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Molecular & Cellular Proteomics

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Table of Contents

November 2012; Volume 11,Issue 11

Review

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    Inference and Validation of Protein Identifications
    Manfred Claassen
    Molecular & Cellular Proteomics November 1, 2012, First published on August 3, 2012, 11 (11) 1097-1104; https://doi.org/10.1074/mcp.R111.014795

Research

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    Quantitative Proteomics Reveals Regulation of Karyopherin Subunit Alpha-2 (KPNA2) and Its Potential Novel Cargo Proteins in Nonsmall Cell Lung Cancer
    Chun-I Wang, Kun-Yi Chien, Chih-Liang Wang, Hao-Ping Liu, Chia-Chen Cheng, Yu-Sun Chang, Jau-Song Yu and Chia-Jung Yu
    Molecular & Cellular Proteomics November 1, 2012, First published on July 25, 2012, 11 (11) 1105-1122; https://doi.org/10.1074/mcp.M111.016592
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    Proteomic and Transcriptomic Profiling of Staphylococcus aureus Surface LPXTG-proteins: Correlation with agr Genotypes and Adherence Phenotypes
    Mathilde Ythier, Grégory Resch, Patrice Waridel, Alexandre Panchaud, Aurélie Gfeller, Paul Majcherczyk, Manfredo Quadroni and Philippe Moreillon
    Molecular & Cellular Proteomics November 1, 2012, First published on July 25, 2012, 11 (11) 1123-1139; https://doi.org/10.1074/mcp.M111.014191
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    Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum
    Tran Hong Nha Nguyen, Laurent Brechenmacher, Joshua T. Aldrich, Therese R. Clauss, Marina A. Gritsenko, Kim K. Hixson, Marc Libault, Kiwamu Tanaka, Feng Yang, Qiuming Yao, Ljiljana Paša-Tolić, Dong Xu, Henry T. Nguyen and Gary Stacey
    Molecular & Cellular Proteomics November 1, 2012, First published on July 25, 2012, 11 (11) 1140-1155; https://doi.org/10.1074/mcp.M112.018028
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    Complementary Proteome and Transcriptome Profiling in Phosphate-deficient Arabidopsis Roots Reveals Multiple Levels of Gene Regulation
    Ping Lan, Wenfeng Li and Wolfgang Schmidt
    Molecular & Cellular Proteomics November 1, 2012, First published on July 25, 2012, 11 (11) 1156-1166; https://doi.org/10.1074/mcp.M112.020461
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    Integrative Proteomic Profiling of Protein Activity and Interactions Using Protein Arrays
    Se-Hui Jung, Kangseung Lee, Deok-Hoon Kong, Woo Jin Kim, Young-Myeong Kim and Kwon-Soo Ha
    Molecular & Cellular Proteomics November 1, 2012, First published on July 26, 2012, 11 (11) 1167-1176; https://doi.org/10.1074/mcp.M112.016964
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    Profiling Lipid–protein Interactions Using Nonquenched Fluorescent Liposomal Nanovesicles and Proteome Microarrays
    Kuan-Yi Lu, Sheng-Ce Tao, Tzu-Ching Yang, Yu-Hsuan Ho, Chia-Hsien Lee, Chen-Ching Lin, Hsueh-Fen Juan, Hsuan-Cheng Huang, Chin-Yu Yang, Ming-Shuo Chen, Yu-Yi Lin, Jin-Ying Lu, Heng Zhu and Chien-Sheng Chen
    Molecular & Cellular Proteomics November 1, 2012, First published on July 26, 2012, 11 (11) 1177-1190; https://doi.org/10.1074/mcp.M112.017426
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    A Novel Method for the Simultaneous Enrichment, Identification, and Quantification of Phosphopeptides and Sialylated Glycopeptides Applied to a Temporal Profile of Mouse Brain Development
    Giuseppe Palmisano, Benjamin L. Parker, Kasper Engholm-Keller, Sara Eun Lendal, Katarzyna Kulej, Melanie Schulz, Veit Schwämmle, Mark E. Graham, Henrik Saxtorph, Stuart J. Cordwell and Martin R. Larsen
    Molecular & Cellular Proteomics November 1, 2012, First published on July 26, 2012, 11 (11) 1191-1202; https://doi.org/10.1074/mcp.M112.017509
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    Diversity in the Protein N-Glycosylation Pathways Within the Campylobacter Genus
    Harald Nothaft, Nichollas E. Scott, Evgeny Vinogradov, Xin Liu, Rui Hu, Bernadette Beadle, Christopher Fodor, William G. Miller, Jianjun Li, Stuart J. Cordwell and Christine M. Szymanski
    Molecular & Cellular Proteomics November 1, 2012, First published on August 2, 2012, 11 (11) 1203-1219; https://doi.org/10.1074/mcp.M112.021519
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    Aurora B-dependent Regulation of Class IIa Histone Deacetylases by Mitotic Nuclear Localization Signal Phosphorylation
    Amanda J. Guise, Todd M. Greco, Irene Y. Zhang, Fang Yu and Ileana M. Cristea
    Molecular & Cellular Proteomics November 1, 2012, First published on August 2, 2012, 11 (11) 1220-1229; https://doi.org/10.1074/mcp.M112.021030
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    Interactome-wide Analysis Identifies End-binding Protein 1 as a Crucial Component for the Speck-like Particle Formation of Activated Absence in Melanoma 2 (AIM2) Inflammasomes
    Li-Jie Wang, Chia-Wei Hsu, Chiu-Chin Chen, Ying Liang, Lih-Chyang Chen, David M. Ojcius, Ngan-Ming Tsang, Chuen Hsueh, Chih-Ching Wu and Yu-Sun Chang
    Molecular & Cellular Proteomics November 1, 2012, First published on August 6, 2012, 11 (11) 1230-1244; https://doi.org/10.1074/mcp.M112.020594
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    Peptidomics of Three Bothrops Snake Venoms: Insights Into the Molecular Diversification of Proteomes and Peptidomes
    Alexandre K. Tashima, André Zelanis, Eduardo S. Kitano, Danielle Ianzer, Robson L. Melo, Vanessa Rioli, Sávio S. Sant'anna, Ana C. G. Schenberg, Antônio C. M. Camargo and Solange M. T. Serrano
    Molecular & Cellular Proteomics November 1, 2012, First published on August 6, 2012, 11 (11) 1245-1262; https://doi.org/10.1074/mcp.M112.019331
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    Five Friends of Methylated Chromatin Target of Protein-Arginine-Methyltransferase[Prmt]-1 (Chtop), a Complex Linking Arginine Methylation to Desumoylation
    Pavlos Fanis, Nynke Gillemans, Ali Aghajanirefah, Farzin Pourfarzad, Jeroen Demmers, Fatemehsadat Esteghamat, Ratna K. Vadlamudi, Frank Grosveld, Sjaak Philipsen and Thamar B. van Dijk
    Molecular & Cellular Proteomics November 1, 2012, First published on August 7, 2012, 11 (11) 1263-1273; https://doi.org/10.1074/mcp.M112.017194
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    The Amyloid Precursor Protein (APP) Family Members are Key Players in S-adenosylmethionine Formation by MAT2A and Modify BACE1 and PSEN1 Gene Expression-Relevance for Alzheimer's Disease
    Andreas Schrötter, Kathy Pfeiffer, Fouzi El Magraoui, Harald W. Platta, Ralf Erdmann, Helmut E. Meyer, Rupert Egensperger, Katrin Marcus and Thorsten Müller
    Molecular & Cellular Proteomics November 1, 2012, First published on August 9, 2012, 11 (11) 1274-1288; https://doi.org/10.1074/mcp.M112.019364
  • Open Access
    Protein-protein-interaction Network Organization of the Hypusine Modification System
    Henning Sievert, Simone Venz, Oscar Platas-Barradas, Vishnu M. Dhople, Martin Schaletzky, Claus-Henning Nagel, Melanie Braig, Michael Preukschas, Nora Pällmann, Carsten Bokemeyer, Tim H. Brümmendorf, Ralf Pörtner, Reinhard Walther, Kent E. Duncan, Joachim Hauber and Stefan Balabanov
    Molecular & Cellular Proteomics November 1, 2012, First published on August 10, 2012, 11 (11) 1289-1305; https://doi.org/10.1074/mcp.M112.019059
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    The Protein Composition of the Digestive Fluid from the Venus Flytrap Sheds Light on Prey Digestion Mechanisms
    Waltraud X. Schulze, Kristian W. Sanggaard, Ines Kreuzer, Anders D. Knudsen, Felix Bemm, Ida B. Thøgersen, Andrea Bräutigam, Line R. Thomsen, Simon Schliesky, Thomas F. Dyrlund, Maria Escalante-Perez, Dirk Becker, Jörg Schultz, Henrik Karring, Andreas Weber, Peter Højrup, Rainer Hedrich and Jan J. Enghild
    Molecular & Cellular Proteomics November 1, 2012, First published on August 12, 2012, 11 (11) 1306-1319; https://doi.org/10.1074/mcp.M112.021006
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    Secretomic Analysis Identifies Alpha-1 Antitrypsin (A1AT) as a Required Protein in Cancer Cell Migration, Invasion, and Pericellular Fibronectin Assembly for Facilitating Lung Colonization of Lung Adenocarcinoma Cells
    Ying-Hua Chang, Shu-Hui Lee, I-Chuang Liao, Shin-Huei Huang, Hung-Chi Cheng and Pao-Chi Liao
    Molecular & Cellular Proteomics November 1, 2012, First published on August 15, 2012, 11 (11) 1320-1339; https://doi.org/10.1074/mcp.M112.017384
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    A Deep Exploration of the Transcriptome and “Excretory/Secretory” Proteome of Adult Fascioloides magna
    Cinzia Cantacessi, Jason Mulvenna, Neil D. Young, Martin Kasny, Petr Horak, Ammar Aziz, Andreas Hofmann, Alex Loukas and Robin B. Gasser
    Molecular & Cellular Proteomics November 1, 2012, First published on August 16, 2012, 11 (11) 1340-1353; https://doi.org/10.1074/mcp.M112.019844
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    Proteomics and Deep Sequencing Comparison of Seasonally Active Venom Glands in the Platypus Reveals Novel Venom Peptides and Distinct Expression Profiles
    Emily S. W. Wong, David Morgenstern, Ehtesham Mofiz, Sara Gombert, Katrina M. Morris, Peter Temple-Smith, Marilyn B. Renfree, Camilla M. Whittington, Glenn F. King, Wesley C. Warren, Anthony T. Papenfuss and Katherine Belov
    Molecular & Cellular Proteomics November 1, 2012, First published on August 16, 2012, 11 (11) 1354-1364; https://doi.org/10.1074/mcp.M112.017491
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    Proteomic Characterization of Phagosomal Membrane Microdomains During Phagolysosome Biogenesis and Evolution
    Guillaume Goyette, Jonathan Boulais, Nicholas J. Carruthers, Christian R. Landry, Isabelle Jutras, Sophie Duclos, Jean-François Dermine, Stephen W. Michnick, Sylvie LaBoissière, Gilles Lajoie, Luis Barreiro, Pierre Thibault and Michel Desjardins
    Molecular & Cellular Proteomics November 1, 2012, First published on August 20, 2012, 11 (11) 1365-1377; https://doi.org/10.1074/mcp.M112.021048
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    Adenoviral E4 Gene Stimulates Secretion of Pigmental Epithelium Derived Factor (PEDF) that Maintains Long-term Survival of Human Glomerulus-derived Endothelial Cells
    Marina Jerebtsova, Namita Kumari, Yuri Obuhkov and Sergei Nekhai
    Molecular & Cellular Proteomics November 1, 2012, First published on August 21, 2012, 11 (11) 1378-1388; https://doi.org/10.1074/mcp.M112.020313
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    Total ApoE and ApoE4 Isoform Assays in an Alzheimer's Disease Case-control Study by Targeted Mass Spectrometry (n = 669): A Pilot Assay for Methionine-containing Proteotypic Peptides
    Romain Simon, Marion Girod, Catherine Fonbonne, Arnaud Salvador, Yohann Clément, Pierre Lantéri, Philippe Amouyel, Jean Charles Lambert and Jérôme Lemoine
    Molecular & Cellular Proteomics November 1, 2012, First published on August 23, 2012, 11 (11) 1389-1403; https://doi.org/10.1074/mcp.M112.018861
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    Potentially Novel Candidate Biomarkers for Head and Neck Squamous Cell Carcinoma Identified Using an Integrated Cell Line-based Discovery Strategy
    Lusia Sepiashvili, Angela Hui, Vladimir Ignatchenko, Willa Shi, Susie Su, Wei Xu, Shao Hui Huang, Brian O'Sullivan, John Waldron, Jonathan C. Irish, Bayardo Perez-Ordonez, Fei-Fei Liu and Thomas Kislinger
    Molecular & Cellular Proteomics November 1, 2012, First published on August 23, 2012, 11 (11) 1404-1415; https://doi.org/10.1074/mcp.M112.020933
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    Functional Interaction of the Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 1 Polymorphism and HLA-B27 in Vivo
    Noel García-Medel, Alejandro Sanz-Bravo, Dung Van Nguyen, Begoña Galocha, Patricia Gómez-Molina, Adrián Martín-Esteban, Carlos Alvarez-Navarro and José A. López de Castro
    Molecular & Cellular Proteomics November 1, 2012, First published on August 23, 2012, 11 (11) 1416-1429; https://doi.org/10.1074/mcp.M112.019588
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    Native Tandem and Ion Mobility Mass Spectrometry Highlight Structural and Modular Similarities in Clustered-Regularly-Interspaced Shot-Palindromic-Repeats (CRISPR)-associated Protein Complexes From Escherichia coli and Pseudomonas aeruginosa
    Esther van Duijn, Ioana M. Barbu, Arjan Barendregt, Matthijs M. Jore, Blake Wiedenheft, Magnus Lundgren, Edze R. Westra, Stan J. J. Brouns, Jennifer A. Doudna, John van der Oost and Albert J. R. Heck
    Molecular & Cellular Proteomics November 1, 2012, First published on August 23, 2012, 11 (11) 1430-1441; https://doi.org/10.1074/mcp.M112.020263
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    Dicer-dependent and -independent Argonaute2 Protein Interaction Networks in Mammalian Cells
    Anne Frohn, H. Christian Eberl, Julia Stöhr, Elke Glasmacher, Sabine Rüdel, Vigo Heissmeyer, Matthias Mann and Gunter Meister
    Molecular & Cellular Proteomics November 1, 2012, First published on August 23, 2012, 11 (11) 1442-1456; https://doi.org/10.1074/mcp.M112.017756
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    Major Histocompatibility Complex Class II+ Invariant Chain Negative Breast Cancer Cells Present Unique Peptides that Activate Tumor-specific T Cells from Breast Cancer Patients
    Olesya Chornoguz, Alexei Gapeev, Michael C. O'Neill and Suzanne Ostrand-Rosenberg
    Molecular & Cellular Proteomics November 1, 2012, First published on August 31, 2012, 11 (11) 1457-1467; https://doi.org/10.1074/mcp.M112.019232

Technological Innovation and Resources

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    Topograph, a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements
    Edward J. Hsieh, Nicholas J. Shulman, Dao-Fu Dai, Evelyn S. Vincow, Pabalu P. Karunadharma, Leo Pallanck, Peter S. Rabinovitch and Michael J. MacCoss
    Molecular & Cellular Proteomics November 1, 2012, First published on August 3, 2012, 11 (11) 1468-1474; https://doi.org/10.1074/mcp.O112.017699
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    Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics
    Amelia C. Peterson, Jason D. Russell, Derek J. Bailey, Michael S. Westphall and Joshua J. Coon
    Molecular & Cellular Proteomics November 1, 2012, First published on August 3, 2012, 11 (11) 1475-1488; https://doi.org/10.1074/mcp.O112.020131
  • Open Access
    A Method for Large-scale Identification of Protein Arginine Methylation
    Thomas Uhlmann, Vincent L. Geoghegan, Benjamin Thomas, Gabriela Ridlova, David C. Trudgian and Oreste Acuto
    Molecular & Cellular Proteomics November 1, 2012, First published on August 3, 2012, 11 (11) 1489-1499; https://doi.org/10.1074/mcp.M112.020743
  • Open Access
    Expert System for Computer-assisted Annotation of MS/MS Spectra
    Nadin Neuhauser, Annette Michalski, Jürgen Cox and Matthias Mann
    Molecular & Cellular Proteomics November 1, 2012, First published on August 10, 2012, 11 (11) 1500-1509; https://doi.org/10.1074/mcp.M112.020271
  • Open Access
    Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae
    Peter Henriksen, Sebastian A. Wagner, Brian T. Weinert, Satyan Sharma, Giedrė Bačinskaja, Michael Rehman, André H. Juffer, Tobias C. Walther, Michael Lisby and Chunaram Choudhary
    Molecular & Cellular Proteomics November 1, 2012, First published on August 2, 2012, 11 (11) 1510-1522; https://doi.org/10.1074/mcp.M112.017251
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In this issue

Molecular & Cellular Proteomics: 11 (11)
Molecular & Cellular Proteomics
Vol. 11, Issue 11
1 Nov 2012
  • Table of Contents
  • Table of Contents (PDF)
  • Cover (PDF)
  • About the Cover
  • Index by author
  • Ed Board (PDF)
  • Front Matter (PDF)

Issue highlights

  • Dicer-dependent and -independent Argonaute2 Protein Interaction Networks in Mammalian Cells
  • Proteomic Characterization of Phagosomal Membrane Microdomains During Phagolysosome Biogenesis and Evolution
  • Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics
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