| Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues*[S] R Bruderer, OM Bernhardt, T Gandhi, SM Miladinoviĉ, LY Cheng, ... Molecular & Cellular Proteomics 14 (5), 1400-1410, 2015 | 918 | 2015 |
| Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results R Bruderer, OM Bernhardt, T Gandhi, Y Xuan, J Sondermann, M Schmidt, ... Molecular & Cellular Proteomics 16 (12), 2296-2309, 2017 | 380 | 2017 |
| Cdc48/p97 promotes reformation of the nucleus by extracting the kinase Aurora B from chromatin K Ramadan, R Bruderer, FM Spiga, O Popp, T Baur, M Gotta, HH Meyer Nature 450 (7173), 1258-1262, 2007 | 322 | 2007 |
| Purification and identification of endogenous polySUMO conjugates R Bruderer, MH Tatham, A Plechanovova, I Matic, AK Garg, RT Hay EMBO reports 12 (2), 142-148, 2011 | 207 | 2011 |
| The AAA ATPase p97/VCP interacts with its alternative co-factors, Ufd1-Npl4 and p47, through a common bipartite binding mechanism RM Bruderer, C Brasseur, HH Meyer Journal of Biological Chemistry 279 (48), 49609-49616, 2004 | 188 | 2004 |
| Surpassing 10000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy J Muntel, T Gandhi, L Verbeke, OM Bernhardt, T Treiber, R Bruderer, ... Molecular omics 15 (5), 348-360, 2019 | 149 | 2019 |
| Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance'[S] R Bruderer, J Muntel, S Müller, OM Bernhardt, T Gandhi, O Cominetti, ... Molecular & Cellular Proteomics 18 (6), 1242-1254, 2019 | 145 | 2019 |
| High‐precision iRT prediction in the targeted analysis of data‐independent acquisition and its impact on identification and quantitation R Bruderer, OM Bernhardt, T Gandhi, L Reiter Proteomics 16 (15-16), 2246-2256, 2016 | 142 | 2016 |
| Comparison of protein quantification in a complex background by DIA and TMT workflows with fixed instrument time J Muntel, J Kirkpatrick, R Bruderer, T Huang, O Vitek, A Ori, L Reiter Journal of proteome research 18 (3), 1340-1351, 2019 | 111 | 2019 |
| A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes I Piazza, N Beaton, R Bruderer, T Knobloch, C Barbisan, L Chandat, ... Nature communications 11 (1), 4200, 2020 | 90 | 2020 |
| Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition J Vowinckel, A Zelezniak, R Bruderer, M Mülleder, L Reiter, M Ralser Scientific Reports 8 (1), 4346, 2018 | 78 | 2018 |
| Ubiquitylation of the chemokine receptor CCR7 enables efficient receptor recycling and cell migration K Schaeuble, MA Hauser, AV Rippl, R Bruderer, C Otero, M Groettrup, ... Journal of cell science 125 (19), 4463-4474, 2012 | 52 | 2012 |
| Combining precursor and fragment information for improved detection of differential abundance in data independent acquisition T Huang, R Bruderer, J Muntel, Y Xuan, O Vitek, L Reiter Molecular & Cellular Proteomics 19 (2), 421-430, 2020 | 49 | 2020 |
| Different syngeneic tumors show distinctive intrinsic tumor-immunity and mechanisms of actions (MOA) of anti-PD-1 treatment Y Jin, X An, B Mao, R Sun, R Kumari, X Chen, Y Shan, M Zang, L Xu, ... Scientific Reports 12 (1), 3278, 2022 | 37 | 2022 |
| Classification of mouse B cell types using surfaceome proteotype maps M van Oostrum, M Müller, F Klein, R Bruderer, H Zhang, PGA Pedrioli, ... Nature communications 10 (1), 5734, 2019 | 35 | 2019 |
| New targeted approaches for the quantification of data‐independent acquisition mass spectrometry R Bruderer, J Sondermann, CC Tsou, A Barrantes‐Freer, C Stadelmann, ... Proteomics 17 (9), 1700021, 2017 | 34 | 2017 |
| Systematic comparison of strategies for the enrichment of lysosomes by data independent acquisition J Singh, E Kaade, J Muntel, R Bruderer, L Reiter, M Thelen, D Winter Journal of proteome research 19 (1), 371-381, 2019 | 27 | 2019 |
| Biomarker candidates for tumors identified from deep-profiled plasma stem predominantly from the low abundant area M Tognetti, K Sklodowski, S Müller, D Kamber, J Muntel, R Bruderer, ... Journal of proteome research 21 (7), 1718-1735, 2022 | 22 | 2022 |
| Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker MT Mackmull, L Nagel, F Sesterhenn, J Muntel, J Grossbach, P Stalder, ... Nature structural & molecular biology 29 (10), 978-989, 2022 | 17 | 2022 |
| Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance L Wrobel, SM Hill, A Djajadikerta, M Fernandez-Estevez, C Karabiyik, ... Nature Communications 13 (1), 4146, 2022 | 12 | 2022 |
