Z04

Advanced Proteomics

Funding period: 2017-2025

Project Z04

Project Leaders

Prof. Dr. Jeroen Krijgsveld

Prof. Dr. Jeroen Krijgsveld

 Project Leader Z04

Abstract

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.

Project-related Publications

DEAD box RNA helicases act as nucleotide exchange factors for casein kinase 2

Fatti E, Hirth A, Švorinić A, Günther M, Stier G, Cruciat CM, Acebrón SP, Papageorgiou D, Sinning I, Krijgsveld J, Höfer T, Niehrs C. Sci Signal. 2023 Apr 25;16(782):eabp8923. doi: 10.1126/scisignal.abp8923. Epub 2023 Apr 25. PMID: 37098120

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Cracking chromatin with proteomics: From chromatome to histone modifications

Sigismondo G, Papageorgiou DN, Krijgsveld J. Proteomics. 2022 May 28:e2100206. doi: 10.1002/pmic.202100206. Online ahead of print. PMID: 35633285

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Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons

Bunina D, Abazova N, Diaz N, Noh KM, Krijgsveld J, Zaugg JB. Cell Syst. 2020 Jun 24;10(6):480-494.e8. doi: 10.1016/j.cels.2020.05.003. Epub 2020 Jun 17.

PMID: 32553182

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Protease‐resistant streptavidin for interaction proteomics

Rafiee MR, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. Mol Syst Biol. 2020 May;16(5):e9370. PMID: 32400114

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Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity

Carnesecchi J, Sigismondo G, Domsch K, Baader CEP, Rafiee MR, Krijgsveld J, Lohmann I. Nat Commun. 2020 Mar 13;11(1):1388. doi: 10.1038/s41467-020-15223-x. PMID: 32170121

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Automated sample preparation with SP3 for low-input clinical proteomics

Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. Mol Syst Biol. 2020 Jan;16(1):e9111. doi: 10.15252/msb.20199111. PMID: 32129943

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The human RNAbinding proteome and its dynamics during arsenite-induced translational arrest

Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. Cell. 2019 Jan 10;176(1-2):391-403.e19. doi: 10.1016/j.cell.2018.11.004. Epub 2018 Dec 6. PMID: 30528433

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Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

Hughes CS, Moggridge S, Müller T, Sorensen PH, Morin GB, Krijgsveld J. Nat Protoc. 2019 Jan;14(1):68-85. doi: 10.1038/s41596-018-0082-x.
PMID: 30464214

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Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)

Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M. Mol Cell Proteomics. 2018 Apr;17(4):810-825. doi: 10.1074/mcp.RA117.000189. Epub 2018 Jan 23. PMID: 29363612

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Expanding the circuitry of pluripotency by selective isolation of chromatin-associated proteins

Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J. Mol Cell. 2016 Nov 3;64(3):624-635. doi: 10.1016/j.molcel.2016.09.019. Epub 2016 Oct 20. PMID: 27773674

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Selective enrichment of newly synthesized proteins for quantitative secretome analysis

Eichelbaum K, Winter M, Berriel Diaz M, Herzig S, Krijgsveld J. Nat Biotechnol. 2012 Oct;30(10):984-90. doi: 10.1038/nbt.2356. Epub 2012 Sep 23.
PMID: 23000932

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