Table of Contents

Research

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  Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

  Lukas Reiter, Manfred Claassen, Sabine P. Schrimpf, Marko Jovanovic, Alexander Schmidt, Joachim M. Buhmann, Michael O. Hengartner and Ruedi Aebersold

  Molecular & Cellular Proteomics November 1, 2009, First published on July 16, 2009, 8 (11) 2405-2417; https://doi.org/10.1074/mcp.M900317-MCP200
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  A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation

  Vinh Nguyen, Lulu Cao, Jonathan T. Lin, Norris Hung, Anna Ritz, Kebing Yu, Radu Jianu, Samuel P. Ulin, Benjamin J. Raphael, David H. Laidlaw, Laurent Brossay and Arthur R. Salomon

  Molecular & Cellular Proteomics November 1, 2009, First published on July 14, 2009, 8 (11) 2418-2431; https://doi.org/10.1074/mcp.M800307-MCP200
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  Heterochromatin Protein 1 Is Extensively Decorated with Histone Code-like Post-translational Modifications

  Gary LeRoy, John T. Weston, Barry M. Zee, Nicolas L. Young, Mariana D. Plazas-Mayorca and Benjamin A. Garcia

  Molecular & Cellular Proteomics November 1, 2009, First published on June 30, 2009, 8 (11) 2432-2442; https://doi.org/10.1074/mcp.M900160-MCP200
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  Label-free Quantitative Proteomics Analysis of Etiolated Maize Seedling Leaves during Greening

  Zhuo Shen, Ping Li, Rui-Juan Ni, Mark Ritchie, Chuan-Ping Yang, Gui-Feng Liu, Wei Ma, Guan-Jun Liu, Ling Ma, Shu-Juan Li, Zhi-Gang Wei, Hong-Xia Wang and Bai-Chen Wang

  Molecular & Cellular Proteomics November 1, 2009, First published on August 7, 2009, 8 (11) 2443-2460; https://doi.org/10.1074/mcp.M900187-MCP200
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  Proline-rich Sequence Recognition

  Michael Kofler, Michael Schuemann, Christian Merz, Daniela Kosslick, Andreas Schlundt, Astrid Tannert, Michael Schaefer, Reinhard Lührmann, Eberhard Krause and Christian Freund

  Molecular & Cellular Proteomics November 1, 2009, First published on May 30, 2009, 8 (11) 2461-2473; https://doi.org/10.1074/mcp.M900191-MCP200
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  Proline-rich Sequence Recognition

  Andreas Schlundt, Jana Sticht, Kirill Piotukh, Daniela Kosslick, Nadin Jahnke, Sandro Keller, Michael Schuemann, Eberhard Krause and Christian Freund

  Molecular & Cellular Proteomics November 1, 2009, First published on June 20, 2009, 8 (11) 2474-2486; https://doi.org/10.1074/mcp.M800337-MCP200
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  Differential 14-3-3 Affinity Capture Reveals New Downstream Targets of Phosphatidylinositol 3-Kinase Signaling

  Fanny Dubois, Franck Vandermoere, Aurélie Gernez, Jane Murphy, Rachel Toth, Shuai Chen, Kathryn M. Geraghty, Nick A. Morrice and Carol MacKintosh

  Molecular & Cellular Proteomics November 1, 2009, First published on August 1, 2009, 8 (11) 2487-2499; https://doi.org/10.1074/mcp.M800544-MCP200
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  Proteomic Analysis of Microtubule-associated Proteins during Macrophage Activation

  Prerna C. Patel, Katherine H. Fisher, Eric C. C. Yang, Charlotte M. Deane and Rene E. Harrison

  Molecular & Cellular Proteomics November 1, 2009, First published on August 2, 2009, 8 (11) 2500-2514; https://doi.org/10.1074/mcp.M900190-MCP200
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  Affinity Enrichment and Characterization of Mucin Core-1 Type Glycopeptides from Bovine Serum

  Zsuzsanna Darula and Katalin F. Medzihradszky

  Molecular & Cellular Proteomics November 1, 2009, First published on August 12, 2009, 8 (11) 2515-2526; https://doi.org/10.1074/mcp.M900211-MCP200
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  A Mixed Integer Linear Optimization Framework for the Identification and Quantification of Targeted Post-translational Modifications of Highly Modified Proteins Using Multiplexed Electron Transfer Dissociation Tandem Mass Spectrometry

  Peter A. DiMaggio, Nicolas L. Young, Richard C. Baliban, Benjamin A. Garcia and Christodoulos A. Floudas

  Molecular & Cellular Proteomics November 1, 2009, First published on August 7, 2009, 8 (11) 2527-2543; https://doi.org/10.1074/mcp.M900144-MCP200
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  Recombinant Surface Proteomics as a Tool to Analyze Humoral Immune Responses in Bovines Infected by Mycoplasma mycoides Subsp. mycoides Small Colony Type

  Carl Hamsten, Maja Neiman, Jochen M. Schwenk, Marica Hamsten, John B. March and Anja Persson

  Molecular & Cellular Proteomics November 1, 2009, First published on August 20, 2009, 8 (11) 2544-2554; https://doi.org/10.1074/mcp.M900009-MCP200
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  The Mouse C2C12 Myoblast Cell Surface N-Linked Glycoproteome

  Rebekah L. Gundry, Kimberly Raginski, Yelena Tarasova, Irina Tchernyshyov, Damaris Bausch-Fluck, Steven T. Elliott, Kenneth R. Boheler, Jennifer E. Van Eyk and Bernd Wollscheid

  Molecular & Cellular Proteomics November 1, 2009, First published on August 4, 2009, 8 (11) 2555-2569; https://doi.org/10.1074/mcp.M900195-MCP200
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  Outside the Unusual Cell Wall of the Hyperthermophilic Archaeon Aeropyrum pernix K1

  Gianna Palmieri, Raffaele Cannio, Immacolata Fiume, Mosé Rossi and Gabriella Pocsfalvi

  Molecular & Cellular Proteomics November 1, 2009, First published on July 28, 2009, 8 (11) 2570-2581; https://doi.org/10.1074/mcp.M900012-MCP200
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  Glucose-regulated Protein 78 Is an Intracellular Antiviral Factor against Hepatitis B Virus

  Yan Ma, Jun Yu, Henry L. Y. Chan, Yang-chao Chen, Hua Wang, Ying Chen, Chu-yan Chan, Minnie Y. Y. Go, Sau-na Tsai, Sai-ming Ngai, Ka-fai To, Joanna H. M. Tong, Qing-Yu He, Joseph J. Y. Sung, Hsiang-fu Kung, Christopher H. K. Cheng and Ming-liang He

  Molecular & Cellular Proteomics November 1, 2009, First published on August 11, 2009, 8 (11) 2582-2594; https://doi.org/10.1074/mcp.M900180-MCP200
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  iTRAQ-based Proteomics Profiling Reveals Increased Metabolic Activity and Cellular Cross-talk in Angiogenic Compared with Invasive Glioblastoma Phenotype

  Uros Rajcevic, Kjell Petersen, Jaco C. Knol, Maarten Loos, Sébastien Bougnaud, Oleg Klychnikov, Ka Wan Li, Thang V. Pham, Jian Wang, Hrvoje Miletic, Zhao Peng, Rolf Bjerkvig, Connie R. Jimenez and Simone P. Niclou

  Molecular & Cellular Proteomics November 1, 2009, First published on August 12, 2009, 8 (11) 2595-2612; https://doi.org/10.1074/mcp.M900124-MCP200