Optimizing a ultrahigh pressure liquid chromatography-time of flight-mass spectrometry approach using a novel sub-2 μm core–shell particle for in depth lipidomic profiling of Caenorhabditis elegans

•Sub-2-μm core–shell column for lipid separation.•Enhanced separation of isomeric species.•Higher coverage of the Caenorhabditis elegans lipidome.

Lipid profiling or lipidomics is currently applied in many different research fields. It refers to the global analysis of a samples lipid content using different analytical chemistry methods, with mass spectrometry as the mostly employed technology. We developed a comprehensive in-depth analysis method for the lipidome of the soil-dwelling nematode Caenorhabitis elegans, a widely used model organism. Four different columns were compared with a generic gradient and a novel sub-2-μm core–shell column, Waters Cortecs C18, showed superior performance in case of chromatographic peak characteristics, e.g. plate numbers and number of detected lipid features. Retention time deviation was generally less than 1% within one column and below 5% for columns from different batches. Intensity variation was lower than 30% for most detected features. Improved chromatographic separation showed enhanced resolution for isomeric lipids and allowed collection of highly detailed MS/MS spectra for lipid identification. In total 1304 lipid features were detected in positive ionization mode and 265 in negative mode. Lipids from different classes were annotated and MS/MS spectra obtained by data dependent fragmentation were used for identification purposes.