Search Results - "DELANGHE, Bernard"

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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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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Building ProteomeTools based on a complete synthetic human proteome by Zolg, Daniel P, Wilhelm, Mathias, Schnatbaum, Karsten, Zerweck, Johannes, Knaute, Tobias, Delanghe, Bernard, Bailey, Derek J, Gessulat, Siegfried, Ehrlich, Hans-Christian, Weininger, Maximilian, Yu, Peng, Schlegl, Judith, Kramer, Karl, Schmidt, Tobias, Kusebauch, Ulrike, Deutsch, Eric W, Aebersold, Ruedi, Moritz, Robert L, Wenschuh, Holger, Moehring, Thomas, Aiche, Stephan, Huhmer, Andreas, Reimer, Ulf, Kuster, Bernhard

“…The ProteomeTools project provides the proteomics community with a physical synthetic tryptic peptide resource and a digital LC-MS/MS data resource covering…”
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Expanding the Use of Spectral Libraries in Proteomics by Deutsch, Eric W, Perez-Riverol, Yasset, Chalkley, Robert J, Wilhelm, Mathias, Tate, Stephen, Sachsenberg, Timo, Walzer, Mathias, Käll, Lukas, Delanghe, Bernard, Böcker, Sebastian, Schymanski, Emma L, Wilmes, Paul, Dorfer, Viktoria, Kuster, Bernhard, Volders, Pieter-Jan, Jehmlich, Nico, Vissers, Johannes P. C, Wolan, Dennis W, Wang, Ana Y, Mendoza, Luis, Shofstahl, Jim, Dowsey, Andrew W, Griss, Johannes, Salek, Reza M, Neumann, Steffen, Binz, Pierre-Alain, Lam, Henry, Vizcaíno, Juan Antonio, Bandeira, Nuno, Röst, Hannes

“…The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the…”
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Author Correction: 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

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The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence by Hansen, Anne-Marie, Chaerkady, Raghothama, Sharma, Jyoti, Díaz-Mejía, J Javier, Tyagi, Nidhi, Renuse, Santosh, Jacob, Harrys K C, Pinto, Sneha M, Sahasrabuddhe, Nandini A, Kim, Min-Sik, Delanghe, Bernard, Srinivasan, Narayanaswamy, Emili, Andrew, Kaper, James B, Pandey, Akhilesh

“…While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To…”
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The RiboMaP Spectral Annotation Method Applied to Various ADP-Ribosylome Studies Including INF-γ-Stimulated Human Cells and Mouse Tissues by Singh, Sasha A, Kuraoka, Shiori, Pestana, Diego Vinicius Santinelli, Nasir, Waqas, Delanghe, Bernard, Aikawa, Masanori

“…ADP-ribosylation is a post-translational modification that is catalyzed by the ADP-ribosyltransferase enzyme family. Major emphasis to date has been…”
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A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry by Chaerkady, Raghothama, Kelkar, Dhanashree S, Muthusamy, Babylakshmi, Kandasamy, Kumaran, Dwivedi, Sutopa B, Sahasrabuddhe, Nandini A, Kim, Min-Sik, Renuse, Santosh, Pinto, Sneha M, Sharma, Rakesh, Pawar, Harsh, Sekhar, Nirujogi Raja, Mohanty, Ajeet Kumar, Getnet, Derese, Yang, Yi, Zhong, Jun, Dash, Aditya P, MacCallum, Robert M, Delanghe, Bernard, Mlambo, Godfree, Kumar, Ashwani, Keshava Prasad, T S, Okulate, Mobolaji, Kumar, Nirbhay, Pandey, Akhilesh

“…Anopheles gambiae is a major mosquito vector responsible for malaria transmission, whose genome sequence was reported in 2002. Genome annotation is a…”
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Comprehensive proteomic analysis of human bile by Barbhuiya, Mustafa A., Sahasrabuddhe, Nandini A., Pinto, Sneha M., Muthusamy, Babylakshmi, Singh, Tekcham D., Nanjappa, Vishalakshi, Keerthikumar, Shivakumar, Delanghe, Bernard, Harsha, H. C., Chaerkady, Raghothama, Jalaj, Visvajit, Gupta, Sanjeev, Shrivastav, Braj R., Tiwari, Pramod K., Pandey, Akhilesh

“…Bile serves diverse functions from metabolism to transport. In addition to acids and salts, bile is composed of proteins secreted or shed by the hepatobiliary…”
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A Combined Gas-Phase Separation Strategy for ADP-ribosylated Peptides by Kasai, Taku, Kuraoka, Shiori, Higashi, Hideyuki, Delanghe, Bernard, Aikawa, Masanori, Singh, Sasha A.

“…ADP-ribosylation (ADPr) is a post-translational modification that is best studied using mass spectrometry. Method developments that are permissive with low…”
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A Novel Lipidomics Workflow for Improved Human Plasma Identification and Quantification Using RPLC-MSn Methods and Isotope Dilution Strategies by Rampler, Evelyn, Criscuolo, Angela, Zeller, Martin, El Abiead, Yasin, Schoeny, Harald, Hermann, Gerrit, Sokol, Elena, Cook, Ken, Peake, David A, Delanghe, Bernard, Koellensperger, Gunda

“…Lipid identification and quantification are essential objectives in comprehensive lipidomics studies challenged by the high number of lipids, their chemical…”
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INFERYS rescoring: Boosting peptide identifications and scoring confidence of database search results by Zolg, Daniel P, Gessulat, Siegfried, Paschke, Carmen, Graber, Michael, Rathke-Kuhnert, Magnus, Seefried, Florian, Fitzemeier, Kai, Berg, Frank, Lopez-Ferrer, Daniel, Horn, David, Henrich, Christoph, Huhmer, Andreas, Delanghe, Bernard, Frejno, Martin

“…Database search engines for bottom-up proteomics largely ignore peptide fragment ion intensities during the automated scoring of tandem mass spectra against…”
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Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides by Gabriel, Wassim, The, Matthew, Zolg, Daniel P., Bayer, Florian P., Shouman, Omar, Lautenbacher, Ludwig, Schnatbaum, Karsten, Zerweck, Johannes, Knaute, Tobias, Delanghe, Bernard, Huhmer, Andreas, Wenschuh, Holger, Reimer, Ulf, Médard, Guillaume, Kuster, Bernhard, Wilhelm, Mathias

“…The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown…”
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A Novel Spectral Annotation Strategy Streamlines Reporting of Mono-ADP-ribosylated Peptides Derived from Mouse Liver and Spleen in Response to IFN-γ by Kuraoka, Shiori, Higashi, Hideyuki, Yanagihara, Yoshihiro, Sonawane, Abhijeet R., Mukai, Shin, Mlynarchik, Andrew K., Whelan, Mary C., Hottiger, Michael O., Nasir, Waqas, Delanghe, Bernard, Aikawa, Masanori, Singh, Sasha A.

“…Mass-spectrometry-enabled ADP-ribosylation workflows are developing rapidly, providing researchers a variety of ADP-ribosylome enrichment strategies and mass…”
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A Comprehensive Map of the Human Urinary Proteome by Marimuthu, Arivusudar, O’Meally, Robert. N, Chaerkady, Raghothama, Subbannayya, Yashwanth, Nanjappa, Vishalakshi, Kumar, Praveen, Kelkar, Dhanashree S, Pinto, Sneha M, Sharma, Rakesh, Renuse, Santosh, Goel, Renu, Christopher, Rita, Delanghe, Bernard, Cole, Robert. N, Harsha, H. C, Pandey, Akhilesh

“…The study of the human urinary proteome has the potential to offer significant insights into normal physiology as well as disease pathology. The information…”
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Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides by Kim, Min-Sik, Zhong, Jun, Kandasamy, Kumaran, Delanghe, Bernard, Pandey, Akhilesh

“…CID has become a routine method for fragmentation of peptides in shotgun proteomics, whereas electron transfer dissociation (ETD) has been described as a…”
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Water Vapor Adsorption/Desorption on Two Fully Characterized Commercial Activated Carbons by Plantier, Frédéric, Marques Fernandes, Kamila, Malheiro, Carine, Delanghe, Bernard, Miqueu, Christelle

“…The adsorption/desorption isotherms of water vapor are measured on two commercial activated carbons (ACs) at three temperatures (353, 369, and 386 K) by means…”
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In-depth Quantitative Cardiac Proteomics Combining Electron Transfer Dissociation and the Metalloendopeptidase Lys-N with the SILAC Mouse by Scholten, Arjen, Mohammed, Shabaz, Low, Teck Y., Zanivan, Sara, van Veen, Toon A.B., Delanghe, Bernard, Heck, Albert J.R.

“…In quantitative proteomics stable isotope labeling has progressed from cultured cells toward the total incorporation of labeled atoms or amino acids into whole…”
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Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells by Chaerkady, Raghothama, Letzen, Brian, Renuse, Santosh, Sahasrabuddhe, Nandini A., Kumar, Praveen, All, Angelo H., Thakor, Nitish V., Delanghe, Bernard, Gearhart, John D., Pandey, Akhilesh, Kerr, Candace L.

“…Oligodendrocytes (OLs) are glial cells of the central nervous system, which produce myelin. Cultured OLs provide immense therapeutic opportunities for treating…”
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A Fully Automated Workflow for Glycopeptide Analysis by Saba, Julian, Viner, Rosa, Shan, Paul, Xin, Lei, Wigmore, Cassandra, Delanghe, Bernard

“…We have shown in the past the importance of electron‐transfer dissociation (ETD) and higher energy collision dissociation (HCD) provide complementary…”
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