Search Results - "Pedrioli, Patrick"

Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA by Peter, Matthias, Pedrioli, Patrick G. A, Hofmann, Kay, Leidel, Sebastian, Costanzo, Michael, Bucher, Tamara, Brost, Renée, Boone, Charles, Schmidt, Alexander, Aebersold, Ruedi

“…Ubiquitin-like proteins (UBLs) can change protein function, localization or turnover by covalent attachment to lysine residues. Although UBLs achieve this…”
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Activation of the canonical IKK complex by K63/M1-linked hybrid ubiquitin chains by Emmerich, Christoph H., Ordureau, Alban, Strickson, Sam, Arthur, J. Simon C., Pedrioli, Patrick G. A., Komander, David, Cohen, Philip

“…Polyubiquitin (pUb) chains formed between the C terminus of ubiquitin and lysine 63 (K63) or methionine 1 (M1) of another ubiquitin have been implicated in the…”
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Phosphorylation of CRTC3 by the salt-inducible kinases controls the interconversion of classically activated and regulatory macrophages by Clark, Kristopher, MacKenzie, Kirsty F, Petkevicius, Kasparas, Kristariyanto, Yosua, Zhang, Jiazhen, Choi, Hwan Geun, Peggie, Mark, Plater, Lorna, Pedrioli, Patrick G. A, McIver, Ed, Gray, Nathanael S, Arthur, J. Simon C, Cohen, Philip

“…Macrophages acquire strikingly different properties that enable them to play key roles during the initiation, propagation, and resolution of inflammation…”
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Surfaceome dynamics reveal proteostasis-independent reorganization of neuronal surface proteins during development and synaptic plasticity by van Oostrum, Marc, Campbell, Benjamin, Seng, Charlotte, Müller, Maik, tom Dieck, Susanne, Hammer, Jacqueline, Pedrioli, Patrick G. A., Földy, Csaba, Tyagarajan, Shiva K., Wollscheid, Bernd

“…Neurons are highly compartmentalized cells with tightly controlled subcellular protein organization. While brain transcriptome, connectome and global proteome…”
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Reproducible Determination of High-Density Lipoprotein Proteotypes by Goetze, Sandra, Frey, Kathrin, Rohrer, Lucia, Radosavljevic, Silvija, Krützfeldt, Jan, Landmesser, Ulf, Bueter, Marco, Pedrioli, Patrick G. A, von Eckardstein, Arnold, Wollscheid, Bernd

“…High-density lipoprotein (HDL) is a heterogeneous mixture of blood-circulating multimolecular particles containing many different proteins, lipids, and RNAs…”
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Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses by Rosenberger, George, Bludau, Isabell, Schmitt, Uwe, Heusel, Moritz, Hunter, Christie L, Liu, Yansheng, MacCoss, Michael J, MacLean, Brendan X, Nesvizhskii, Alexey I, Pedrioli, Patrick G A, Reiter, Lukas, Röst, Hannes L, Tate, Stephen, Ting, Ying S, Collins, Ben C, Aebersold, Ruedi

“…The statistical concepts for false discovery rate control long applied in the field of data-dependent acquisition (DDA) mass spectrometry-based proteomics can…”
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Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures by Tyagi, Kshitiz, Pedrioli, Patrick G A

“…Maintenance of protein quality control has implications in various processes such as neurodegeneration and ageing. To investigate how environmental insults…”
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Trans-proteomic pipeline: a pipeline for proteomic analysis by Pedrioli, Patrick G A

“…Mass spectrometry has quickly become an essential tool in molecular biology laboratories. Here, we describe the Trans-Proteomic Pipeline, a collection of…”
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Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial by Čuklina, Jelena, Lee, Chloe H, Williams, Evan G, Sajic, Tatjana, Collins, Ben C, Rodríguez Martínez, María, Sharma, Varun S, Wendt, Fabian, Goetze, Sandra, Keele, Gregory R, Wollscheid, Bernd, Aebersold, Ruedi, Pedrioli, Patrick G A

“…Advancements in mass spectrometry‐based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much‐needed…”
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Mitochondrial NAD+ Controls Nuclear ARTD1-Induced ADP-Ribosylation by Hopp, Ann-Katrin, Teloni, Federico, Bisceglie, Lavinia, Gondrand, Corentin, Raith, Fabio, Nowak, Kathrin, Muskalla, Lukas, Howald, Anna, Pedrioli, Patrick G.A., Johnsson, Kai, Altmeyer, Matthias, Pedrioli, Deena M. Leslie, Hottiger, Michael O.

“…In addition to its role as an electron transporter, mitochondrial nicotinamide adenine dinucleotide (NAD+) is an important co-factor for enzymatic reactions,…”
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Proteogenetic drug response profiling elucidates targetable vulnerabilities of myelofibrosis by Wildschut, Mattheus H. E., Mena, Julien, Dördelmann, Cyril, van Oostrum, Marc, Hale, Benjamin D., Settelmeier, Jens, Festl, Yasmin, Lysenko, Veronika, Schürch, Patrick M., Ring, Alexander, Severin, Yannik, Bader, Michael S., Pedrioli, Patrick G. A., Goetze, Sandra, van Drogen, Audrey, Balabanov, Stefan, Skoda, Radek C., Lopes, Massimo, Wollscheid, Bernd, Theocharides, Alexandre P. A., Snijder, Berend

“…Myelofibrosis is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. Myelofibrosis patients frequently carry driver mutations in…”
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Classification of mouse B cell types using surfaceome proteotype maps by van Oostrum, Marc, Müller, Maik, Klein, Fabian, Bruderer, Roland, Zhang, Hui, Pedrioli, Patrick G. A., Reiter, Lukas, Tsapogas, Panagiotis, Rolink, Antonius, Wollscheid, Bernd

“…System-wide quantification of the cell surface proteotype and identification of extracellular glycosylation sites is challenging when samples are limited…”
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Hydrophilic Strong Anion Exchange (hSAX) Chromatography for Highly Orthogonal Peptide Separation of Complex Proteomes by Ritorto, Maria Stella, Cook, Ken, Tyagi, Kshitiz, Pedrioli, Patrick G. A, Trost, Matthias

“…Due to its compatibility and orthogonality to reversed phase (RP) liquid chromatography (LC) separation, ion exchange chromatography, and mainly strong cation…”
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PGE2 Induces Macrophage IL-10 Production and a Regulatory-like Phenotype via a Protein Kinase A–SIK–CRTC3 Pathway by MacKenzie, Kirsty F., Clark, Kristopher, Naqvi, Shaista, McGuire, Victoria A., Nöehren, Gesa, Kristariyanto, Yosua, van den Bosch, Mirjam, Mudaliar, Manikhandan, McCarthy, Pierre C., Pattison, Michael J., Pedrioli, Patrick G. A., Barton, Geoff J., Toth, Rachel, Prescott, Alan, Arthur, J. Simon C.

“…Abstract The polarization of macrophages into a regulatory-like phenotype and the production of IL-10 plays an important role in the resolution of…”
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PRAMEL7 and CUL2 decrease NuRD stability to establish ground-state pluripotency by Rupasinghe, Meneka, Bersaglieri, Cristiana, Leslie Pedrioli, Deena M, Pedrioli, Patrick GA, Panatta, Martina, Hottiger, Michael O, Cinelli, Paolo, Santoro, Raffaella

“…Pluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, their gene…”
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The SysteMHC Atlas project by Shao, Wenguang, Pedrioli, Patrick G A, Wolski, Witold, Scurtescu, Cristian, Schmid, Emanuel, Vizcaíno, Juan A, Courcelles, Mathieu, Schuster, Heiko, Kowalewski, Daniel, Marino, Fabio, Arlehamn, Cecilia S L, Vaughan, Kerrie, Peters, Bjoern, Sette, Alessandro, Ottenhoff, Tom H M, Meijgaarden, Krista E, Nieuwenhuizen, Natalie, Kaufmann, Stefan H E, Schlapbach, Ralph, Castle, John C, Nesvizhskii, Alexey I, Nielsen, Morten, Deutsch, Eric W, Campbell, David S, Moritz, Robert L, Zubarev, Roman A, Ytterberg, Anders Jimmy, Purcell, Anthony W, Marcilla, Miguel, Paradela, Alberto, Wang, Qi, Costello, Catherine E, Ternette, Nicola, van Veelen, Peter A, van Els, Cécile A C M, Heck, Albert J R, de Souza, Gustavo A, Sollid, Ludvig M, Admon, Arie, Stevanovic, Stefan, Rammensee, Hans-Georg, Thibault, Pierre, Perreault, Claude, Bassani-Sternberg, Michal, Aebersold, Ruedi, Caron, Etienne

“…Abstract Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility…”
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High-throughput identification of repurposable neuroactive drugs with potent anti-glioblastoma activity by Lee, Sohyon, Weiss, Tobias, Bühler, Marcel, Mena, Julien, Lottenbach, Zuzanna, Wegmann, Rebekka, Sun, Miaomiao, Bihl, Michel, Augustynek, Bartłomiej, Baumann, Sven P., Goetze, Sandra, van Drogen, Audrey, Pedrioli, Patrick G. A., Penton, David, Festl, Yasmin, Buck, Alicia, Kirschenbaum, Daniel, Zeitlberger, Anna M., Neidert, Marian C., Vasella, Flavio, Rushing, Elisabeth J., Wollscheid, Bernd, Hediger, Matthias A., Weller, Michael, Snijder, Berend

“…Glioblastoma, the most aggressive primary brain cancer, has a dismal prognosis, yet systemic treatment is limited to DNA-alkylating chemotherapies. New…”
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tRNA tKᵁᵁᵁ, tQᵁᵁᴳ, and tEᵁᵁC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding by Rezgui, Vanessa Anissa Nathalie, Tyagi, Kshitiz, Ranjan, Namit, Konevega, Andrey L, Mittelstaet, Joerg, Rodnina, Marina V, Peter, Matthias, Pedrioli, Patrick G A

“…tRNA modifications are crucial to ensure translation efficiency and fidelity. In eukaryotes, the URM1 and ELP pathways increase cellular resistance to various…”
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A tissue-based draft map of the murine MHC class I immunopeptidome by Schuster, Heiko, Shao, Wenguang, Weiss, Tobias, Pedrioli, Patrick G.A., Roth, Patrick, Weller, Michael, Campbell, David S., Deutsch, Eric W., Moritz, Robert L., Planz, Oliver, Rammensee, Hans-Georg, Aebersold, Ruedi, Caron, Etienne

“…The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I…”
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A common open representation of mass spectrometry data and its application to proteomics research by Aebersold, Ruedi, Pedrioli, Patrick G A, Eng, Jimmy K, Hubley, Robert, Vogelzang, Mathijs, Deutsch, Eric W, Raught, Brian, Pratt, Brian, Nilsson, Erik, Angeletti, Ruth H, Apweiler, Rolf, Cheung, Kei, Costello, Catherine E, Hermjakob, Henning, Huang, Sequin, Julian, Randall K, Kapp, Eugene, McComb, Mark E, Oliver, Stephen G, Omenn, Gilbert, Paton, Norman W, Simpson, Richard, Smith, Richard, Taylor, Chris F, Zhu, Weimin

“…A broad range of mass spectrometers are used in mass spectrometry (MS)-based proteomics research. Each type of instrument possesses a unique design, data…”
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