Lipidomics
4D lipidomics and lipid fluxomics on trapped ion mobility and Orbitrap mass spectrometry platforms.
We combine liquid chromatography, trapped ion mobility, high-resolution accurate mass, and MS/MS to annotate lipids at the molecular species level, with collision cross section (CCS) as an additional identifier. Measurements are embedded in standardized sample preparation, internal-standard-based quantification, and systematic QC.
Platforms
- Bruker timsMetabo (trapped ion mobility)
- Bruker timsTOF Pro 2 (trapped ion mobility)
- Thermo Orbitrap Exploris 240
- Thermo Q Exactive Plus (2×)
- UHPLC front ends; nano-UPLC in development
What 4D adds
Each lipid feature is described by four orthogonal properties: retention time, collision cross section, accurate mass, and MS/MS fragmentation.
- Separation of isobaric and isomeric species that co-elute
- CCS as a reproducible identifier that supports annotation across studies
- Cleaner MS/MS spectra through mobility-resolved fragmentation
- Annotation confidence reported according to Lipidomics Standards Initiative guidelines
Workflows
Workflow choice follows the research question.
- Untargeted lipidomics for discovery and phenotyping
- Semi-targeted panels for defined lipid classes
- Structural characterization of selected species on request
- Stable-isotope tracer studies (fluxomics)
- Integration with targeted metabolite and fatty acid analyses of the CFM
Four dimensions per lipid
Figure 1. 4D lipidomics. Lipid features are characterized by retention time (1), ion mobility expressed as collision cross section (2), accurate mass (3), and MS/MS fragmentation (4), enabling separation of co-eluting isomers and annotation at the molecular species level.
Lipid fluxomics
Stable-isotope labelled precursors are incorporated into specific lipid moieties. Isotopologue-resolved mass spectrometry then shows how quickly lipids are synthesized, remodeled, and turned over, information that steady-state abundance cannot provide. Tracer choice, labelling time courses, and data processing are tailored per project, in cell models, model organisms, and patient-derived material.
Figure 2. Tracer-based lipidomics. Labelled head groups (e.g. d9-choline), glycerol backbones (e.g. ¹³C₃-glycerol), or fatty acids (e.g. d9-oleate) produce characteristic mass shifts in the isotopologue distribution of lipid species, from which pathway activity is derived.
Coverage
Lipid classes
Glycerophospholipids including ether lipids and plasmalogens, lysophospholipids, cardiolipins, sphingolipids, and neutral lipids (TG, DG, CE). Sterols and fatty acids via complementary targeted assays.
Sample types
Plasma and serum, cultured cells including patient fibroblasts and iPSC-derived models, tissues, and model organisms. Sample requirements are agreed during intake.
Data analysis
Processing, annotation, statistics, and pathway-level interpretation by the CFM bioinformatics team, with FAIR data handling supported by ACDC.
Lipidomics at NExTLi builds on more than two decades of lipid research at the Laboratory Genetic Metabolic Diseases, Amsterdam UMC, including ether lipid, peroxisomal, and mitochondrial lipid metabolism.