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Lipidomic profiling allows 100s if not 1000s of lipids in a sample to be detected and quantified. Modern lipidomics techniques are ultra-sensitive assays that enable the discovery of novel biomarkers in a variety of fields and provide new insight in mechanistic investigations. Despite much progress in lipidomics, there remains, as for all high throughput “omics” strategies, the need to develop strategies to standardize and integrate quality control into studies in order to enhance robustness, reproducibility, and usability of studies within specific fields and beyond.    Objectives  We aimed to understand how much results from lipid profiling in the model organism  Caenorhabditis elegans  are influenced by different culture conditions in different laboratories.    Methods  In this work we have undertaken an inter-laboratory study, comparing the lipid profiles of N2 wild type  C .  elegans  and  daf-2 ( e1370 ) mutants lacking a functional insulin receptor. Sample were collected from worms grown in four separate laboratories under standardized growth conditions. We used an UPLC-UHR-ToF–MS system allowing chromatographic separation before MS analysis.    Results  We found common qualitative changes in several marker lipids in samples from the individual laboratories. On the other hand, even in this controlled experimental system, the exact fold-changes for each marker varied between laboratories.    Conclusion  Our results thus reveal a serious limitation to the reproducibility of current lipid profiling experiments and reveal challenges to the integration of such data from different laboratories.    Supplementary Information  The online version contains supplementary material available at 10.1007/s11306-021-01775-6.

Comparison of lipidome profiles of Caenorhabditis elegans—results from an inter-laboratory ring trial