DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics von Midha, Mukul K., Campbell, David S., Kapil, Charu, Kusebauch, Ulrike, Hoopmann, Michael R., Bader, Samuel L., Moritz, Robert L.

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Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome von 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.

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Building ProteomeTools based on a complete synthetic human proteome von 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

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PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline von 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

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A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis von Picotti, Paola, Clément-Ziza, Mathieu, Lam, Henry, Campbell, David S., Schmidt, Alexander, Deutsch, Eric W., Röst, Hannes, Sun, Zhi, Rinner, Oliver, Reiter, Lukas, Shen, Qin, Michaelson, Jacob J., Frei, Andreas, Alberti, Simon, Kusebauch, Ulrike, Wollscheid, Bernd, Moritz, Robert L., Beyer, Andreas, Aebersold, Ruedi

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Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity von Herrmann, Marietta, Babler, Anne, Moshkova, Irina, Gremse, Felix, Kiessling, Fabian, Kusebauch, Ulrike, Nelea, Valentin, Kramann, Rafael, Moritz, Robert L, McKee, Marc D, Jahnen-Dechent, Willi

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1 von Deutsch, Eric W, Overall, Christopher M, Van Eyk, Jennifer E, Baker, Mark S, Paik, Young-Ki, Weintraub, Susan T, Lane, Lydie, Martens, Lennart, Vandenbrouck, Yves, Kusebauch, Ulrike, Hancock, William S, Hermjakob, Henning, Aebersold, Ruedi, Moritz, Robert L, Omenn, Gilbert S

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PASSEL: The PeptideAtlas SRMexperiment library von Farrah, Terry, Deutsch, Eric W., Kreisberg, Richard, Sun, Zhi, Campbell, David S., Mendoza, Luis, Kusebauch, Ulrike, Brusniak, Mi-Youn, Hüttenhain, Ruth, Schiess, Ralph, Selevsek, Nathalie, Aebersold, Ruedi, Moritz, Robert L.

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Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-derived Exosomal Proteins Following Epithelial-Mesenchymal Transition von Tauro, Bow J., Mathias, Rommel A., Greening, David W., Gopal, Shashi K., Ji, Hong, Kapp, Eugene A., Coleman, Bradley M., Hill, Andrew F., Kusebauch, Ulrike, Hallows, Janice L., Shteynberg, David, Moritz, Robert L., Zhu, Hong-Jian, Simpson, Richard J.

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A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS von Midha, Mukul K., Kusebauch, Ulrike, Shteynberg, David, Kapil, Charu, Bader, Samuel L., Reddy, Panga Jaipal, Campbell, David S., Baliga, Nitin S., Moritz, Robert L.

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State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet von Deutsch, Eric W, Sun, Zhi, Campbell, David, Kusebauch, Ulrike, Chu, Caroline S, Mendoza, Luis, Shteynberg, David, Omenn, Gilbert S, Moritz, Robert L

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Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins von Kusebauch, Ulrike, Hernández-Castellano, Lorenzo E., Bislev, Stine L., Moritz, Robert L., Røntved, Christine M., Bendixen, Emøke

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Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector von Kumar, Sudhir, Haile, Meseret T, Hoopmann, Michael R, Tran, Linh T, Michaels, Samantha A, Morrone, Seamus R, Ojo, Kayode K, Reynolds, Laura M, Kusebauch, Ulrike, Vaughan, Ashley M, Moritz, Robert L, Kappe, Stefan H I, Swearingen, Kristian E

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Mycobacterium tuberculosis supports protein tyrosine phosphorylation von Kusebauch, Ulrike, Ortega, Corrie, Ollodart, Anja, Rogers, Richard S., Sherman, David R., Moritz, Robert L., Grundner, Christoph

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An activated form of ADAM10 is tumor selective and regulates cancer stem-like cells and tumor growth von Atapattu, Lakmali, Saha, Nayanendu, Chheang, Chanly, Eissman, Moritz F, Xu, Kai, Vail, Mary E, Hii, Linda, Llerena, Carmen, Liu, Zhanqi, Horvay, Katja, Abud, Helen E, Kusebauch, Ulrike, Moritz, Robert L, Ding, Bi-Sen, Cao, Zhongwei, Rafii, Shahin, Ernst, Matthias, Scott, Andrew M, Nikolov, Dimitar B, Lackmann, Martin, Janes, Peter W

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A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon von Lorenzetti, Alan P R, Kusebauch, Ulrike, Zaramela, Lívia S, Wu, Wei-Ju, de Almeida, João P P, Turkarslan, Serdar, L G de Lomana, Adrián, Gomes-Filho, José V, Vêncio, Ricardo Z N, Moritz, Robert L, Koide, Tie, Baliga, Nitin S

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Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics von Kusebauch, Ulrike, Deutsch, Eric W., Campbell, David S., Sun, Zhi, Farrah, Terry, Moritz, Robert L.

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A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS von Kusebauch, Ulrike, Lorenzetti, Alan P. R., Campbell, David S., Pan, Min, Shteynberg, David, Kapil, Charu, Midha, Mukul K., López García de Lomana, Adrián, Baliga, Nitin S., Moritz, Robert L.

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ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry von Brusniak, Mi-Youn K, Kwok, Sung-Tat, Christiansen, Mark, Campbell, David, Reiter, Lukas, Picotti, Paola, Kusebauch, Ulrike, Ramos, Hector, Deutsch, Eric W, Chen, Jingchun, Moritz, Robert L, Aebersold, Ruedi

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Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut von Diener, Christian, Hoge, Anna C. H., Kearney, Sean M., Kusebauch, Ulrike, Patwardhan, Sushmita, Moritz, Robert L., Erdman, Susan E., Gibbons, Sean M.

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