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
2021
12
1

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
2021
18
6
604-617

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
2021
20
6
3388-3394

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
93
25
8687-8692

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
2021
12
1

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
2021
20
100076