Search Results - "Köcher, Thomas"

Universal and Confident Phosphorylation Site Localization Using phosphoRS by Taus, Thomas, Köcher, Thomas, Pichler, Peter, Paschke, Carmen, Schmidt, Andreas, Henrich, Christoph, Mechtler, Karl

“…An algorithm for the assignment of phosphorylation sites in peptides is described. The program uses tandem mass spectrometry data in conjunction with the…”
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Quantitative Phosphoproteomics of the Ataxia Telangiectasia-Mutated (ATM) and Ataxia Telangiectasia-Mutated and Rad3-related (ATR) Dependent DNA Damage Response in Arabidopsis thaliana[S] by Roitinger, Elisabeth, Hofer, Manuel, Köcher, Thomas, Pichler, Peter, Novatchkova, Maria, Yang, Jianhua, Schlögelhofer, Peter, Mechtler, Karl

“…The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is an important biological regulatory mechanism. In the context of…”
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Ultra-High-Pressure RPLC Hyphenated to an LTQ-Orbitrap Velos Reveals a Linear Relation between Peak Capacity and Number of Identified Peptides by Köcher, Thomas, Swart, Remco, Mechtler, Karl

“…Currently, unbiased protein identification is mostly performed by directly coupling reversed-phase liquid chromatography (RPLC) via electrospray ionization to…”
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Mass spectrometry-based functional proteomics: from molecular machines to protein networks by Kocher, Thomas, Superti-Furga, Giulio

“…The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A…”
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Kynurenine importation by SLC7A11 propagates anti-ferroptotic signaling by Fiore, Alessandra, Zeitler, Leonie, Russier, Marion, Groß, Annette, Hiller, Maria-Kathrin, Parker, Joanne L., Stier, Luca, Köcher, Thomas, Newstead, Simon, Murray, Peter J.

“…IDO1 oxidizes tryptophan (TRP) to generate kynurenine (KYN), the substrate for 1-carbon and NAD metabolism, and is implicated in pro-cancer pathophysiology and…”
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Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis by Bonnay, François, Veloso, Ana, Steinmann, Victoria, Köcher, Thomas, Abdusselamoglu, Merve Deniz, Bajaj, Sunanjay, Rivelles, Elisa, Landskron, Lisa, Esterbauer, Harald, Zinzen, Robert P., Knoblich, Juergen A.

“…Metabolic reprogramming is a key feature of many cancers, but how and when it contributes to tumorigenesis remains unclear. Here we demonstrate that metabolic…”
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Anti-ferroptotic mechanism of IL4i1-mediated amino acid metabolism by Zeitler, Leonie, Fiore, Alessandra, Meyer, Claudia, Russier, Marion, Zanella, Gaia, Suppmann, Sabine, Gargaro, Marco, Sidhu, Sachdev S, Seshagiri, Somasekar, Ohnmacht, Caspar, Köcher, Thomas, Fallarino, Francesca, Linkermann, Andreas, Murray, Peter J

“…Interleukin-4-induced-1 (IL4i1) is an amino acid oxidase secreted from immune cells. Recent observations have suggested that IL4i1 is pro-tumorigenic via…”
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SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis by Muhar, Matthias, Ebert, Anja, Neumann, Tobias, Umkehrer, Christian, Jude, Julian, Wieshofer, Corinna, Rescheneder, Philipp, Lipp, Jesse J, Herzog, Veronika A, Reichholf, Brian, Cisneros, David A, Hoffmann, Thomas, Schlapansky, Moritz F, Bhat, Pooja, von Haeseler, Arndt, Köcher, Thomas, Obenauf, Anna C, Popow, Johannes, Ameres, Stefan L, Zuber, Johannes

“…Defining direct targets of transcription factors and regulatory pathways is key to understanding their roles in physiology and disease. We combined SLAM-seq…”
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Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets by Rix, Uwe, Hantschel, Oliver, Dürnberger, Gerhard, Remsing Rix, Lily L., Planyavsky, Melanie, Fernbach, Nora V., Kaupe, Ines, Bennett, Keiryn L., Valent, Peter, Colinge, Jacques, Köcher, Thomas, Superti-Furga, Giulio

“…The BCR-ABL tyrosine kinase inhibitor imatinib represents the current frontline therapy in chronic myeloid leukemia. Because many patients develop imatinib…”
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Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients by Köcher, Thomas, Pichler, Peter, Swart, Remco, Mechtler, Karl

“…The majority of proteome-wide studies rely on the high separation power of two-dimensional liquid chromatography–tandem mass spectrometry (2D LC-MS/MS), often…”
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Peptide Labeling with Isobaric Tags Yields Higher Identification Rates Using iTRAQ 4-Plex Compared to TMT 6-Plex and iTRAQ 8-Plex on LTQ Orbitrap by Pichler, Peter, Köcher, Thomas, Holzmann, Johann, Mazanek, Michael, Taus, Thomas, Ammerer, Gustav, Mechtler, Karl

“…Peptide labeling with isobaric tags has become a popular technique in quantitative shotgun proteomics. Using two different samples viz. a protein mixture and…”
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The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response by Asanović, Igor, Strandback, Emilia, Kroupova, Alena, Pasajlic, Djurdja, Meinhart, Anton, Tsung-Pin, Pai, Djokovic, Nemanja, Anrather, Dorothea, Schuetz, Thomas, Suskiewicz, Marcin Józef, Sillamaa, Sirelin, Köcher, Thomas, Beveridge, Rebecca, Nikolic, Katarina, Schleiffer, Alexander, Jinek, Martin, Hartl, Markus, Clausen, Tim, Penninger, Josef, Macheroux, Peter, Weitzer, Stefan, Martinez, Javier

“…The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a…”
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High Precision Quantitative Proteomics Using iTRAQ on an LTQ Orbitrap: A New Mass Spectrometric Method Combining the Benefits of All by Köcher, Thomas, Pichler, Peter, Schutzbier, Michael, Stingl, Christoph, Kaul, Axel, Teucher, Nils, Hasenfuss, Gerd, Penninger, Josef M, Mechtler, Karl

“…The development of quantitative techniques in mass spectrometry has generated the ability to systematically monitor protein expression. Isobaric tags for…”
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ABCC1 and glutathione metabolism limit the efficacy of BCL-2 inhibitors in acute myeloid leukemia by Ebner, Jessica, Schmoellerl, Johannes, Piontek, Martin, Manhart, Gabriele, Troester, Selina, Carter, Bing Z., Neubauer, Heidi, Moriggl, Richard, Szakács, Gergely, Zuber, Johannes, Köcher, Thomas, Andreeff, Michael, Sperr, Wolfgang R., Valent, Peter, Grebien, Florian

“…The BCL-2 inhibitor Venetoclax is a promising agent for the treatment of acute myeloid leukemia (AML). However, many patients are refractory to Venetoclax, and…”
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General Statistical Modeling of Data from Protein Relative Expression Isobaric Tags by Breitwieser, Florian P, Müller, André, Dayon, Loïc, Köcher, Thomas, Hainard, Alexandre, Pichler, Peter, Schmidt-Erfurth, Ursula, Superti-Furga, Giulio, Sanchez, Jean-Charles, Mechtler, Karl, Bennett, Keiryn L, Colinge, Jacques

“…Quantitative comparison of the protein content of biological samples is a fundamental tool of research. The TMT and iTRAQ isobaric labeling technologies allow…”
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Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa‐Porthos axis in Drosophila by Emtenani, Shamsi, Martin, Elliot T, Gyoergy, Attila, Bicher, Julia, Genger, Jakob‐Wendelin, Köcher, Thomas, Akhmanova, Maria, Guarda, Mariana, Roblek, Marko, Bergthaler, Andreas, Hurd, Thomas R, Rangan, Prashanth, Siekhaus, Daria E

“…Cellular metabolism must adapt to changing demands to enable homeostasis. During immune responses or cancer metastasis, cells leading migration into…”
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AIF-regulated oxidative phosphorylation supports lung cancer development by Rao, Shuan, Mondragón, Laura, Pranjic, Blanka, Hanada, Toshikatsu, Stoll, Gautier, Köcher, Thomas, Zhang, Peng, Jais, Alexander, Lercher, Alexander, Bergthaler, Andreas, Schramek, Daniel, Haigh, Katharina, Sica, Valentina, Leduc, Marion, Modjtahedi, Nazanine, Pai, Tsung-Pin, Onji, Masahiro, Uribesalgo, Iris, Hanada, Reiko, Kozieradzki, Ivona, Koglgruber, Rubina, Cronin, Shane J., She, Zhigang, Quehenberger, Franz, Popper, Helmut, Kenner, Lukas, Haigh, Jody J., Kepp, Oliver, Rak, Malgorzata, Cai, Kaican, Kroemer, Guido, Penninger, Josef M.

“…Cancer is a major and still increasing cause of death in humans. Most cancer cells have a fundamentally different metabolic profile from that of normal tissue…”
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Reduced coenzyme Q synthesis confers non-target site resistance to the herbicide thaxtomin A by Casey, Chloe, Köcher, Thomas, Champion, Clément, Jandrasits, Katharina, Mosiolek, Magdalena, Bonnot, Clémence, Dolan, Liam

“…Herbicide resistance in weeds is a growing threat to global crop production. Non-target site resistance is problematic because a single resistance allele can…”
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Quality control in LC-MS/MS by Köcher, Thomas, Pichler, Peter, Swart, Remco, Mechtler, Karl

“…In the last 15 years, MS-based protein characterization has expanded at a rapid rate. This success is built upon constantly improving instrumentation and a…”
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Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up by Köcher, Thomas, Pichler, Peter, De Pra, Mauro, Rieux, Laurent, Swart, Remco, Mechtler, Karl

“…LC‐MS/MS is the most commonly used technique for the identification and characterization of proteins. The efficiency of the electrospray process is a critical…”
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