Project Z04

Project leader: Jeroen Krijgsveld

Advanced Proteomics

Project Z04 will provide access to a platform for mass spectrometry-based proteome analysis. The group has a longstanding interest and expertise in the development and application of innovative proteomic methods, aimed to gain insight in proteome dynamics, to characterize specific sub-proteomes, to enable low-input proteome analysis, and to streamline sample handling in automated workflows. Support for global proteome profiling, nascent proteomics, secretome analysis, and identification of protein interactions will be provided to gain a better understanding of Wnt signaling, trafficking and downstream signaling. In addition, technologies for temporal and spatial proteome analysis will be advanced to uncover the dynamics of Wnt signaling.

Hochentwickelte Massenspektrometrie

Das Z04-Zentralprojekt wird dem Konsortium Zugang zu verschiedenen Massenspektrometrie-Methoden zur Proteom-Analyse zur Verfügung stellen. Die Arbeitsgruppe hat langjährige Erfahrung bezüglich der Entwicklung und Anwendung verschiedener Methoden hinsichtlich der Analyse spezifischer Teilproteome und bei der automatischen Probenvorbereitung für die Proteomik. Im Rahmen des SFB 1324 werden wir Unterstützung bei der globalen Proteom- und Phoshoproteom-Analyse, Sekretomanalyse sowie bei der Identifizierung von Interaktionspartnern gewährleisten, wodurch neue Erkenntnisse hinsichtlich des Wnt-Signalwegs, der Transportmechanismen und der nachgeschalteten Faktoren gewonnen werden können.

Project-related publications

  • Bunina D, Abazova N, Diaz N, Noh K-M*, Krijgsveld J*, Zaugg JB*. 2020. Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons. *Joint senior authors. Cell Syst. 10(6):480-494.e8. PMID: 32553182
  • Rafiee MR, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. 2020. Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol. 16(5):e9370. PMID: 32400114
  • Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. 2020. Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol. 16(1):e9111. PMID: 32129943.
  • Kuhn TC, Knobel J, Burkert-Rettenmaier S, Li X, Meyer IS, Jungmann A, Sicklinger F, Backs J, Lasitschka F, Müller OJ, Katus HA, Krijgsveld J*, Leuschner F*. 2020. Secretome analysis of cardiomyocytes identifies PCSK6 as a novel player in cardiac remodeling after myocardial infarction. *Joint senior authors. Circulation. 141:1628–1644. PMID: 32100557.
  • Carnesecchi J, Sigismondo G, Domsch K, Baader CEP, Rafiee MR, Krijgsveld J and Lohmann I. 2020. Multilevel and lineage-specific interactome of the Hox transcription factor Ubx contributes to its functional specificity. Nature Communications. 11(1): 1388. PMID: 32170121
  • Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. 2019. The human RNAbinding proteome and its dynamics during arsenite-induced translational arrest. Cell. 176(1-2):391-
    403. PMID: 30528433
  • Hughes, C., S. Moggridge, T. Müller, P. Sorensen, G. Morin, and J. Krijgsveld. 2019. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nature Protocols. 14(1):68-85. PMID: 30464214
  • Buczak, K., A. Ori, J.M. Kirkpatrick, K. Holzer, D. Dauch, S. Roessler, V. Endris, F. Lasitschka, L. Parca, A. Schmidt, L. Zender, P. Schirmacher, J. Krijgsveld, S. Singer, and M. Beck. 2018. Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC). Mol. Cell. Proteomics. 17:810–825. PMID: 29363612
  • Rafiee, M.-R., C. Girardot, G. Sigismondo, J. Krijgsveld. 2016. Expanding the circuitry of pluripotency by selective isolation of chromatin-associated proteins. Mol Cell. 64(3):624-635. PMID: 27773674
  • Eichelbaum, K., M. Winter, M. Berriel Diaz, S. Herzig, and J. Krijgsveld. 2012. Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nature Biotechnology. 30:984-990. PMID: 23000932