Lipids, Lipidomics, and Spatial Lipidomics

Lipids are essential molecules that play crucial roles in energy storage, cell membrane integrity, and signaling processes within biological systems. The study of these vital substances falls under the domain of lipidomics, a field that explores the complex lipid profiles within cells and tissues to unveil their roles in health and disease. NExTLi, the National Expert center for Translational Lipidomics, is dedicated to pioneering research in lipidomics by offering comprehensive services and expertise to researchers aiming to unravel the mysteries of lipid metabolism and its implications.

Building upon the foundation of traditional lipidomics in the Amsterdam UMC Core Facility Metabolomics, spatial lipidomics introduces an additional layer of complexity by mapping the distribution of lipids within tissues. This approach allows for the visualization of lipid diversity at a microscopic scale, offering insights into the spatial heterogeneity of lipids and their functional roles in various physiological and pathological contexts. While our current capabilities enable us to offer a wide range of lipidomics services, we are on the brink of expanding our technological arsenal to include spatial lipidomics (see Figure) —an advancement that hinges on the successful acquisition of a spatial omics instrument. This initiative is part of a Research Infrastructure (RI) grant we have submitted to the Netherlands Organisation for Scientific research (NWO), aimed at further enhancing our services to the research community. By integrating advanced imaging techniques, NExTLi provides unparalleled insights into the lipid landscape, aiding researchers in identifying novel biomarkers and therapeutic targets.

Mass spectrometry imaging and spatial lipidomics

To characterize molecules in context of tissue at the single cell resolution, mass spectrometry imaging (MSI) is used to scan a surface with a laser thereby ionizing molecules which are then detected and quantified by mass spectrometry, where MSI measuring lipids is termed spatial lipidomics. Recent technological developments in MSI have significantly improved its efficiency and precision. Instruments are available that combine the optimized ionization of molecules from the investigated surface (the tissue) with advanced ion mobility capabilities. The latter is important since it enables the separation of isobaric species, which is especially relevant for lipids, which can have many structural isomers.

At NExTLi, we are committed to supporting the research community through our specialized services in lipidomics and, hopefully in the near future, spatial lipidomics. By leveraging our expertise and state-of-the-art technologies, we offer researchers the tools and knowledge necessary to advance our understanding of lipid functions and their impact on human health.

Lipidomics

NExTLi provides different lipidomics services that encompass 2D, 3D and 4D lipidomics. We also can do tracer-based lipidomics. But what does this mean? This is explained below.

2D, 3D and 4D lipidomics?

Lipidomics can be performed at different dimensional depths ranging from 2D- to 4D-lipidomics, see Figure 1, where every stage is indicated by a number between brackets. 2D-lipidomics = (1) + (3) uses liquid chromatographic separation of the lipid, yielding retention time = RT = (1), followed by mass spectrometric detection of the lipid (3), termed MS1, expressed as m/z = mass over charge. 3D-lipidomics = (1) + (3) + (4) usually adds fragmentation of the lipid (4), termed MS2 or MS/MS, to the chromatographic and MS1 dimension to gather more structural information, thereby enhancing identification. In 4D-lipidomics (1) + (2) + (3) + (4), ion mobility (2), expressed as the collisional cross section (CCS), is added, which is a physical constant representing the shape/surface area of the molecule. Ion mobility can be used to separate molecules even if they have the same m/z in the MS1 stage. This allows the identification of more lipids at a higher structural level and certainty.

Ion mobility?

We mention the term ion mobility as one of the dimensions that is used to make the mixture of lipids less complex. Ion mobility is technique that enables the separation of metabolites with the same exact mass but different 3-dimensional conformations. This advanced ion mobility approach is ideally suited for lipidomics as it increases the number of identifiable lipids, enhances compound identification confidence, and in some cases eliminates the need for chromatographic separation, which is especially important for applications where chromatographic separation is not possible, such as mass spectrometry imaging. A nice use-case is presented Figure 2.

Tracer-based lipidomics?

Tracer-based lipidomics and fluxomics utilize non-radioactive stable isotopes to investigate lipid metabolic processes, focusing on the synthesis, modification, and turnover of lipids in biological systems, see Figure 3. These stable isotopes, distinguishable by their heavier mass via mass spectrometry, enable the tracking of lipid molecule changes. Fluxomics builds upon this and tracks changes over time which allows the determination of the rates of metabolic reactions and pathways at the cellular, tissue, or organism level, offering an extensive understanding of metabolic flux and its regulation. Both tracer-based lipidomics and fluxomics can also be performed for spatial omics, providing spatio-temporal information on lipid metabolism.

Technologies

NExTLi’s technological arsenal is equipped with state-of-the-art instruments and corresponding bioinformatics workflows designed to meet the broad spectrum of research needs within the field of lipidomics. Our facility harnesses cutting-edge analytical tools to provide comprehensive lipid analysis, detailed lipid profiling, and pioneering spatial lipidomics services.

Current Instrumentation

Mass spectrometers for lipidomics: Our core capabilities include a four high-resolution Orbitrap mass spectrometers and the innovative timsTOF Pro 2 system featuring advanced ion mobility. These platforms facilitate 2D, 3D, and 4D lipidomics analyses, offering unparalleled sensitivity, specificity, and throughput for the quantitative and qualitative analysis of lipidomes. In addition, we have 8 triple quad mass spectrometers and 2 GC(MS)s that also can be used for (targeted) lipid measurements, such as total fatty acids.

Future Instrumentation

Spatial omics instrument: Awaiting the successful acquisition through an RI grant application to the NWO, NExTLi plans to integrate a spatial omics instrument into our facility. This advanced tool will allow us to map the distribution of lipids within tissues at the single-cell level, opening new avenues for understanding lipid function and distribution in health and disease contexts.

Advanced bioinformatics and data processing

NExTLi stands at the forefront of bioinformatics and data processing within the lipidomics field, integrating sophisticated computational strategies to decipher complex lipid data. Our team harnesses custom-developed algorithms and state-of-the-art software to analyze, interpret, and visualize lipidomics datasets, enabling precise identification and quantification of lipid species across various biological samples. With a focus on enhancing the accuracy and efficiency of lipidomics research, we provide researchers with comprehensive data analysis support, from experimental design to insightful biological interpretation. Our bioinformatics infrastructure is designed to manage large-scale lipidomics data, applying advanced statistical methods and machine learning techniques to uncover novel lipid biomarkers and metabolic pathways. At NExTLi, we are dedicated to pushing the boundaries of what’s possible in lipidomics data analysis, offering researchers powerful tools to drive forward their scientific inquiries.

Through the synergistic use of these instruments and bioinformatics/data processing workflows, NExTLi is at the forefront of lipidomics research, offering unparalleled expertise and services to the scientific community. Our commitment to technological advancement and precision analysis positions us as a leader in the exploration of lipid function and metabolism, propelling the field toward new scientific discoveries and therapeutic approaches.