Proteomics and protein analysis

Proteomics and protein analysis

State-of-the-art infrastructure for proteome-wide quantitative analysis

The proteomics and protein analysis facility provides a state-of the-art infrastructure for proteome-wide quantitative analyses as well as the structural and quantitative investigation of proteins, to aid in the understanding of their biological roles. Included here are new developments in mass spectrometry, stable isotope labeling-based sample multiplexing and separation technologies resulting in great sensitivity and speed of analysis.


  • Identification and quantification of proteins in complex mixtures out of solution or separated by PAGE
  • Identification and quantification of various covalent modifications (PTMs)
  • Identification and characterization of isolated proteins, protein complexes or protein fragments
  • Proteome-wide quantitative analyses

Proteome-wide quantitative analyses require planning, time and commitment from the user and our facility, and we provide individual training and assistance with the experimental setup and data analysis.

Jan Seebacher: Platform head, proteomics

Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M (2020) Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation.

Mol Cell. 2020 Mar 19;77(6):1222-1236.e13

Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J (2020) Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2.

EMBO J. 2020 Jan 15;39(2):e102591

Deshpande I, Keusch JJ, Challa K, Iesmantavicius V, Gasser SM, Gut H (2019) The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.

EMBO J. 2019 Oct 15;38(20):e101744

Fontana GA, Hess D, Reinert JK, Mattarocci S, Falquet B, Klein D, Shore D, Thomä NH, Rass U (2019) Rif1 S-acylation mediates DNA double-strand break repair at the inner nuclear membrane.

Nat Commun. 2019 Jun 10;10(1):2535

Redolfi J, Zhan Y, Valdes-Quezada C, Kryzhanovska M, Guerreiro I, Iesmantavicius V, Pollex T, Grand RS, Mulugeta E, Kind J, Tiana G, Smallwood SA, de Laat W, Giorgetti L (2019) DamC reveals principles of chromatin folding in vivo without crosslinking and ligation.

Nat Struct Mol Biol. 2019 Jun;26(6):471-480

Villegas F, Lehalle D, Mayer D, Rittirsch M, Stadler MB, Zinner M, Olivieri D, Vabres P, Duplomb-Jego L, De Bont ESJM, Duffourd Y, Duijkers F, Avila M, Geneviève D, Houcinat N, Jouan T, Kuentz P, Lichtenbelt KD, Thauvin-Robinet C, St-Onge J, Thevenon J, van Gassen KLI, van Haelst M, van Koningsbruggen S, Hess D, Smallwood SA, Rivière JB, Faivre L, Betschinger J (2019) Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3.

Cell Stem Cell. 2019 Feb 7;24(2):257-270.e8

Saito M, Hess D, Eglinger J, Fritsch AW, Kreysing M, Weinert BT, Choudhary C, Matthias P (2019) Acetylation of intrinsically disordered regions regulates phase separation.

Nat Chem Biol. 2019 Jan;15(1):51-61

Ginno PA, Burger L, Seebacher J, Iesmantavicius V, Schübeler D (2018) Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape.

Nat Commun. 2018 Oct 2;9(1):4048

Schnellmann R, Sack R, Hess D, Annis DS, Mosher DF, Apte SS, Chiquet-Ehrismann R (2018) A Selective Extracellular Matrix Proteomics Approach Identifies Fibronectin Proteolysis by A Disintegrin-like and Metalloprotease Domain with Thrombospondin Type 1 Motifs (ADAMTS16) and Its Impact on Spheroid Morphogenesis.

Mol Cell Proteomics. 2018 Jul;17(7):1410-1425

Ostapcuk V, Mohn F, Carl SH, Basters A, Hess D, Iesmantavicius V, Lampersberger L, Flemr M, Pandey A, Thomä NH, Betschinger J, Bühler M (2018) Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes.

Nature. 2018 May;557(7707):739-743

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY (2018) Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor RbM15/spenito to the m6 a machinery component Wtap/Fl(2)d

Genes Dev. 2018 Mar 1;32(5-6):415-429

Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M (2017) The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1.

Mol Cell. 2017 Jul 20;67(2):294-307.e9

Hauer MH, Seeber A, Singh V, Thierry R, Sack R, Amitai A, Kryzhanovska M, Eglinger J, Holcman D, Owen-Hughes T, Gasser SM (2017) Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates.

Nat Struct Mol Biol. 2017 Feb;24(2):99-107

Miyake Y, Keusch JJ, Wang L, Saito M, Hess D, Wang X, Melancon BJ, Helquist P, Gut H, Matthias P (2016) Structural insights into HDAC6 tubulin deacetylation and its selective inhibition.

Nat Chem Biol. 2016 Sep;12(9):748-54

Grzmil M, Seebacher J, Hess D, Behe M, Schibli R, Moncayo G, Frank S, Hemmings BA (2016) Inhibition of MNK pathways enhances cancer cell response to chemotherapy with temozolomide and targeted radionuclide therapy.

Cell Signal. 2016 Sep;28(9):1412-21

Poli J, Gerhold CB, Tosi A, Hustedt N, Seeber A, Sack R, Herzog F, Pasero P, Shimada K, Hopfner KP, Gasser SM (2016) Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress.

Genes Dev. 2016 Feb 1;30(3):337-54

Rüegger S, Miki TS, Hess D, Großhans H (2015) The ribonucleotidyl transferase USIP-1 acts with SART3 to promote U6 snRNA recycling.

Nucleic Acids Res. 2015 Mar 31;43(6):3344-57

Zhang L, Tang F, Terracciano L, Hynx D, Kohler R, Bichet S, Hess D, Cron P, Hemmings BA, Hergovich A, Schmitz-Rohmer D (2015) NDR functions as a physiological YAP1 kinase in the intestinal epithelium.

Curr Biol. 2015 Feb 2;25(3):296-305

Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM (2015) Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.

Mol Cell. 2015 Jan 22;57(2):273-89

Arnold A, Rahman MM, Lee MC, Muehlhaeusser S, Katic I, Gaidatzis D, Hess D, Scheckel C, Wright JE, Stetak A, Boag PR, Ciosk R (2014) Functional characterization of C. elegans Y-box-binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes.

Nucleic Acids Res. 2014 Dec 1;42(21):13353-69

Lingaraju GM, Bunker RD, Cavadini S, Hess D, Hassiepen U, Renatus M, Fischer ES, Thomä NH (2014) Crystal structure of the human COP9 signalosome.

Nature. 2014 Aug 14;512(7513):161-5

MacDonald G, Nalvarte I, Smirnova T, Vecchi M, Aceto N, Dolemeyer A, Frei A, Lienhard S, Wyckoff J, Hess D, Seebacher J, Keusch JJ, Gut H, Salaun D, Mazzarol G, Disalvatore D, Bentires-Alj M, Di Fiore PP, Badache A, Hynes NE (2014) Memo is a copper-dependent redox protein with an essential role in migration and metastasis.

Sci Signal. 2014 Jun 10;7(329):ra56

Scharenberg MA, Pippenger BE, Sack R, Zingg D, Ferralli J, Schenk S, Martin I, Chiquet-Ehrismann R (2014) TGF-ß-induced differentiation into myofibroblasts involves specific regulation of two MKL1 isoforms.

J Cell Sci. 2014 Mar 1;127(Pt 5):1079-91

Grzmil M, Huber RM, Hess D, Frank S, Hynx D, Moncayo G, Klein D, Merlo A, Hemmings BA (2014) MNK1 pathway activity maintains protein synthesis in rapalog-treated gliomas.

J Clin Invest. 2014 Feb;124(2):742-54

Loedige I, Gaidatzis D, Sack R, Meister G, Filipowicz W (2013) The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function.

Nucleic Acids Res. 2013 Jan 7;41(1):518-32

Towbin BD, González-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM (2012) Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery.

Cell. 2012 Aug 31;150(5):934-47

Chen CI, Keusch JJ, Klein D, Hess D, Hofsteenge J, Gut H (2012) Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation.

EMBO J. 2012 Jul 18;31(14):3183-97

Kueng S, Tsai-Pflugfelder M, Oppikofer M, Ferreira HC, Roberts E, Tsai C, Roloff TC, Sack R, Gasser SM (2012) Regulating repression: roles for the sir4 N-terminus in linker DNA protection and stabilization of epigenetic states.

PLoS Genet. 2012;8(5):e1002727

Xue G, Restuccia DF, Lan Q, Hynx D, Dirnhofer S, Hess D, Rüegg C, Hemmings BA (2012) Akt/PKB-mediated phosphorylation of Twist1 promotes tumor metastasis via mediating cross-talk between PI3K/Akt and TGF-β signaling axes.

Cancer Discov. 2012 Mar;2(3):248-59

Schmitges FW, Prusty AB, Faty M, Stützer A, Lingaraju GM, Aiwazian J, Sack R, Hess D, Li L, Zhou S, Bunker RD, Wirth U, Bouwmeester T, Bauer A, Ly-Hartig N, Zhao K, Chan H, Gu J, Gut H, Fischle W, Müller J, Thomä NH (2011) Histone methylation by PRC2 is inhibited by active chromatin marks.

Mol Cell. 2011 May 6;42(3):330-41


Platform/Service Head

Jan Seebacher (Platform head, proteomics)

Technical/Research associates

Daniel Hess (Platform head, protein analysis)
Vytautas Iesmantavicius (Research associate, proteomics)


Postdoctoral fellows

Vytautas Iesmantavicius (2015-2017, Postdoctoral fellow)
Helene Rogniaux (2000-2002, Postdoctoral fellow)

Technical/Research associates

Ragna Sack (2011-2016, Research associate in mass spectrometry)
Ragna Sack (2002-2011, Technical/Research associate)
Dominique Klein (2009-2011, Technical/Research associate)
Reto Portmann (2003-2008, Technical/Research associate)
Anne Ulvestad (2000-2003, Technical/Research associate)
Renate Matthies (1985-2002, Technical/Research associate)


Martin Stalder (2008, Undergraduate)
Jasmin Althaus (2003-2004, Undergraduate)

Biography of Jan Seebacher

Software and Tools

Test - Not in use for now