Search Results - "Kuster, Bernhard"

Defining the carrier proteome limit for single-cell proteomics by Cheung, Tommy K., Lee, Chien-Yun, Bayer, Florian P., McCoy, Atticus, Kuster, Bernhard, Rose, Christopher M.

“…Single-cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method to quantify multiplexed single-cell proteomes. While this technique has…”
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Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning by Gessulat, Siegfried, Schmidt, Tobias, Zolg, Daniel Paul, Samaras, Patroklos, Schnatbaum, Karsten, Zerweck, Johannes, Knaute, Tobias, Rechenberger, Julia, Delanghe, Bernard, Huhmer, Andreas, Reimer, Ulf, Ehrlich, Hans-Christian, Aiche, Stephan, Kuster, Bernhard, Wilhelm, Mathias

“…In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral…”
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Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS by Bian, Yangyang, Zheng, Runsheng, Bayer, Florian P., Wong, Cassandra, Chang, Yun-Chien, Meng, Chen, Zolg, Daniel P., Reinecke, Maria, Zecha, Jana, Wiechmann, Svenja, Heinzlmeir, Stephanie, Scherr, Johannes, Hemmer, Bernhard, Baynham, Mike, Gingras, Anne-Claude, Boychenko, Oleksandr, Kuster, Bernhard

“…Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but…”
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A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets[S] by Savitski, Mikhail M., Wilhelm, Mathias, Hahne, Hannes, Kuster, Bernhard, Bantscheff, Marcus

“…Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data…”
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Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present by Bantscheff, Marcus, Lemeer, Simone, Savitski, Mikhail M., Kuster, Bernhard

“…Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also…”
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Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics by Wilhelm, Mathias, Zolg, Daniel P., Graber, Michael, Gessulat, Siegfried, Schmidt, Tobias, Schnatbaum, Karsten, Schwencke-Westphal, Celina, Seifert, Philipp, de Andrade Krätzig, Niklas, Zerweck, Johannes, Knaute, Tobias, Bräunlein, Eva, Samaras, Patroklos, Lautenbacher, Ludwig, Klaeger, Susan, Wenschuh, Holger, Rad, Roland, Delanghe, Bernard, Huhmer, Andreas, Carr, Steven A., Clauser, Karl R., Krackhardt, Angela M., Reimer, Ulf, Kuster, Bernhard

“…Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for…”
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TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach[S] by Zecha, Jana, Satpathy, Shankha, Kanashova, Tamara, Avanessian, Shayan C., Kane, M. Harry, Clauser, Karl R., Mertins, Philipp, Carr, Steven A., Kuster, Bernhard

“…Isobaric labeling using tandem mass tags (TMTs) is increasingly applied for deep-scale proteomic studies in a multitude of organisms and addressing diverse…”
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Quantitative mass spectrometry in proteomics: a critical review by Bantscheff, Marcus, Schirle, Markus, Sweetman, Gavain, Rick, Jens, Kuster, Bernhard

“…The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging…”
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Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling by Zecha, Jana, Gabriel, Wassim, Spallek, Ria, Chang, Yun-Chien, Mergner, Julia, Wilhelm, Mathias, Bassermann, Florian, Kuster, Bernhard

“…Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ…”
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A deep proteome and transcriptome abundance atlas of 29 healthy human tissues by Wang, Dongxue, Eraslan, Basak, Wieland, Thomas, Hallström, Björn, Hopf, Thomas, Zolg, Daniel Paul, Zecha, Jana, Asplund, Anna, Li, Li‐hua, Meng, Chen, Frejno, Martin, Schmidt, Tobias, Schnatbaum, Karsten, Wilhelm, Mathias, Ponten, Frederik, Uhlen, Mathias, Gagneur, Julien, Hahne, Hannes, Kuster, Bernhard

“…Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to…”
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Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis by Ruprecht, Benjamin, Zaal, Esther A, Zecha, Jana, Wu, Wei, Berkers, Celia R, Kuster, Bernhard, Lemeer, Simone

“…HER2/ERBB2-overexpressing breast cancers targeted effectively by the small-molecule kinase inhibitor lapatinib frequently acquire resistance to this drug. In…”
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Mass-spectrometry-based draft of the Arabidopsis proteome by Mergner, Julia, Frejno, Martin, List, Markus, Papacek, Michael, Chen, Xia, Chaudhary, Ajeet, Samaras, Patroklos, Richter, Sandra, Shikata, Hiromasa, Messerer, Maxim, Lang, Daniel, Altmann, Stefan, Cyprys, Philipp, Zolg, Daniel P., Mathieson, Toby, Bantscheff, Marcus, Hazarika, Rashmi R., Schmidt, Tobias, Dawid, Corinna, Dunkel, Andreas, Hofmann, Thomas, Sprunck, Stefanie, Falter-Braun, Pascal, Johannes, Frank, Mayer, Klaus F. X., Jürgens, Gerd, Wilhelm, Mathias, Baumbach, Jan, Grill, Erwin, Schneitz, Kay, Schwechheimer, Claus, Kuster, Bernhard

“…Plants are essential for life and are extremely diverse organisms with unique molecular capabilities 1 . Here we present a quantitative atlas of the…”
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A multivariate approach to the integration of multi-omics datasets by Meng, Chen, Kuster, Bernhard, Culhane, Aedín C, Gholami, Amin Moghaddas

“…To leverage the potential of multi-omics studies, exploratory data analysis methods that provide systematic integration and comparison of multiple layers of…”
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Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion by Martinelli, Silvia, Anderzhanova, Elmira A., Bajaj, Thomas, Wiechmann, Svenja, Dethloff, Frederik, Weckmann, Katja, Heinz, Daniel E., Ebert, Tim, Hartmann, Jakob, Geiger, Thomas M., Döngi, Michael, Hafner, Kathrin, Pöhlmann, Max L., Jollans, Lee, Philipsen, Alexandra, Schmidt, Susanne V., Schmidt, Ulrike, Maccarrone, Giuseppina, Stein, Valentin, Hausch, Felix, Turck, Christoph W., Schmidt, Mathias V., Gellner, Anne-Kathrin, Kuster, Bernhard, Gassen, Nils C.

“…The stress response is an essential mechanism for maintaining homeostasis, and its disruption is implicated in several psychiatric disorders. On the cellular…”
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Mass-spectrometry-based draft of the human proteome by Wilhelm, Mathias, Schlegl, Judith, Hahne, Hannes, Gholami, Amin Moghaddas, Lieberenz, Marcus, Savitski, Mikhail M., Ziegler, Emanuel, Butzmann, Lars, Gessulat, Siegfried, Marx, Harald, Mathieson, Toby, Lemeer, Simone, Schnatbaum, Karsten, Reimer, Ulf, Wenschuh, Holger, Mollenhauer, Martin, Slotta-Huspenina, Julia, Boese, Joos-Hendrik, Bantscheff, Marcus, Gerstmair, Anja, Faerber, Franz, Kuster, Bernhard

“…Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all…”
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Proteome activity landscapes of tumor cell lines determine drug responses by Frejno, Martin, Meng, Chen, Ruprecht, Benjamin, Oellerich, Thomas, Scheich, Sebastian, Kleigrewe, Karin, Drecoll, Enken, Samaras, Patroklos, Hogrebe, Alexander, Helm, Dominic, Mergner, Julia, Zecha, Jana, Heinzlmeir, Stephanie, Wilhelm, Mathias, Dorn, Julia, Kvasnicka, Hans-Michael, Serve, Hubert, Weichert, Wilko, Kuster, Bernhard

“…Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular…”
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Correction: Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies by Abbas, Qussai, Wilhelm, Mathias, Kuster, Bernhard, Poppenberger, Brigitte, Frishman, Dmitrij

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Meltome atlas—thermal proteome stability across the tree of life by Jarzab, Anna, Kurzawa, Nils, Hopf, Thomas, Moerch, Matthias, Zecha, Jana, Leijten, Niels, Bian, Yangyang, Musiol, Eva, Maschberger, Melanie, Stoehr, Gabriele, Becher, Isabelle, Daly, Charlotte, Samaras, Patroklos, Mergner, Julia, Spanier, Britta, Angelov, Angel, Werner, Thilo, Bantscheff, Marcus, Wilhelm, Mathias, Klingenspor, Martin, Lemeer, Simone, Liebl, Wolfgang, Hahne, Hannes, Savitski, Mikhail M., Kuster, Bernhard

“…We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from…”
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Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies by Abbas, Qussai, Wilhelm, Mathias, Kuster, Bernhard, Poppenberger, Brigitte, Frishman, Dmitrij

“…Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease…”
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Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics by Zecha, Jana, Meng, Chen, Zolg, Daniel Paul, Samaras, Patroklos, Wilhelm, Mathias, Kuster, Bernhard

“…The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass…”
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