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Technical University of Munich

Prof. Dr. Mathias Wilhelm

Professur für Computational Mass Spectrometry

https://www1.ls.tum.de/en/compms/group-members/people/mathias-wilhelm/

Publications

2024

  • Abbas, Qussai; Wilhelm, Mathias; Kuster, Bernhard; Poppenberger, Brigitte; Frishman, Dmitrij: Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies. BMC Genomics 25 (1), 2024 more…
  • Eckert, Stephan; Berner, Nicola; Kramer, Karl; Schneider, Annika; Müller, Julian; Lechner, Severin; Brajkovic, Sarah; Sakhteman, Amirhossein; Graetz, Christian; Fackler, Jonas; Dudek, Michael; Pfaffl, Michael W.; Knolle, Percy; Wilhelm, Stephanie; Kuster, Bernhard: Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics. Nature Biotechnology, 2024 more…
  • The, Matthew; Picciani, Mario; Jensen, Cecilia; Gabriel, Wassim; Kuster, Bernhard; Wilhelm, Mathias: AI-Assisted Processing Pipeline to Boost Protein Isoform Detection. In: Protein Bioinformatics. Springer US, 2024 more…

2023

  • Knecht, Sascha; Eberl, H. Christian; Kreisz, Norbert; Ugwu, Ukamaka Juliet; Starikova, Tatiana; Kuster, Bernhard; Wilhelm, Stephanie: An introduction to analytical challenges, approaches and applications in mass-spectrometry-based secretomics. Molecular & Cellular Proteomics, 2023, 100636 more…
  • Kücükdisli, Murat; Bel-Abed, Hassen; Cirillo, Davide; Lo, Wen-Ting; Efrém, Nina-Louisa; Horatscheck, André; Perepelittchenko, Liudmila; Prokofeva, Polina; Ehret, Theresa A. L.; Radetzki, Silke; Neuenschwander, Martin; Specker, Edgar; Médard, Guillaume; Müller, Susanne; Wilhelm, Stephanie; Kuster, Bernhard; von Kries, Jens Peter; Haucke, Volker; Nazaré, Marc: Structural Basis for Highly Selective Class II Alpha Phosphoinositide-3-Kinase Inhibition. Journal of Medicinal Chemistry, 2023 more…
  • Lee, Chien-Yun; The, Matthew; Meng, Chen; Bayer, Florian P; Putzker, Kerstin; Müller, Julian; Streubel, Johanna; Woortman, Julia; Sakhteman, Amirhossein; Resch, Moritz; Schneider, Annika; Wilhelm, Stephanie; Kuster, Bernhard: Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics. Molecular Systems Biology, 2023 more…
  • Picciani, Mario; Gabriel, Wassim; Giurcoiu, Victor‐George; Shouman, Omar; Hamood, Firas; Lautenbacher, Ludwig; Jensen, Cecilia Bang; Müller, Julian; Kalhor, Mostafa; Soleymaniniya, Armin; Kuster, Bernhard; The, Matthew; Wilhelm, Mathias: Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit. PROTEOMICS, 2023 more…
  • Reinecke, Maria; Brear, Paul; Vornholz, Larsen; Berger, Benedict-Tilmann; Seefried, Florian; Wilhelm, Stephanie; Samaras, Patroklos; Gyenis, Laszlo; Litchfield, David William; Médard, Guillaume; Müller, Susanne; Ruland, Jürgen; Hyvönen, Marko; Wilhelm, Mathias; Kuster, Bernhard: Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nature Chemical Biology, 2023 more…
  • Tretter, Celina; de Andrade Krätzig, Niklas; Pecoraro, Matteo; Lange, Sebastian; Seifert, Philipp; von Frankenberg, Clara; Untch, Johannes; Zuleger, Gabriela; Wilhelm, Mathias; Zolg, Daniel P.; Dreyer, Florian S.; Bräunlein, Eva; Engleitner, Thomas; Uhrig, Sebastian; Boxberg, Melanie; Steiger, Katja; Slotta-Huspenina, Julia; Ochsenreither, Sebastian; von Bubnoff, Nikolas; Bauer, Sebastian; Boerries, Melanie; Jost, Philipp J.; Schenck, Kristina; Dresing, Iska; Bassermann, Florian; Friess, Helmut; Reim, Daniel; Grützmann, Konrad; Pfütze, Katrin; Klink, Barbara; Schröck, Evelin; Haller, Bernhard; Kuster, Bernhard; Mann, Matthias; Weichert, Wilko; Fröhling, Stefan; Rad, Roland; Hiltensperger, Michael; Krackhardt, Angela M.: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nature Communications 14 (1), 2023 more…
  • Zecha, Jana; Bayer, Florian P.; Wiechmann, Svenja; Woortman, Julia; Berner, Nicola; Müller, Julian; Schneider, Annika; Kramer, Karl; Abril-Gil, Mar; Hopf, Thomas; Reichart, Leonie; Chen, Lin; Hansen, Fynn M.; Lechner, Severin; Samaras, Patroklos; Eckert, Stephan; Lautenbacher, Ludwig; Reinecke, Maria; Hamood, Firas; Prokofeva, Polina; Vornholz, Larsen; Falcomatà, Chiara; Dorsch, Madeleine; Schröder, Ayla; Venhuizen, Anton; Wilhelm, Stephanie; Médard, Guillaume; Stoehr, Gabriele; Ruland, Jürgen; Grüner, Barbara M.; Saur, Dieter; Buchner, Maike; Ruprecht, Benjamin; Hahne, Hannes; The, Matthew; Wilhelm, Mathias; Kuster, Bernhard: Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science 380 (6640), 2023, 93-101 more…

2022

  • Bozilovic, Jelena; Eing, Lorenz; Berger, Benedict-Tilman; Adhikari, Bikash; Weckesser, Janik; Berner, Nicola B.; Wilhelm, Stephanie; Kuster, Bernhard; Wolf, Elmar; Knapp, Stefan: Novel, highly potent PROTACs targeting AURORA-A kinase. Current Research in Chemical Biology 2, 2022, 100032 more…
  • Gabriel, Wassim; The, Matthew; Zolg, Daniel P.; Bayer, Florian P.; Shouman, Omar; Lautenbacher, Ludwig; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Huhmer, Andreas; Wenschuh, Holger; Reimer, Ulf; Médard, Guillaume; Kuster, Bernhard; Wilhelm, Mathias: Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides. Analytical Chemistry 94 (20), 2022, 7181-7190 more…
  • Giansanti, Piero; Samaras, Patroklos; Bian, Yangyang; Meng, Chen; Coluccio, Andrea; Frejno, Martin; Jakubowsky, Hannah; Dobiasch, Sophie; Hazarika, Rashmi R.; Rechenberger, Julia; Calzada-Wack, Julia; Krumm, Johannes; Mueller, Sebastian; Lee, Chien-Yun; Wimberger, Nicole; Lautenbacher, Ludwig; Hassan, Zonera; Chang, Yun-Chien; Falcomatà, Chiara; Bayer, Florian P.; Bärthel, Stefanie; Schmidt, Tobias; Rad, Roland; Combs, Stephanie E.; The, Matthew; Johannes, Frank; Saur, Dieter; de Angelis, Martin Hrabe; Wilhelm, Mathias; Schneider, Günter; Kuster, Bernhard: Mass spectrometry-based draft of the mouse proteome. Nature Methods 19 (7), 2022, 803-811 more…
  • Hamood, Firas; Bayer, Florian P.; Wilhelm, Mathias; Kuster, Bernhard; The, Matthew: SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering. Molecular & Cellular Proteomics, 2022, 100238 more…
  • Krumm, Johannes; Sekine, Keisuke; Samaras, Patroklos; Brazovskaja, Agnieska; Breunig, Markus; Yasui, Ryota; Kleger, Alexander; Taniguchi, Hideki; Wilhelm, Mathias; Treutlein, Barbara; Camp, J. Gray; Kuster, Bernhard: High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Reports 38 (13), 2022, 110604 more…
  • Lechner, Severin; Malgapo, Martin Ian P.; Grätz, Christian; Steimbach, Raphael R.; Baron, Agnes; Rüther, Patrick; Nadal, Simon; Stumpf, Carmen; Loos, Christina; Ku, Xin; Prokofeva, Polina; Lautenbacher, Ludwig; Heimburg, Tino; Würf, Vivian; Meng, Chen; Wilhelm, Mathias; Sippl, Wolfgang; Kleigrewe, Karin; Pauling, Josch K.; Kramer, Karl; Miller, Aubry K.; Pfaffl, Michael W.; Linder, Maurine E.; Kuster, Bernhard; Médard, Guillaume: Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nature Chemical Biology, 2022 more…
  • The, Matthew; Samaras, Patroklos; Kuster, Bernhard; Wilhelm, Mathias: Re-analysis of ProteomicsDB using an accurate, sensitive and scalable false discovery rate estimation approach for protein groups. Molecular & Cellular Proteomics, 2022, 100437 more…
  • Zecha, Jana; Gabriel, Wassim; Spallek, Ria; Chang, Yun-Chien; Mergner, Julia; Wilhelm, Mathias; Bassermann, Florian; Kuster, Bernhard: Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling. Nature Communications 13 (1), 2022 more…
  • Zecha, Jana; Gabriel, Wassim; Spallek, Ria; Chang, Yun-Chien; Mergner, Julia; Wilhelm, Mathias; Bassermann, Florian; Kuster, Bernhard: Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling. Nature Communications 13 (1), 2022 more…

2021

  • Alfaro, Javier Antonio; Bohländer, Peggy; Dai, Mingjie; Filius, Mike; Howard, Cecil J.; van Kooten, Xander F.; Ohayon, Shilo; Pomorski, Adam; Schmid, Sonja; Aksimentiev, Aleksei; Anslyn, Eric V.; Bedran, Georges; Cao, Chan; Chinappi, Mauro; Coyaud, Etienne; Dekker, Cees; Dittmar, Gunnar; Drachman, Nicholas; Eelkema, Rienk; Goodlett, David; Hentz, Sébastien; Kalathiya, Umesh; Kelleher, Neil L.; Kelly, Ryan T.; Kelman, Zvi; Kim, Sung Hyun; Kuster, Bernhard; Rodriguez-Larrea, David; Lindsay, Stuart; Maglia, Giovanni; Marcotte, Edward M.; Marino, John P.; Masselon, Christophe; Mayer, Michael; Samaras, Patroklos; Sarthak, Kumar; Sepiashvili, Lusia; Stein, Derek; Wanunu, Meni; Wilhelm, Mathias; Yin, Peng; Meller, Amit; Joo, Chirlmin: The emerging landscape of single-molecule protein sequencing technologies. Nature Methods 18 (6), 2021, 604-617 more…
  • Bian, Yangyang; The, Matthew; Giansanti, Piero; Mergner, Julia; Zheng, Runsheng; Wilhelm, Mathias; Boychenko, Alexander; Kuster, Bernhard: Identification of 7 000–9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC–MS/MS. Analytical Chemistry, 2021 more…
  • Lautenbacher, Ludwig; Samaras, Patroklos; Muller, Julian; Grafberger, Andreas; Shraideh, Marwin; Rank, Johannes; Fuchs, Simon T; Schmidt, Tobias K; The, Matthew; Dallago, Christian; Wittges, Holger; Rost, Burkhard; Krcmar, Helmut; Kuster, Bernhard; Wilhelm, Mathias: ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Research, 2021 more…
  • Verbruggen, Steven; Gessulat, Siegfried; Gabriels, Ralf; Matsaroki, Anna; Van de Voorde, Hendrik; Kuster, Bernhard; Degroeve, Sven; Martens, Lennart; Van Criekinge, Wim; Wilhelm, Mathias; Menschaert, Gerben: Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics. Molecular & Cellular Proteomics 20, 2021, 100076 more…
  • Wilhelm, Mathias; Zolg, Daniel P.; Graber, Michael; Gessulat, Siegfried; Schmidt, Tobias; Schnatbaum, Karsten; Schwencke-Westphal, Celina; Seifert, Philipp; de Andrade Krätzig, Niklas; Zerweck, Johannes; Knaute, Tobias; Bräunlein, Eva; Samaras, Patroklos; Lautenbacher, Ludwig; Klaeger, Susan; Wenschuh, Holger; Rad, Roland; Delanghe, Bernard; Huhmer, Andreas; Carr, Steven A.; Clauser, Karl R.; Krackhardt, Angela M.; Reimer, Ulf; Kuster, Bernhard: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nature Communications 12 (1), 2021 more…

2020

  • Frejno, Martin; Meng, Chen; Ruprecht, Benjamin; Oellerich, Thomas; Scheich, Sebastian; Kleigrewe, Karin; Drecoll, Enken; Samaras, Patroklos; Hogrebe, Alexander; Helm, Dominic; Mergner, Julia; Zecha, Jana; Heinzlmeir, Stephanie; Wilhelm, Mathias; Dorn, Julia; Kvasnicka, Hans-Michael; Serve, Hubert; Weichert, Wilko; Kuster, Bernhard: Proteome activity landscapes of tumor cell lines determine drug responses. Nature Communications 11 (1), 2020 more…
  • Jarzab, Anna; Kurzawa, Nils; Hopf, Thomas; Moerch, Matthias; Zecha, Jana; Leijten, Niels; Bian, Yangyang; Musiol, Eva; Maschberger, Melanie; Stoehr, Gabriele; Becher, Isabelle; Daly, Charlotte; Samaras, Patroklos; Mergner, Julia; Spanier, Britta; Angelov, Angel; Werner, Thilo; Bantscheff, Marcus; Wilhelm, Mathias; Klingenspor, Martin; Lemeer, Simone; Liebl, Wolfgang; Hahne, Hannes; Savitski, Mikhail M.; Kuster, Bernhard: Meltome atlas—thermal proteome stability across the tree of life. Nature Methods 17 (5), 2020, 495-503 more…
  • Mergner, Julia; Frejno, Martin; List, Markus; Papacek, Michael; Chen, Xia; Chaudhary, Ajeet; Samaras, Patroklos; Richter, Sandra; Shikata, Hiromasa; Messerer, Maxim; Lang, Daniel; Altmann, Stefan; Cyprys, Philipp; Zolg, Daniel P.; Mathieson, Toby; Bantscheff, Marcus; Hazarika, Rashmi R.; Schmidt, Tobias; Dawid, Corinna; Dunkel, Andreas; Hofmann, Thomas; Sprunck, Stefanie; Falter-Braun, Pascal; Johannes, Frank; Mayer, Klaus F. X.; Jürgens, Gerd; Wilhelm, Mathias; Baumbach, Jan; Grill, Erwin; Schneitz, Kay; Schwechheimer, Claus; Kuster, Bernhard: Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 579 (7799), 2020, 409-414 more…
  • Mergner, Julia; Frejno, Martin; Messerer, Maxim; Lang, Daniel; Samaras, Patroklos; Wilhelm, Mathias; Mayer, Klaus F. X.; Schwechheimer, Claus; Kuster, Bernhard: Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis. Scientific Data 7 (1), 2020 more…
  • Searle, Brian C.; Swearingen, Kristian E.; Barnes, Christopher A.; Schmidt, Tobias; Gessulat, Siegfried; Küster, Bernhard; Wilhelm, Mathias: Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nature Communications 11 (1), 2020 more…

2019

  • Gessulat, Siegfried; Schmidt, Tobias; Zolg, Daniel Paul; Samaras, Patroklos; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Rechenberger, Julia; Delanghe, Bernard; Huhmer, Andreas; Reimer, Ulf; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias: Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nature Methods 16 (6), 2019, 509-518 more…
  • Rechenberger, Julia; Samaras, Patroklos; Jarzab, Anna; Behr, Juergen; Frejno, Martin; Djukovic, Ana; Sanz, Jaime; González-Barberá, Eva M.; Salavert, Miguel; López-Hontangas, Jose Luis; Xavier, Karina B.; Debrauwer, Laurent; Rolain, Jean-Marc; Sanz, Miguel; Garcia-Garcera, Marc; Wilhelm, Mathias; Ubeda, Carles; Kuster, Bernhard: Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae. Proteomes 7 (1), 2019, 2 more…
  • Reinecke, Maria; Heinzlmeir, Stephanie; Wilhelm, Mathias; Médard, Guillaume; Klaeger, Susan; Kuster, Bernhard: Kinobeads: A Chemical Proteomic Approach for Kinase Inhibitor Selectivity Profiling and Target Discovery. Target Discovery and Validation: Methods and Strategies for Drug Discovery, 2019, 97--130 more…
  • Reinecke, Maria; Ruprecht, Benjamin; Poser, Sandra; Wiechmann, Svenja; Wilhelm, Mathias; Heinzlmeir, Stephanie; Kuster, Bernhard; Médard, Guillaume: Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors. ACS Chemical Biology 14 (4), 2019, 655-664 more…
  • Samaras, Patroklos; Schmidt, Tobias; Frejno, Martin; Gessulat, Siegfried; Reinecke, Maria; Jarzab, Anna; Zecha, Jana; Mergner, Julia; Giansanti, Piero; Ehrlich, Hans-Christian; Aiche, Stephan; Rank, Johannes; Kienegger, Harald; Krcmar, Helmut; Kuster, Bernhard; Wilhelm, Mathias: ProteomicsDB: a multi-omics and multi-organism resource for life science research. Nucleic Acids Research, 2019 more…
  • Seefried, Florian; Schmidt, Tobias; Reinecke, Maria; Heinzlmeir, Stephanie; Kuster, Bernhard; Wilhelm, Mathias: CiRCus: A Framework to Enable Classification of Complex High-Throughput Experiments. Journal of Proteome Research 18 (4), 2019, 1486-1493 more…
  • Verbruggen, Steven; Ndah, Elvis; Van Criekinge, Wim; Gessulat, Siegfried; Kuster, Bernhard; Wilhelm, Mathias; Van Damme, Petra; Menschaert, Gerben: PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Molecular & Cellular Proteomics 18 (8 suppl 1), 2019, S126-S140 more…
  • Wang, Dongxue; Eraslan, Basak; Wieland, Thomas; Hallström, Björn; Hopf, Thomas; Zolg, Daniel Paul; Zecha, Jana; Asplund, Anna; Li, Li‐hua; Meng, Chen; Frejno, Martin; Schmidt, Tobias; Schnatbaum, Karsten; Wilhelm, Mathias; Ponten, Frederik; Uhlen, Mathias; Gagneur, Julien; Hahne, Hannes; Kuster, Bernhard: A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Molecular Systems Biology 15 (2), 2019 more…

2018

  • Deutsch, Eric W.; Perez-Riverol, Yasset; Chalkley, Robert J.; Wilhelm, Mathias; Tate, Stephen; Sachsenberg, Timo; Walzer, Mathias; Käll, Lukas; Delanghe, Bernard; Böcker, Sebastian; Schymanski, Emma L.; Wilmes, Paul; Dorfer, Viktoria; Kuster, Bernhard; Volders, Pieter-Jan; Jehmlich, Nico; Vissers, Johannes P. C.; Wolan, Dennis W.; Wang, Ana Y.; Mendoza, Luis; Shofstahl, Jim; Dowsey, Andrew W.; Griss, Johannes; Salek, Reza M.; Neumann, Steffen; Binz, Pierre-Alain; Lam, Henry; Vizcaíno, Juan Antonio; Bandeira, Nuno; Röst, Hannes: Expanding the Use of Spectral Libraries in Proteomics. Journal of Proteome Research 17 (12), 2018, 4051-4060 more…
  • Lee, Chien-Yun; Wang, Dongxue; Wilhelm, Mathias; Zolg, Daniel P.; Schmidt, Tobias; Schnatbaum, Karsten; Reimer, Ulf; Pontén, Fredrik; Uhlén, Mathias; Hahne, Hannes; Kuster, Bernhard: Mining the Human Tissue Proteome for Protein Citrullination. Molecular & Cellular Proteomics 17 (7), 2018, 1378-1391 more…
  • Mathew, Nimitha R; Baumgartner, Francis; Braun, Lukas; O'Sullivan, David; Thomas, Simone; Waterhouse, Miguel; Müller, Tony A; Hanke, Kathrin; Taromi, Sanaz; Apostolova, Petya; Illert, Anna L; Melchinger, Wolfgang; Duquesne, Sandra; Schmitt-Graeff, Annette; Osswald, Lena; Yan, Kai-Li; Weber, Arnim; Tugues, Sonia; Spath, Sabine; Pfeifer, Dietmar; Follo, Marie; Claus, Rainer; Lübbert, Michael; Rummelt, Christoph; Bertz, Hartmut; Wäsch, Ralph; Haag, Johanna; Schmidts, Andrea; Schultheiss, Michael; Bettinger, Dominik; Thimme, Robert; Ullrich, Evelyn; Tanriver, Yakup; Vuong, Giang Lam; Arnold, Renate; Hemmati, Philipp; Wolf, Dominik; Ditschkowski, Markus; Jilg, Cordula; Wilhelm, Konrad; Leiber, Christian; Gerull, Sabine; Halter, Jörg; Lengerke, Claudia; Pabst, Thomas; Schroeder, Thomas; Kobbe, Guido; Rösler, Wolf; Doostkam, Soroush; Meckel, Stephan et al.: Sorafenib promotes graft-versus-leukemia activity in mice and humans through IL-15 production in FLT3-ITD-mutant leukemia cells. Nature Medicine 24 (3), 2018, 282-291 more…
  • Mathew, Nimitha R; Baumgartner, Francis; Braun, Lukas; O'Sullivan, David; Thomas, Simone; Waterhouse, Miguel; Müller, Tony A; Hanke, Kathrin; Taromi, Sanaz; Apostolova, Petya; Illert, Anna L; Melchinger, Wolfgang; Duquesne, Sandra; Schmitt-Graeff, Annette; Osswald, Lena; Yan, Kai-Li; Weber, Arnim; Tugues, Sonia; Spath, Sabine; Pfeifer, Dietmar; Follo, Marie; Claus, Rainer; Lübbert, Michael; Rummelt, Christoph; Bertz, Hartmut; Wäsch, Ralph; Haag, Johanna; Schmidts, Andrea; Schultheiss, Michael; Bettinger, Dominik; Thimme, Robert; Ullrich, Evelyn; Tanriver, Yakup; Vuong, Giang Lam; Arnold, Renate; Hemmati, Philipp; Wolf, Dominik; Ditschkowski, Markus; Jilg, Cordula; Wilhelm, Konrad; Leiber, Christian; Gerull, Sabine; Halter, Jörg; Lengerke, Claudia; Pabst, Thomas; Schroeder, Thomas; Kobbe, Guido; Rösler, Wolf; Doostkam, Soroush; Meckel, Stephan et al.: Erratum: Sorafenib promotes graft-versus-leukemia activity in mice and humans through IL-15 production in FLT3-ITD-mutant leukemia cells. Nature Medicine 24 (4), 2018, 526--526 more…
  • Zecha, Jana; Meng, Chen; Zolg, Daniel Paul; Samaras, Patroklos; Wilhelm, Mathias; Kuster, Bernhard: Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. Molecular & Cellular Proteomics 17 (5), 2018, 974-992 more…
  • Zolg, Daniel Paul; Wilhelm, Mathias; Schmidt, Tobias; Médard, Guillaume; Zerweck, Johannes; Knaute, Tobias; Wenschuh, Holger; Reimer, Ulf; Schnatbaum, Karsten; Kuster, Bernhard: ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides. Molecular & Cellular Proteomics 17 (9), 2018, 1850-1863 more…

2017

  • Frejno, Martin; Zenezini Chiozzi, Riccardo; Wilhelm, Mathias; Koch, Heiner; Zheng, Runsheng; Klaeger, Susan; Ruprecht, Benjamin; Meng, Chen; Kramer, Karl; Jarzab, Anna; Heinzlmeir, Stephanie; Johnstone, Elaine; Domingo, Enric; Kerr, David; Jesinghaus, Moritz; Slotta‐Huspenina, Julia; Weichert, Wilko; Knapp, Stefan; Feller, Stephan M; Kuster, Bernhard: Pharmacoproteomic characterisation of human colon and rectal cancer. Molecular Systems Biology 13 (11), 2017, 951 more…
  • Heinzlmeir, Stephanie; Lohse, Jonas; Treiber, Tobias; Kudlinzki, Denis; Linhard, Verena; Gande, Santosh Lakshmi; Sreeramulu, Sridhar; Saxena, Krishna; Liu, Xiaofeng; Wilhelm, Mathias; Schwalbe, Harald; Kuster, Bernhard; Médard, Guillaume: Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors. ChemMedChem 12 (12), 2017, 999-1011 more…
  • Klaeger, Susan; Heinzlmeir, Stephanie; Wilhelm, Mathias; Polzer, Harald; Vick, Binje; Koenig, Paul-Albert; Reinecke, Maria; Ruprecht, Benjamin; Petzoldt, Svenja; Meng, Chen; Zecha, Jana; Reiter, Katrin; Qiao, Huichao; Helm, Dominic; Koch, Heiner; Schoof, Melanie; Canevari, Giulia; Casale, Elena; Depaolini, Stefania Re; Feuchtinger, Annette; Wu, Zhixiang; Schmidt, Tobias; Rueckert, Lars; Becker, Wilhelm; Huenges, Jan; Garz, Anne-Kathrin; Gohlke, Bjoern-Oliver; Zolg, Daniel Paul; Kayser, Gian; Vooder, Tonu; Preissner, Robert; Hahne, Hannes; Tõnisson, Neeme; Kramer, Karl; Götze, Katharina; Bassermann, Florian; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Walch, Axel; Greif, Philipp A.; Schneider, Sabine; Felder, Eduard Rudolf; Ruland, Juergen; Médard, Guillaume; Jeremias, Irmela; Spiekermann, Karsten; Kuster, Bernhard: The target landscape of clinical kinase drugs. Science 358 (6367), 2017, eaan4368 more…
  • Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias: ProteomicsDB. Nucleic Acids Research, 2017 more…
  • Wilhelm, Mathias; Hahne, Hannes; Savitski, Mikhail; Marx, Harald; Lemeer, Simone; Bantscheff, Marcus; Kuster, Bernhard: Wilhelm et al. reply. Nature 547 (7664), 2017, E23-E23 more…
  • Yu, Peng; Petzoldt, Svenja; Wilhelm, Mathias; Zolg, Daniel Paul; Zheng, Runsheng; Sun, Xuefei; Liu, Xiaodong; Schneider, Günter; Huhmer, Andreas; Kuster, Bernhard: Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis. Analytical Chemistry 89 (17), 2017, 8884-8891 more…
  • Zolg, Daniel P; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W; Aebersold, Ruedi; Moritz, Robert L; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard: Building ProteomeTools based on a complete synthetic human proteome. Nature Methods 14 (3), 2017, 259-262 more…
  • Zolg, Daniel Paul; Wilhelm, Mathias; Yu, Peng; Knaute, Tobias; Zerweck, Johannes; Wenschuh, Holger; Reimer, Ulf; Schnatbaum, Karsten; Kuster, Bernhard: PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration. PROTEOMICS 17 (21), 2017, 1700263 more…

2016

  • Heinzlmeir, S. ; Kudlinzki, D. ; Sreeramulu, S. ; Klaeger, S. ; Gande, S. ; Linhard, V. ; Wilhelm, M. ; Qiao, H. ; Helm, D. ; Ruprecht, B. ; Saxena, K. ; Medard, G. ; Schwalbe, H. ; Kuster, B.: Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs. ACS Chem Biol, 2016 more…
  • Koch, Heiner; Wilhelm, Mathias; Ruprecht, Benjamin; Beck, Scarlet; Frejno, Martin; Klaeger, Susan; Kuster, Bernhard: Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells. Journal of Proteome Research 15 (12), 2016, 4490-4504 more…
  • Yu, Peng; Hahne, Hannes; Wilhelm, Mathias; Kuster, Bernhard: Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics. Analytical and Bioanalytical Chemistry 409 (4), 2016, 1049-1057 more…

2015

  • Hao, Yanqi; Colak, Recep; Teyra, Joan; Corbi-Verge, Carles; Ignatchenko, Alexander; Hahne, Hannes; Wilhelm, Mathias; Kuster, Bernhard; Braun, Pascal; Kaida, Daisuke; Kislinger, Thomas; Kim, Philip M.: Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Reports 12 (2), 2015, 183-189 more…
  • Médard, Guillaume; Pachl, Fiona; Ruprecht, Benjamin; Klaeger, Susan; Heinzlmeir, Stephanie; Helm, Dominic; Qiao, Huichao; Ku, Xin; Wilhelm, Mathias; Kuehne, Thomas; Wu, Zhixiang; Dittmann, Antje; Hopf, Carsten; Kramer, Karl; Kuster, Bernhard: Optimized Chemical Proteomics Assay for Kinase Inhibitor Profiling. Journal of Proteome Research 14 (3), 2015, 1574-1586 more…
  • Savitski, Mikhail M.; Wilhelm, Mathias; Hahne, Hannes; Kuster, Bernhard; Bantscheff, Marcus: A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets. Molecular & Cellular Proteomics 14 (9), 2015, 2394-2404 more…

2014

  • Helm, Dominic; Vissers, Johannes P. C.; Hughes, Christopher J.; Hahne, Hannes; Ruprecht, Benjamin; Pachl, Fiona; Grzyb, Arkadiusz; Richardson, Keith; Wildgoose, Jason; Maier, Stefan K.; Marx, Harald; Wilhelm, Mathias; Becher, Isabelle; Lemeer, Simone; Bantscheff, Marcus; Langridge, James I.; Kuster, Bernhard: Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics. Molecular & Cellular Proteomics 13 (12), 2014, 3709-3715 more…
  • Wilhelm, Mathias; Schlegl, Judith; Hahne, Hannes; Gholami, Amin Moghaddas; Lieberenz, Marcus; Savitski, Mikhail M.; Ziegler, Emanuel; Butzmann, Lars; Gessulat, Siegfried; Marx, Harald; Mathieson, Toby; Lemeer, Simone; Schnatbaum, Karsten; Reimer, Ulf; Wenschuh, Holger; Mollenhauer, Martin; Slotta-Huspenina, Julia; Boese, Joos-Hendrik; Bantscheff, Marcus; Gerstmair, Anja; Faerber, Franz; Kuster, Bernhard: Mass-spectrometry-based draft of the human proteome. Nature 509 (7502), 2014, 582-587 more…

2013

  • Gholami, Amin Moghaddas; Hahne, Hannes; Wu, Zhixiang; Auer, Florian Johann; Meng, Chen; Wilhelm, Mathias; Kuster, Bernhard: Global Proteome Analysis of the NCI-60 Cell Line Panel. Cell Reports 4 (3), 2013, 609-620 more…
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