SPS' Digest

Issue 25, 2-Dec-2005

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Quick jumps to articles in: Bioinformatics (15) / Biological applications (18) / Biomedical and clinical applications (36) / Eukaryotic Cells And Tissues (7) / Prokaryotes (13) / Pharmacology and Toxicology (1) / Protein Array (2) / Protein Characterization - PTMs (3) / Protein-protein interaction (3) / Quantitation (4) / Review (15) / Methodology (16) / Meeting (1) / Other (2) /

In this issue, 132 articles have been selected from:

Am J Respir Crit Care Med, Early Edition, 17-Nov-2005 (1 article)
Anal Biochem, Early Edition, 2-Nov-2005->26-Oct-2005 (2 articles)
Anal Chem, Volume 77, Issues 21+22+23, 2005 (13 articles)
Anat Rec A Discov Mol Cell Evol Biol, Early Edition, 10-Nov-2005 (1 article)
Angew Chem Int Ed Engl, Early Edition, 3-Nov-2005 (1 article)
Appl Environ Microbiol, Volume 71, Issue 11, 2005 (2 articles)
BMC Bioinformatics, Volume 6, Issue 1, 2005 (2 articles)
Basic Res Cardiol, Early Edition, 11-Nov-2005 (1 article)
Biochim Biophys Acta, Early Edition, 21-Oct-2005->24-Oct-2005 (2 articles)
Bioorg Med Chem Lett, Early Edition, 11-Nov-2005 (1 article)
Biophys J, Early Edition, 18-Nov-2005 (1 article)
Biotechnol Adv, Early Edition, 7-Nov-2005 (1 article)
Cancer Cell, Volume 8, Issue 5, 2005 (1 article)
Cancer Lett, Volume 230, Issue 2, 2005 (1 article)
Cancer Res, Volume 65, Issues 21+22, 2005 (4 articles)
Chin J Physiol, Volume 48, Issue 3, 2005 (1 article)
Circulation, Volume 112, Issue 19, 2005 (1 article)
Clin Adv Hematol Oncol, Volume 1, Issue 8, 2003 (1 article)
Clin Cancer Res, Volume 11, Issue 22, 2005 (1 article)
Clin Chem, Volume 51, Issue 12, 2005 (1 article)
Comp Biochem Physiol C Toxicol Pharmacol, Early Edition, 5-Nov-2005 (1 article)
Curr Opin Neurol, Volume 18, Issue 6, 2005 (1 article)
Curr Top Microbiol Immunol, Volume 295, 2005 (1 article)
Current Proteomics, Volume 2, Issue 3, 2005 (5 articles)
Diab Vasc Dis Res, Volume 2, Issue 2, 2005 (1 article)
Endocrinology, Early Edition, 3-Nov-2005 (1 article)
Exp Gerontol, Early Edition, 20-Nov-2005 (1 article)
Expert Opin Ther Targets, Volume 9, Issue 6, 2005 (1 article)
Expert Rev Proteomics, Volume 2, Issue 6, 2005 (8 articles)
FEBS Lett, Early Edition, 24-Oct-2005 (1 article)
Free Radic Res, Volume 39, Issues 11+12, 2005 (2 articles)
Gastroenterology, Volume 129, Issue 5, 2005 (1 article)
Immunome Res, Volume 1, Issue 1, 2005 (2 articles)
In Silico Biol, Volume 5, Issue 4, 2005 (1 article)
J Agric Food Chem, Volume 53, Issue 23, 2005 (1 article)
J Androl, Early Edition, 8-Nov-2005 (1 article)
J Bacteriol, Volume 187, Issue 23, 2005 (5 articles)
J Biol Chem, Early Edition, 28-Oct-2005 (1 article)
J Cancer Res Clin Oncol, Early Edition, 28-Oct-2005 (1 article)
J Clin Endocrinol Metab, Early Edition, 22-Nov-2005 (1 article)
J Immunol, Volume 175, Issue 10, 2005 (1 article)
J Ind Microbiol Biotechnol, Early Edition, 25-Nov-2005 (1 article)
J Insur Med, Volume 37, Issue 3, 2005 (1 article)
J Neurochem, Early Edition, 3-Nov-2005 (1 article)
J Neurosci Res, Early Edition, 4-Nov-2005 (1 article)
J Proteome Res, Early Edition, 11/25/2005->12/02/2005 (8 articles)
J Toxicol Environ Health A, Volume 69, Issue 1, 2006 (1 article)
Life Sci, Early Edition, 8-Nov-2005 (1 article)
Mass Spectrom Rev, Early Edition, 11-Nov-2005 (2 articles)
Mech Ageing Dev, Early Edition, 14-Nov-2005 (1 article)
Med Res Rev, Early Edition, 10-Nov-2005 (1 article)
Methods Enzymol, Volume 396PE, 2005 (2 articles)
Mol Biochem Parasitol, Early Edition, 19-Oct-2005->21-Oct-2005 (2 articles)
Mol Cell Biol, Volume 25, Issue 23, 2005 (1 article)
Mol Cell Proteomics, Volume 4, Issue 11, 2005 (12 articles)
Mol Cells, Volume 20, Issue 2, 2005 (1 article)
Nat Methods, Volume 2, Issues 11+12, 2005 (2 articles)
Neurobiol Aging, Early Edition, 3-Nov-2005 (1 article)
Neurobiol Aging, Volume 27, Issue 1, 2006 (1 article)
Nucl Acids Res, Volume 33, Issue 19, 2005 (1 article)
Pathol Res Pract, Volume 201, Issue 12, 2005 (1 article)
Pediatr Transplant, Volume 9, Issue 6, 2005 (1 article)
Photosynth Res, Early Edition, 15-Nov-2005 (1 article)
Plant Methods, Volume 1, Issue 1, 2005 (2 articles)
Plant Physiol Biochem, Early Edition, 29-Sep-2005 (1 article)
Proc Natl Acad Sci U S A, Early Edition, 14-Nov-2005->17-Nov-2005 (2 articles)
Proc Natl Acad Sci U S A, Volume 102, Issue 47, 2005 (1 article)
Protein Pept Lett, Volume 12, Issue 8, 2005 (1 article)
Rapid Commun Mass Spectrom, Volume 19, Issue 23, 2005 (1 article)
Rapid Commun Mass Spectrom, Volume 20, Issue 1, 2005 (1 article)
Structure (Camb), Volume 13, Issue 11, 2005 (1 article)
Toxicon, Early Edition, 9-Nov-2005 (1 article)

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

Quick jumps to articles in: Bioinformatics (15) / Biological applications (18) / Biomedical and clinical applications (36) / Eukaryotic Cells And Tissues (7) / Prokaryotes (13) / Pharmacology and Toxicology (1) / Protein Array (2) / Protein Characterization - PTMs (3) / Protein-protein interaction (3) / Quantitation (4) / Review (15) / Methodology (16) / Meeting (1) / Other (2) /

Bioinformatics

Possible Detection of Pancreatic Cancer by Plasma Protein Profiling
Honda K, Hayashida Y, Umaki T, Okusaka T, Kosuge T, Kikuchi S, Endo M, Tsuchida A, Aoki T, Itoi T, Moriyasu F, Hirohashi S, Yamada T
Cancer Res (2005) 65(22): 10613-10622

Top-down proteomics for rapid identification of intact microorganisms
Demirev PA, Feldman AB, Kowalski P, Lin JS
Anal Chem (2005) 77(22): 7455-61

NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing
Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM
Anal Chem (2005) 77(22): 7265-73

Multicomponent Internal Recalibration of an LC-FTICR-MS Analysis Employing a Partially Characterized Complex Peptide Mixture: Systematic and Random Errors
Yanofsky CM, Bell AW, Lesimple S, Morales F, Lam TT, Blakney GT, Marshall AG, Carrillo B, Lekpor K, Boismenu D, Kearney RE
Anal Chem (2005) 77(22): 7246-7254

Comparison of Large Proteomic Datasets
Maurer, Martin H
Current Proteomics (2005) 2(3): 179-189

Protein Structure Prediction Using an Augmented Homology Modeling Method: Key Importance of Iterative-Procedures for Obtaining Consistent Quality Models
McDonald, S.; Mylvaganam, S.; Shenderovich, M.; Tseitin, V.; Fisher, C.; Raghunathan, G.; Zheng, J.; Kodandapani, R.; Dudek, M.; Muthuchi-dambaram Prabhakaran,; Ramnarayan, Kal
Current Proteomics (2005) 2(3): 233-258

What is mzXML good for?
Simon M Lin, Lihua Zhu, Andrew Q Winter, Maciek Sasinowski, Warren A Kibbe
Expert Review of Proteomics (2005) 2(6): 839-845

Bioinformatics approaches in clinical proteomics
Eric T Fung, Scot R Weinberger, Ed Gavin, Fujun Zhang
Expert Review of Proteomics (2005) 2(6): 847-862

IMGT, the international ImMunoGeneTics information system(R): a standardized approach for immunogenetics and immunoinformatics
Lefranc MP
Immunome Res (2005) 1(1): 3

An algorithmic framework for genome-wide modeling and analysis of translation networks
Mehra A, Hatzimanikatis V
Biophys J Early Edition: published 18-Nov-2005

MASPIC: Intensity-Based Tandem Mass Spectrometry Scoring Scheme That Improves Peptide Identification at High Confidence
Chandrasegaran Narasimhan, David L. Tabb, Nathan C. VerBerkmoes, Melissa R. Thompson, Robert L. Hettich, and Edward C. Uberbacher
ANALYTICAL CHEMISTRY (2005) 77(23): 7581-7593

KEGG-based pathway visualization tool for complex omics data
Arakawa K, Kono N, Yamada Y, Mori H, Tomita M
In Silico Biol (2005) 5(4): 0039

Computational identification of strain-, species- and genus-specific proteins
Mazumder R, Natale DA, Murthy S, Thiagarajan R, Wu CH
BMC Bioinformatics (2005) 6(1): 279

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process
Wolski WE, Lalowski M, Martus P, Herwig R, Giavalisco P, Gobom J, Sickmann A, Lehrach H, Reinert K
BMC Bioinformatics (2005) 6: 285

Farm animal genomics and informatics: an update
Fadiel A, Anidi I, Eichenbaum KD
Nucl Acids Res (2005) 33(19): 6308-18

Biological applications

Comparison of the partial proteomes of the venoms of Brazilian spiders of the genus Phoneutria
Richardson M, Pimenta AM, Bemquerer MP, Santoro MM, Beirao PS, Lima ME, Figueiredo SG, Bloch C Jr, Vasconcelos EA, Campos FA, Gomes PC, Cordeiro MN
Comp Biochem Physiol C Toxicol Pharmacol Early Edition: published 5-Nov-2005

Evaluation of Nonstarch Polysaccharides and Oligosaccharide Content of Different Soybean Varieties (Glycine max) by Near-Infrared Spectroscopy and Proteomics
Hollung K, Overland M, Hrustic M, Sekulic P, Miladinovic J, Martens H, Narum B, Sahlstrom S, Sorensen M, Storebakken T, Skrede A
J Agric Food Chem (2005) 53(23): 9112-9121

Transcriptomic and proteomic patterns of systemic inflammation in on-pump and off-pump coronary artery bypass grafting
Tomic V, Russwurm S, Moller E, Claus RA, Blaess M, Brunkhorst F, Bruegel M, Bode K, Bloos F, Wippermann J, Wahlers T, Deigner HP, Thiery J, Reinhart K, Bauer M
Circulation (2005) 112(19): 2912-20

SARS Proteomics Reveals Viral Secrets
Garman E
Structure (Camb) (2005) 13(11): 1582-3

Proteomic analysis of the entomopathogenic nematode Steinernema feltiae IS-6 IJs under evaporative and osmotic stresses
Chen S, Glazer I, Gollop N, Cash P, Argo E, Innes A, Stewart E, Davidson I, Wilson MJ
Mol Biochem Parasitol Early Edition: published 21-Oct-2005

The Potential of Ecotoxicoproteomics in Environmental Monitoring: Biomarker Profiling in Mussel Plasma Using Proteinchip Array Technology
Bjornstad A, Larsen BK, Skadsheim A, Jones MB, Andersen OK
J Toxicol Environ Health A (2006) 69(1): 77-96

Protein Nitration in Biological Aging: Proteomic and Tandem Mass Spectrometric Characterization of Nitrated Sites
Kanski J, Schoneich C
Methods Enzymol (2005) 396PE: 160-171

Kinetics and strain variation of phagosome proteins of Entamoeba histolytica by proteomic analysis
Okada M, Huston CD, Oue M, Mann BJ, Petri WA Jr, Kita K, Nozaki T
Mol Biochem Parasitol Early Edition: published 19-Oct-2005

Proteomic identification of glyceraldehyde 3-phosphate dehydrogenase as an inhibitory target of hydrogen peroxide in Arabidopsis
Hancock JT, Henson D, Nyirenda M, Desikan R, Harrison J, Lewis M, Hughes J, Neill SJ
Plant Physiol Biochem Early Edition: published 29-Sep-2005

Estimation of the mtDNA mutation rate in aging mice by proteome analysis and mathematical modeling
Mao L, Zabel C, Wacker MA, Nebrich G, Sagi D, Schrade P, Bachmann S, Kowald A, Klose J
Exp Gerontol Early Edition: published 20-Nov-2005

Capillary affinity electrophoresis using lectins for the analysis of milk oligosaccharide structure and its application to bovine colostrum oligosaccharides
Nakajima K, Kinoshita M, Matsushita N, Urashima T, Suzuki M, Suzuki A, Kakehi K
Anal Biochem Early Edition: published 26-Oct-2005

Amnesic shellfish poisoning toxins in bivalve molluscs in Ireland
James KJ, Gillman M, Amandi MF, Lopez-Rivera A, Puente PF, Lehane M, Mitrovic S, Furey A
Toxicon Early Edition: published 9-Nov-2005

ETO-2 Associates with SCL in Erythroid Cells and Megakaryocytes and Provides Repressor Functions in Erythropoiesis
Schuh AH, Tipping AJ, Clark AJ, Hamlett I, Guyot B, Iborra FJ, Rodriguez P, Strouboulis J, Enver T, Vyas P, Porcher C
Mol Cell Biol (2005) 25(23): 10235-10250

Decreased levels of CXC-chemokines in serum of benzene-exposed workers identified by array-based proteomics
Vermeulen R, Lan Q, Zhang L, Gunn L, McCarthy D, Woodbury RL, McGuire M, Podust VN, Li G, Chatterjee N, Mu R, Yin S, Rothman N, Smith MT
Proc Natl Acad Sci U S A Early Edition: published 14-Nov-2005

Compositional Characterization of the Cytoskeleton of NK-Like Cells
Xiaobo Meng and John A. Wilkins
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/18/2005

The Lipolytic Proteome of Mouse Adipose Tissue
Ruth Birner-Gruenberger, Heidrun Susani-Etzerodt, Markus Waldhuber, Gernot Riesenhuber, Hannes Schmidinger, Gerald Rechberger, Manfred Kollroser, Juliane G. Strauss, Achim Lass, Robert Zimmermann, Guenter Haemmerle, Rudolf Zechner, and Albin Hermetter
Mol Cell Proteomics (2005) 4(11): 1710-1717

Establishment of epidermal cell lines derived from the skin of the Atlantic bottlenose dolphin (Tursiops truncatus)
Yu J, Kindy MS, Ellis BC, Baatz JE, Peden-Adams M, Ellingham TJ, Wolff DJ, Fair PA, Gattoni-Celli S
Anat Rec A Discov Mol Cell Evol Biol Early Edition: published 10-Nov-2005

Identification of proteins in the accessory sex gland fluid associated with fertility indexes of dairy bulls: a proteomic approach
Moura AA, Koc H, Chapman DA, Killian GJ
J Androl Early Edition: published 8-Nov-2005

Biomedical and clinical applications

Rheumatoid Arthritis, a complex multifactorial disease: On the way toward individualized medicine
Glocker MO, Guthke R, Kekow J, Thiesen HJ
Med Res Rev Early Edition: published 10-Nov-2005

Myocardial preconditioning and remote renal preconditioning Identifying a protective factor using proteomic methods?
Lang SC, Elsasser A, Scheler C, Vetter S, Tiefenbacher CP, Kubler W, Katus HA, Vogt AM
Basic Res Cardiol Early Edition: published 11-Nov-2005

Biomarkers for neurodegenerative diseases
Henley SM, Bates GP, Tabrizi SJ
Curr Opin Neurol (2005) 18(6): 698-705

Mitochondrial dysfunction in cardiac ischemia-reperfusion injury: ROS from complex I, without inhibition
Tompkins AJ, Burwell LS, Digerness SB, Zaragoza C, Holman WL, Brookes PS
Biochim Biophys Acta Early Edition: published 21-Oct-2005

Large-scale identification of human biliary proteins from a cholesterol stone patient using a proteomic approach
Zhou H, Chen B, Li RX, Sheng QH, Li SJ, Zhang L, Li L, Xia QC, Wang HY, Zeng R
Rapid Commun Mass Spectrom (2005) 19(23): 3569-3578

Sleep deprivation-induced protein changes in basal forebrain: Implications for synaptic plasticity
Basheer R, Brown R, Ramesh V, Begum S, McCarley RW
J Neurosci Res Early Edition: published 4-Nov-2005

Proteomic Scan for Tyrosinase Peptide Antigenic Pattern in Vitiligo and Melanoma: Role of Sequence Similarity and HLA-DR1 Affinity
Lucchese A, Willers J, Mittelman A, Kanduc D, Dummer R
J Immunol (2005) 175(10): 7009-20

Redox proteomics identification of oxidized proteins in Alzheimer's disease hippocampus and cerebellum: An approach to understand pathological and biochemical alterations in AD
Sultana R, Boyd-Kimball D, Poon HF, Cai J, Pierce WM, Klein JB, Merchant M, Markesbery WR, Butterfield DA
Neurobiol Aging Early Edition: published 3-Nov-2005

How proteomics reveals potential biomarkers in brain diseases
Oliver Schmidt, Thomas Schulenborg, Helmut E Meyer, Katrin Marcus, Michael Hamacher
Expert Review of Proteomics (2005) 2(6): 901-913

Proteomics of TGF- signaling and its impact on breast cancer
Serhiy Souchelnytskyi
Expert Review of Proteomics (2005) 2(6): 925-935

SELDI-MS-based expression profiling of ductal invasive and lobular invasive human breast carcinomas
Traub F, Feist H, Kreipe HH, Pich A
Pathol Res Pract (2005) 201(12): 763-770

Proteomic analysis on multi-drug resistant cells HL-60/DOX of acute myeloblastic leukemia
Chen CY, Jia JH, Zhang MX, Meng YS, Kong DX, Pan XL, Yu XP
Chin J Physiol (2005) 48(3): 115-20

Novel Biomarkers of Human Growth Hormone Action from Serum Proteomic Profiling using Protein Chip Mass Spectrometry
Chung L, Clifford D, Buckley M, Baxter RC
J Clin Endocrinol Metab Early Edition: published 22-Nov-2005

Possible prediction of chemoradiosensitivity of esophageal cancer by serum protein profiling
Hayashida Y, Honda K, Osaka Y, Hara T, Umaki T, Tsuchida A, Aoki T, Hirohashi S, Yamada T
Clin Cancer Res (2005) 11(22): 8042-7

Proteomic characterization of oxidative dysfunction in human umbilical vein endothelial cells (HUVEC) induced by exposure to oxidized LDL
Kinumi T, Ogawa Y, Kimata J, Saito Y, Yoshida Y, Niki E
Free Radic Res (2005) 39(12): 1335-44

Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain
Korolainen MA, Goldsteins G, Nyman TA, Alafuzoff I, Koistinaho J, Pirttila T
Neurobiol Aging (2006) 27(1): 42-53

Combined Top-Down and Bottom-Up Mass Spectrometric Approach to Characterization of Biomarkers for Renal Disease
Michael J. Chalmers, Colin Logan Mackay, Christopher L. Hendrickson, Stefan Wittke, Michael Walden, Harald Mischak, Danilo Fliser, Ingo Just, and Alan G. Marshall
ANALYTICAL CHEMISTRY (2005) 77(22): 7163-7171

Complement C3a and C4a Increased in Plasma of Patients with Aspirin-induced Asthma
Lee SH, Rhim T, Choi YS, Min JW, Kim SH, Cho SY, Paik YK, Park CS
Am J Respir Crit Care Med Early Edition: published 17-Nov-2005

Proteome studies of CSF in AD patients
Davidsson P, Sjogren M
Mech Ageing Dev Early Edition: published 14-Nov-2005

Differential regulation of anti-inflammatory proteins in human rheumatoid synoviocyte MH7A cell by celecoxib and ibuprofen
Heum Park J, Cho Han D, Kim J, Hyung Hong S, Lee SK, Seog Yoon K, Min Kim J, Son KH, Miyazawa K, Kwon BM
Life Sci Early Edition: published 8-Nov-2005

The Role of Peroxiredoxin II in Radiation-Resistant MCF-7 Breast Cancer Cells
Wang T, Tamae D, Lebon T, Shively JE, Yen Y, Li JJ
Cancer Res (2005) 65(22): 10338-10346

Novel Molecular Signaling and Classification of Human Clinically Nonfunctional Pituitary Adenomas Identified by Gene Expression Profiling and Proteomic Analyses
Moreno CS, Evans CO, Zhan X, Okor M, Desiderio DM, Oyesiku NM
Cancer Res (2005) 65(22): 10214-10222

Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression
Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM
Cancer Cell (2005) 8(5): 393-406

Decreased levels of CXC-chemokines in serum of benzene-exposed workers identified by array-based proteomics
Roel Vermeulen, Qing Lan, Luoping Zhang, Laura Gunn, Diane McCarthy, Ronald L. Woodbury, Marielena McGuire, Vladimir N. Podust, Guilan Li, Nilanjan Chatterjee, Ruidong Mu, Songnian Yin, Nathaniel Rothman, and Martyn T. Smith
PNAS (2005) 102(47): 17041-17046

Principal Component Analysis of the Conformational Freedom within the EF-Hand Superfamily
Elena Babini, Ivano Bertini, Francesco Capozzi, Claudio Luchinat, # Alessandro Quattrone, and Maria Turano
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/11/2005

Identification of Human Hepatocellular Carcinoma-Related Biomarkers by Two-Dimensional Difference Gel Electrophoresis and Mass Spectrometry
I-Neng Lee, Chien-Hung Chen, Jin-Chuan Sheu Hsuan-Shu Lee, Guan-Tarn Huang, Chen-Yin Yu, Fung-Jou Lu, and Lu-Ping Chow
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/11/2005

Proteomics-based Identification of Human Acute Leukemia Antigens That Induce Humoral Immune Response
Jiu-wei Cui, Wei-hua Li, Jie Wang, Ai-ling Li, Hui-yan Li, Hong-xia Wang, Kun He, Wei Li, Li-hua Kang, Ming Yu, Bei-fen Shen, Guan-Jun Wang, and Xue-min Zhang
Mol Cell Proteomics (2005) 4(11): 1718-1724

Proteomic Analysis of Formalin-fixed Prostate Cancer Tissue
Brian L. Hood, Marlene M. Darfler, Thomas G. Guiel, Bungo Furusato, David A. Lucas, Bradley R. Ringeisen, Isabell A. Sesterhenn, Thomas P. Conrads, Timothy D. Veenstra, and David B. Krizman
Mol Cell Proteomics (2005) 4(11): 1741-1753

The Human Platelet Membrane Proteome Reveals Several New Potential Membrane Proteins
Jan Moebius, Rene Peiman Zahedi, Urs Lewandrowski, Claudia Berger, Ulrich Walter, and Albert Sickmann
Mol Cell Proteomics (2005) 4(11): 1754-1761

Organ mRNA and plasma proteome changes in the adjuvant-induced arthritis model: responses to disease induction and therapy with the estrogen receptor-{beta} selective agonist ERB-041
Follettie MT, Pinard M, Keith JC Jr, Wang L, Chelsky D, Hayward C, Kearney P, Thibault P, Paramithiotis E, Dorner AJ, Harris HA
Endocrinology Early Edition: published 3-Nov-2005

Alterations of Protein Expression in Macrophages in Response to Candida albicans Infection
Shin YK, Kim KY, Paik YK
Mol Cells (2005) 20(2): 271-9

Cerebrospinal fluid proteomic analysis reveals dysregulation of methionine aminopeptidase-2 expression in human and mouse neurofibromatosis 1-associated glioma
Dasgupta B, Yi Y, Hegedus B, Weber JD, Gutmann DH
Cancer Res (2005) 65(21): 9843-50

Proteomic analysis on metastasis-associated proteins of human hepatocellular carcinoma tissues
Song HY, Liu YK, Feng JT, Cui JF, Dai Z, Zhang LJ, Feng JX, Shen HL, Tang ZY
J Cancer Res Clin Oncol Early Edition: published 28-Oct-2005

Analysis of NOD2-mediated proteome response to muramyl-dipeptide in HEK293 cells
Weichart D, Gobom J, Klopfleisch S, Hasler R, Gustavsson N, Billmann S, Lehrach H, Seegert D, Schreiber S, Rosenstiel P
J Biol Chem Early Edition: published 28-Oct-2005

American gastroenterological association future trends committee report: the application of genomic and proteomic technologies to digestive disease diagnosis and treatment and their likely impact on gastroenterology clinical practice
Lazaridis KN, Juran BD
Gastroenterology (2005) 129(5): 1720-52

Possible Detection of Pancreatic Cancer by Plasma Protein Profiling
Honda K, Hayashida Y, Umaki T, Okusaka T, Kosuge T, Kikuchi S, Endo M, Tsuchida A, Aoki T, Itoi T, Moriyasu F, Hirohashi S, Yamada T
Cancer Res (2005) 65(22): 10613-10622

Eukaryotic Cells And Tissues

Systematic Evaluation of Sample Preparation Methods for Gel-Based Human Urinary Proteomics: Quantity, Quality, and Variability
Visith Thongboonkerd, Somchai Chutipongtanate, and Rattiyaporn Kanlaya
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/25/2005

Analysis of Leaf Proteome after UV-B Irradiation in Maize Lines Differing in Sensitivity
Paula Casati, Xing Zhang, Alma L. Burlingame, and Virginia Walbot
Mol Cell Proteomics (2005) 4(11): 1673-1685

Gametes Alter the Oviductal Secretory Proteome
A. Stephen Georgiou, Edita Sostaric, Chi H. Wong, Ambrosius P. L. Snijders, Phillip C. Wright, Harry D. Moore, and Alireza Fazeli
Mol Cell Proteomics (2005) 4(11): 1785-1796

A Two-dimensional Electrophoresis Proteomic Reference Map and Systematic Identification of 1367 Proteins from a Cell Suspension Culture of the Model Legume Medicago truncatula
Zhentian Lei, Aaron M. Elmer, Bonnie S. Watson, Richard A. Dixon, Pedro J. Mendes, and Lloyd W. Sumner
Mol Cell Proteomics (2005) 4(11): 1812-1825

A Catalogue of Human Saliva Proteins Identified by Free Flow Electrophoresis-based Peptide Separation and Tandem Mass Spectrometry
Hongwei Xie, Nelson L. Rhodus, Robert J. Griffin, John V. Carlis, and Timothy J. Griffin
Mol Cell Proteomics (2005) 4(11): 1826-1830

Proteome Analysis of Nelore Bull (Bos taurus indicus) Seminal Plasma
Assump Ao TI, Fontes W, Sousa MV, Ricart CA
Protein Pept Lett (2005) 12(8): 813-7

Immunoisolation of two synaptic vesicle pools from synaptosomes: a proteomics analysis
Morciano M, Burre J, Corvey C, Karas M, Zimmermann H, Volknandt W
J Neurochem Early Edition: published 3-Nov-2005

Prokaryotes

Classification and identification of bacteria using mass spectrometry-based proteomics
Jacek P Dworzanski, A Peter Snyder
Expert Review of Proteomics (2005) 2(6): 863-878

Protein Complexes in the Archaeon Methanothermobacter thermautotrophicus Analyzed by Blue Native/SDS-PAGE and Mass Spectrometry
Murtada H. Farhoud, Hans J. C. T. Wessels, Peter J. M. Steenbakkers, Sandy Mattijssen, Ron A. Wevers, Baziel G. van Engelen, Mike S. M. Jetten, Jan A. Smeitink, Lambert P. van den Heuvel, and Jan T. Keltjens
Mol Cell Proteomics (2005) 4(11): 1653-1663

Mass Spectrometry-Based Proteomics Combined with Bioinformatic Tools for Bacterial Classification
Jacek P. Dworzanski, Samir V. Deshpande, Rui Chen, Rabih E. Jabbour, A. Peter Snyder, Charles H. Wick, and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/02/2005

Top-Down Proteomics for Rapid Identification of Intact Microorganisms
Plamen A. Demirev, Andrew B. Feldman, Paul Kowalski, and Jeffrey S. Lin
ANALYTICAL CHEMISTRY (2005) 77(22): 7455-7461

Proteome analysis and comparison of Clostridium acetobutylicum ATCC 824 and Spo0A strain variants
Sullivan L, Bennett GN
J Ind Microbiol Biotechnol Early Edition: published 25-Nov-2005

Up-expression of NapA and other oxidative stress proteins is a compensatory response to loss of major Helicobacter pylori stress resistance factors
Olczak AA, Wang G, Maier RJ
Free Radic Res (2005) 39(11): 1173-82

The Pseudomonas aeruginosa Proteome during Anaerobic Growth
Wu M, Guina T, Brittnacher M, Nguyen H, Eng J, Miller SI
J Bacteriol (2005) 187(23): 8185-8190

Proteomic Characterization of Yersinia pestis Virulence
Chromy BA, Choi MW, Murphy GA, Gonzales AD, Corzett CH, Chang BC, Fitch JP, McCutchen-Maloney SL
J Bacteriol (2005) 187(23): 8172-8180

Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C1 Metabolic Pathways in Burkholderia xenovorans LB400
Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD
J Bacteriol (2005) 187(23): 7996-8005

sinI- and expR-Dependent Quorum Sensing in Sinorhizobium meliloti
Gao M, Chen H, Eberhard A, Gronquist MR, Robinson JB, Rolfe BG, Bauer WD
J Bacteriol (2005) 187(23): 7931-7944

Increased Excision of the Salmonella Prophage ST64B Caused by a Deficiency in Dam Methylase
Alonso A, Pucciarelli MG, Figueroa-Bossi N, Garcia-Del Portillo F
J Bacteriol (2005) 187(23): 7901-7911

Bactericidal Actions of a Silver Ion Solution on Escherichia coli, Studied by Energy-Filtering Transmission Electron Microscopy and Proteomic Analysis
Yamanaka M, Hara K, Kudo J
Appl Environ Microbiol (2005) 71(11): 7589-93

Proteomic Signature of Lactococcus lactis NCDO763 Cultivated in Milk
Gitton C, Meyrand M, Wang J, Caron C, Trubuil A, Guillot A, Mistou MY
Appl Environ Microbiol (2005) 71(11): 7152-63

Pharmacology and Toxicology

Identification and Characterization of Peptides and Proteins in Doping Control Analysis
Thevis, Mario; Schanzer, Wilhelm
Current Proteomics (2005) 2(3): 191-208

Protein Array

Biomarker discovery using protein microarray technology platforms: antibody-antigen complex profiling
Dawn Mattoon, Gregory Michaud, Janie Merkel, Barry Schweitzer
Expert Review of Proteomics (2005) 2(6): 879-889

Development of an Internally Controlled Antibody Microarray
Eric W. Olle, Arun Sreekumar, Roscoe L. Warner, Shannon D. McClintock,Arul M. Chinnaiyan, Michael R. Bleavins, Timothy D. Anderson, and Kent J. Johnson
Mol Cell Proteomics (2005) 4(11): 1664-1672

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Protein Characterization / PTMs

Combining metaloxide affinity chromatography (MOAC) and selective mass spectrometry for robust identification of in vivophosphorylation sites
Wolschin F, Weckwerth W
Plant Methods (2005) 1(1): 9

Phosphoproteomic Analysis of Rat Liver by High Capacity IMAC and LC-MS/MS
Katrin Moser and Forest M. White
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/02/2005

Identification of Unusual Bacterial Glycosylation by Tandem Mass Spectrometry Analyses of Intact Proteins
Michael Schirm, Ian C. Schoenhofen, Susan M. Logan, Karen C. Waldron, and Pierre Thibault
ANALYTICAL CHEMISTRY (2005) 77(23): 7774-7782

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Protein-protein interaction

Unraveling the Dopamine Receptor Signalplex by DRIPs and DRAPs
Kabbani, N.; Hannan, M. A.; Levenson, R
Current Proteomics (2005) 2(3): 209-223

Defining Viral Protein Interactomes Using the Yeast Two-Hybrid Assay
Diefenbach, E.; Cunningham, A. L.; Diefenbach, R. J
Current Proteomics (2005) 2(3): 225-231

A proteomic snapshot of the human heat shock protein 90 interactome
Falsone SF, Gesslbauer B, Tirk F, Piccinini AM, Kungl AJ
FEBS Lett Early Edition: published 24-Oct-2005

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Quantitation

Stable Isotope Labeling of Arabidopsis thaliana Cells and Quantitative Proteomics by Mass Spectrometry
Albrecht Gruhler, Waltraud X. Schulze, Rune Matthiesen, Matthias Mann,and Ole N. Jensen
Mol Cell Proteomics (2005) 4(11): 1697-1709

Quantitative Proteomic Analysis of Drug-Induced Changes in Mycobacteria
Minerva A. Hughes, Jeffrey C. Silva, Scott J. Geromanos, and Craig A. Townsend
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/02/2005

Measurement of the Isotope Enrichment of Stable Isotope-Labeled Proteins Using High-Resolution Mass Spectra of Peptides
Michael J. MacCoss, Christine C. Wu, Dwight E. Matthews, and John R. Yates, III
ANALYTICAL CHEMISTRY (2005) 77(23): 7646-7653

Improved 2-nitrobenzenesulfenyl method: optimization of the protocol and improved enrichment for labeled peptides
Matsuo EI, Toda C, Watanabe M, Iida T, Masuda T, Minohata T, Ando E, Tsunasawa S, Nishimura O
Rapid Commun Mass Spectrom (2005) 20(1): 31-38

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Review

Oxidative stress response: a proteomic view
Thierry Rabilloud, Mireille Chevallet, Sylvie Luche, Emmanuelle Leize-Wagner
Expert Review of Proteomics (2005) 2(6): 949-956

What is mzXML good for?
Simon M Lin, Lihua Zhu, Andrew Q Winter, Maciek Sasinowski, Warren A Kibbe
Expert Review of Proteomics (2005) 2(6): 839-845

Bioinformatics approaches in clinical proteomics
Eric T Fung, Scot R Weinberger, Ed Gavin, Fujun Zhang
Expert Review of Proteomics (2005) 2(6): 847-862

Biomarker discovery using protein microarray technology platforms: antibody-antigen complex profiling
Dawn Mattoon, Gregory Michaud, Janie Merkel, Barry Schweitzer
Expert Review of Proteomics (2005) 2(6): 879-889

Thioredoxins inArabidopsis and other plants
Meyer Y, Reichheld JP, Vignols F
Photosynth Res Early Edition: published 15-Nov-2005

The application of proteomics to diabetes
Scott EM, Carter AM, Findlay JB
Diab Vasc Dis Res (2005) 2(2): 54-60

Individualised cancer therapeutics: dream or reality?
Senzer N, Shen Y, Hill C, Nemunaitis J
Expert Opin Ther Targets (2005) 9(6): 1189-201

Autoantibodies in breast cancer sera: candidate biomarkers and reporters of tumorigenesis
Fernandez Madrid F
Cancer Lett (2005) 230(2): 187-98

Transplantation proteomics
Traum AZ, Schachter AD
Pediatr Transplant (2005) 9(6): 700-11

Protein Posttranslational Modifications: The Chemistry of Proteome Diversifications
Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr
Angew Chem Int Ed Engl Early Edition: published 3-Nov-2005

Functional proteome and expression analysis of sporozoites and hepatic stages of malaria development
Blair PL, Carucci DJ
Curr Top Microbiol Immunol (2005) 295: 417-38

Practical cancer genetics, genomics and proteomics
Gruber MP, Geraci MW
J Insur Med (2005) 37(3): 190-200

Genomics, metagenomics and proteomics in biomining microorganisms
Valenzuela L, Chi A, Beard S, Orell A, Guiliani N, Shabanowitz J, Hunt DF, Jerez CA
Biotechnol Adv Early Edition: published 7-Nov-2005

Automated protein identification by tandem mass spectrometry: Issues and strategies
Hernandez P, Muller M, Appel RD
Mass Spectrom Rev Early Edition: published 11-Nov-2005

The role of mass spectrometry in plant systems biology
Glinski M, Weckwerth W
Mass Spectrom Rev Early Edition: published 11-Nov-2005

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Methodology

Liquid-based free-flow electrophoresis-reversed-phase HPLC: a proteomic tool
Moritz RL, Simpson RJ
Nat Methods (2005) 2(11): 863-73

Efficient solubilization buffers for two-dimensional gel electrophoresis of acidic and basic proteins extracted from wheat seeds
Chinnasamy G, Rampitsch C
Biochim Biophys Acta Early Edition: published 24-Oct-2005

Pooled ORF Expression Technology (POET): Using Proteomics to Screen Pools of Open Reading Frames for Protein Expression
William K. Gillette, Dominic Esposito, Peter H. Frank, Ming Zhou, Li-Rong Yu, Catherine Jozwik, Xiuying Zhang, Brighid McGowan, David M. Jacobowitz, Harvey B. Pollard, Tong Hao, David E. Hill, Marc Vidal, Thomas P. Conrads, Timothy D. Veenstra, and James L. Hartley
Mol Cell Proteomics (2005) 4(11): 1647-1652

Enrichment and Identification of Cysteine-Containing Peptides from Tryptic Digests of Performic Oxidized Proteins by Strong Cation Exchange LC and MALDI-TOF/TOF MS
Jingquan Dai, Jinglan Wang, Yangjun Zhang, Zhuang Lu, Bing Yang, Xiaohai Li, Yun Cai, and Xiaohong Qian
ANALYTICAL CHEMISTRY (2005) 77(23): 7594-7604

Enhanced Characterization of Complex Proteomic Samples Using LC-MALDI MS/MS: Exclusion of Redundant Peptides from MS/MS Analysis in Replicate Runs
Hsuan-shen Chen, Tomas Rejtar, Victor Andreev, Eugene Moskovets, and Barry L. Karger
ANALYTICAL CHEMISTRY (2005) 77(23): 7816-7825

Protein/RNA coextraction and small two-dimensional polyacrylamide gel electrophoresis for proteomic/gene expression analysis of renal cancer biopsies
Barbero G, Carta F, Giribaldi G, Mandili G, Crobu S, Ceruti C, Fontana D, Destefanis P, Turrini F
Anal Biochem Early Edition: published 2-Nov-2005

Microfluidic Electrocapture for Separation of Peptides
Juan Astorga-Wells, Susanne Vollmer, Sam Tryggvason, Tomas Bergman, and Hans Jörnvall
ANALYTICAL CHEMISTRY (2005) 77(22): 7131-7136

Preanalytical Impact of Sample Handling on Proteome Profiling Experiments with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
Findeisen P, Sismanidis D, Riedl M, Costina V, Neumaier M
Clin Chem (2005) 51(12): 2409-2411

Suppression of Matrix Clusters and Enhancement of Peptide Signals in MALDI-TOF Mass Spectrometry Using Nitrilotriacetic Acid
Jong-Seo Kim, Ji-Young Kim, and Hie-Joon Kim
ANALYTICAL CHEMISTRY (2005) 77(22): 7483-7488

Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides
McDonald L, Robertson DH, Hurst JL, Beynon RJ
Nat Methods (2005) 2(12): 955-7

Isoelectric Point-Based Prefractionation of Proteins from Crude Biological Samples Prior to Two-Dimensional Gel Electrophoresis
Ziad J. Sahab, Yewseok Suh, and Qing-Xiang Amy Sang
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/18/2005

Microfluidic platform for liquid chromatography-tandem mass spectrometry analyses of complex Peptide mixtures
Xie J, Miao Y, Shih J, Tai YC, Lee TD
Anal Chem (2005) 77(21): 6947-53

Quantitative mass spectral evidence for the absence of circulating brain natriuretic peptide (BNP-32) in severe human heart failure
Hawkridge AM, Heublein DM, Bergen HR 3rd, Cataliotti A, Burnett JC Jr, Muddiman DC
Proc Natl Acad Sci U S A Early Edition: published 17-Nov-2005

Detection and Identification of S-Nitrosylated Proteins in Endothelial Cells
Martinez-Ruiz A, Lamas S
Methods Enzymol (2005) 396PE: 131-139

Development of chemically stable solid phases for the target isolation with reduced nonspecific binding proteins
Takahashi T, Shiyama T, Hosoya K, Tanaka A
Bioorg Med Chem Lett Early Edition: published 11-Nov-2005

Blue-Native PAGE in plants: a tool in analysis of protein-protein interactions
Eubel H, Braun HP, Millar AH
Plant Methods (2005) 1(1): 11

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Meeting

First Meeting on Developments in Protein Interaction Analysis DiPIA 2005
Eric D Roush, Kara M Herlihy
Expert Review of Proteomics (2005) 2(6): 833-835

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Other

Immunome Research
Petrovsky N
Immunome Res (2005) 1(1): 1

The promise of proteomics
Liotta LA, Petricoin EF 3rd
Clin Adv Hematol Oncol (2003) 1(8): 460-2

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