LipidCreator workbench to probe the lipidomic landscape

• Published in: Nature communications Vol. 11; no. 1; pp. 2057 - 14
• Main Authors: Peng, Bing, Kopczynski, Dominik, Pratt, Brian S., Ejsing, Christer S., Burla, Bo, Hermansson, Martin, Benke, Peter Imre, Tan, Sock Hwee, Chan, Mark Y., Torta, Federico, Schwudke, Dominik, Meckelmann, Sven W., Coman, Cristina, Schmitz, Oliver J., MacLean, Brendan, Manke, Mailin-Christin, Borst, Oliver, Wenk, Markus R., Hoffmann, Nils, Ahrends, Robert
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 28-04-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 119/118; 631/114/794; 631/1647/296; 631/45/608; 82/58; Adult; Assaying; Blood Platelets - metabolism; Calibration; Computer programs; Female; Humanities and Social Sciences; Humans; Knowledge bases (artificial intelligence); Lipidomics - methods; Lipids; Lipids - blood; Lipids - chemistry; Male; Mass spectrometry; Mass spectroscopy; Medicin och hälsovetenskap; multidisciplinary; Platelet Activation; Platelets; Probability; Reproducibility of Results; Science; Science (multidisciplinary); Scientific imaging; Signal Transduction; Software; Software development tools; Spectroscopy; Stable isotopes; Young Adult
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-15960-z

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.
Targeted mass spectrometry enables reproducible and accurate lipid quantification but dedicated software tools to develop targeted lipidomics assays are lacking. Here, the authors develop a targeted lipidomics workbench and lipid knowledgebase for the streamlined generation of targeted assays.