Exploiting the Tumor Proteome Activity Status for Future Cancer Therapies

Publications

Proteome activity landscapes of tumor cell lines determine drug responses

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-17336-9

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

Auteurs: Jana Zecha, Chien-Yun Lee, Florian P. Bayer, Chen Meng, Vincent Grass, Johannes Zerweck, Karsten Schnatbaum, Thomas Michler, Andreas Pichlmair, Christina Ludwig, Bernhard Kuster
Publié dans: Molecular & Cellular Proteomics, Numéro 19/9, 2020, Page(s) 1503-1522, ISSN 1535-9476
Éditeur: 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

Auteurs: Bayer FP, Gander M, Kuster B, The M
Publié dans: Nature Communications, Numéro 14(1), 2023, Page(s) 7902, ISSN 2041-1723
Éditeur: 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

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

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

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

Defining the carrier proteome limit for single-cell proteomics

Auteurs: Tommy K Cheung, Chien-Yun Lee, Florian P Bayer, Atticus McCoy, Bernhard Kuster, Christopher M Rose
Publié dans: Nature Methods, Numéro 18(1), 2021, Page(s) 76-83, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-020-01002-5

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

Auteurs: Firas Hamood, Florian P Bayer, Mathias Wilhelm, Bernhard Kuster, Matthew The
Publié dans: Molecular & Cellular Proteomics, Numéro 21(8), 2022, Page(s) 100238, ISSN 1535-9476
Éditeur: 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

Auteurs: 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
Publié dans: Science, Numéro 380(6640), 2023, Page(s) 93–101, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.ade3925

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

Auteurs: 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
Publié dans: Molecular Systems Biology, Numéro 20(1), 2023, Page(s) 28-55, ISSN 1744-4292
Éditeur: 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

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

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

Auteurs: Jana Zecha, Wassim Gabriel, Ria Spalek, Yun-Chien Chang, Julia Mergner, Mathias Wilhelm, Florian Bassermann, Bernhard Kuster
Publié dans: Nature communications, Numéro 13(1), 2022, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: Nature communications, Numéro 11(1), 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-13973-x

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