Table of Contents

Research

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  Alterations in Protein Regulators of Neurodevelopment in the Cerebrospinal Fluid of Infants with Posthemorrhagic Hydrocephalus of Prematurity

  Diego M. Morales, R. Reid Townsend, James P. Malone, Carissa A. Ewersmann, Elizabeth M. Macy, Terrie E. Inder and David D. Limbrick

  Molecular & Cellular Proteomics June 1, 2012, First published on December 20, 2011, 11 (6) M111.011973; https://doi.org/10.1074/mcp.M111.011973
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  Proteomic Analysis of Mitotic RNA Polymerase II Reveals Novel Interactors and Association With Proteins Dysfunctional in Disease

  André Möller, Sheila Q. Xie, Fabian Hosp, Benjamin Lang, Hemali P. Phatnani, Sonya James, Francisco Ramirez, Gayle B. Collin, Jürgen K. Naggert, M. Madan Babu, Arno L. Greenleaf, Matthias Selbach and Ana Pombo

  Molecular & Cellular Proteomics June 1, 2012, First published on December 22, 2011, 11 (6) M111.011767; https://doi.org/10.1074/mcp.M111.011767
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  Pharmacoproteomic Study of Three Different Chondroitin Sulfate Compounds on Intracellular and Extracellular Human Chondrocyte Proteomes

  Valentina Calamia, Patricia Fernández-Puente, Jesús Mateos, Lucía Lourido, Beatriz Rocha, Eulália Montell, Josep Vergés, Cristina Ruiz-Romero and Francisco J. Blanco

  Molecular & Cellular Proteomics June 1, 2012, First published on December 27, 2011, 11 (6) M111.013417; https://doi.org/10.1074/mcp.M111.013417
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  CD90 is Identified as a Candidate Marker for Cancer Stem Cells in Primary High-Grade Gliomas Using Tissue Microarrays

  Jintang He, Yashu Liu, Thant Zhu, Jianhui Zhu, Francesco DiMeco, Angelo L. Vescovi, Jason A. Heth, Karin M. Muraszko, Xing Fan and David M. Lubman

  Molecular & Cellular Proteomics June 1, 2012, First published on December 27, 2011, 11 (6) M111.010744; https://doi.org/10.1074/mcp.M111.010744
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  Systems Kinomics Demonstrates Congo Basin Monkeypox Virus Infection Selectively Modulates Host Cell Signaling Responses as Compared to West African Monkeypox Virus

  Jason Kindrachuk, Ryan Arsenault, Anthony Kusalik, Kristen N. Kindrachuk, Brett Trost, Scott Napper, Peter B. Jahrling and Joseph E. Blaney

  Molecular & Cellular Proteomics June 1, 2012, First published on December 28, 2011, 11 (6) M111.015701; https://doi.org/10.1074/mcp.M111.015701
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  La Autoantigen Mediates Oxidant Induced De Novo Nrf2 Protein Translation

  Jack Zhang, Thai Nho Dinh, Kyle Kappeler, George Tsaprailis and Qin M. Chen

  Molecular & Cellular Proteomics June 1, 2012, First published on December 29, 2011, 11 (6) M111.015032; https://doi.org/10.1074/mcp.M111.015032
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  On Marathons and Sprints: An Integrated Quantitative Proteomics and Transcriptomics Analysis of Differences Between Slow and Fast Muscle Fibers

  Hannes C. A. Drexler, Aaron Ruhs, Anne Konzer, Luca Mendler, Mark Bruckskotten, Mario Looso, Stefan Günther, Thomas Boettger, Marcus Krüger and Thomas Braun

  Molecular & Cellular Proteomics June 1, 2012, First published on December 30, 2011, 11 (6) M111.010801; https://doi.org/10.1074/mcp.M111.010801
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  LC-MS/MS Analysis of Differentially Expressed Glioblastoma Membrane Proteome Reveals Altered Calcium Signaling and Other Protein Groups of Regulatory Functions

  Ravindra Varma Polisetty, Poonam Gautam, Rakesh Sharma, H. C. Harsha, Sudha C. Nair, Manoj Kumar Gupta, Megha S. Uppin, Sundaram Challa, Aneel Kumar Puligopu, Praveen Ankathi, Aniruddh K. Purohit, Giriraj R. Chandak, Akhilesh Pandey and Ravi Sirdeshmukh

  Molecular & Cellular Proteomics June 1, 2012, First published on January 4, 2012, 11 (6) M111.013565; https://doi.org/10.1074/mcp.M111.013565
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  Comparative Large Scale Characterization of Plant versus Mammal Proteins Reveals Similar and Idiosyncratic N-α-Acetylation Features

  Willy V. Bienvenut, David Sumpton, Aude Martinez, Sergio Lilla, Christelle Espagne, Thierry Meinnel and Carmela Giglione

  Molecular & Cellular Proteomics June 1, 2012, First published on January 5, 2012, 11 (6) M111.015131; https://doi.org/10.1074/mcp.M111.015131
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  Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

  Yoon-Jung Moon, Joseph Kwon, Sung-Ho Yun, Hye Li Lim, Min-Sik Kim, Sung Gyun Kang, Jung-Hyun Lee, Jong-Soon Choi, Seung Il Kim and Young-Ho Chung

  Molecular & Cellular Proteomics June 1, 2012, First published on January 9, 2012, 11 (6) M111.015420; https://doi.org/10.1074/mcp.M111.015420
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  Restricting Fermentative Potential by Proteome Remodeling

  Gérémy Clair, Jean Armengaud and Catherine Duport

  Molecular & Cellular Proteomics June 1, 2012, First published on January 9, 2012, 11 (6) M111.013102; https://doi.org/10.1074/mcp.M111.013102
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  Chitinase-like Proteins are Candidate Biomarkers for Sepsis-induced Acute Kidney Injury

  B. Maddens, B. Ghesquière, R. Vanholder, D. Demon, J. Vanmassenhove, K. Gevaert and E. Meyer

  Molecular & Cellular Proteomics June 1, 2012, First published on January 10, 2012, 11 (6) M111.013094; https://doi.org/10.1074/mcp.M111.013094
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  Metabolomics of Human Cerebrospinal Fluid Identifies Signatures of Malignant Glioma

  Jason W. Locasale, Tamar Melman, Susan Song, Xuemei Yang, Kenneth D. Swanson, Lewis C. Cantley, Eric T. Wong and John M. Asara

  Molecular & Cellular Proteomics June 1, 2012, First published on January 12, 2012, 11 (6) M111.014688; https://doi.org/10.1074/mcp.M111.014688
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  Integrated Proteomic, Transcriptomic, and Biological Network Analysis of Breast Carcinoma Reveals Molecular Features of Tumorigenesis and Clinical Relapse

  Marcin Imielinski, Sangwon Cha, Tomas Rejtar, Elizabeth A. Richardson, Barry L. Karger and Dennis C. Sgroi

  Molecular & Cellular Proteomics June 1, 2012, First published on January 12, 2012, 11 (6) M111.014910; https://doi.org/10.1074/mcp.M111.014910
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  Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

  Ludovic C. Gillet, Pedro Navarro, Stephen Tate, Hannes Röst, Nathalie Selevsek, Lukas Reiter, Ron Bonner and Ruedi Aebersold

  Molecular & Cellular Proteomics June 1, 2012, First published on January 18, 2012, 11 (6) O111.016717; https://doi.org/10.1074/mcp.O111.016717
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  Glycosylation of Human Milk Lactoferrin Exhibits Dynamic Changes During Early Lactation Enhancing Its Role in Pathogenic Bacteria-Host Interactions

  Mariana Barboza, Janneth Pinzon, Saumya Wickramasinghe, John W. Froehlich, Isabelle Moeller, Jennifer T. Smilowitz, L. Renee Ruhaak, Jincui Huang, Bo Lönnerdal, J. Bruce German, Juan F. Medrano, Bart C. Weimer and Carlito B. Lebrilla

  Molecular & Cellular Proteomics June 1, 2012, First published on January 19, 2012, 11 (6) M111.015248; https://doi.org/10.1074/mcp.M111.015248
• Open Access

  Mapping Yeast N-Glycosites with Isotopically Recoded Glycans

  Mark A. Breidenbach, Krishnan K. Palaniappan, Austin A. Pitcher and Carolyn R. Bertozzi

  Molecular & Cellular Proteomics June 1, 2012, First published on January 19, 2012, 11 (6) M111.015339; https://doi.org/10.1074/mcp.M111.015339
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  Interaction Proteomics Identify NEURL4 and the HECT E3 Ligase HERC2 as Novel Modulators of Centrosome Architecture

  Abdallah K. Al-Hakim, Mikhail Bashkurov, Anne-Claude Gingras, Daniel Durocher and Laurence Pelletier

  Molecular & Cellular Proteomics June 1, 2012, First published on January 19, 2012, 11 (6) M111.014233; https://doi.org/10.1074/mcp.M111.014233
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  Quantitative Analysis of the Chromatin Proteome in Disease Reveals Remodeling Principles and Identifies High Mobility Group Protein B2 as a Regulator of Hypertrophic Growth

  Sarah Franklin, Haodong Chen, Scherise Mitchell-Jordan, Shuxun Ren, Yibin Wang and Thomas M. Vondriska

  Molecular & Cellular Proteomics June 1, 2012, First published on January 23, 2012, 11 (6) M111.014258; https://doi.org/10.1074/mcp.M111.014258
• Open Access

  The Proteomic Profile of Circulating Pentraxin 3 (PTX3) Complex in Sepsis Demonstrates the Interaction with Azurocidin 1 and Other Components of Neutrophil Extracellular Traps

  Kenji Daigo, Naotaka Yamaguchi, Takeshi Kawamura, Koichi Matsubara, Shuying Jiang, Riuko Ohashi, Yukio Sudou, Tatsuhiko Kodama, Makoto Naito, Kenji Inoue and Takao Hamakubo

  Molecular & Cellular Proteomics June 1, 2012, First published on January 25, 2012, 11 (6) M111.015073; https://doi.org/10.1074/mcp.M111.015073
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  Proteomic Analysis of Zebrafish Caudal Fin Regeneration

  Sandeep Saxena, Sachin K. Singh, Mula G. Meena Lakshmi, Vuppalapaty Meghah, Bhawna Bhatti, Cherukuvada V. Brahmendra Swamy, Curam S. Sundaram and Mohammed M. Idris

  Molecular & Cellular Proteomics June 1, 2012, First published on January 25, 2012, 11 (6) M111.014118; https://doi.org/10.1074/mcp.M111.014118
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  A Proteome Comparison Between Physiological Angiogenesis and Angiogenesis in Glioblastoma

  Dana A. M. Mustafa, Lennard J. Dekker, Christoph Stingl, Andreas Kremer, Marcel Stoop, Peter A. E. Sillevis Smitt, Johan M. Kros and Theo M. Luider

  Molecular & Cellular Proteomics June 1, 2012, First published on January 25, 2012, 11 (6) M111.008466; https://doi.org/10.1074/mcp.M111.008466
• Open Access

  Multi High-Throughput Approach for Highly Selective Identification of Vaccine Candidates: the Group A Streptococcus Case

  Giuliano Bensi, Marirosa Mora, Giovanna Tuscano, Massimiliano Biagini, Emiliano Chiarot, Mauro Bombaci, Sabrina Capo, Fabiana Falugi, Andrea G. O. Manetti, Paolo Donato, Erwin Swennen, Marilena Gallotta, Manuela Garibaldi, Vittoria Pinto, Nico Chiappini, James M. Musser, Robert Janulczyk, Massimo Mariani, Maria Scarselli, John L. Telford, Renata Grifantini, Nathalie Norais, Immaculada Margarit and Guido Grandi

  Molecular & Cellular Proteomics June 1, 2012, First published on January 27, 2012, 11 (6) M111.015693; https://doi.org/10.1074/mcp.M111.015693
• Open Access

  Evaluation and Properties of the Budding Yeast Phosphoproteome

  Grigoris D. Amoutzias, Ying He, Kathryn S. Lilley, Yves Van de Peer and Stephen G. Oliver

  Molecular & Cellular Proteomics June 1, 2012, First published on January 27, 2012, 11 (6) M111.009555; https://doi.org/10.1074/mcp.M111.009555
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  Identification of Candidate Biomarkers for Early Detection of Human Lung Squamous Cell Cancer by Quantitative Proteomics

  Gu-Qing Zeng, Pang-Fei Zhang, Xingming Deng, Feng-Lei Yu, Cui Li, Yan Xu, Hong Yi, Mao-Yu Li, Rong Hu, Jian-Hong Zuo, Xin-Hui Li, Xun-Xun Wan, Jia-Quan Qu, Qiu-Yan He, Jian-Huang Li, Xu Ye, Yu Chen, Jiao-Yang Li and Zhi-Qiang Xiao

  Molecular & Cellular Proteomics June 1, 2012, First published on January 31, 2012, 11 (6) M111.013946; https://doi.org/10.1074/mcp.M111.013946
• Open Access

  Global Stability of Plasma Proteomes for Mass Spectrometry-Based Analyses

  Lisa J. Zimmerman, Ming Li, Wendell G. Yarbrough, Robbert J. C. Slebos and Daniel C. Liebler

  Molecular & Cellular Proteomics June 1, 2012, First published on February 1, 2012, 11 (6) M111.014340; https://doi.org/10.1074/mcp.M111.014340
• Open Access

  Rapid Identification of Monospecific Monoclonal Antibodies Using a Human Proteome Microarray

  Jun Seop Jeong, Lizhi Jiang, Edisa Albino, Josean Marrero, Hee Sool Rho, Jianfei Hu, Shaohui Hu, Carlos Vera, Diane Bayron-Poueymiroy, Zully Ann Rivera-Pacheco, Leonardo Ramos, Cecil Torres-Castro, Jiang Qian, Joseph Bonaventura, Jef D. Boeke, Wendy Y. Yap, Ignacio Pino, Daniel J. Eichinger, Heng Zhu and Seth Blackshaw

  Molecular & Cellular Proteomics June 1, 2012, First published on February 3, 2012, 11 (6) O111.016253; https://doi.org/10.1074/mcp.O111.016253
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  Altered Expression of Sialylated Glycoproteins in Breast Cancer Using Hydrazide Chemistry and Mass Spectrometry

  Yuan Tian, Francisco J. Esteva, Jin Song and Hui Zhang

  Molecular & Cellular Proteomics June 1, 2012, First published on February 7, 2012, 11 (6) M111.011403; https://doi.org/10.1074/mcp.M111.011403
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  Cross-talk between Receptor Tyrosine Kinase and Tumor Necrosis Factor-α Signaling Networks Regulates Apoptosis but not Proliferation

  Elsa M. Beyer and Gavin MacBeath

  Molecular & Cellular Proteomics June 1, 2012, First published on February 8, 2012, 11 (6) M111.013292; https://doi.org/10.1074/mcp.M111.013292
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  Heterogenous Turnover of Sperm and Seminal Vesicle Proteins in the Mouse Revealed by Dynamic Metabolic Labeling

  Amy J. Claydon, Steven A. Ramm, Andrea Pennington, Jane L. Hurst, Paula Stockley and Robert Beynon

  Molecular & Cellular Proteomics June 1, 2012, First published on February 13, 2012, 11 (6) M111.014993; https://doi.org/10.1074/mcp.M111.014993
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  Systematic Identification of the HSP90 Regulated Proteome

  Zhixiang Wu, Amin Moghaddas Gholami and Bernhard Kuster

  Molecular & Cellular Proteomics June 1, 2012, First published on February 14, 2012, 11 (6) M111.016675; https://doi.org/10.1074/mcp.M111.016675
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  Protein Interaction Profiling of the p97 Adaptor UBXD1 Points to a Role for the Complex in Modulating ERGIC-53 Trafficking

  Dale S. Haines, J. Eugene Lee, Stephen L. Beauparlant, Dane B. Kyle, Willem den Besten, Michael J. Sweredoski, Robert L. J. Graham, Sonja Hess and Raymond J. Deshaies

  Molecular & Cellular Proteomics June 1, 2012, First published on February 14, 2012, 11 (6) M111.016444; https://doi.org/10.1074/mcp.M111.016444
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  Human Biomarker Discovery and Predictive Models for Disease Progression for Idiopathic Pneumonia Syndrome Following Allogeneic Stem Cell Transplantation

  Daniela M. Schlatzer, Jean-Eudes Dazard, Rob M. Ewing, Serguei Ilchenko, Sara E. Tomcheko, Saada Eid, Vincent Ho, Greg Yanik, Mark R. Chance and Kenneth R. Cooke

  Molecular & Cellular Proteomics June 1, 2012, First published on February 15, 2012, 11 (6) M111.015479; https://doi.org/10.1074/mcp.M111.015479
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  TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics

  Jun Zhong, Min-Sik Kim, Raghothama Chaerkady, Xinyan Wu, Tai-Chung Huang, Derese Getnet, Christopher J. Mitchell, Shyam M. Palapetta, Jyoti Sharma, Robert N. O'Meally, Robert N. Cole, Akinori Yoda, Albrecht Moritz, Marc M. Loriaux, John Rush, David M. Weinstock, Jeffrey W. Tyner and Akhilesh Pandey

  Molecular & Cellular Proteomics June 1, 2012, First published on February 16, 2012, 11 (6) M112.017764; https://doi.org/10.1074/mcp.M112.017764
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  A Profile of an Endosymbiont-enriched Fraction of the Coral Stylophora pistillata Reveals Proteins Relevant to Microbial-Host Interactions

  Andrew J. Weston, Walter C. Dunlap, J. Malcolm Shick, Anke Klueter, Katrina Iglic, Ana Vukelic, Antonio Starcevic, Malcolm Ward, Mark L. Wells, Charles G. Trick and Paul F. Long

  Molecular & Cellular Proteomics June 1, 2012, First published on February 20, 2012, 11 (6) M111.015487; https://doi.org/10.1074/mcp.M111.015487