Mass Spectrometry Unit
Our facility is providing mass spectrometry service to all departments and groups of the institute and is currently equipped with a state-of-the-art Orbitrap Velos hybrid mass spectrometer (Thermo Scientific) that is online coupled to an EASY nano-HPLC from Proxeon. This setup allows the reproducible chromatographic separations of even highly complex samples containing thousands of peptides and their subsequent identification and characterization by mass spectrometry. Database searches can be performed either on a dedicated Mascot Server (Matrix Science), by the Sequest algorithm implemented in the Proteome Discoverer software (Thermo Scientific) as well as by the recently developed Andromeda machine, which is part of the MaxQuant Software Suite (Jürgen Cox, Matthias Mann; Max Planck Institute for Biochemistry, Martinsried) and which is our main workhorse.
Since the composition of the proteome is not static and is modulated by changes in the cellular environment (e.g. by the presence or absence of cytokines, growth factors, drugs, nutrients etc), it is equally important to also address the question of quantitative changes of the identified proteins. We therefore offer the possibility to perform relative quantitation experiments using the SILAC-technique (SILAC = Stable Isotope Labeling with Amino Acids in Culture) or by the adoption of isobaric tags (iTRAQ®; AB Sciex). In cases where metabolic or chemical labeling is not practical we have implemented a label-free quantitation protocol.
We apply a mass spectrometry approach in addition to other areas of interest such as the description of protein-protein interactions, changes affecting the subcellular distribution of proteins or the characterization of post-translational modifications, such as phosphorylation, acetylation and ubiquitylation.
We furthermore aid in the strategic planning of experiments where mass spectrometry will be part of the experimental workflow and provide help with sample preparation at all levels. Our facility features separate lab space for this purpose, where all steps from electrophoresis to sample clean-up are carried out.
Supervision is provided to researchers who wish to prepare their samples on their own.
Luxán G, Stewen J, Díaz N, Kato K, Maney SK, Pitulescu ME, Nagelmann N, Drexler HCA, Zeuschner D, Faber C, Schillers H, Hermann S, Wiseman J, Vaquerizas JM, Pitulescu M, and Adams RH. Endothelial EphB4 maintains vascular integrity and transport function in adult heart. eLife (accepted)
Israel S, Casser E, Drexler HCA, Fuellen G, Boiani M. A framework for TRIM21-mediated protein depletion in early mouse embryos: recapitulation of Tead4 null phenotype over three days. BMC Genomics. 2019 Oct 21;20(1):755. doi: 10.1186/s12864-019-6106-2
Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L. An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo. Sci Rep. 2019 Sep 16;9(1):13356. doi: 10.1038/s41598-019-49817-3.
Drexler HCA, Vockel M, Polaschegg C, Frye M, Peters K, Vestweber D. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2. Mol Cell Proteomics. 2019 Oct;18(10):2058-2077. doi: 10.1074/mcp.RA119.001716. Epub 2019 Aug 19.
Holthenrich A, Drexler HCA, Chehab T, Naß J, Gerke V. Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von Willebrand factor secretion. Blood. 2019 Sep 19;134(12):979-982. doi: 10.1182/blood.2019000786. Epub 2019 Jul 1.
Braun LJ, Zinnhardt M, Vockel M, Drexler HCA, Peters K, Vestweber D (2019). VE-PTP inhibition stabilizes endothelial junctions by activating FGD5. EMBO Rep. pii: e47046. doi: 10.15252/embr.201847046. [Epub ahead of print]
Marrone L, Drexler HCA, Wang J, Tripathi P, Distler T, Heisterkamp P, Anderson EN, Kour S, Moraiti A, Maharana S, Bhatnagar R, Belgard TG, Tripathy V, Kalmbach N, Hosseinzadeh Z, Crippa V, Abo-Rady M, Wegner F, Poletti A, Troost D, Aronica E, Busskamp V, Weis J, Pandey UB, Hyman AA, Alberti S, Goswami A, Sterneckert J (2019). FUS pathology in ALS is linked to alterations in multiple ALS-associated proteins and rescued by drugs stimulating autophagy. Acta Neuropathol 138(1):67-84. doi: 10.1007/s00401-019-01998-x
Reinhardt L, Kordes S, Reinhardt P, Glatza M, Baumann M, Drexler HCA, Menninger S, Zischinsky G, Eickhoff J, Fröb C, Bhattarai P, Arulmozhivarman G, Marrone L, Janosch A, Adachi K, Stehling M, Anderson EN, Abo-Rady M, Bickle M, Pandey UB, Reimer MM, Kizil C, Schöler HR, Nussbaumer P, Klebl B, Sterneckert JL (2019). Dual Inhibition of GSK3β and CDK5 Protects the Cytoskeleton of Neurons from Neuroinflammatory-Mediated Degeneration In Vitro and In Vivo. Stem Cell Reports 12:502-517.
Mallik M, Catinozzi M, Hug CB, Zhang L, Wagner M, Bussmann J, Bittern J, Mersmann S, Klämbt C, Drexler HCA, Huynen MA, Vaquerizas JM, Storkebaum E (2018). Xrp1 genetically interacts with the ALS-associated FUS orthologue caz and mediates its toxicity. J Cell Biol 217:3947-3964.
Böser A, Drexler HCA, Bartscherer K (2018). Tissue Extracts for Quantitative Mass Spectrometry of Planarian Proteins Using SILAC. Methods Mol Biol 1774:539-553.
Sarin LP, Kienast SD, Leufken J, Ross RL, Dziergowska A, Debiec K, Sochacka E, Limbach PA, Fufezan C, Drexler HCA, Leidel SA (2018). Nano LC-MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels. RNA 24:1403-1417.
Höing S, Yeh T-Y, Baumann M, Martinez NE, Habenberger P, Kremer L, Drexler HCA, Küchler P, Reinhardt P, Choidas A, Zischinsky M-L, Zischinsky G, Nandini S, Ledray AP, Ketcham SA, Reinhardt L, Abo-Rady M, Glatza M, King SJ, Nussbaumer P, Ziegler S, Klebl B, Schroer TA, Schöler HR, Waldmann H, Sterneckert J. Dynarrestin, a Novel Inhibitor of Cytoplasmic Dynein. Cell Chemical Biology, Volume 25, Issue 4, p357–369.e6, 19 April 2018. DOI: https://doi.org/10.1016/j.chembiol.2017.12.014
Wang B, Pfeiffer MJ, Drexler HCA, Fuellen G, Boiani M. Proteomic analysis of mouse oocytes identifies PRMT7 as reprogramming factor that replaces SOX2 in the induction of pluripotent stem cells. J Proteome Res. May 26, 2016; DOI: 10.1021/acs.jproteome.5b01083
Alings F, Sarin LP, Fufezan C, Drexler HCA, Leidel SA. An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast. RNA. 2015 Feb;21(2):202-12. doi: 10.1261/rna.048199.114. Epub 2014 Dec 12.
Pfeiffer MJ, Taher L, Drexler HCA, Suzuki Y, Makałowski W, Schwarzer C, Wang B, Fuellen G, Boiani M. Differences in embryo quality are associated with differences in oocyte composition: A proteomic study in inbred mice. Proteomics. 2014 Nov 4. doi: 10.1002/pmic.201400334. [Epub ahead of print]
Gaumann AK, Drexler HCA, Lang SA, Stoeltzing O, Diermeier-Daucher S, Buchdunger E, Wood J, Bold G, Breier G. The inhibition of tyrosine kinase receptor signalling in leiomyosarcoma cells using the small molecule kinase inhibitor PTK787/ZK222584 (Vatalanib®). Int J Oncol. 2014 Dec;45(6):2267-77. doi: 10.3892/ijo.2014.2683. Epub 2014 Sep 29.
Rocha SF, Schiller M, Jing D, Li H, Butz S,Vestweber D,Biljes D, Drexler HCA, Nieminen-Kelha M, Vajkoczy P, Adams S, Benedito R, Adams RH, Esm1 Modulates Endothelial Tip Cell Behavior and Vascular Permeability by Enhancing VEGF Bioavailability. Circulation Res, 2014 Aug 29;115(6):581-90. doi: 10.1161/CIRCRESAHA.115.304718. Epub 2014 Jul 23
Schwarzer C, Siatkowski M, Pfeiffer MJ, Baeumer N, Drexler HCA, Wang B, Fuellen G, Boiani M., Maternal age effect on mouse oocytes: new biological insight from proteomic analysis. Reproduction, 2014, 148, 55-72
Shintani Y, Drexler HCA, Kioka H, Terracciano CMN, Coppen SR, Imamura H, Akao M, Nakai J, Wheeler AP, Higo S, Nakayama H, Takashima S, Yashiro K, Suzuki K. Toll-like receptor 9 protects non-immune cells from stress by modulating mitochondrial ATP synthesis through the inhibition of SERCA2. EMBO Reports, Apr;15(4):438-45. doi: 10.1002/embr.201337945. Epub 2014 Mar 7
Boeser A, Drexler HCA, Reuter H, Schmitz H, Wu G, Schöler HR, Gentile L, Bartscherer K. SILAC Proteomics of Planarians Identifies Ncoa5 as a Conserved Component of Pluripotent Stem Cells. Cell Reports 2013, 5, 1142-1155.
Esch D, Vahokoski J, Groves MR, Pogenberg V, Cojocaru V, Vom Bruch H, Han D, Drexler HCA, Araúzo-Bravo MJ, Ng CKL, Jauch R, Wilmanns M & Schöler HR. A unique Oct4 interface is crucial for reprogramming to pluripotency. Nat Cell Biol 2013, 15, 295-301
Nakayama M, Nakayama A, van Lessen M, Yamamoto H, Hoffmann S, Drexler HCA, Itoh N, Hirose T, Breier G, Vestweber D, Cooper JA, Ohno S, Kaibuchi K & Adams RH. Spatial regulation of VEGF receptor endocytosis in angiogenesis. Nat Cell Biol 2013, 15, 249-260
Drexler HCA, Ruhs A, Konzer A, Mendler L, Bruckskotten M, Looso M, Günther S, Boettger T, Krüger M, and Braun T. On marathons and sprints: an integrated quantitative proteomics and transcriptomics analysis of differences between slow and fast muscle fibers. Mol Cell Proteomics published 30 December 2011, 10.1074/mcp.M111.010801
Pfeiffer MJ, Siatkowski M, Paudel Y, Balbach ST, Baeumer N, Crosetto N, Drexler HCA, Fuellen G, Boiani M. Proteomic analysis of mouse oocytes reveals 28 candidate factors of the "reprogrammome". J Proteome Res. 2011 May 6;10(5):2140-53. Epub 2011 Mar 29.