Mass spectrometry and NMR spectroscopy are key technologies in determining molecular compounds in cellular systems. The Core Facility Mass Spectrometry & NMR Spectroscopy provides its technologies and applications, Lipidomics, Proteomics, and Metabolomics to a wide range of basic, translational and clinical research. Cutting-edge technologies enable us to determine several thousand individual lipids, small molecule metabolites and proteins, and we are constantly striving to adapt our portfolio of methods and workflows to the latest innovations and scientific needs. Sophisticated, tailored data analysis as well as the option of multiomic integration of metabolomic, lipidomic and proteomic data generate high added value for biomedical scientists and provide a holistic picture of cellular/metabolic processes.
Deep lipidomics profiling
Our LC-MS-based lipidomics platform runs on the Orbitrap Velos Pro and Orbitrap Eclipse. We use either reverse-phase chromatography, which separates lipids according to their hydrophobic fatty acids, or HILIC, which separates lipids according to their polar head groups. In addition to LC-MS of more complex lipids, the analysis of fatty acids is covered by GC-MS. Our portfolio covers fatty acids (and their derivatives), phospholipids, glycerolipids, sphingolipids, sterols, and prenols from the biological-functional areas of cellular membranes, energy storage, and signal transduction. This results in a standard portfolio that includes the lipid classes PC, PE, PI, PG, PS, CL, SM, Cer, HexCer, TG, DG, FA, and Chol.
Lipoprotein profiling
In addition to the lipidomics described above, we offer lipoprotein profiling using NMR, which can also be used in a clinical setting. The Avance Neo 600 nuclear magnetic resonance spectrometer can be routinely used for robust and quantitative analysis of VLDL, IDL, LDL, and HDL, including 16 lipoprotein subclasses and 41 serum/plasma metabolites.
LC-MS Metabolomics
LC-MS-based determination of low-molecular-weight metabolites is currently the most sensitive and comprehensive form of metabolomics analysis. The Core Facility uses an Orbitrap Q-Exactive or an Orbitrap Tribrid Eclipse for this type of analysis. Depending on requirements, both devices are equipped with either reversed-phase chromatography or HILIC. Our proprietary workflows, databases, and metabolic maps are centered around the robust analysis of metabolites involved in a variety of cellular metabolic processes. At the customer's request, the evaluation can include either basic differential statistics or in-depth statistics (MVA, enrichment analysis, metabolic pathway mapping, etc.) and visualization of metabolic networks.
NMR Metabolomics
In addition to the LC-MS metabolomics described above, we offer NMR metabolomics using Bruker's IVDr kit. This is performed on the Avance Neo 600 MHz NMR spectrometer and can be used on urine and serum/plasma in a clinical setting. The extremely high stability and favorable quantitative properties are the ideal prerequisites for conducting comparative long-term clinical studies (e.g., plasma biomarkers). Currently, the Bruker IVDr Metabolomics Kit records 41 metabolites and 112 lipoprotein-associated parameters absolutely quantitatively, at a throughput rate of 48 samples per day.
The aim of proteomics is to identify and quantify as many proteins and peptides as possible with high reliability and reproducibility. The challenge here is to extract as much information as possible from samples that are usually very complex. In the Core Facility, the Orbitrap Exploris 480 and the maXis II ETD (Q-ToF) are used exclusively for proteomics. The steps involved in a typical proteomics experiment are tissue lysis, proteolytic digestion, chromatographic separation using nanoHPLC, and peptide identification using a mass spectrometer. With these capabilities, we can offer relative protein quantification (LFQ), characterization of extracellular vesicles, and identification and localization of post-translational modifications. In addition, it is possible to determine the molecular weight of intact, undigested proteins.
Multi-omics data integration provides a comprehensive overview of biological processes and is an essential component in the further development of molecular sciences. As we have all three mass spectrometry-based omics technologies (proteomics, metabolomics, lipidomics) at our disposal, we are in the advantageous position of being able to combine them via multi-omics, thereby creating significant added value. This approach is made possible by our in-house developed multi-extraction protocol, where hydrophobic lipids, hydrophilic metabolites, and proteins are sequentially isolated from a sample extraction and can then be fed into the corresponding omics analyses. Since proteins, metabolites, and lipids are linked in metabolic interactions at the cellular level, researchers can identify existing connections much more clearly in a multi-omics approach, thereby reducing the complexity of individual data sets.
