LipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation - DIA lipid mediator validation

ABSTRACT:

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.

In MTBLS1382, to validate lipid mediator species identified with the Qtrap instrument (https://www.ebi.ac.uk/metabolights/MTBLS1381), the Thermo QEx HF was used to perform high resolution MS full scan (HR-FS) and data independent acquisition (DIA) analyses between 200-400 m/z with a 20 m/z step size. DIA method preparation and data analysis were performed with Skyline. We used LipidCreator as an external tool in Skyline to generate a collision-energy specific transition list for the mediators 12-HETE, 13-HODE, 15-HETE, arachidonic acid (AA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and thromboxane B2 (TXB2) and their deuterated counterparts 12-HETE-d8, 13-HODE-d4, 15-HETE-d8, AA-d8, DHA-d5, EPA-d5 and TXB2-d4, at a normalized collision energy NCE=21. We also used LipidCreator's relative fragment intensity prediction model to generate a custom spectral library for the light and heavy mediators. We transfered both the transition list and the spectral library directly from LipidCreator to Skyline and exported the dot product values after manual fragment peaks review.

Studies linked to this manuscript include;

MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HF

MTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTof

MTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid Profiling

MTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard

MTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identification

MTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator Profiling

MTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase

SUBMITTER: Nils Hoffmann 

PROVIDER: MTBLS1382 | MetaboLights | 2020-04-15

REPOSITORIES: MetaboLights