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Andrej Shevchenko

MPI-CBG | Research Group Leader

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  • Basic Research

    Proteomics, Lipidomics

  • Technology & Resources

    Proteomics, Lipidomics

Project Description

Shotgun lipidomics relies on the direct infusion of total lipid extracts of cells or tissues into a high resolution mass spectrometer. Lipids and internal standards spiked before the extraction are analysed together and this contributes to robust and accurate quantification. However, shotgun spectra are exceedingly complex and their confident interpretation requires high resolving power of employed mass spectrometers. We are working on implementing ultra-high resolution mass spectrometry in quantitative shotgun profiling of total extracts. Mass resolution exceeding 1 million allows to resolve fine isotopic structures of lipid molecules which dramatically increases confidence of lipid species assignment. The technology opens up new perspectives in lipidome-wide quantification of lipids flux and spatial organisation of tissue lipidomes.

Fig.: Shotgun spectrum of a total lipid extract

  • Collection of Lipid Center relevant Publications

    2018
    Vvedenskaya O, Wang Y, Ackerman JM, Knittelfelder O, Shevchenko A. Analytical challenges in human plasma lipidomics: A winding path towards the truth. Trends Analyt Chem, in press Art. No. doi: 10.1016/j.trac.2018.10.013 (2018)

    Rennert C, Vlaic S, Marbach-Breitrück E, Thiel C, Sales S, Shevchenko A, Gebhardt R, Matz-Soja M. The Diurnal Timing of Starvation Differently Impacts Murine Hepatic Gene Expression and Lipid Metabolism – A Systems Biology Analysis Using Self-Organizing Maps. Front Physiol. 2018 Sep 10;9:1180.

    Brankatschk M, Gutmann T, Knittelfelder O, Palladini A, Prince E, Grzybek M, Brankatschk B, Shevchenko A, Coskun Ü, Eaton S. A Temperature-Dependent Switch in Feeding Preference Improves Drosophila Development and Survival in the Cold. Dev Cell. 2018 Sep 24;46(6):781-793.e4.

    Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J Lipid Res. 2018 Oct;59(10):2001-2017

    Knittelfelder O, Traikov S, Vvedenskaya O, Schuhmann A, Segeletz S, Shevchenko A, Shevchenko A. Shotgun Lipidomics Combined with Laser Capture Microdissection: A Tool To Analyze Histological Zones in Cryosections of Tissues. Anal Chem. 2018 Aug 21;90(16):9868-9878

    Bonzón-Kulichenko E, Moltó E, Pintado C, Fernández A, Arribas C, Schwudke D, Gallardo N, Shevchenko A, Andrés A. Changes in Visceral Adipose Tissue Plasma Membrane Lipid Composition in Old Rats Are Associated With Adipocyte Hypertrophy With Aging. J Gerontol A Biol Sci Med Sci. 2018 Aug 10;73(9):1139-1146

    Kumar M, Joseph SR, Augsburg M, Bogdanova A, Drechsel D, Vastenhouw NL, Buchholz F, Gentzel M, Shevchenko A. MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting. Mol Cell Proteomics. 2018 Feb;17(2):384-396

    2017
    Schuhmann K, Srzentić K, Nagornov KO, Thomas H, Gutmann T, Coskun Ü, Tsybin YO, Shevchenko A. Monitoring Membrane Lipidome Turnover by Metabolic (15)N Labeling and Shotgun Ultra-High-Resolution Orbitrap Fourier Transform Mass Spectrometry. Anal Chem. 2017 Dec 5;89(23):12857-12865

    Bowden JA, Heckert A, Ulmer CZ, Jones CM, Koelmel JP, Abdullah L, Ahonen L, Alnouti Y, Armando AM, Asara JM, Bamba T, Barr JR, Bergquist J, Borchers CH, Brandsma J, Breitkopf SB, Cajka T, Cazenave-Gassiot A, Checa A, Cinel MA, Colas RA, Cremers S, Dennis EA, Evans JE, Fauland A, Fiehn O, Gardner MS, Garrett TJ, Gotlinger KH, Han J, Huang Y, Neo AH, Hyötyläinen T, Izumi Y, Jiang H, Jiang H, Jiang J, Kachman M, Kiyonami R, Klavins K, Klose C, Köfeler HC, Kolmert J, Koal T, Koster G, Kuklenyik Z, Kurland IJ, Leadley M, Lin K, Maddipati KR, McDougall D, Meikle PJ, Mellett NA, Monnin C, Moseley MA, Nandakumar R, Oresic M, Patterson R, Peake D, Pierce JS, Post M, Postle AD, Pugh R, Qiu Y, Quehenberger O, Ramrup P, Rees J, Rembiesa B, Reynaud D, Roth MR, Sales S, Schuhmann K, Schwartzman ML, Serhan CN, Shevchenko A, Somerville SE, St John-Williams L, Surma MA, Takeda H, Thakare R, Thompson JW, Torta F, Triebl A, Trötzmüller M, Ubhayasekera SJK, Vuckovic D, Weir JM, Welti R, Wenk MR, Wheelock CE, Yao L, Yuan M, Zhao XH, Zhou S. Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J Lipid Res. 2017 Dec;58(12):2275-2288

    Anitei M, Stange C, Czupalla C, Niehage C, Schuhmann K, Sala P, Czogalla A, Pursche T, Coskun Ü, Shevchenko A, Hoflack B. Spatiotemporal Control of Lipid Conversion, Actin-Based Mechanical Forces, and Curvature Sensors during Clathrin/AP-1-Coated Vesicle Biogenesis. Cell Rep. 2017 Aug 29;20(9):2087-2099.

    Schwudke D, Shevchenko A, Hoffmann N, Ahrends R. Lipidomics informatics for life-science. J Biotechnol. 2017 Nov 10;261:131-136

    Sales S, Knittelfelder O, Shevchenko A. Lipidomics of Human Blood Plasma by High-Resolution Shotgun Mass Spectrometry. Methods Mol Biol. 2017;1619:203-212.

    Schuhmann K, Thomas H, Ackerman JM, Nagornov KO, Tsybin YO, Shevchenko A. Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics. Anal Chem. 2017 Jul 5;89(13):7046-7052.

    Ocaña-Morgner C, Sales S, Rothe M, Shevchenko A, Jessberger R. Tolerogenic versus Immunogenic Lipidomic Profiles of CD11c(+) Immune Cells and Control of Immunogenic Dendritic Cell Ceramide Dynamics. J Immunol. 2017 Jun 1;198(11):4360-4372

    Sellin J, Schulze H, Paradis M, Gosejacob D, Papan C, Shevchenko A, Psathaki OE, Paululat A, Thielisch M, Sandhoff K, Hoch M. Characterization of Drosophila Saposin-related mutants as a model for lysosomal sphingolipid storage diseases. Dis Model Mech. 2017 Jun 1;10(6):737-750

    Ciucci S, Ge Y, Durán C, Palladini A, Jiménez-Jiménez V, Martínez-Sánchez LM, Wang Y, Sales S, Shevchenko A, Poser SW, Herbig M, Otto O, Androutsellis-Theotokis A, Guck J, Gerl MJ, Cannistraci CV. Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies. Sci Rep. 2017 Mar 13;7:43946

    Shevchenko A, Yang Y, Knaust A, Verbavatz JM, Mai H, Wang B, Wang C, Shevchenko A. Open sesame: Identification of sesame oil and oil soot ink in organic deposits of Tang Dynasty lamps from Astana necropolis in China. PLoS One. 2017 Feb 24;12(2):e0158636

    Hwang S, Gustafsson HT, O’Sullivan C, Bisceglia G, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM. Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells. Cell Rep. 2017 Dec 26;21(13):3807-3818

    Mesut Bilgin, Andrej Shevchenko. Quantification of endogenous endocannabinoids by LC-MS/MS. In: Lipidomics. (Eds.) Paul Wood (Neuromethods ; 125).,New York,Springer (2017),99-107 Ch. 7

    2016
    Bilgin M, Born P, Fezza F, Heimes M, Mastrangelo N, Wagner N, Schultz C, Maccarrone M, Eaton S, Nadler A, Wilm M, Shevchenko A. Lipid Discovery by Combinatorial Screening and Untargeted LC-MS/MS. Sci Rep. 2016 Jun 17;6:27920

    Sales S, Graessler J, Ciucci S, Al-Atrib R, Vihervaara T, Schuhmann K, Kauhanen D, Sysi-Aho M, Bornstein SR, Bickle M, Cannistraci CV, Ekroos K, Shevchenko A. Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome. Sci Rep. 2016 Jun 14;6:27710

    Ayciriex S, Gerber H, Osuna GM, Chami M, Stahlberg H, Shevchenko A, Fraering PC. The lipidome associated with the γ-secretase complex is required for its integrity and activity. Biochem J. 2016 Feb 1;473(3):321-34

    Chiang YN, Tan KJ, Chung H, Lavrynenko O, Shevchenko A, Yew JY. Steroid Hormone Signaling Is Essential for Pheromone Production and Oenocyte Survival. PLoS Genet. 2016 Jun 22;12(6):e1006126.

    Kopprasch S, Dheban S, Schuhmann K, Xu A, Schulte KM, Simeonovic CJ, Schwarz PE, Bornstein SR, Shevchenko A, Graessler J. Detection of Independent Associations of Plasma Lipidomic Parameters with Insulin Sensitivity Indices Using Data Mining Methodology. PLoS One. 2016 Oct 13;11(10):e0164173

    2015
    Hebbar S, Sahoo I, Matysik A, Argudo Garcia I, Osborne KA, Papan C, Torta F, Narayanaswamy P, Fun XH, Wenk MR, Shevchenko A, Schwudke D, Kraut R. Ceramides And Stress Signalling Intersect With Autophagic Defects In Neurodegenerative Drosophila blue cheese (bchs) Mutants. Sci Rep. 2015 Dec 7;5:15926

    Lavrynenko O, Rodenfels J, Carvalho M, Dye NA, Lafont R, Eaton S, Shevchenko A. The ecdysteroidome of Drosophila: influence of diet and development. Development. 2015 Nov 1;142(21):3758-68

    Zeigerer A, Bogorad RL, Sharma K, Gilleron J, Seifert S, Sales S, Berndt N, Bulik S, Marsico G, D’Souza RCJ, Lakshmanaperumal N, Meganathan K, Natarajan K, Sachinidis A, Dahl A, Holzhütter HG, Shevchenko A, Mann M, Koteliansky V, Zerial M. Regulation of liver metabolism by the endosomal GTPase Rab5. Cell Rep. 2015 May 12;11(6):884-892

    Bilgin M, Bindila L, Graessler J, Shevchenko A. Quantitative profiling of endocannabinoids in lipoproteins by LC-MS/MS. Anal Bioanal Chem. 2015 Jul;407(17):5125-31

    Khaliullina H, Bilgin M, Sampaio JL, Shevchenko A, Eaton S. Endocannabinoids are conserved inhibitors of the Hedgehog pathway. Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3415-20

    Habeck M, Haviv H, Katz A, Kapri-Pardes E, Ayciriex S, Shevchenko A, Ogawa H, Toyoshima C, Karlish SJ. Stimulation, inhibition, or stabilization of Na,K-ATPase caused by specific lipid interactions at distinct sites. J Biol Chem. 2015 Feb 20;290(8):4829-42

    Böttger J, Arnold K, Thiel C, Rennert C, Aleithe S, Hofmann U, Vlaic S, Sales S, Shevchenko A, Matz-Soja M. RNAi in murine hepatocytes: the agony of choice–a study of the influence of lipid-based transfection reagents on hepatocyte metabolism. Arch Toxicol. 2015 Sep;89(9):1579-88