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SPS' Digest

Issue 23, 28-Sep-2005

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Quick jumps to articles in: Bioinformatics (19) / Biological applications (16) / Biomedical and clinical applications (28) / Eukaryotic Cells And Tissues (10) / Prokaryotes (4) / Pharmacology and Toxicology (3) / Protein Array (2) / Protein Characterization - PTMs (11) / Protein-protein interaction (4) / Quantitation (5) / Review (18) / Methodology (21) / Meeting (2) / Other (6) /

In this issue, 146 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 (19) / Biological applications (16) / Biomedical and clinical applications (28) / Eukaryotic Cells And Tissues (10) / Prokaryotes (4) / Pharmacology and Toxicology (3) / Protein Array (2) / Protein Characterization - PTMs (11) / Protein-protein interaction (4) / Quantitation (5) / Review (18) / Methodology (21) / Meeting (2) / Other (6) /

Bioinformatics

Dynamic covariation between gene expression and proteome characteristics
Taghavi M, Siermala M, Lehtinen TO, Vihinen M
BMC Bioinformatics (2005) 6(1): 215

PIMWalkertrade mark: Visualising Protein Interaction Networks Using the HUPO PSI Molecular Interaction Format
Meil A, Durand P, Wojcik J
Appl Bioinformatics (2005) 4(2): 137-9

Sequence-based discovery of the human and rodent peroxisomal proteome
Kurochkin IV, Nagashima T, Konagaya A, Schonbach C
Appl Bioinformatics (2005) 4(2): 93-104

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants
Wolski WE, Lalowski M, Jungblut P, Reinert K
BMC Bioinformatics (2005) 6: 203

DCCP and DICP: Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins
Hao Wu, Yan Yang, Sheng-Juan Jiang, Ling-Ling Chen, Hai-Xia Gao, Qing-Shan Fu, Feng Li, Bin-Guang Ma, and Hong-Yu Zhang
Genomics Proteomics Bioinformatics (2005) 3(1): 52-57

From XML to RDF: how semantic web technologies will change the design of 'omic' standards
Wang X, Gorlitsky R, Almeida JS
Nat Biotechnol (2005) 23(9): 1099-103

Inferring protein domain interactions from databases of interacting proteins
Robert Riley, Christopher Lee, Chiara Sabatti, David Eisenberg
Genome Biology (2005) 6(10): R89

Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution
Nandi S, Mehra N, Lynn AM, Bhattacharya A
BMC Genomics (2005) 6(1): 116

5(th) HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK - Setting the Analysis Frame
Stephan C, Hamacher M, Bluggel M, Korting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schafer H, Martens L, Jones P, Muller M, Auyeung K, Taylor C, Binz PA, Thiele H, Parkinson D, Meyer HE, Apweiler R
Proteomics (2005) 5(14): 3560-3562

An ontology for carcinoma classification for clinical bioinformatics
Kumar A, Yip YL, Smith B, Marwede D, Novotny D
Stud Health Technol Inform (2005) 116: 635-40

Species-Specific Bacteria Identification Using Differential Mobility Spectrometry and Bioinformatics Pattern Recognition
Shnayderman M, Mansfield B, Yip P, Clark HA, Krebs MD, Cohen SJ, Zeskind JE, Ryan ET, Dorkin HL, Callahan MV, Stair TO, Gelfand JA, Gill CJ, Hitt B, Davis CE
Anal Chem (2005) 77(18): 5930-5937

Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
Kawano S, Hashimoto K, Miyama T, Goto S, Kanehisa M
Bioinformatics Early Edition: published 13-Sep-2005

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
Xing Y, Lee C
Proc Natl Acad Sci U S A Early Edition: published 12-Sep-2005

In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network
Heinemann M, Kummel A, Ruinatscha R, Panke S
Biotechnol Bioeng Early Edition: published 9-Sep-2005

A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry
Xiao-jun Li, Eugene C. Yi, Christopher J. Kemp, Hui Zhang, and Ruedi Aebersold
Mol Cell Proteomics (2005) 4(9): 1328-1340

Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data
William R. Cannon, Kristin H. Jarman, Bobbie-Jo M. Webb-Robertson, Douglas J. Baxter, Christopher S. Oehmen, Kenneth D. Jarman, Alejandro Heredia-Langner, # Kenneth J. Auberry, and Gordon A. Anderson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/16/2005

Using cross-correlation normalized for peptide length to optimize peptide identification in shotgun proteomics
Ying W, Gong Y, Zhang Y, Cai Y, Dong H, Qian X
Rapid Commun Mass Spectrom (2005) 19(20): 2983-2985

PSST-2.0: Protein Data Bank Sequence Search Tool
Ananthalakshmi P, Samayamohan K, Chokalingam C, Mayilarasi C, Sekar K
Appl Bioinformatics (2005) 4(2): 141-5

A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules
Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT, Watkins DI, Mothe BR, Sette A
Vaccine Early Edition: published 29-Aug-2005

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Biological applications

Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies
Salasznyk RM, Westcott AM, Klees RF, Ward DF, Xiang Z, Vandenberg S, Bennett K, Plopper GE
Stem Cells Dev (2005) 14(4): 354-66

A proteomic approach to study protein variation in GM durum wheat in relation to technological properties of semolina
Di Luccia A, Lamacchia C, Fares C, Padalino L, Mamone G, La Gatta B, Gambacorta G, Faccia M, Di Fonzo N, La Notte E
Ann Chim (2005) 95(6): 405-14

The v-SNARE Vti1a regulates insulin stimulated glucose transport and ACRP30 secretion in 3T3L1 adipocytes
Bose A, Guilherme A, Huang S, Hubbard AC, Lane CR, Soriano NA, Czech MP
J Biol Chem Early Edition: published 29-Aug-2005

Proteomic identification of proteins conjugated to ISG15 in mouse and human cells
Giannakopoulos NV, Luo JK, Papov V, Zou W, Lenschow DJ, Jacobs BS, Borden EC, Li J, Virgin HW, Zhang DE
Biochem Biophys Res Commun Early Edition: published 31-Aug-2005

Characterisation of the role of the RabGAP AS160 in insulin-regulated GLUT4 trafficking
Larance M, Ramm G, Stockli J, van Dam EM, Winata S, Wasinger V, Simpson F, Graham M, Junutula JR, Guilhaus M, James DE
J Biol Chem Early Edition: published 8-Sep-2005

Proteomic Identification of Insulin-like Growth Factor-binding Protein-6 Induced by Sublethal H2O2 Stress from Human Diploid Fibroblasts
Lifang Xie, George Tsaprailis, and Qin M. Chen
Mol Cell Proteomics (2005) 4(9): 1273-1283

A Combined Proteome and Microarray Investigation of Inorganic Phosphate-induced Pre-osteoblast Cells
Kelly A. Conrads, Ming Yi, Kerri A. Simpson, David A. Lucas, Corinne E. Camalier, Li-Rong Yu, Timothy D. Veenstra, Robert M. Stephens, Thomas P. Conrads, and George R. Beck, Jr
Mol Cell Proteomics (2005) 4(9): 1284-1296

Expression Clustering Reveals Detailed Co-expression Patterns of Functionally Related Proteins during B Cell Differentiation: A Proteomic Study Using a Combination of One-Dimensional Gel Electrophoresis, LC-MS/MS, and Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)
Edwin P. Romijn, Chantal Christis, Marnix Wieffer, Joost W. Gouw, Asier Fullaondo, Peter van der Sluijs, Ineke Braakman, and Albert J. R. Heck
Mol Cell Proteomics (2005) 4(9): 1297-1310

Accelerated Discovery of Novel Protein Function in Cultured Human Cells
Emily Hodges, Jenny Stjerndahl Redelius, Weilin Wu, and Christer Hoog
Mol Cell Proteomics (2005) 4(9): 1319-1327

The Subunit Structure and Dynamics of the 20S Proteasome in Chicken Skeletal Muscle
Julia R. Hayter, Mary K. Doherty, Colin Whitehead, Heather McCormack, Simon J. Gaskell, and Robert J. Beynon
Mol Cell Proteomics (2005) 4(9): 1370-1381

Characterization of the Drosophila melanogaster Mitochondrial Proteome
Jana Alonso, Javier M. Rodriguez, Luis Alberto Baena-López, and Juan F. Santarén
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/16/2005

Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach
Regonesi ME, Del Favero M, Basilico F, Briani F, Benazzi L, Tortora P, Mauri P, Deho G
Biochimie Early Edition: published 30-Aug-2005

Plasma proteomic analysis of the acute phase response of rainbow trout (Oncorhynchus mykiss) to intraperitoneal inflammation and LPS injection
Russell S, Hayes MA, Simko E, Lumsden JS
Dev Comp Immunol Early Edition: published 30-Aug-2005

From Dormant to Germinating Spores of Streptomyces coelicolor A3(2): New Perspectives from the crp Null Mutant
André Piette, # Adeline Derouaux, # Pascal Gerkens, Elke E. E. Noens, Gabriel Mazzucchelli, Sébastien Vion, Henk K. Koerten, Fritz Titgemeyer, Edwin De Pauw, Pierre Leprince, Gilles P. van Wezel, Moreno Galleni, and Sébastien Rigali
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/23/2005

Identification and Characterization of Deamidation Sites in the Conserved Regions of Human Immunoglobulin Gamma Antibodies
Dirk Chelius, Douglas S. Rehder, and Pavel V. Bondarenko
ANALYTICAL CHEMISTRY (2005) 77(18): 6004-6011

Proteomics in nutrition research: principles, technologies and applications
Winkelmann I, Johnson IT, Mariman E, Wenzel U, Daniel H
Br J Nutr (2005) 94(3): 302-314

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Biomedical and clinical applications

Proteomics in Acute Myelogenous Leukaemia (AML): Methodological Strategies and Identification of Protein Targets for Novel Antileukaemic Therapy
Anensen N, Wergeland L, Mc Cormack E, Bruserud O, Gjertsen BT
Curr Drug Targets (2005) 6(6): 631-46

Differential protein expression in the prefrontal white matter of human alcoholics: a proteomics study
James G, Sheedy D, Harper C, Matsumoto I
Mol Psychiatry Early Edition: published 20-Sep-2005

Proteomic analysis of childhood leukemia
Hegedus CM, Gunn L, Skibola CF, Zhang L, Shiao R, Fu S, Dalmasso EA, Metayer C, Dahl GV, Buffler PA, Smith MT
Leukemia Early Edition: published 1-Sep-2005

Proteomic determination of widespread detergent insolubility, including Abeta but not tau, early in the pathogenesis of Alzheimer's disease
Woltjer RL, Cimino PJ, Boutte AM, Schantz AM, Montine KS, Larson EB, Bird T, Quinn JF, Zhang J, Montine TJ
FASEB J Early Edition: published 29-Aug-2005

Proteomic Analysis of Sputum from Adults and Children with Cystic Fibrosis and from Control Subjects
Sloane AJ, Lindner RA, Prasad SS, Sebastian LT, Pedersen SK, Robinson M, Bye PT, Nielson DW, Harry JL
Am J Respir Crit Care Med Early Edition: published 15-Sep-2005

Detection of acute tubulointerstitial rejection by proteomic analysis of urinary samples in renal transplant recipients
Wittke S, Haubitz M, Walden M, Rohde F, Schwarz A, Mengel M, Mischak H, Haller H, Gwinner W
Am J Transplant (2005) 5(10): 2479-88

Discriminatory proteomic biomarker analysis identifies free hemoglobin in the cerebrospinal fluid of women with severe preeclampsia
Norwitz ER, Tsen LC, Park JS, Fitzpatrick PA, Dorfman DM, Saade GR, Buhimschi CS, Buhimschi IA
Am J Obstet Gynecol (2005) 193(3 Suppl): 957-64

Decreased Asialotransferrin in Cerebrospinal Fluid of Patients with Childhood-Onset Ataxia and Central Nervous System Hypomyelination/Vanishing White Matter Disease
Vanderver A, Schiffmann R, Timmons M, Kellersberger KA, Fabris D, Hoffman EP, Maletkovic J, Hathout Y
Clin Chem Early Edition: published 9-Sep-2005

Proteomic analysis of colonic myofibroblasts and effect on colon cancer cell proliferation
Chen AL, Soman KV, Rychahou PG, Luxon BA, Evers BM
Surgery (2005) 138(2): 382-90

Differentially Expressed Proteins in the Pancreas of Diet-induced Diabetic Mice
Linghua Qiu, Edward O. List, and John J. Kopchick
Mol Cell Proteomics (2005) 4(9): 1311-1318

Epitomics: serum screening for the early detection of cancer on microarrays using complex panels of tumor antigens
Draghici S, Chatterjee M, Tainsky MA
Expert Rev Mol Diagn (2005) 5(5): 735-43

Proteomic analysis of parkin knockout mice: alterations in energy metabolism, protein handling and synaptic function
Periquet M, Corti O, Jacquier S, Brice A
J Neurochem Early Edition: published 7-Sep-2005

Use of proteomic patterns as a novel screening tool in pre-eclampsia
Myers J, Macleod M, Reed B, Harris N, Mires G, Baker P
J Obstet Gynaecol (2004) 24(8): 873-4

Identification of 2 serum biomarkers of renal cell carcinoma by surface enhanced laser desorption/ionization mass spectrometry
Hara T, Honda K, Ono M, Naito K, Hirohashi S, Yamada T
J Urol (2005) 174(4 Pt 1): 1213-7

Serum proteomics study of the squamous cell carcinoma antigen 1 in tongue cancer
Huang X, Wei Y, Li L, Wen Y, Yang J, Liu B, Song X, Zhao J
Oral Oncol Early Edition: published 3-Sep-2005

PARK7 and Nucleoside Diphosphate Kinase A as Plasma Markers for the Early Diagnosis of Stroke
Allard L, Burkhard PR, Lescuyer P, Burgess JA, Walter N, Hochstrasser DF, Sanchez JC
Clin Chem Early Edition: published 1-Sep-2005

Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry
Schwartz SA, Weil RJ, Thompson RC, Shyr Y, Moore JH, Toms SA, Johnson MD, Caprioli RM
Cancer Res (2005) 65(17): 7674-81

Differential Proteomic Analysis of Bronchoalveolar Lavage Fluid in Asthmatics following Segmental Antigen Challenge
Jiang Wu, Michiko Kobayashi, Eric A. Sousa, Wei Liu, Jie Cai, Samuel J. Goldman, Andrew J. Dorner, Steven J. Projan, Mani S. Kavuru, Yongchang Qiu, and Mary Jane Thomassen
Mol Cell Proteomics (2005) 4(9): 1251-1264

MALDI-TOF Mass Spectrometry Analysis of Cerebrospinal Fluid Tryptic Peptide Profiles to Diagnose Leptomeningeal Metastases in Patients with Breast Cancer
Lennard J. Dekker, Willem Boogerd, Guenther Stockhammer, Johannes C. Dalebout, Ivar Siccama, Pingpin Zheng, Johannes M. Bonfrer, Jan J. Verschuuren, Guido Jenster, Marcel M. Verbeek, Theo M. Luider, and Peter A. Sillevis Smitt
Mol Cell Proteomics (2005) 4(9): 1341-1349

Analysis of Intimal Proteoglycans in Atherosclerosis-prone and Atherosclerosis-resistant Human Arteries by Mass Spectrometry
Paul Talusan, Shahinaz Bedri, Suping Yang, Taj Kattapuram, Nilsa Silva, Peter J. Roughley, and James R. Stone
Mol Cell Proteomics (2005) 4(9): 1350-1357

Profiling of Alopecia Areata Autoantigens Based on Protein Microarray Technology
Angelika Lueking, Otmar Huber, Christopher Wirths, Kirsten Schulte, Karola M. Stieler, Ulrike Blume-Peytavi, Axel Kowald, Karin Hensel-Wiegel, Rudolf Tauber, Hans Lehrach, Helmut E. Meyer, and Dolores J. Cahill
Mol Cell Proteomics (2005) 4(9): 1382-1390

A Dataset of Human Cornea Proteins Identified by Peptide Mass Fingerprinting and Tandem Mass Spectrometry
Henrik Karring, Ida B. Thogersen, Gordon K. Klintworth, Torben Moller-Pedersen, and Jan J. Enghild
Mol Cell Proteomics (2005) 4(9): 1406-1408

Comparative Plasma Proteome Analysis of Lymphoma-Bearing SJL Mice
Vadiraja B. Bhat, Man Ho Choi, John S. Wishnok, and Steven R. Tannenbaum
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/02/2005

Characterization of Proteins in Human Pancreatic Cancer Serum Using Differential Gel Electrophoresis and Tandem Mass Spectrometry
Kenneth H. Yu, Anil K. Rustgi, and Ian A. Blair
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Expression Profiling of Herpesvirus and Vaccinia Virus Proteins Using a High-Throughput Baculovirus Screening System
Mian Gao, # Nicole Brufatto, Tricia Chen, Laura Lea Murley, Rosanne Thalakada, Megan Domagala, Bryan Beattie, Daniel Mamelak, ,& Vicki Athanasopoulos, David Johnson, Grant McFadden, Christian Burks, and Lori Frappier
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/23/2005

Proteomic Evidence for Roles for Nucleolin and Poly[ADP-ribosyl] Transferase in Drug Resistance
Zongming Fu and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/23/2005

Proteomic analysis of corticobasal degeneration: a case study of corticobasal degeneration at the proteome level
Ji J, Ru B
J Neuropsychiatry Clin Neurosci (2005) 17(3): 364-71

Proteomic Patterns of Preinvasive Bronchial Lesions
Shyr Y, Yildiz PB, Gonzalez AL, Li H, Zhang X, Chaurand P, Yanagisawa K, Slovis BS, Miller RF, Ninan M, Miller YE, Franklin WA, Caprioli RM, Carbone DP, Massion PP
Am J Respir Crit Care Med Early Edition: published 22-Sep-2005

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Eukaryotic Cells And Tissues

A proteomic analysis of salivary glands of female Anopheles gambiae mosquito
Kalume DE, Okulate M, Zhong J, Reddy R, Suresh S, Deshpande N, Kumar N, Pandey A
Proteomics Early Edition: published 29-Aug-2005

A comparative proteomic analysis of the rat brain during rebound hyperphagia induced by space-restriction
Ishihara K, Nakata K, Yamagishi N, Iwasaki S, Kiriike N, Hatayama T
Mol Cell Biochem (2005) 276(1-2): 21-9

Proteomic analysis of supernatants of stored red blood cell products
Anniss AM, Glenister KM, Killian JJ, Sparrow RL
Transfusion (2005) 45(9): 1426-33

Proteome analysis of a rat liver nuclear insoluble protein fraction and localization of a novel protein, ISP36, to compartments in the interchromatin space
Segawa M, Niino K, Mineki R, Kaga N, Murayama K, Sugimoto K, Watanabe Y, Furukawa K, Horigome T
FEBS J (2005) 272(17): 4327-38

The protein composition of honeybee venom reconsidered by a proteomic approach
Nico Peiren, Frank Vanrobaeys, Dirk C. de Graaf, Bart Devreese, Jozef Van Beeumen and Frans J. Jacobs
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics (2005) 1752(1): 1-5

Proteome analysis of chicken embryonic gonads: Identification of major proteins from cultured gonadal primordial germ cells
Han BK, Kim JN, Shin JH, Kim JK, Jo DH, Kim H, Han JY
Mol Reprod Dev Early Edition: published 13-Sep-2005

Myocardial subproteomic analysis of a constitutively active Rac1 expressing transgenic mouse with lethal myocardial hypertrophy
Buscemi N, Murray C, Doherty-Kirby A, Lajoie G, Sussman MA, Van Eyk JE
Am J Physiol Heart Circ Physiol Early Edition: published 9-Sep-2005

Signalization and cytoskeleton activity through myosin IB during the early steps of phagocytosis in Entamoeba histolytica: a proteomic approach
Marion S, Laurent C, Guillen N
Cell Microbiol (2005) 7(10): 1504-18

Synapse proteomics of multiprotein complexes: en route from genes to nervous system diseases
Grant SG, Marshall MC, Page KL, Cumiskey MA, Armstrong JD
Hum Mol Genet Early Edition: published 8-Sep-2005

Differential expression of the fast skeletal muscle proteome following chronic low-frequency stimulation
Donoghue P, Doran P, Dowling P, Ohlendieck K
Biochim Biophys Acta Early Edition: published 1-Sep-2005

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Prokaryotes

Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions
Nandakumar MP, Muthuvijayan V, Marten MR
Biotechnol Bioeng Early Edition: published 22-Sep-2005

Metaproteomic analysis of Chesapeake Bay microbial communities
Hanson TE, Ginter JM, Wang K, Chen F
Saline Systems (2005) 1: 7.

Identification and Characterization of the Sulfolobus solfataricus P2 Proteome
Poh Kuan Chong and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Comparative proteomics using 2-D gel electrophoresis and mass spectrometry as tools to dissect stimulons and regulons in bacteria with sequenced or partially sequenced genomes
Encarnacion S, Hernandez M, Martinez-Batallar G, Contreras S, Del Carmen Vargas M, Mora J
Biol Proced Online (2005) 7: 117-35

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Pharmacology and Toxicology

Effects of formaldehyde inhalation on lung of rats
Yang YH, Xi ZG, Chao FH, Yang DF
Biomed Environ Sci (2005) 18(3): 164-8

Chemical Effects in Biological Systems - Data Dictionary (CEBS-DD): A Compendium of Terms for the Capture and Integration of Biological Study Design Description, Conventional Phenotypes and 'Omics Data
Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR, Brown R, Bruno M, Cunningham ML, Dix D, Eastin W, Frade C, Garcia A, Heinloth A, Irwin R, Madenspacher J, Merrick BA, Papoian T, Paules R, Rocca-Serra P, Sansone AS, Stevens J, Tomer K, Yang C, Waters M
Toxicol Sci Early Edition: published 8-Sep-2005

Identification of oxidative stress-related proteins for predictive screening of hepatotoxicity using a proteomic approach
Yamamoto T, Kikkawa R, Yamada H, Horii I
J Toxicol Sci (2005) 30(3): 213-27

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Protein Array

Screening microarrays of novel monoclonal antibodies for binding to T-, B- and myeloid leukaemia cells
Belov L, Huang P, Chrisp JS, Mulligan SP, Christopherson RI
J Immunol Methods Early Edition: published 24-Aug-2005

Antigen microarray profiling of autoantibodies in rheumatoid arthritis
Hueber W, Kidd BA, Tomooka BH, Lee BJ, Bruce B, Fries JF, Sonderstrup G, Monach P, Drijfhout JW, van Venrooij WJ, Utz PJ, Genovese MC, Robinson WH
Arthritis Rheum (2005) 52(9): 2645-2655

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Protein Characterization / PTMs

MALDI Mass Spectrometry Analysis of High Molecular Weight Proteins from Whole Bacterial Cells: Pretreatment of Samples with Surfactants
Mohammed A. Meetani and Kent J. Voorhees
Journal of the American Society for Mass Spectrometry (2005) 16(9): 1422-1426

Immobilization of Aminophenylboronic Acid on Magnetic Beads for the Direct Determination of Glycoproteins by Matrix Assisted Laser Desorption Ionization Mass Spectrometry
Jeong Heon Lee, Yangsun Kim, Mi Young Ha, Eun Kyu Lee and Jaebum Choo
Journal of the American Society for Mass Spectrometry (2005) 16(9): 1456-1460

Phosphoproteome Analysis of HeLa Cells Using Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)
Ramars Amanchy, Dario E. Kalume, Akiko Iwahori, Jun Zhong, and Akhilesh Pandey
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Phosphatase-Directed Phosphorylation-Site Determination: A Synthesis of Methods for the Detection and Identification of Phosphopeptides
Matthew P. Torres, Roopa Thapar, William F. Marzluff, and Christoph H. Borchers
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Selective Sampling of Phosphopeptides for Detection by MALDI Mass Spectrometry
Zhang H, Zhang C, Lajoie GA, Yeung KK
Anal Chem (2005) 77(18): 6078-84

Normalization of relative peptide ratios derived from in-gel digests: applications to protein variant analysis at the peptide level
Bergen HR 3rd, Muddiman DC, O'brien JF, Hoyer JD
Rapid Commun Mass Spectrom (2005) 19(19): 2871-2877

Probing Lysine Acetylation in Proteins: Strategies, Limitations, and Pitfalls of in Vitro Acetyltransferase Assays
Wilma Dormeyer, Melanie Ott, and Martina Schnolzer
Mol Cell Proteomics (2005) 4(9): 1226-1239

Time-resolved Mass Spectrometry of Tyrosine Phosphorylation Sites in the Epidermal Growth Factor Receptor Signaling Network Reveals Dynamic Modules
Yi Zhang, Alejandro Wolf-Yadlin, Phillip L. Ross, Darryl J. Pappin, John Rush, Douglas A. Lauffenburger, and Forest M. White
Mol Cell Proteomics (2005) 4(9): 1240-1250

Dynamic Changes in Protein-Protein Interaction and Protein Phosphorylation Probed with Amine-reactive Isotope Tag
Marcus B. Smolka, Claudio P. Albuquerque, Sheng-hong Chen, Kristina H.Schmidt, Xiao X. Wei, Richard D. Kolodner, and Huilin Zhou
Mol Cell Proteomics (2005) 4(9): 1358-1369

Optimizing Thiophosphorylation in the Presence of Competing Phosphorylation with MALDI-TOF-MS Detection
Laurie L. Parker, Alexander B. Schilling, Stephen J. Kron, and Stephen B. H. Kent
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/16/2005

Fe3O4/TiO2 Core/Shell Nanoparticles as Affinity Probes for the Analysis of Phosphopeptides Using TiO2 Surface-Assisted Laser Desorption/Ionization Mass Spectrometry
Cheng-Tai Chen and Yu-Chie Chen
ANALYTICAL CHEMISTRY (2005) 77(18): 5912-5919

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Protein-protein interaction

A human protein-protein interaction network: a resource for annotating the proteome
Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE
Cell (2005) 122(6): 957-68

Inferring protein domain interactions from databases of interacting proteins
Robert Riley, Christopher Lee, Chiara Sabatti, David Eisenberg
Genome Biology (2005) 6(10): R89

Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin
McCracken S, Longman D, Marcon E, Moens P, Downey M, Nickerson JA, Jessberger R, Wilde A, Caceres JF, Emili A, Blencowe BJ
J Biol Chem Early Edition: published 13-Sep-2005

Methods for the Detection of Paxillin Post-translational Modifications and Interacting Proteins by Mass Spectrometry
Melanie J. Schroeder, Donna J. Webb, Jeffrey Shabanowitz, Alan F. Horwitz, and Donald F. Hunt
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/16/2005

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Quantitation

Quantitative MS for proteomics: teaching a new dog old tricks
MacCoss MJ, Matthews DE
Anal Chem (2005) 77(15): 294A-302A

N-terminal isotope tagging with propionic anhydride: Proteomic analysis of myogenic differentiation of C2C12 cells
Nam HW, Simpson R, Kim YS
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 12-Sep-2005

Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein
Yasushi Ishihama, Yoshiya Oda, Tsuyoshi Tabata, Toshitaka Sato, Takeshi Nagasu, Juri Rappsilber, and Matthias Mann
Mol Cell Proteomics (2005) 4(9): 1265-1272

Quantitative Neuropeptidomics of Microwave-irradiated Mouse Brain and Pituitary
Fa-Yun Che, Jihyeon Lim, Hui Pan, Reeta Biswas, and Lloyd D. Fricker
Mol Cell Proteomics (2005) 4(9): 1391-1405

Identification and Quantification of Differentially Expressed Proteins in E-Cadherin Deficient SCC9 Cells and SCC9 Transfectants Expressing E-Cadherin by Dimethyl Isotope Labeling, LC-MALDI MS and MS/MS J. Proteome Res. 2005, 4, 1419-1426
Chengjie Ji, Laiji Li, Mulu Gebre, Manijeh Pasdar, and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/16/2005

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Review

Genetics, genomics and proteomics in atherosclerosis research
Binder BR, Yla-Herttuala S
Ann Med (2005) 37(5): 323-32

The potential of proteomics and peptidomics for allergy and asthma research
Crameri R
Allergy (2005) 60(10): 1227-37

Proteomics of Metal Transport and Metal-Associated Diseases
Kulkarni PP, She YM, Smith SD, Roberts EA, Sarkar B
Chemistry Early Edition: published 31-Aug-2005

Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry
Guan JQ, Chance MR
Trends Biochem Sci Early Edition: published 26-Aug-2005

The nuclear membrane proteome: extending the envelope
Schirmer EC, Gerace L
Trends Biochem Sci Early Edition: published 24-Aug-2005

Functional Genomics meets neurodegenerative disorders Part II: Application and data integration
David DC, Gotz J
Prog Neurobiol Early Edition: published 14-Sep-2005

Functional Genomics meets neurodegenerative disorders Part I: Transcriptomic and proteomic technology
Hoerndli F, Gotz J
Prog Neurobiol Early Edition: published 13-Sep-2005

Phosphoproteomics: new insights into cellular signaling
Mumby M, Brekken D
Genome Biology (2005) 6(9): 230

Emerging issues of the expression profiling technologies for the study of gynecologic cancer
Pappa KI, Anagnou NP
Am J Obstet Gynecol (2005) 193(3 Suppl): 908-18

Transcriptomics and proteomics: tools for optimising phytoremediation activities
Coleman JO, Haslam RP, Downie AL
Z Naturforsch [C] (2005) 60(7-8): 544-8

Molecular diagnostics of malignant disorders
Rose MG, Degar BA, Berliner N
Clin Adv Hematol Oncol (2004) 2(10): 650-60

Interactome: Gateway into systems biology
Cusick M, Klitgord N, Vidal M, Hill DE
Hum Mol Genet Early Edition: published 14-Sep-2005

Systems biology in the cell nucleus
Gorski S, Misteli T
J Cell Sci (2005) 118(Pt 18): 4083-92

Toxicogenomics concepts and applications to study hepatic effects of food additives and chemicals
Stierum R, Heijne W, Kienhuis A, van Ommen B, Groten J
Toxicol Appl Pharmacol Early Edition: published 30-Aug-2005

CSF biomarkers for Alzheimer's disease: use in early diagnosis and evaluation of drug treatment
Blennow K
Expert Rev Mol Diagn (2005) 5(5): 661-72

Protein function from sequence and structure data
Domingues FS, Lengauer T
Appl Bioinformatics (2003) 3(1): 3-12

SELDI-TOF mass spectrometry for cancer biomarker discovery and serum proteomic diagnostics
Simpkins F, Czechowicz JA, Liotta L, Kohn EC
Pharmacogenomics (2005) 6(6): 647-53

Chaperomics: In Vivo GroEL Function Defined
Ellis RJ
Curr Biol (2005) 15(17): R661-3

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Methodology

Threshold values for detergents in protein and peptide samples for mass spectrometry
Li X, Franz T
Rapid Commun Mass Spectrom (2005) 19(20): 2986-2988

An optimized protein in-gel digest method for reliable proteome characterization by MALDI-TOF-MS analysis
Mohottalage S, Goegan P, Vincent R
Anal Biochem Early Edition: published 13-Sep-2005

Formation of phosphopeptide-metal ion complexes in liquid chromatography/electrospray mass spectrometry and their influence on phosphopeptide detection
Liu S, Zhang C, Campbell JL, Zhang H, Yeung KK, Han VK, Lajoie GA
Rapid Commun Mass Spectrom (2005) 19(19): 2747-2756

Optimization of protein identification from digests as analyzed by capillary isoelectric focusing-mass spectrometry
Henricus F. Storms, Robert van der Heijden, Ubbo R. Tjaden and Jan van der Greef
J Chromatogr B (2005) 824(1-2): 189-200

Interactions Between Sodium Dodecyl Sulfate Micelles and Peptides During Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) of Proteolytic Digests
Rama Tummala, Kari B. Green-Church and Patrick A. Limbach
Journal of the American Society for Mass Spectrometry (2005) 16(9): 1438-1446

LC-nanospray-MS/MS analysis of hydrophobic proteins from membrane protein complexes isolated by blue-native electrophoresis
Fandino AS, Rais I, Vollmer M, Elgass H, Schagger H, Karas M
J Mass Spectrom (2005) 40(9): 1223-1231

Phosphatase-Directed Phosphorylation-Site Determination: A Synthesis of Methods for the Detection and Identification of Phosphopeptides
Matthew P. Torres, Roopa Thapar, William F. Marzluff, and Christoph H. Borchers
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands
Thulasiraman V, Lin S, Gheorghiu L, Lathrop J, Lomas L, Hammond D, Boschetti E
Electrophoresis (2005) 26(18): 3561-3571

Protein identification assisted by the prediction of retention time in liquid chromatography/tandem mass spectrometry
Wang Y, Zhang J, Gu X, Zhang XM
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 10-Sep-2005

Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma
Chou PH, Chen SH, Liao HK, Lin PC, Her GR, Lai AC, Chen JH, Lin CC, Chen YJ
Anal Chem (2005) 77(18): 5990-5997

Proteomic Analysis with Integrated Multiple Dimensional Liquid Chromatography/Mass Spectrometry Based on Elution of Ion Exchange Column Using pH Steps
Dai J, Shieh CH, Sheng QH, Zhou H, Zeng R
Anal Chem (2005) 77(18): 5793-9

Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS
Crockett DK, Lin Z, Vaughn CP, Lim MS, Elenitoba-Johnson KS
Lab Invest Early Edition: published 5-Sep-2005

Phosphoproteome Analysis of HeLa Cells Using Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)
Ramars Amanchy, Dario E. Kalume, Akiko Iwahori, Jun Zhong, and Akhilesh Pandey
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Effect of Immunoaffinity Depletion of Human Serum during Proteomic Investigations
Anastasia K. Yocum, Kenneth Yu, Tomoyuki Oe, and Ian A Blair
JOURNAL OF PROTEOME RESEARCH Early Edition: published 09/09/2005

Consecutive Ion Activation for Top Down Mass Spectrometry: Improved Protein Sequencing by Nozzle-Skimmer Dissociation
Huili Zhai, Xuemei Han, Kathrin Breuker, and Fred W. McLafferty
ANALYTICAL CHEMISTRY (2005) 77(18): 5777-5784

Data pre-processing in liquid chromatography-mass spectrometry based proteomics
Zhang X, Asara JM, Adamec J, Ouzzani M, Elmagarmid AK
Bioinformatics Early Edition: published 8-Sep-2005

Protein-Reactive Natural Products
Drahl C, Cravatt BF, Sorensen EJ
Angew Chem Int Ed Engl (2005) 44(36): 5788-5809

Proteohistography--Direct Analysis of Tissue with High Sensitivity and High Spatial Resolution Using ProteinChip Technology
Ernst G, Melle C, Schimmel B, Bleul A, von Eggeling F
J Histochem Cytochem Early Edition: published 7-Sep-2005

Nanosecond Laser-Induced Photochemical Oxidation Method for Protein Surface Mapping with Mass Spectrometry
Thin Thin Aye, Teck Yew Low, and Siu Kwan Sze
ANALYTICAL CHEMISTRY (2005) 77(18): 5814-5822

Determination of Phosphorus-, Copper-, and Zinc-Containing Human Brain Proteins by LA-ICPMS and MALDI-FTICR-MS
J. Sabine Becker, Miroslav Zoriy, J. Susanne Becker, Carola Pickhardt, Eugen Damoc, Gabor Juhacz, Miklos Palkovits, and Michael Przybylski
ANALYTICAL CHEMISTRY (2005) 77(18): 5851-5860

Structural Analysis of an N-Glycan with "1-4 Bisecting Branch" from Human Serum IgG by Negative-Ion MSn Spectral Matching and Exoglycosidase Digestion
Yasuhiro Takegawa, Kisaburo Deguchi, Hiroaki Nakagawa, and Shin-Ichiro Nishimura
ANALYTICAL CHEMISTRY (2005) 77(18): 6062-6068

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Meeting

Report on the 1(st )International Conference of the Hellenic Proteomics Society in Athens, Greece
Fountoulakis M, Vlahou A
Proteomics Early Edition: published 29-Aug-2005

Beyond Genome - Proteomics: the future of biomedicine
Zhang WW
Pharmacogenomics (2005) 6(6): 555-62

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Other

$104 million proteomics initiative gets green light
[No authors listed]
J Natl Cancer Inst (2005) 97(18): 1324-5

Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis
Elena SF
Arch Virol Early Edition: published 20-Sep-2005

The clinical use of tumor makers in select cancers: are you confident enough to discuss them with your patients?
Sanchez Yamamoto D, Hallquist Viale P, Roesser K, Lin A
Oncol Nurs Forum (2005) 32(5): 1013-22; quiz 1023-4

Protein Identification: The Good, the Bad, and the Ugly
Ralph A. Bradshaw, Alma L. Burlingame, Steve Carr, and Ruedi Aebersold
Mol Cell Proteomics (2005) 4(9): 1221-1222

Revised Draft Guidelines for Proteomic Data Publication
Mol Cell Proteomics (2005) 4(9): 1223-1225

Proteomics' new order
[No authors listed]
Nature (2005) 437(7056): 169-70

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