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

Charlotte Soneson , Vytautas Iesmantavicius, Daniel Hess, Michael B Stadler, Jan Seebacher (2023) einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data

Journal of Open Source Software, 8(89), 5750

Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, Bühler M (2023) Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.

RNA. 2023 Aug;29(8):1140-1165

Welte T, Goulois A, Stadler MB, Hess D, Soneson C, Neagu A, Azzi C, Wisser MJ, Seebacher J, Schmidt I, Estoppey D, Nigsch F, Reece-Hoyes J, Hoepfner D, Großhans H (2023) Convergence of multiple RNA-silencing pathways on GW182/TNRC6.

Mol Cell. 2023 Jul 20;83(14):2478-2492.e8

Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thomä NH (2023) Cooperation between bHLH transcription factors and histones for DNA access.

Nature. 2023 Jul;619(7969):385-393

Kuzdere T, Flury V, Schalch T, Iesmantavicius V, Hess D, Bühler M (2023) Differential phosphorylation of Clr4(SUV39H) by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis.

EMBO Rep. 2023 Jan 9;24(1):e55928

Amante RJ, Auf der Maur P, Richina V, Sethi A, Iesmantavicius V, Bonenfant D, Aceto N, Bentires-Alj M (2022) Protein Tyrosine Phosphatase SHP2 Controls Interleukin-8 Expression in Breast Cancer Cells.

J Mammary Gland Biol Neoplasia. 2022 Jun;27(2):145-153

Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6.

Nat Commun. 2022 Feb 25;13(1):1059

Delaney CE, Methot SP, Kalck V, Seebacher J, Hess D, Gasser SM, Padeken J (2022) SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity.

Nat Struct Mol Biol. 2022 Feb;29(2):85-96

Challa K, Seebacher J, Gasser SM (2021) Sucrose gradient chromatin enrichment for quantitative proteomics analysis in budding yeast.

STAR Protoc. 2021 Dec 17;2(4):100825

Hurst V, Challa K, Jonas F, Forey R, Sack R, Seebacher J, Schmid CD, Barkai N, Shimada K, Gasser SM, Poli J (2021) A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress.

EMBO J. 2021 Sep 27;:e108439

Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D (2021) BANP opens chromatin and activates CpG-island-regulated genes.

Nature. 2021 Aug;596(7870):133-137

Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J (2021) The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency.

J Biol Chem. 2021 Aug;297(2):100947

Nörpel J, Cavadini S, Schenk AD, Graff-Meyer A, Hess D, Seebacher J, Chao JA, Bhaskar V. (2021) Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture.

PLoS Biol. 2021 Jul 23;19(7):e3001344

Gudipati RK, Braun K, Gypas F, Hess D, Schreier J, Carl SH, Ketting RF, Großhans H (2021) Protease-mediated processing of Argonaute proteins controls small RNA association.

Mol Cell. 2021 Jun 3;81(11):2388-2402.e8

Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J (2021) Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells.

EMBO J. 2021 Apr 28;:e106818

Hendaoui I, Lahmar A, Campo L, Mebarki S, Bichet S, Hess D, Degen M, Kchir N, Charrada-Ben Farhat L, Hefaiedh R, Ruiz C, Terracciano LM, Tucker RP, Hendaoui L, Chiquet-Ehrismann R (2021) Tenascin-W Is a Novel Stromal Marker in Biliary Tract Cancers.

Front Immunol. 2020;11:630139

Challa K, Schmid CD, Kitagawa S, Cheblal A, Iesmantavicius V, Seeber A, Amitai A, Seebacher J, Hauer MH, Shimada K, Gasser SM (2021) Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair.

Mol Cell. 2021 Feb 18;81(4):811-829.e6

Saito M, Iestamantavicius V, Hess D, Matthias P (2020) Monitoring Acetylation of the RNA Helicase DDX3X, a Protein Critical for Formation of Stress Granules.

Methods Mol Biol. 2021;2209:217-234

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


Platform/Service Head

In current position since 2012
» Contact details

Technical/Research associates

In current position since 1995
» Contact details

In current position since 2017
» Contact details


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