Contributors:Matt McCormick, Sebastien Jourdain, Don Smyth, Alexis Girault, Wei Ouyang, Scott Wittenburg, Jade Bilkey
Viewer: Add initial support for per-comp lut/pwf (c0d45c2)
Contributors:Kopczynski, Dominik, Peng, Bing, Hoffmann, Nils, Pratt, Brian, Ahrends, Robert
LipidCreator release 1.1.0 - Build 734
March 30th, 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.
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.
- 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
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'
LipidCreator provides several predefined data sets for a number of organisms
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.
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.
LipidCreator's source code is available at https://github.com/lifs-tools/lipidcreator.
Contributors:benkrikler, Eshwen Bhal, linacre
New post-processing command to reshape outputs of fast-carpenter, see PR #28
Contributors:Juniper L. Simonis
Tools for interacting with the publicly available California Delta Fish Salvage Database, including continuous deployment of data access, analysis, and presentation.
parameters’ primary goal is to provide utilities for processing the parameters of various statistical models (see here for a list of supported models). Beyond computing p-values, CIs, Bayesian indices and other measures for a wide variety of models, this package implements features like bootstrapping of parameters and models, feature reduction (feature extraction and variable selection).