Z04

Advanced Proteomics

Funding period: 2017-2029

Project Z04

Project Leaders

Prof. Dr. Jeroen Krijgsveld

 Project Leader Z04

Abstract

Project Z04 will offer a platform for cutting-edge mass spectrometry-based proteome analysis to investigate proteome composition and dynamics. We will support a broad range of applications, including global proteome profiling, secretome analysis, phosphoproteomics, protein interactions, and single-cell proteomics studies, to understand Wnt signaling, trafficking, and downstream pathways. Furthermore, we will apply advanced methods for temporal, spatial, and single-cell proteome analysis to uncover the functional dynamics of Wnt signaling.

Project-related Publications

Combined MEK and PARP inhibition enhances radiation response in rectal cancer

Xiao Q, Riedesser JE, Mulholland T, Li Z, Buchloh J, Albrecht P, Yang X, Li M, Venkatachalam N, Skabkina O, Klupsch A, Eichhorn E, Wang L, Belle S, Schulte N, Schmitz D, Froelich MF, Trikhirhisthit K, Valentini E, Boonekamp KE, Petersen Y, Miersch T, Burgermeister E, Herskind C, Veldwijk MR, Brochhausen C, Ihnatko R, Krijgsveld J, Kurth I, Zhu Y, Ma Y, Cao K, Boutros M, Ebert MP, Zhan T, Betge J. Cell Rep Med. 2025 Aug 5:102284. doi: 10.1016/j.xcrm.2025.102284. Online ahead of print.

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DEAD box RNA helicases are pervasive protein kinase interactors and activators

Hirth A, Fatti E, Netz E, Acebron SP, Papageorgiou D, Švorinić A, Cruciat CM, Karaulanov E, Gopanenko A, Zhu T, Sinning I, Krijgsveld J, Kohlbacher O, Niehrs C. Genome Res. 2024 Jul 23;34(6):952-966. doi: 10.1101/gr.278264.123. PMID: 38986579

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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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