Mathias Wilhelm

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 56

Top Topics

Liquid Chromatography

Mass Spectrometry

Top Venues

Nature communications

Journal of proteome research

bioRxiv : the preprint server for biology

This page only lists publications with an associated author ORCID identifier.

Publications

Jennifer A Korchak, Erin D Jeffery, Saikat Bandyopadhyay, Ben T Jordan, Micah D Lehe, Emily F Watts, Aidan Fenix, Mathias Wilhelm, Gloria M Sheynkman
IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection. Journal of the American Society for Mass Spectrometry (2024)
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Matthew Chambers, Elias Kahl, Fengchao Yu, Wassim Gabriel, Dulguun Bold, Tobias Schmidt, Kai Li, Brendan X MacLean, Alexey I Nesvizhskii, Mathias Wilhelm
Koina: Democratizing machine learning for proteomics research. bioRxiv : the preprint server for biology (2024)
Jennifer A Korchak, Erin D Jeffery, Saikat Bandyopadhyay, Ben T Jordan, Micah Lehe, Emily F Watts, Aidan Fenix, Mathias Wilhelm, Gloria M Sheynkman
IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. bioRxiv : the preprint server for biology (2024)
Daniela Klaproth-Andrade, Johannes Hingerl, Yanik Bruns, Nicholas H Smith, Jakob Träuble, Mathias Wilhelm, Julien Gagneur
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing. Nature communications 15 (1) (2024)
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Matthew Chambers, Elias Kahl, Fengchao Yu, Wassim Gabriel, Dulguun Bold, Tobias Schmidt, Kai Li, Brendan X MacLean, Alexey I Nesvizhskii, Mathias Wilhelm
Koina: Democratizing machine learning for proteomics research. bioRxiv : the preprint server for biology (2024)
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Matthew Chambers, Elias Kahl, Fengchao Yu, Wassim Gabriel, Dulguun Bold, Tobias Schmidt, Kai Li, Brendan X MacLean, Alexey I Nesvizhskii, Mathias Wilhelm
Koina: Democratizing machine learning for proteomics research. bioRxiv : the preprint server for biology (2024)
Jennifer A Korchak, Erin D Jeffery, Saikat Bandyopadhyay, Ben T Jordan, Micah Lehe, Emily F Watts, Aidan Fenix, Mathias Wilhelm, Gloria M Sheynkman
IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. bioRxiv : the preprint server for biology (2024)
Charlotte Adams, Wassim Gabriel, Kris Laukens, Mario Picciani, Mathias Wilhelm, Wout Bittremieux, Kurt Boonen
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nature communications 15 (1) (2024)
Markus Hoffmann, Julian M Poschenrieder, Massimiliano Incudini, Sylvie Baier, Amelie Fritz, Andreas Maier, Michael Hartung, Christian Hoffmann, Nico Trummer, Klaudia Adamowicz, Mario Picciani, Evelyn Scheibling, Maximilian V Harl, Ingmar Lesch, Hunor Frey, Simon Kayser, Paul Wissenberg, Leon Schwartz, Leon Hafner, Aakriti Acharya, Lena Hackl, Gordon Grabert, Sung-Gwon Lee, Gyuhyeok Cho, Matthew E Cloward, Jakub Jankowski, Hye Kyung Lee, Olga Tsoy, Nina Wenke, Anders Gorm Pedersen, Klaus Bønnelykke, Antonio Mandarino, Federico Melograna, Laura Schulz, Héctor Climente-González, Mathias Wilhelm, Luigi Iapichino, Lars Wienbrandt, David Ellinghaus, Kristel Van Steen, Michele Grossi, Priscilla A Furth, Lothar Hennighausen, Alessandra Di Pierro, Jan Baumbach, Tim Kacprowski, Markus List, David B Blumenthal
Network medicine-based epistasis detection in complex diseases: ready for quantum computing. Nucleic acids research (2024)
Charlotte Adams, Wassim Gabriel, Kris Laukens, Mario Picciani, Mathias Wilhelm, Wout Bittremieux, Kurt Boonen
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nature communications 15 (1) (2024)
Celina Tretter, Niklas de Andrade Krätzig, Matteo Pecoraro, Sebastian Lange, Philipp Seifert, Clara von Frankenberg, Johannes Untch, Gabriela Zuleger, Mathias Wilhelm, Daniel P Zolg, Florian S Dreyer, Eva Bräunlein, Thomas Engleitner, Sebastian Uhrig, Melanie Boxberg, Katja Steiger, Julia Slotta-Huspenina, Sebastian Ochsenreither, Nikolas von Bubnoff, Sebastian Bauer, Melanie Börries, Philipp J Jost, Kristina Schenck, Iska Dresing, Florian Bassermann, Helmut Friess, Daniel Reim, Konrad Grützmann, Katrin Pfütze, Barbara Klink, Evelin Schröck, Bernhard Haller, Bernhard Kuster, Matthias Mann, Wilko Weichert, Stefan Fröhling, Roland Rad, Michael Hiltensperger, Angela M Krackhardt
Author Correction: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nature communications 15 (1) (2024)
Jennifer A Korchak, Erin D Jeffery, Saikat Bandyopadhyay, Ben T Jordan, Micah Lehe, Emily F Watts, Aidan Fenix, Mathias Wilhelm, Gloria M Sheynkman
IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. bioRxiv : the preprint server for biology (2024)
Daniela Klaproth-Andrade, Johannes Hingerl, Yanik Bruns, Nicholas H Smith, Jakob Träuble, Mathias Wilhelm, Julien Gagneur
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing. Nature communications 15 (1) (2024)
Celina Tretter, Niklas de Andrade Krätzig, Matteo Pecoraro, Sebastian Lange, Philipp Seifert, Clara von Frankenberg, Johannes Untch, Gabriela Zuleger, Mathias Wilhelm, Daniel P Zolg, Florian S Dreyer, Eva Bräunlein, Thomas Engleitner, Sebastian Uhrig, Melanie Boxberg, Katja Steiger, Julia Slotta-Huspenina, Sebastian Ochsenreither, Nikolas von Bubnoff, Sebastian Bauer, Melanie Börries, Philipp J Jost, Kristina Schenck, Iska Dresing, Florian Bassermann, Helmut Friess, Daniel Reim, Konrad Grützmann, Katrin Pfütze, Barbara Klink, Evelin Schröck, Bernhard Haller, Bernhard Kuster, Matthias Mann, Wilko Weichert, Stefan Fröhling, Roland Rad, Michael Hiltensperger, Angela M Krackhardt
Author Correction: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nature communications 15 (1) (2024)
Jennifer A Korchak, Erin D Jeffery, Saikat Bandyopadhyay, Ben T Jordan, Micah Lehe, Emily F Watts, Aidan Fenix, Mathias Wilhelm, Gloria M Sheynkman
IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. bioRxiv : the preprint server for biology (2024)
Jennifer A Korchak, Erin D Jeffery, Saikat Bandyopadhyay, Ben T Jordan, Micah D Lehe, Emily F Watts, Aidan Fenix, Mathias Wilhelm, Gloria M Sheynkman
IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection. Journal of the American Society for Mass Spectrometry (2024)
Markus Hoffmann, Julian M Poschenrieder, Massimiliano Incudini, Sylvie Baier, Amelie Fritz, Andreas Maier, Michael Hartung, Christian Hoffmann, Nico Trummer, Klaudia Adamowicz, Mario Picciani, Evelyn Scheibling, Maximilian V Harl, Ingmar Lesch, Hunor Frey, Simon Kayser, Paul Wissenberg, Leon Schwartz, Leon Hafner, Aakriti Acharya, Lena Hackl, Gordon Grabert, Sung-Gwon Lee, Gyuhyeok Cho, Matthew E Cloward, Jakub Jankowski, Hye Kyung Lee, Olga Tsoy, Nina Wenke, Anders Gorm Pedersen, Klaus Bønnelykke, Antonio Mandarino, Federico Melograna, Laura Schulz, Héctor Climente-González, Mathias Wilhelm, Luigi Iapichino, Lars Wienbrandt, David Ellinghaus, Kristel Van Steen, Michele Grossi, Priscilla A Furth, Lothar Hennighausen, Alessandra Di Pierro, Jan Baumbach, Tim Kacprowski, Markus List, David B Blumenthal
Network medicine-based epistasis detection in complex diseases: ready for quantum computing. Nucleic acids research (2024)
Mario Picciani, Wassim Gabriel, Victor-George Giurcoiu, Omar Shouman, Firas Hamood, Ludwig Lautenbacher, Cecilia Bang Jensen, Julian Müller, Mostafa Kalhor, Armin Soleymaniniya, Bernhard Kuster, Matthew The, Mathias Wilhelm
Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit. Proteomics (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Cristina Chiva, Zahra Elhamraoui, Amanda Solé, Marc Serret, Mathias Wilhelm, Eduard Sabidó
Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification. Analytical chemistry (2023)
Chris D McGann, William D Barshop, Jesse D Canterbury, Chuwei Lin, Wassim Gabriel, Jingjing Huang, David Bergen, Vlad Zabrouskov, Rafael D Melani, Mathias Wilhelm, Graeme C McAlister, Devin K Schweppe
Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics. Journal of proteome research (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias K Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of proteome research 22 (3) (2023)
Maria Reinecke, Paul D Brear, Larsen Vornholz, Benedict-Tilmann Berger, Florian Seefried, Stephanie Wilhelm, Patroklos Samaras, Laszlo Gyenis, David William Litchfield, Guillaume Médard, Susanne Müller, Jürgen Ruland, Marko Hyvönen, Mathias Wilhelm, Bernhard Kuster
Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nature chemical biology (2023)
Jana Zecha, Florian P Bayer, Svenja Wiechmann, Julia Woortman, Nicola Berner, Julian Müller, Annika Schneider, Karl Kramer, Mar Abril-Gil, Thomas A Hopf, Leonie Reichart, Lin Chen, Fynn M Hansen, Severin Lechner, Patroklos Samaras, Stephan Eckert, Ludwig Lautenbacher, Maria Reinecke, Firas Hamood, Polina Prokofeva, Larsen Vornholz, Chiara Falcomatà, Madeleine Dorsch, Ayla Schröder, Anton Venhuizen, Stephanie Wilhelm, Guillaume Médard, Gabriele Stoehr, Juergen Ruland, Barbara M Grüner, Dieter Saur, Maike Buchner, Benjamin Ruprecht, Hannes Hahne, Matthew The, Mathias Wilhelm, Bernhard Kuster
Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science (New York, N.Y.) (2023)
Celina Tretter, Niklas de Andrade Krätzig, Matteo Pecoraro, Sebastian Lange, Philipp Seifert, Clara von Frankenberg, Johannes Untch, Gabriela Zuleger, Mathias Wilhelm, Daniel P Zolg, Florian S Dreyer, Eva Bräunlein, Thomas Engleitner, Sebastian Uhrig, Melanie Boxberg, Katja Steiger, Julia Slotta-Huspenina, Sebastian Ochsenreither, Nikolas von Bubnoff, Sebastian Bauer, Melanie Börries, Philipp J Jost, Kristina Schenck, Iska Dresing, Florian Bassermann, Helmut Friess, Daniel Reim, Konrad Grützmann, Katrin Pfütze, Barbara Klink, Evelin Schröck, Bernhard Haller, Bernhard Kuster, Matthias Mann, Wilko Weichert, Stefan Fröhling, Roland Rad, Michael Hiltensperger, Angela M Krackhardt
Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nature communications 14 (1) (2023)
Markus Hoffmann, Julian M Poschenrieder, Massimiliano Incudini, Sylvie Baier, Amelie Fitz, Andreas Maier, Michael Hartung, Christian Hoffmann, Nico Trummer, Klaudia Adamowicz, Mario Picciani, Evelyn Scheibling, Maximilian V Harl, Ingmar Lesch, Hunor Frey, Simon Kayser, Paul Wissenberg, Leon Schwartz, Leon Hafner, Aakriti Acharya, Lena Hackl, Gordon Grabert, Sung-Gwon Lee, Gyuhyeok Cho, Matthew E Cloward, Jakub Jankowski, Hye Kyung Lee, Olga Tsoy, Nina Kerstin Wenke, Anders Gorm Pedersen, Klaus Bønnelykke, Antonio Mandarino, Federico Melograna, Laura Schulz, Héctor Climente-Gonzalez, Mathias Wilhelm, Luigi Iapichino, Lars Wienbrandt, David Ellinghaus, Kristel Van Steen, Michele Grossi, Priscilla A Furth, Lothar Hennighausen, Alessandra Di Pierro, Jan Baumbach, Tim Kacprowski, Markus List, David B Blumenthal
Network medicine-based epistasis detection in complex diseases: ready for quantum computing. medRxiv : the preprint server for health sciences (2023)
Jana Zecha, Wassim Gabriel, Ria Spallek, Yun-Chien Chang, Julia Mergner, Mathias Wilhelm, Florian Bassermann, Bernhard Kuster
Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling. Nature communications 13 (1) (2022)
Markus Ekvall, Patrick Truong, Wassim Gabriel, Mathias Wilhelm, Lukas Käll
Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities. Journal of proteome research 21 (5) (2022)
Piero Giansanti, Patroklos Samaras, Yangyang Bian, Chen Meng, Andrea Coluccio, Martin Frejno, Hannah Jakubowsky, Sophie Dobiasch, Rashmi R Hazarika, Julia Woortman, 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 K Schmidt, Roland Rad, Stephanie E Combs, Matthew The, Frank Johannes, Dieter Saur, Martin Hrabě de Angelis, Mathias Wilhelm, Günter Schneider, Bernhard Kuster
Mass spectrometry-based draft of the mouse proteome. Nature methods 19 (7) (2022)
Severin Lechner, Martin Ian P Malgapo, Christian Graetz, Raphael R Steimbach, Agnes Baron, Patrick Leopold Rüther, Simon Nadal, Carmen Stumpf, Christina Loos, Xin Ku, Polina Prokofeva, Ludwig Lautenbacher, Tino Heimburg, Vivian Würf, Chen Meng, Mathias Wilhelm, Wolfgang Sippl, Karin Kleigrewe, Josch K Pauling, Karl Kramer, Aubry K Miller, Michael W Pfaffl, Maurine E Linder, Bernhard Kuster, Guillaume Médard
Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nature chemical biology 18 (8) (2022)
Magnus Palmblad, Sebastian Böcker, Sven Degroeve, Oliver Kohlbacher, Lukas Käll, William Stafford Noble, Mathias Wilhelm
Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. Journal of proteome research 21 (4) (2022)
Wassim Gabriel, Matthew The, Daniel P Zolg, Florian P Bayer, Omar Shouman, Ludwig Lautenbacher, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute, Bernard Delanghe, Andreas Huhmer, Holger Wenschuh, Ulf Reimer, Guillaume Médard, Bernhard Kuster, Mathias Wilhelm
Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides. Analytical chemistry 94 (20) (2022)
Wassim Gabriel, Victor-George Giurcoiu, Ludwig Lautenbacher, Mathias Wilhelm
Predicting fragment intensities and retention time of iTRAQ- and TMTPro-labeled peptides with Prosit-TMT. Proteomics 22 (19-20) (2022)
Mathias Wilhelm, Daniel P Zolg, Michael Graber, Siegfried Gessulat, Tobias K Schmidt, Karsten Schnatbaum, Celina Tretter, Philipp Seifert, Niklas de Andrade Krätzig, Johannes Zerweck, Tobias Knaute, Eva Bräunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A Carr, Karl R Clauser, Angela M Krackhardt, Ulf Reimer, Bernhard Kuster
Author Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nature communications 12 (1) (2021)
Javier Antonio Alfaro, Peggy Bohländer, Mingjie Dai, Mike Filius, Cecil J Howard, Xander F van Kooten, Shilo Ohayon, Adam Pomorski, Sonja Schmid, Aleksei Aksimentiev, Eric V Anslyn, Georges Bedran, Chan Cao, Mauro Chinappi, Etienne Coyaud, Cees Dekker, Gunnar Dittmar, Nicholas Drachman, Rienk Eelkema, David Goodlett, Sébastien Hentz, Umesh Kalathiya, Michael P Snyder, Ryan T Kelly, Zvi Kelman, Sung Hyun Kim, Bernhard Kuster, David Rodriguez-Larrea, Stuart Lindsay, Giovanni Maglia, Edward M Marcotte, John P Marino, Christophe D Masselon, Michael Mayer, Patroklos Samaras, Kumar Sarthak, Lusia Sepiashvili, Derek Stein, Meni Wanunu, Mathias Wilhelm, Peng Yin, Amit Meller, Chirlmin Joo
The emerging landscape of single-molecule protein sequencing technologies. Nature methods 18 (6) (2021)
Tobias K Schmidt, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, Yasset Perez Riverol, Eric W Deutsch, Bernhard Kuster, Mathias Wilhelm
Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. Journal of proteome research 20 (6) (2021)
Yangyang Bian, Matthew The, Piero Giansanti, Julia Mergner, Runsheng Zheng, Mathias Wilhelm, Alexander Boychenko, Bernhard Kuster
Identification of 7 000-9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC-MS/MS. Analytical chemistry 93 (25) (2021)
Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Bjoern Andreas Gruening, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W Deutsch, Juan Antonio Vizcaino, Mingze Bai, Timo Sachsenberg, Lev I Levitsky, Yasset Perez Riverol
A proteomics sample metadata representation for multiomics integration and big data analysis. Nature communications 12 (1) (2021)
Ludwig Lautenbacher, Patroklos Samaras, Julian Muller, Andreas Grafberger, Marwin Shraideh, Johannes Rank, Simon T Fuchs, Tobias K Schmidt, Matthew The, Christian Dallago, Holger Wittges, Burkhard Rost, Helmut Krcmar, Bernhard Kuster, Mathias Wilhelm
ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic acids research (2021)
Mathias Wilhelm, Daniel P Zolg, Michael Graber, Siegfried Gessulat, Tobias K Schmidt, Karsten Schnatbaum, Celina Tretter, Philipp Seifert, Niklas de Andrade Krätzig, Johannes Zerweck, Tobias Knaute, Eva Bräunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A Carr, Karl R Clauser, Angela M Krackhardt, Ulf Reimer, Bernhard Kuster
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nature communications 12 (1) (2021)
Julia Mergner, Martin Frejno, Markus List, Michael Papacek, Xia Chen, Ajeet Chaudhary, Patroklos Samaras, Sandra Richter, Hiromasa Shikata, Maxim Messerer, Daniel Lang, Stefan Altmann, Philipp Cyprys, Daniel P Zolg, Toby Mathieson, Marcus Bantscheff, Rashmi R Hazarika, Tobias K Schmidt, Corinna Dawid, Andreas Dunkel, Thomas Hofmann, Stefanie Sprunck, Pascal Falter-Braun, Frank Johannes, Klaus F X Mayer, Gerd Jürgens, Mathias Wilhelm, Jan Baumbach, Erwin Grill, Kay Schneitz, Claus Schwechheimer, Bernhard Kuster
Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 579 (7799) (2020)
Anna Jarzab, Nils Kurzawa, Thomas Hopf, Matthias Moerch, Jana Zecha, Niels Leijten, Yangyang Bian, Eva Musiol, Melanie Maschberger, Gabriele Stoehr, Isabelle Becher, Charlotte Daly, Patroklos Samaras, Julia Mergner, Britta Spanier, Angel Angelov, Thilo Werner, Marcus Bantscheff, Mathias Wilhelm, Martin Klingenspor, Simone Lemeer, Wolfgang Liebl, Hannes Hahne, Mikhail M Savitski, Bernhard Kuster
Meltome atlas-thermal proteome stability across the tree of life. Nature methods 17 (5) (2020)
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 Wilhelm, Mathias Wilhelm, Julia Dorn, Hans Michael Kvasnicka, Hubert Serve, Wilko Weichert, Bernhard Kuster
Proteome activity landscapes of tumor cell lines determine drug responses. Nature communications 11 (1) (2020)
Brian C Searle, Kristian E Swearingen, Christopher A Barnes, Tobias K Schmidt, Siegfried Gessulat, Bernhard Kuster, Mathias Wilhelm
Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nature communications 11 (1) (2020)
Julia Woortman, Patroklos Samaras, Anna Jarzab, Juergen Behr, Martin Frejno, Ana Djukovic, Jaime Sanz, Eva M González-Barberá, Miguel Salavert, Jose Luis López-Hontangas, Karina B Xavier, Laurent Debrauwer, Jean-Marc Rolain, Miguel Angel Sanz, Marc Garcia-Garcera, Mathias Wilhelm, Carles Ubeda, Bernhard Kuster
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae. Proteomes 7 (1) (2019)
Maria Reinecke, Benjamin Ruprecht, Sandra Poser, Svenja Wiechmann, Mathias Wilhelm, Stephanie Wilhelm, Bernhard Kuster, Guillaume Médard
Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors. ACS chemical biology 14 (4) (2019)
Siegfried Gessulat, Tobias Schmidt, Daniel Paul Zolg, Patroklos Samaras, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute, Julia Rechenberger, Bernard Delanghe, Andreas Huhmer, Ulf Reimer, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nature methods 16 (6) (2019)
Florian Seefried, Tobias K Schmidt, Maria Reinecke, Stephanie Wilhelm, Bernhard Kuster, Mathias Wilhelm
CiRCus: A Framework to Enable Classification of Complex High-Throughput Experiments. Journal of proteome research 18 (4) (2019)
Eric W Deutsch, Yasset Perez Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P C Vissers, Dennis W Wolan, Ana Y Wang, Luis Mendoza, Jim Shofstahl, Andrew W Dowsey, Johannes Griss, Reza M Salek, Steffen Neumann, Pierre-Alain Binz, Henry H N Lam, Juan Antonio Vizcaino, Nuno Bandeira, Hannes L Röst
Expanding the Use of Spectral Libraries in Proteomics. Journal of proteome research 17 (12) (2018)
Daniel Paul Zolg, Mathias Wilhelm, Tobias Schmidt, Guillaume Médard, Johannes Zerweck, Tobias Knaute, Holger Wenschuh, Ulf Reimer, Karsten Schnatbaum, Bernhard Kuster
ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides. Molecular & cellular proteomics : MCP 17 (9) (2018)
Chien-Yun Lee, Dongxue Wang, Mathias Wilhelm, Daniel P Zolg, Tobias Schmidt, Karsten Schnatbaum, Ulf Reimer, Fredrik Pontén, Mathias Uhlén, Hannes Hahne, Bernhard Kuster
Mining the Human Tissue Proteome for Protein Citrullination. Molecular & cellular proteomics : MCP 17 (7) (2018)
Susan Klaeger, Stephanie Wilhelm, Mathias Wilhelm, Harald Polzer, Binje Vick, Paul-Albert Koenig, Maria Reinecke, Benjamin Ruprecht, Svenja Petzoldt, Chen Meng, Jana Zecha, Katrin Reiter, Huichao Qiao, Dominic Helm, Heiner Koch, Melanie Schoof, Giulia Canevari, Elena Casale, Stefania Re Depaolini, Annette Feuchtinger, Zhixiang Wu, Tobias K Schmidt, Lars Rueckert, Wilhelm Becker, Jan Huenges, Anne-Kathrin Garz, Bjoern-Oliver Gohlke, Daniel Paul Zolg, Gian Kayser, Tonu Vooder, Robert Preissner, Hannes Hahne, Neeme Tõnisson, Karl Kramer, Katharina Götze, Florian Bassermann, Judith Schlegl, Hans-Christian Ehrlich, Stephan Aiche, Axel Walch, Philipp A Greif, Sabine Schneider, Eduard Rudolf Felder, Juergen Ruland, Guillaume Médard, Irmela Jeremias, Karsten Spiekermann, Bernhard Kuster
The target landscape of clinical kinase drugs. Science (New York, N.Y.) 358 (6367) (2018)