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 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 as well as to select external collaborators. We provide expert assistance 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 sample lysis to sample clean-up are carried out.

We are currently equipped with a Q Exactive HF Orbitrap mass spectrometer (Thermo Scientific) as well as with a state-of-the-art Bruker timsTOF pro system (since 01/2020). Both mass spectrometry systems are online-coupled to nano HPLC instruments. This setup allows for the reproducible chromatographic separations of even highly complex samples containing thousands of peptides and their sensitive and reliable identification by mass spectrometry.

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 in many instances of equal interest not only to identify proteins but also to address the question of quantitative changes of the identified proteins. We therefore offer the possibility to perform relative quantitation experiments using either label-free methods, the introduction of isobaric tags (TMT) and other chemical labels, or by using the SILAC-technique (SILAC = Stable Isotope Labelling with Amino Acids in Culture).

Database searches are generally performed by using MaxQuant and its built-in Andromeda search engine (Jürgen Cox, Matthias Mann; Max Planck Institute for Biochemistry, Martinsried), which has been our main workhorse since 2008. However, we also have access to other tools such as PEAKS (for de-novo sequencing) or Spectronaut (for the analysis of measurements made in DIA mode). More recently, index-based open search engines have been developed, which rapidly gain popularity (fragpipe/MSFragger, DIA-NN, MetaMorpheus). They render the search process considerably faster and also allow to more broadly address the presence of known and unknown post-translational modifications.

Whenever possible and reasonable we finally attempt to not only provide results as difficult-to-read long lists but also perform an initial bioinformatic analysis of the data, including statistics, differential expression analysis, enrichment calculations etc. using tools such as Perseus, R, Cytoscape and various web-based tools, which altogether renders mass spectrometry results more accessible and useful.



Duethorn B, Groll F, Rieger B, Drexler HCA, Brinkmann H, Kremer L, Stehling M, Borowski MT, Mildner K, Zeuschner D, Zernicka-Goetz M, Stemmler MP, Busch KB, Vaquerizas JM, Bedzhov I (2022). Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism. Nat Commun. 2022 Feb 1;13(1):610. doi: 10.1038/s41467-022-28139-5​.​​​​

​Han D, Wu G, Chen R, Drexler HCA, MacCarthy CM, Kim KP, Adachi K, Gerovska D, Mavrommatis L, Bedzhov I, Araúzo-Bravo MJ, Schöler HR (2022). A balanced Oct4 interactome is crucial for maintaining pluripotency. Sci Adv. 2022 Feb 18;8(7):eabe4375. doi: 10.1126/sciadv.abe4375. Epub 2022 Feb 16.​

​​​​Taher L, Israel S, Drexler HCA, Makalowski, W, Suzuki, Y, Fuellen, G, Boiani, M. The proteome, not the transcriptome, predicts that oocyte superovulation affects embryonic phenotypes in mice. Sci Rep, 2021, 12 09. 11:23731. 10.1038/s41598-021-03054-9.​

​​​​​​Di Persio S, Tekath T, Siebert-Kuss LM, Cremers J-F, Wistuba J, Li X, Meyer zu Hörste G, Drexler HCA, Wyrwoll MJ, Tüttelmann F, Dugas M, Kliesch S, Schlatt S, Laurentino S, Neuhaus N. Single-cell RNA-seq unravels alterations of the human spermatogonial stem cell compartment in patients with impaired spermatogenesis. Cell Reports Medicine, 2021, 2(9),

​​​​​​Mall EM, Lecanda A, Drexler HCA, Raz E, Schöler HR, Schlatt S (2021). Heading towards a dead end: The role of DND1 in germ line differentiation of human iPSCs. PLoS One 16:e0258427.

​​​​​​Liu  Y , Chen Q , Han D , Schoeler H , Fabian J, Stehling M, Jeong H-W , Drexler HCA , Adams  RH. Dopamine signaling regulates hematopoietic stem and progenitor cell function​. Blood, 2021, doi: 10.1182/blood.2020010419. 

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

Lepa C, Hoppe S, Stöber A, Skryabin BV, Sievers LK, Heitplatz B, Ciarimboli G, Neugebauer U, Lindenmeyer MT, Cohen CD, Drexler HCA, Boor P, Weide T, Pavenstädt H, George B. TrkC Is Essential for Nephron Function and Trans-Activates Igf1R Signaling. J Am Soc Nephrol. 2021 Feb;32(2):357-374. doi: 10.1681/ASN.2020040424. Epub 2020 Dec 30. PMID: 33380522

Starost L, Lindner M, Herold M, Xu YKT, Drexler HCA, Heß K, Ehrlich M, Ottoboni L, Ruffini F, Stehling M, Röpke A, Thomas C, Schöler HR, Antel J, Winkler J, Martino G, Klotz L, Kuhlmann T. Extrinsic immune cell-derived, but not intrinsic oligodendroglial factors contribute to oligodendroglial differentiation block in multiple sclerosis. Acta Neuropathol. 2020 Nov; 140(5):715-736. doi: 10.1007/s00401-020-02217-8. Epub 2020 Sep 7. PMID: 32894330

Margraf A, Germena G, Drexler HCA, Rossaint J, Ludwig N, Prystaj B, Mersmann S, Thomas K, Block H, Gottschlich W, Liu C, Krenn PW, Haller H, Heitplatz B, Meyer Zu Brickwedde M, Moser M, Vestweber D, Zarbock A. The integrin linked kinase is required for chemokine-triggered high affinity conformation of neutrophil β2-integrin LFA1. Blood. 2020 Jul 30; doi: 10.1182/blood.2020004948. Online ahead of print. PMID: 32730588

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 2019 Nov 29;8:e45863. doi: 10.7554/eLife.45863. PMID: 31782728

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:

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.

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