Search Results - "Scheltema, Richard"

Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage by Liaci, A. Manuel, Steigenberger, Barbara, Telles de Souza, Paulo Cesar, Tamara, Sem, Gröllers-Mulderij, Mariska, Ogrissek, Patrick, Marrink, Siewert J., Scheltema, Richard A., Förster, Friedrich

“…The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic reticulum (ER), where it removes signal peptides (SPs) from a large…”
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Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment by Cox, Jürgen, Neuhauser, Nadin, Michalski, Annette, Scheltema, Richard A, Olsen, Jesper V, Mann, Matthias

“…A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe…”
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Direct Proteomic Quantification of the Secretome of Activated Immune Cells by Meissner, Felix, Scheltema, Richard A., Mollenkopf, Hans-Joachim, Mann, Matthias

“…Protein secretion allows communication of distant cells in an organism and controls a broad range of physiological functions. We describe a quantitative,…”
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Efficient and robust proteome-wide approaches for cross-linking mass spectrometry by Klykov, Oleg, Steigenberger, Barbara, Pektaş, Sibel, Fasci, Domenico, Heck, Albert J. R., Scheltema, Richard A.

“…Cross-linking mass spectrometry (XL-MS) has received considerable interest, owing to its potential to investigate protein–protein interactions (PPIs) in an…”
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Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4 by Benda, Christian, Ebert, Judith, Scheltema, Richard A., Schiller, Herbert B., Baumgärtner, Marc, Bonneau, Fabien, Mann, Matthias, Conti, Elena

“…The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system. We investigated the molecular…”
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How paired PSII–LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry by Albanese, Pascal, Tamara, Sem, Saracco, Guido, Scheltema, Richard A., Pagliano, Cristina

“…Grana are a characteristic feature of higher plants’ thylakoid membranes, consisting of stacks of appressed membranes enriched in Photosystem II (PSII) and…”
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Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification by Liu, Fan, Lössl, Philip, Scheltema, Richard, Viner, Rosa, Heck, Albert J. R.

“…We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links…”
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Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei by Fasci, Domenico, van Ingen, Hugo, Scheltema, Richard A., Heck, Albert J.R.

“…Cells organize their actions partly through tightly controlled protein-protein interactions—collectively termed the interactome. Here we use crosslinking mass…”
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Towards a structurally resolved human protein interaction network by Burke, David F., Bryant, Patrick, Barrio-Hernandez, Inigo, Memon, Danish, Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Dunham, Alistair S., Albanese, Pascal, Keller, Andrew, Scheltema, Richard A., Bruce, James E., Leitner, Alexander, Kundrotas, Petras, Beltrao, Pedro, Elofsson, Arne

“…Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to studying their…”
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Time‐ and compartment‐resolved proteome profiling of the extracellular niche in lung injury and repair by Schiller, Herbert B, Fernandez, Isis E, Burgstaller, Gerald, Schaab, Christoph, Scheltema, Richard A, Schwarzmayr, Thomas, Strom, Tim M, Eickelberg, Oliver, Mann, Matthias

“…The extracellular matrix (ECM) is a key regulator of tissue morphogenesis and repair. However, its composition and architecture are not well characterized…”
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PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis by Scheltema, Richard A, Jankevics, Andris, Jansen, Ritsert C, Swertz, Morris A, Breitling, Rainer

“…The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these…”
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Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning by Nieuwkoop, Thijs, Terlouw, Barbara R, Stevens, Katherine G, Scheltema, Richard A, de Ridder, Dick, van der Oost, John, Claassens, Nico J

“…Abstract It has been known for decades that codon usage contributes to translation efficiency and hence to protein production levels. However, its role in…”
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Visualization of translation and protein biogenesis at the ER membrane by Gemmer, Max, Chaillet, Marten L., van Loenhout, Joyce, Cuevas Arenas, Rodrigo, Vismpas, Dimitrios, Gröllers-Mulderij, Mariska, Koh, Fujiet A., Albanese, Pascal, Scheltema, Richard A., Howes, Stuart C., Kotecha, Abhay, Fedry, Juliette, Förster, Friedrich

“…The dynamic ribosome–translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome 1 , 2 . It…”
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Fast and Accurate Disulfide Bridge Detection by Heissel, Søren, He, Yi, Jankevics, Andris, Shi, Yuqi, Molina, Henrik, Viner, Rosa, Scheltema, Richard A.

“…Recombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multibillion dollar industry. Essential here is the quality control…”
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Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding by Taschner, Michael, Basquin, Jérôme, Steigenberger, Barbara, Schäfer, Ingmar B, Soh, Young‐Min, Basquin, Claire, Lorentzen, Esben, Räschle, Markus, Scheltema, Richard A, Gruber, Stephan

“…Eukaryotic cells employ three SMC (structural maintenance of chromosomes) complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA…”
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Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion by Mirzakhanyan, Yeva, Jankevics, Andris, Scheltema, Richard A, Gershon, Paul David

“…An outstanding problem in the understanding of poxvirus biology is the molecular structure of the mature virion. Via deep learning methods combined with…”
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Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology by Klykov, Oleg, Kopylov, Mykhailo, Carragher, Bridget, Heck, Albert J.R., Noble, Alex J., Scheltema, Richard A.

“…Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems…”
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PhoX: An IMAC-Enrichable Cross-Linking Reagent by Steigenberger, Barbara, Pieters, Roland J, Heck, Albert J. R, Scheltema, Richard A

“…Chemical cross-linking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by…”
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SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components by Scheltema, Richard A, Mann, Matthias

“…With the advent of high-throughput mass spectrometry (MS)-based proteomics, the magnitude and complexity of the performed experiments has increased…”
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Structural Proteomics Applied to Plant Membrane Protein Complexes by Albanese, Pascal, Tamara, Sem, Scheltema, Richard A., Pagliano, Cristina

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