Mass Spectrometry Unit

Mass Spectrometry Unit

The large scale analysis of proteins by mass spectrometry has gained significant momentum during the last few years by several key technological developments affecting instrumentation as well as analysis software, which in combination enable researchers to sensitively resolve the protein composition of cells or of tissues (The “Proteome”) to a very high degree.

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.


Israel S, Drexler HCA, Fuellen G, and Boiani M. The COP9 signalosome subunit 3 is necessary for early embryo survival by way of a stable protein deposit in mouse oocytes. Mol Hum Reprod, 2021, accepted

Lai KY, Rizzato M, Aydin I, Villalonga-Planells R, Drexler HCA, and Schelhaas M. A Ran-binding protein facilitates nuclear import of human papillomavirus type 16. PLoS Pathog, 2021, 17, e1009580

Schreiber A, Boff L, Anhlan D, Krischuns T, Brunotte L, Schuberth C, Wedlich-Söldner R, Drexler H, and Ludwig S. Dissecting the mechanism of signaling-triggered nuclear export of newly synthesized influenza virus ribonucleoprotein complexes. Proc Natl Acad Sci U S A, 2020, 117, 16557-16566

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.

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