Skip to content
Technical University of Munich

Publications

SearchNote: This “quick search” only finds text in the shown fields, not in abstracts or keywords. The search term must have at least 3 letters.

2025

  • Abele, Miriam; Soleymaniniya, Armin; Bayer, Florian P.; Lomp, Nina; Doll, Etienne; Meng, Chen; Neuhaus, Klaus; Scherer, Siegfried; Wenning, Mareike; Wantia, Nina; Kuster, Bernhard; Wilhelm, Mathias; Ludwig, Christina: Proteomic diversity in bacteria: Insights and implications for bacterial identification. Molecular & Cellular Proteomics, 2025, 100917 more…
  • Gabriel, Wassim; Gonzalez, Rebecca Meelker; Laposchan, Sophia; Riedel, Erik; Dündar, Gönül; Poppenberger, Brigitte; Wilhelm, Mathias; Lee, Chien-Yun: Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes. Molecular & Cellular Proteomics, 2025, 100924 more…
  • Hamood, Firas; Gabriel, Wassim; Pfeiffer, Pia; Kuster, Bernhard; Wilhelm, Mathias; The, Matthew: ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer. Journal of Proteome Research 24 (4), 2025, 2173-2180 more…
  • Müller, Julian; Bayer, Florian P.; Wilhelm, Mathias; Schuh, Maximilian G.; Kuster, Bernhard; The, Matthew: PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways. Nature Communications 16 (1), 2025 more…
  • Xiao, Zixuan; Tüshaus, Johanna; Kuster, Bernhard; The, Matthew; Wilhelm, Mathias: SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run. Journal of Proteome Research, 2025 more…
  • Zhang, Ning; Tang, Li; Li, Songgang; Liu, Lu; Gao, Mengjuan; Wang, Sisheng; Chen, Daiying; Zhao, Yichao; Zheng, Ruiqing; Soleymaniniya, Armin; Zhang, Lingran; Wang, Wenkang; Yang, Xia; Ren, Yan; Sun, Congwei; Wilhelm, Mathias; Wang, Daowen; Li, Min; Chen, Feng: Integration of multi-omics data accelerates molecular analysis of common wheat traits. Nature Communications 16 (1), 2025 more…

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…
  • Adams, Charlotte; Gabriel, Wassim; Laukens, Kris; Picciani, Mario; Wilhelm, Mathias; Bittremieux, Wout; Boonen, Kurt: Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nature Communications 15 (1), 2024 more…
  • Beltrao, Pedro; Van Den Bossche, Tim; Gabriels, Ralf; Holstein, Tanja; Kockmann, Tobias; Nameni, Alireza; Panse, Christian; Schlapbach, Ralph; Lautenbacher, Ludwig; Mattanovich, Matthias; Nesvizhskii, Alexey; Van Puyvelde, Bart; Scheid, Jonas; Schwämmle, Veit; Strauss, Maximilian; Susmelj, Anna Klimovskaia; The, Matthew; Webel, Henry; Wilhelm, Mathias; Winkelhardt, Dirk; Wolski, Witold E.; Xi, Muyao: Proceedings of the EuBIC-MS developers meeting 2023. Journal of Proteomics 305, 2024, 105246 more…
  • Elhamraoui, Zahra; Borràs, Eva; Wilhelm, Mathias; Sabidó, Eduard: Theoretical Assessment of Indistinguishable Peptides in Mass Spectrometry-Based Proteomics. Analytical Chemistry 96 (40), 2024, 15829-15833 more…
  • Gabriel, Wassim; Picciani, Mario; The, Matthew; Wilhelm, Mathias: Deep Learning-Assisted Analysis of Immunopeptidomics Data. In: Methods in Molecular Biology. Springer US, 2024 more…
  • Gabriel, Wassim; Shouman, Omar; Schröder, Eva Ayla; Böß l, Florian; Wilhelm, Mathias: PROSPECT PTMs: Rich Labeled Tandem Mass Spectrometry Dataset of Modified Peptides for Machine Learning in Proteomics. Advances in Neural Information Processing Systems, Curran Associates, Inc., 2024 more…
  • He, Fuchu; Aebersold, Ruedi; Baker, Mark S.; Bian, Xiuwu; Bo, Xiaochen; Chan, Daniel W.; Chang, Cheng; Chen, Luonan; Chen, Xiangmei; Chen, Yu-Ju; Cheng, Heping; Collins, Ben C.; Corrales, Fernando; Cox, Jürgen; E, Weinan; Van Eyk, Jennifer E.; Fan, Jia; Faridi, Pouya; Figeys, Daniel; Gao, George Fu; Gao, Wen; Gao, Zu-Hua; Goda, Keisuke; Goh, Wilson Wen Bin; Gu, Dongfeng; Guo, Changjiang; Guo, Tiannan; He, Yuezhong; Heck, Albert J. R.; Hermjakob, Henning; Hunter, Tony; Iyer, Narayanan Gopalakrishna; Jiang, Ying; Jimenez, Connie R.; Joshi, Lokesh; Kelleher, Neil L.; Li, Ming; Li, Yang; Lin, Qingsong; Liu, Cui Hua; Liu, Fan; Liu, Guang-Hui; Liu, Yansheng; Liu, Zhihua; Low, Teck Yew; Lu, Ben; Mann, Matthias; Meng, Anming; Moritz, Robert L.; Nice, Edouard et al.: π-HuB: the proteomic navigator of the human body. Nature 636 (8042), 2024, 322-331 more…
  • Hoffmann, Markus; Poschenrieder, Julian M; Incudini, Massimiliano; Baier, Sylvie; Fritz, Amelie; Maier, Andreas; Hartung, Michael; Hoffmann, Christian; Trummer, Nico; Adamowicz, Klaudia; Picciani, Mario; Scheibling, Evelyn; Harl, Maximilian V; Lesch, Ingmar; Frey, Hunor; Kayser, Simon; Wissenberg, Paul; Schwartz, Leon; Hafner, Leon; Acharya, Aakriti; Hackl, Lena; Grabert, Gordon; Lee, Sung-Gwon; Cho, Gyuhyeok; Cloward, Matthew E; Jankowski, Jakub; Lee, Hye Kyung; Tsoy, Olga; Wenke, Nina; Pedersen, Anders Gorm; Bønnelykke, Klaus; Mandarino, Antonio; Melograna, Federico; Schulz, Laura; Climente-González, Héctor; Wilhelm, Mathias; Iapichino, Luigi; Wienbrandt, Lars; Ellinghaus, David; Van Steen, Kristel; Grossi, Michele; Furth, Priscilla A; Hennighausen, Lothar; Di Pierro, Alessandra; Baumbach, Jan; Kacprowski, Tim; List, Markus; Blumenthal, David B: Network medicine-based epistasis detection in complex diseases: ready for quantum computing. Nucleic Acids Research 52 (17), 2024, 10144-10160 more…
  • Kalhor, Mostafa; Lapin, Joel; Picciani, Mario; Wilhelm, Mathias: Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors into Peptide Identification. Molecular & Cellular Proteomics, 2024, 100798 more…
  • Klaproth-Andrade, Daniela; Hingerl, Johannes; Bruns, Yanik; Smith, Nicholas H.; Träuble, Jakob; Wilhelm, Mathias; Gagneur, Julien: Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing. Nature Communications 15 (1), 2024 more…
  • Korchak, Jennifer A.; Jeffery, Erin D.; Bandyopadhyay, Saikat; Jordan, Ben T.; Lehe, Micah D.; Watts, Emily F.; Fenix, Aidan; Wilhelm, Mathias; Sheynkman, Gloria M.: IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection. Journal of the American Society for Mass Spectrometry 35 (11), 2024, 2614-2630 more…
  • The, Matthew; Picciani, Mario; Jensen, Cecilia; Gabriel, Wassim; Kuster, Bernhard; Wilhelm, Mathias: AI-Assisted Processing Pipeline to Boost Protein Isoform Detection. In: Methods in Molecular Biology. Springer US, 2024 more…

2023

  • Chiva, Cristina; Elhamraoui, Zahra; Solé, Amanda; Serret, Marc; Wilhelm, Mathias; Sabidó, Eduard: Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification. Analytical Chemistry 95 (37), 2023, 13746-13749 more…
  • McGann, Chris D.; Barshop, William D.; Canterbury, Jesse D.; Lin, Chuwei; Gabriel, Wassim; Huang, Jingjing; Bergen, David; Zabrouskov, Vlad; Melani, Rafael D.; Wilhelm, Mathias; McAlister, Graeme C.; Schweppe, Devin K.: Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics. Journal of Proteome Research 22 (9), 2023, 2836-2846 more…
  • Neely, Benjamin A.; Dorfer, Viktoria; Martens, Lennart; Bludau, Isabell; Bouwmeester, Robbin; Degroeve, Sven; Deutsch, Eric W.; Gessulat, Siegfried; Käll, Lukas; Palczynski, Pawel; Payne, Samuel H.; Rehfeldt, Tobias Greisager; Schmidt, Tobias; Schwämmle, Veit; Uszkoreit, Julian; Vizcaíno, Juan Antonio; Wilhelm, Mathias; Palmblad, Magnus: Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research 22 (3), 2023, 681-696 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 24 (8), 2023 more…
  • 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 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

  • Ekvall, Markus; Truong, Patrick; Gabriel, Wassim; Wilhelm, Mathias; Käll, Lukas: Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities. Journal of Proteome Research 21 (5), 2022, 1359-1364 more…
  • Gabriel, Wassim; Giurcoiu, Victor; Lautenbacher, Ludwig; Wilhelm, Mathias: Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT. PROTEOMICS, 2022, 2100257 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, 2022 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, 2022 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…
  • 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 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…
  • Palmblad, Magnus; Böcker, Sebastian; Degroeve, Sven; Kohlbacher, Oliver; Käll, Lukas; Noble, William Stafford; Wilhelm, Mathias: Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. Journal of Proteome Research 21 (4), 2022, 1204-1207 more…
  • Shouman, Omar; Gabriel, Wassim; Giurcoiu, Victor-George; Sternlicht, Vitor; Wilhelm, Mathias: PROSPECT: Labeled Tandem Mass Spectrometry Dataset for Machine Learning in Proteomics. Advances in Neural Information Processing Systems, Curran Associates, Inc., 2022 more…
  • 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 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 93 (25), 2021, 8687-8692 more…
  • Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M.; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; Grüning, Björn; Föll, Melanie Christine; Griss, Johannes; Vaudel, Marc; Audain, Enrique; Locard-Paulet, Marie; Turewicz, Michael; Eisenacher, Martin; Uszkoreit, Julian; Van Den Bossche, Tim; Schwämmle, Veit; Webel, Henry; Schulze, Stefan; Bouyssié, David; Jayaram, Savita; Duggineni, Vinay Kumar; Samaras, Patroklos; Wilhelm, Mathias; Choi, Meena; Wang, Mingxun; Kohlbacher, Oliver; Brazma, Alvis; Papatheodorou, Irene; Bandeira, Nuno; Deutsch, Eric W.; Vizcaíno, Juan Antonio; Bai, Mingze; Sachsenberg, Timo; Levitsky, Lev I.; Perez-Riverol, Yasset: A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications 12 (1), 2021 more…
  • Lechner, Severin; Malgapo, Martin; Grätz, Christian; Baron, Agnes; Rüther, Patrick Leopold; Nadal, Simon; Stumpf, Carmen; Loos, Christina; Ku, Xin; Prokofeva, Polina; Lautenbacher, Ludwig; Heimburg, Tino; Würf, Vivian; Meng, Chen; Sippl, Wolfgang; Wilhelm, Mathias; Kleigrewe, Karin; Pauling, Josch; Kramer, Karl; Pfaffl, Michael; Linder, Maurine; Kuster, Bernhard; Médard, Guillaume: Target deconvolution of HDAC pharmacopoeia highlights MBLAC2 as common off-target. 2021 more…
  • 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 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…
  • Zhang, Shuhao; Plauth, Max; Eberhardt, Felix; Polze, Andreas; Lehmann, Jens; Sejdiu, Gezim; Jabeen, Hajira; Servadei, Lorenzo; Möstl, Christian; Bär, Florian; Netzeband, André; Schmidt, Rainer; Knigge, Marlene; Hecht, Sonja; Prifti, Loina; Krcmar, Helmut; Sapegin, Andrey; Jaeger, David; Cheng, Feng; Meinel, Christoph; Friedrich, Tobias; Rothenberger, Ralf; Sutton, Andrew M.; Sidorova, Julia A.; Lundberg, Lars; Rosander, Oliver; Sköld, Lars; Di Varano, Igor; van der Walt, Estée; Eloff, Jan H. P.; Fabian, Benjamin; Baumann, Annika; Ermakova, Tatiana; Kelkel, Stefan; Choudhary, Yash; Cooray, Thilini; Rodríguez, Jorge; Medina-Pérez, Miguel Angel; Trejo, Luis A.; Barrera-Animas, Ari Yair; Monroy-Borja, Raúl; López-Cuevas, Armando; Ramírez-Márquez, José Emmanuel; Grohmann, Maria; Niederleithinger, Ernst; Podapati, Sasidhar; Schmidt, Christopher; Huegle, Johannes; de Oliveira, Roberto C. L.; Soares, Fábio Mendes et al.: HPI Future SOC Lab – Proceedings 2017. Universitätsverlag Potsdam, 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 – 4. In: Target Discovery and Validation. John Wiley & Sons, Ltd, 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), 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…
  • 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…
  • 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 46 (D1), 2017, D1271-D1281 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, Stephanie; Kudlinzki, Denis; Sreeramulu, Sridhar; Klaeger, Susan; Gande, Santosh Lakshmi; Linhard, Verena; Wilhelm, Mathias; Qiao, Huichao; Helm, Dominic; Ruprecht, Benjamin; Saxena, Krishna; Médard, Guillaume; Schwalbe, Harald; Kuster, Bernhard: Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs. ACS Chemical Biology 11 (12), 2016, 3400-3411 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

  • Froehlich, John W.; Dodds, Eric D.; Wilhelm, Mathias; Serang, Oliver; Steen, Judith A.; Lee, Richard S.: A Classifier Based on Accurate Mass Measurements to Aid Large Scale, Unbiased Glycoproteomics. Molecular & Cellular Proteomics 12 (4), 2013, 1017-1025 more…
  • 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…
  • Hoffmann, Nils; Wilhelm, Mathias; Doebbe, Anja; Niehaus, Karsten; Stoye, Jens: BiPACE 2D—graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinformatics 30 (7), 2013, 988-995 more…

2012

  • Hoffmann, Nils; Keck, Matthias; Neuweger, Heiko; Wilhelm, Mathias; Högy, Petra; Niehaus, Karsten; Stoye, Jens: Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics 13 (1), 2012 more…
  • Wilhelm, Mathias; Kirchner, Marc; Steen, Judith A.J.; Steen, Hanno: mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets. Molecular & Cellular Proteomics 11 (1), 2012, O111.011379 more…
To top