A: The laboratory is split 50/50 between proteomics and lipidomics research. While working on protein analysis, such as identifying protein interaction networks or characterizing the proteomes of organisms that are related very distantly to organisms with sequenced genomes, we also attempt to better quantify the lipidome of various organelles, cells and tissues.
Q: WHAT ARE YOUR PRIMARY GOALS?
A: In lipidomics, we forge the alliance with developmental biology. The primary goal of the group is to combine lipidomics with developmental biology. As organisms grow and develop from a single cell, newly differentiated tissues require their own unique membrane lipid composition. We hope to characterize these tailored changes to better understand how inherited defects in lipid metabolism cause disease. We are equally interested in lipidomes of membrane microdomains and the biological significance of its remarkable complexity.
Q: WHY DID YOU INCORPORATE THE TRIVERSA NANOMATE® INTO YOUR LABORATORY?
A: We had a need for automated nanoflow direct-infusion capabilities. Shotgun lipidomics relies on low and stable flow rates, and the TriVersa NanoMate® has this demonstrated ability. We have purchased three additional instruments because they allow us to rapidly switch between lipids and proteomic analysis.
Q: DO YOU HAVE ANY PUBLICATIONS OF PRESENTATIONS USING THE TRIVERSA NANOMATE®? Publication Highlight 2021: Hormone-Sensitive Lipase Couples Intergenerational Sterol Metabolism to Reproductive Success Christoph Heier Is a corresponding author , Oskar Knittelfelder, Harald F Hofbauer, Wolfgang Mende, Ingrid Pörnbacher, Laura Schiller, Gabriele Schoiswohl, Hao Xie, Sebastian Grönke, Andrej Shevchenko, Ronald P Kühnlein
Hormone-sensitive lipase (Hsl) was identified as an ancestral regulator of SE degradation, which improves intergenerational sterol transfer and reproductive success in flies.
Other Publications:
Knittelfelder, O., Prince, E., Sales, S., Fritzsche, E., Woehner, T., Brankatschk, M., Shevchenko, A. (2020) Sterols as dietary markers for Drosophila melanogaster. BBA – Molecular and Cell Biology of Lipids, 1865 (7), 1388-1981. DOI: 10.1016/j.bbalip.2020.158683
Trautenberg, L.C., Knittelfelder, O., Hofmann, C., Shevchenko, A., Brankatschk, M., Prince, E. (2020) How to use the development of individual Drosophila larvae as a metabolic sensor. Journal of Insect Biology, 126, 0022-1910. DOI: 10.1016/j.jinsphys.2020.104095
Wang, Y., Hinz, S., Uckermann, O., Hoenscheid, P., von Schoenfels, W., Burmesiter, G., Hendricks, A., Ackerman, J.M., Baretton, G.B., Hampe, J., Brosch, M., Schafmayer, C., Shevchenko, A., Seissig, S. (2020) Shotgun lipidomics-based characterization of the landscape of lipid metabolism in colorectal cancer. BBA – Molecular and Cell Biology of Lipids, 1865 (3), 1388-1981. DOI: 10.1016/j.bbalip.2019.158579
Finkelstein, S. Gospe III, S.M., Schuhmann, K., Shevkenko, A., Arshavsky, V.M., Lobanova, E.S. (2020) Phophoinositide profile of the mouse retina. Cells 9(6), 1417. DOI: 10.3390/cells9061417
Brankatschk, M., Gutmann, T., Knittelfelder, O., Palladini, A., Prince, E., Grzybek, M., Brankatschk, B., Shevchenko, A., Coskun, U., Eaton, S. (2018) A temperature-dependent switch in feeding preference improves drosphila development and survival in the cold. Developmental Cell, 46, 6, 781-793.e4. DOI: 10.1016/j.devcel.2018.05.028
Fernandez, C., Sandin, M., Sampaio, J.L., Almgren, P., Narkiewicz, K., Hoffmann, M., Hedner, T., Wahlstrand, B., Simons, K., Shevchenko, A., James, P., Melander, O. (2013) Plasma lipid composition and risk of developing cardiovascular disease. PLOS One. DOI: 10.1371/journal.pone.0071846
Ghosh, A., Kling, T., Snaidero, N., Sampaio, J.L., Shevchenko, A., Gras, H., Geurten, B., Goepfert, M.C., Schulz, J.B., Voigt, A., Simons, M. (2013) A global in vivo drosophila RNAi screen identifies a key role of ceramide phosphothanolamine for glial ensheathment of axons. PLOS Genetics. DOI: 10.1371/journal.pgen.1003980
Schuhmann, K., Almeida, R., Baumert, M., Herzog, R., Bornstein, S.R. and Shevchenko, A. (2012) Shotgun lipidomics on a LTQ Orbitrap mass spectrometer by successive switching between acquisition polarity modes. J. Mass. Spectrom., 47: 96-104. DOI: 10.1002/jms.2031
Carvalho, M., Sampaio, J.L., Palm, W., Brankatschk, M., Eaton, S., Shevchenko, A. (2012) Effects of diet and development on the Drosophila lipidome. Mol Syst Biol, 8:600. DOI: 10.1038/msb.2012.29
Luerschner, L. Richter, D., Hannibal-Bach, H.K., Gaebler, A., Shevchenko, A., Ejsing, C.S., Thiele, C. (2012) Exogenous ether lipids predominantly target mitochondria. PLOS ONE. DOI: 10.1371/journal.pone.0031342
Sampaio, J.L., Gerl, M.J., Klose, C., Ejsing, C.S., Beug, H., Simons, K., Shevchenko, A. (2011) Membrane lipidome of an epithelial cell line. PNAS, 108 (5), 1903-1907. DOI: 10.1073/pnas.1019267108
Ejsing, C.S., Sampaio, J.L., Surendranath, V., Duchoslav, E., Ekroos, K., Klemm, R.W., Simons, K., Shevchenko, A. (2009) Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry. PNAS, 106 (7), 2136-2141. DOI: 10.1073/pnas.0811700106
A: One of the topics of our lab is the interaction of insect pheromones and their analogues with pheromone-binding proteins (PBPs) which are part of an extremely sensitive multi-component pheromone detection system.
We utilize binding assays to determine the function of the PBPs through affinity measurements of the protein-ligand receptors, calculate binding constants, the spatial arrangement of the complex and do modeling. In addition, point-mutated PBPs are used for a better understanding of the contribution of individual amino acids to the binding event.
Q: How does the TriVersa NanoMate® (TVNM) align with your research goals?
A: The TVNM enabled us to develop a high-throughput method to study protein-ligand-interactions for large series of different pheromones and their analogues.
As the binding energies involved are very low and we need to preserve the native structure of the molecules, the soft-ionization conditions of the TVNM are perfect for us. Further, these studies are difficult with classic electrospray, due to the stickiness of the samples. They create problems from short cleaning cycles and produce contaminations.
In contrast, the established method with the TVNM is reliable and stable, and it eliminates the sticky sample issues. In addition, multiple experiments with very low quantities of protein (1 nmol) at different cone-voltage conditions are possible.
We recently added the LESA™ (Liquid Extraction Surface Analysis) capability to the TVNM. This enables us to detect putative signal molecules on leaf surfaces and to track down their production and storage sites by comparing the data with extracts from samples derived from the inner compartments of the leaves.
Q: To whom would you recommend the TriVersa NanoMate for their research?
A: I would recommend the TriVersa NanoMate to everybody because it is a universal source. With direct infusion, coupling for fraction collection and surface analysis, it may replace all ionization sources.
Automated static nano-ESI/MS/MS (Infusion MS/MS) is an easy-to-use and high-throughput approach to analyte identification. It is particularly useful in the field of shotgun lipidomics, which itself has great potential for biomarker discovery and gained some significant attention in the last couple of years (Schuhmann et al. 2012; Jung et al. 2011; Han et al. 2011).
In order to simplify shotgun lipidomic approaches even further, the TriVersa NanoMate can now change nano-ESI spray polarity within the same infusion experiment.
In many cases of routine protein identification, processing times become the major bottleneck at the core facility. Although a nano-LC/MS/MS approach is recognized as a general strategy for protein identification, the typical 30-120 min run-time prohibits fast turnaround times. The TriVersa NanoMate offers a more rapid approach for the infusion of the protein digest, with only a 2-5 min run-time per sample.
Presented by: John P. Shockcor, Director of Life Sciences Business Development, Waters Corp., Visiting Fellow, Dept. of Biochemistry, University of Cambridge, UK
Description: Profiling low level components in a complex mixture of small molecules can be a challenging task. Although it may be possible to detect many low level components in a complex mixture, characterization is often hindered because fragmentation of these low level components yields peaks below the limit of detection. This problem can be alleviated by using a TriVersa NanoMate assisted approach. In this webinar we will describe how a TriVersa NanoMate coupled to a SYNAPT G2 Hybrid QTof Ion-Mobility Mass Spectrometer can provide critical fragmentation information needed to characterize low level components in lipidomics, drug metabolism studies and natural product profiling. This approach is ideally suited to the use of time-aligned-parallel fragmentation (TAP) which are illustrated by a number of examples.
In this webinar, Dr. Han describes how he uses the TriVersa NanoMate’s chip-based nanoelectrospray ionization capabilities in infusion mode to obtain more information from complex samples and faster lipids analysis with no sample-to-sample carryover. The interests of Dr. Han’s laboratory have been focused on the altered lipid metabolism, trafficking, and homeostasis under patho(physio)logical conditions. Currently, there are three specific areas explored in his laboratory including (1) extension of the shotgun lipidomics technology for increased penetrance into the low abundance regime of a cellular lipidome with emphasis on high throughput, and bioinformatics; (2) investigation of the biochemical mechanisms underlying the altered lipid content and composition in metabolic syndrome; and (3) identification of the biochemical mechanisms responsible for the sulfatide depletion and ceramide elevation at the very earliest stages of Alzheimer’s disease.
Presented by: Xianlin Han, Ph.D., Professor, Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute
