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Technische Universität München

ProteomicsDB - resource for life science research

ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research.

The development of ProteomicsDB started as a protein-centric in-memory database for exploration of large collections of quantitative mass spectrometry-based proteomics data. The contents and types of available data have grown ever since. The current version also includes RNA-Seq expression data, drug-target interactions and cell line viability data. Due to its generic design, all analytical features available for the original human resource seamlessly transfer to other organisms such as mouse, arabidopsis and rice which were recently added.

The major focus over the last two years was to adopt and implement the FAIR concept (findability, accessibility, interoperability and reusability). A new application programming interface (API) has been released that provides systematic access to essentially all data in ProteomicsDB. Additionally, a new open-source user interface (UI) is available and constantly extended. It showcases the advantages of FAIR and provides an interactive web app for easy access to the scientific community.

Available theses and research projects

Interested? Do you want to contribute? Are you looking for a research project, thesis, internship or simply a diversion? Visit our Open Research Projects and find topics related to [PrDB] or other projects.

Primary literature

SucheHinweis: Die „Schnellsuche“ findet nur Text in den angezeigten Feldern; nicht in Abstracts oder Schlagwörtern. Der Suchbegriff muss mindestens 3 Buchstaben lang sein.

2023

  • Piller, Andrea; Brajkovic, Sarah; Abbas, Qussai; Andrade‐Galan, Paula; Aydin, Ezgi; Corongiu, Gianluca; Giordano, Guido; Haljiti, Genc; Hein, Sophia; Pan, Jiuyue; Picciani, Mario; Ramirez, Veronica; Röhrl, Patrick; Saylan, Cemil Can; Soleymaniniya, Armin; Urzinger, Sebastian; Würstl, Lukas; Avramova, Viktoriya; Dawid, Corinna; Frishman, Dmitrij; Gutjahr, Caroline; Hückelhoven, Ralph; Ludwig, Christina; Pauling, Josch; Schön, Chris‐Carolin; Schwechheimer, Claus; Wilhelm, Mathias; Wilhelm, Stephanie; Poppenberger, Brigitte; Küster, Bernhard: The Proteomes that Feed the World. Lebensmittelchemie 77 (S1), 2023 mehr…
  • 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 mehr…
  • 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 mehr…

2022

  • 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, 2022 mehr…
  • 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, 2022 mehr…
  • 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 mehr…
  • The, Matthew; Samaras, Patroklos; Kuster, Bernhard; Wilhelm, Mathias: Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups. Molecular & Cellular Proteomics 21 (12), 2022, 100437 mehr…

2021

  • Schmidt, Tobias; Samaras, Patroklos; Dorfer, Viktoria; Panse, Christian; Kockmann, Tobias; Bichmann, Leon; van Puyvelde, Bart; Perez-Riverol, Yasset; Deutsch, Eric W.; Kuster, Bernhard; Wilhelm, Mathias: Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. Journal of Proteome Research 20 (6), 2021, 3388-3394 mehr…

2020

  • 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 mehr…

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 mehr…
  • 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 mehr…

2017

  • 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 46 (D1), 2017, D1271-D1281 mehr…
  • 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 mehr…

2015

  • 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 mehr…

2014

  • 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 mehr…
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