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TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore TIMS2Rescore: 一种基于MS2Rescore的数据相关采集并行累积和串行分段优化的数据驱动重新分心管道 Declercq, Arthur; Devreese, Robbe; Scheid, Jonas; Jachmann, Caroline; van den Bossche, Tim; Preikschat, Annica; Gomez-Zepeda, David; Rijal, Jeewan Babu; Hirschler, Aurelie; Krieger, Jonathan R.; Srikumar, Tharan; Rosenberger, George; Martelli, Claudia; Trede, Dennis; Carapito, Christine; Tenzer, Stefan; Walz, Juliane S.; Degroeve, Sven; Bouwmeester, Robbin; Martens, Lennart; Gabriels, Ralf 分享 收藏
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Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis Rosenberger, George; Li, Wenxue; Turunen, Mikko; He, Jing; Subramaniam, Prem S.; Pampou, Sergey; Griffin, Aaron T.; Karan, Charles; Kerwin, Patrick; Murray, Diana; Honig, Barry; Liu, Yansheng; Califano, Andrea 分享 收藏
OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data Pfeuffer, Julianus; Bielow, Chris; Wein, Samuel; Jeong, Kyowon; Netz, Eugen; Walter, Axel; Alka, Oliver; Nilse, Lars; Colaianni, Pasquale Domenico; Mccloskey, Douglas; Kim, Jihyung; Rosenberger, George; Bichmann, Leon; Walzer, Mathias; Veit, Johannes; Boudaud, Bertrand; Bernt, Matthias; Patikas, Nikolaos; Pilz, Matteo; Startek, Michal Piotr; Kutuzova, Svetlana; Heumos, Lukas; Charkow, Joshua; Sing, Justin Cyril; Feroz, Ayesha; Siraj, Arslan; Weisser, Hendrik; Dijkstra, Tjeerd M. H.; Perez-Riverol, Yasset; Roest, Hannes; Kohlbacher, Oliver; Sachsenberg, Timo 分享 收藏
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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts Demichev, Vadim; Szyrwiel, Lukasz; Yu, Fengchao; Teo, Guo Ci; Rosenberger, George; Niewienda, Agathe; Ludwig, Daniela; Decker, Jens; Kaspar-Schoenefeld, Stephanie; Lilley, Kathryn S.; Muelleder, Michael; Nesvizhskii, Alexey, I; Ralser, Markus 分享 收藏
Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses Chen, Qian; Coto-Llerena, Mairene; Suslov, Aleksei; Teixeira, Raphael Dias; Fofana, Isabel; Nuciforo, Sandro; Hofmann, Maike; Thimme, Robert; Hensel, Nina; Lohmann, Volker; Ng, Charlotte K. Y.; Rosenberger, George; Wieland, Stefan; Heim, Markus H. 分享 收藏
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics Bichmann, Leon; Gupta, Shubham; Rosenberger, George; Kuchenbecker, Leon; Sachsenberg, Timo; Ewels, Phil; Alka, Oliver; Pfeuffer, Julianus; Kohlbacher, Oliver; Rost, Hannes 分享 收藏
Systematic detection of functional proteoform groups from bottom-up proteomic datasets Bludau, Isabell; Frank, Max; Doerig, Christian; Cai, Yujia; Heusel, Moritz; Rosenberger, George; Picotti, Paola; Collins, Ben C.; Rost, Hannes; Aebersold, Ruedi 分享 收藏
Global and Site-Specific Effect of Phosphorylation on Protein Turnover 磷酸化对蛋白质周转的全局和位点特异性影响 Wu, Chongde; Ba, Qian; Lu, Dayun; Li, Wenxue; Salovska, Barbora; Hou, Pingfu; Mueller, Torsten; Rosenberger, George; Gao, Erli; Di, Yi; Zhou, Hu; Fornasiero, Eugenio F.; Liu, Yansheng 分享 收藏
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles Rosenberger, George; Heusel, Moritz; Bludau, Isabell; Collins, Ben C.; Martelli, Claudia; Williams, Evan G.; Xue, Peng; Liu, Yansheng; Aebersold, Ruedi; Califano, Andrea 分享 收藏
Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease Robinson, Aaron E.; Binek, Aleksandra; Venkatraman, Vidya; Searle, Brian C.; Holewinski, Ronald J.; Rosenberger, George; Parker, Sarah J.; Basisty, Nathan; Xie, Xueshu; Lund, Peder J.; Saxena, Gautam; Mato, Jose M.; Garcia, Benjamin A.; Schilling, Birgit; Lu, Shelly C.; Van Eyk, Jennifer E. 分享 收藏
Quantitative assessment of drug combination effects in NSCLC cell lines through network-based analysis of functional protein activity Antonini, Chiara; Rosenberger, George; Bianconi, Fortunato; Tomassoni, Lorenzo; Ludovini, Vienna; Baglivo, Sara; Calandrini, Sara; Baldelli, Elisa; Pierobon, Mariaelena; Petricoin, Emanuel F.; Califano, Andrea 分享 收藏
Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases Buljan, Marija; Ciuffa, Rodolfo; van Drogen, Audrey; Vichalkovski, Anton; Mehnert, Martin; Rosenberger, George; Lee, Sohyon; Varjosalo, Markku; Pernas, Lucia Espona; Spegg, Vincent; Snijder, Berend; Aebersold, Ruedi; Gstaiger, Matthias 分享 收藏
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes Bludau, Isabell; Heusel, Moritz; Frank, Max; Rosenberger, George; Hafen, Robin; Banaei-Esfahani, Amir; van Drogen, Audrey; Collins, Ben C.; Gstaiger, Matthias; Aebersold, Ruedi 分享 收藏
Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation Salovska, Barbora; Zhu, Hongwen; Gandhi, Tejas; Frank, Max; Li, Wenxue; Rosenberger, George; Wu, Chongde; Germain, Pierre-Luc; Zhou, Hu; Hodny, Zdenek; Reiter, Lukas; Liu, Yansheng 分享 收藏
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data (vol 32, pg 219, 2014) Rost, Hannes L.; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinovic, Sasa M.; Schubert, Olga T.; Wolski, Witold; Collins, Ben C.; Malmstrom, Johan; Malmstrom, Lars; Aebersold, Ruedi 分享 收藏
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS Heusel, Moritz; Frank, Max; Koehler, Mario; Amon, Sabine; Frommelt, Fabian; Rosenberger, George; Bludau, Isabell; Aulakh, Simran; Linder, Monika, I; Liu, Yansheng; Collins, Ben C.; Gstaiger, Matthias; Kutay, Ulrike; Aebersold, Ruedi 分享 收藏
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