Comet: An open-source MS/MS sequence database search tool von Eng, Jimmy K., Jahan, Tahmina A., Hoopmann, Michael R.

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Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics von Schweppe, Devin K, Eng, Jimmy K, Yu, Qing, Bailey, Derek, Rad, Ramin, Navarrete-Perea, Jose, Huttlin, Edward L, Erickson, Brian K, Paulo, Joao A, Gygi, Steven P

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Extending Comet for Global Amino Acid Variant and Post‐Translational Modification Analysis Using the PSI Extended FASTA Format von Eng, Jimmy K., Deutsch, Eric W.

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In Vivo Conformational Dynamics of Hsp90 and Its Interactors von Chavez, Juan D., Schweppe, Devin K., Eng, Jimmy K., Bruce, James E.

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iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates von Shteynberg, David, Deutsch, Eric W., Lam, Henry, Eng, Jimmy K., Sun, Zhi, Tasman, Natalie, Mendoza, Luis, Moritz, Robert L., Aebersold, Ruedi, Nesvizhskii, Alexey I.

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guided tour of the Trans-Proteomic Pipeline von 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

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A Face in the Crowd: Recognizing Peptides Through Database Search von Eng, Jimmy K., Searle, Brian C., Clauser, Karl R., Tabb, David L.

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Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry von Navare, Arti T., Chavez, Juan D., Zheng, Chunxiang, Weisbrod, Chad R., Eng, Jimmy K., Siehnel, Richard, Singh, Pradeep K., Manoil, Colin, Bruce, James E.

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In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075 von Wu, Xia, Chavez, Juan D., Schweppe, Devin K., Zheng, Chunxiang, Weisbrod, Chad R., Eng, Jimmy K., Murali, Ananya, Lee, Samuel A., Ramage, Elizabeth, Gallagher, Larry A., Kulasekara, Hemantha D., Edrozo, Mauna E., Kamischke, Cassandra N., Brittnacher, Mitchell J., Miller, Samuel I., Singh, Pradeep K., Manoil, Colin, Bruce, James E.

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Development and validation of a spectral library searching method for peptide identification from MS/MS von Lam, Henry, Deutsch, Eric W., Eddes, James S., Eng, Jimmy K., King, Nichole, Stein, Stephen E., Aebersold, Ruedi

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Building consensus spectral libraries for peptide identification in proteomics von Lam, Henry, Deutsch, Eric W, Eddes, James S, Eng, Jimmy K, Stein, Stephen E, Aebersold, Ruedi

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General framework for developing and evaluating database scoring algorithms using the TANDEM search engine von MacLean, Brendan, Eng, Jimmy K., Beavis, Ronald C., McIntosh, Martin

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A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry von Chavez, Juan D, Eng, Jimmy K, Schweppe, Devin K, Cilia, Michelle, Rivera, Keith, Zhong, Xuefei, Wu, Xia, Allen, Terrence, Khurgel, Moshe, Kumar, Akhilesh, Lampropoulos, Athanasios, Larsson, Mårten, Maity, Shuvadeep, Morozov, Yaroslav, Pathmasiri, Wimal, Perez-Neut, Mathew, Pineyro-Ruiz, Coriness, Polina, Elizabeth, Post, Stephanie, Rider, Mark, Tokmina-Roszyk, Dorota, Tyson, Katherine, Vieira Parrine Sant'Ana, Debora, Bruce, James E

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Proteomics Standards Initiative Extended FASTA Format von Binz, Pierre-Alain, Shofstahl, Jim, Vizcaíno, Juan Antonio, Barsnes, Harald, Chalkley, Robert J, Menschaert, Gerben, Alpi, Emanuele, Clauser, Karl, Eng, Jimmy K, Lane, Lydie, Seymour, Sean L, Sánchez, Luis Francisco Hernández, Mayer, Gerhard, Eisenacher, Martin, Perez-Riverol, Yasset, Kapp, Eugene A, Mendoza, Luis, Baker, Peter R, Collins, Andrew, Van Den Bossche, Tim, Deutsch, Eric W

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An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis von Kapp, Eugene A., Schütz, Frédéric, Connolly, Lisa M., Chakel, John A., Meza, Jose E., Miller, Christine A., Fenyo, David, Eng, Jimmy K., Adkins, Joshua N., Omenn, Gilbert S., Simpson, Richard J.

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The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5 von Aderem, Alan, Hayashi, Fumitaka, Smith, Kelly D, Ozinsky, Adrian, Hawn, Thomas R, Yi, Eugene C, Goodlett, David R, Eng, Jimmy K, Akira, Shizuo, Underhill, David M

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A common open representation of mass spectrometry data and its application to proteomics research von Aebersold, Ruedi, Pedrioli, Patrick G A, Eng, Jimmy K, Hubley, Robert, Vogelzang, Mathijs, Deutsch, Eric W, Raught, Brian, Pratt, Brian, Nilsson, Erik, Angeletti, Ruth H, Apweiler, Rolf, Cheung, Kei, Costello, Catherine E, Hermjakob, Henning, Huang, Sequin, Julian, Randall K, Kapp, Eugene, McComb, Mark E, Oliver, Stephen G, Omenn, Gilbert, Paton, Norman W, Simpson, Richard, Smith, Richard, Taylor, Chris F, Zhu, Weimin

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Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry von Aebersold, Ruedi, Tao, W Andy, Wollscheid, Bernd, O'Brien, Robert, Eng, Jimmy K, Li, Xiao-jun, Bodenmiller, Bernd, Watts, Julian D, Hood, Leroy

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The Fasted/Fed Mouse Metabolic Acetylome: N6-Acetylation Differences Suggest Acetylation Coordinates Organ-Specific Fuel Switching von Yang, Li, Vaitheesvaran, Bhavapriya, Hartil, Kirsten, Robinson, Alan J, Hoopmann, Michael R, Eng, Jimmy K, Kurland, Irwin J, Bruce, James E

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Sites of ubiquitin attachment in Saccharomyces cerevisiae von Starita, Lea M., Lo, Russell S., Eng, Jimmy K., von Haller, Priska D., Fields, Stanley

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