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.
Services
- 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.
Contact
Jan Seebacher: Platform head, proteomics
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):e55928Amante 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):145-153Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC center dot DNA center dot Cdc6.
Nat Commun. 2022 Feb 25;13(1):1059Delaney 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):85-96Challa K, Seebacher J, Gasser SM (2021) Sucrose gradient chromatin enrichment for quantitative proteomics analysis in budding yeast.
STAR Protoc. 2021 Dec 17;2(4):100825Hurst 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;:e108439Grand 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):133-137Olivieri 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):100947Nörpel 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):e3001344Gudipati 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.e8Olivieri 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;:e106818Hendaoui 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;11:630139Challa 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.e6Saito 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;2209:217-234Tuck 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.e13Mayer 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):e102591Deshpande 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):e101744Fontana 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):2535Redolfi 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):471-480Villegas 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.e8Saito 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):51-61Ginno 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):4048Schnellmann 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):1410-1425Ostapcuk 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):739-743Knuckles 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):415-429Flury 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.e9Hauer 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):99-107Miyake 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):748-54Grzmil 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):1412-21Poli 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
Members
Platform/Service Head

In current position since 2012
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Technical/Research associates

In current position since 1995
» Contact details

In current position since 2017
» Contact details