LipidCreator workbench to probe the lipidomic landscape

Abstract

Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.

New software tools, databases, and resources in metabolomics: updates from 2020

“…LipidCreator, is available both as a Skyline plugin and a standalone/command-line operation, is a lipid building block-based workbench and knowledgebase for semi-automatic generation of targeted lipidomics MS assays and in silico spectral libraries (Peng et al 2020 ). It can support diverse lipid categories, allows SRM/ parallel reaction monitoring (PRM) assay generation for both labeled and unlabeled lipid species and their derived fragment ions, allows in silico spectral library generation and CEs optimization and the entire workflow can be integrated into Konstanz Information Miner (KNIME™) and Galaxy workflows as a native node.…”

Ceramide Levels and COVID-19 Respiratory Distress, a Causal Relationship

“…Figure 3a shows the identification, categorization and quantification of identified lipid metabolites: PS = Phosphatidylserine, Cer = Ceramides, PE = Phosphatidylethanolamine, PI = Phosphatidylinositol, PG = Prostaglandin, HexCer = Hexosylceramide, Hex2Cer = DiHexosylceramide, Hex3Cer = TriHexosylceramide by using the combination of obtained peak list of selective ions, obtained MS/MS data, and LIPID CREATOR platform (10). Figure 3b shows the observed retention time (RT) differences between the identified metabolites in the plasma of uninfected and COVID-19-infected individuals.…”

Ceramide Levels and Covid-19 Respiratory Distress, a Causal Relationship

“…After the data preprocessing, the LipidCreator workbench software in Skyline (available at https://lifs.isas.de/lipidcreator) was used for both quantification and qualification of the lipid species present within the plasma samples (10).…”

“…Figure3a, the identification, categorization and quantification of identified lipid metabolites : PS = Phosphatidylserine, Cer = Ceramides, PE = Phosphatidylethanolamine, PI = Phosphatidylinositol, PG = Prostaglandin, HexCer = Hexosylceramide, Hex2Cer = DiHexosylceramide, Hex3Cer = TriHexosylceramide was possible by using the combination of obtained peak list of selective ions, obtained MS/MS data, and LIPID CREATOR platform(10). Figure3b, shows the observed retention time (RT) differences between the identified metabolites in plasma of uninfected and Covid-19 infected individuals.…”