| 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 Miladinoviæ, LY Cheng, ... Molecular & Cellular Proteomics 14 (5), 1400-1410, 2015 | 728 | 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 | 289 | 2017 |
| A multicenter study benchmarks software tools for label-free proteome quantification P Navarro, J Kuharev, LC Gillet, OM Bernhardt, B MacLean, HL Röst, ... Nature biotechnology 34 (11), 1130-1136, 2016 | 272 | 2016 |
| Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries DB Bekker-Jensen, OM Bernhardt, A Hogrebe, A Martinez-Val, L Verbeke, ... Nature communications 11 (1), 787, 2020 | 189 | 2020 |
| Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry N Selevsek, CY Chang, LC Gillet, P Navarro, OM Bernhardt, L Reiter, ... Molecular & Cellular Proteomics 14 (3), 739-749, 2015 | 176 | 2015 |
| 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 | 129 | 2016 |
| 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 | 118 | 2019 |
| 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 | 109 | 2019 |
| Spectronaut: a fast and efficient algorithm for MRM-like processing of data independent acquisition (SWATH-MS) data OM Bernhardt, N Selevsek, LC Gillet, O Rinner, P Picotti, R Aebersold, ... Biognosys. ch, 2012 | 52 | 2012 |
| MassIVE. quant: a community resource of quantitative mass spectrometry–based proteomics datasets M Choi, J Carver, C Chiva, M Tzouros, T Huang, TH Tsai, B Pullman, ... Nature methods 17 (10), 981-984, 2020 | 33 | 2020 |
| Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry*[S] F Müller, L Kolbowski, OM Bernhardt, L Reiter, J Rappsilber Molecular & Cellular Proteomics 18 (4), 786-795, 2019 | 30 | 2019 |
| Revealing dynamic protein acetylation across subcellular compartments J Baeza, AJ Lawton, J Fan, MJ Smallegan, I Lienert, T Gandhi, ... Journal of proteome research 19 (6), 2404-2418, 2020 | 22 | 2020 |
| WITHDRAWN: Heralds of parallel MS: Data-independent acquisition surpassing sequential identification of data dependent acquisition in proteomics. R Bruderer, OM Bernhardt, T Gandhi, Y Xuan, J Sondermann, M Schmidt, ... Molecular & Cellular Proteomics: MCP, mcp. M116. 065730-mcp. M116. 065730, 2017 | 5 | 2017 |
| Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition (DIA) without the need for spectral libraries DB Bekker-Jensen, OM Bernhardt, A Hogrebe, AM del Val, L Verbeke, ... BioRxiv, 657858, 2019 | 4 | 2019 |
| Quantifying dynamic protein acetylation using quantitative stoichiometry J Baeza, AJ Lawton, J Fan, MJ Smallegan, I Lienert, T Gandhi, ... Preprint at https://www. biorxiv. org/content/10.1101/472530v1. full, 2018 | 3 | 2018 |
| Having a free lunch: A combined DIA+ DDA approach towards spectral library generation T Gandhi, L Verbeke, OM Bernhardt, R Bruderer, J Muntel, L Reiter | 1 | 2017 |
| Substantial Downregulation of Mitochondrial and Peroxisomal Proteins during Acute Kidney Injury revealed by Data-Independent Acquisition Proteomics JB Burton, A Silva-Barbosa, J Bons, JP Rose, K Pfister, F Simona, ... bioRxiv, 2023.02. 26.530107, 2023 | | 2023 |
| Discovery of MHC class I and class II neoantigens in lung cancer in needle biopsy tissue samples using an optimized high-throughput workflow IE Shapiro, L Raess, M Tognetti, T Temu, OM Bernhardt, Y Feng, ... Cancer Research 82 (12_Supplement), 1374-1374, 2022 | | 2022 |
| A Tale of Two-Data Independent Acquisition applied to maximize proteome coverage and throughput RM Bruderer, OM Bernhardt, T Gandhi, J Muntel, S Muller, P Mironova, ... Molecular & Cellular Proteomics 16 (8), S25-S25, 2017 | | 2017 |
| This article has been withdrawn by the authors. This article did not comply with the editorial guidelines of MCP. Specifically, single peptide based protein identifications of … R Bruderer, OM Bernhardt, T Gandhi, Y Xuan, J Sondermann, M Schmidt, ... | | 2017 |
