SPS' Digest

Issue 26, 23-Dec-2005

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Quick jumps to articles in: Bioinformatics (13) / Biological applications (31) / Biomedical and clinical applications (40) / Eukaryotic Cells And Tissues (4) / Prokaryotes (7) / Pharmacology and Toxicology (1) / Protein Array (2) / Protein Characterization - PTMs (11) / Protein-protein interaction (8) / Quantitation (5) / Review (11) / Methodology (45) / Books (1) / Meeting (2) / Other (6) /

In this issue, 185 articles have been selected from:

Anal Chem, Volume 77, Issues 23+24, 2005 (5 articles)
Appl Bioinformatics, Volume 4, Issue 4, 2005 (1 article)
Appl Environ Microbiol, Volume 71, Issue 12, 2005 (1 article)
Arch Microbiol, Early Edition, 26-Nov-2005 (1 article)
Arthritis Rheum, Volume 52, Issue 12, 2005 (1 article)
BMC Bioinformatics, Volume 6, Issue 1, 2005 (2 articles)
BMC Neurol, Volume 5, Issue 1, 2005 (1 article)
Biochem Biophys Res Commun, Early Edition, 17-Nov-2005 (1 article)
Biochem Biophys Res Commun, Volume 339, Issue 2, 2006 (1 article)
Biochem J, Early Edition, 14-Dec-2005 (1 article)
Biochemistry, Volume 44, Issue 50, 2005 (1 article)
Biogerontology, Volume 6, Issue 4, 2005 (1 article)
Bioinformatics, Early Edition, 13-Dec-2005 (1 article)
Bioinformatics, Volume 21, Issue 24, 2005 (1 article)
Biomedical Digital Libraries, Volume 2, 2005 (1 article)
Cancer Res, Volume 65, Issue 23, 2005 (1 article)
Carcinogenesis, Early Edition, 12-Dec-2005 (1 article)
Chembiochem, Early Edition, 12-Dec-2005 (1 article)
Circulation, Early Edition, 12-Dec-2005 (1 article)
Clin Cancer Res, Volume 11, Issue 23, 2005 (1 article)
Clin Chem Lab Med, Volume 43, Issue 12, 2005 (1 article)
Complexus, Volume 2, Issue 2, 2005 (1 article)
Crit Rev Oncol Hematol, Early Edition, 6-Dec-2005 (1 article)
Curr Diab Rep, Volume 5, Issue 6, 2005 (1 article)
Electrophoresis, Early Edition, 16-Dec-2005 (1 article)
Electrophoresis, Volume 26, Issues 23+24, 2005 (6 articles)
Endocrine, Volume 28, Issue 1, 2005 (1 article)
Eur J Pharmacol, Early Edition, 25-Nov-2005 (1 article)
Exp Biol Med (Maywood), Volume 230, Issue 11, 2005 (5 articles)
FEBS Lett, Early Edition, 6-Dec-2005 (1 article)
Genes Dev, Volume 19, Issue 23, 2005 (1 article)
Genome Biology, Volume 6, Issue 12, 2005 (1 article)
Glycobiology, Early Edition, 29-Nov-2005 (1 article)
Int J Gynecol Cancer, Volume 15, Issue Suppl 3, 2005 (2 articles)
Int J Med Microbiol, Volume 295, Issue 8, 2005 (1 article)
Int J Oncol, Volume 28, Issue 1, 2006 (2 articles)
J Alzheimers Dis, Volume 8, Issue 3, 2005 (1 article)
J Am Soc Mass Spectrom, Early Edition, 9-Dec-2005 (1 article)
J Bacteriol, Volume 188, Issue 1, 2006 (1 article)
J Biochem Mol Biol, Volume 38, Issue 6, 2005 (2 articles)
J Biol Chem, Early Edition, 13-Dec-2005->29-Nov-2005 (3 articles)
J Clin Invest, Volume 115, Issue 12, 2005 (1 article)
J Neurochem, Volume 95, Issue 5, 2005 (1 article)
J Neurovirol, Volume 11, Issue 6, 2005 (1 article)
J Nutr, Volume 135, Issue 12, 2005 (1 article)
J Proteome Res, Early Edition, 12/09/2005->12/16/2005 (16 articles)
J Proteome Res, Volume 4, Issue 6, 2005 (60 articles)
Kidney Int Suppl, Volume , Issue 99, 2005 (1 article)
Liver Int, Volume 25, Issue 6, 2005 (1 article)
Methods Enzymol, Volume 399, 2005 (3 articles)
Methods Mol Biol, Volume 310, 2005 (4 articles)
Methods, Early Edition, 9-Dec-2005 (1 article)
Microbiology, Volume 151, Issue Pt 12, 2005 (1 article)
Mol Cell Biochem, Volume 275, Issue 1-2, 2005 (1 article)
Mol Cell Proteomics, Volume 4, Issue 12, 2005 (17 articles)
Mol Divers, Volume 9, Issue 4, 2005 (1 article)
Mol Microbiol, Volume 58, Issue 5, 2005 (1 article)
Nat Biotechnol, Early Edition, 27-Nov-2005 (1 article)
Nat Clin Pract Oncol, Volume 2, Issue 12, 2005 (1 article)
Nature, Volume 438, Issue 7068, 2005 (1 article)
Neuroscience, Early Edition, 6-Dec-2005 (1 article)
Novartis Found Symp, Volume 269: 35-42; discussion 43-6, 2005 (1 article)
Oncogene, Early Edition, 28-Nov-2005 (1 article)
Parasitology, Volume 131, Issue Pt 6, 2005 (1 article)
Photosynth Res, Volume 79, Issue 3, 2004 (1 article)
Proc Natl Acad Sci U S A, Early Edition, 12-Dec-2005 (1 article)
Proc Natl Acad Sci U S A, Volume 102, Issue 50, 2005 (1 article)
Reproduction, Volume 130, Issue 6, 2005 (1 article)
Science, Early Edition, 8-Dec-2005 (1 article)
Surgeon, Volume 3, Issue 6, 2005 (1 article)
Trends Plant Sci, Early Edition, 11-Dec-2005 (1 article)

Disclaimer: The selection and categorisation reflect the views and understandings of contributors (i.e. SPS members).

Quick jumps to articles in: Bioinformatics (13) / Biological applications (31) / Biomedical and clinical applications (40) / Eukaryotic Cells And Tissues (4) / Prokaryotes (7) / Pharmacology and Toxicology (1) / Protein Array (2) / Protein Characterization - PTMs (11) / Protein-protein interaction (8) / Quantitation (5) / Review (11) / Methodology (45) / Books (1) / Meeting (2) / Other (6) /

Bioinformatics

A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics
Mathias Uhlen, Erik Bjorling, Charlotta Agaton, Cristina Al-Khalili Szigyarto, Bahram Amini, Elisabet Andersen, Ann-Catrin Andersson, Pia Angelidou, Anna Asplund, Caroline Asplund, Lisa Berglund, Kristina Bergstrom, Harry Brumer, Dijana Cerjan, Marica Ekstrom, Adila Elobeid, Cecilia Eriksson, Linn Fagerberg, Ronny Falk, Jenny Fall, Mattias Forsberg, Marcus Gry Bjorklund, Kristoffer Gumbel, Asif Halimi, Inga Hallin, Carl Hamsten, Marianne Hansson, My Hedhammar, Gorel Hercules, Caroline Kampf, Karin Larsson, Mats Lindskog, Wald Lodewyckx, Jan Lund, Joakim Lundeberg, Kristina Magnusson, Erik Malm, Peter Nilsson, Jenny Odling, Per Oksvold, Ingmarie Olsson, Emma Oster, Jenny Ottosson, Linda Paavilainen, Anja Persson, Rebecca Rimini, Johan Rockberg, Marcus Runeson, Asa Sivertsson, Anna Skollermo, Johanna Steen, Maria Stenvall, Fredrik Sterky, Sara Stromberg, Marten Sundberg, Hanna Tegel, Samuel Tourle, Eva Wahlund, Annelie Walden, Jinghong Wan, Henrik Wernerus, Joakim Westberg, Kenneth Wester, Ulla Wrethagen, Lan Lan Xu, Sophia Hober, and Fredrik Ponten
Mol Cell Proteomics (2005) 4(12): 1920-1932

Software-induced variance in two-dimensional gel electrophoresis image analysis
Wheelock AM, Buckpitt AR
Electrophoresis (2005) 26(23): 4508-4520

Identification of post-translational modifications by blind search of mass spectra
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA
Nat Biotechnol Early Edition: published 27-Nov-2005

Feature Selection for Classification of SELDI-TOF-MS Proteomic Profiles
Hauskrecht M, Pelikan R, Malehorn DE, Bigbee WL, Lotze MT, Zeh HJ, Whitcomb DC, Lyons-Weiler J
Appl Bioinformatics (2005) 4(4): 227-46

Quality classification of tandem mass spectrometry data
Salmi J, Moulder R, Filen JJ, Nevalainen OS, Nyman TA, Lahesmaa R, Aittokallio T
Bioinformatics Early Edition: published 13-Dec-2005

Efficient Analysis and Extraction of MS/MS Result Data from Mascot(TM) Result Files
Grosse-Coosmann F, Boehm AM, Sickmann A
BMC Bioinformatics (2005) 6(1): 290

An SVM-based system for predicting protein subnuclear localizations
Lei Z, Dai Y
BMC Bioinformatics (2005) 6: 291

Improving Mass and Liquid Chromatography Based Identification of Proteins Using Bayesian Scoring
Sharon S. Chen, Eric W. Deutsch, Eugene C. Yi, Xiao-jun Li, David R. Goodlett, and Ruedi Aebersold
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2174-2184

Strategy to Design Improved Proteomic Experiments Based on Statistical Analyses of the Chemical Properties of Identified Peptides
Martin Ethier and Daniel Figeys
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2201-2206

VEMS 3.0: Algorithms and Computational Tools for Tandem Mass Spectrometry Based Identification of Post-translational Modifications in Proteins
Rune Matthiesen, Morten Beck Trelle, Peter H jrup, Jakob Bunkenborg, and Ole N. Jensen
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2338-2347

Proteomics-Grade de Novo Sequencing Approach
Mikhail M. Savitski, Michael L. Nielsen, Frank Kjeldsen, and Roman A. Zubarev
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2348-2354

"Plasmo2D": An Ancillary Proteomic Tool to Aid Identification of Proteins from Plasmodium falciparum
Amit Khachane, Ranjit Kumar, Sanyam Jain, Samta Jain, Gowrishankar Banumathy, Varsha Singh, Saurabh Nagpal, and Utpal Tatu
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2369-2374

Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments
Adam Rauch, Matthew Bellew, Jimmy Eng, Matthew Fitzgibbon, Ted Holzman, Peter Hussey, Mark Igra, Brendan Maclean, Chen Wei Lin, Andrea Detter, Ruihua Fang, Vitor Faca, Phil Gafken, Heidi Zhang, Jeffrey Whitaker, David States, Sam Hanash, Amanda Paulovich, and Martin W. McIntosh
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/09/2005

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Biological applications

Proteomic Analysis of Schistosoma mansoni Cercarial Secretions
Giselle M. Knudsen, Katalin F. Medzihradszky, Kee-Chong Lim, ElizabethHansell, and James H. McKerrow
Mol Cell Proteomics (2005) 4(12): 1862-1875

B7/CD28 Costimulation of T Cells Induces a Distinct Proteome Pattern
Kai Kronfeld, Elisabeth Hochleitner, Simone Mendler, Jutta Goldschmidt, Rudolf Lichtenfels, Friedrich Lottspeich, Hinrich Abken, and Barbara Seliger
Mol Cell Proteomics (2005) 4(12): 1876-1887

Analysis of BCL6-interacting Proteins by Tandem Mass Spectrometry
Rodney R. Miles, David K. Crockett, Megan S. Lim, and Kojo S. J. Elenitoba-Johnson
Mol Cell Proteomics (2005) 4(12): 1898-1909

A proteomic analysis of mammalian preimplantation embryonic development
Katz-Jaffe MG, Linck DW, Schoolcraft WB, Gardner DK
Reproduction (2005) 130(6): 899-905

Quantitative proteomic analysis of Myc-induced apoptosis: A direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4
Shiio Y, Suh KS, Lee H, Yuspa SH, Eisenman RN, Aebersold R
J Biol Chem Early Edition: published 29-Nov-2005

Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations
Nie L, Wu G, Zhang W
Biochem Biophys Res Commun Early Edition: published 17-Nov-2005

Identification of Differentially Expressed Proteins during Larval Molting of Helicoverpa armigera
Xiao-Fan Zhao, Hong-Juan He, Du-Juan Dong, and Jin-Xing Wang
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Dynamics of Arabidopsis thaliana soluble proteome in response to different nutrient culture conditions
Sarry JE, Kuhn L, Le Lay P, Garin J, Bourguignon J
Electrophoresis Early Edition: published 16-Dec-2005

Cytoskeletal networks and pathways involved in endocytosis
Drubin DG, Kaksonen M, Toret C, Sun Y
Novartis Found Symp (2005) 269: 35-42; discussion 43-6: 223-30

Defining the role of the E. coli chaperone SECB using comparative proteomics
Baars L, Ytterberg AJ, Drew D, Wagner S, Thilo C, van Wijk KJ, de Gier JW
J Biol Chem Early Edition: published 13-Dec-2005

The cell-shape protein MreC interacts with extracytoplasmic proteins including cell wall assembly complexes in Caulobacter crescentus
Divakaruni AV, Ogorzalek Loo RR, Xie Y, Loo JA, Gober JW
Proc Natl Acad Sci U S A Early Edition: published 12-Dec-2005

Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation
Dopson M, Baker-Austin C, Bond PL
Microbiology (2005) 151(Pt 12): 4127-37

Estrogen regulation of the rat anterior pituitary gland proteome
Blake CA, Brown LM, Duncan MW, Hunsucker SW, Helmke SM
Exp Biol Med (Maywood) (2005) 230(11): 800-7

Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: synthesis of active site-directed probes
Ovaa H, Galardy PJ, Ploegh HL
Methods Enzymol (2005) 399: 468-78

Proteomic analysis of ubiquitin conjugates in yeast
Peng J, Cheng D
Methods Enzymol (2005) 399: 367-81

Proteomic analysis of rat hippocampus after repeated psychosocial stress
Carboni L, Piubelli C, Pozzato C, Astner H, Arban R, Righetti PG, Hamdan M, Domenici E
Neuroscience Early Edition: published 6-Dec-2005

A method for direct application of human plasmin on a dithiothreitol-containing agarose stacking gel system
Choi NS, Chung DM, Yoon KS, Maeng PJ, Kim SH
J Biochem Mol Biol (2005) 38(6): 763-5

Proteomic analysis and extensive protein identification from dry, germinating Arabidopsis seeds and young seedlings
Fu Q, Wang BC, Jin X, Li HB, Han P, Wei KH, Zhang XM, Zhu YX
J Biochem Mol Biol (2005) 38(6): 650-60

Proteomic analysis of a 120 kDa protein complex in cyst fluid of Taenia solium metacestode and preliminary evaluation of its value for the serodiagnosis of neurocysticercosis
Lee EG, Bae YA, Jeong YT, Chung JY, Je EY, Kim SH, Na BK, Ju JW, Kim TS, Ma L, Cho SY, Kong Y
Parasitology (2005) 131(Pt 6): 867-79

Direct Proteomic Mapping of Streptomyces Luteogriseus Strain 103 and cnn1 and Insights into Antibiotic Biosynthesis
Yu-xia Wang and Ying-Jin Yuan
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 1999-2006

Global Analysis of the Hortaea werneckii Proteome: Studying Steroid Response in Yeast
Maja Matis, Marija akelj-Mavri , and Jasna Peter-Katalini
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2043-2051

Order from Chaos: Observing Hormesis at the Proteome Level
Milan Randi and Ernesto Estrada
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2133-2136

Proteomic Analysis of Cellular Response to Microcystin in Human Amnion FL Cells
Wen-yu Fu, Li-hong Xu, and Ying-nian Yu
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2207-2215

Proteomic Analysis of the Sarcosine-Insoluble Outer Membrane Fraction of Pseudomonas aeruginosa Responding to Ampicilin, Kanamycin, and Tetracycline Resistance
Xuanxian Peng, Changxin Xu, Haixia Ren, Xiangmin Lin, Lina Wu, and Sanying Wang
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2257-2265

Profiling of Myelin Proteins by 2D-Gel Electrophoresis and Multidimensional Liquid Chromatography Coupled to MALDI TOF-TOF Mass Spectrometry
Frank Vanrobaeys, Rudy Van Coster, Goedele Dhondt, Bart Devreese, and Jozef Van Beeumen
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2283-2293

Formation of Truncated Proteins and High-Molecular-Mass Aggregates upon Soft Illumination of Photosynthetic Proteins
Sara Rinalducci, Natascia Campostrini, Paolo Antonioli, Pier Giorgio Righetti, Peter Roepstorff, and Lello Zolla
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2327-2337

Identification of an OprD Homologue in Acinetobacter baumannii
Myrielle Dupont, Jean-Marie Pagès, Daniel Lafitte, Axel Siroy, and Claude Bollet
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2386-2390

Mammalian Embryonic Cerebrospinal Fluid Proteome Has Greater Apolipoprotein and Enzyme Pattern Complexity than the Avian Proteome
Carolina Parada, Ángel Gato, and David Bueno
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2420-2428

Enhanced Proteome Profiling by Inhibiting Proteolysis with Small Heat Shock Proteins
Mee-Jung Han, Jeong Wook Lee, and Sang Yup Lee
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2429-2434

Proteomic Analysis of Apical Microvillous Membranes of Syncytiotrophoblast Cells Reveals A High Degree of Similarity with Lipid Rafts
Alberto Paradela, Susana B. Bravo, Mauricio Henríquez, Gloria Riquelme, Francisco Gavilanes, José M. González-Ros, and Juan P. Albar
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2435-2441

Insulin-dependent Interactions of Proteins with GLUT4 Revealed through Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)
Leonard J. Foster, # Assaf Rudich, # Ilana Talior, # Nish Patel, Xudong Huang, L. Michelle Furtado, Philip J. Bilan, Matthias Mann, and Amira Klip
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/09/2005

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Biomedical and clinical applications

Proteomic Analysis of Pancreatic Ductal Carcinoma Cells after Combined Treatment with Gemcitabine and Trichostatin A
Daniela Cecconi, Massimo Donadelli, Aldo Scarpa, Alberto Milli, Marta Palmieri, Mahmoud Hamdan, Liliana B. Areces, Juri Rappsilber, and Pier Giorgio Righetti
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 1909-1916

Comparison of Normal and Breast Cancer Cell Lines Using Proteome, Genome, and Interactome Data
Anil J. Patwardhan, Eric F. Strittmatter, David G. Camp II, Richard D. Smith, and Maria G. Pallavicini
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 1952-1960

Analysis of Protein Expression during Oxidative Stress in Breast Epithelial Cells Using a Stable Isotope Labeled Proteome Internal Standard
Yuan Yan, Valerie M. Weaver, and Ian A. Blair
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2007-2014

In Search of Secreted Protein Biomarkers for the Anti-inflammatory Effect of 2-Adrenergic Receptor Agonists: Application of DIGE Technology in Combination with Multivariate and Univariate Data Analysis Tools
Kitty C. M. Verhoeckx, Marco Gaspari, Sabina Bijlsma, Jan van der Greef, Renger F. Witkamp, Robert P. Doornbos, and Richard J. T. Rodenburg
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2015-2023

Steatosis-Induced Proteomic Changes in Liver Mitochondria Evidenced by Two-Dimensional Differential In-Gel Electrophoresis
Pierre Douette, Rachel Navet, Pascal Gerkens, Edwin de Pauw, Pierre Leprince, Claudine Sluse-Goffart, and Francis E. Sluse
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2024-2031

Resetting the Epigenetic Histone Code in the MRL-lpr/lpr Mouse Model of Lupus by Histone Deacetylase Inhibition
Benjamin A. Garcia, Scott A. Busby, Jeffrey Shabanowitz, Donald F. Hunt, and Nilamadhab Mishra
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2032-2042

Characterization of Human Tear Proteome Using Multiple Proteomic Analysis Techniques
Nan Li, Nan Wang, Jing Zheng, X. Michael Liu, O. William Lever, Paul M. Erickson, and Liang Li
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2052-2061

Identification of Human Hepatocellular Carcinoma-Related Biomarkers by Two-Dimensional Difference Gel Electrophoresis and Mass Spectrometry
I-Neng Lee, Chien-Hung Chen, Jin-Chuan Sheu Hsuan-Shu Lee, Guan-Tarn Huang, Chen-Yin Yu, Fung-Jou Lu, and Lu-Ping Chow
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2062-2069

Genomic and Proteomic Analysis of Mammary Tumors Arising in Transgenic Mice
Lu Xie, Baogang J. Xu, Agnieszka E. Gorska, Yu Shyr, Sarah A. Schwartz, Nikki Cheng, Shawn Levy, Brian Bierie, Richard M. Caprioli, and Harold L. Moses
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2088-2098

Unbiased Examination of Changes in Plasma Membrane Proteins in Drug Resistant Cancer Cells
Amir M. Rahbar and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2148-2153

Proteomic Analysis of Protein Expression and Oxidative Modification in R6/2 Transgenic Mice: A Model of Huntington Disease
Marzia Perluigi, H. Fai Poon, William Maragos, William M. Pierce, Jon B. Klein, Vittorio Calabrese, Chiara Cini, Carlo De Marco, and D. Allan Butterfield
Mol Cell Proteomics (2005) 4(12): 1849-1861

Comparative Proteomic Analysis of Intra- and Interindividual Variation in Human Cerebrospinal Fluid
Yan Hu, James P. Malone, Anne M. Fagan, R. Reid Townsend, and David M.Holtzman
Mol Cell Proteomics (2005) 4(12): 2000-2009

Proteomic Analysis of Ubiquitinated Proteins from Human MCF-7 Breast Cancer Cells by Immunoaffinity Purification and Mass Spectrometry
Julian Vasilescu, Jeffrey C. Smith, Martin Ethier, and Daniel Figeys
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2192-2200

Proteomic Analysis Using Protein Chips to Detect Biomarkers in Cervical and Amniotic Fluid in Women with Intra-Amniotic Inflammation
Ulla Rüetschi, Åsa Rosén, Gösta Karlsson, Henrik Zetterberg, Lars Rymo, Henrik Hagberg, and Bo Jacobsson
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2236-2242

Identification of Class II HLA-DRB1 03-Bound Measles Virus Peptides by 2D-Liquid Chromatography Tandem Mass Spectrometry
Kenneth L. Johnson, Inna G. Ovsyannikova, Gregory A. Poland, and David C. Muddiman
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2243-2249

The Protein Expression of Streptococcus pyogenes Is Significantly Influenced by Human Plasma
Björn P. Johansson, Fredrik Levander, Ulrich von Pawel-Rammingen, Tord Berggård, Lars Björck, and Peter James
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2302-2311

Detection of Hypothetical Proteins in Human Fetal Perireticular Nucleus
Felix Hepner, Jae-Kyung Myung, Norbert Ulfig, Arnold Pollak, and Gert Lubec
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2379-2385

Identification of biomarkers for breast cancer in nipple aspiration and ductal lavage fluid
Li J, Zhao J, Yu X, Lange J, Kuerer H, Krishnamurthy S, Schilling E, Khan SA, Sukumar S, Chan DW
Clin Cancer Res (2005) 11(23): 8312-20

A chronic fatigue syndrome - related proteome in human cerebrospinal fluid
Baraniuk JN, Casado B, Maibach H, Clauw DJ, Pannell LK, Hess S
BMC Neurol (2005) 5(1): 22

Discovery of new rheumatoid arthritis biomarkers using the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry ProteinChip approach
de Seny D, Fillet M, Meuwis MA, Geurts P, Lutteri L, Ribbens C, Bours V, Wehenkel L, Piette J, Malaise M, Merville MP
Arthritis Rheum (2005) 52(12): 3801-3812

Different expression of calgizzarin (S100A11) in normal colonic epithelium, adenoma and colorectal carcinoma
Melle C, Ernst G, Schimmel B, Bleul A, Mothes H, Kaufmann R, Settmacher U, Von Eggeling F
Int J Oncol (2006) 28(1): 195-200

Protein Dysregulation in Mouse Hippocampus Polytransgenic for Chromosome 21 Structures in the Down Syndrome Critical Region
Joo-Ho Shin, Talin Gulesserian, Emmanuelle Verger, Jean-Maurice Delabar, and Gert Lubec
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

The proteomics of sickle cell disease: profiling of erythrocyte membrane proteins by 2D-DIGE and tandem mass spectrometry
Kakhniashvili DG, Griko NB, Bulla LA Jr, Goodman SR
Exp Biol Med (Maywood) (2005) 230(11): 787-92

Cerebrospinal fluid proteomics and human immunodeficiency virus dementia: Preliminary observations
Berger JR, Avison M, Mootoor Y, Beach C
J Neurovirol (2005) 11(6): 557-62

Is tailored therapy feasible in oncology?
Gasparini G, Longo R, Torino F, Gattuso D, Morabito A, Toffoli G
Crit Rev Oncol Hematol Early Edition: published 6-Dec-2005

Proteomic approach in the search of new cardiovascular biomarkers
Gallego-Delgado J, Lazaro A, Osende JI, Barderas MG, Blanco-Colio LM, Duran MC, Martin-Ventura JL, Vivanco F, Egido J
Kidney Int Suppl (2005) (99): S103-7.

Proteome profiling of human epithelial ovarian cancer cell line TOV-112D
Gagne JP, Gagne P, Hunter JM, Bonicalzi ME, Lemay JF, Kelly I, Le Page C, Provencher D, Mes-Masson AM, Droit A, Bourgais D, Poirier GG
Mol Cell Biochem (2005) 275(1-2): 25-55

Chemoprevention of breast cancer, proteomic discovery of genistein action in the rat mammary gland
Rowell C, Carpenter DM, Lamartiniere CA
J Nutr (2005) 135(12): 2953S-9S

Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics
Nagaraja GM, Othman M, Fox BP, Alsaber R, Pellegrino CM, Zeng Y, Khanna R, Tamburini P, Swaroop A, Kandpal RP
Oncogene Early Edition: published 28-Nov-2005

A proteomic analysis of penicillin resistance in Streptococcus pneumoniae reveals a novel role for PstS, a subunit of the phosphate ABC transporter
Soualhine H, Brochu V, Menard F, Papadopoulou B, Weiss K, Bergeron MG, Legare D, Drummelsmith J, Ouellette M
Mol Microbiol (2005) 58(5): 1430-40

Proteomic profiling of cerebrospinal fluid identifies biomarkers for amyotrophic lateral sclerosis
Ranganathan S, Williams E, Ganchev P, Gopalakrishnan V, Lacomis D, Urbinelli L, Newhall K, Cudkowicz ME, Brown RH Jr, Bowser R
J Neurochem (2005) 95(5): 1461-71

Comparing calpain- and caspase-3-degradation patterns in traumatic brain injury by differential proteome analysis
Liu MC, Akle V, Zheng W, Dave JR, Tortella FC, Hayes RL, Wang KK
Biochem J Early Edition: published 14-Dec-2005

Metabolomic Identification of Novel Biomarkers of Myocardial Ischemia
Sabatine MS, Liu E, Morrow DA, Heller E, McCarroll R, Wiegand R, Berriz GF, Roth FP, Gerszten RE
Circulation Early Edition: published 12-Dec-2005

A proteomic investigation into a human gastric cancer cell line BGC823 treated with diallyl trisulfide
Li N, Guo R, Li W, Shao J, Li S, Zhao K, Chen X, Xu N, Liu S, Lu Y
Carcinogenesis Early Edition: published 12-Dec-2005

Ovarian cancer: is the news good enough?
Poveda A
Int J Gynecol Cancer (2005) 15(Suppl 3): 298-306

Ovarian cancer in the proteomics era: diagnosis, prognosis, and therapeutics targets
Boyce EA, Kohn EC
Int J Gynecol Cancer (2005) 15(Suppl 3): 266-73

Altered protein expression and protein nitration pattern during d-galactosamine-induced cell death in human hepatocytes: a proteomic analysis
Rodriguez-Ariza A, Lopez-Sanchez LM, Gonzalez R, Corrales FJ, Lopez P, Bernardos A, Muntane J
Liver Int (2005) 25(6): 1259-69

Using proteomics and network analysis to elucidate the consequences of synaptic protein oxidation in a PS1+AbetaPP mouse model of Alzheimer's disease
Soreghan BA, Lu BW, Thomas SN, Duff K, Rakhmatulin EA, Nikolskaya T, Chen T, Yang AJ
J Alzheimers Dis (2005) 8(3): 227-41

Proteomics as a tool for clinically relevant biomarker discovery and validation
Duncan MW, Hunsucker SW
Exp Biol Med (Maywood) (2005) 230(11): 808-17

Proteomics of the anterior pituitary gland as a model for studying the physiology of a heterogeneous organ
Blake CA, Helmke SM
Exp Biol Med (Maywood) (2005) 230(11): 793-9

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Eukaryotic Cells And Tissues

Preparation of postsynaptic density fraction from hippocampal slices and proteomic analysis
Dosemeci A, Tao-Cheng JH, Vinade L, Jaffe H
Biochem Biophys Res Commun (2006) 339(2): 687-694

Two-dimensional gel electrophoresis maps of the proteome and phosphoproteome of primitively cultured rat mesangial cells
Jiang XS, Tang LY, Cao XJ, Zhou H, Xia QC, Wu JR, Zeng R
Electrophoresis (2005) 26(23): 4540-4562

A hydroponic rice seedling culture model system for investigating proteome of salt stress in rice leaf
Kim DW, Rakwal R, Agrawal GK, Jung YH, Shibato J, Jwa NS, Iwahashi Y, Iwahashi H, Kim DH, Shim IS, Usui K
Electrophoresis (2005) 26(23): 4521-4539

Molecular diversity of rat brain proteins as revealed by proteomic analysis
Yang JW, Juranville JF, Hoger H, Fountoulakis M, Lubec G
Mol Divers (2005) 9(4): 385-96

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Prokaryotes

Proteome Analysis of Streptococcus thermophilus Grown in Milk Reveals Pyruvate Formate-Lyase as the Major Upregulated Protein
Derzelle S, Bolotin A, Mistou MY, Rul F
Appl Environ Microbiol (2005) 71(12): 8597-8605

Proteome analyses of Staphylococcus aureus in growing and non-growing cells: A physiological approach
Kohler C, Wolff S, Albrecht D, Fuchs S, Becher D, Buttner K, Engelmann S, Hecker M
Int J Med Microbiol (2005) 295(8): 547-65

Two-Dimensional Fluorescence Difference Gel Electrophoretic Analysis of Streptococcus mutans Biofilms
Catherine Rathsam, Ruth E. Eaton, Christine L. Simpson, Gina V. Browne, Valentina A. Valova, Derek W. S. Harty, and Nicholas A. Jacques
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2161-2173

Challenges in the Overall Analysis of Microbial Proteomes
Alexander Scherl, Jean-Charles Sanchez, Denis F. Hochstrasser
Complexus (2005) 2(2): 79-86

Reconstruction and Regulation of the Central Catabolic Pathway in the Thermophilic Propionate-Oxidizing Syntroph Pelotomaculum thermopropionicum
Kosaka T, Uchiyama T, Ishii S, Enoki M, Imachi H, Kamagata Y, Ohashi A, Harada H, Ikenaga H, Watanabe K
J Bacteriol (2006) 188(1): 202-10

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ, Lopez-Hoyo N, Jiang L, Piccirillo S, Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M, Grayhack EJ
Genes Dev (2005) 19(23): 2816-26

Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools
Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A, Lillehaug JR, Eidhammer I, Jensen HB
Arch Microbiol Early Edition: published 26-Nov-2005

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Pharmacology and Toxicology

Biomarker discovery in rat plasma for estrogen receptor-alpha action
Holt TG, Flick RB, Rohde E, Griffin P, Rohrer SP
Electrophoresis (2005) 26(23): 4486-4494

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Protein Array

Serum Microarrays for Large Scale Screening of Protein Levels
Magdalena Janzi, Jenny Odling, Qiang Pan-Hammarstrom, Martenn Sundberg, Joakim Lundeberg, Mathias Uhlen, Lennart Hammarstrom, and Peter Nilsson
Mol Cell Proteomics (2005) 4(12): 1942-1947

One-Step Fractionation of Complex Proteomes Enables Detection of Low Abundant Analytes Using Antibody-Based Microarrays
Johan Ingvarsson, Malin Lindstedt, Carl A. K. Borrebaeck, and Christer Wingren
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

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Protein Characterization / PTMs

Quantitative Analysis of Protein Phosphorylation in Mouse Brain by Hypothesis-Driven Multistage Mass Spectrometry
Mi Jin, Helen Bateup, Júlio C. Padovan, Paul Greengard, Angus C. Nairn, and Brian T. Chait
ANALYTICAL CHEMISTRY (2005) 77(24): 7845-7851

Rapid and Sensitive Identification of Major Histocompatibility Complex Class I-associated Tumor Peptides by Nano-LC MALDI MS/MS
Sandra Hofmann, Matthias Gluckmann, Sandra Kausche, Andrea Schmidt, Carsten Corvey, Rudolf Lichtenfels, Christoph Huber, Christian Albrecht, Michael Karas, and Wolfgang Herr
Mol Cell Proteomics (2005) 4(12): 1888-1897

Collisional Activation by MALDI Tandem Time-of-flight Mass Spectrometry Induces Intramolecular Migration of Amide Hydrogens in Protonated Peptides
Thomas J. D. Jorgensen, Nicolai Bache, Peter Roepstorff, Henrik Gardsvoll, and Michael Ploug
Mol Cell Proteomics (2005) 4(12): 1910-1919

Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry
Tao Liu, Wei-Jun Qian, Marina A. Gritsenko, David G. Camp II, Matthew E. Monroe, Ronald J. Moore, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2070-2080

Poly(Glycidyl Methacrylate/Divinylbenzene)-IDA-FeIII in Phosphoproteomics
Nurul H. Aprilita, Christian W. Huck, Rania Bakry, Isabel Feuerstein, Guenther Stecher, Sandra Morandell, Hong-Lei Huang, Taras Stasyk, Lukas A. Huber, and Guenther K. Bonn
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2312-2319

Analysis of Total N-Glycans in Cell Membrane Fractions of Cancer Cells Using a Combination of Serotonin Affinity Chromatography and Normal Phase Chromatography
Ryosuke Naka, Satoru Kamoda, Aya Ishizuka, Mitsuhiro Kinoshita, and Kazuaki Kakehi
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Identification of novel phospholipid binding proteins in Saccharomyces cerevisiae
Fernandez-Murray JP, McMaster CR
FEBS Lett Early Edition: published 6-Dec-2005

Structural Conservation of Mouse and Rat Zona Pellucida Glycoproteins. Probing the Native Rat Zona Pellucida Proteome by Mass Spectrometry
Boja ES, Hoodbhoy T, Garfield M, Fales HM
Biochemistry (2005) 44(50): 16445-16460

Glycomic survey mapping of zebrafish identifies unique sialylation pattern
Guerardel Y, Chang LY, Maes E, Huang CJ, Khoo KH
Glycobiology Early Edition: published 29-Nov-2005

Global analysis of protein phosphorylation in yeast
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M
Nature (2005) 438(7068): 679-84

Quantitative Phosphoproteomic Analysis of the Tumor Necrosis Factor Pathway
Greg T. Cantin, John D. Venable, Daniel Cociorva, and John R. Yates, III
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/09/2005

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Protein-protein interaction

Prediction of protein-protein interactions using random decision forest framework
Xue-Wen Chen and Mei Liu
Bioinformatics (2005) 21(24): 4394-4400

Combining chemical genetics and proteomics to identify protein kinase substrates
Noah Dephoure, Russell W. Howson, Justin D. Blethrow, Kevan M. Shokat, and Erin K. O'Shea
PNAS (2005) 102(50): 17940-17945 Open Access

Proteomics uncovers proteins interacting electrostatically with thioredoxin in chloroplasts
Balmer Y, Koller A, Val GD, Schurmann P, Buchanan BB
Photosynth Res (2004) 79(3): 275-80

Comparative proteomic analysis of nucleic acid-binding proteins in ten human tumor cell lines
Afjehi-Sadat L, Engidawork E, Slavc I, Lubec G
Int J Oncol (2006) 28(1): 173-90

Effect of Protein Backbone Folding on the Stability of Protein-Ligand Complexes
Ernesto Estrada, Eugenio Uriarte, and Santiago Vilar
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Phosphate Stabilization of Intermolecular Interactions
Shelley N. Jackson, Hay-Yan J. Wang, Alfred Yergey, and Amina S. Woods
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular Dynamics and Molecular Field Analysis
Tingjun Hou, William McLaughlin, Benzhuo Lu, Ken Chen, and Wei Wang
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Proteomic analysis of beta 1-adrenergic receptor interactions with PDZ scaffold proteins
He J, Bellini M, Inuzuka H, Xu J, Xiong Y, Yang X, Castleberry AM, Hall RA
J Biol Chem Early Edition: published 29-Nov-2005

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Quantitation

Cell Surface Labeling and Mass Spectrometry Reveal Diversity of Cell Surface Markers and Signaling Molecules Expressed in Undifferentiated Mouse Embryonic Stem Cells
Kazuto Nunomura, Kohji Nagano, Chiharu Itagaki, Masato Taoka, Nobuko Okamura, Yoshio Yamauchi, Sumio Sugano, Nobuhiro Takahashi, Tomonori Izumi, and Toshiaki Isobe
Mol Cell Proteomics (2005) 4(12): 1968-1976

High Throughput Quantitative Glycomics and Glycoform-focused Proteomics of Murine Dermis and Epidermis
Rie Uematsu, Jun-ichi Furukawa, Hiroaki Nakagawa, Yasuro Shinohara, Kisaburo Deguchi, Kenji Monde, and Shin-Ichiro Nishimura
Mol Cell Proteomics (2005) 4(12): 1977-1989

Quantifying Peptide Signal in MALDI-TOF Mass Spectrometry Data
Timothy W. Randolph, Bree L. Mitchell, Dale F. McLerran, Paul D. Lampe, and Ziding Feng
Mol Cell Proteomics (2005) 4(12): 1990-1999

In-Gel Stable-Isotope Labeling (ISIL): A Strategy for Mass Spectrometry-Based Relative Quantification
John M. Asara, Xiang Zhang, Bin Zheng, Heather H. Christofk, Ning Wu, and Lewis C. Cantley
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Ultra-Sensitive Immunoassays Using Multi-Photon-Detection in Diagnostic Proteomics of Blood
Andrzej K. Drukier, Natascha Ossetrova, Elena Schors, Larry R. Brown, John Tomaszewski, Richard Sainsbury, and Jasminka Godovac-Zimmermann
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2375-2378

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Review

Advances, Challenges, and Limitations in Serum-Proteome-Based Cancer Diagnosis
Matthias P. A. Ebert, Murray Korc, Peter Malfertheiner, and Christoph Röcken
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/09/2005

Human Liver Proteome Project: Plan, Progress, and Perspectives
Fuchu He
Mol Cell Proteomics (2005) 4(12): 1841-1848

Bioinformatics and Proteomics Approaches for Aging Research
Raghothama C, Harsha HC, Prasad CK, Pandey A
Biogerontology (2005) 6(4): 227-232

Challenges in the Overall Analysis of Microbial Proteomes
Alexander Scherl, Jean-Charles Sanchez, Denis F. Hochstrasser
Complexus (2005) 2(2): 79-86

Cell wall proteins: a new insight through proteomics
Jamet E, Canut H, Boudart G, Pont-Lezica RF
Trends Plant Sci Early Edition: published 11-Dec-2005

SELDI-TOF proteomic analysis and cancer detection
Henderson NA, Steele RJ
Surgeon (2005) 3(6): 422

Platelet genomics and proteomics in human health and disease
Macaulay IC, Carr P, Gusnanto A, Ouwehand WH, Fitzgerald D, Watkins NA
J Clin Invest (2005) 115(12): 3370-3377

Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy
Caprioli RM
Cancer Res (2005) 65(23): 10642-5

Pharmacogenomics and cardiovascular drugs: Need for integrated biological system with phenotypes and proteomic markers
Siest G, Marteau JB, Maumus S, Berrahmoune H, Jeannesson E, Samara A, Batt AM, Visvikis-Siest S
Eur J Pharmacol Early Edition: published 25-Nov-2005

Proteomics and diabetic nephropathy
Merchant ML, Klein JB
Curr Diab Rep (2005) 5(6): 464-9

Genetics and proteomics of pituitary tumors
Asa SL, Ezzat S
Endocrine (2005) 28(1): 43-8

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Methodology

High-Throughput Identification of In-Gel Digested Proteins by Rapid, Isocratic HPLC/MS/MS
Yue Chen, Sung Chan Kim, and Yingming Zhao
ANALYTICAL CHEMISTRY (2005) 77(24): 8179-8184

Fluorescent Proteins as Proteomic Probes
Ileana M. Cristea, Rosemary Williams, Brian T. Chait, and Michael P. Rout
Mol Cell Proteomics (2005) 4(12): 1933-1941

Tube-Gel Digestion: A Novel Proteomic Approach for High Throughput Analysis of Membrane Proteins
Xiaoning Lu and Haining Zhu
Mol Cell Proteomics (2005) 4(12): 1948-1958

Exploring the Hidden Human Urinary Proteome via Ligand Library Beads
Annalisa Castagna, Daniela Cecconi, Lau Sennels, Juri Rappsilber, Luc Guerrier, Frederic Fortis, Egisto Boschetti, Lee Lomas, and Pier Giorgio Righetti
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 1917-1930

Comparative Study of [Three] LC-MALDI Workflows for the Analysis of Complex Proteomic Samples
Stephen J. Hattan, Jason Marchese, Nikita Khainovski, Steve Martin, and Peter Juhasz
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 1931-1941

Improving Solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 Proteins Expressed into Esherichia coli
Irina Kataeva, Jessie Chang, Hao Xu, Chi-Hao Luan, Jizhong Zhou, Vladimir N. Uversky, Dawei Lin, Peter Horanyi, Z. J. Liu, Lars G. Ljungdahl, John Rose, Ming Luo, and Bi-Cheng Wang
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 1942-1951

Compositional Characterization of the Cytoskeleton of NK-Like Cells
Xiaobo Meng and John A. Wilkins
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2081-2087

Differential Dimethyl Labeling of N-Termini of Peptides after Guanidination for Proteome Analysis
Chengjie Ji, Nan Guo, and Liang Li
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2099-2108

Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap
Jesper V. Olsen, Lyris M. F. de Godoy, Guoqing Li, Boris Macek, Peter Mortensen, Reinhold Pesch, Alexander Makarov, Oliver Lange, Stevan Horning, and Matthias Mann
Mol Cell Proteomics (2005) 4(12): 2010-2021

Method for Qualitative Comparisons of Protein Mixtures Based on Enzyme-Catalyzed Stable-Isotope Incorporation
Ekaterina Mirgorodskaya, Erich Wanker, Albrecht Otto, Hans Lehrach, and Johan Gobom
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2109-2116

Differential Radioactive Proteomic Analysis of Microdissected Renal Cell Carcinoma Tissue by 54 cm Isoelectric Focusing in Serial Immobilized pH Gradient Gels
Slobodan Poznanovi , Wojciech Wozny, Gerhard P. Schwall, Chaturvedula Sastri, Christian Hunzinger, Werner Stegmann, André Schrattenholz, Alexander Buchner, Rainer Gangnus, Renate Burgemeister, and Michael A. Cahill
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2117-2125

Solution Isoelectric Focusing for Peptide Analysis: Comparative Investigation of an Insoluble Nuclear Protein Fraction
Yanming An, Zongming Fu, Peter Gutierrez, and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2126-2132

Strategy for Allosteric Analysis Based on Protein-Patterned Stationary Phase in Microfluidic Chip
Hongyan Bi, Xuexiang Weng, Haiyun Qu, Jilie Kong, Pengyuan Yang, and Baohong Liu
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2154-2160

Perturbation and Interpretation of Nitrogen Isotope Distribution Patterns in Proteomics
Ambrosius P. L. Snijders, Bart de Koning, and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2185-2191

Mass Spectrometric Peptide Fingerprinting of Proteins after Western Blotting on Polyvinylidene Fluoride and Enhanced Chemiluminescence Detection
Ruth Menque Methogo, Geneviève Dufresne-Martin, Patrice Leclerc, Richard Leduc, and Klaus Klarskov
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2216-2224

A Method for the Rapid and Efficient Elution of Native Affinity-Purified Protein A Tagged Complexes
Caterina Strambio-de-Castillia, Jaclyn Tetenbaum-Novatt, Brian S. Imai, Brian T. Chait, and Michael P. Rout
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2250-2256

Isoelectric Point-Based Prefractionation of Proteins from Crude Biological Samples Prior to Two-Dimensional Gel Electrophoresis
Ziad J. Sahab, Yewseok Suh, and Qing-Xiang Amy Sang
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2266-2272

Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides
Manfred Heller, Mingliang Ye, Philippe E. Michel, Patrick Morier, Daniel Stalder, Martin A. Jünger, Ruedi Aebersold, Frédéric Reymond, and Joël S. Rossier
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2273-2282

Prefractionation of Cerebrospinal Fluid to Enhance Glycoprotein Concentration Prior to Structural Determination with FT-ICR Mass Spectrometry
Carina Sihlbom, Pia Davidsson, and Carol L Nilsson
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2294-2301

Proteome Analysis of Isolated Perfused Organ Effluent as a Novel Model for Protein Biomarker Discovery
John M. Koomen, Christopher R. Wilson, Patrick Guthrie, Matthew J. Androlewicz, Ryuji Kobayashi, and Heinrich Taegtmeyer
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

A Proteomics Approach to Identify Long-Term Molecular Changes in Rat Medial Prefrontal Cortex Resulting from Sucrose Self-Administration
Michel C. Van den Oever, Sabine Spijker, Ka Wan Li, Connie R. Jiménez, Eisuke Koya, Roel C. Van der Schors, Yvonne Gouwenberg, Rob Binnekade, Taco J. De Vries, Anton N. M. Schoffelmeer, and August B. Smit
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Derivatized Cellulose Combined with MALDI-TOF MS: A New Tool for Serum Protein Profiling
Isabel Feuerstein, Matthias Rainer, Katussevani Bernardo, Günther Stecher, Christian W. Huck, Kurt Kofler, Alexandre Pelzer, Wolfgang Horninger, Helmut Klocker, Georg Bartsch, and Günther K. Bonn
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2320-2326

One-Pot Glyco-Affinity Precipitation Purification for Enhanced Proteomics: The Flexible Alignment of Solution-Phase Capture/Release and Solid-Phase Separation
Xue-Long Sun, Carolyn A. Haller , XiaoYi Wu , Vincent P. Conticello, and Elliot L. Chaikof
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2355-2359

Study of the Fragmentation Patterns of the Phosphate-Arginine Noncovalent Bond
Shelley N. Jackson, Hay-Yan J. Wang, and Amina S. Woods
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2360-2363

Serial Isoelectric Focusing as an Effective and Economic Way to Obtain Maximal Resolution and High-Throughput in 2D-Based Comparative Proteomics of Scarce Samples: Proof-of-Principle
Murtada H. Farhoud^,, Hans J. C. T. Wessels, Ron A. Wevers, Baziel G. van Engelen, Lambert P. van den Heuvel, and Jan A. Smeitink
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2364-2368

Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method
Haixing Wang, Wei-Jun Qian, Heather M. Mottaz, Therese R. W. Clauss, David J. Anderson, Ronald J. Moore, David G. Camp, II, Arshad H. Khan, Daniel M. Sforza, Maria Pallavicini, Desmond J. Smith, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2397-2403

Efficient Method for the Proteomic Analysis of Fixed and Embedded Tissues
Darryl Erik Palmer-Toy, Bryan Krastins, David A. Sarracino, Joseph B. Nadol, Jr., and Saumil N. Merchant
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2404-2411

A Double-Vented Tetraphasic Continuous Column Approach to MuDPIT Analysis on Long Capillary Columns Demonstrates Superior Proteomic Coverage
Andrew W. Guzzetta and Allis S. Chien
JOURNAL OF PROTEOME RESEARCH (2005) 4(6): 2412-2419

Counting the Zinc-Proteins Encoded in the Human Genome
Claudia Andreini , Lucia Banci , Ivano Bertini , and Antonio Rosato
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/16/2005

Multiplex multidimensional nanoLC-MS system for targeted proteomic analyses
Bonneil E, Tessier S, Carrier A, Thibault P
Electrophoresis (2005) 26(24): 4575-4589

An Open Design Microfabricated Nib-Like Nanoelectrospray Emitter Tip on a Conducting Silicon Substrate for the Application of the Ionization Voltage
Le Gac S, Arscott S, Rolando C
J Am Soc Mass Spectrom Early Edition: published 9-Dec-2005

Peptide mass fingerprinting: protein identification using MALDI-TOF mass spectrometry
Webster J, Oxley D
Methods Mol Biol (2005) 310: 227-40

Fabrication of protein function microarrays for systems-oriented proteomic analysis
Blackburn JM, Hart DJ
Methods Mol Biol (2005) 310: 197-216

High-throughput purification of hexahistidine-tagged proteins expressed in E. coli
Murphy MB, Doyle SA
Methods Mol Biol (2005) 310: 123-30

Screening for the expression of soluble recombinant protein in Escherichia coli
Doyle SA
Methods Mol Biol (2005) 310: 115-21

Purification of mitotic spindles from cultured human cells
Sillje HH, Nigg EA
Methods Early Edition: published 9-Dec-2005

Protein Function Microarrays Based on Self-Immobilizing and Self-Labeling Fusion Proteins
Sielaff I, Arnold A, Godin G, Tugulu S, Klok HA, Johnsson K
Chembiochem Early Edition: published 12-Dec-2005

Herpesviral Protein Networks and Their Interaction with the Human Proteome
Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala S, Roupelieva M, Rose D, Fossum E, Haas J
Science Early Edition: published 8-Dec-2005

Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: crystallography, activity profiling, and protease identification
Galardy P, Ploegh HL, Ovaa H
Methods Enzymol (2005) 399: 120-31

Enhanced Characterization of Complex Proteomic Samples Using LC-MALDI MS/MS: Exclusion of Redundant Peptides from MS/MS Analysis in Replicate Runs
Chen HS, Rejtar T, Andreev V, Moskovets E, Karger BL
Anal Chem (2005) 77(23): 7816-25

Making Broad Proteome Protein Measurements in 1-5 min Using High-Speed RPLC Separations and High-Accuracy Mass Measurements
Shen Y, Strittmatter EF, Zhang R, Metz TO, Moore RJ, Li F, Udseth HR, Smith RD, Unger KK, Kumar D, Lubda D
Anal Chem (2005) 77(23): 7763-73

Enrichment and Identification of Cysteine-Containing Peptides from Tryptic Digests of Performic Oxidized Proteins by Strong Cation Exchange LC and MALDI-TOF/TOF MS
Dai J, Wang J, Zhang Y, Lu Z, Yang B, Li X, Cai Y, Qian X
Anal Chem (2005) 77(23): 7594-604

Large-scale muLC-MS/MS for silver- and Coomassie blue-stained polyacrylamide gels
Zhu W, Venable J, Giometti CS, Khare T, Tollaksen S, Ahrendt AJ, Yates JR 3rd
Electrophoresis (2005) 26(23): 4495-4507

Separation of human serum proteins using the Beckman-Coulter PF2Dtrade mark system: analysis of ion exchange-based first dimension chromatography
Levreri I, Musante L, Petretto A, Bruschi M, Candiano G, Melioli G
Clin Chem Lab Med (2005) 43(12): 1327-33

Integration of Multidimensional Chromatographic Protein Separations with a Combined "Top-Down" and "Bottom-Up" Proteomic Strategy
Kevin M. Millea, Ira S. Krull, Steven A. Cohen, John C. Gebler, and Scott J. Berger
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/09/2005

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Books

Proteomics: Biomedical and Pharmaceutical Applications | Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology
Jeffrey C. Smith, Daniel Figeys, Ettore Appella
J Proteome Res (2005) 4(6): 1905

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Meeting

Meeting News: Human Protein Atlas unveiled | Proteomics repositories will exchange data
Katie Cottingham
J Proteome Res (2005) 4(6): 1902

Defining the proteome
J�rg Bernhardt
Genome Biology (2005) 6(12): 360

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Other

Calendar
Mol Cell Proteomics (2005) 4(12): 2022-2023

The "impact factor" revisited
Dong P, Loh M, Mondry A
Biomedical Digital Libraries (2005) 2: 7

Government & Society: Proteomics gets out of a fix | PSI creates MIAPE: Gel Electrophoresis
Linda Sage, Katie Cottingham
J Proteome Res (2005) 4(6): 1903-1904

Defining the proteome
Bernhardt J
Genome Biol (2005) 6(12): 360

Epidemiology informing clinical practice: from bills of mortality to population laboratories
Potter JD
Nat Clin Pract Oncol (2005) 2(12): 625-34

Physiological proteomics: cells, organs, biological fluids, and biomarkers
Blake CA
Exp Biol Med (Maywood) (2005) 230(11): 785-6

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