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SPS' Digest

Issue 30, 09-May-2006

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Quick jumps to articles in: Bioinformatics (17) / Biological applications (82) / Biomedical and clinical applications (44) / Eukaryotic Cells And Tissues (16) / Prokaryotes (12) / Pharmacology and Toxicology (10) / Protein Array (4) / Protein Characterization - PTMs (10) / Protein-protein interaction (2) / Quantitation (5) / Review (12) / Methodology (43) / Books (1) / Meeting (1) / Other (13) /

In this issue, 269 articles have been selected from:
Disclaimer: The selection and categorisation reflect the views and understandings of contributors (i.e. SPS members).

Quick jumps to articles in: Bioinformatics (17) / Biological applications (82) / Biomedical and clinical applications (44) / Eukaryotic Cells And Tissues (16) / Prokaryotes (12) / Pharmacology and Toxicology (10) / Protein Array (4) / Protein Characterization - PTMs (10) / Protein-protein interaction (2) / Quantitation (5) / Review (12) / Methodology (43) / Books (1) / Meeting (1) / Other (13) /

Bioinformatics

Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data
Zhang X, Lu X, Shi Q, Xu XQ, Leung HC, Harris LN, Iglehart JD, Miron A, Liu JS, Wong WH
BMC Bioinformatics (2006) 7(1): 197

GARBAN II: An integrative framework for extracting biological information from proteomic and genomic data
Victoriano Segura, Adam Podhorski, Elizabeth Guruceaga, José L. Sevilla, Fernando J. Corrales, Angel Rubio
PROTEOMICS (2006) 6(S1): S12-S15

Selection and combination of machine learning classifiers for prediction of linear B-cell epitopes on proteins
Sollner J
J Mol Recognit Early Edition: published 7-Apr-2006

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data
Zhang Z, Sun S, Zhu X, Chang S, Liu X, Yu C, Bu D, Chen R
BMC Bioinformatics (2006) 7(1): 222

Mass Analysis Peptide Sequence Prediction (MAPSP)
Martin Eisenacher, Jurgen de Braaf, and Simone Konig
Bioinformatics (2006) 22(8): 1002-1003

AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
Major SM, Nishizuka S, Morita D, Rowland R, Sunshine M, Shankavaram U, Washburn F, Asin D, Kouros-Mehr H, Kane D, Weinstein JN
BMC Bioinformatics (2006) 7(1): 192

Integration of Two-Dimensional LC-MS with Multivariate Statistics for Comparative Analysis of Proteomic Samples
Gaspari M, Verhoeckx KC, Verheij ER, van der Greef J
Anal Chem (2006) 78(7): 2286-96

The Web as an educational tool for/in learning/teaching bioinformatics statistics
Oliver J, Pisano ME, Alonso T, Roca P
Med Inform Internet Med (2005) 30(4): 255-66

Structural Bioinformatics. By Philip E. Bourne and Helge Weissig (Eds.)
Lorenza Bordoli, Torsten Schwede
PROTEOMICS (2006) 6(8): 2626-2627

Enhanced Peptide Mass Fingerprinting through High Mass Accuracy: Exclusion of Non-Peptide Signals Based on Residual Mass
Eric D. Dodds, Hyun Joo An, Paul J. Hagerman, and Carlito B. Lebrilla
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/21/2006

An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints
Lee TY, Horng JT, Juan HF, Huang HD, Wu LC, Tsai MF, Huang HC
J Comput Chem (2006) 27(9): 1020-1032

A protein database constructed from low-coverage genomic sequence of Bacillus megaterium and its use for accelerated proteomic analysis
Sun J, Wang W, Hundertmark C, Zeng AP, Jahn D, Deckwer WD
J Biotechnol Early Edition: published 24-Mar-2006

Diffusion kernel-based logistic regression models for protein function prediction
Lee H, Tu Z, Deng M, Sun F, Chen T
OMICS (2006) 10(1): 40-55

Composition-Modified Matrices Improve Identification of Homologs of Saccharomyces cerevisiae Low-Complexity Glycoproteins
Coronado JE, Attie O, Epstein SL, Qiu WG, Lipke PN
Eukaryot Cell (2006) 5(4): 628-37

Prima: Peptide robust identification from ms/ms spectra
Liu J, Ma B, Li M
J Bioinform Comput Biol (2006) 4(1): 125-38

ModifiComb, a New Proteomic Tool for Mapping Substoichiometric Post-translational Modifications, Finding Novel Types of Modifications, and Fingerprinting Complex Protein Mixtures
Mikhail M. Savitski, Michael L. Nielsen, and Roman A. Zubarev
Mol Cell Proteomics (2006) 5(5): 935-948

Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations
Wu X, Zhu L, Guo J, Zhang DY, Lin K
Nucl Acids Res (2006) 34(7): 2137-50

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Biological applications

A proteomic approach to the identification of new tPA receptors in pancreatic cancer cells
Oriol Roda, Cristina Chiva, Gemma Espuña, Hans-J. Gabius, Francisco X. Real, Pilar Navarro, David Andreu
PROTEOMICS (2006) 6(S1): S36-S41

Application of Capture-Recapture Models to Estimation of Protein Count in MudPIT Experiments
Koziol JA, Feng AC, Schnitzer JE
Anal Chem (2006) 78(9): 3203-7

Proteomic analysis of differential protein expression in early process of pancreatic regeneration in pancreatectomized rats
Yang M, Liu W, Wang CY, Liu T, Zhou F, Tao J, Wang Y, Li MT
Acta Pharmacol Sin (2006) 27(5): 568-78

Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view
Mireille Chevallet, Pierre Lescuyer, Hélène Diemer, Alain van Dorsselaer, Emmanuelle Leize-Wagner, Thierry Rabilloud
ELECTROPHORESIS (2006) 27(8): 1574-1583

Environmental proteomics and metallomics
Juan López-Barea, José Luis Gómez-Ariza
PROTEOMICS (2006) 6(S1): S51-S62

Spatial learning induces predominant downregulation of cytosolic proteins in the rat hippocampus
Henninger N, Feldmann RE Jr, Futterer CD, Schrempp C, Maurer MH, Waschke KF, Kuschinsky W, Schwab S
Genes Brain Behav Early Edition: published 27-Apr-2006

Immune-mediated beta-cell destruction in vitro and in vivo-A pivotal role for galectin-3
Karlsen AE, Storling ZM, Sparre T, Larsen MR, Mahmood A, Storling J, Roepstorff P, Wrzesinski K, Larsen PM, Fey S, Nielsen K, Heding P, Ricordi C, Johannesen J, Kristiansen OP, Christensen UB, Kockum I, Luthman H, Nerup J, Pociot F
Biochem Biophys Res Commun Early Edition: published 29-Mar-2006

Identification of proteins cleaved downstream of caspase activation in monocytes undergoing macrophage differentiation
Cathelin S, Rebe C, Haddaoui L, Simioni N, Verdier F, Fontenay M, Launay S, Mayeux P, Solary E
J Biol Chem Early Edition: published 24-Apr-2006

Proteomic analysis of the tegument and excretory-secretory products of adult Schistosoma bovis worms
Ricardo Pérez-Sánchez, Alicia Ramajo-Hernández, Vicente Ramajo-Martín, Ana Oleaga
PROTEOMICS (2006) 6(S1): S226-S236

Serum protein pattern during cow pregnancy: Acute-phase proteins increase in the peripartum period
Fausto Cairoli, Massimiliano Battocchio, Maria Cristina Veronesi, Daniela Brambilla, Francesca Conserva, Ivano Eberini, Robin Wait, Elisabetta Gianazza
ELECTROPHORESIS (2006) 27(8): 1617-1625

Physical and Genetic Interactions Link Hox Function with Diverse Transcription Factors and Cell Signaling Proteins
Sarah E. Bondos, Xin-Xing Tan, and Kathleen S. Matthews
Mol Cell Proteomics (2006) 5(5): 824-834

Comparative proteomic analysis to study molecular events during gonad development in mice
Wilhelm D, Huang E, Svingen T, Stanfield S, Dinnis D, Koopman P
Genesis (2006) 44(4): 168-176

Two-dimensional electrophoresis study of in vitro pellicle formation and dental caries susceptibility
Vitorino R, de Morais Guedes S, Ferreira R, Lobo MJ, Duarte J, Ferrer-Correia AJ, Tomer KB, Domingues PM, Amado FM
Eur J Oral Sci (2006) 114(2): 147-53

Proteotyping of human haptoglobin by MALDI-TOF profiling: Phenotype distribution in a population of toxic oil syndrome patients
Carlos Rodriguez, Carmen Quero, Ana Dominguez, Miguel Trigo, Manuel Posada de la Paz, Emilio Gelpi, Joaquin Abian
PROTEOMICS (2006) 6(S1): S272-S281

Proteome analysis of silk gland proteins from the silkworm, Bombyx mori
Pingbo Zhang, Yoichi Aso, Kohji Yamamoto, Yutaka Banno, Yongqiang Wang, Kozo Tsuchida, Yutaka Kawaguchi, Hiroshi Fujii
PROTEOMICS (2006) 6(8): 2586-2599

Plasmodium post-genomics: better the bug you know?
Kooij TW, Janse CJ, Waters AP
Nat Rev Microbiol Early Edition: published 3-Apr-2006

Proteome of amyloplasts isolated from developing wheat endosperm presents evidence of broad metabolic capability
Balmer Y, Vensel WH, Dupont FM, Buchanan BB, Hurkman WJ
J Exp Bot Early Edition: published 4-Apr-2006

High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of cytoplasmatic protein complexes from Chlorobium tepidum
Aivaliotis M, Karas M, Tsiotis G
Photosynth Res Early Edition: published 19-Apr-2006

DNA Microarray and Proteomic Analyses of the RpoS Regulon in Geobacter sulfurreducens
Nunez C, Esteve-Nunez A, Giometti C, Tollaksen S, Khare T, Lin W, Lovley DR, Methe BA
J Bacteriol (2006) 188(8): 2792-800

Identification of Novel Proteases and Immunomodulators in the Secretions of Schistosome Cercariae That Facilitate Host Entry
Rachel S. Curwen, Peter D. Ashton, Shobana Sundaralingam, and R. Alan Wilson
Mol Cell Proteomics (2006) 5(5): 835-844

Protective effect of D609 against amyloid-beta(1-42)-induced oxidative modification of neuronal proteins: Redox proteomics study
Sultana R, Newman SF, Abdul HM, Cai J, Pierce WM, Klein JB, Merchant M, Butterfield DA
J Neurosci Res Early Edition: published 21-Apr-2006

Characterization of the microtubule proteome during post-diapause development of Artemia franciscana
O'connell PA, Pinto DM, Chisholm KA, Macrae TH
Biochim Biophys Acta Early Edition: published 5-Apr-2006

Salivary diagnostics powered by nanotechnologies, proteomics and genomics
Wong DT
J Am Dent Assoc (2006) 137(3): 313-21

Proteomic profiling of metalloprotease activities with cocktails of active-site probes
Sieber SA, Niessen S, Hoover HS, Cravatt BF
Nat Chem Biol Early Edition: published 26-Mar-2006

Psychrophilic microorganisms: challenges for life
D'Amico S, Collins T, Marx JC, Feller G, Gerday C
EMBO Rep (2006) 7(4): 385-9

Comparative proteomic analysis reveals a function of the novel death receptor-associated protein BRE in the regulation of prohibitin and p53 expression and proliferation
Mei Kuen Tang, Chun Mei Wang, Sze Wan Shan, Yiu Loon Chui, Arthur Kar Keung Ching, Pak Ham Chow, Lars Grotewold, John Yeuk Hon Chan , Kenneth Ka Ho Lee
PROTEOMICS (2006) 6(8): 2376-2385

Oxidation-reduction respiratory chains and ATP synthase complex are localized in detergent-resistant lipid rafts
Ki-Bum Kim, Joong-Won Lee, Chang Seok Lee, Bong-Woo Kim, Hyo-Jung Choo, Soon-Young Jung, Sung-Gil Chi, Young-Sil Yoon, Gyesoon Yoon, Young-Gyu Ko
PROTEOMICS (2006) 6(8): 2444-2453

A Proteomic Approach Towards the Analysis of Salt Tolerance in Rhizobium etli and Sinorhizobium meliloti Strains
Shamseldin A, Nyalwidhe J, Werner D
Curr Microbiol (2006) 52(5): 333-9

Proteomic analysis of acidic chaperones, and stress proteins in extreme halophile Halobacterium NRC-1: A comparative proteomic approach to study heat shock response
Shukla HD
Proteome Sci (2006) 4(1): 6

Proteome Analysis of an Aerobic Hyperthermophilic Crenarchaeon, Aeropyrum pernix K1
Syuji Yamazaki, Jun Yamazaki, Keiko Nishijima, Rie Otsuka, Miyako Mise, Hanako Ishikawa, Kazumi Sasaki, Shin-ichi Tago, and Katsumi Isono
Mol Cell Proteomics (2006) 5(5): 811-823

Identification of regulators of germ layer morphogenesis using proteomics in zebrafish
Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg CP
J Cell Sci Early Edition: published 25-Apr-2006

Proteolysis and Toxoplasma invasion
Carruthers VB
Int J Parasitol Early Edition: published 13-Mar-2006

Proteomic analysis of detergent-resistant membranes from Candida albicans
María Insenser, César Nombela, Gloria Molero, Concha Gil
PROTEOMICS (2006) 6(S1): S74-S81

An ecotoxicoproteomic approach (SELDI-TOF mass spectrometry) to biomarker discovery in crab exposed to pollutants under laboratory conditions
Gomiero A, Pampanin DM, Bjornstad A, Larsen BK, Provan F, Lyng E, Andersen OK
Aquat Toxicol Early Edition: published 21-Apr-2006

Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology
Amme S, Matros A, Schlesier B, Mock HP
J Exp Bot Early Edition: published 30-Mar-2006

Proteomic analysis of p38? mitogen-activated protein kinase-regulated changes in membrane fractions of RAS-transformed fibroblasts
Patricia Alfonso, Ignacio Dolado, Aneta Swat, Antonio Núñez, Ana Cuadrado, Angel R. Nebreda, J. Ignacio Casal
PROTEOMICS (2006) 6(S1): S262-S271

Proteomic Profiling of ClpXP Substrates after DNA Damage Reveals Extensive Instability within SOS Regulon
Neher SB, Villen J, Oakes EC, Bakalarski CE, Sauer RT, Gygi SP, Baker TA
Mol Cell (2006) 22(2): 193-204

Proteomic analysis of a fraction enriched in cell envelope proteins of Acinetobacter baumannii
Sara Martí, Javier Sánchez-Céspedes, Eliandre Oliveira, David Bellido, Ernest Giralt, Jordi Vila
PROTEOMICS (2006) 6(S1): S82-S87

Mitochondrial UCPs: New insights into regulation and impact
Sluse FE, Jarmuszkiewicz W, Navet R, Douette P, Mathy G, Sluse-Goffart CM
Biochim Biophys Acta Early Edition: published 6-Mar-2006

A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression
Liu HC, Soderblom EJ, Goshe MB
J Virol Methods Early Edition: published 22-Mar-2006

The heat shock response of Synechocystis sp. PCC 6803 analysed by transcriptomics and proteomics
Suzuki I, Simon WJ, Slabas AR
J Exp Bot Early Edition: published 30-Mar-2006

Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome
Collins MO, Husi H, Yu L, Brandon JM, Anderson CN, Blackstock WP, Choudhary JS, Grant SG
J Neurochem (2006) 97(Suppl 1): 16-23

Regulation of the cadmium stress response through SCF-like ubiquitin ligases: comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammalian cells
Baudouin-Cornu P, Labarre J
Biochimie Early Edition: published 23-Mar-2006

The dopamine transporter proteome
Torres GE
J Neurochem (2006) 97(Suppl 1): 3-10

Screening for new metabolites from marine microorganisms
Schweder T, Lindequist U, Lalk M
Adv Biochem Eng Biotechnol (2005) 96: 1-48

Proteomic Profiling of Accessory Structures from the Mouse Sperm Flagellum
Wenlei Cao, George L. Gerton, and Stuart B. Moss
Mol Cell Proteomics (2006) 5(5): 801-810

Study of transaldolase deficiency in urine samples by capillary LC-MS/MS
György Vas, Karina Conkrite, Wendy Amidon, Yueming Qian, Katalin Bánki, András Perl
Journal of Mass Spectrometry (2006) 41(4): 463-469

Proteomic analysis of rat aorta during atherosclerosis induced by high cholesterol diet and injection of vitamin D3
Almofti MR, Huang Z, Yang P, Rui Y, Yang P
Clin Exp Pharmacol Physiol (2006) 33(4): 305-9

Differential Expression Profiling of the Hepatic Proteome in a Rat Model of Dioxin Resistance: CORRELATION WITH GENOMIC AND TRANSCRIPTOMIC ANALYSES
Roberta Pastorelli, Donatella Carpi, Roberta Campagna, Luisa Airoldi, Raimo Pohjanvirta, Matti Viluksela, Helen Hakansson, Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, and Roberto Fanelli
Mol Cell Proteomics (2006) 5(5): 882-894

Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D difference in-gel electrophoresis
Michael R. Eman, Elsa Regan-Klapisz, Martijn W. H. Pinkse, Inge M. Koop, Johan Haverkamp, Albert J. R. Heck, Arie J. Verkleij, Jan A. Post
ELECTROPHORESIS (2006) 27(8): 1669-1682

Glutamine regulates the expression of proteins with a potential health-promoting effect in human intestinal Caco-2 cells
Kaatje Lenaerts, Edwin Mariman, Freek Bouwman, Johan Renes
PROTEOMICS (2006) 6(8): 2454-2464

Identification and characterization of a novel bovine oocyte-specific secreted protein gene
Tremblay K, Vigneault C, McGraw S, Morin G, Sirard MA
Gene Early Edition: published 29-Mar-2006

Utility of proteomics to assess pollutant response of clams from the Doñana bank of Guadalquivir Estuary (SW Spain)
Antonio Romero-Ruiz, Montserrat Carrascal, José Alhama, José Luis Gómez-Ariza, Joaquín Abian, Juan López-Barea
PROTEOMICS (2006) 6(S1): S245-S255

OMICS-driven biomarker discovery in nutrition and health
Kussmann M, Raymond F, Affolter M
J Biotechnol Early Edition: published 3-Apr-2006

Genetic and proteomic evidences support the localization of yeast enolase in the cell surface
Elena López-Villar, Lucía Monteoliva, Martin R. Larsen, Emmanuelle Sachon, Mohammed Shabaz, Mercedes Pardo, Jesús Pla, Concha Gil, Peter Roepstorff , César Nombela
PROTEOMICS (2006) 6(S1): S107-S118

Host-pathogen systems biology
Forst CV
Drug Discov Today (2006) 11(5-6): 220-7

Proteomic analysis of quorum sensing in Rhizobium leguminosarum biovar viciae UPM791
Laura Cantero, José Manuel Palacios, Tomás Ruiz-Argüeso, Juan Imperial
PROTEOMICS (2006) 6(S1): S97-S106

Detection and Quantification of Protein Biomarkers from Fewer than 10 Cells
Saju Nettikadan, Korinna Radke, James Johnson, Juntao Xu, Michael Lynch, Curtis Mosher, and Eric Henderson
Mol Cell Proteomics (2006) 5(5): 895-901

Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
Gao W, Liu Y, Giometti CS, Tollaksen SL, Khare T, Wu L, Klingeman DM, Fields MW, Zhou J
BMC Genomics (2006) 7(1): 76

Comprehensive Identification of Phosphorylation Sites in Postsynaptic Density Preparations
Jonathan C. Trinidad, Christian G. Specht, Agnes Thalhammer, Ralf Schoepfer, and Alma L. Burlingame
Mol Cell Proteomics (2006) 5(5): 914-922

Conformational diversity of the Goodpasture antigen, the noncollagenous-1 domain of the ?3 chain of collagen IV
Juan J. Calvete, Fernando Revert, Mario Blanco, Javier Cervera, Céline Tárrega, Libia Sanz, Francisco Revert-Ros, Froilán Granero, Enrique Pérez-Payá, Billy G. Hudson, Juan Saus
PROTEOMICS (2006) 6(S1): S237-S244

A Phosphatase Holoenzyme Comprised of Shoc2/Sur8 and the Catalytic Subunit of PP1 Functions as an M-Ras Effector to Modulate Raf Activity
Rodriguez-Viciana P, Oses-Prieto J, Burlingame A, Fried M, McCormick F
Mol Cell (2006) 22(2): 217-30

Characterization of Storage Proteins in Wild (Glycine soja) and Cultivated (Glycine max) Soybean Seeds Using Proteomic Analysis
Natarajan SS, Xu C, Bae H, Caperna TJ, Garrett WM
J Agric Food Chem (2006) 54(8): 3114-3120

Predicting the subcellular localization of viral proteins within a mammalian host cell
Scott MS, Oomen R, Thomas DY, Hallett MT
Virol J (2006) 3(1): 24

Gamma-secretase-dependent proteolysis of CD44 promotes neoplastic transformation of rat fibroblastic cells
Pelletier L, Guillaumot P, Freche B, Luquain C, Christiansen D, Brugiere S, Garin J, Manie SN
Cancer Res (2006) 66(7): 3681-7

Protein expression in a transformed trabecular meshwork cell line: proteome analysis
Steely HT, Dillow GW, Bian L, Grundstad J, Braun TA, Casavant TL, McCartney MD, Clark AF
Mol Vis (2006) 12: 372-83.

Proteomic analysis of tobacco mosaic virus-infected tomato (Lycopersicon esculentum M.) fruits and detection of viral coat protein
Juan Casado-Vela, Susana Sellés, Roque Bru Martínez
PROTEOMICS (2006) 6(S1): S196-S206

Isolation and characterization of mitochondrial ribosomes and ribosomal subunits from Leishmania tarentolae
Maslov DA, Sharma MR, Butler E, Falick AM, Gingery M, Agrawal RK, Spremulli LL, Simpson L
Mol Biochem Parasitol Early Edition: published 24-Mar-2006

Proteome analysis of the sarcoplasmic fraction of pig semimembranosus muscle: implications on meat color development
Sayd T, Morzel M, Chambon C, Franck M, Figwer P, Larzul C, Le Roy P, Monin G, Cherel P, Laville E
J Agric Food Chem (2006) 54(7): 2732-7

Proteome analysis to study signal transduction of G protein-coupled receptors
Pluder F, Morl K, Beck-Sickinger AG
Pharmacol Ther Early Edition: published 24-Apr-2006

Proteome Changes after Metabolic Engineering to Enhance Aerobic Mineralization of cis-1,2-Dichloroethylene
Jintae Lee, Li Cao, Saw Yen Ow, Martin E. Barrios-Llerena, Wilfred Chen, Thomas K. Wood, and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/28/2006

Differential proteome profiles in E2F2-deficient T lymphocytes
Mikel Azkargorta, Jesus M. Arizmendi, Felix Elortza, Nere Alkorta, Ana M. Zubiaga, Asier Fullaondo
PROTEOMICS (2006) 6(S1): S42-S50

Protein responses in blue mussels (Mytilus edulis) exposed to organic pollutants: A combined CYP-antibody/proteomic approach
Jonsson H, Schiedek D, Grosvik BE, Goksoyr A
Aquat Toxicol Early Edition: published 5-Apr-2006

Quantitative Proteomics of the Archaeon Methanococcus maripaludis Validated by Microarray Analysis and Real Time PCR
Qiangwei Xia, Erik L. Hendrickson, Yi Zhang, Tiansong Wang, Fred Taub,Brian C. Moore, Iris Porat, William B. Whitman, Murray Hackett, and John A. Leigh
Mol Cell Proteomics (2006) 5(5): 868-881

Proteomic analysis of macrophages stimulated by lipopolysaccharide: Lipopolysaccharide inhibits the cleavage of nucleophosmin
Xiulian Zhang, Yasuhiro Kuramitsu, Masanori Fujimoto, Eiko Hayashi, Xiaoqin Yuan, Kazuyuki Nakamura
ELECTROPHORESIS (2006) 27(8): 1659-1668

Protein stability promotes evolvability
Jesse D. Bloom, Sy T. Labthavikul, Christopher R. Otey, and Frances H. Arnold
PNAS Early Edition: published 31 March 2006

Proteomic Approach to Identification of Proteins Reactive for Abasic Sites in DNA
Robert A. Rieger, Elena I. Zaika, Weiping Xie, Francis Johnson, ArthurP. Grollman, Charles R. Iden, and Dmitry O. Zharkov
Mol Cell Proteomics (2006) 5(5): 858-867

A proteomic approach for dissecting H-Ras signaling networks in NIH/3T3 mouse embryonic fibroblast cells
Jung Wook Park, Seyoon Kim, Young Yil Bahk
PROTEOMICS (2006) 6(8): 2433-2443

Identification of substrates of the extracellular protease ADAMTS1 by DIGE proteomic analysis
Francesc Canals, Nuria Colomé, Cristina Ferrer, María del Carmen Plaza-Calonge, Juan Carlos Rodríguez-Manzaneque
PROTEOMICS (2006) 6(S1): S28-S35

In-depth analysis of the membrane and cytosolic proteome of red blood cells
Pasini EM, Kirkegaard M, Mortensen P, Lutz HU, Thomas A, Mann M
Blood Early Edition: published 18-Apr-2006

The cryptome: a subset of the proteome, comprising cryptic peptides with distinct bioactivities
Autelitano DJ, Rajic A, Smith AI, Berndt MC, Ilag LL, Vadas M
Drug Discov Today (2006) 11(7-8): 306-14

Mapping of alkaline proteins in bovine skeletal muscle
Thibault Chaze, Julien Bouley, Christophe Chambon, Christiane Barboiron, Brigitte Picard
PROTEOMICS (2006) 6(8): 2571-2575

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Biomedical and clinical applications

Proteomic analysis of acute myeloid leukemia: Identification of potential early biomarkers and therapeutic targets
Chary López-Pedrera, José Manuel Villalba, Emilio Siendones, Nuria Barbarroja, Consuelo Gómez-Díaz, Antonio Rodríguez-Ariza, Paula Buendía, Antonio Torres, Francisco Velasco
PROTEOMICS (2006) 6(S1): S293-S299

Expanding the protein catalogue in the proteome reference map of human breast cancer cells
Ida Pucci-Minafra, Patrizia Cancemi, Simona Fontana, Luigi Minafra, Salvatore Feo, Michel Becchi, Anne-Marie Freyria, Salvatore Minafra
PROTEOMICS (2006) 6(8): 2609-2625

Hypoxia in breast cancer: role of blood flow, oxygen diffusion distances, and anemia in the development of oxygen depletion
Vaupel P, Mayer A, Briest S, Hockel M
Adv Exp Med Biol (2005) 566: 333-42

Cytokeratin-20 and seminal vesicle secretory protein VI as possible marker proteins in urinary bladder preneoplastic lesions induced by N-butyl-N-(4-hydroxybutyl) nitrosamine
Kim HJ, Sohng I, Hwang CH, Park JY
Int J Urol (2006) 13(2): 142-7

Altered protein profile in chronic myeloid leukemia chronic phase identified by a comparative proteomic study
Pizzatti L, Sa LA, de Souza JM, Bisch PM, Abdelhay E
Biochim Biophys Acta Early Edition: published 10-Mar-2006

Proteomic Analysis of Hemangioblastoma Cyst Fluid
Glasker S, Vortmeyer AO, Lonser RR, Lubensky IA, Okamoto H, Xia JB, Li J, Milne E, Kowalak JA, Oldfield EH, Zhuang Z
Cancer Biol Ther Early Edition: published 6-May-2006

Searching for markers of Creutzfeldt-Jakob disease in cerebrospinal fluid by two-dimensional mapping
Chiara Piubelli, Michele Fiorini, Gianluigi Zanusso, Alberto Milli, Elisa Fasoli, Salvatore Monaco, Pier Giorgio Righetti
PROTEOMICS (2006) 6(S1): S256-S261

Eye lens proteomics
Hoehenwarter W, Klose J, Jungblut PR
Amino Acids Early Edition: published 4-Apr-2006

Differential protein expression of murine macrophages upon interaction with Candida albicans
Laura Martínez-Solano, César Nombela, Gloria Molero, Concha Gil
PROTEOMICS (2006) 6(S1): S133-S144

Teaching molecular genetics: Chapter 3 - Proteomics in nephrology
Groenen PJ, van den Heuvel LP
Pediatr Nephrol Early Edition: published 30-Mar-2006

Analysis of porcine peripheral blood mononuclear cells proteome by 2-DE and MS: Analytical and biological variability in the protein expression level and protein identification
María Ramirez-Boo, Juan J. Garrido, Samuel Ogueta, Juan J. Calvete, Consuelo Gómez-Díaz, Ángela Moreno
PROTEOMICS (2006) 6(S1): S215-S225

Hcc-2, a novel mammalian ER thioredoxin that is differentially expressed in hepatocellular carcinoma
Nissom PM, Lo SL, Lo JC, Ong PF, Lim JW, Ou K, Liang RC, Seow TK, Chung MC
FEBS Lett Early Edition: published 20-Mar-2006

Glomerular podocytes contain neuron-like functional synaptic vesicles
Rastaldi MP, Armelloni S, Berra S, Calvaresi N, Corbelli A, Giardino LA, Li M, Wang GQ, Fornasieri A, Villa A, Heikkila E, Soliymani R, Boucherot A, Cohen CD, Kretzler M, Nitsche A, Ripamonti M, Malgaroli A, Pesaresi M, Forloni GL, Schlondorff D, Holthofer H, D'Amico G
FASEB J Early Edition: published 3-Apr-2006

A Systems Approach to Clinical Oncology: Focus on Breast Cancer
Abramovitz M, Leyland-Jones BR
Proteome Sci (2006) 4(1): 5

Biomarker discovery in breast cancer serum using 2-D differential gel electrophoresis/ MALDI-TOF/TOF and data validation by routine clinical assays
Hong-Lei Huang, Taras Stasyk, Sandra Morandell, Hans Dieplinger, Gerda Falkensammer, Andrea Griesmacher, Maurice Mogg, Martin Schreiber, Isabel Feuerstein, Christian W. Huck, Guenther Stecher, Guenther K. Bonn, Lukas A. Huber
ELECTROPHORESIS (2006) 27(8): 1641-1650

Immunomics: discovering new targets for vaccines and therapeutics
De Groot AS
Drug Discov Today (2006) 11(5-6): 203-9

Proteomic analysis of prodigiosin-induced apoptosis in a breast cancer mitoxantrone-resistant (MCF-7 MR) cell line
Monge M, Vilaseca M, Soto-Cerrato V, Montaner B, Giralt E, Perez-Tomas R
Invest New Drugs Early Edition: published 5-Apr-2006

Inner ear proteomics of mouse models for deafness, a discovery strategy
Zheng QY, Rozanas CR, Thalmann I, Chance MR, Alagramam KN
Brain Res Early Edition: published 4-Apr-2006

Breast cancer proteomics by laser capture microdissection, sample pooling, 54-cm IPG IEF, and differential iodine radioisotope detection
Neubauer H, Clare SE, Kurek R, Fehm T, Wallwiener D, Sotlar K, Nordheim A, Wozny W, Schwall GP, Poznanovic S, Sastri C, Hunzinger C, Stegmann W, Schrattenholz A, Cahill MA
Electrophoresis (2006) 27(9): 1840-1852

Neuroblastoma detection using serum proteomic profiling: a novel mining technique for cancer?
Sandoval JA, Dobrolecki LE, Huang J, Grosfeld JL, Hickey RJ, Malkas LH
J Pediatr Surg (2006) 41(4): 639-46

Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry
Engwegen JY, Gast MC, Schellens JH, Beijnen JH
Trends Pharmacol Sci Early Edition: published 3-Apr-2006

The heterogeneity of human mesenchymal stem cell preparations-Evidence from simultaneous analysis of proteomes and transcriptomes
Wagner W, Feldmann RE Jr, Seckinger A, Maurer MH, Wein F, Blake J, Krause U, Kalenka A, Burgers HF, Saffrich R, Wuchter P, Kuschinsky W, Ho AD
Exp Hematol (2006) 34(4): 536-48

Detection and identification of heat shock protein 10 as a biomarker in colorectal cancer by protein profiling
Christian Melle, Ralf Bogumil, Günther Ernst, Bettina Schimmel, Annett Bleul, Ferdinand von Eggeling
PROTEOMICS (2006) 6(8): 2600-2608

Proteomics-based analysis of a pair of glioma cell lines with different tumor forming characteristics
Zhou L, Wang Y, Zhang YT, Geng YP, Si LS, Wang YL
Neurosci Lett Early Edition: published 24-Mar-2006

Proteomic analysis of plasma from patients with systemic lupus erythematosus: Increased presence of haptoglobin ?2 polypeptide chains over the ?1 isoforms
Esther J. Pavón, Pilar Muñoz, Antonio Lario, Victoria Longobardo, Montserrat Carrascal, Joaquín Abián, Ana B. Martin, Salvador A. Arias, José-Luis Callejas-Rubio, Ricardo Sola, Francisco Navarro-Pelayo, Enrique Raya-Alvarez, Norberto Ortego-Centeno, Mercedes Zubiaur, Jaime Sancho
PROTEOMICS (2006) 6(S1): S282-S292

Rat brain proteome in morphine dependence
Bierczynska-Krzysik A, Bonar E, Drabik A, Noga M, Suder P, Dylag T, Dubin A, Kotlinska J, Silberring J
Neurochem Int Early Edition: published 30-Mar-2006

Present status of clinical proteomic analysis for the early detection and determination of therapeutic strategy in lung cancer
Hirano T, Kato H
Ann Thorac Cardiovasc Surg (2006) 12(1): 4-9

The C Terminus of Lens Aquaporin 0 Interacts with the Cytoskeletal Proteins Filensin and CP49
Rose KM, Gourdie RG, Prescott AR, Quinlan RA, Crouch RK, Schey KL
Invest Ophthalmol Vis Sci (2006) 47(4): 1562-70

Differential expression of proteins in kidney, eye, aorta, and serum of diabetic and non-diabetic rats
Cho WC, Yip TT, Chung WS, Leung AW, Cheng CH, Yue KK
J Cell Biochem Early Edition: published 5-Apr-2006

Profiling cancer stem cells using protein array technology
Nishizuka S
Eur J Cancer Early Edition: published 25-Apr-2006

Aberrant expression of cytoskeleton proteins in hippocampus from patients with mesial temporal lobe epilepsy
Yang JW, Czech T, Felizardo M, Baumgartner C, Lubec G
Amino Acids Early Edition: published 4-Apr-2006

Profiling of the Tetraspanin Web of Human Colon Cancer Cells
Francois Le Naour, Magali Andre, Celine Greco, Martine Billard, Bernard Sordat, Jean-Francois Emile, Francois Lanza, Claude Boucheix, and Eric Rubinstein
Mol Cell Proteomics (2006) 5(5): 845-857

Proteomic analysis of serum marker proteins in recipient mice with liver cirrhosis after bone marrow cell transplantation
Yuichiro Yokoyama, Shuji Terai, Tsuyoshi Ishikawa, Koji Aoyama, Yohei Urata, Yoshio Marumoto, Hiroshi Nishina, Kazuyuki Nakamura, Kiwamu Okita , Isao Sakaida
PROTEOMICS (2006) 6(8): 2564-2570

Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid
Guerreiro N, Gomez-Mancilla B, Charmont S
Proteome Sci (2006) 4(1): 7

Expression of peroxiredoxin and thioredoxin in human lung cancer and paired normal lung
Park JH, Kim YS, Lee HL, Shim JY, Lee KS, Oh YJ, Shin SS, Choi YH, Park KJ, Park RW, Hwang SC
Respirology (2006) 11(3): 269-75

Identification of anti-infective targets through comparative proteomics
Burchmore R
Expert Rev Anti Infect Ther (2006) 4(2): 163-5

Identification of differentially expressed, tumor-associated proteins in oral squamous cell carcinoma by proteomic analysis
Turhani D, Krapfenbauer K, Thurnher D, Langen H, Fountoulakis M
Electrophoresis (2006) 27(7): 1417-1423

The MALDI TOF Mass Spectrometric View of the Plasma Proteome and Peptidome
Hortin GL
Clin Chem Early Edition: published 27-Apr-2006

Profiling of membrane proteins from human macrophages: Comparison of two approaches
Marie-Christine Slomianny, Annabelle Dupont, Fatiha Bouanou, Olivia Beseme, Anne-Laure Guihot, Philippe Amouyel, Jean-Claude Michalski, Florence Pinet
PROTEOMICS (2006) 6(8): 2365-2375

Urinary protein expression patterns in children with sleep-disordered breathing: Preliminary findings
Krishna J, Shah ZA, Merchant M, Klein JB, Gozal D
Sleep Med Early Edition: published 22-Mar-2006

Plasma proteomic profiling: Search for lung cancer diagnostic and early detection markers
Ali IU, Xiao Z, Malone W, Smith M, Conrads TP, Veenstra TD, Greenwald P, Luke BT, McLarty JW
Oncol Rep (2006) 15(5): 1367-72

Modifications in the human T cell proteome induced by intracellular HIV-1 Tat protein expression
Mayte Coiras, Emilio Camafeita, Tomás Ureña, Juan Antonio López, Francisco Caballero, Belén Fernández, María Rosa López-Huertas, Mayte Pérez-Olmeda, José Alcamí
PROTEOMICS (2006) 6(S1): S63-S73

Defining the dopamine transporter proteome by convergent biochemical and in silico analyses
Maiya R, Ponomarev I, Linse KD, Harris RA, Mayfield RD
Genes Brain Behav Early Edition: published 27-Apr-2006

Animal models of asthma: Innovative methods of lung research and new pharmacological targets
Braun A, Tschernig T
Exp Toxicol Pathol Early Edition: published 31-Mar-2006

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Eukaryotic Cells And Tissues

A proteomic approach to study pea (Pisum sativum) responses to powdery mildew (Erysiphe pisi)
Miguel Curto, Emilio Camafeita, Juan A. Lopez, Ana M. Maldonado, Diego Rubiales, Jesús V. Jorrín
PROTEOMICS (2006) 6(S1): S163-S174

The human heart proteome: Two-dimensional maps using narrow-range immobilised pH gradients
Jules A. Westbrook, Jun X. Wheeler, Robin Wait, Sandy Y. Welson, Michael J. Dunn
ELECTROPHORESIS (2006) 27(8): 1547-1555

Identification of a Vacuolar Sucrose Transporter in Hordeum vulgare and Arabidopsis thaliana Mesophyll Cells by a Tonoplast Proteomic Approach
Endler A, Meyer S, Schelbert S, Schneider T, Weschke W, Peters SW, Keller F, Baginsky S, Martinoia E, Schmidt UG
Plant Physiol Early Edition: published 31-Mar-2006

Towards the identification of late-embryogenic-abundant phosphoproteome in Arabidopsis by 2-DE and MS
Sami Irar, Eliandre Oliveira, Montserrat Pagès, Adela Goday
PROTEOMICS (2006) 6(S1): S175-S185

Proteomic profiling of human urine using multi-dimensional protein identification technology
Ru QC, Katenhusen RA, Zhu LA, Silberman J, Yang S, Orchard TJ, Brzeski H, Liebman M, Ellsworth DL
J Chromatogr A (2006) 1111(2): 166-74

Two-dimensional electrophoresis protein profile of the phytopathogenic fungus Botrytis cinerea
Francisco Javier Fernández-Acero, Inmaculada Jorge, Enrique Calvo, Inmaculada Vallejo, María Carbú, Emilio Camafeita, Juan Antonio López, Jesús Manuel Cantoral, Jesús Jorrín
PROTEOMICS (2006) 6(S1): S88-S96

Effects of salinity levels on proteome of Suaeda aegyptiaca leaves
Hossein Askari, Johan Edqvist, Mohsen Hajheidari, Mohammad Kafi, Ghasem Hosseini Salekdeh
PROTEOMICS (2006) 6(8): 2542-2554

Mapping the Arabidopsis organelle proteome
Tom P. J. Dunkley, Svenja Hester, Ian P. Shadforth, John Runions, Thilo Weimar, Sally L. Hanton, Julian L. Griffin, Conrad Bessant, Federica Brandizzi, Chris Hawes, Rod B. Watson, Paul Dupree, and Kathryn S. Lilley
PNAS (2006) 103(17): 6518-6523

Variation in the holm oak leaf proteome at different plant developmental stages, between provenances and in response to drought stress
Inmaculada Jorge, Rafael M. Navarro, Christof Lenz, David Ariza, Jesús Jorrín
PROTEOMICS (2006) 6(S1): S207-S214

A mass spectrometric approach to identify arbuscular mycorrhiza-related proteins in root plasma membrane fractions
Benoît Valot, Luc Negroni, Michel Zivy, Silvio Gianinazzi, Eliane Dumas-Gaudot
PROTEOMICS (2006) 6(S1): S145-S155

Shotgun identification of proteins from uredospores of the bean rust Uromyces appendiculatus
Bret Cooper, Wesley M. Garrett, Kimberly B. Campbell
PROTEOMICS (2006) 6(8): 2477-2484

Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.)
Michaela Sauer, Andreas Jakob, Alfred Nordheim, Frank Hochholdinger
PROTEOMICS (2006) 6(8): 2530-2541

Post-translational modifications, but not transcriptional regulation, of major chloroplast RNA-binding proteins are related to Arabidopsis seedling development
Bai-Chen Wang, Hong-Xia Wang, Jian-Xun Feng, Da-Zhe Meng, Li-Jia Qu, Yu-Xian Zhu
PROTEOMICS (2006) 6(8): 2555-2563

Maize response to acute arsenic toxicity as revealed by proteome analysis of plant shoots
Raquel Requejo, Manuel Tena
PROTEOMICS (2006) 6(S1): S156-S162

Defining the Mitochondrial Proteomes from Five Rat Organs in a Physiologically Significant Context Using 2D Blue-Native/SDS-PAGE
Nicole H. Reifschneider, Sataro Goto, Hideko Nakamoto, Ryoya Takahashi, Michiru Sugawa, Norbert A. Dencher, and Frank Krause
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/14/2006

Proteomic analyses of Oryza sativa mature pollen reveal novel proteins associated with pollen germination and tube growth
Shaojun Dai, Lei Li, Taotao Chen, Kang Chong, Yongbiao Xue, Tai Wang
PROTEOMICS (2006) 6(8): 2504-2529

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Prokaryotes

The dynamic proteome of Lyme disease Borrelia
Norris SJ
Genome Biol (2006) 7(3): 209

Proteomic Analysis of Extracellular Proteins from Escherichia coli W3110
M. P. Nandakumar, Agnes Cheung, and Mark R. Marten
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/14/2006

Selecting thioredoxins for disulphide proteomics: Target proteomes of three thioredoxins from the cyanobacterium Synechocystis sp. PCC 6803
María Esther Pérez-Pérez, Francisco J. Florencio, Marika Lindahl
PROTEOMICS (2006) 6(S1): S186-S195

Mapping and comprehensive analysis of the extracellular and cell surface proteome of the human pathogen Corynebacterium diphtheriae
Nicole Hansmeier, Tzu-Chiao Chao, Jörn Kalinowski, Alfred Pühler, Andreas Tauch
PROTEOMICS (2006) 6(8): 2465-2476

Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB
Laura Tomás-Gallardo, Inés Canosa, Eduardo Santero, Emilio Camafeita, Enrique Calvo, Juan A. López, Belén Floriano
PROTEOMICS (2006) 6(S1): S119-S132

Proteomic Study of Peptide Deformylase Inhibition in Streptococcus pneumoniae and Staphylococcus aureus
Wang W, White R, Yuan Z
Antimicrob Agents Chemother (2006) 50(5): 1656-63

ADP-Ribosylation of Cyclophilin A by Pseudomonas aeruginosa Exoenzyme S
Dinovo AA, Schey KL, Vachon WS, McGuffie EM, Olson JC, Vincent TS
Biochemistry (2006) 45(14): 4664-4673

An important role of a ?probable ATP-binding component of ABC transporter? during the process of Pseudomonas aeruginosa resistance to fluoroquinolone
Jinsong Zhou, Dongyun Hao, Xudong Wang, Teimei Liu, Chengyan He, Feng Xie, Yanhong Sun, Jin Zhang
PROTEOMICS (2006) 6(8): 2495-2503

Identification of two putative rickettsial adhesins by proteomic analysis
Renesto P, Samson L, Ogata H, Azza S, Fourquet P, Gorvel JP, Heinzen RA, Raoult D
Res Microbiol Early Edition: published 28-Feb-2006

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

Proteins unique to intraphagosomally grown Mycobacterium tuberculosis
Jens Mattow, Frank Siejak, Kristine Hagens, Dörte Becher, Dirk Albrecht, Alexander Krah, Frank Schmidt, Peter R. Jungblut, Stefan H. E. Kaufmann , Ulrich E. Schaible
PROTEOMICS (2006) 6(8): 2485-2494

Differential proteomic analysis in the study of prokaryotes stress resistance
Renzone G, D'Ambrosio C, Arena S, Rullo R, Ledda L, Ferrara L, Scaloni A
Ann Ist Super Sanita (2005) 41(4): 459-468

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Pharmacology and Toxicology

Proteomic analysis and the antimetastatic effect of N-(4-methyl)phenyl-O-(4-methoxy) phenyl-thionocarbamate-induced apoptosis in human melanoma SK-MEL-28 cells
Choi SL, Choi YS, Kim YK, Sung ND, Kho CW, Park BC, Kim EM, Lee JH, Kim KM, Kim MY, Myung PK
Arch Pharm Res (2006) 29(3): 224-34

Preliminary proteomic analysis of indomethacin's effect on tumor transplanted with colorectal cancer cell in nude mice
Wang YJ, Zhang GY, Xiao ZQ, Wang HM, Chen ZC
J Biochem Mol Biol (2006) 39(2): 171-7

Proteomics study of anthrax lethal toxin-treated murine macrophages
Jeffrey F. Kuhn, Patric Hoerth, Silvia T. Hoehn, Tobias Preckel, Kenneth B. Tomer
ELECTROPHORESIS (2006) 27(8): 1584-1597

Effect of a single in ovo injection of 2,3,7,8-tetrachlorodibenzo-p-dioxin on protein expression in liver and ovary of the one-day-old chick analyzed by fluorescent two-dimensional difference gel electrophoresis and mass spectrometry
Veerle Bruggeman, Gert Van den Bergh, Stefan Clerens, Linn Dumez, Okanlawon Onagbesan, Lutgarde Arckens, Eddy Decuypere
PROTEOMICS (2006) 6(8): 2576-2585

Functional proteomics of resveratrol-induced colon cancer cell apoptosis: Caspase-6-mediated cleavage of lamin A is a major signaling loop
Shao Chin Lee, Jason Chan, Marie-Veronique Clement, Shazib Pervaiz
PROTEOMICS (2006) 6(8): 2386-2394

An integrated study of acute effects of valproic Acid in the liver using metabonomics, proteomics, and transcriptomics platforms
Schnackenberg LK, Jones RC, Thyparambil S, Taylor JT, Han T, Tong W, Hansen DK, Fuscoe JC, Edmondson RD, Beger RD, Dragan YP
OMICS (2006) 10(1): 1-14

Pharmacoproteomics
Turck CW
Handb Exp Pharmacol (2005) (169): 547-60

Proteomic approach to study the cytotoxicity of dioscin (saponin)
Ying Wang, Yim Hing Cheung, Zhiqi Yang, Jen-Fu Chiu, Chi-Ming Che, Qing-Yu He
PROTEOMICS (2006) 6(8): 2422-2432

Quantitative analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels
Hakan Sarioglu, Stefanie Brandner, Carola Jacobsen, Thomas Meindl, Alexander Schmidt, Josef Kellermann, Friedrich Lottspeich, Ulrich Andrae
PROTEOMICS (2006) 6(8): 2407-2421

New pharmacological treatment approaches for anxiety disorders
Strohle A
Handb Exp Pharmacol (2005) (169): 503-26

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Protein Array

A more practical strategy for interfacing microscale solution phase IEF with commercially available very narrow range IPG strips for optimal protein separation
Lee K, Zuo X, Speicher DW
Electrophoresis Early Edition: published 5-Apr-2006

Immunological synapse arrays: Patterned protein surfaces that modulate immunological synapse structure formation in T cells
Junsang Doh and Darrell J. Irvine
PNAS Early Edition: published 3 April 2006

Multiplexed protein measurement: technologies and applications of protein and antibody arrays
Kingsmore SF
Nat Rev Drug Discov (2006) 5(4): 310-321

Low viscous separation media for genomics and proteomics analysis on microchip electrophoresis system
Jabasini M, Murakami Y, Kaji N, Tokeshi M, Baba Y
Biol Pharm Bull (2006) 29(4): 595-604

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Protein Characterization / PTMs

Proteome Analysis of Human Hair Shaft: From Protein Identification to Posttranslational Modification
Young Jin Lee, Robert H. Rice, and Young Moo Lee
Mol Cell Proteomics (2006) 5(5): 789-800

Proteomic analysis of nitrated and 4-hydroxy-2-nonenal-modified serum proteins during aging
Kim CH, Zou Y, Kim DH, Kim ND, Yu BP, Chung HY
J Gerontol A Biol Sci Med Sci (2006) 61(4): 332-8

Systematic characterization of phosphorylation sites in NFATc2 by linear ion trap mass spectrometry
Margarita Villar, Inmaculada Ortega-Pérez, Felipe Were, Eva Cano, Juan Miguel Redondo, Jesús Vázquez
PROTEOMICS (2006) 6(S1): S16-S27

Mass spectrometry for protein identification and the study of post translational modifications
Salzano AM, Crescenzi M
Ann Ist Super Sanita (2005) 41(4): 443-450

Radiolytic Protein Footprinting with Mass Spectrometry to Probe the Structure of Macromolecular Complexes
Takamoto K, Chance MR
Annu Rev Biophys Biomol Struct Early Edition: published 28-Feb-2006

Phosphoproteome Profiling of Human Skin Fibroblast Cells in Response to Low- and High-Dose Irradiation
Feng Yang, David L. Stenoien, Eric F. Strittmatter, Junhua Wang, Lianghao Ding, Mary S. Lipton, Matthew E. Monroe, Carrie D. Nicora, Marina A. Gristenko, Keqi Tang, Ruihua Fang, Joshua N. Adkins, David G. Camp, II, David J. Chen, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/14/2006

Proteomics approaches to study the redox state of Cysteine containing proteins
Camerini S, Polci ML, Bachi A
Ann Ist Super Sanita (2005) 41(4): 451-457

Phosphoproteome analysis of the human mitotic spindle
Marjaana Nousiainen, Herman H. W. Sillje, Guido Sauer, Erich A. Nigg, and Roman Korner
PNAS (2006) 103(14): 5391-5396

Neuroproteomics of the Synapse and Drug Addiction
Abul-Husn NS, Devi LA
J Pharmacol Exp Ther Early Edition: published 27-Apr-2006

Selective detection and identification of phosphopeptides by dansyl MS/MS/MS fragmentation
Amoresano A, Monti G, Cirulli C, Marino G
Rapid Commun Mass Spectrom (2006) 20(9): 1400-1404

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Protein-protein interaction

Isolating the whole complex of target proteins of FK506 using affinity resins from novel solid phases
Takahashi T, Shiyama T, Mori T, Hosoya K, Tanaka A
Anal Bioanal Chem Early Edition: published 7-Apr-2006

Landscape of the hnRNP K protein-protein interactome
Micha? Mikula, Artur Dzwonek, Jakub Karczmarski, Tymon Rubel, Micha? Dadlez, Lucjan S. Wyrwicz, Karol Bomsztyk, Jerzy Ostrowski
PROTEOMICS (2006) 6(8): 2395-2406

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Quantitation

Enhanced Analysis of Metastatic Prostate Cancer Using Stable Isotopes and High Mass Accuracy Instrumentation
Patrick A. Everley, Corey E. Bakalarski, Joshua E. Elias, Carol G. Waghorne, Sean A. Beausoleil, Scott A. Gerber, Brendan K. Faherty, Bruce R. Zetter, and Steven P. Gygi
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/21/2006

Proteome Changes after Metabolic Engineering to Enhance Aerobic Mineralization of cis-1,2-Dichloroethylene
Jintae Lee, Li Cao, Saw Yen Ow, Martin E. Barrios-Llerena, Wilfred Chen, Thomas K. Wood, and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/28/2006

Differentially isotope-coded N-terminal protein sulphonation: Combining protein identification and quantification
Elisabeth Guillaume, Alexandre Panchaud, Michael Affolter, Valérie Desvergnes, Martin Kussmann
PROTEOMICS (2006) 6(8): 2338-2349

Stable Isotope Tagging of Epitopes: A Highly Selective Strategy For The Identification Of Major Histocompatibility Complex Class I-Associated Peptides Induced Upon Viral Infection
Hugo D. Meiring, Ernst C. Soethout, Martien C. M. Poelen, Dennis Mooibroek, Ronald Hoogerbrugge, Hans Timmermans, Claire J. Boog, Albert J. R. Heck, Ad P. J. M. de Jong, and Cecile A. C. M. van Els
Mol Cell Proteomics (2006) 5(5): 902-913

Quantitative proteomics using 16O/18O labeling and linear ion trap mass spectrometry
Daniel López-Ferrer, Antonio Ramos-Fernández, Salvador Martínez-Bartolomé, Predestinación García-Ruiz, Jesús Vázquez
PROTEOMICS (2006) 6(S1): S4-S11

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Review

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

Microfabricated devices: A new sample introduction approach to mass spectrometry
Iulia M. Lazar, Jakub Grym, Frantisek Foret
Mass Spectrometry Reviews (2006) 25(4): 573-594

Personalized medicine and development of targeted therapies: the upcoming challenge for diagnostic molecular pathology. A review
Dietel M, Sers C
Virchows Arch Early Edition: published 22-Apr-2006

Array of Informatics: Applications in Modern Research
Anna Kozarova, Steven Petrinac, Adnan Ali, and John W. Hudson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/07/2006

Functional genomics, new tools in malaria research
Di Girolamo F, Raggi C, Bultrini E, Lanfrancotti A, Silvestrini F, Sargiacomo M, Birago C, Pizzi E, Alano P, Ponzi M
Ann Ist Super Sanita (2005) 41(4): 469-477

Proteomics: recent applications and new technologies
Elrick MM, Walgren JL, Mitchell MD, Thompson DC
Basic Clin Pharmacol Toxicol (2006) 98(5): 432-41

Protein identification and expression analysis using mass spectrometry
Kolker E, Higdon R, Hogan JM
Trends Microbiol Early Edition: published 5-Apr-2006

Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
Andrea Sinz
Mass Spectrometry Reviews (2006) 25(4): 663-682

Proteomics-driven progress in neurodegeneration research
Michael Fountoulakis, Sophia Kossida
ELECTROPHORESIS (2006) 27(8): 1556-1573

Proteomic technology for biomarker profiling in cancer: an update
Alaoui-Jamali MA, Xu YJ
J Zhejiang Univ Sci B (2006) 7(6): 411-20

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000
David J. Harvey
Mass Spectrometry Reviews (2006) 25(4): 595-662

Homo sapiens proteomics: clinical perspectives
Del Boccio P, Urbani A
Ann Ist Super Sanita (2005) 41(4): 479-482

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Methodology

Nitrotyrosine proteome survey in asthma identifies oxidative mechanism of catalase inactivation
Ghosh S, Janocha AJ, Aronica MA, Swaidani S, Comhair SA, Xu W, Zheng L, Kaveti S, Kinter M, Hazen SL, Erzurum SC
J Immunol (2006) 176(9): 5587-97

Multi-dimensional HPLC/MS of the nucleolar proteome using HPLC-chip/MS
Vollmer M, Horth P, Rozing G, Coute Y, Grimm R, Hochstrasser D, Sanchez JC
J Sep Sci (2006) 29(4): 499-509

Development of a novel 2D proteomics approach for the identification of proteins secreted by primary chondrocytes after stimulation by IL-1 and oncostatin M
Catterall JB, Rowan AD, Sarsfield S, Saklatvala J, Wait R, Cawston TE
Rheumatology (Oxford) Early Edition: published 27-Mar-2006

Differential detergent fractionation for non-electrophoretic bovine peripheral blood monocyte proteomics reveals proteins involved in professional antigen presentation
Lee SR, Pharr GT, Cooksey AM, McCarthy FM, Boyd BL, Pinchuk LM
Dev Comp Immunol Early Edition: published 13-Mar-2006

A mass spectrometry compatible silver staining method for protein incorporating a new silver sensitizer in sodium dodecyl sulfate-polyacrylamide electrophoresis gels
Li-Tai Jin, Sun-Young Hwang, Gyurng-Soo Yoo, Jung-Kap Choi
PROTEOMICS (2006) 6(8): 2334-2337

Sequencing covalent modifications of membrane proteins
Whitelegge JP, Laganowsky A, Nishio J, Souda P, Zhang H, Cramer WA
J Exp Bot Early Edition: published 30-Mar-2006

Top-down Protein Sequencing and MS3 on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer
Boris Macek, Leonie F. Waanders, Jesper V. Olsen, and Matthias Mann
Mol Cell Proteomics (2006) 5(5): 949-958

Src Homology 2 Domain-based High Throughput Assays for Profiling Downstream Molecules in Receptor Tyrosine Kinase Pathways
Takuro Yaoi, Sangpen Chamnongpol, Xin Jiang, and Xianqiang Li
Mol Cell Proteomics (2006) 5(5): 959-968

More Sensitive and Quantitative Proteomic Measurements Using Very Low Flow Rate Porous Silica Monolithic LC Columns with Electrospray Ionization-Mass Spectrometry
Quanzhou Luo, Keqi Tang, Feng Yang, Ayesha Elias, Yufeng Shen, Ronald J. Moore, Rui Zhao, Kim K. Hixson, Sandra S. Rossie, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/07/2006

Detection of serum hepcidin in renal failure and inflammation by using ProteinChip System(R)
Tomosugi N, Kawabata H, Wakatabe R, Higuchi M, Yamaya H, Umehara H, Ishikawa I
Blood Early Edition: published 18-Apr-2006

Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform-independent separation
Zurbig P, Renfrow MB, Schiffer E, Novak J, Walden M, Wittke S, Just I, Pelzing M, Neususs C, Theodorescu D, Root KE, Ross MM, Mischak H
Electrophoresis Early Edition: published 27-Apr-2006

A proteomic approach to investigate potential biomarkers directed against membrane-associated breast cancer proteins
Ludovic Canelle, Jordane Bousquet, Cedric Pionneau, Julie Hardouin, Genevieve Choquet-Kastylevsky, Raymonde Joubert-Caron, Michel Caron
ELECTROPHORESIS (2006) 27(8): 1609-1616

Improved mass spectrometry compatibility is afforded by ammoniacal silver staining
Mireille Chevallet, Hélène Diemer, Sylvie Luche, Alain van Dorsselaer, Thierry Rabilloud, Emmanuelle Leize-Wagner
PROTEOMICS (2006) 6(8): 2350-2354

Analysis of human serum by liquid chromatography-mass spectrometry: Improved sample preparation and data analysis
Govorukhina NI, Reijmers TH, Nyangoma SO, van der Zee AG, Jansen RC, Bischoff R
J Chromatogr A Early Edition: published 28-Mar-2006

Functionalized magnetic micro- and nanoparticles: Optimization and application to mu-chip tryptic digestion
Bilkova Z, Slovakova M, Minc N, Futterer C, Cecal R, Horak D, Benes M, le Potier I, Krenkova J, Przybylski M, Viovy JL
Electrophoresis (2006) 27(9): 1811-1824

From Gene to HSQC in under Five Hours: High-Throughput NMR Proteomics
Keppetipola S, Kudlicki W, Nguyen BD, Meng X, Donovan KJ, Shaka AJ
J Am Chem Soc (2006) 128(14): 4508-9

O-Linked N-Acetylglucosamine Proteomics of Postsynaptic Density Preparations Using Lectin Weak Affinity Chromatography and Mass Spectrometry
Keith Vosseller, Jonathan C. Trinidad, Robert J. Chalkley, Christian G. Specht, Agnes Thalhammer, Aenoch J. Lynn, June O. Snedecor, Shenheng Guan, Katalin F. Medzihradszky, David A. Maltby, Ralf Schoepfer, and Alma L. Burlingame
Mol Cell Proteomics (2006) 5(5): 923-934

Direct Protein Detection from Biological Media through Electrospray-Assisted Laser Desorption Ionization/Mass Spectrometry
Min-Zong Huang, Hsiu-Jung Hsu, Jen-Yih Lee, Jingyueh Jeng, and Jentaie Shiea
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/07/2006

Comparison of indirect and direct approaches using ion-trap and Fourier transform ion cyclotron resonance mass spectrometry for exploring viperid venom proteomes
Fox JW, Ma L, Nelson K, Sherman NE, Serrano SM
Toxicon Early Edition: published 28-Mar-2006

Contribution of cell culture additives to the two-dimensional protein patterns of mouse macrophages
Ingrid Miller, Marta Radwan, Birgit Strobl, Mathias Müller, Manfred Gemeiner
ELECTROPHORESIS (2006) 27(8): 1626-1629

New approaches to high-throughput structure characterization of SH3 complexes: The example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae
Musi V, Birdsall B, Fernandez-Ballester G, Guerrini R, Salvatori S, Serrano L, Pastore A
Protein Sci (2006) 15(4): 795-807

Miniaturized Solid-Phase Extraction and Sample Preparation for MALDI MS Using a Microfabricated Integrated Selective Enrichment Target
Simon Ekström, Lars Wallman, Daniel Hök, György Marko-Varga, and Thomas Laurell
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/21/2006

A versatile method for deciphering plant membrane proteomes
Rolland N, Ferro M, Ephritikhine G, Marmagne A, Ramus C, Brugiere S, Salvi D, Seigneurin-Berny D, Bourguignon J, Barbier-Brygoo H, Joyard J, Garin J
J Exp Bot Early Edition: published 4-Apr-2006

Derivatization by 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate for enhancing the ionization yield of small peptides and glycopeptides in matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry
Roman Ullmer, Alexander Plematl, Andreas Rizzi
Rapid Communications in Mass Spectrometry (2006) 20(9): 1469-1479

Sample sonication after trichloroacetic acid precipitation increases protein recovery from cultured hippocampal neurons, and improves resolution and reproducibility in two-dimensional gel electrophoresis
Bruno J. Manadas, Konstantinos Vougas, Michael Fountoulakis, Carlos B. Duarte
ELECTROPHORESIS (2006) 27(9): 1825-1831

Optimizing the surface plasmon resonance/mass spectrometry interface for functional proteomics applications: How to avoid and utilize nonspecific adsorption
Helén Larsericsdotter, Östen Jansson, Andrei Zhukov, Daphne Areskoug, Sven Oscarsson, Jos Buijs
PROTEOMICS (2006) 6(8): 2355-2364

Deviation from the mobile proton model in amino-modified peptides: implications for multiple reaction monitoring analysis of peptides
Locke SJ, Leslie AD, Melanson JE, Pinto DM
Rapid Commun Mass Spectrom (2006) 20(10): 1525-1530

Protein tryptic digests analyzed by carrier ampholyte-based capillary electrophoresis coupled to ESI-MS
Jean-Marc Busnel, Stéphanie Descroix, Thomas Le Saux, Shigeru Terabe, Marie-Claire Hennion, Gabriel Peltre
ELECTROPHORESIS (2006) 27(8): 1481-1488

Aqueous Two-Phase Partitioning for Proteomic Monitoring of Cell Surface Biomarkers in Human Peripheral Blood Mononuclear Cells
Henrik Everberg, Ragna Peterson, Sabina Rak, Folke Tjerneld, and Cecilia Emanuelsson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/07/2006

Laser-microdissection for cell type- and compartment-specific analyses on genomic and proteomic level
Fink L, Kwapiszewska G, Wilhelm J, Bohle RM
Exp Toxicol Pathol Early Edition: published 31-Mar-2006

Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization
Matthias Berg, Axel Parbel, Harald Pettersen, David Fenyö, Lennart Björkesten
Rapid Communications in Mass Spectrometry (2006) 20(10): 1558-1562

Relative and absolute quantitative shotgun proteomics: targeting low-abundance proteins in Arabidobsis thaliana
Wienkoop S, Weckwerth W
J Exp Bot Early Edition: published 30-Mar-2006

Comparison of CID spectra of singly charged polypeptide antibiotic precursor ions obtained by positive-ion vacuum MALDI IT/RTOF and TOF/RTOF, AP-MALDI-IT and ESI-IT mass spectrometry
Ernst Pittenauer, Martin Zehl, Omar Belgacem, Emmanuel Raptakis, Robert Mistrik, Günter Allmaier
Journal of Mass Spectrometry (2006) 41(4): 421-447

A perspective on the use of iTRAQTM reagent technology for protein complex and profiling studies
Zieske LR
J Exp Bot Early Edition: published 30-Mar-2006

Improved 2-DE of microorganisms after acidic extraction
Ben R. Herbert, Jasmine Grinyer, John T. McCarthy, Mitchell Isaacs, Elizabeth J. Harry, Helena Nevalainen, Mathew D. Traini, Sybille Hunt, Ben Schulz, Matthew Laver, Anthony R. Goodall, Joanne Packer, Jenny L. Harry, Keith L. Williams
ELECTROPHORESIS (2006) 27(8): 1630-1640

Exploring human plasma proteome strategies: High efficiency in-solution digestion protocol for multi-dimensional protein identification technology
Ru QC, Zhu LA, Katenhusen RA, Silberman J, Brzeski H, Liebman M, Shriver CD
J Chromatogr A (2006) 1111(2): 175-91

Application of quantum dots in quantitative proteomics for multiplex colour system assay
Khalifeh K, Ranjbar B
Med Hypotheses Early Edition: published 28-Mar-2006

Use of Solution-IEF-Fractionation Leads to Separation of 2673 Mouse Brain Proteins Including 255 Hydrophobic Structures
Jae-Kyung Myung and Gert Lubec
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/14/2006

Ion-interaction-capillary zone electrophoresis of cationic proteomic peptide standards
Popa TV, Mant CT, Hodges RS
J Chromatogr A (2006) 1111(2): 192-9

Combining protein identification and quantification: C-terminal isotope-coded tagging using sulfanilic acid
Alexandre Panchaud, Elisabeth Guillaume, Michael Affolter, Fabien Robert, Philippe Moreillon, Martin Kussmann
Rapid Communications in Mass Spectrometry (2006) 20(10): 1585-1594

Optimization of protein extraction and solubilization for mature grape berry clusters
Delphine Vincent, Matthew D. Wheatley, Grant R. Cramer
ELECTROPHORESIS (2006) 27(9): 1853-1865

Selective detection and identification of phosphopeptides by dansyl MS/MS/MS fragmentation
Angela Amoresano, Gianluca Monti, Claudia Cirulli, Gennaro Marino
Rapid Communications in Mass Spectrometry (2006) 20(9): 1400-1404

Nanoporous Surfaces as Harvesting Agents for Mass Spectrometric Analysis of Peptides in Human Plasma
Marco Gaspari, Mark Ming-Cheng Cheng, Rosa Terracciano, Xuewu Liu, A. Jasper Nijdam, Lisa Vaccari, Enzo di Fabrizio, Emanuel F. Petricoin, Lance A. Liotta, Giovanni Cuda, Salvatore Venuta, # and Mauro Ferrari #
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/07/2006

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Books

LC/MS: A Practical User's Guide. By Marvin C. McMaster
Kasper Juel Pedersen
PROTEOMICS (2006) 6(8): 2627

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Meeting

OUT OF CÓRDOBA
José Antonio Bárcena, Juan José Calvete, Angela Moreno-López, Jesús V. Jorrín-Novo
PROTEOMICS (2006) 6(S1): S1-S3

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Other

Proteomics reveals proteins in paint
Mukhopadhyay R
Anal Chem (2006) 78(5): 1379

Professor Michael J. Dunn is celebrating his 60th birthday
Hans-Joachim Kraus
PROTEOMICS (2006) 6(8): 2333

Celebrating the 65th Birthday of Professor Pier Giorgio Righetti
Nancy Stellwagen
ELECTROPHORESIS (2006) 27(8): 1435

Calendar
Mol Cell Proteomics (2006) 5(5): 969-970

Product News: Proteomics 8/2006
PROTEOMICS (2006) 6(8): 2628-2632

Cover Picture: Proteomics Supplement 1/2006
PROTEOMICS (2006) 6(S1): published 18 Apr 2006

Publishing proteomic data
Latterich M
Proteome Sci (2006) 4(1): 8

Reporting Protein Identification Data: The next Generation of Guidelines
Ralph A. Bradshaw, Alma L. Burlingame, Steven Carr, and Ruedi Aebersold
Mol Cell Proteomics (2006) 5(5): 787-788

Company News: Proteomics 8/2006
PROTEOMICS (2006) 6(8): 2632

Focus issue: peering into the proteome
Adler EM
Sci STKE (2006) 2006(331): eg5

Contents: Proteomics Supplement 1/2006
PROTEOMICS (2006) 6(S1): published 18 Apr 2006

Contents: Proteomics 8/2006
PROTEOMICS (2006) 6(8): published 12 Apr 2006

Cover Picture: Proteomics 8/2006
PROTEOMICS (2006) 6(8): published 12 Apr 2006

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