Search Results - "Bernhardt, Oliver M."

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries by Bekker-Jensen, Dorte B., Bernhardt, Oliver M., Hogrebe, Alexander, Martinez-Val, Ana, Verbeke, Lynn, Gandhi, Tejas, Kelstrup, Christian D., Reiter, Lukas, Olsen, Jesper V.

“…Quantitative phosphoproteomics has transformed investigations of cell signaling, but it remains challenging to scale the technology for high-throughput…”
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Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results by Bruderer, Roland, Bernhardt, Oliver M., Gandhi, Tejas, Xuan, Yue, Sondermann, Julia, Schmidt, Manuela, Gomez-Varela, David, Reiter, Lukas

“…Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an…”
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Reproducible and Consistent Quantification of the Saccharomyces cerevisiae Proteome by SWATH-mass spectrometry by Selevsek, Nathalie, Chang, Ching-Yun, Gillet, Ludovic C., Navarro, Pedro, Bernhardt, Oliver M., Reiter, Lukas, Cheng, Lin-Yang, Vitek, Olga, Aebersold, Ruedi

“…Targeted mass spectrometry by selected reaction monitoring (S/MRM) has proven to be a suitable technique for the consistent and reproducible quantification of…”
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MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets by Choi, Meena, Carver, Jeremy, Chiva, Cristina, Tzouros, Manuel, Huang, Ting, Tsai, Tsung-Heng, Pullman, Benjamin, Bernhardt, Oliver M., Hüttenhain, Ruth, Teo, Guo Ci, Perez-Riverol, Yasset, Muntel, Jan, Müller, Maik, Goetze, Sandra, Pavlou, Maria, Verschueren, Erik, Wollscheid, Bernd, Nesvizhskii, Alexey I., Reiter, Lukas, Dunkley, Tom, Sabidó, Eduard, Bandeira, Nuno, Vitek, Olga

“…MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry–based proteomics, which is compatible with all…”
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Surpassing 10 000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy by Muntel, Jan, Gandhi, Tejas, Verbeke, Lynn, Bernhardt, Oliver M, Treiber, Tobias, Bruderer, Roland, Reiter, Lukas

“…Comprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry…”
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High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation by Bruderer, Roland, Bernhardt, Oliver M., Gandhi, Tejas, Reiter, Lukas

“…Targeted analysis of data‐independent acquisition (DIA) data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome…”
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Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues[S] by Bruderer, Roland, Bernhardt, Oliver M., Gandhi, Tejas, Miladinović, Saša M., Cheng, Lin-Yang, Messner, Simon, Ehrenberger, Tobias, Zanotelli, Vito, Butscheid, Yulia, Escher, Claudia, Vitek, Olga, Rinner, Oliver, Reiter, Lukas

“…The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content…”
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Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry[S] by Müller, Fränze, Kolbowski, Lars, Bernhardt, Oliver M., Reiter, Lukas, Rappsilber, Juri

“…We present here a simple, user friendly and automated new quantitative cross-linking mass spectrometry (QCLMS) workflow comprising data-independent acquisition…”
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A multicenter study benchmarks software tools for label-free proteome quantification by Navarro, Pedro, Kuharev, Jörg, Gillet, Ludovic C, Bernhardt, Oliver M, MacLean, Brendan, Röst, Hannes L, Tate, Stephen A, Tsou, Chih-Chiang, Reiter, Lukas, Distler, Ute, Rosenberger, George, Perez-Riverol, Yasset, Nesvizhskii, Alexey I, Aebersold, Ruedi, Tenzer, Stefan

“…LFQbench, a software tool to assess the quality of label-free quantitative proteomics analyses, enables developers to benchmark and improve analytic methods…”
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Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance'[S] by Bruderer, Roland, Muntel, Jan, Müller, Sebastian, Bernhardt, Oliver M., Gandhi, Tejas, Cominetti, Ornella, Macron, Charlotte, Carayol, Jérôme, Rinner, Oliver, Astrup, Arne, Saris, Wim H.M., Hager, Jörg, Valsesia, Armand, Dayon, Loïc, Reiter, Lukas

“…We established a robust capillary-flow data-independent acquisition MS platform capable of measuring 31 plasma proteomes per day without the need of repeated…”
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MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale by Kohler, Devon, Staniak, Mateusz, Tsai, Tsung-Heng, Huang, Ting, Shulman, Nicholas, Bernhardt, Oliver M., MacLean, Brendan X., Nesvizhskii, Alexey I., Reiter, Lukas, Sabido, Eduard, Choi, Meena, Vitek, Olga

“…The MSstats R-Bioconductor family of packages is widely used for statistical analyses of quantitative bottom-up mass spectrometry-based proteomic experiments…”
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Revealing Dynamic Protein Acetylation across Subcellular Compartments by Baeza, Josue, Lawton, Alexis J, Fan, Jing, Smallegan, Michael J, Lienert, Ian, Gandhi, Tejas, Bernhardt, Oliver M, Reiter, Lukas, Denu, John M

“…Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances in mass spectrometry have enabled…”
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150 Class I and II neoantigen mapping in MSI-high colorectal cancer in needle biopsy size tissue samples by Shapiro, Ilja E, Raess, Luca, Tognetti, Marco, Temu, Tikira, Bernhardt, Oliver M, Bruderer, Roland, Feng, Yuehan, Woodsmith, Jonathan, Reiter, Lukas

“…BackgroundColorectal cancer (CRC) is currently the second most common cause of cancer related mortality in the world. One of the hallmarks of CRC is its…”
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Abstract 5376: Quantitative profiling of HLA class I and class II antigens and neoantigens in tissue biopsy and PBMC samples using an optimized mass spectrometry-based workflow by Shapiro, Ilja E., Tognetti, Marco, Temu, Tikira, Bernhardt, Oliver M., Redfern, Daniel, Feng, Yuehan, Bruderer, Roland, Reiter, Lukas

“…Abstract Major histocompatibility complex (MHC) molecules play a central role in orchestrating immune responses by presenting antigenic peptides derived from…”
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Abstract 1374: Discovery of MHC class I and class II neoantigens in lung cancer in needle biopsy tissue samples using an optimized high-throughput workflow by Shapiro, Ilja E., Raess, Luca, Tognetti, Marco, Temu, Tikira, Bernhardt, Oliver M., Feng, Yuehan, Bruderer, Roland, Reiter, Lukas

“…Abstract Human leukocyte antigen-associated peptides, known as immunopeptides, play an essential role in adaptive immunity by activating and ensuring the…”
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Abstract 2991: Complementarity of class I and II neoantigen mapping in MSI-high colorectal cancer in needle biopsy size tissue samples by Shapiro, Ilja E., Räss, Luca, Below, Christopher R., Tognetti, Marco, Temu, Tikira, Bernhardt, Oliver M., Bruderer, Roland, Woodsmith, Jonathan, Reiter, Lukas

“…Abstract Colorectal cancer (CRC) is currently the second most common cause of cancer related mortality in the world. One of the hallmarks of CRC is its complex…”
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A multi-center study benchmarks software tools for label-free proteome quantification by Navarro, Pedro, Kuharev, Jörg, Gillet, Ludovic C, Bernhardt, Oliver M., MacLean, Brendan, Röst, Hannes L., Tate, Stephen A., Tsou, Chih-Chiang, Reiter, Lukas, Distler, Ute, Rosenberger, George, Perez-Riverol, Yasset, Nesvizhskii, Alexey I., Aebersold, Ruedi, Tenzer, Stefan

“…The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition…”
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Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry by Müller, Fränze, Kolbowski, Lars, Bernhardt, Oliver M, Reiter, Lukas, Rappsilber, Juri

“…Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine…”
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Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance by Bruderer, Roland, Muntel, Jan, Müller, Sebastian, Bernhardt, Oliver M, Gandhi, Tejas, Cominetti, Ornella, Macron, Charlotte, Carayol, Jérôme, Rinner, Oliver, Astrup, Arne, Saris, Wim H M, Hager, Jörg, Valsesia, Armand, Dayon, Loïc, Reiter, Lukas

“…Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our…”
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Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance by Bruderer, Roland, Muntel, Jan, Müller, Sebastian, Bernhardt, Oliver M, Gandhi, Tejas, Cominetti, Ornella, Macron, Charlotte, Carayol, Jérôme, Rinner, Oliver, Astrup, Arne, Saris, Wim H M, Hager, Jörg, Valsesia, Armand, Dayon, Loïc, Reiter, Lukas

“…Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our…”
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