Full Text Journal Articles by
Author Benjamin Ruprecht

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Publisher Correction: A mass spectrometry-based proteome map of drug action in lung cancer cell lines.

Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew Christopher, Rafael B Fernandez, Li Zheng, Brian D Dill, Huijun Wang, Yuting Xu, Andy Liaw, Jonathan D Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R Tata, Victoria Kutilek, Ivan Cornella-Taracido, An Chi,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Chem Biol (Nature chemical biology)
[2020, 16(10):1149]

Cited: 0 times

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A mass spectrometry-based proteome map of drug action in lung cancer cell lines.

Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew Christopher, Rafael B Fernandez, Li Zheng, Brian D Dill, Huijun Wang, Yuting Xu, Andy Liaw, Jonathan D Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R Tata, Victoria Kutilek, Ivan Cornella-Taracido, An Chi,

Mass spectrometry-based discovery proteomics is an essential tool for the proximal readout of cellular drug action. Here, we apply a robust proteomic workflow to rapidly profile the proteomes of five lung cancer cell lines in response to more than 50 drugs. Integration of millions of quantitative protein-drug associations substantially improved ... Read more >>

Nat. Chem. Biol. (Nature chemical biology)
[2020, 16(10):1111-1119]

Cited: 0 times

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Proteome activity landscapes of tumor cell lines determine drug responses.

Martin Frejno, Chen Meng, Benjamin Ruprecht, Thomas Oellerich, Sebastian Scheich, Karin Kleigrewe, Enken Drecoll, Patroklos Samaras, Alexander Hogrebe, Dominic Helm, Julia Mergner, Jana Zecha, Stephanie Heinzlmeir, Mathias Wilhelm, Julia Dorn, Hans-Michael Kvasnicka, Hubert Serve, Wilko Weichert, Bernhard Kuster,

Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular mechanisms of drug action. We extend this paradigm to measuring proteome activity landscapes by acquiring and integrating quantitative data for 10,000 proteins and 55,000 phosphorylation sites (p-sites) from 125 ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):3639]

Cited: 0 times

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Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors.

Maria Reinecke, Benjamin Ruprecht, Sandra Poser, Svenja Wiechmann, Mathias Wilhelm, Stephanie Heinzlmeir, Bernhard Kuster, Guillaume Médard,

Chemical proteomic approaches utilizing immobilized, broad-selective kinase inhibitors (Kinobeads) have proven valuable for the elucidation of a compound's target profile under close-to-physiological conditions and often revealed potentially synergistic or toxic off-targets. Current Kinobeads enrich more than 300 native protein kinases from cell line or tissue lysates but do not systematically ... Read more >>

ACS Chem Biol (ACS chemical biology)
[2019, 14(4):655-664]

Cited: 2 times

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Preferential microRNA targeting revealed by in vivo competitive binding and differential Argonaute immunoprecipitation.

Stanislas Werfel, Simon Leierseder, Benjamin Ruprecht, Bernhard Kuster, Stefan Engelhardt,

MicroRNAs (miRNAs) have been described to simultaneously inhibit hundreds of targets, albeit to a modest extent. It was recently proposed that there could exist more specific, exceptionally strong binding to a subgroup of targets. However, it is unknown, whether this is the case and how such targets can be identified. ... Read more >>

Nucleic Acids Res (Nucleic acids research)
[2017, 45(17):10218-10228]

Cited: 7 times

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Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis.

Benjamin Ruprecht, Esther A Zaal, Jana Zecha, Wei Wu, Celia R Berkers, Bernhard Kuster, Simone Lemeer,

HER2/ERBB2-overexpressing breast cancers targeted effectively by the small-molecule kinase inhibitor lapatinib frequently acquire resistance to this drug. In this study, we employed explorative mass spectrometry to profile proteome, kinome, and phosphoproteome changes in an established model of lapatinib resistance to systematically investigate initial inhibitor response and subsequent reprogramming in resistance. ... Read more >>

Cancer Res. (Cancer research)
[2017, 77(8):1842-1853]

Cited: 19 times

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Optimized Enrichment of Phosphoproteomes by Fe-IMAC Column Chromatography.

Benjamin Ruprecht, Heiner Koch, Petra Domasinska, Martin Frejno, Bernhard Kuster, Simone Lemeer,

Phosphorylation is among the most important post-translational modifications of proteins and has numerous regulatory functions across all domains of life. However, phosphorylation is often substoichiometric, requiring selective and sensitive methods to enrich phosphorylated peptides from complex cellular digests. Various methods have been devised for this purpose and we have recently ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2017, 1550:47-60]

Cited: 6 times

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High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests.

Benjamin Ruprecht, Jana Zecha, Daniel P Zolg, Bernhard Kuster,

Despite recent advances in mass spectrometric sequencing speed and improved sensitivity, the in-depth analysis of proteomes still widely relies on off-line peptide separation and fractionation to deal with the enormous molecular complexity of shotgun digested proteomes. While a multitude of methods has been established for off-line peptide separation using HPLC ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2017, 1550:83-98]

Cited: 6 times

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Hydrophilic Strong Anion Exchange (hSAX) Chromatography Enables Deep Fractionation of Tissue Proteomes.

Benjamin Ruprecht, Dongxue Wang, Riccardo Zenezini Chiozzi, Li-Hua Li, Hannes Hahne, Bernhard Kuster,

The bottom-up proteomic analysis of cell line and tissue samples to a depth > 10,000 proteins still represents a considerable challenge because of the sheer number of peptides generated by proteolytic digestions and the high dynamic range of protein expression. As a result, comprehensive protein coverage requires multidimensional peptide separation. ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2017, 1550:69-82]

Cited: 4 times

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Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs.

Stephanie Heinzlmeir, Denis Kudlinzki, Sridhar Sreeramulu, Susan Klaeger, Santosh Lakshmi Gande, Verena Linhard, Mathias Wilhelm, Huichao Qiao, Dominic Helm, Benjamin Ruprecht, Krishna Saxena, Guillaume Médard, Harald Schwalbe, Bernhard Kuster,

The receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays important roles in oncogenesis, metastasis, and treatment resistance, yet therapeutic targeting, drug discovery, or investigation of EPHA2 biology is hampered by the lack of appropriate inhibitors and structural information. Here, we used chemical proteomics to survey 235 clinical kinase inhibitors ... Read more >>

ACS Chem. Biol. (ACS chemical biology)
[2016, 11(12):3400-3411]

Cited: 11 times

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Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells.

Heiner Koch, Mathias Wilhelm, Benjamin Ruprecht, Scarlet Beck, Martin Frejno, Susan Klaeger, Bernhard Kuster,

Although substantial progress has been made regarding the use of molecularly targeted cancer therapies, resistance almost invariably develops and presents a major clinical challenge. The tumor microenvironment can rescue cancer cells from kinase inhibitors by growth-factor-mediated induction of pro-survival pathways. Here we show that epidermal growth factor receptor (EGFR) inhibition ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2016, 15(12):4490-4504]

Cited: 5 times

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MALDI-TOF and nESI Orbitrap MS/MS identify orthogonal parts of the phosphoproteome.

Benjamin Ruprecht, Christoph Roesli, Simone Lemeer, Bernhard Kuster,

Phosphorylation is a reversible posttranslational protein modification which plays a pivotal role in intracellular signaling. Despite extensive efforts, phosphorylation site mapping of proteomes is still incomplete motivating the exploration of alternative methods that complement existing workflows. In this study, we compared tandem mass spectrometry (MS/MS) on matrix assisted laser desorption/ionization ... Read more >>

Proteomics (Proteomics)
[2016, 16(10):1447-1456]

Cited: 3 times

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Evaluation of Kinase Activity Profiling Using Chemical Proteomics.

Benjamin Ruprecht, Jana Zecha, Stephanie Heinzlmeir, Guillaume Médard, Simone Lemeer, Bernhard Kuster,

Protein kinases are important mediators of intracellular signaling and are reversibly activated by phosphorylation. Immobilized kinase inhibitors can be used to enrich these often low-abundance proteins, to identify targets of kinase inhibitors, or to probe their selectivity. It has been suggested that the binding of kinases to affinity beads reflects ... Read more >>

ACS Chem. Biol. (ACS chemical biology)
[2015, 10(12):2743-2752]

Cited: 12 times

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Optimized chemical proteomics assay for kinase inhibitor profiling.

Guillaume Médard, Fiona Pachl, Benjamin Ruprecht, Susan Klaeger, Stephanie Heinzlmeir, Dominic Helm, Huichao Qiao, Xin Ku, Mathias Wilhelm, Thomas Kuehne, Zhixiang Wu, Antje Dittmann, Carsten Hopf, Karl Kramer, Bernhard Kuster,

Solid supported probes have proven to be an efficient tool for chemical proteomics. The kinobeads technology features kinase inhibitors covalently attached to Sepharose for affinity enrichment of kinomes from cell or tissue lysates. This technology, combined with quantitative mass spectrometry, is of particular interest for the profiling of kinase inhibitors. ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2015, 14(3):1574-1586]

Cited: 39 times

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Proteomic analysis of phosphorylation in cancer.

Benjamin Ruprecht, Simone Lemeer,

Constitutive activity of kinases is known to be crucial for a tumor to maintain its malignant phenotype, a phenomenon which is often referred to as oncogene addiction. The in-depth analysis of aberrant signaling pathways by the analysis of protein phosphorylation has become feasible through recent advances in proteomics technology. In ... Read more >>

Expert Rev Proteomics (Expert review of proteomics)
[2014, 11(3):259-267]

Cited: 14 times

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DMSO enhances electrospray response, boosting sensitivity of proteomic experiments.

Hannes Hahne, Fiona Pachl, Benjamin Ruprecht, Stefan K Maier, Susan Klaeger, Dominic Helm, Guillaume Médard, Matthias Wilm, Simone Lemeer, Bernhard Kuster,

We report that low percentages of dimethylsulfoxide (DMSO) in liquid chromatography solvents lead to a strong enhancement of electrospray ionization of peptides, improving the sensitivity of protein identification in bottom-up proteomics by up to tenfold. The method can be easily implemented on any LC-MS/MS system without modification to hardware or ... Read more >>

Nat. Methods (Nature methods)
[2013, 10(10):989-991]

Cited: 80 times

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Characterization of a chemical affinity probe targeting Akt kinases.

Fiona Pachl, Patrik Plattner, Benjamin Ruprecht, Guillaume Médard, Norbert Sewald, Bernhard Kuster,

Protein kinases are key regulators of cellular processes, and aberrant function is often associated with human disease. Consequently, kinases represent an important class of therapeutic targets and about 20 kinase inhibitors (KIs) are in clinical use today. Detailed knowledge about the selectivity of KIs is important for the correct interpretation ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2013, 12(8):3792-3800]

Cited: 10 times

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Comparing immobilized kinase inhibitors and covalent ATP probes for proteomic profiling of kinase expression and drug selectivity.

Simone Lemeer, Corina Zörgiebel, Benjamin Ruprecht, Kristian Kohl, Bernhard Kuster,

Kinases are involved in the regulation of many cellular processes and aberrant kinase signaling has been implicated in human disease. As a consequence, kinases are attractive drug targets. Assessing kinase function and drug selectivity in a more physiological context is challenging and often hampered by the generally low expression level ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2013, 12(4):1723-1731]

Cited: 18 times

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Extremely slow Li ion dynamics in monoclinic Li2TiO3--probing macroscopic jump diffusion via 7Li NMR stimulated echoes.

Benjamin Ruprecht, Martin Wilkening, Reinhard Uecker, Paul Heitjans,

A thorough understanding of ion dynamics in solids, which is a vital topic in modern materials and energy research, requires the investigation of diffusion properties on a preferably large dynamic range by complementary techniques. Here, a polycrystalline sample of Li(2)TiO(3) was used as a model substance to study Li motion ... Read more >>

Phys Chem Chem Phys (Physical chemistry chemical physics : PCCP)
[2012, 14(34):11974-11980]

Cited: 6 times

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