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Software Open Access

LipidCreator 1.1.1.747

Kopczynski, Dominik; Peng, Bing; Hoffmann, Nils; Pratt, Brian; Ahrends, Robert

Researcher(s)
Ejsing, Christer S; Burla, Bo; Hermansson, Martin; Benke, Peter Imre; Tan, Sock Hwee; Chan, Mark Y; Torta, Federico; Schwudke, Dominik; Meckelmann, Sven; Coman, Cristina; Schmitz, Oliver J; MacLean, Brendan; Borst, Oliver; Wenk, Markus R; Manke, Mailin-Christin

LipidCreator release 1.1.1 - Build 747

December 21st, 2020

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), cholesterol and its derivates (Ch, ChE), 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 1012 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 1.1.1 - 747

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 and 18.04, 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.

Installation for standalone mode:
No installation required, please click on 'LipidCreator.exe' to run the software.

Installation as external program in Skyline:
 1) Open Skyline with a blank document
 2) Go in the menu on 'Tools' -> 'External Tools...'
 3) Click on 'Add' -> 'From File'
 4) Browse to the 'LipidCreator.zip' archive and select it
 5) Confirm your selection two times
 6) To run LipidCreator, go in the menu on 'Tools' -> 'LipidCreator'

Demo
 
LipidCreator provides several predefined data sets for a number of organisms
and tissues.
 1) Start LipidCreator
 2) Click in the menu on 'File' -> 'Import Predefined' -> 'Yeast' -> 'Lipidome'
 3) After loading, click on 'Review Lipids'. The new window shows 406 precursors.
 4) 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 our support form at https://lifs.isas.de/support with the support category
'Lipid Creator'. Please include your Operating System, Skyline version (if
applicable), and the full LipidCreator version, which is available from the
'Help' -> 'About' menu dialog.

Source Code

LipidCreator's source code is available at https://github.com/lifs-tools/lipidcreator.

Files (18.7 MB)
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LipidCreator.zip
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