Exploiting the Tumor Proteome Activity Status for Future Cancer Therapies

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Proteome activity landscapes of tumor cell lines determine drug responses

Author(s): Martin Frejno, Chen Meng, Benjamin Ruprecht, Thomas Oellerich, Sebastian Scheich, Karin Kleigrewe, Enken Drecoll, Patroklos Samaras, Alexander Hogrebe, Dominic Helm, Julia Mergner, Jana Zecha, Stephanie Heinzlmeir, Mathias Wilhelm, Julia Dorn, Hans-Michael Kvasnicka, Hubert Serve, Wilko Weichert, Bernhard Kuster
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17336-9

Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics

Author(s): Stephan Eckert, Nicola Berner, Karl Kramer, Annika Schneider, Julian Müller, Severin Lechner, Sarah Brajkovic, Amirhossein Sakhteman, Christian Graetz, Jonas Fackler, Michael Dudek, Michael W. Pfaffl, Percy Knolle, Stephanie Wilhelm, Bernhard Kuster
Published in: Nature Biotechnology, 2024, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-024-02218-y

Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

Author(s): Jana Zecha, Chien-Yun Lee, Florian P. Bayer, Chen Meng, Vincent Grass, Johannes Zerweck, Karsten Schnatbaum, Thomas Michler, Andreas Pichlmair, Christina Ludwig, Bernhard Kuster
Published in: Molecular & Cellular Proteomics, Issue 19/9, 2020, Page(s) 1503-1522, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra120.002164

CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves

Author(s): Bayer FP, Gander M, Kuster B, The M
Published in: Nature Communications, Issue 14(1), 2023, Page(s) 7902, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-43696-z

Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue

Author(s): Stephan Eckert, Yun-Chien Chang, Florian P Bayer, Matthew The, Peer-Hendrik Kuhn, Wilko Weichert, Bernhard Kuster
Published in: Journal of Proteome Research, Issue 20(12), 2021, Page(s) 5402-5411, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00695

Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting

Author(s): Bian Y, Bayer FP, Chang YC, Meng C, Hoefer S, Deng N, Zheng R, Boychenko O, Kuster B.
Published in: Analytical Chemistry, 2021, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c00257

Identification of 7 000-9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC-MS/MS.

Author(s): Yangyang Bian; Yangyang Bian; Piero Giansanti; Julia Mergner; Runsheng Zheng; Mathias Wilhelm; Alexander Boychenko; Bernhard Kuster
Published in: Analytical Chemistry, Issue 93(25), 2021, Page(s) 8687-8692, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c00738

ProteomicsDB: toward a FAIR open-source resource for life-science research

Author(s): Lautenbacher, L., Samaras, P., Muller, J., Grafberger, A., Shraideh, M., Rank, J., Fuchs, S. T., Schmidt, T. K., The, M., Dallago, C., Wittges, H., Rost, B., Krcmar, H., Kuster, B. & Wilhelm, M.
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1026

Mass spectrometry-based draft of the mouse proteome

Author(s): Piero Giansanti, Patroklos Samaras, Yangyang Bian, Chen Meng, Andrea Coluccio, Martin Frejno, Hannah Jakubowsky, Sophie Dobiasch, Rashmi R Hazarika, Julia Rechenberger, Julia Calzada-Wack, Johannes Krumm, Sebastian Mueller, Chien-Yun Lee, Nicole Wimberger, Ludwig Lautenbacher, Zonera Hassan, Yun-Chien Chang, Chiara Falcomatà, Florian P Bayer, Stefanie Bärthel, Tobias Schmidt, Roland Rad, Stephan
Published in: Nature Methods, 2022, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01526-y

Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors.

Author(s): Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B.
Published in: Nature Chemical Biology, 2023, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-023-01459-3

SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering

Author(s): Firas Hamood, Florian P Bayer, Mathias Wilhelm, Bernhard Kuster, Matthew The
Published in: Molecular & Cellular Proteomics, Issue 21(8), 2022, Page(s) 100238, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100238

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics

Author(s): Zecha J, Bayer FP, Wiechmann S, Woortman J, Berner N, Müller J, Schneider A, Kramer K, Abril-Gil M, Hopf T, Reichart L, Chen L, Hansen FM, Lechner S, Samaras P, Eckert S, Lautenbacher L, Reinecke M, Hamood F, Prokofeva P, Vornholz L, Falcomatà C, Dorsch M, Schröder A, Venhuizen A, Wilhelm S, Médard G, Stoehr G, Ruland J, Grüner BM, Saur D, Buchner M, Ruprecht B, Hahne H, The M, Wilhelm M, Kus
Published in: Science, Issue 380(6640), 2023, Page(s) 93–101, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.ade3925

Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics

Author(s): Lee CY, The M, Meng C, Bayer FP, Putzker K, Müller J, Streubel J, Woortman J, Sakhteman A, Resch M, Schneider A, Wilhelm S, Kuster B
Published in: Molecular Systems Biology, Issue 20(1), 2023, Page(s) 28-55, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-023-00004-7

Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups

Author(s): Matthew The, Patroklos Samaras, Bernhard Kuster, Mathias Wilhelm
Published in: Molecular & Cellular Proteomics, Issue 21(12), 2022, Page(s) 100437, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100437

Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics

Author(s): Yun-Chien Chang, Christian Gnann, Raphael R. Steimbach, Florian P. Bayer, Severin Lechner, Amirhossein Sakhteman, Miriam Abele, Jana Zecha, Jakob Trendel, Matthew The, Emma Lundberg, Aubry K. Miller, Bernhard Kuster
Published in: Cell Reports, Issue 43, 2024, Page(s) 114272, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2024.114272

Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling

Author(s): Jana Zecha, Wassim Gabriel, Ria Spalek, Yun-Chien Chang, Julia Mergner, Mathias Wilhelm, Florian Bassermann, Bernhard Kuster
Published in: Nature communications, Issue 13(1), 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27639-0

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS

Author(s): Yangyang Bian, Runsheng Zheng, Florian P. Bayer, Cassandra Wong, Yun-Chien Chang, Chen Meng, Daniel P. Zolg, Maria Reinecke,Jana Zecha, Svenja Wiechmann, Stephanie Heinzlmeir, Johannes Scherr, Bernhard Hemmer,Mike Baynham, Anne-Claude Gingras, Oleksandr Boychenko, and Bernhard Kuster
Published in: Nature communications, Issue 11(1), 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-13973-x

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