SPS' Digest

Issue 29, 31-Mar-2006

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Quick jumps to articles in: Bioinformatics (29) / Biological applications (35) / Biomedical and clinical applications (55) / Eukaryotic Cells And Tissues (19) / Prokaryotes (7) / Pharmacology and Toxicology (6) / Protein Characterization - PTMs (27) / Protein-protein interaction (6) / Quantitation (9) / Review (22) / Methodology (61) / Books (1) / Meeting (1) /

In this issue, 277 articles have been selected from:

Acta Anaesthesiol Scand, Volume 50, Issue 4, 2006 (1 article)
Am J Nephrol, Volume 26, Issue 2, 2006 (1 article)
Anal Bioanal Chem, Early Edition, 23-Mar-2006 (1 article)
Anal Chem, Early Edition, 03/17/2006->03/10/2006 (9 articles)
Anal Chem, Volume 78, Issues 5+6, 2006 (7 articles)
Anesth Analg, Volume 102, Issue 4, 2006 (1 article)
Annu Rev Immunol, Volume 24, 2006 (1 article)
Arterioscler Thromb Vasc Biol, Early Edition, 16-Mar-2006 (1 article)
BMC Bioinformatics, Volume 7, Issue 1, 2006 (2 articles)
BMC Cancer, Volume 6, Issue 1, 2006 (1 article)
BMC Genomics, Volume 7, Issue 1, 2006 (2 articles)
Biochemistry, Volume 45, Issue 9, 2006 (1 article)
Bioinformatics, Early Edition, 7-Mar-2006 (1 article)
Bioinformatics, Volume 22, Issue 7, 2006 (2 articles)
Biol Sci Space, Volume 19, Issues 2+3, 2005 (2 articles)
Biomaterials, Early Edition, 22-Feb-2006 (1 article)
Biomol Eng, Early Edition, 6-Mar-2006 (1 article)
Bioorg Med Chem Lett, Early Edition, 20-Mar-2006 (1 article)
Biotechniques, Volume Suppl, 2005 (2 articles)
Blood Cells Mol Dis, Early Edition, 21-Feb-2006 (1 article)
Blood, Early Edition, 28-Feb-2006 (1 article)
Brain Res, Early Edition, 13-Mar-2006 (1 article)
Cancer Res, Volume 66, Issue 5, 2006 (1 article)
Cancer, Early Edition, 3-Mar-2006 (1 article)
Cell Microbiol, Volume 8, Issue 4, 2006 (1 article)
Chem Res Toxicol, Volume 18, Issue 10, 2005 (1 article)
Chembiochem, Early Edition, 27-Feb-2006 (1 article)
Clin Chim Acta, Early Edition, 23-Feb-2006 (1 article)
Curr Opin Oncol, Volume 18, Issue 3, 2006 (1 article)
Diabetes Educ, Volume 32, Issue 2, 2006 (1 article)
Electrophoresis, Early Edition, 3-Mar-2006->23-Mar-2006 (4 articles)
Electrophoresis, Volume 27, Issues 5-6+7, 2006 (7 articles)
Eukaryot Cell, Volume 5, Issue 3, 2006 (1 article)
Eur Neuropsychopharmacol, Early Edition, 3-Mar-2006 (1 article)
Free Radic Biol Med, Volume 40, Issue 7, 2006 (1 article)
Fut Oncol, Volume 1, Issue 1, 2005 (1 article)
Insect Biochem Mol Biol, Volume 36, Issue 3, 2006 (1 article)
Int J Cancer, Early Edition, 23-Mar-2006 (1 article)
Int J Gynecol Cancer, Volume 16, Issue Suppl 1, 2006 (1 article)
Int J Parasitol, Early Edition, 28-Feb-2006 (1 article)
Invest Ophthalmol Vis Sci, Volume 47, Issue 3, 2006 (2 articles)
J Agric Food Chem, Volume 54, Issue 6, 2006 (3 articles)
J Alzheimers Dis, Volume 8, Issue 4, 2005 (2 articles)
J Am Diet Assoc, Volume 106, Issue 3, 2006 (1 article)
J Am Med Inform Assoc, Early Edition, 24-Feb-2006 (1 article)
J Anim Sci, Volume 84, Issue 4, 2006 (1 article)
J Bacteriol, Volume 188, Issue 7, 2006 (1 article)
J Biomol Tech, Volume 16, Issue 4, 2005 (8 articles)
J Card Fail, Volume 12, Issue 1, 2006 (1 article)
J Cell Biochem, Early Edition, 21-Mar-2006 (2 articles)
J Chromatogr A, Early Edition, 6-Mar-2006->27-Feb-2006 (2 articles)
J Chromatogr B, Early Edition, 3-Mar-2006->27-Feb-2006 (3 articles)
J Exp Bot, Early Edition, 2-Mar-2006->21-Mar-2006 (5 articles)
J Insect Physiol, Early Edition, 27-Feb-2006 (1 article)
J Mass Spectrom, Volume 41, Issue 3, 2006 (1 article)
J Neurochem, Early Edition, 3-Mar-2006 (1 article)
J Pathol, Volume 208, Issue 5, 2006 (1 article)
J Proteome Res, Early Edition, 03/10/2006->03/31/2006 (23 articles)
J Proteome Res, Volume 5, Issue 3, 2006 (24 articles)
J Sep Sci, Volume 29, Issue 3, 2006 (1 article)
J Toxicol Sci, Volume 31, Issue 1, 2006 (1 article)
J Virol, Volume 80, Issue 6, 2006 (1 article)
J Zhejiang Univ Sci B, Volume 7, Issue 3, 2006 (1 article)
Lancet Oncol, Volume 7, Issue 3, 2006 (1 article)
Mass Spectrom Rev, Early Edition, 28-Feb-2006 (1 article)
Mass Spectrom Rev, Volume 25, Issue 3, 2006 (3 articles)
Microbiol Mol Biol Rev, Volume 70, Issue 1, 2006 (1 article)
Microbiology, Volume 152, Issue Pt 3, 2006 (1 article)
Mol Biochem Parasitol, Early Edition, 9-Feb-2006 (1 article)
Mol Cell Proteomics, Volume 5, Issues 3+4, 2006 (27 articles)
Mol Nutr Food Res, Volume 50, Issue 1, 2006 (1 article)
Mol Plant Microbe Interact, Volume 19, Issue 2, 2006 (1 article)
Nat Biotechnol, Volume 24, Issue 3, 2006 (1 article)
Nat Genet, Volume 38, Issue 3, 2006 (1 article)
Nat Med, Early Edition, 19-Mar-2006 (1 article)
Nephron Physiol, Volume 103, Issue 3, 2006 (1 article)
Neurobiol Aging, Early Edition, 4-Mar-2006 (1 article)
Neurobiol Dis, Early Edition, 17-Mar-2006 (1 article)
Neurol Res, Volume 28, Issue 2, 2006 (1 article)
Osteoarthritis Cartilage, Early Edition, 3-Mar-2006 (1 article)
Philos Trans R Soc Lond B Biol Sci, Volume 361, Issue 1467, 2006 (2 articles)
Physiol Biochem Zool, Volume 79, Issue 2, 2006 (1 article)
Physiol Res, Early Edition, 23-Mar-2006 (1 article)
Plant Physiol, Early Edition, 16-Mar-2006 (1 article)
Proc Natl Acad Sci U S A, Early Edition, 20-Mar-2006 (1 article)
Protein Sci, Early Edition, 7-Mar-2006 (1 article)
Proteome Sci, Volume 4, 2006 (4 articles)
Proteomics, Volume 6, Issues 6+7, 2006 (58 articles)
Rapid Commun Mass Spectrom, Volume 20, Issues 7+8, 2006 (2 articles)
Rheumatology (Oxford), Early Edition, 7-Mar-2006 (1 article)
Toxicon, Early Edition, 18-Mar-2006 (1 article)
Transfusion, Volume 46, Issue 3, 2006 (1 article)
Trends Biotechnol, Early Edition, 16-Mar-2006 (1 article)
Vet Parasitol, Early Edition, 27-Feb-2006 (1 article)
Virol J, Volume 3, Issue 1, 2006 (1 article)

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

Quick jumps to articles in: Bioinformatics (29) / Biological applications (35) / Biomedical and clinical applications (55) / Eukaryotic Cells And Tissues (19) / Prokaryotes (7) / Pharmacology and Toxicology (6) / Protein Characterization - PTMs (27) / Protein-protein interaction (6) / Quantitation (9) / Review (22) / Methodology (61) / Books (1) / Meeting (1) /

Bioinformatics

Correlation and Convolution Analysis of Peptide Mass Spectra
Matthew J. Sniatynski, Jason C. Rogalski, Michael D. Hoffman, and Juergen Kast
ANALYTICAL CHEMISTRY Early Edition: published 03/24/2006

Optimizing search conditions for the mass fingerprint-based identification of proteins
Elena Ossipova, David Fenyö, Jan Eriksson
PROTEOMICS (2006) 6(7): 2079-2085

Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
Kristian Flikka, Lennart Martens, Joël Vandekerckhove, Kris Gevaert, Ingvar Eidhammer
PROTEOMICS (2006) 6(7): 2086-2094

Feature extraction in the analysis of proteomic mass spectra
Xuena Wang, Wei Zhu, Kith Pradhan, Chen Ji, Yeming Ma, Oliver John Semmes, James Glimm, Joseph Mitchell
PROTEOMICS (2006) 6(7): 2095-2100

Identification of Proteins from Non-model Organisms Using Mass Spectrometry: Application to a Hibernating Mammal
Kevin P. Russeth, LeeAnn Higgins, and Matthew T. Andrews
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/10/2006

Computational Methods for Comparison of Large Genomic and Proteomic Datasets Reveal Protein Markers of Metastatic Cancer
Yingchun Wang, Rachel Hanley, and Richard L. Klemke
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Detection and Identification of Protein Isoforms Using Cluster Analysis of MALDI-MS Mass Spectra
Rikard Alm, Peter Johansson, Karin Hjern , Cecilia Emanuelsson, Markus Ringnér, and Jari Häkkinen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Processing and classification of protein mass spectra
Melanie Hilario, Alexandros Kalousis, Christian Pellegrini, Markus Müller
Mass Spectrometry Reviews (2006) 25(3): 409-449

Improved Classification of Mass Spectrometry Database Search Results Using Newer Machine Learning Approaches
Peter J. Ulintz, Ji Zhu, Zhaohui S. Qin, and Philip C. Andrews
Mol Cell Proteomics (2006) 5(3): 497-509

In Silico Identification of New Secretory Peptide Genes in Drosophila melanogaster
Feng Liu, Geert Baggerman, Wannes D'Hertog, Peter Verleyen, Liliane Schoofs, and Geert Wets
Mol Cell Proteomics (2006) 5(3): 510-522

Fast and Accurate Method for Identifying High-Quality Protein-Interaction Modules by Clique Merging and Its Application to Yeast
Chi Zhang, Song Liu, and Yaoqi Zhou
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data: Toward More Efficient Identification of Post-translational Modifications, Sequence Polymorphisms, and Novel Peptides
Alexey I. Nesvizhskii, Franz F. Roos, Jonas Grossmann, Mathijs Vogelzang, James S. Eddes, Wilhelm Gruissem, Sacha Baginsky, and Ruedi Aebersold
Mol Cell Proteomics (2006) 5(4): 652-670

Bioinformatic challenges for the next decade(s)
Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M
Philos Trans R Soc Lond B Biol Sci (2006) 361(1467): 525-7

From genomes to systems: the path with yeast
Oliver SG
Philos Trans R Soc Lond B Biol Sci (2006) 361(1467): 477-82

IsoSVM - Distinguishing isoforms and paralogs on the protein level
Spitzer M, Lorkowski S, Cullen P, Sczyrba A, Fuellen G
BMC Bioinformatics (2006) 7(1): 110

EST2Prot: Mapping EST sequences to proteins
Shafer P, Lin DM, Yona G
BMC Genomics (2006) 7(1): 41

SPLASH: Systematic proteomics laboratory analysis and storage hub
Siaw Ling Lo, Tao You, Qingsong Lin, Shashikant B. Joshi, Maxey C. M. Chung, Choy Leong Hew
PROTEOMICS (2006) 6(6): 1758-1769

MapQuant: Open-source software for large-scale protein quantification
Kyriacos C. Leptos, David A. Sarracino, Jacob D. Jaffe, Bryan Krastins, George M. Church
PROTEOMICS (2006) 6(6): 1770-1782

PRISM: A data management system for high-throughput proteomics
Gary R. Kiebel, Ken J. Auberry, Navdeep Jaitly, David A. Clark, Matthew E. Monroe, Elena S. Peterson, Nikola Toli?, Gordon A. Anderson, Richard D. Smith
PROTEOMICS (2006) 6(6): 1783-1790

An XML-based System for Synthesis of Data from Disparate Databases
Kurc T, Janies DA, Johnson AD, Langella S, Oster S, Hastings S, Habib F, Camerlengo T, Ervin D, Catalyurek UV, Saltz JH
J Am Med Inform Assoc Early Edition: published 24-Feb-2006

Estimating Probabilities of Peptide Database Identifications to LC-FTICR-MS Observations
Anderson KK, Monroe ME, Daly DS
Proteome Sci (2006) 4: 1

Reproducibility of LC-MS-based protein identification
Berg M, Parbel A, Pettersen H, Fenyo D, Bjorkesten L
J Exp Bot Early Edition: published 21-Mar-2006

2DDB - a bioinformatics solution for analysis of quantitative proteomics data
Malmstrom L, Marko-Varga G, Westergren-Thosson G, Laurell T, Malmstrom J
BMC Bioinformatics (2006) 7(1): 158

Fishing for biomarkers: analyzing mass spectrometry data with the new ClinProTools software
Ketterlinus R, Hsieh SY, Teng SH, Lee H, Pusch W
Biotechniques (2005) Suppl: 37-40.

Complex Graph Matrix Representations and Characterizations of Proteomic Maps and Chemically Induced Changes to Proteomes
Krishnan Balasubramanian, Kanan Khokhani, and Subhash C. Basak
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/31/2006

Predicting the Solvent Accessibility of Transmembrane Residues from Protein Sequence
Zheng Yuan, Fasheng Zhang, Melissa J. Davis, Mikael Bodén, and Rohan D. Teasdale
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/31/2006

InSilicoSpectro: An Open-Source Proteomics Library
Jacques Colinge, Alexandre Masselot, Pablo Carbonell, and Ron D. Appel
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 619-624

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application
Sandhya Xirasagar, Scott F. Gustafson, Cheng-Cheng Huang, Qinyan Pan, Jennifer Fostel, Paul Boyer, B. Alex Merrick, Kenneth B. Tomer, Denny D. Chan, Kenneth J. Yost, III, Danielle Choi, Nianqing Xiao, Stanley Stasiewicz, Pierre Bushel, and Michael D. Waters
Bioinformatics (2006) 22(7): 874-882

Pro-CrossLink. Software Tool for Protein Cross-Linking and Mass Spectrometry
Qiuxia Gao, Song Xue, Catalin E. Doneanu, Scott A. Shaffer, David R. Goodlett, and Sidney D. Nelson
ANALYTICAL CHEMISTRY Early Edition: published 03/10/2006

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Biological applications

A proteomics approach to survey the antigenicity of the influenza virus by mass spectrometry
Bethny Morrissey, Kevin M. Downard
PROTEOMICS (2006) 6(7): 2034-2041

A functional proteomics approach for the detection of nuclear proteins based on derepressed importin alpha
Erik Blazek, Michael Meisterernst
PROTEOMICS (2006) 6(7): 2070-2078

Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: Identification of new proteins at the DNA replication factory
Jean-Christophe Meile, Ling Juan Wu, S. Dusko Ehrlich, Jeff Errington, Philippe Noirot
PROTEOMICS (2006) 6(7): 2135-2146

Proteomic analysis of Candida albicans yeast and hyphal cell wall and associated proteins
Roger O. Ebanks, Kenneth Chisholm, Stewart McKinnon, Malcolm Whiteway, Devanand M. Pinto
PROTEOMICS (2006) 6(7): 2147-2156

The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses
Jean-Emmanuel Sarry, Lauriane Kuhn, Céline Ducruix, Alexandra Lafaye, Christophe Junot, Véronique Hugouvieux, Agnès Jourdain, Olivier Bastien, Julie B. Fievet, Dominique Vailhen, Badia Amekraz, Christophe Moulin, Eric Ezan, Jérôme Garin, Jacques Bourguignon
PROTEOMICS (2006) 6(7): 2180-2198

Proteomic analysis reveals the spatial heterogeneity of immobilized Taxus cuspidata cells in support matrices
Jing-Sheng Cheng, Ying-Jin Yuan
PROTEOMICS (2006) 6(7): 2199-2207

Human colostrum: Identification of minor proteins in the aqueous phase by proteomics
David J. Palmer, Van C. Kelly, Anne-Marie Smit, Sulee Kuy, Catriona G. Knight , Garth J. Cooper
PROTEOMICS (2006) 6(7): 2208-2216

Analysis of chicken serum proteome and differential protein expression during development in single-comb White Leghorn hens
San-Yuan Huang, Jyh-Hung Lin, Yu-Huey Chen, Chin-Kai Chuang, Yu-Fang Chiu, Ming-Yu Chen, Hsin-Hsin Chen, Wen-Chuan Lee
PROTEOMICS (2006) 6(7): 2217-2224

Proteomics analysis revealed changes in rat bronchoalveolar lavage fluid proteins associated with oil mist exposure
Yung-Shan Lee, Pang-Wei Chen, Perng-Jy Tsai, Shu-Hui Su, Pao-Chi Liao
PROTEOMICS (2006) 6(7): 2236-2250

Proteomics profiling of epidermal mucus secretion of a cichlid (Symphysodon aequifasciata) demonstrating parental care behavior
Kenny Chong, Shashikant Joshi, Lam Toong Jin, Alexander Chong Shu-Chien
PROTEOMICS (2006) 6(7): 2251-2258

Proteomic analysis of the Gallus gallus embryo at stage-29 of development
David Agudo, Francisco Gómez-Esquer, Gema Díaz-Gil, Fernando Martínez-Arribas, José Delcán, José Schneider, María Angustias Palomar, Rafael Linares
PROTEOMICS (2006) 6(7): 2326

Comparative Proteomic Analysis Provides New Insights into Chilling Stress Responses in Rice
Shun-Ping Yan, Qun-Ye Zhang, Zhang-Cheng Tang, Wei-Ai Su, and Wei-NingSun
Mol Cell Proteomics (2006) 5(3): 484-496

Characterization of Histone H2A and H2B Variants and Their Post-translational Modifications by Mass Spectrometry
Debora Bonenfant, Michele Coulot, Harry Towbin, Patrick Schindler, andJan van Oostrum
Mol Cell Proteomics (2006) 5(3): 541-552

Quantitative Proteomic Comparison of Rat Mitochondria from Muscle, Heart, and Liver
Francesca Forner, Leonard J. Foster, Stefano Campanaro, Giorgio Valle,and Matthias Mann
Mol Cell Proteomics (2006) 5(4): 608-619

High Expression of Antioxidant Proteins in Dendritic Cells: Possible Implications in Atherosclerosis
Aymeric Rivollier, Laure Perrin-Cocon, Sylvie Luche, Helene Diemer, Jean-Marc Strub, Daniel Hanau, Alain van Dorsselaer, Vincent Lotteau, Chantal Rabourdin-Combe, Thierry Rabilloud, and Christine Servet-Delprat
Mol Cell Proteomics (2006) 5(4): 726-736

2-DE proteome analysis of a proliferating and differentiating human neuronal stem cell line (ReNcell VM)
Raimund Hoffrogge, Stefan Mikkat, Christian Scharf, Susanne Beyer, Hilmar Christoph, Jens Pahnke, Eilhard Mix, Matthias Berth, Adelinde Uhrmacher, Igor Z. Zubrzycki, Erik Miljan, Uwe Völker, Arndt Rolfs
PROTEOMICS (2006) 6(6): 1833-1847

Proteomics in Myzus persicae: Effect of aphid host plant switch
Francis F, Gerkens P, Harmel N, Mazzucchelli G, De Pauw E, Haubruge E
Insect Biochem Mol Biol (2006) 36(3): 219-27

Identification of the nucleocapsid, tegument, and envelope proteins of the shrimp white spot syndrome virus virion
Tsai JM, Wang HC, Leu JH, Wang AH, Zhuang Y, Walker PJ, Kou GH, Lo CF
J Virol (2006) 80(6): 3021-9

Models of blood coagulation
Mann KG, Brummel-Ziedins K, Orfeo T, Butenas S
Blood Cells Mol Dis Early Edition: published 21-Feb-2006

Genomic and proteomic approaches in comparative biochemistry and physiology
Storey KB
Physiol Biochem Zool (2006) 79(2): 324-32

Moving pieces in a taxonomic puzzle: Venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones)
Nascimento DG, Rates B, Santos DM, Verano-Braga T, Barbosa-Silva A, Dutra AA, Biondi I, Martin-Eauclaire MF, Lima ME, Pimenta AM
Toxicon Early Edition: published 18-Mar-2006

Proteomic analysis of Arabidopsis root gravitropism
Kamada M, Higashitani A
Biol Sci Space (2005) 19(3): 148-154

Proteomics Study on the Variation of Protein Expression and Phosphorylations caused by Radiation in Cultured Grial Cells
Miura Y, Kano M, Toda T, Suzuki S
Biol Sci Space (2005) 19(2): 98-99

Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view
Chevallet M, Lescuyer P, Diemer H, van Dorsselaer A, Leize-Wagner E, Rabilloud T
Electrophoresis Early Edition: published 20-Mar-2006

Proteomic analysis of differentially expressed proteins in fungal elicitor-treated Arabidopsis cell cultures
Chivasa S, Hamilton JM, Pringle RS, Ndimba BK, Simon WJ, Lindsey K, Slabas AR
J Exp Bot Early Edition: published 17-Mar-2006

Human Protein Atlas charts a diverse terrain
Saviranta P, Kallioniemi O
Trends Biotechnol Early Edition: published 16-Mar-2006

Functions of the tegument of schistosomes: Clues from the proteome and lipidome
Van Hellemond JJ, Retra K, Brouwers JF, van Balkom BW, Yazdanbakhsh M, Shoemaker CB, Tielens AG
Int J Parasitol Early Edition: published 28-Feb-2006

Changes in the muscle proteome after compensatory growth in pigs
Lametsch R, Kristensen L, Larsen MR, Therkildsen M, Oksbjerg N, Ertbjerg P
J Anim Sci (2006) 84(4): 918-24

Proteomic analysis of seed filling in Brassica napus: Developmental characterization of metabolic isozymes using high-resolution two-dimensional gel electrophoresis
Hajduch M, Casteel JE, Hurrelmeyer KE, Song Z, Agrawal GK, Thelen JJ
Plant Physiol Early Edition: published 16-Mar-2006

Application of Two-Dimensional Gel Electrophoresis To Interrogate Alterations in the Proteome of Gentically Modified Crops. 3. Assessing Unintended Effects
Ruebelt MC, Lipp M, Reynolds TL, Schmuke JJ, Astwood JD, Dellapenna D, Engel KH, Jany KD
J Agric Food Chem (2006) 54(6): 2169-2177

Application of Two-Dimensional Gel Electrophoresis To Interrogate Alterations in the Proteome of Genetically Modified Crops. 2. Assessing Natural Variability
Ruebelt MC, Lipp M, Reynolds TL, Astwood JD, Engel KH, Jany KD
J Agric Food Chem (2006) 54(6): 2162-2168

Application of Two-Dimensional Gel Electrophoresis To Interrogate Alterations in the Proteome of Genetically Modified Crops. 1. Assessing Analytical Validation
Ruebelt MC, Leimgruber NK, Lipp M, Reynolds TL, Nemeth MA, Astwood JD, Engel KH, Jany KD
J Agric Food Chem (2006) 54(6): 2154-2161

Identification of developmentally-regulated proteins in Leishmania panamensis by proteome profiling of promastigotes and axenic amastigotes
Walker J, Vasquez JJ, Gomez MA, Drummelsmith J, Burchmore R, Girard I, Ouellette M
Mol Biochem Parasitol Early Edition: published 9-Feb-2006

Proteomic Analysis of Mature Melanosomes from the Retinal Pigmented Epithelium
Sassan M. Azarian, Ian McLeod, Concepcion Lillo, Daniel Gibbs, John R. Yates, and David S. Williams
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 521-529

Proteomic Analysis of Mice Hippocampus in Simulated Microgravity Environment
Poonam Sarkar, Shubhashish Sarkar, Vani Ramesh, Barbara E. Hayes, Renard L. Thomas, Bobby L. Wilson, Helen Kim, Stephen Barnes, Anil Kulkarni, Neal Pellis, and Govindarajan T. Ramesh
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 548-553

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Biomedical and clinical applications

Pilot Study Using SELDI-TOF-MS Based Proteomic Profile for the Identification of Diagnostic Biomarkers of Thyroid Proliferative Diseases
R. Suriano, Y. Lin, B. T. Ashok, S. D. Schaefer, S. P. Schantz, J. Geliebter, and R. K. Tiwari
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Proteomic Analysis of the Mode of Antibacterial Action of Silver Nanoparticles
Chun-Nam Lok, Chi-Ming Ho, Rong Chen, Qing-Yu He, Wing-Yiu Yu, Hongzhe Sun, Paul Kwong-Hang Tam, # Jen-Fu Chiu, and Chi-Ming Che
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Neuroproteomics in neurotrauma
Andrew K. Ottens, Firas H. Kobeissy, Erin C. Golden, Zhiqun Zhang, William E. Haskins, Su-Shing Chen, Ronald L. Hayes, Kevin K.W. Wang, Nancy D. Denslow
Mass Spectrometry Reviews (2006) 25(3): 380-408

A multidimensional proteomic approach to identify hypertrophy-associated proteins
Merry L. Lindsey, Danielle K. Goshorn, Susana Comte-Walters, Jennifer W. Hendrick, Elizabeth Hapke, Michael R. Zile, Kevin Schey
PROTEOMICS (2006) 6(7): 2225-2235

Overexpression and elevated serum levels of phosphoglycerate kinase 1 in pancreatic ductal adenocarcinoma
Tsann-Long Hwang, Ying Liang, Kuan-Yi Chien, Jau-Song Yu
PROTEOMICS (2006) 6(7): 2259-2272

Differential Protein Expression Profiling by iTRAQ-2DLC-MS/MS of Lung Cancer Cells Undergoing Epithelial-Mesenchymal Transition Reveals a Migratory/Invasive Phenotype
Venkateshwar G. Keshamouni, George Michailidis, Catherine S. Grasso, Shalini Anthwal, John R. Strahler, Angela Walker, Douglas A. Arenberg, Raju C. Reddy, Sudhakar Akulapalli, # Victor J. Thannickal, Theodore J. Standiford, Philip C. Andrews, and Gilbert S. Omenn
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Apocrine Cysts of the Breast: Biomarkers, Origin, Enlargement, and Relation with Cancer Phenotype
Julio E. Celis, Pavel Gromov, Jose M. A. Moreira, Teresa Cabezon, Esbern Friis, Ilse M. M. Vejborg, Gottfried Proess, Fritz Rank, and Irina Gromova
Mol Cell Proteomics (2006) 5(3): 462-483

Proteomic identification of alterations in metabolic enzymes and signaling proteins in hypokalemic nephropathy
Visith Thongboonkerd, Somchai Chutipongtanate, Rattiyaporn Kanlaya, Napat Songtawee, Supachok Sinchaikul, Paisal Parichatikanond, Shui-Tein Chen, Prida Malasit
PROTEOMICS (2006) 6(7): 2273-2285

Identification of plasma protein biomarkers associated with idiopathic pulmonary arterial hypertension
Vahitha B. Abdul-Salam, Gideon A. Paul, J. Omar Ali, Simon R. Gibbs, Dinah Rahman, Graham W. Taylor, Martin R. Wilkins, Robert J. Edwards
PROTEOMICS (2006) 6(7): 2286-2294

Diagnosis of congenital disorders of glycosylation type-I using protein chip technology
Kevin Mills, Philippa Mills, Marie Jackson, Viki Worthington, Clare Beesley, Anúska Mann, Peter Clayton, Stephanie Grunewald, Geoffrey Keir, Liz Young, James Langridge, Nasi Mian, Bryan Winchester
PROTEOMICS (2006) 6(7): 2295-2304

Differential post-translational modifications of transthyretin in Alzheimer's disease: A study of the cerebral spinal fluid
Antonino Biroccio, Piero del Boccio, Marta Panella, Sergio Bernardini, Carmine Di Ilio, Domenico Gambi, Paolo Stanzione, Paolo Sacchetta, Giorgio Bernardi, Alessandro Martorana, Giorgio Federici, Alessandro Stefani, Andrea Urbani
PROTEOMICS (2006) 6(7): 2305-2313

Proteomic analysis of nasal cells from cystic fibrosis patients and non-cystic fibrosis control individuals: Search for novel biomarkers of cystic fibrosis lung disease
Mónica Roxo-Rosa, Gonçalo da Costa, Theo M. Luider, Bob J. Scholte, Ana V. Coelho, Margarida D. Amaral, Deborah Penque
PROTEOMICS (2006) 6(7): 2314-2325

Subcellular and Functional Proteomic Analysis of the Cellular Responses Induced by Helicobacter pylori
Chia-Hsin Chan, Chia-Cheng Ko, Jan-Gowth Chang, Sung-Fang Chen, Ming-Shiang Wu, Jaw-Town Lin, and Lu-Ping Chow
Mol Cell Proteomics (2006) 5(4): 702-713

Identification of parotid salivary biomarkers in Sjogren's syndrome by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry and two-dimensional difference gel electrophoresis
Ryu OH, Atkinson JC, Hoehn GT, Illei GG, Hart TC
Rheumatology (Oxford) Early Edition: published 7-Mar-2006

Convergence of the proteomic pattern in cancer
Muller U, Ernst G, Melle C, Guthke R, von Eggeling F
Bioinformatics Early Edition: published 7-Mar-2006

Proteomic analysis of brain tissue from an Alzheimer's disease mouse model by two-dimensional difference gel electrophoresis
Sizova D, Charbaut E, Delalande F, Poirier F, High AA, Parker F, Van Dorsselaer A, Duchesne M, Diu-Hercend A
Neurobiol Aging Early Edition: published 4-Mar-2006

Proteomic-based prediction of clinical behavior in adult acute lymphoblastic leukemia
Albitar M, Potts SJ, Giles FJ, O'brien S, Keating M, Thomas D, Clarke C, Jilani I, Aguilar C, Estey E, Kantarjian H
Cancer Early Edition: published 3-Mar-2006

Plasma proteomic pattern as biomarkers for ovarian cancer
Lin YW, Lin CY, Lai HC, Chiou JY, Chang CC, Yu MH, Chu TY
Int J Gynecol Cancer (2006) 16(Suppl 1): 139-46

Differential protein expression in hypertrophic heart with and without hypertension in spontaneously hypertensive rats
Xian Jin, Li Xia, Li-Shun Wang, Jun-Zhi Shi, Ying Zheng, Wen-Li Chen, Lei Zhang, Zhen-Guo Liu, Guo-Qiang Chen, Ning-Yuan Fang
PROTEOMICS (2006) 6(6): 1948-1956

Protein profiling the effects of in vitro hyperoxic exposure on fetal rabbit lung
Phillip Henschke, Henrik Vorum, Bent Honoré, Gregory Edward Rice
PROTEOMICS (2006) 6(6): 1957-1962

Surface-enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors
Gabriel Ricolleau, Catherine Charbonnel, Laurence Lodé, Delphine Loussouarn, Marie-Pierre Joalland, Ralf Bogumil, Sabine Jourdain, Stéphane Minvielle, Mario Campone, Régine Déporte-Fety, Loïc Campion, Pascal Jézéquel
PROTEOMICS (2006) 6(6): 1963-1975

Proteomic analysis of membrane microdomains derived from both failing and non-failing human hearts
Cristina Banfi, Maura Brioschi, Robin Wait, Shajna Begum, Elisabetta Gianazza, Pasquale Fratto, Gianluca Polvani, Ettore Vitali, Alessandro Parolari, Luciana Mussoni, Elena Tremoli
PROTEOMICS (2006) 6(6): 1976-1988

Intermittent administration of morphine alters protein expression in rat nucleus accumbens
Ka Wan Li, Connie R. Jimenez, Roel C. van der Schors, Martin P. Hornshaw, Anton N. M. Schoffelmeer, August B. Smit
PROTEOMICS (2006) 6(6): 2003-2008

The Human Liver Proteome Project (HLPP) Workshop during the 4th HUPO World Congress
Junjie Zheng, Xue Gao, Laura Beretta, Fuchu He
PROTEOMICS (2006) 6(6): 1716-1718

Fibrinogen {gamma} Overexpression in Pancreatic Cancer Identified by Large-scale Proteomic Analysis of Serum Samples
Bloomston M, Zhou JX, Rosemurgy AS, Frankel W, Muro-Cacho CA, Yeatman TJ
Cancer Res (2006) 66(5): 2592-9

Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis
Theodorescu D, Wittke S, Ross MM, Walden M, Conaway M, Just I, Mischak H, Frierson HF
Lancet Oncol (2006) 7(3): 230-40

Pox proteomics: mass spectrometry analysis and identification of Vaccinia virion proteins
Yoder JD, Chen TS, Gagnier CR, Vemulapalli S, Maier CS, Hruby DE
Virol J (2006) 3(1): 10

Proteomic analysis of uveal melanoma reveals novel potential markers involved in tumor progression
Zuidervaart W, Hensbergen PJ, Wong MC, Deelder AM, Tensen CP, Jager MJ, Gruis NA
Invest Ophthalmol Vis Sci (2006) 47(3): 786-93

Preoperatively molecular staging with CM10 ProteinChip and SELDI-TOF-MS for colorectal cancer patients
Xu WH, Chen YD, Hu Y, Yu JK, Wu XG, Jiang TJ, Zheng S, Zhang SZ
J Zhejiang Univ Sci B (2006) 7(3): 235-40

Proteins pattern alteration in AZT-treated K562 cells detected by two-dimensional gel electrophoresis and peptide mass fingerprinting
D'Andrea G, Lizzi A, Venditti S, Di Francesco L, Giorgi A, Mignogna G, Oratore A, Bozzi A
Proteome Sci (2006) 4: 4

Proteomic analysis of Down's syndrome patients with gout
Chen YC, Wang PW, Pan TL, Wallace CG, Chen CJ
Clin Chim Acta Early Edition: published 23-Feb-2006

Proteomic Analysis Reveals Significant Alternations of Cardiac Small Heat Shock Protein Expression in Congestive Heart Failure
Dohke T, Wada A, Isono T, Fujii M, Yamamoto T, Tsutamoto T, Horie M
J Card Fail (2006) 12(1): 77-84

Bystander effects are induced by CENU treatment and associated with altered protein secretory activity of treated tumor cells A relay for chemotherapy?
Demidem A, Morvan D, Madelmont JC
Int J Cancer Early Edition: published 23-Mar-2006

Proteomic Analysis of Rat Plasma by SELDI-TOF-MS under the Condition of Prevention of Progressive Adriamycin Nephropathy Using Oral Adsorbent AST-120
Ishikawa I, Hayama T, Yoshida S, Asaka M, Tomosugi N, Watanabe M, Yamato H, Sugano M
Nephron Physiol (2006) 103(3): p125-p130

Comparative proteomic analysis of apoptosis induced by sodium selenite in human acute promyelocytic leukemia NB4 cells
Dong H, Ying T, Li T, Cao T, Wang J, Yuan J, Feng E, Han B, Hua F, Yang Y, Yuan J, Wang H, Xu C
J Cell Biochem Early Edition: published 21-Mar-2006

Comparative proteomics of cerebrospinal fluid in neuropathologically-confirmed Alzheimer's disease and non-demented elderly subjects
Castano EM, Roher AE, Esh CL, Kokjohn TA, Beach T
Neurol Res (2006) 28(2): 155-63

A proteomic approach to investigate potential biomarkers directed against membrane-associated breast cancer proteins
Canelle L, Bousquet J, Pionneau C, Hardouin J, Choquet-Kastylevsky G, Joubert-Caron R, Caron M
Electrophoresis Early Edition: published 20-Mar-2006

Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis
Decramer S, Wittke S, Mischak H, Zurbig P, Walden M, Bouissou F, Bascands JL, Schanstra JP
Nat Med Early Edition: published 19-Mar-2006

Proteomic Profiling of Urinary Protein Excretion in the Factor H-Deficient Mouse
Braun MC, Li L, Ke B, Dubinsky WP, Pickering MC, Chang JY
Am J Nephrol (2006) 26(2): 127-135

Identification of protein biomarkers for schizophrenia and bipolar disorder in the postmortem prefrontal cortex using SELDI-TOF-MS ProteinChip profiling combined with MALDI-TOF-PSD-MS analysis
Novikova SI, He F, Cutrufello NJ, Lidow MS
Neurobiol Dis Early Edition: published 17-Mar-2006

Transcriptomic and proteomic analyses of rhabdomyosarcoma cells reveal differential cellular gene expression in response to enterovirus 71 infection
Leong WF, Chow VT
Cell Microbiol (2006) 8(4): 565-80

Volatile anesthetics evoke prolonged changes in the proteome of the left ventricule myocardium: defining a molecular basis of cardioprotection?
Kalenka A, Maurer MH, Feldmann RE, Kuschinsky W, Waschke KF
Acta Anaesthesiol Scand (2006) 50(4): 414-27

Proteomics as a tool for assessment of therapeutics in transfusion medicine: evaluation of prothrombin complex concentrates
Brigulla M, Thiele T, Scharf C, Breitner-Ruddock S, Venz S, Volker U, Greinacher A
Transfusion (2006) 46(3): 377-85

Identification of differentially expressed, tumor-associated proteins in oral squamous cell carcinoma by proteomic analysis
Dritan Turhani, Kurt Krapfenbauer, Dietmar Thurnher, Hanno Langen, Michael Fountoulakis
ELECTROPHORESIS (2006) 27(7): 1417-1423

Comparative Proteomics of Ovarian Epithelial Tumors
Hee Jung An, Nam Hoon Cho, Yong Kyu Park, Sei Kwang Kim,⁴ Yoon Pyo Choi, Suki Kang, Boxiao Ding, and Dong Su Kim
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/31/2006

Using Chemometrics and Statistics To Improve Proteomics Biomarker Discovery
Clifford H. SpiegelmanRuth PfeifferMitchell Gail
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 461-462

Proteomic Analysis of Human Immunodeficiency Virus Using Liquid Chromatography/Tandem Mass Spectrometry Effectively Distinguishes Specific Incorporated Host Proteins
Andrew C. S. Saphire, Philippe A. Gallay, and Steven J. Bark
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 530-538

Effects of Subminimum Inhibitory Concentrations of Antibiotics on the Pasteurella multocida Proteome
Bindu Nanduri, Mark L. Lawrence, Carolyn R. Boyle, Mahalingam Ramkumar, and Shane C. Burgess
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 572-580

Functional Proteomics Approach to Investigate the Biological Activities of cDNAs Implicated in Breast Cancer
Abigail E. Witt, Lisa M. Hines, Nicole L. Collins, Yanhui Hu, Ruwanthi N. Gunawardane, Donna Moreira, Jacob Raphael, Daniel Jepson, Malvika Koundinya, Andreas Rolfs, Barbara Taron, Steven J. Isakoff, Joan S. Brugge, and Joshua LaBaer
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 599-610

Comparative Proteomics of Pulmonary Tumors with Neuroendocrine Differentiation
Nam Hoon Cho, Eun Suk Koh, Dong Wha Lee, Haeryoung Kim, Youn Pyo Choi, Sang Ho Cho, and Dong Su Kim
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 643-650

The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studies
Michael Hamacher, Christian Stephan, Martin Blüggel, Daniel Chamrad, Gerhard Körting, Lennart Martens, Michael Müller, Henning Hermjakob, David Parkinson, Andrew Dowsey, Kai A. Reidegeld, Katrin Marcus, Michael J. Dunn, Helmut E. Meyer, Rolf Apweiler
PROTEOMICS (2006) 6(6): 1719-1721

Multiplex detection of surface molecules on colorectal cancers
Peter Ellmark, Larissa Belov, Pauline Huang, C. Soon Lee, Michael J. Solomon, Daniel K. Morgan, Richard I. Christopherson
PROTEOMICS (2006) 6(6): 1791-1802

Proteomic characterization of the effects of clofibrate on protein expression in rat liver
Jean-François Léonard, Martine Courcol, Claire Mariet, Aurore Charbonnier, Eric Boitier, Marc Duchesne, Fabienne Parker, Bruno Genet, Françoise Supatto, Ruth Roberts, Jean-Charles Gautier
PROTEOMICS (2006) 6(6): 1915-1933

Proteomic analysis in human breast cancer: Identification of a characteristic protein expression profile of malignant breast epithelium
Gernot Hudelist, Christian F. Singer, Kerstin I. D. Pischinger, Klaus Kaserer, Mahmood Manavi, Ernst Kubista, Klaus F. Czerwenka
PROTEOMICS (2006) 6(6): 1989-2002

Proteome analysis of multidrug resistance in vincristine-resistant human gastric cancer cell line SGC7901/VCR
Yi-Xuan Yang, Zhi-Qiang Xiao, Zhu-Chu Chen, Gui-Ying Zhang, Hong Yi, Peng-Fei Zhang, Jian-Ling li, Guo Zhu
PROTEOMICS (2006) 6(6): 2009-2021

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Eukaryotic Cells And Tissues

Characterization of the Maize Xylem Sap Proteome
Sophie Alvarez, Jason Q. D. Goodger, Ellen L. Marsh, Sixue Chen, Victor S. Asirvatham, and Daniel P. Schachtman
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Maturation of Human Neutrophil Phagosomes Includes Incorporation of Molecular Chaperones and Endoplasmic Reticulum Quality Control Machinery
Christopher Burlak, Adeline R. Whitney, David J. Mead, Ted Hackstadt, and Frank R. DeLeo
Mol Cell Proteomics (2006) 5(4): 620-634

Characterization of an RNA Granule from Developing Brain
George Elvira, Sylwia Wasiak, Vanessa Blandford, Xin-Kang Tong, Alexandre Serrano, Xiaotang Fan, Maria del Rayo Sanchez-Carbente, Florence Servant, Alexander W. Bell, Daniel Boismenu, Jean-Claude Lacaille, Peter S. McPherson, Luc DesGroseillers, and Wayne S. Sossin
Mol Cell Proteomics (2006) 5(4): 635-651

Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals
Knoll-Gellida A, Andre M, Gattegno T, Forgue J, Admon A, Babin PJ
BMC Genomics (2006) 7(1): 46

Posttranslational, Translational, and Transcriptional Responses to Nitric Oxide Stress in Cryptococcus neoformans: Implications for Virulence
Missall TA, Pusateri ME, Donlin MJ, Chambers KT, Corbett JA, Lodge JK
Eukaryot Cell (2006) 5(3): 518-29

Mitochondrial proteomic characterization of human normal articular chondrocytes
Ruiz-Romero C, Lopez-Armada MJ, Blanco FJ
Osteoarthritis Cartilage Early Edition: published 3-Mar-2006

Differential protein expression in brain capillary endothelial cells induced by hypoxia and posthypoxic reoxygenation
Reiner F. Haseloff, Eberhard Krause, Marina Bigl, Kerstin Mikoteit, Danica Stanimirovic, Ingolf E. Blasig
PROTEOMICS (2006) 6(6): 1803-1809

A proteomic analysis of 14-3-3 binding proteins from developing barley grains
Ross D. Alexander, Peter C. Morris
PROTEOMICS (2006) 6(6): 1886-1896

Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction
Christof Rampitsch, Natalia V. Bykova, Brent McCallum, Eva Beimcik, Werner Ens
PROTEOMICS (2006) 6(6): 1897-1907

A 2-D liquid-phase chromatography for proteomic analysis in plant tissues
Pirondini A, Visioli G, Malcevschi A, Marmiroli N
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 27-Feb-2006

Identification of new immune induced molecules in the haemolymph of Drosophila melanogaster by 2D-nanoLC MS/MS
Verleyen P, Baggerman G, D'Hertog W, Vierstraete E, Husson SJ, Schoofs L
J Insect Physiol Early Edition: published 27-Feb-2006

Identification of members of the annexin family in the detergent-insoluble fraction of rat Morris hepatoma plasma membranes
Clifton JG, Brown MK, Huang F, Li X, Reutter W, Hofmann W, Hixson DC, Josic D
J Chromatogr A Early Edition: published 27-Feb-2006

Proteomics of the retinal pigment epithelium reveals altered protein expression at progressive stages of age-related macular degeneration
Nordgaard CL, Berg KM, Kapphahn RJ, Reilly C, Feng X, Olsen TW, Ferrington DA
Invest Ophthalmol Vis Sci (2006) 47(3): 815-22

Soy extract has different effects compared with the isolated isoflavones on the proteome of homocysteine-stressed endothelial cells
Fuchs D, Dirscherl B, Schroot JH, Daniel H, Wenzel U
Mol Nutr Food Res (2006) 50(1): 58-69

Comparative proteome analysis of rat brain and coronary microvascular endothelial cells
Lu L, Yang PY, Rui YC, Kang H, Zhang J, Zhang JP, Feng WH
Physiol Res Early Edition: published 23-Mar-2006

Proteomic comparison of needles from blister rust-resistant and susceptible Pinus strobus seedlings reveals upregulation of putative disease resistance proteins
Smith JA, Blanchette RA, Burnes TA, Jacobs JJ, Higgins L, Witthuhn BA, David AJ, Gillman JH
Mol Plant Microbe Interact (2006) 19(2): 150-60

Liquid Tissue: proteomic profiling of formalin-fixed tissues
Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, Conrads TP, Veenstra TD, Krizman DB
Biotechniques (2005) Suppl: 32-5.

Identification of Novel Centrosomal Proteins in Dictyostelium discoideum by Comparative Proteomic Approaches
Yvonne Reinders, Irene Schulz, Ralph Gräf, and Albert Sickmann
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 589-598

Comparative Profiling of the Mammalian Mitochondrial Proteome: Multiple Aconitase-2 Isoforms Including N-formylkynurenine Modifications as Part of a Protein Biomarker Signature for Reactive Oxidative Species
Christian Hunzinger, Wojciech Wozny, Gerhard P. Schwall, Slobodan Poznanovi , Werner Stegmann, Helmut Zengerling, Rainer Schoepf, Karlfried Groebe, Michael A. Cahill, Heinz D. Osiewacz, Nora Jägemann, Monika Bloch, Norbert A. Dencher, Frank Krause, and André Schrattenholz
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 625-633

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Prokaryotes

Proteome analysis of sorbitol fermentation specific protein in Vibrio cholerae by 2-DE and MS
Zou QingHua, Yan XiaoMei, Li BoQing, Zeng Xun, Zhou Jun, Zhang JianZhong
PROTEOMICS (2006) 6(6): 1848-1855

Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling
Alexandra Resch, Stefan Leicht, Marc Saric, Linda Pásztor, Andreas Jakob, Friedrich Götz, Alfred Nordheim
PROTEOMICS (2006) 6(6): 1867-1877

Comparative proteome approach to characterize the high-pressure stress response of Lactobacillus sanfranciscensis DSM 20451T
Sebastian Hörmann, Carsten Scheyhing, Jürgen Behr, Melanie Pavlovic, Matthias Ehrmann, Rudi F. Vogel
PROTEOMICS (2006) 6(6): 1878-1885

Growth-induced changes in the proteome of Helicobacter pylori
Uwins C, Deitrich C, Argo E, Stewart E, Davidson I, Cash P
Electrophoresis (2006) 27(5-6): 1136-1146

Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal
Budde I, Steil L, Scharf C, Volker U, Bremer E
Microbiology (2006) 152(Pt 3): 831-53

Phenotypic Characterization of Streptococcus pneumoniae Biofilm Development
Allegrucci M, Hu FZ, Shen K, Hayes J, Ehrlich GD, Post JC, Sauer K
J Bacteriol (2006) 188(7): 2325-35

Proteome of the Bacterium Mycoplasma penetrans
Mario Ferrer-Navarro, Antonio Gómez, Oscar Yanes, Raquel Planell, Francesc Xavier Avilés, Jaume Piñol, Josep Antoni Pérez Pons, and Enrique Querol
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 688-694

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Pharmacology and Toxicology

Surface enhanced laser desorption ionization spectrometry reveals biomarkers for drug treatment but not dose
Cloud P. Paweletz, Matthew C. Wiener, Jeffrey R. Sachs, Roger Meurer, Margaret S. Wu, Kenney K. Wong, Nathan A. Yates, Ronald C. Hendrickson
PROTEOMICS (2006) 6(7): 2101-2107

Proteins Associated with Cisplatin Resistance in Ovarian Cancer Cells Identified by Quantitative Proteomic Technology and Integrated with mRNA Expression Levels
Jennifer J. Stewart, James T. White, Xiaowei Yan, Steven Collins, Charles W. Drescher, Nicole D. Urban, Leroy Hood, and Biaoyang Lin
Mol Cell Proteomics (2006) 5(3): 433-443

Proteomic analysis of rat hippocampus and frontal cortex after chronic treatment with fluoxetine or putative novel antidepressants: CRF1 and NK1 receptor antagonists
Carboni L, Vighini M, Piubelli C, Castelletti L, Milli A, Domenici E
Eur Neuropsychopharmacol Early Edition: published 3-Mar-2006

Investigation of proteomic biomarkers in in vivo hepatotoxicity study of rat liver: toxicity differentiation in hepatotoxicants
Yamamoto T, Kikkawa R, Yamada H, Horii I
J Toxicol Sci (2006) 31(1): 49-60

Immunochemical and proteomic analysis of covalent adducts formed by quinone methide tumor promoters in mouse lung epithelial cell lines
Meier BW, Gomez JD, Zhou A, Thompson JA
Chem Res Toxicol (2005) 18(10): 1575-85

Pharmacoproteomics of 4-Phenylbutyrate-Treated IB3-1 Cystic Fibrosis Bronchial Epithelial Cells
Om V. Singh, Neeraj Vij, Peter J. Mogayzel, Jr., Cathy Jozwik, Harvey B. Pollard, and Pamela L. Zeitlin
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 562-571

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Protein Characterization / PTMs

Characterization of Protein Expression and Folding in Cell-Free Systems by MALDI-TOF Mass Spectrometry
Lisa M. Jungbauer and Silvia Cavagnero
ANALYTICAL CHEMISTRY Early Edition: published 03/24/2006

Method to Site-Specifically Identify and Quantitate Carbonyl End Products of Protein Oxidation Using Oxidation-Dependent Element Coded Affinity Tags (O-ECAT) and NanoLiquid Chromatography Fourier Transform Mass Spectrometry
Susan Lee, Nicolas L. Young, Paul A. Whetstone, Sarah M. Cheal, W. Henry Benner, Carlito B. Lebrilla, and Claude F. Meares
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 539-547

Quantitative Phosphotyrosine Proteomics of EphB2 Signaling by Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)
Guoan Zhang, Daniel S. Spellman, Edward Y. Skolnik, and Thomas A. Neubert
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 581-588

PhosTShunter: A Fast and Reliable Tool to Detect Phosphorylated Peptides in Liquid Chromatography Fourier Transform Tandem Mass Spectrometry Data Sets
Thomas Köcher, Mikhail M. Savitski, Michael L. Nielsen, and Roman A. Zubarev
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 659-668

Tools for Glycoproteomic Analysis: Size Exclusion Chromatography Facilitates Identification of Tryptic Glycopeptides with N-linked Glycosylation Sites
Gerardo Alvarez-Manilla, James Atwood III, Yan Guo, Nicole Lynn Warren, Ron Orlando, and Michael Pierce
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 701-708

Strategy for Simulation of CID Spectra of N-Linked Oligosaccharides toward Glycomics
Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Norihiro Kikuchi, Takashi Angata, Mitsuru Nakamura, Hide-Ki Ishida, and Hisashi Narimatsu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Improved Identification of SUMO Attachment Sites Using C-Terminal SUMO Mutants and Tailored Protease Digestion Strategies
James A. Wohlschlegel, Erica S. Johnson, Steven I. Reed, and John R. Yates, III
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Novel Protein Phosphorylation Site Identification in Spinach Stroma Membranes by Titanium Dioxide Microcolumns and Tandem Mass Spectrometry
Sara Rinalducci, Martin R. Larsen, Shabaz Mohammed, and Lello Zolla
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes
Alain Lévine, Françoise Vannier, Cédric Absalon, Lauriane Kuhn, Peter Jackson, Elaine Scrivener, Valérie Labas, Joëlle Vinh, Patrick Courtney, Jérôme Garin, Simone J. Séror
PROTEOMICS (2006) 6(7): 2157-2173

Identification of Sites of Mannose 6-Phosphorylation on Lysosomal Proteins
David E. Sleat, Haiyan Zheng, Meiqian Qian, and Peter Lobel
Mol Cell Proteomics (2006) 5(4): 686-701

Phosphate-binding Tag, a New Tool to Visualize Phosphorylated Proteins
Eiji Kinoshita, Emiko Kinoshita-Kikuta, Kei Takiyama, and Tohru Koike
Mol Cell Proteomics (2006) 5(4): 749-757

Differential Phosphoprotein Labeling (DIPPL), a Method for Comparing Live Cell Phosphoproteomes Using Simultaneous Analysis of 33P- and 32P-Labeled Proteins
Andreas Wyttenbach and Aviva M. Tolkovsky
Mol Cell Proteomics (2006) 5(3): 553-559

Concanavalin A-captured Glycoproteins in Healthy Human Urine
Linjie Wang, Fuxin Li, Wei Sun, Shuzhen Wu, Xiaorong Wang, Ling Zhang,Dexian Zheng, Jue Wang, and Youhe Gao
Mol Cell Proteomics (2006) 5(3): 560-562

Quantitation of protein phosphorylation in pregnant rat uteri using stable isotope dimethyl labeling coupled with IMAC
Sheng-Yu Huang, Mei-Ling Tsai, Chin-Jen Wu, Jue-Liang Hsu, Shih-Hsin Ho, Shu-Hui Chen
PROTEOMICS (2006) 6(6): 1722-1734

Identification of novel phosphoproteins in signaling pathways triggered by latent membrane protein 1 using functional proteomics technology
Guangrong Yan, Lili Li, Yongguang Tao, Sufang Liu, Yiping Liu, Wei Luo, Yong Wu, Min Tang, Zigang Dong, Ya Cao
PROTEOMICS (2006) 6(6): 1810-1821

Detection of Phosphopeptides Using Fe(III)-Nitrilotriacetate Complexes Immobilized on a MALDI Plate
Jamie D. Dunn, J. Throck Watson, and Merlin L. Bruening
ANALYTICAL CHEMISTRY (2006) 78(5): 1574-1580

MALDI QqTOF MS Combined with Off-line HPLC for Characterization of Protein Primary Structure and Post-Translational Modifications
Krokhin OV, Ens W, Standing KG
J Biomol Tech (2005) 16(4): 429-40

Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: application to proteins isolated by gel electrophoresis
Sachon E, Mohammed S, Bache N, Jensen ON
Rapid Commun Mass Spectrom (2006) 20(7): 1127-1134

A Novel Approach for Screening the Proteome for Changes in Protein Conformation
Pierce A, Dewaal E, Vanremmen H, Richardson A, Chaudhuri A
Biochemistry (2006) 45(9): 3077-3085

On-Bead Chemical Synthesis and Display of Phosphopeptides for Affinity Pull-Down Proteomics
Brandt M, Madsen JC, Bunkenborg J, Jensen ON, Gammeltoft S, Jensen KJ
Chembiochem Early Edition: published 27-Feb-2006

Probing mucin-type O-linked glycosylation in living animals
Dube DH, Prescher JA, Quang CN, Bertozzi CR
Proc Natl Acad Sci U S A Early Edition: published 20-Mar-2006

Nitric Oxide and Posttranslational Modification of the Vascular Proteome. S-Nitrosation of Reactive Thiols
Handy DE, Loscalzo J
Arterioscler Thromb Vasc Biol Early Edition: published 16-Mar-2006

Protein and proteome phosphorylation stoichiometry analysis by element mass spectrometry
Kruger R, Kubler D, Pallisse R, Burkovski A, Lehmann WD
Anal Chem (2006) 78(6): 1987-94

Highly sensitive multistage mass spectrometry enables small-scale analysis of protein glycosylation from two-dimensional polyacrylamide gels
Nobuaki Takemori, Naoka Komori, Hiroyuki Matsumoto
ELECTROPHORESIS (2006) 27(7): 1394-1406

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)
Fengfeng Zhou, Yu Xue, Xuebiao Yao, and Ying Xu
Bioinformatics (2006) 22(7): 894-896

Structural Characterization of Glycopeptides by N-terminal Protein Ladder Sequencing
Yusuke Suzuki, Minoru Suzuki, Yoshiaki Nakahara, Yukishige Ito, Emi Ito, Naoko Goto, Kozo Miseki, Junko Iida, and Akemi Suzuki
ANALYTICAL CHEMISTRY Early Edition: published 03/10/2006

Infrared Multiphoton Dissociation and Electron Capture Dissociation of High-Mannose Type Glycopeptides
Julie T. Adamson and Kristina Håkansson
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 493-501

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Protein-protein interaction

An evaluation of in vitro protein-protein interaction techniques: Assessing contaminating background proteins
Jenika M. Howell, Tara L. Winstone, Jens R. Coorssen, Raymond J. Turner
PROTEOMICS (2006) 6(7): 2050-2069

Surface plasmon resonance imaging protein arrays for analysis of triple protein interactions of HPV, E6, E6AP, and p53
Hyeon-Su Ro, Byung Hoon Koh, Sun Ok Jung, Hyun Kyu Park, Yong-Beom Shin, Min-Gon Kim, Bong Hyun Chung
PROTEOMICS (2006) 6(7): 2108-2111

Proteomic analysis of the binding partners to enteropathogenic Escherichia coli virulence proteins expressed in Saccharomyces cerevisiae
Philip R. Hardwidge, Sam Donohoe, Ruedi Aebersold, B. Brett Finlay
PROTEOMICS (2006) 6(7): 2174-2179

Construction and Application of a Yeast Surface-displayed Human cDNA Library to Identify Post-translational Modification-dependent Protein-Protein Interactions
Scott Bidlingmaier and Bin Liu
Mol Cell Proteomics (2006) 5(3): 533-540

The dopamine transporter proteome
Torres GE
J Neurochem Early Edition: published 3-Mar-2006

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A
Nat Genet (2006) 38(3): 285-93

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Quantitation

Comparative Study of Three Proteomic Quantitative Methods, DIGE, cICAT, and iTRAQ, Using 2D Gel- or LC-MALDI TOF/TOF
Wells W. Wu, Guanghui Wang, Seung Joon Baek, and Rong-Fong Shen
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 651-658

Label-Free Protein Quantification Using LC-Coupled Ion Trap or FT Mass Spectrometry: Reproducibility, Linearity, and Application with Complex Proteomes
Guanghui Wang, Wells W. Wu, Weihua Zeng, Chung-Lin Chou, and Rong-Fong Shen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/24/2006

Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins
Leigh Anderson and Christie L. Hunter
Mol Cell Proteomics (2006) 5(4): 573-588

Simultaneous Qualitative and Quantitative Analysis of theEscherichia coli Proteome: A Sweet Tale
Jeffrey C. Silva, Richard Denny, Craig Dorschel, Marc V. Gorenstein, Guo-Zhong Li, Keith Richardson, Daniel Wall, and Scott J. Geromanos
Mol Cell Proteomics (2006) 5(4): 589-607

Signal Maps for Mass Spectrometry-based Comparative Proteomics
Amol Prakash, Parag Mallick, Jeffrey Whiteaker, Heidi Zhang, Amanda Paulovich, Mark Flory, Hookeun Lee, Ruedi Aebersold, and Benno Schwikowski
Mol Cell Proteomics (2006) 5(3): 423-432

Relative and absolute quantitative expression profiling of cytochromes P450 using isotope-coded affinity tags
Rosalind E. Jenkins, Neil R. Kitteringham, Christie L. Hunter, Sally Webb, Tony J. Hunt, Robert Elsby, Rod B. Watson, Dominic Williams, Stephen R. Penningtonand, B. Kevin Park
PROTEOMICS (2006) 6(6): 1934-1947

Quantitative proteomics reveals post-translational control as a regulatory factor in primary hematopoietic stem cells
Unwin RD, Smith DL, Blinco D, Wilson CL, Miller CJ, Evans CA, Jaworska E, Baldwin SA, Barnes K, Pierce A, Spooncer E, Whetton AD
Blood Early Edition: published 28-Feb-2006

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein
Pawlik TM, Hawke DH, Liu Y, Krishnamurthy S, Fritsche H, Hunt KK, Kuerer HM
BMC Cancer (2006) 6(1): 68

Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: application to proteins isolated by gel electrophoresis
E. Sachon, S. Mohammed, N. Bache, O. N. Jensen
Rapid Communications in Mass Spectrometry (2006) 20(7): 1127-1134

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Review

Proteobionics: Biomimetics in Proteomics
Andrei P. Sommer and Eleonora Gheorghiu
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 611-618

Population proteomics: An emerging discipline to study metapopulation ecology
David G. Biron, Hugh D. Loxdale, Fleur Ponton, Hercules Moura, Laurent Marché, Christophe Brugidou, Frédéric Thomas
PROTEOMICS (2006) 6(6): 1712-1715

Protein and peptide arrays: Recent trends and new directions
Cretich M, Damin F, Pirri G, Chiari M
Biomol Eng Early Edition: published 6-Mar-2006

Glucose Signaling in Saccharomyces cerevisiae
Santangelo GM
Microbiol Mol Biol Rev (2006) 70(1): 253-82

Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer
Gulmann C, Sheehan K, Kay E, Liotta L, Petricoin E 3rd
J Pathol (2006) 208(5): 595-606

Real and imaginary artefacts in proteome analysis via two-dimensional maps
Righetti PG
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 3-Mar-2006

Immune control of Babesia bovis infection
Brown WC, Norimine J, Knowles DP, Goff WL
Vet Parasitol Early Edition: published 27-Feb-2006

Microfabricated devices: A new sample introduction approach to mass spectrometry
Lazar IM, Grym J, Foret F
Mass Spectrom Rev Early Edition: published 28-Feb-2006

Nutrigenomics, proteomics, metabolomics, and the practice of dietetics
Trujillo E, Davis C, Milner J
J Am Diet Assoc (2006) 106(3): 403-13

Proteomic biomarker discovery in cerebrospinal fluid for neurodegenerative diseases
Zhang J, Goodlett DR, Montine TJ
J Alzheimers Dis (2005) 8(4): 377-86

Biomarkers for Alzheimer's disease - Clinical needs and application
Galasko D
J Alzheimers Dis (2005) 8(4): 339-46

Cancer biomarkers: knowing the present and predicting the future
Zetter BR, Chatterjee SK
Fut Oncol (2005) 1(1): 37-50

Proteomics-driven progress in neurodegeneration research
Fountoulakis M, Kossida S
Electrophoresis Early Edition: published 23-Mar-2006

What is the future of diabetic wound care?
Sweitzer SM, Fann SA, Borg TK, Baynes JW, Yost MJ
Diabetes Educ (2006) 32(2): 197-210

Application of mass spectrometry to the discovery of biomarkers for detection of prostate cancer
Semmes OJ, Malik G, Ward M
J Cell Biochem Early Edition: published 21-Mar-2006

Disease mechanism and biomarkers of oral squamous cell carcinoma
Brinkman BM, Wong DT
Curr Opin Oncol (2006) 18(3): 228-233

Technologies to shape the future: proteomics applications in anesthesiology and critical care medicine
Atkins JH, Johansson JS
Anesth Analg (2006) 102(4): 1207-16

Arabidopsis thaliana proteomics: from proteome to genome
Baginsky S, Gruissem W
J Exp Bot Early Edition: published 21-Mar-2006

Proteomics studies of post-translational modifications in plants
Kwon SJ, Choi EY, Choi YJ, Ahn JH, Park OK
J Exp Bot Early Edition: published 21-Mar-2006

MULTIPLEXED PROTEIN ARRAY PLATFORMS FOR ANALYSIS OF AUTOIMMUNE DISEASES
Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ
Annu Rev Immunol (2006) 24: 391-418.

Mitochondrial uncoupling proteins: New insights from functional and proteomic studies
Douette P, Sluse FE
Free Radic Biol Med (2006) 40(7): 1097-107

Inner ear proteomics: A fad or hear to stay
Thalmann I
Brain Res Early Edition: published 13-Mar-2006

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Methodology

Label-Free Detection of Single Protein Molecules Using Deep UV Fluorescence Lifetime Microscopy
Qiang Li and Stefan Seeger
ANALYTICAL CHEMISTRY Early Edition: published 03/17/2006

Direct-Write Fabrication of Functional Protein Matrixes Using a Low-Cost Q-Switched Laser
Bryan Kaehr, Nusret Erta , Rex Nielson, Richard Allen, Ryan T. Hill, Matthew Plenert, and Jason B. Shear
ANALYTICAL CHEMISTRY Early Edition: published 03/24/2006

Modular Stop and Go Extraction Tips with Stacked Disks for Parallel and Multidimensional Peptide Fractionation in Proteomics
Yasushi Ishihama, Juri Rappsilber, and Matthias Mann
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/10/2006

Secretory Protein Enrichment and Analysis: An Optimized Approach Applied on Cancer Cell Lines Using 2D LC-MS/MS
Flaubert Mbeunkui, Oystein Fodstad, and Lewis K. Pannell
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/10/2006

Trade-Off between High Sensitivity and Increased Potential for False Positive Peptide Sequence Matches Using a Two-Dimensional Linear Ion Trap for Tandem Mass Spectrometry-Based Proteomics
Hongwei Xie and Timothy J. Griffin
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Advances in proteomics data analysis and display using an accurate mass and time tag approach
Jennifer S.D. Zimmer, Matthew E. Monroe, Wei-Jun Qian, Richard D. Smith
Mass Spectrometry Reviews (2006) 25(3): 450-482

Simultaneous Reduction and Alkylation of Protein Disulfides in a Centrifugal Ultrafiltration Device Prior to Two-Dimensional Gel Electrophoresis
Gary B. Smejkal, Chunqin Li, Myra H. Robinson, Alexander V. Lazarev, Nathan P. Lawrence, and Elena Chernokalskaya
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Comparative Analysis of Protein O-Glycosylation in Arthritis by Stable Isotope Coding and Serial Lectin Affinity Chromatography
Malaika O. Durham, Andrew Hilgenbrink, Phillip Low, and Fred E. Regnier
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/17/2006

Toward the Complete Membrane Proteome: High Coverage of Integral Membrane Proteins Through Transmembrane Peptide Detection
Frank Fischer, Dirk Wolters, Matthias Rogner, and Ansgar Poetsch
Mol Cell Proteomics (2006) 5(3): 444-453

Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry
Jennifer L. Frahm, Brian E. Howard, Steffen Heber, David C. Muddiman
Journal of Mass Spectrometry (2006) 41(3): 281-288

C-terminal sequencing method for proteins in polyacrylamide gel by the reaction of acetic anhydride
Kenji Miyazaki, Akira Tsugita
PROTEOMICS (2006) 6(7): 2026-2033

Selective detection of 2-nitrobenzenesulfenyl-labeled peptides by matrix-assisted laser desorption/ionization-time of flight mass spectrometry using a novel matrix
Ei-ichi Matsuo, Chikako Toda, Makoto Watanabe, Noriyuki Ojima, Shunsuke Izumi, Koichi Tanaka, Susumu Tsunasawa, Osamu Nishimura
PROTEOMICS (2006) 6(7): 2042-2049

A broad-spectrum fluorescence-based peptide library for the rapid identification of protease substrates
Daniel A. Thomas, Peter Francis, Carla Smith, Steven Ratcliffe, Nicholas J. Ede, Corinne Kay, Gareth Wayne, Steve L. Martin, Keith Moore, Augustin Amour, Nigel M. Hooper
PROTEOMICS (2006) 6(7): 2112-2120

Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach
Ruihua Fang, Dwayne A. Elias, Matthew E. Monroe, Yufeng Shen, Martin Mcintosh, Pei Wang, Carrie D. Goddard, Stephen J. Callister, Ronald J. Moore, Yuri A. Gorby, Joshua N. Adkins, Jim K. Fredrickson, Mary S. Lipton, and Richard D. Smith
Mol Cell Proteomics (2006) 5(4): 714-725

A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions: Application in Ubiquitin Profiling and Protein Complex Identification Combined with in vivoCross-Linking
Christian Tagwerker, Karin Flick, Meng Cui, Cortnie Guerrero, Yimeng Dou, Bernhard Auer, Pierre Baldi, Lan Huang, and Peter Kaiser
Mol Cell Proteomics (2006) 5(4): 737-748

Multiplex Analysis of Intracellular Signaling Pathways in Lymphoid Cells by Microbead Suspension Arrays
Imran H. Khan, Sara Mendoza, Paul Rhyne, Melanie Ziman, Joseph Tuscano, Dominic Eisinger, Hsing-Jien Kung, and Paul A. Luciw
Mol Cell Proteomics (2006) 5(4): 758-768

Microwave-assisted Protein Preparation and Enzymatic Digestion in Proteomics
Wei Sun, Shijuan Gao, Linjie Wang, Yong Chen, Shuzhen Wu, Xiaorong Wang, Dexian Zheng, and Youhe Gao
Mol Cell Proteomics (2006) 5(4): 769-776

Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-Fourier transform mass spectrometer
Zheng X, Baker H, Hancock WS
J Chromatogr A Early Edition: published 6-Mar-2006

Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM
Nat Biotechnol (2006) 24(3): 333-8

High-speed biomarker identification utilizing porous silicon nanovial arrays and MALDI-TOF mass spectrometry
Finnskog D, Jaras K, Ressine A, Malm J, Marko-Varga G, Lilja H, Laurell T
Electrophoresis (2006) 27(5-6): 1093-1103

Comparison of the Paul ion trap to the linear ion trap for use in global proteomics
Leah S. Riter, Karen M. Gooding, Barry D. Hodge, Randall K. Julian Jr
PROTEOMICS (2006) 6(6): 1735-1740

Octadecylated Silica Monolith Capillary Column with Integrated Nanoelectrospray Ionization Emitter for Highly Efficient Proteome Analysis
Chuanhui Xie, Mingliang Ye, Xiaogang Jiang, Wenhai Jin, and Hanfa Zou
Mol Cell Proteomics (2006) 5(3): 454-461

Sulfonation Chemistry as a Powerful Tool for MALDI TOF/TOF de Novo Sequencing and Post-Translational Modification Analysis
Conrotto P, Hellman U
J Biomol Tech (2005) 16(4): 441-52

Surfactant Sodium Lauryl Sulfate Enhances Skin Vaccination: Molecular Characterization via a Novel Technique using Ultrafiltration Capillaries and Mass Spectrometric Proteomics
Chun-Ming Huang, Chao-Cheng Wang, Mikako Kawai, Stephen Barnes, and Craig A. Elmets
Mol Cell Proteomics (2006) 5(3): 523-532

Concentration and desalting of Peptide and protein samples with a newly developed c18 membrane in a microspin column format
Naldrett MJ, Zeidler R, Wilson KE, Kocourek A
J Biomol Tech (2005) 16(4): 423-8

Proteomic changes in bovine heart mitochondria with age: using a novel technique for organelle separation and enrichment
Kiri AN, Tran HC, Drahos KL, Lan W, McRorie DK, Horn MJ
J Biomol Tech (2005) 16(4): 371-9

Comparison of Golgi apparatus and endoplasmic reticulum proteins from livers of juvenile and aged rats using a novel technique for separation and enrichment of organelles
Drahos KL, Tran HC, Kiri AN, Lan W, McRorie DK, Horn MJ
J Biomol Tech (2005) 16(4): 347-55

Outer membrane vesicles from group B Neisseria meningitidis ?gna33 mutant: Proteomic and immunological comparison with detergent-derived outer membrane vesicles
Germano Ferrari, Ignazio Garaguso, Jeannette Adu-Bobie, Francesco Doro, Anna Rita Taddei, Alessia Biolchi, Brunella Brunelli, Marzia Monica Giuliani, Mariagrazia Pizza, Nathalie Norais, Guido Grandi
PROTEOMICS (2006) 6(6): 1856-1866

Annotated proteome of a human T-cell lymphoma
Crockett DK, Seiler CE 3rd, Elenitoba-Johnson KS, Lim MS
J Biomol Tech (2005) 16(4): 341-6

Multidimensional fractionation of the bovine skeletal muscle proteome
Cruzado-Park ID, Betgovargez E, Ratnayake C, Simonian MH
J Biomol Tech (2005) 16(4): 311-5

Characterization of proteins in the human serum proteome
Betgovargez E, Knudson V, Simonian MH
J Biomol Tech (2005) 16(4): 306-10

Identification of Proteins in Renaissance Paintings by Proteomics
Caroline Tokarski, Elisabeth Martin, Christian Rolando, and Cécile Cren-Olivé
ANALYTICAL CHEMISTRY (2006) 78(5): 1494-1502

DNA-Directed Protein Immobilization for Simultaneous Detection of Multiple Analytes by Surface Plasmon Resonance Biosensor
Christina Boozer, Jon Ladd, Shengfu Chen, and Shaoyi Jiang
ANALYTICAL CHEMISTRY (2006) 78(5): 1515-1519

New Escherichia coli outer membrane proteins identified through prediction and experimental verification
Marani P, Wagner S, Baars L, Genevaux P, De Gier JW, Nilsson I, Casadio R, Von Heijne G
Protein Sci Early Edition: published 7-Mar-2006

Pulsed Hydrogen/Deuterium Exchange MS/MS for Studying the Relationship between Noncovalent Protein Complexes in Solution and in the Gas Phase after Electrospray Ionization
Belal M. Hossain and Lars Konermann
ANALYTICAL CHEMISTRY (2006) 78(5): 1613-1619

Proteomic analysis of the mouse brain following protein enrichment by preparative electrophoresis
Xixi E, Dimitraki P, Vougas K, Kossida S, Lubec G, Fountoulakis M
Electrophoresis Early Edition: published 3-Mar-2006

Identification of Carboxyl-Terminal Peptide Fragments of Parathyroid Hormone in Human Plasma at Low-Picomolar Levels by Mass Spectrometry
Chao-Xuan Zhang, Brittney V. Weber, Jerdravee Thammavong, Thomas A. Grover, and David S. Wells
ANALYTICAL CHEMISTRY (2006) 78(5): 1636-1643

Improved Protein Recovery in Reversed-Phase Liquid Chromatography by the Use of Ultrahigh Pressures
John W. Eschelbach and James W. Jorgenson
ANALYTICAL CHEMISTRY (2006) 78(5): 1697-1706

Protein cleavage strategies for an improved analysis of the membrane proteome
Fischer F, Poetsch A
Proteome Sci (2006) 4: 2

Optimizing the Use of TRIzol-extracted Proteins in Surface Enhanced Laser Desorption/ Ionization (SELDI) Analysis
Man T, Li Y, Dang T, Shen J, Perlaky L, Lau C
Proteome Sci (2006) 4: 3

An accurate and reproducible method for proteome profiling of the effects of salt stress in the rice leaf lamina
Parker R, Flowers TJ, Moore AL, Harpham NV
J Exp Bot Early Edition: published 2-Mar-2006

Proteomic study of muscle sarcoplasmic proteins using AUT-PAGE/SDS-PAGE as two-dimensional gel electrophoresis
Picariello G, De Martino A, Mamone G, Ferranti P, Addeo F, Faccia M, Spagnamusso S, Di Luccia A
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 23-Feb-2006

A novel glass slide-based peptide array support with high functionality resisting non-specific protein adsorption
Beyer M, Felgenhauer T, Ralf Bischoff F, Breitling F, Stadler V
Biomaterials Early Edition: published 22-Feb-2006

A novel droplet-tap sample-loading method for two-dimensional gel electrophoresis
Long XH, Lin JF, Zhang YZ
Anal Bioanal Chem Early Edition: published 23-Mar-2006

Development of activity-based probes for trypsin-family serine proteases
Pan Z, Jeffery DA, Chehade K, Beltman J, Clark JM, Grothaus P, Bogyo M, Baruch A
Bioorg Med Chem Lett Early Edition: published 20-Mar-2006

Preliminary approaches for the development of a high-performance liquid chromatography/electrospray ionization tandem mass spectrometry method for the detection and label-free semi-quantitation of the main storage proteins of Lupinus albus in foods
Locati D, Morandi S, Zanotti M, Arnoldi A
Rapid Commun Mass Spectrom (2006) 20(8): 1305-1316

Copper-coated microsprayer interface for on-line sheathless capillary electrophoresis electrospray mass spectrometry of carbohydrates
Zamfir AD, Dinca N, Sisu E, Peter-Katalinic J
J Sep Sci (2006) 29(3): 414-22

Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis
Zora Nováková, Petr Man, Petr Novák, Pavel Hozák, Zden?k Hodný
ELECTROPHORESIS (2006) 27(7): 1277-1287

High-throughput sodium dodecyl sulfate polyacrylamide gel electrophoresis by linking conventional gel plates with automated liquid handler via Gel Adaptor
Satoshi Sugawa, Tatsuzo Kawano, Yukinori Nara, Tetsu Isomura
ELECTROPHORESIS (2006) 27(7): 1300-1302

High-sensitivity staining of proteins for one- and two-dimensional gel electrophoresis using post migration covalent staining with a ruthenium fluorophore
Caroline Tokarski, Cécile Cren-Olivé, Marianne Fillet, Christian Rolando
ELECTROPHORESIS (2006) 27(7): 1407-1416

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Reproducibility: Implication of Multiple Injections
Poh Kuan Chong, Chee Sian Gan, Trong Khoa Pham, and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/31/2006

Selective Isolation of Lysine-Free Tryptic Peptides Delimited by Arginine Residues: A New Tool for Proteome Analysis
Aniel S nchez, Luis J. Gonz lez, Yassel Ramos, L zaro Betancourt, Jeovanis Gil, Vladimir Besada, Jorge Fern ndez-de-Cossio, Félix Alvarez, and Gabriel Padrón
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/31/2006

Capillary Isoelectric Focusing Coupled with Dynamic Imaging Detection: A One-Dimensional Separation for Two-Dimensional Protein Characterization
Zhen Liu, Tibebe Lemma, and Janusz Pawliszyn
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/31/2006

Different Impact of Staining Procedures Using Visible Stains and Fluorescent Dyes for Large-Scale Investigation of Proteomes by MALDI-TOF Mass Spectrometry
François Chevalier, Delphine Centeno, Valérie Rofidal, Marc Tauzin, Olivier Martin, Nicolas Sommerer, and Michel Rossignol
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 512-520

Analysis of Intact Tissue by Intermediate-Pressure MALDI on a Linear Ion Trap Mass Spectrometer
Timothy J. Garrett and Richard A. Yost
ANALYTICAL CHEMISTRY Early Edition: published 03/10/2006

Integration of a Two-Phase Partition Method into Proteomics Research on Rat Liver Plasma Membrane Proteins
Rui Cao, Xuanwen Li, Zhen Liu, Xia Peng, Weijun Hu, Xianchun Wang, Ping Chen, Jingyun Xie, and Songping Liang
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 634-642

IMS-IMS and IMS-IMS-IMS/MS for Separating Peptide and Protein Fragment Ions
Samuel I. Merenbloom, Stormy L. Koeniger, Stephen J. Valentine, Manolo D. Plasencia, and David E. Clemmer
ANALYTICAL CHEMISTRY Early Edition: published 03/10/2006

140 Mouse Brain Proteins Identified by Ca2+-Calmodulin Affinity Chromatography and Tandem Mass Spectrometry
Tord Berggård, Giorgio Arrigoni, Olof Olsson, Malin Fex, Sara Linse, and Peter James
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 669-687

Effects of Modified Digestion Schemes on the Identification of Proteins from Complex Mixtures
Aaron A. Klammer and Michael J. MacCoss
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 695-700

Matrix with High Salt Tolerance for the Analysis of Peptide and Protein Samples by Desorption/Ionization Time-of-Flight Mass Spectrometry
Songyun Xu, Mingliang Ye, Danke Xu, Xin Li, Chensong Pan, and Hanfa Zou
ANALYTICAL CHEMISTRY Early Edition: published 03/17/2006

Analysis of Membrane Proteins from Human Chronic Myelogenous Leukemia Cells: Comparison of Extraction Methods for Multidimensional LC-MS/MS
Mariah C. Ruth, William M. Old, Michelle A. Emrick, Karen Meyer-Arendt, Lauren D. Aveline-Wolf, Kevin G. Pierce, Alex M. Mendoza, Joel R. Sevinsky, Micah Hamady, Robin D. Knight, Katheryn A. Resing, and Natalie G. Ahn
JOURNAL OF PROTEOME RESEARCH (2006) 5(3): 709-719

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Books

Book Review: The Evolution from Protein Chemistry to Proteomics. By R. L. Lundblad
Pier Giorgio Righetti
PROTEOMICS (2006) 6(7): 2328-2329

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Meeting

Meetings Diary: Proteomics 7/2006
PROTEOMICS (2006) 6(7): 2330-2332

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