Search Results - "Deutsch, Eric W."

File Formats Commonly Used in Mass Spectrometry Proteomics by Deutsch, Eric W.

“…The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to…”
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The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics by Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan A

“…Abstract The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of…”
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The ProteomeXchange consortium at 10 years: 2023 update by Deutsch, Eric W, Bandeira, Nuno, Perez-Riverol, Yasset, Sharma, Vagisha, Carver, Jeremy J, Mendoza, Luis, Kundu, Deepti J, Wang, Shengbo, Bandla, Chakradhar, Kamatchinathan, Selvakumar, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan Antonio

“…Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources…”
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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition by Deutsch, Eric W, Csordas, Attila, Sun, Zhi, Jarnuczak, Andrew, Perez-Riverol, Yasset, Ternent, Tobias, Campbell, David S, Bernal-Llinares, Manuel, Okuda, Shujiro, Kawano, Shin, Moritz, Robert L, Carver, Jeremy J, Wang, Mingxun, Ishihama, Yasushi, Bandeira, Nuno, Hermjakob, Henning, Vizcaíno, Juan Antonio

“…The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and…”
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PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows by Deutsch, Eric W, Lam, Henry, Aebersold, Ruedi

“…A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the…”
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination by Vizcaíno, Juan A, Deutsch, Eric W, Wang, Rui, Csordas, Attila, Reisinger, Florian, Ríos, Daniel, Dianes, José A, Sun, Zhi, Farrah, Terry, Bandeira, Nuno, Binz, Pierre-Alain, Xenarios, Ioannis, Eisenacher, Martin, Mayer, Gerhard, Gatto, Laurent, Campos, Alex, Chalkley, Robert J, Kraus, Hans-Joachim, Albar, Juan Pablo, Martinez-Bartolomé, Salvador, Apweiler, Rolf, Omenn, Gilbert S, Martens, Lennart, Jones, Andrew R, Hermjakob, Henning

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Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics by Deutsch, Eric W., Mendoza, Luis, Shteynberg, David, Slagel, Joseph, Sun, Zhi, Moritz, Robert L.

“…Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics…”
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Extending Comet for Global Amino Acid Variant and Post‐Translational Modification Analysis Using the PSI Extended FASTA Format by Eng, Jimmy K., Deutsch, Eric W.

“…Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard…”
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A cross-platform toolkit for mass spectrometry and proteomics by Chambers, Matthew C, Maclean, Brendan, Burke, Robert, Amodei, Dario, Ruderman, Daniel L, Neumann, Steffen, Gatto, Laurent, Fischer, Bernd, Pratt, Brian, Egertson, Jarrett, Hoff, Katherine, Kessner, Darren, Tasman, Natalie, Shulman, Nicholas, Frewen, Barbara, Baker, Tahmina A, Brusniak, Mi-Youn, Paulse, Christopher, Creasy, David, Flashner, Lisa, Kani, Kian, Moulding, Chris, Seymour, Sean L, Nuwaysir, Lydia M, Lefebvre, Brent, Kuhlmann, Frank, Roark, Joe, Rainer, Paape, Detlev, Suckau, Hemenway, Tina, Huhmer, Andreas, Langridge, James, Connolly, Brian, Chadick, Trey, Holly, Krisztina, Eckels, Josh, Deutsch, Eric W, Moritz, Robert L, Katz, Jonathan E, Agus, David B, MacCoss, Michael, Tabb, David L, Mallick, Parag

“…Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and…”
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iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates by Shteynberg, David, Deutsch, Eric W., Lam, Henry, Eng, Jimmy K., Sun, Zhi, Tasman, Natalie, Mendoza, Luis, Moritz, Robert L., Aebersold, Ruedi, Nesvizhskii, Alexey I.

“…The combination of tandem mass spectrometry and sequence database searching is the method of choice for the identification of peptides and the mapping of…”
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The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases by Vizcaíno, Juan Antonio, Kubiniok, Peter, Kovalchik, Kevin A., Ma, Qing, Duquette, Jérôme D., Mongrain, Ian, Deutsch, Eric W., Peters, Bjoern, Sette, Alessandro, Sirois, Isabelle, Caron, Etienne

“…Immunopeptidomics is a rapidly evolving field that is catalyzed by neoantigen discovery and cancer immunotherapy. Emulating the path of other omic disciplines,…”
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Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome by Kusebauch, Ulrike, Campbell, David S., Deutsch, Eric W., Chu, Caroline S., Spicer, Douglas A., Brusniak, Mi-Youn, Slagel, Joseph, Sun, Zhi, Stevens, Jeffrey, Grimes, Barbara, Shteynberg, David, Hoopmann, Michael R., Blattmann, Peter, Ratushny, Alexander V., Rinner, Oliver, Picotti, Paola, Carapito, Christine, Huang, Chung-Ying, Kapousouz, Meghan, Lam, Henry, Tran, Tommy, Demir, Emek, Aitchison, John D., Sander, Chris, Hood, Leroy, Aebersold, Ruedi, Moritz, Robert L.

“…The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding…”
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The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays by Schwenk, Jochen M, Omenn, Gilbert S, Sun, Zhi, Campbell, David S, Baker, Mark S, Overall, Christopher M, Aebersold, Ruedi, Moritz, Robert L, Deutsch, Eric W

“…Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome…”
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The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource by van Wijk, Klaas J, Leppert, Tami, Sun, Qi, Boguraev, Sascha S, Sun, Zhi, Mendoza, Luis, Deutsch, Eric W

“…We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana…”
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Universal Spectrum Identifier for mass spectra by Deutsch, Eric W., Perez-Riverol, Yasset, Carver, Jeremy, Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Binz, Pierre-Alain, Pullman, Benjamin, Sun, Zhi, Shofstahl, Jim, Bittremieux, Wout, Mak, Tytus D., Klein, Joshua, Zhu, Yunping, Lam, Henry, Vizcaíno, Juan Antonio, Bandeira, Nuno

“…Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be…”
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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 by Deutsch, Eric W, Lane, Lydie, Overall, Christopher M, Bandeira, Nuno, Baker, Mark S, Pineau, Charles, Moritz, Robert L, Corrales, Fernando, Orchard, Sandra, Van Eyk, Jennifer E, Paik, Young-Ki, Weintraub, Susan T, Vandenbrouck, Yves, Omenn, Gilbert S

“…The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied…”
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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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PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline by Shteynberg, David D, Deutsch, Eric W, Campbell, David S, Hoopmann, Michael R, Kusebauch, Ulrike, Lee, Dave, Mendoza, Luis, Midha, Mukul K, Sun, Zhi, Whetton, Anthony D, Moritz, Robert L

“…Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions,…”
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guided tour of the Trans-Proteomic Pipeline by Deutsch, Eric W, Mendoza, Luis, Shteynberg, David, Farrah, Terry, Lam, Henry, Tasman, Natalie, Sun, Zhi, Nilsson, Erik, Pratt, Brian, Prazen, Bryan, Eng, Jimmy K, Martin, Daniel B, Nesvizhskii, Alexey I, Aebersold, Ruedi

“…The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data…”
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mzML—a Community Standard for Mass Spectrometry Data by Martens, Lennart, Chambers, Matthew, Sturm, Marc, Kessner, Darren, Levander, Fredrik, Shofstahl, Jim, Tang, Wilfred H., Römpp, Andreas, Neumann, Steffen, Pizarro, Angel D., Montecchi-Palazzi, Luisa, Tasman, Natalie, Coleman, Mike, Reisinger, Florian, Souda, Puneet, Hermjakob, Henning, Binz, Pierre-Alain, Deutsch, Eric W.

“…Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods,…”
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