Ubuntu 16.04 or higher* (with 'mono-complete' package installed, only 64 bit)
- at least 256MB main memory or higher
- LipidCreator has been tested on Ubuntu 16.04, 18.04 and 20.04, as well as on
Debian 10 (Buster). Other Linux distributions should also work, but have not
been tested.
Note: If you install Skyline first, all necessary .NET framework libraries will be installed
automatically! Later versions of Windows 8 and 10 already ship with up-to-date versions of .NET
installed. These also do not require additional installation.
Windows
With Skyline
LipidCreator has been tested with Skyline 19.1, 64 bit, 20.1, 64 bit and 21.1, 64 bit. Please follow the installation instructions on the Skyline homepage if you do not have Skyline installed already.
Installation from the Skyline Tool Store
The preferred way to install the latest release versions of LipidCreator is to install it from the Skyline Tool Store:
- Open Skyline with a blank document
- Go to the "Tools" > "Tool Store..." menu
- Scroll down and select "LipidCreator" for installation
- Wait for the installation to complete
- LipidCreator can now be started via "Tools" > "LipidCreator"
Manual Installation from ZIP
You can install the LipidCreator zip file (name must be LipidCreator.zip), e.g. for testing purposes, as an external tool:
- Go to "Tools" > "External Tools" and click on "Add"
- Select the LipidCreator.zip file
- Wait for the installation to complete
- Click "OK" on the "External Tools" dialog.
- LipidCreator can now be started via "Tools" > "LipidCreator"
Stand-Alone
If you locate the LipidCreator.exe file, either in your Skyline installation under the "Tools" folder, or within the LipidCreator folder extracted from the zip archive, you need to double click on it to start in stand-alone mode. It is also possible to start LipidCreator from the command line.
Linux / Ubuntu
To run LipidCreator, locate the directory containing LipidCreator.exe, open a terminal and type
mono LipidCreator.exe
Please note that there may be issues with the repainting of certain windows and controls (scrollable areas) due to the not 100% compatible Mono implementation.
Demo
LipidCreator provides several predefined data sets for a number of organisms
and tissues.
- Start LipidCreator
- Click in the menu on 'File' -> 'Import Predefined' -> 'Yeast' -> 'Lipidome'
- After loading, click on 'Review Lipids'. The new window shows 406 precursors.
- Click on 'Continue' to get the final list containing 5674 transitions for the
yeast lipidome which can be used / stored for further method development.
This demo can be performed in few seconds.
Tutorials
After LipidCreator has been started, four interactive tutorials can be started
from the 'Home' tab, namely:
- PRM tutorial
- SRM tutorial
- heavy labeled isotope tutorial
- collision energy tutorial
Additionally, a text version (pdf) is available in LipidCreator, please click
on 'Help' -> 'Documentation' within LipidCreator's menu.
Help & Support
If you experience any issues with LipidCreator, we kindly ask you to report them
using the GitHub issue system at https://github.com/lifs-tools/issues.
Please include your Operating System, Skyline version (if
applicable), and the full LipidCreator version, which is available from the
'Help' -> 'About' menu dialog.