The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
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
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Journal Article
The ProteomeXchange consortium at 10 years: 2023 update
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
Published in Nucleic acids research (06.01.2023)
Published in Nucleic acids research (06.01.2023)
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Journal Article
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
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
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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Journal Article
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
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
Published in Nature biotechnology (01.03.2014)
Published in Nature biotechnology (01.03.2014)
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Journal Article
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics
Deutsch, Eric W., Mendoza, Luis, Shteynberg, David, Slagel, Joseph, Sun, Zhi, Moritz, Robert L.
Published in Proteomics. Clinical applications (01.08.2015)
Published in Proteomics. Clinical applications (01.08.2015)
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Journal Article
A cross-platform toolkit for mass spectrometry and proteomics
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
Published in Nature biotechnology (01.10.2012)
Published in Nature biotechnology (01.10.2012)
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Journal Article
iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates
Shteynberg, David, Deutsch, Eric W., Lam, Henry, Eng, Jimmy K., Sun, Zhi, Tasman, Natalie, Mendoza, Luis, Moritz, Robert L., Aebersold, Ruedi, Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (01.12.2011)
Published in Molecular & cellular proteomics (01.12.2011)
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Journal Article
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
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.
Published in Cell (28.07.2016)
Published in Cell (28.07.2016)
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Journal Article
The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
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
Published in Journal of proteome research (01.12.2017)
Published in Journal of proteome research (01.12.2017)
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Journal Article
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases
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
Published in Molecular & cellular proteomics (01.01.2020)
Published in Molecular & cellular proteomics (01.01.2020)
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Journal Article
Universal Spectrum Identifier for mass spectra
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
Published in Nature methods (01.07.2021)
Published in Nature methods (01.07.2021)
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Journal Article
Building ProteomeTools based on a complete synthetic human proteome
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
Published in Nature methods (01.03.2017)
Published in Nature methods (01.03.2017)
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Journal Article
PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
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
Published in Journal of proteome research (06.12.2019)
Published in Journal of proteome research (06.12.2019)
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Journal Article
guided tour of the Trans-Proteomic Pipeline
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
Published in Proteomics (Weinheim) (01.03.2010)
Published in Proteomics (Weinheim) (01.03.2010)
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Journal Article
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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
Published in Journal of proteome research (06.12.2019)
Published in Journal of proteome research (06.12.2019)
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Journal Article
mzML—a Community Standard for Mass Spectrometry Data
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.
Published in Molecular & cellular proteomics (01.01.2011)
Published in Molecular & cellular proteomics (01.01.2011)
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