Regulation of Pluripotency and Cellular Reprogramming by the Ubiquitin-Proteasome System von Buckley, Shannon M., Aranda-Orgilles, Beatriz, Strikoudis, Alexandros, Apostolou, Effie, Loizou, Evangelia, Moran-Crusio, Kelly, Farnsworth, Charles L., Koller, Antonius A., Dasgupta, Ramanuj, Silva, Jeffrey C., Stadtfeld, Matthias, Hochedlinger, Konrad, Chen, Emily I., Aifantis, Iannis

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Immunoaffinity Enrichment and Mass Spectrometry Analysis of Protein Methylation von Guo, Ailan, Gu, Hongbo, Zhou, Jing, Mulhern, Daniel, Wang, Yi, Lee, Kimberly A., Yang, Vicky, Aguiar, Mike, Kornhauser, Jon, Jia, Xiaoying, Ren, Jianmin, Beausoleil, Sean A., Silva, Jeffrey C., Vemulapalli, Vidyasiri, Bedford, Mark T., Comb, Michael J.

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Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow[S] von Svinkina, Tanya, Gu, Hongbo, Silva, Jeffrey C., Mertins, Philipp, Qiao, Jana, Fereshetian, Shaunt, Jaffe, Jacob D., Kuhn, Eric, Udeshi, Namrata D., Carr, Steven A.

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Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures von Li, Guo-Zhong, Vissers, Johannes P.C, Silva, Jeffrey C, Golick, Dan, Gorenstein, Marc V, Geromanos, Scott J

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Calorie restriction alters mitochondrial protein acetylation von Schwer, Bjoern, Eckersdorff, Mark, Li, Yu, Silva, Jeffrey C., Fermin, Damian, Kurtev, Martin V., Giallourakis, Cosmas, Comb, Michael J., Alt, Frederick W., Lombard, David B.

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Identification of the Acetylation and Ubiquitin-Modified Proteome during the Progression of Skeletal Muscle Atrophy von Ryder, Daniel J, Judge, Sarah M, Beharry, Adam W, Farnsworth, Charles L, Silva, Jeffrey C, Judge, Andrew R

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Quantitative Proteomic Analysis by Accurate Mass Retention Time Pairs von Silva, Jeffrey C, Denny, Richard, Dorschel, Craig A, Gorenstein, Marc, Kass, Ignatius J, Li, Guo-Zhong, McKenna, Therese, Nold, Michael J, Richardson, Keith, Young, Phillip, Geromanos, Scott

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A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling von Patterson, Heide Christine, Gerbeth, Carolin, Thiru, Prathapan, Vögtle, Nora F., Knoll, Marko, Shahsafaei, Aliakbar, Samocha, Kaitlin E., Huang, Cher X., Harden, Mark Michael, Song, Rui, Chen, Cynthia, Kao, Jennifer, Shi, Jiahai, Salmon, Wendy, Shaul, Yoav D., Stokes, Matthew P., Silva, Jeffrey C., Bell, George W., MacArthur, Daniel G., Ruland, Jürgen, Meisinger, Chris, Lodish, Harvey F.

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HDAC4 does not act as a protein deacetylase in the postnatal murine brain in vivo von Mielcarek, Michal, Seredenina, Tamara, Stokes, Matthew P, Osborne, Georgina F, Landles, Christian, Inuabasi, Linda, Franklin, Sophie A, Silva, Jeffrey C, Luthi-Carter, Ruth, Beaumont, Vahri, Bates, Gillian P

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RHEX, a novel regulator of human erythroid progenitor cell expansion and erythroblast development von Verma, Rakesh, Su, Su, McCrann, Donald J, Green, Jennifer M, Leu, Karen, Young, Peter R, Schatz, Peter J, Silva, Jeffrey C, Stokes, Matthew P, Wojchowski, Don M

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detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS von Geromanos, Scott J, Vissers, Johannes P.C, Silva, Jeffrey C, Dorschel, Craig A, Li, Guo-Zhong, Gorenstein, Marc V, Bateman, Robert H, Langridge, James I

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Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion von Gu, Hongbo, Ren, Jian Min, Jia, Xiaoying, Levy, Tyler, Rikova, Klarisa, Yang, Vicky, Lee, Kimberly A., Stokes, Matthew P., Silva, Jeffrey C.

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Integrative Genomic and Proteomic Analyses Identify Targets for Lkb1-Deficient Metastatic Lung Tumors von Carretero, Julian, Shimamura, Takeshi, Rikova, Klarisa, Jackson, Autumn L., Wilkerson, Matthew D., Borgman, Christa L., Buttarazzi, Matthew S., Sanofsky, Benjamin A., McNamara, Kate L., Brandstetter, Kathleyn A., Walton, Zandra E., Gu, Ting-Lei, Silva, Jeffrey C., Crosby, Katherine, Shapiro, Geoffrey I., Maira, Sauveur-Michel, Ji, Hongbin, Castrillon, Diego H., Kim, Carla F., García-Echeverría, Carlos, Bardeesy, Nabeel, Sharpless, Norman E., Hayes, Neil D., Kim, William Y., Engelman, Jeffrey A., Wong, Kwok-Kin

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PTMScan Direct: Identification and Quantification of Peptides from Critical Signaling Proteins by Immunoaffinity Enrichment Coupled with LC-MS/MS von Stokes, Matthew P., Farnsworth, Charles L., Moritz, Albrecht, Silva, Jeffrey C., Jia, Xiaoying, Lee, Kimberly A., Guo, Ailan, Polakiewicz, Roberto D., Comb, Michael J.

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Affi-BAMS™: A Robust Targeted Proteomics Microarray Platform to Measure Histone Post-Translational Modifications von Hamza, Ghaith M, Miele, Eric, Wojchowski, Don M, Toran, Paul, Worsfold, Camilla R, Anthonymuthu, Tamil S, Bergo, Vladislav B, Zhang, Andrew X, Silva, Jeffrey C

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Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics von Hamza, Ghaith M, Bergo, Vladislav B, Mamaev, Sergey, Wojchowski, Don M, Toran, Paul, Worsfold, Camilla R, Castaldi, M Paola, Silva, Jeffrey C

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Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale von Silva, Jeffrey C, Denny, Richard, Dorschel, Craig, Gorenstein, Marc V, Li, Guo-Zhong, Richardson, Keith, Wall, Daniel, Geromanos, Scott J

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Interrogating cAMP-dependent Kinase Signaling in Jurkat T Cells via a Protein Kinase A Targeted Immune-precipitation Phosphoproteomics Approach von Giansanti, Piero, Stokes, Matthew P., Silva, Jeffrey C., Scholten, Arjen, Heck, Albert J.R.

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Ubiquitin Ligase Substrate Identification through Quantitative Proteomics at Both the Protein and Peptide Levels von Lee, Kimberly A., Hammerle, Lisa P., Andrews, Paul S., Stokes, Matthew P., Mustelin, Tomas, Silva, Jeffrey C., Black, Roy A., Doedens, John R.

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Systems-wide Analysis of K-Ras, Cdc42, and PAK4 Signaling by Quantitative Phosphoproteomics von Gnad, Florian, Young, Amy, Zhou, Wei, Lyle, Karen, Ong, Christy C., Stokes, Matthew P., Silva, Jeffrey C., Belvin, Marcia, Friedman, Lori S., Koeppen, Hartmut, Minden, Audrey, Hoeflich, Klaus P.

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