SPS' Digest

Issue 20, 11-Jul-2005

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Quick jumps to articles in: Bioinformatics (29) / Biological applications (22) / Biomedical and clinical applications (45) / Eukaryotic Cells And Tissues (21) / Prokaryotes (9) / Pharmacology and Toxicology (9) / Protein Array (9) / Protein Characterization - PTMs (12) / Protein-protein interaction (5) / Quantitation (7) / Review (28) / Methodology (47) / Books (1) / Meeting (2) / Other (9) /

In this issue, 254 articles have been selected from:

Am J Nephrol, Volume 25, Issue 4, 2005 (1 article)
Am J Pharmacogenomics, Volume 5, Issue 3, 2005 (1 article)
Am J Respir Crit Care Med, Early Edition, 9-Jun-2005 (1 article)
Anal Biochem, Early Edition, 9-Jun-2005->10-Jun-2005 (2 articles)
Anal Chem, Volume 77, Issues 11+12, 2005 (3 articles)
Bioinformatics, Early Edition, 9-Jun-2005 (1 article)
Bioinformatics, Volume 21, Issues Suppl 1+13, 2005 (2 articles)
Biotechnol Bioeng, Early Edition, 9-Jun-2005->15-Jun-2005 (2 articles)
Brain Res Mol Brain Res, Early Edition, 30-May-2005 (1 article)
Brief Funct Genomic Proteomic, Volume 4, Issue 1, 2005 (6 articles)
C R Biol, Volume 328, Issue 5, 2005 (1 article)
Can J Microbiol, Volume 51, Issue 3, 2005 (1 article)
Cancer Detect Prev, Volume 29, Issue 3, 2005 (1 article)
Cancer Lett, Early Edition, 27-May-2005 (1 article)
Cell, Volume 121, Issue 5, 2005 (1 article)
Chem Biol Interact, Volume 153-154, 2005 (1 article)
Chem Res Toxicol, Volume 18, Issue 6, 2005 (2 articles)
Clin Chem, Early Edition, 10-Jun-2005 (1 article)
Clin Chim Acta, Early Edition, 3-Jun-2005->18-Jun-2005 (6 articles)
Curr Top Dev Biol, Volume 67, 2005 (1 article)
Dermatology, Volume 210, Issue 4, 2005 (1 article)
Dis Markers, Volume 21, Issue 2, 2005 (1 article)
Drug Discov Today, Volume 10, Issue 11, 2005 (2 articles)
Electrophoresis, Early Edition, 20-Jun-2005->30-May-2005 (12 articles)
Electrophoresis, Volume 26, Issue 12, 2005 (3 articles)
Endocr Relat Cancer, Volume 12, Issue 2, 2005 (1 article)
Eur J Cancer, Early Edition, 10-Jun-2005 (1 article)
Eur J Gastroenterol Hepatol, Volume 17, Issue 7, 2005 (1 article)
Eur Urol, Early Edition, 15-Jun-2005 (1 article)
Expert Rev Mol Diagn, Volume 5, Issue 3, 2005 (1 article)
Expert Rev Proteomics, Volume 2, Issue 2, 2005 (8 articles)
FEBS Lett, Volume 579, Issue 15, 2005 (1 article)
FEMS Microbiol Lett, Volume 247, Issue 1, 2005 (1 article)
IDrugs, Volume 4, Issue 11, 2001 (2 articles)
IEEE Eng Med Biol Mag, Volume 24, Issue 3, 2005 (3 articles)
In Silico Biol, Volume 5, Issues 1+2, 2005 (2 articles)
Insect Biochem Mol Biol, Volume 35, Issue 8, 2005 (1 article)
Int J Oncol, Volume 27, Issue 1, 2005 (1 article)
J Am Soc Mass Spectrom, Early Edition, 25-May-2005->26-May-2005 (3 articles)
J Bacteriol, Volume 187, Issue 12, 2005 (1 article)
J Biochem Mol Biol, Volume 38, Issue 3, 2005 (1 article)
J Biol Chem, Early Edition, 25-May-2005 (1 article)
J Biomed Inform, Early Edition, 14-Jun-2005 (1 article)
J Cell Mol Med, Volume 9, Issue 2, 2005 (1 article)
J Korean Med Sci, Volume 20, Issue 3, 2005 (1 article)
J Mass Spectrom, Volume 40, Issue 6, 2005 (1 article)
J Proteome Res, Early Edition, 06/17/2005->07/01/2005 (27 articles)
J Proteome Res, Volume 4, Issue 3, 2005 (27 articles)
J Psychiatr Res, Early Edition, 28-May-2005 (1 article)
J Virol, Volume 79, Issue 12, 2005 (1 article)
Kidney Int, Volume 68, Issue 1, 2005 (1 article)
Leuk Res, Early Edition, 2-Jun-2005 (1 article)
Mar Biotechnol (NY), Early Edition, 4-Jun-2005 (1 article)
Mass Spectrom Rev, Early Edition, 14-Jun-2005 (1 article)
Methods Inf Med, Volume 44, Issue 2, 2005 (1 article)
Microbiology, Volume 151, Issue Pt 6, 2005 (2 articles)
Mol Cell Proteomics, Early Edition, 21-Jun-2005 (1 article)
Mol Cell Proteomics, Volume 4, Issues 6+7, 2005 (20 articles)
Nat Rev Mol Cell Biol, Early Edition, 15-Jun-2005 (1 article)
Nephrology (Carlton), Volume 10, Issue 3, 2005 (1 article)
Neurobiol Aging, Early Edition, 9-Jun-2005 (1 article)
Nucl. Acids Res., Volume 33, Issues Suppl_2+10, 2005 (6 articles)
OMICS, Volume 9, Issue 2, 2005 (1 article)
Oncogene, Early Edition, 6-Jun-2005 (1 article)
Phytochemistry, Early Edition, 15-Jun-2005 (1 article)
Plant Physiol, Early Edition, 10-Jun-2005 (1 article)
Plant Physiol, Volume 138, Issue 2, 2005 (2 articles)
Proc Natl Acad Sci U S A, Early Edition, 6-Jun-2005 (1 article)
Proteome Sci, Volume 3, Issue 1, 2005 (3 articles)
Proteomics, Early Edition, 13-Jun-2005 (1 article)
Proteomics, Volume 5, Issues 9+10, 2005 (47 articles)
Rapid Commun Mass Spectrom, Volume 19, Issues 12+13, 2005 (2 articles)
Reprod Biol Endocrinol, Volume 3, Issue 1, 2005 (1 article)
Reproduction, Volume 129, Issue 6, 2005 (1 article)
Rheumatology (Oxford), Early Edition, 31-May-2005 (1 article)
Science, Volume 308, Issues 5726+5727, 2005 (2 articles)
Stud Health Technol Inform, Volume 112, 2005 (1 article)
Theriogenology, Early Edition, 10-Jun-2005 (1 article)
Toxicol Appl Pharmacol, Volume 206, Issue 2, 2005 (3 articles)
Trends Biotechnol, Volume 23, Issue 6, 2005 (1 article)
World J Gastroenterol, Volume 11, Issue 22, 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 (29) / Biological applications (22) / Biomedical and clinical applications (45) / Eukaryotic Cells And Tissues (21) / Prokaryotes (9) / Pharmacology and Toxicology (9) / Protein Array (9) / Protein Characterization - PTMs (12) / Protein-protein interaction (5) / Quantitation (7) / Review (28) / Methodology (47) / Books (1) / Meeting (2) / Other (9) /

Bioinformatics

A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples
Shin H, Markey MK
J Biomed Inform Early Edition: published 14-Jun-2005

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry
Dequan Li, Yan Fu, Ruixiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong Zeng, Qiang Yang, Simin He, and Wen Gao
Bioinformatics (2005) 21(13): 3049-3050

Modeling and Designing a Proteomics Application on PROTEUS
Cannataro M, Cuda G, Veltri P
Methods Inf Med (2005) 44(2): 221-226

Using Ontologies in PROTEUS for Modeling Proteomics Data Mining Applications
Cannataro M, Guzzi PH, Mazza T, Tradigo G, Veltri P
Stud Health Technol Inform (2005) 112: 17-26

Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
Ari Frank, Stephen Tanner, Vineet Bafna, and Pavel Pevzner
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/17/2005

Canonical Labeling of Proteome Maps
Milan Randi , Nella Ler , Damir Vuki evi , Dejan Plav i , Brian D. Gute, and Subhash C. Basak
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser
A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, and F. Meyer
Nucl. Acids Res. (2005) 33(Suppl_2): W710-W716

GPS: a comprehensive www server for phosphorylation sites prediction
Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, and Xuebiao Yao
Nucl. Acids Res. (2005) 33(Suppl_2): W184-W187

KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, and Jorng-Tzong Horng
Nucl. Acids Res. (2005) 33(Suppl_2): W226-W229

DiANNA: a web server for disulfide connectivity prediction
F. Ferre and P. Clote
Nucl. Acids Res. (2005) 33(Suppl_2): W230-W232

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
Brian D. Halligan, Victor Ruotti, Simon N. Twigger, and Andrew S. Greene
Nucl. Acids Res. (2005) 33(Suppl_2): W376-W381

Three-Dimensional Visualization of Protein Expression in Mouse Brain Structures Using Imaging Mass Spectrometry
Crecelius AC, Cornett DS, Caprioli RM, Williams B, Dawant BM, Bodenheimer B
J Am Soc Mass Spectrom Early Edition: published 26-May-2005

An Automated Method for the Analysis of Stable Isotope Labeling Data in Proteomics
Zhang X, Hines W, Adamec J, Asara JM, Naylor S, Regnier FE
J Am Soc Mass Spectrom Early Edition: published 25-May-2005

Large Scale Analysis of MASCOT Results Using a Mass Accuracy-Based THreshold (MATH) Effectively Improves Data Interpretation
Paul A. Rudnick, Yueju Wang, Erin Evans, Cheng S. Lee, and Brian M. Balgley
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/01/2005

The use of proteotypic peptide libraries for protein identification
Robertson Craig, John P. Cortens, Ronald C. Beavis
Rapid Communications in Mass Spectrometry (2005) 19(13): 1844-1850

The Integr8 project - a resource for genomic and proteomic data
Pruess M, Kersey P, Apweiler R
In Silico Biol (2004) 5(2): 0017

Who tangos with GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools
Lee V, Camon E, Dimmer E, Barrell D, Apweiler R
In Silico Biol (2005) 5(1): 5-8

Quantitative analysis of proteomics using data mining. An automated system for constructing assays quickly and precisely
Yen CY, Helmke SM, Cios KJ, Perryman MB, Duncan MW
IEEE Eng Med Biol Mag (2005) 24(3): 67-72

Enabling proteomics discovery through visual analysis. The peptide permutation and protein prediction tool
Havre SL, Singhal M, Payne DA, Lipton MS, Webb-Robertson BJ
IEEE Eng Med Biol Mag (2005) 24(3): 50-7

Key challenges in proteomics and proteoinformatics. Progress in proteins
Hamady M, Cheung TH, Resing K, Cios KJ, Knight R
IEEE Eng Med Biol Mag (2005) 24(3): 34-40

Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
Jianghong An, Maxim Totrov, and Ruben Abagyan
Mol Cell Proteomics (2005) 4(6): 752-761

A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results
D. Brent Weatherly, James A. Astwood, III, Todd A. Minning, Cameron Cavola, Rick L. Tarleton, and Ron Orlando
Mol Cell Proteomics (2005) 4(6): 762-772

Refined phylogenetic profiles method for predicting protein-protein interactions
Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y
Bioinformatics Early Edition: published 9-Jun-2005

Genome update: prediction of secreted proteins in 225 bacterial proteomes
Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Ponten T, Ussery DW
Microbiology (2005) 151(Pt 6): 1725-7

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M
Bioinformatics (2005) 21(Suppl 1): i302-i310

Protein length in eukaryotic and prokaryotic proteomes
Brocchieri L, Karlin S
Nucl Acids Res (2005) 33(10): 3390-400

Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions
Bastien O, Roy S, Marechal E
C R Biol (2005) 328(5): 445-53

Robust Method for Proteome Analysis by MS/MS Using an Entire Translated Genome: Demonstration on the Ciliome of Tetrahymena thermophila
Jeffrey C. Smith, Julian G. B. Northey, Jyoti Garg, Ronald E. Pearlman, and K. W. Michael Siu
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 909-919

Decoding two-dimensional polyacrylamide gel electrophoresis complex maps by autocovariance function: A simplified approach useful for proteomics
Pietrogrande MC, Marchetti N, Tosi A, Dondi F, Righetti PG
Electrophoresis Early Edition: published 20-Jun-2005

Biological applications

Proteome Profiling for Assessing Diversity: Analysis of Individual Heads of Drosophila melanogaster Using LC-Ion Mobility-MS
John A. Taraszka, Xinfeng Gao, Stephen J. Valentine, Renã A. Sowell, Stormy L. Koeniger, David F. Miller, Thomas C. Kaufman, and David E. Clemmer
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation
Kratchmarova I, Blagoev B, Haack-Sorensen M, Kassem M, Mann M
Science (2005) 308(5727): 1472-7

Mass spectrometry-based analytical tools for the molecular protein characterization of human plasma lipoproteins
Manfred Heller, Daniel Stalder, Evelyn Schlappritzi, Gertraud Hayn, Urs Matter, Andr� Haeberli
PROTEOMICS (2005) 5(10): 2619-2630

Proteomic identification of less oxidized brain proteins in aged senescence-accelerated mice following administration of antisense oligonucleotide directed at the Abeta region of amyloid precursor protein
Poon HF, Farr SA, Banks WA, Pierce WM, Klein JB, Morley JE, Butterfield DA
Brain Res Mol Brain Res Early Edition: published 30-May-2005

Comparative proteome analysis revealed up-regulation of transthyretin in rat brain under chronic clozapine treatment
Chen ML, Chen CH
J Psychiatr Res Early Edition: published 28-May-2005

An emerging role for comprehensive proteome analysis in human pregnancy research
Shankar R, Gude N, Cullinane F, Brennecke S, Purcell AW, Moses EK
Reproduction (2005) 129(6): 685-696

Proteomic and microscopic analysis of biofilms formed by Listeria monocytogenes 568
Hefford MA, D'Aoust S, Cyr TD, Austin JW, Sanders G, Kheradpir E, Kalmokoff ML
Can J Microbiol (2005) 51(3): 197-208

Mapping the Proteome of Drosophila melanogaster: Analysis of Embryos and Adult Heads by LC-IMS-MS Methods
John A. Taraszka, Ruwan Kurulugama, Renã A. Sowell, Stephen J. Valentine, Stormy L. Koeniger, Randy J. Arnold, David F. Miller, Thomas C. Kaufman, and David E. Clemmer
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Analysis of Polyubiquitin Conjugates Reveals That the Rpn10 Substrate Receptor Contributes to the Turnover of Multiple Proteasome Targets
Thibault Mayor, J. Russell Lipford, Johannes Graumann, Geoffrey T. Smith, and Raymond J. Deshaies
Mol Cell Proteomics (2005) 4(6): 741-751

Modulation of Differentiation-related Gene 1 Expression by Cell Cycle Blocker Mimosine, Revealed by Proteomic Analysis
Zizheng Dong, Randy J. Arnold, Youyun Yang, Myung Hee Park, Petra Hrncirova, Yehia Mechref, Milos V. Novotny, and Jian-Ting Zhang
Mol Cell Proteomics (2005) 4(7): 993-1001

Precise and Parallel Characterization of Coding Polymorphisms, Alternative Splicing, and Modifications in Human Proteins by Mass Spectrometry
Michael J. Roth, Andrew J. Forbes, Michael T. Boyne, II, Yong-Bin Kim,Dana E. Robinson, and Neil L. Kelleher
Mol Cell Proteomics (2005) 4(7): 1002-1008

Proteomic approach to blossom-end rot in tomato fruits (Lycopersicon esculentum M.): Antioxidant enzymes and the pentose phosphate pathway
Juan Casado-Vela, Susana Sell�s, Roque Bru Mart�nez
PROTEOMICS (2005) 5(10): 2488-2496

A proteome approach defines protective functions of tobacco leaf trichomes
Steffen Amme, Twan Rutten, Michael Melzer, Guido Sonsmann, Johannes P. C. Vissers, Bernhard Schlesier, Hans-Peter Mock
PROTEOMICS (2005) 5(10): 2508-2518

Proteomic profiling of facial development in chick embryos
Jonathan E. Mangum, Peter G. Farlie, Michael J. Hubbard
PROTEOMICS (2005) 5(10): 2542-2550

Holistic differential analysis of embryo-induced alterations in the proteome of bovine endometrium in the preattachment period
Frank J. Berendt, Thomas Fr�hlich, Susanne E. M. Schmidt, Horst-Dieter Reichenbach, Eckhard Wolf, Georg J. Arnold
PROTEOMICS (2005) 5(10): 2551-2560

A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity
Carine Froment, Sandrine Uttenweiler-Joseph, Marie-Pierre Bousquet-Dubouch, Mariette Matondo, Jean-Philippe Borges, Charlotte Esmenjaud, Christelle Lacroix, Bernard Monsarrat, Odile Burlet-Schiltz
PROTEOMICS (2005) 5(9): 2351-2363

Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues
Mijalski T, Harder A, Halder T, Kersten M, Horsch M, Strom TM, Liebscher HV, Lottspeich F, Hrabe de Angelis M, Beckers J
Proc Natl Acad Sci U S A Early Edition: published 6-Jun-2005

Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology
Khan SM, Franke-Fayard B, Mair GR, Lasonder E, Janse CJ, Mann M, Waters AP
Cell (2005) 121(5): 675-87

Comparison of Tuber Proteomes of Potato Varieties, Landraces, and Genetically Modified Lines
Lehesranta SJ, Davies HV, Shepherd LV, Nunan N, McNicol JW, Auriola S, Koistinen KM, Suomalainen S, Kokko HI, Karenlampi SO
Plant Physiol Early Edition: published 10-Jun-2005

Developmental changes of heat-shock proteins in porcine testis by a proteomic analysis
Huang SY, Tam MF, Hsu YT, Lin JH, Chen HH, Chuang CK, Chen MY, King YT, Lee WC
Theriogenology Early Edition: published 10-Jun-2005

Identification of Mycobacterium tuberculosis H37Rv Integral Membrane Proteins by One-Dimensional Gel Electrophoresis and Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry
Ying Xiong, Michael J. Chalmers, # Fei Philip Gao, Timothy A. Cross, and Alan G. Marshall
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 855-861

Integrative Proteomics: Functional and Molecular Characterization of a Particular Glutamate-Related Neuregulin Isoform
Simone Schillo, Vojislav Pejovi , Christian Hunzinger, Torsten Hansen, Slobodan Poznanovi , Jörg Kriegsmann, Werner J. Schmidt, and André Schrattenholz
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 900-908

Biomedical and clinical applications

Proteomic Identification of Potential Susceptibility Factors in Drug-Induced Liver Disease
Welch KD, Wen B, Goodlett DR, Yi EC, Lee H, Reilly TP, Nelson SD, Pohl LR
Chem Res Toxicol (2005) 18(6): 924-933

Proteomic Analysis of Primary Cultures of Human Adipose-derived Stem Cells: Modulation by Adipogenesis
James P. DeLany, Z. Elizabeth Floyd, Sanjin Zvonic, Andrea Smith, Amy Gravois, Eric Reiners, Xiying Wu, Gail Kilroy, Michael Lefevre, and Jeffrey M. Gimble
Mol Cell Proteomics (2005) 4(6): 731-740

Quantitative Protein Expression Analysis Of CLL B Cells from Mutated and Unmutated IgVH Subgroups Using Acid-Cleavable Isotope-Coded Affinity Tag Reagents
David R. Barnidge, Diane F. Jelinek, David C. Muddiman, and Neil E. Kay
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/17/2005

Proteome profile of human urine with two-dimensional liquid phase fractionation
Monica Soldi, Cecilia Sarto, Cristina Valsecchi, Fulvio Magni, Vanessa Proserpio, Davide Ticozzi, Paolo Mocarelli
PROTEOMICS (2005) 5(10): 2641-2647

Perspective: A Program to Improve Protein Biomarker Discovery for Cancer
Ruedi Aebersold, Leigh Anderson, Richard Caprioli, Brian Druker, Leland Hartwell, and Richard Smith
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/10/2005

Proteomic analysis of ursolic acid-induced apoptosis in cervical carcinoma cells
Yim EK, Lee KH, Namkoong SE, Um SJ, Park JS
Cancer Lett Early Edition: published 27-May-2005

The use of proteomics in biomarker discovery in neurodegenerative diseases
Davidsson P, Sjogren M
Dis Markers (2005) 21(2): 81-92

Proteome analysis of liver cells expressing a full-length hepatitis C virus (HCV) replicon and biopsy specimens of posttransplantation liver from HCV-infected patients
Jacobs JM, Diamond DL, Chan EY, Gritsenko MA, Qian W, Stastna M, Baas T, Camp DG 2nd, Carithers RL Jr, Smith RD, Katze MG
J Virol (2005) 79(12): 7558-69

Global Phosphoproteome of HT-29 Human Colon Adenocarcinoma Cells
Ji-Eun Kim, Steven R. Tannenbaum, and Forest M. White
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Quest for Novel Cardiovascular Biomarkers by Proteomic Analysis
Fernando Vivanco, Jose L. Martín-Ventura, # Mari Carmen Duran, Maria G. Barderas, Luis Blanco-Colio, Verónica M. Dardé, Sebastián Mas, Olivier Meilhac, # Jean B. Michel, # Jose Tuñón, and Jesús Egido
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Identification and Quantification of Differentially Expressed Proteins in E-Cadherin Deficient SCC9 Cells and SCC9 Transfectants Expressing E-Cadherin by Dimethyl Isotope Labeling, LC-MALDI MS and MS/MS
Chengjie Ji, Laiji Li, Mulu Gebre, Manijeh Pasdar, and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

MALDI-TOF mass spectrometry analysis of cerebrospinal fluid tryptic peptide profiles to diagnose leptomeningeal metastases in breast cancer patients
Dekker LJ, Boogerd W, Stockhammer G, Dalebout JC, Siccama I, Zheng P, Bonfrer JM, Verschuuren JJ, Jenster G, Verbeek MM, Luider TM, Sillevis Smitt PA
Mol Cell Proteomics Early Edition: published 21-Jun-2005

Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery
Seibert V, Ebert MP, Buschmann T
Brief Funct Genomic Proteomic (2005) 4(1): 16-26

Proteomic changes in the pressure overloaded right ventricle after 6 weeks in young rats: Correlations with the degree of hypertrophy
Matthijs J. Faber, Michiel Dalinghaus, Inge M. Lankhuizen, Karel Bezstarosti, Dick H. W. Dekkers, Dirk J. Duncker, Willem A. Helbing, Jos M. J. Lamers
PROTEOMICS (2005) 5(10): 2519-2530

Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer
Martin W. Volmer, Kai St�hler, Marc Zapatka, Anna Sch�neck, Susanne Klein-Scory, Wolff Schmiegel, Helmut E. Meyer, Irmgard Schwarte-Waldhoff
PROTEOMICS (2005) 5(10): 2587-2601

Identification of fatty acid binding proteins as markers associated with the initiation and/or progression of renal cell carcinoma
Barbara Seliger, Rudolf Lichtenfels, Derek Atkins, J�rgen Bukur, Thomas Halder, Michael Kersten, Alois Harder, Angelika Ackermann, Barbara Malenica, Walburgis Brenner, Monica Zobawa, Friedrich Lottspeich
PROTEOMICS (2005) 5(10): 2631-2640

Two-dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy
Kumar Sharma, SoHee Lee, Steven Han, Sungchun Lee, Barbara Francos, Peter McCue, Richard Wassell, M. Alexander Shaw, Satish P. RamachandraRao
PROTEOMICS (2005) 5(10): 2648-2655

Application of fluorescence difference gel electrophoresis saturation labelling for the analysis of microdissected precursor lesions of pancreatic ductal adenocarcinoma
Barabara Sitek, Jutta L�ttges, Katrin Marcus, G�nter Kl�ppel, Wolff Schmiegel, Helmut E. Meyer, Stephan A. Hahn, Kai St�hler
PROTEOMICS (2005) 5(10): 2665-2679

Protein profile changes in the human breast cancer cell line MCF-7 in response to SEL1L gene induction
Laura Bianchi, Cristina Canton, Luca Bini, Rosaria Orlandi, Sylvie M�nard, Alessandro Armini, Monica Cattaneo, Vitaliano Pallini, Luigi Rossi Bernardi, Ida Biunno
PROTEOMICS (2005) 5(9): 2433-2442

Francisella tularensis live vaccine strain: Proteomic analysis of membrane proteins enriched fraction
Ivona P�vkov�, Martin Hub�lek, Jana Zechovsk�, Juraj Len?o, Ji?� Stul�k
PROTEOMICS (2005) 5(9): 2460-2467

Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets
Maria Zellner, Wolfgang Winkler, Hubert Hayden, Michael Diestinger, Maja Eliasen, Bernd Gesslbauer, Ingrid Miller, Martina Chang, Andreas Kungl, Erich Roth, Rudolf Oehler
ELECTROPHORESIS (2005) 26(12): 2481-2489

Low molecular weight proteomic information distinguishes metastatic from benign pheochromocytoma
Brouwers FM, Petricoin EF 3rd, Ksinantova L, Breza J, Rajapakse V, Ross S, Johann D, Mannelli M, Shulkin BL, Kvetnansky R, Eisenhofer G, Walther MM, Hitt BA, Conrads TP, Veenstra TD, Mannion DP, Wall MR, Wolfe GM, Fusaro VA, Liotta LA, Pacak K
Endocr Relat Cancer (2005) 12(2): 263-72

Comparative proteome analysis of untreated and Helicobacter pylori-treated HepG2
Zhang Y, Fan XG, Chen R, Xiao ZQ, Feng XP, Tian XF, Chen ZH
World J Gastroenterol (2005) 11(22): 3485-9

Proteomic analysis of differentially expressed proteins between metastatic and non-metastatic human colorectal carcinoma cell lines
Ying-Tao Z, Yi-Ping G, Lu-Sheng S, Yi-Li W
Eur J Gastroenterol Hepatol (2005) 17(7): 725-732

Abnormalities in Nitric Oxide and its Derivatives in Lung Cancer
Masri FA, Comhair SA, Koeck T, Stuehr DJ, Xu W, Janocha A, Ghosh S, Dweik RA, Golish J, Kinter M, Erzurum SC, Aulak KS
Am J Respir Crit Care Med Early Edition: published 9-Jun-2005

Pancreatic cancer-associated diabetes mellitus: An open field for proteomic applications
Basso D, Greco E, Fogar P, Pucci P, Flagiello A, Baldo G, Giunco S, Valerio A, Navaglia F, Zambon CF, Pedrazzoli S, Plebani M
Clin Chim Acta Early Edition: published 6-Jun-2005

A proteomic approach in the study of an animal model of Parkinson's disease
De Iuliis A, Grigoletto J, Recchia A, Giusti P, Arslan P
Clin Chim Acta Early Edition: published 7-Jun-2005

Identification of differentially expressed proteins in oral squamous cell carcinoma using a global proteomic approach
Koike H, Uzawa K, Nakashima D, Shimada K, Kato Y, Higo M, Kouzu Y, Endo Y, Kasamatsu A, Tanzawa H
Int J Oncol (2005) 27(1): 59-67

Proteomics analysis of H-RAS-mediated oncogenic transformation in a genetically defined human ovarian cancer model
Young T, Mei F, Liu J, Bast RC, Kurosky A, Cheng X
Oncogene Early Edition: published 6-Jun-2005

Early Prediction of Acute Renal Injury Using Urinary Proteomics
Nguyen MT, Ross GF, Dent CL, Devarajan P
Am J Nephrol (2005) 25(4): 318-326

Identification of leukemia-associated antigens in chronic myeloid leukemia by proteomic analysis
Zou L, Wu Y, Pei L, Zhong D, Gen M, Zhao T, Wu J, Ni B, Mou Z, Han J, Chen Y, Zhi Y
Leuk Res Early Edition: published 2-Jun-2005

Impact of diabetic nephropathy and angiotensin II receptor blockade on urinary polypeptide patterns
Rossing K, Mischak H, Parving HH, Christensen PK, Walden M, Hillmann M, Kaiser T
Kidney Int (2005) 68(1): 193-205

Identification of differentially expressed proteins during human urinary bladder cancer progression
Memon AA, Chang JW, Oh BR, Yoo YJ
Cancer Detect Prev (2005) 29(3): 249-55

Identification of proteins differentially expressed in the conventional renal cell carcinoma by proteomic analysis
Hwa JS, Park HJ, Jung JH, Kam SC, Park HC, Kim CW, Kang KR, Hyun JS, Chung KH
J Korean Med Sci (2005) 20(3): 450-5

Chemoprevention of genome, transcriptome, and proteome alterations induced by cigarette smoke in rat lung
Izzotti A, Bagnasco M, Cartiglia C, Longobardi M, Balansky RM, Merello A, Lubet RA, De Flora S
Eur J Cancer Early Edition: published 10-Jun-2005

Oxidative modification and down-regulation of Pin1 in Alzheimer's disease hippocampus: A redox proteomics analysis
Sultana R, Boyd-Kimball D, Poon HF, Cai J, Pierce WM, Klein JB, Markesbery WR, Zhou XZ, Lu KP, Butterfield DA
Neurobiol Aging Early Edition: published 9-Jun-2005

Molecular biomarkers for the study of childhood leukemia
Smith MT, McHale CM, Wiemels JL, Zhang L, Wiencke JK, Zheng S, Gunn L, Skibola CF, Ma X, Buffler PA
Toxicol Appl Pharmacol (2005) 206(2): 237-45

Proteome Analysis of Gelatin-Bound Urinary Proteins from Patients with Bladder Cancers
Saito M, Kimoto M, Araki T, Shimada Y, Fujii R, Oofusa K, Hide M, Usui T, Yoshizato K
Eur Urol Early Edition: published 15-Jun-2005

A two dimensional electrophoresis preliminary approach to human hepatocarcinoma differentiation induced by PPAR-agonists
Bottoni P, Giardina B, Martorana GE, Zuppi C, De Sole P, Rossi C, Scatena R
J Cell Mol Med (2005) 9(2): 462-7

Global Protein Shotgun Expression Profiling of Proliferating MCF-7 Breast Cancer Cells
Charanjit Sandhu, Michael Connor, Thomas Kislinger, Joyce Slingerland, and Andrew Emili
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 674-689

Proteomic Studies on Low- and High-Grade Human Brain Astrocytomas
Federico Odreman, Marco Vindigni, Marlen Lujardo Gonzales, Benedetta Niccolini, Giovanni Candiano, Bruno Zanotti, Miran Skrap, Stefano Pizzolitto, Giorgio Stanta, and Alessandro Vindigni
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 698-708

Comparative Analysis of the Tear Protein Expression in Blepharitis Patients Using Two-Dimensional Electrophoresis
Bon-Suk Koo , Do-Yeon Lee , Hyo-Shin Ha, Jae-Chan Kim, and Chan-Wha Kim
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 719-724

Diagnostic Potential of Tear Proteomic Patterns in Sjögren's Syndrome
Naohisa Tomosugi, Kazuko Kitagawa, Nobuo Takahashi, Susumu Sugai, and Isao Ishikawa
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 820-825

Differential Expression of Proteins in Response to Ceramide-Mediated Stress Signal in Colon Cancer Cells by 2-D Gel Electrophoresis and MALDI-TOF-MS
M. Fillet, C. Cren-Olivé, A.-F. Renert, J. Piette, F. Vandermoere, Ch. Rolando, and M-P. Merville
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 870-880

Differential Protein Expression Profiles of Gastric Epithelial Cells Following Helicobacter pylori Infection Using ProteinChips
Soumita Das, Johanna C. Sierra, Kizhake V. Soman, Giovanni Suarez, Amin A. Mohammad, Tu Anh T. Dang, Bruce A. Luxon, and Victor E. Reyes ^,
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 920-930

Eukaryotic Cells And Tissues

Mass Spectrometric Analysis of the Schistosoma mansoni Tegumental Sub-proteome
Bas W. M. van Balkom, Renske A. van Gestel, Jos F. H. M. Brouwers, Jeroen Krijgsveld, Aloysius G. M. Tielens, Albert J. R. Heck, and Jaap J. van Hellemond
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 958-966

Targeted Proteomic Analysis of 14-3-3{varsigma}, a p53 Effector Commonly Silenced in Cancer
Anne Benzinger, Nemone Muster, Heike B. Koch, John R. Yates, III, and Heiko Hermeking
Mol Cell Proteomics (2005) 4(6): 785-795

Human Tissue Profiling with Multidimensional Protein Identification Technology
Gerard Cagney, Stephen Park, Clement Chung, Bianca Tong, Colm O'Dushlaine, Denis C. Shields, and Andrew Emili
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/08/2005

Quantitative Analysis of Severe Acute Respiratory Syndrome (SARS)-associated Coronavirus-infected Cells Using Proteomic Approaches: Implications for Cellular Responses to Virus Infection
Xiao-Sheng Jiang, Liu-Ya Tang, Jie Dai, Hu Zhou, Su-Jun Li, Qi-Chang Xia, Jia-Rui Wu, and Rong Zeng
Mol Cell Proteomics (2005) 4(7): 902-913

Carbonylated proteins in bronchoalveolar lavage of patients with sarcoidosis, pulmonary fibrosis associated with systemic sclerosis and idiopathic pulmonary fibrosis
Paola Rottoli, Barbara Magi, Riccardo Cianti, Elena Bargagli, Cecilia Vagaggini, Nikolaos Nikiforakis, Vitaliano Pallini, Luca Bini
PROTEOMICS (2005) 5(10): 2612-2618

Proteomic Profiling of Human Pleural Effusion Using Two-Dimensional Nano Liquid Chromatography Tandem Mass Spectrometry
Yu-Chang Tyan, Hsin-Yi Wu, Wu-Wei Lai, Wu-Chou Su, and Pao-Chi Liao
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/10/2005

Proteomic approach to probe for larval proteins of the mussel Mytilus galloprovincialis
Lopez JL, Abalde SL, Fuentes J
Mar Biotechnol (NY) Early Edition: published 4-Jun-2005

Proteome Dynamics during C2C12 Myoblast Differentiation
Thomas Kislinger, Anthony O. Gramolini, Yan Pan, Khaled Rahman, David H. MacLennan, and Andrew Emili
Mol Cell Proteomics (2005) 4(7): 887-901

"Subcellular Proteomics" of Neuromelanin Granules Isolated from the Human Brain
Florian Tribl, Manfred Gerlach, Katrin Marcus, Esther Asan, Thomas Tatschner, Thomas Arzberger, Helmut E. Meyer, Gerhard Bringmann, and Peter Riederer
Mol Cell Proteomics (2005) 4(7): 945-957

Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry
Sabine P. Schrimpf, Virginia Meskenaite, Erich Brunner, Dorothea Rutishauser, Pascal Walther, Jimmy Eng, Ruedi Aebersold, Peter Sonderegger
PROTEOMICS (2005) 5(10): 2531-2541

Proteomics of the rat gut: Analysis of the myenteric plexus-longitudinal muscle preparation
Laure Marvin-Guy, Lu�sa V. Lopes, Michael Affolter, Marie-Claude Courtet-Compondu, Sandrine Wagni�re, Gabriela E. Bergonzelli, Laurent B. Fay, Martin Kussmann
PROTEOMICS (2005) 5(10): 2561-2569

Differential protein expression in anatomical zones of the prostate
Helena Lexander, Bo Franz�n, Daniel Hirschberg, Susanne Becker, Magnus Hellstr�m, Tomas Bergman, Hans J�rnvall, Gert Auer, Lars Egevad
PROTEOMICS (2005) 5(10): 2570-2576

Comparison of protein expression in human deltoideus and vastus lateralis muscles using two-dimensional gel electrophoresis
Daniele Capitanio, Agnese Vigan�, Enzo Ricci, Paolo Cerretelli, Robin Wait, Cecilia Gelfi
PROTEOMICS (2005) 5(10): 2577-2586

The hemolymph proteome of Anopheles gambiae
Paskewitz SM, Shi L
Insect Biochem Mol Biol (2005) 35(8): 815-24

Studies on substantially increased proteins in follicular fluid of bovine ovarian follicular cysts using 2-D PAGE and MALDI-TOF MS
Maniwa J, Izumi S, Isobe N, Terada T
Reprod Biol Endocrinol (2005) 3(1): 23

Stem cell proteomes: A profile of human mesenchymal stem cells derived from umbilical cord blood
Feldmann RE Jr, Bieback K, Maurer MH, Kalenka A, Burgers HF, Gross B, Hunzinger C, Kluter H, Kuschinsky W, Eichler H
Electrophoresis Early Edition: published 21-Jun-2005

The role of proteomics in the assessment of premature rupture of fetal membranes
Thadikkaran L, Crettaz D, Siegenthaler MA, Gallot D, Sapin V, Iozzo RV, Queloz PA, Schneider P, Tissot JD
Clin Chim Acta Early Edition: published 18-Jun-2005

Protein mapping of the salivary complex from a hematophagous leech
Ricci-Silva ME, Konno K, Faria F, Radis-Baptista G, Fontes W, Stocklin R, Michalet S, Yamane T, Chudzinski-Tavassi AM
OMICS (2005) 9(2): 194-208

Organelle Proteomics of Rat Synaptic Proteins: Correlation-Profiling by Isotope-Coded Affinity Tagging in Conjunction with Liquid Chromatography-Tandem Mass Spectrometry to Reveal Post-synaptic Density Specific Proteins
Ka wan Li, Martin P. Hornshaw, Jan van Minnen, Karl-Heinz Smalla, Eckart D. Gundelfinger, and August B. Smit
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 725-733

Proteome Analysis of Primary Neurons and Astrocytes from Rat Cerebellum
Jae-Won Yang, Regina Rodrigo, Vicente Felipo, and Gert Lubec
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 768-788

Protein Profiling of Human Pancreatic Islets by Two-Dimensional Gel Electrophoresis and Mass Spectrometry
Meftun Ahmed, Jens Forsberg, and Peter Bergsten
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 931-940

Prokaryotes

Proteomic expression analysis of colorectal cancer by two-dimensional differential gel electrophoresis
Patricia Alfonso, Antonio N��ez, Juan Madoz-Gurpide, Luis Lombardia, Lydia S�nchez, J. Ignacio Casal
PROTEOMICS (2005) 5(10): 2602-2611

Inventory of the Proteins in Neisseria meningitidis Serogroup B Strain MC58
Giuseppina Mignogna, Alessandra Giorgi, Paola Stefanelli, Arianna Neri, Gianni Colotti, Bruno Maras, and M. Eugenia Schininà
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/10/2005

Proteome analysis of a recombinant Bacillus megaterium strain during heterologous production of a glucosyltransferase
Wang W, Hollmann R, Fuerch T, Nimtz M, Malten M, Jahn D, Deckwer WD
Proteome Sci (2005) 3(1): 4

Global topology analysis of the Escherichia coli inner membrane proteome
Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G
Science (2005) 308(5726): 1321-3

Proteomic analysis of cell surface proteins from Clostridium difficile
Anne Wright, Robin Wait, Shajna Begum, Ben Crossett, Judit Nagy, Katherine Brown, Neil Fairweather
PROTEOMICS (2005) 5(9): 2443-2452

Art-loving bugs: The resurrection of Spinello Aretino from Pisa's cemetery
Paolo Antonioli, Giacomo Zapparoli, Pamela Abbruscato, Claudia Sorlini, Giancarlo Ranalli, Pier Giorgio Righetti
PROTEOMICS (2005) 5(9): 2453-2459

Integrative Genomic, Transcriptional, and Proteomic Diversity in Natural Isolates of the Human Pathogen Burkholderia pseudomallei
Ou K, Ong C, Koh SY, Rodrigues F, Sim SH, Wong D, Ooi CH, Ng KC, Jikuya H, Yau CC, Soon SY, Kesuma D, Lee MA, Tan P
J Bacteriol (2005) 187(12): 4276-85

Preliminary Proteomic Analysis of Thiobacillus ferrooxidans Growing on Elemental Sulphur and Fe(2+) Separately
He ZG, Hu YH, Zhong H, Hu WX, Xu J
J Biochem Mol Biol (2005) 38(3): 307-13

Up-regulation of competence- but not stress-responsive proteins accompanies an altered metabolic phenotype in Streptococcus mutans biofilms
Rathsam C, Eaton RE, Simpson CL, Browne GV, Berg T, Harty DW, Jacques NA
Microbiology (2005) 151(Pt 6): 1823-37

Pharmacology and Toxicology

Biomarkers of cadmium and arsenic interactions
Nordberg GF, Jin T, Hong F, Zhang A, Buchet JP, Bernard A
Toxicol Appl Pharmacol (2005) 206(2): 191-7

Metabolomic and proteomic biomarkers for III-V semiconductors: Chemical-specific porphyrinurias and proteinurias
Fowler BA, Conner EA, Yamauchi H
Toxicol Appl Pharmacol (2005) 206(2): 121-30

Proteome analysis of maize roots reveals that oxidative stress is a main contributing factor to plant arsenic toxicity
Requejo R, Tena M
Phytochemistry Early Edition: published 15-Jun-2005

Screening of human serum proteins for uranium binding
Vidaud C, Dedieu A, Basset C, Plantevin S, Dany I, Pible O, Quemeneur E
Chem Res Toxicol (2005) 18(6): 946-53

Plasma Protein Level Changes in Waste Incineration Workers Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin
Mee Jeong Kang, Do-Youn Lee, Won-A Joo, and Chan-Wha Kim
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/17/2005

Application of Two-Dimensional Difference Gel Electrophoresis to Studying Bone Marrow Macrophages and Their in Vivo Responses to Ionizing Radiation
Changwei Chen, Michael T. Boylan, Caroline A. Evans, Antony D. Whetton, and Eric G. Wright
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/17/2005

Combinatorial biomarkers: From early toxicology assays to patient population profiling
Koop R
Drug Discov Today (2005) 10(11): 781-8

Induction of Apoptosis in Mouse Liver by Microcystin-LR: A Combined Transcriptomic, Proteomic, And Simulation Strategy
Ting Chen, Qingsong Wang, Jun Cui, Wei Yang, Qian Shi, Zichun Hua, Jianguo Ji, and Pingping Shen
Mol Cell Proteomics (2005) 4(7): 958-974

Use of 'Omic' technologies to study humans exposed to benzene
Smith MT, Vermeulen R, Li G, Zhang L, Lan Q, Hubbard AE, Forrest MS, McHale C, Zhao X, Gunn L, Shen M, Rappaport SM, Yin S, Chanock S, Rothman N
Chem Biol Interact (2005) 153-154: 123-7.

Protein Array

Determination of Relative Protein Abundance by Internally Normalized Ratio Algorithm with Antibody Arrays
Oskar Andersson, Mark Kozlowski, Tatiana Garachtchenko, Corina Nikoloff, Nancy Lew, David J. Litman, and Grigoriy Chaga
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 758-767

An aptamer-based protein biochip
Stadtherr K, Wolf H, Lindner P
Anal Chem (2005) 77(11): 3437-43

Protein biochips: A new and versatile platform technology for molecular medicine
Lueking A, Cahill DJ, Mullner S
Drug Discov Today (2005) 10(11): 789-94

Making the most of affinity tags
Waugh DS
Trends Biotechnol (2005) 23(6): 316-20

Optimized Normalization for Antibody Microarrays and Application to Serum-Protein Profiling
Darren Hamelinck, Heping Zhou, Lin Li, Cornelius Verweij, Deborah Dillon, Ziding Feng, Jose Costa, and Brian B. Haab
Mol Cell Proteomics (2005) 4(6): 773-784

A novel approach to protein expression profiling using antibody microarrays combined with surface plasmon resonance technology
Kazue Usui-Aoki, Kiyo Shimada, Mihoko Nagano, Makoto Kawai, Hisashi Koga
PROTEOMICS (2005) 5(9): 2396-2401

Protein microarrays for antibody profiling: Specificity and affinity determination on a chip
Oliver Poetz, Ralf Ostendorp, Bodo Brocks, Jochen M. Schwenk, Dieter Stoll, Thomas O. Joos, Markus F. Templin
PROTEOMICS (2005) 5(9): 2402-2411

PanoramaTM Ab Microarray Cell Signaling kit: A unique tool for protein expression analysis
Eliezer Kopf, Dalia Shnitzer, Dorit Zharhary
PROTEOMICS (2005) 5(9): 2412-2416

SPOT synthesis: Reliability of array-based measurement of peptide binding affinity
Weiser AA, Or-Guil M, Tapia V, Leichsenring A, Schuchhardt J, Frommel C, Volkmer-Engert R
Anal Biochem Early Edition: published 9-Jun-2005

Protein Characterization / PTMs

Quantitative detection of phosphoproteins by combination of two-dimensional difference gel electrophoresis and phosphospecific fluorescent staining
Stasyk T, Morandell S, Bakry R, Feuerstein I, Huck CW, Stecher G, Bonn GK, Huber LA
Electrophoresis Early Edition: published 20-Jun-2005

Age-dependent variations of cell response to oxidative stress: Proteomic approach to protein expression and phosphorylation
Miura Y, Kano M, Abe K, Urano S, Suzuki S, Toda T
Electrophoresis Early Edition: published 20-Jun-2005

Tagging-via-Substrate Strategy for Probing O-GlcNAc Modified Proteins
Robert Sprung, Animesh Nandi, Yue Chen, Sung Chan Kim, Deb Barma, John R. Falck, and Yingming Zhao
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 950-957

Identification of Phosphopeptides by MALDI Q-TOF MS in Positive and Negative Ion Modes after Methyl Esterification
Chong-Feng Xu, Yun Lu, Jinghong Ma, Moosa Mohammadi, and Thomas A. Neubert
Mol Cell Proteomics (2005) 4(6): 809-818

A High Throughput Method for the Detection of Metalloproteins on a Microgram Scale
Martin Hogbom, Ulrika B. Ericsson, Robert Lam, M. Amin Bakali H., Ekaterina Kuznetsova, Par Nordlund, and Deborah B. Zamble
Mol Cell Proteomics (2005) 4(6): 827-834

Extended Range Proteomic Analysis (ERPA): A New and Sensitive LC-MS Platform for High Sequence Coverage of Complex Proteins with Extensive Post-translational Modifications-Comprehensive Analysis of Beta-Casein and Epidermal Growth Factor Receptor (EGFR)
Shiaw-Lin Wu, Jeongkwon Kim, William S. Hancock, and Barry Karger
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/17/2005

Glycoproteomics of N-glycosylation by in-gel deglycosylation and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry mapping: Application to congenital disorders of glycosylation
Dijana ?agi, Petra Kienz, Jonas Denecke, Thorsten Marquardt, Jasna Peter-Katalini?
PROTEOMICS (2005) 5(10): 2689-2701

Characterisation of protein microheterogeneity and protein complexes using on-chip immunoaffinity purification-mass spectrometry
Schweigert FJ
Brief Funct Genomic Proteomic (2005) 4(1): 7-15

Phosphotyrosine Proteomic Study of Interferon {alpha} Signaling Pathway Using a Combination of Immunoprecipitation and Immobilized Metal Affinity Chromatography
Haiyan Zheng, Ping Hu, Douglas F. Quinn, and Y. Karen Wang
Mol Cell Proteomics (2005) 4(6): 721-730

Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns
Martin R. Larsen, Tine E. Thingholm, Ole N. Jensen, Peter Roepstorff, and Thomas J. D. Jorgensen
Mol Cell Proteomics (2005) 4(7): 873-886

Characterization of nitroproteome in neuron-like PC12 cells differentiated with nerve growth factor: Identification of two nitration sites in ?-tubulin
Gabriella Tedeschi, Graziella Cappelletti, Armando Negri, Lara Pagliato, Maria G. Maggioni, Rosalba Maci, Severino Ronchi
PROTEOMICS (2005) 5(9): 2422-2432

Glyco-oxidation in diabetes and related diseases
Lapolla A, Fedele D, Traldi P
Clin Chim Acta Early Edition: published 3-Jun-2005

Protein-protein interaction

MultiProtIdent: Identifying Proteins Using Database Search and Protein-Protein Interactions
Hsien-Da Huang, Tzong-Yi Lee, Li-Cheng Wu, Feng-Mao Lin, Hsueh-Fen Juan, Jorng-Tzong Horng, and Ann-Ping Tsou
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 690-697

Structural analysis of a highly acetylated protein using a curved-field reflectron mass spectrometer
Dongxia Wang, Paul Thompson, Philip A. Cole, Robert J. Cotter
PROTEOMICS (2005) 5(9): 2288-2296

Detection and identification of stable oligomeric protein complexes in E. coli inner membranes. A proteomics approach
Spelbrink RE, Kolkman A, Slijper M, Killian JA, de Kruijff B
J Biol Chem Early Edition: published 25-May-2005

SPR-MS in functional proteomics
Buijs J, Franklin GC
Brief Funct Genomic Proteomic (2005) 4(1): 39-47

A Combined Yeast/Bacteria Two-hybrid System: Development and Evaluation
Ilya G. Serebriiskii, Rui Fang, Ekaterina Latypova, Richard Hopkins, Charles Vinson, J. Keith Joung, and Erica A. Golemis
Mol Cell Proteomics (2005) 4(6): 819-826

Quantitation

Quantitative Proteome Analysis Using Differential Stable Isotopic Labeling and Microbore LC-MALDI MS and MS/MS
Chengjie Ji and Liang Li
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 734-742

A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells
Choe LH, Aggarwal K, Franck Z, Lee KH
Electrophoresis Early Edition: published 30-May-2005

Comprehensive Label-Free Method for the Relative Quantification of Proteins from Biological Samples
Richard E. Higgs, Michael D. Knierman, Valentina Gelfanova, Jon P. Butler, and John E. Hale
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Mass spectrometry-based quantitative proteomic profiling
Yan W, Chen SS
Brief Funct Genomic Proteomic (2005) 4(1): 27-38

Quantitative Proteomic Analysis Using Isobaric Protein Tags Enables Rapid Comparison of Changes in Transcript and Protein Levels in Transformed Cells
Richard D. Unwin, Andrew Pierce, Rod B. Watson, David W. Sternberg, and Anthony D. Whetton
Mol Cell Proteomics (2005) 4(7): 924-935

Quantitative analysis of protein expression using amine-specific isobaric tags in Escherichia coli cells expressing rhsA elements
Kunal Aggarwal, Leila H. Choe, Kelvin H. Lee
PROTEOMICS (2005) 5(9): 2297-2308

Innovation: Scoring proteomes with proteotypic peptide probes
Kuster B, Schirle M, Mallick P, Aebersold R
Nat Rev Mol Cell Biol Early Edition: published 15-Jun-2005

Review

Proteome analysis in the clinical chemistry laboratory: Myth or reality?
Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N, Rustichelli C, Antonioli P, Zanusso G, Monaco S, Lomas L, Boschetti E
Clin Chim Acta Early Edition: published 18-Jun-2005

Capillary electrophoresis coupled to mass spectrometry for clinical diagnostic purposes
Fliser D, Wittke S, Mischak H
Electrophoresis Early Edition: published 20-Jun-2005

Proteomics in the Forefront of Cancer Biomarker Discovery
Sudhir Srivastava and Rashmi-Gopal Srivastava
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/17/2005

MALDI Mass Spectrometry for Direct Tissue Analysis: A New Tool for Biomarker Discovery
Michelle L. Reyzer and Richard M. Caprioli
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/08/2005

A streamlined approach to high_throughput proteomics
Andrew N Stephens, Patricia Quach, Elizabeth J Harry
Expert Review of Proteomics (2005) 2(2): 173-185

Host_pathogen interactions: a proteomic view
Celia G Zhang, Brett A Chromy, Sandra L McCutchen_Maloney
Expert Review of Proteomics (2005) 2(2): 187-202

Proteomics for biodefense applications: progress and opportunities
Richard R Drake, Yuping Deng, E Ellen Schwegler, Stefan Gravenstein
Expert Review of Proteomics (2005) 2(2): 203-213

Proteomic approaches for studying chemoresistance in cancer
Pier Giorgio Righetti, Annalisa Castagna, Paolo Antonioli, Daniela Cecconi, Natascia Campostrini, Sabina Carla Righetti
Expert Review of Proteomics (2005) 2(2): 215-228

Proteomics in cancer vaccine development
Stacy H Shoshan, Arie Admon
Expert Review of Proteomics (2005) 2(2): 229-241

Recent advances in 2D electrophoresis: an array of possibilities
Gert Van den Bergh, Lutgarde Arckens
Expert Review of Proteomics (2005) 2(2): 243-252

Shotgun lipidomics: multidimensional MS analysis of cellular lipidomes
Xianlin Han, Richard W Gross
Expert Review of Proteomics (2005) 2(2): 253-264

Does O_GlcNAc play a role in neurodegenerative diseases?
Tony Lefebvre, Celine Guinez, Vanessa Dehennaut, Olivia Beseme_Dekeyser, Willy Morelle, Jean_Claude Michalski
Expert Review of Proteomics (2005) 2(2): 265-275

Proteomics: from Gel Based to Gel Free
Jean-Philippe Lambert, Martin Ethier, Jeffrey C. Smith, and Daniel Figeys
ANALYTICAL CHEMISTRY (2005) 77(12): 3771-3788

Rheumatology: a close encounter with proteomics
Tilleman K, Deforce D, Elewaut D
Rheumatology (Oxford) Early Edition: published 31-May-2005

Proteomics: From Basic Research to Diagnostic Application. A Review of Requirements & Needs
Frank Vitzthum, Fritz Behrens, N. Leigh Anderson, and John H. Shaw
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Proteomics approaches to biomarker detection
Zhou M, Conrads TP, Veenstra TD
Brief Funct Genomic Proteomic (2005) 4(1): 69-75

Clinical Cancer Proteomics: Promises and Pitfalls
Ayodele Alaiya, Mai Al-Mohanna, and Stig Linder
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

The interplay between structure and function in intrinsically unstructured proteins
Tompa P
FEBS Lett (2005) 579(15): 3346-54

Proteomics: The next revolution in laboratory medicine?
Plebani M
Clin Chim Acta Early Edition: published 4-Jun-2005

Molecular markers that predict response to colon cancer therapy
Ahmed FE
Expert Rev Mol Diagn (2005) 5(3): 353-75

Bioinformatics. Current limitations and insights for the future
Rhee SY
Plant Physiol (2005) 138(2): 569-70

Lessons from nature: On the molecular recognition elements of the phosphoprotein binding-domains
Roque AC, Lowe CR
Biotechnol Bioeng Early Edition: published 15-Jun-2005

Prospects for urinary proteomics: Exosomes as a source of urinary biomarkers (Review Article)
Hoorn EJ, Pisitkun T, Zietse R, Gross P, Frokiaer J, Wang NS, Gonzales PA, Star RA, Knepper MA
Nephrology (Carlton) (2005) 10(3): 283-90

Rice proteomics: A cornerstone for cereal food crop proteomes
Agrawal GK, Rakwal R
Mass Spectrom Rev Early Edition: published 14-Jun-2005

Update on proteomics in Arabidopsis. Where do we go from here?
Peck SC
Plant Physiol (2005) 138(2): 591-9

Applying proteomics in clinical trials : assessing the potential and practical limitations in ovarian cancer
Tchabo NE, Liel MS, Kohn EC
Am J Pharmacogenomics (2005) 5(3): 141-8

Proteomics: from gel based to gel free
Lambert JP, Ethier M, Smith JC, Figeys D
Anal Chem (2005) 77(12): 3771-88

14-3-3 protein signaling in development and growth factor responses
Thomas D, Guthridge M, Woodcock J, Lopez A
Curr Top Dev Biol (2005) 67: 285-303

Methodology

Separation techniques hyphenated to electrospray-tandem mass spectrometry in proteomics: Capillary electrophoresis versus nanoliquid chromatography
Pelzing M, Neususs C
Electrophoresis Early Edition: published 20-Jun-2005

A novel technique to specifically analyze the secretome of cells and tissues
Zwickl H, Traxler E, Staettner S, Parzefall W, Grasl-Kraupp B, Karner J, Schulte-Hermann R, Gerner C
Electrophoresis Early Edition: published 20-Jun-2005

Global Whole-Cell FTICR Mass Spectrometric Proteomics Analysis of the Heat Shock Response in the Radioresistant Bacterium Deinococcus radiodurans
Amy K. Schmid, Mary S. Lipton, Heather Mottaz, Matthew E. Monroe, Richard D. Smith, and Mary E. Lidstrom
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 709-718

Direct MS/MS Analysis of Proteins Blotted on Membranes by a Matrix-Assisted Laser Desorption/Ionization-Quadrupole Ion Trap-Time-of-Flight Tandem Mass Spectrometer
Tsuyoshi Nakanishi, Iwao Ohtsu, Masaru Furuta, Eiji Ando, and Osamu Nishimura
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 743-747

Global Proteome Discovery Using an Online Three-Dimensional LC-MS/MS
Jing Wei, Jun Sun, Wen Yu, Arianna Jones, Paul Oeller, Martin Keller, Gary Woodnutt, and Jay M. Short
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 801-808

Optimal Replication and the Importance of Experimental Design for Gel-Based Quantitative Proteomics
Sybille M. N. Hunt, Mervyn R. Thomas, Lucille T. Sebastian, Susanne K. Pedersen, Rebecca L. Harcourt, Andrew J. Sloane, and Marc R. Wilkins
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 809-819

Evaluation of Protein Depletion Methods for the Analysis of Total-, Phospho- and Glycoproteins in Lumbar Cerebrospinal Fluid
Yuko Ogata, M. Cristine Charlesworth, and David C. Muddiman
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 837-845

Sequence Similarity-Based Proteomics in Insects: Characterization of the Larvae Venom of the Brazilian Moth Cerodirphia speciosa
Anna Shevchenko, Mirta Mittelstedt Leal de Sousa, Patrice Waridel, Silvia Tolfo Bittencourt, Marcelo Valle de Sousa, and Andrej Shevchenko
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 862-869

In Vivo Dual-Tagging Proteomic Approach in Studying Signaling Pathways in Immune Response
Tianyi Wang, Sheng Gu, Tapani Ronni, Yu-Chun Du, and Xian Chen
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 941-949

Direct Tandem Mass Spectrometry Reveals Limitations in Protein Profiling Experiments for Plasma Biomarker Discovery
John M. Koomen, Donghui Li, Lian-chun Xiao, Thomas C. Liu, Kevin R. Coombes, James Abbruzzese, and Ryuji Kobayashi
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 972-981

Postfractionation for Enhanced Proteomic Analyses: Routine Electrophoretic Methods Increase the Resolution of Standard 2D-PAGE
R. Hussain Butt and Jens R. Coorssen
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 982-991

Peptide sequencing through N-terminal phosphonylation and electrospray ionization mass spectrometry
Jiangyin Bao, Huiwang Ai, Hua Fu, Yuyang Jiang, Yufen Zhao, Cheng Huang
Journal of Mass Spectrometry (2005) 40(6): 772-776

Increased Protein Identification Capabilities through Novel Tandem MS Calibration Strategies
Si Wu, Nathan K. Kaiser, Da Meng, Gordon A. Anderson, Kai Zhang, and James E. Bruce
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/08/2005

Improvements in two-dimensional gel electrophoresis by utilizing a low cost ?in-house? neutral pH sodium dodecyl sulfate-polyacrylamide gel electrophoresis system
David R. M. Graham, Christopher P. Garnham, Qin Fu, Jeffrey Robbins, Jennifer E. Van Eyk
PROTEOMICS (2005) 5(9): 2309-2314

Development of a high-throughput method for preparing human urine for two-dimensional electrophoresis
Graeme Smith, Derek Barratt, Rachel Rowlinson, Janice Nickson, Robert Tonge
PROTEOMICS (2005) 5(9): 2315-2318

MSight: An image analysis software for liquid chromatography-mass spectrometry
Patricia M. Palagi, Daniel Walther, Manfredo Quadroni, S�bastien Catherinet, Jennifer Burgess, Catherine G. Zimmermann-Ivol, Jean-Charles Sanchez, Pierre-Alain Binz, Denis F. Hochstrasser, Ron D. Appel
PROTEOMICS (2005) 5(9): 2381-2384

Spot overlapping in two-dimensional maps: A serious problem ignored for much too long
Natascia Campostrini, Liliana B. Areces, Juri Rappsilber, Maria Chiara Pietrogrande, Francesco Dondi, Fabio Pastorino, Mirco Ponzoni, Pier Giorgio Righetti
PROTEOMICS (2005) 5(9): 2385-2395

Development of a sample preparation method for fungal proteomics
Shimizu M, Wariishi H
FEMS Microbiol Lett (2005) 247(1): 17-22

Towards validating a method for two-dimensional electrophoresis/silver staining
Schlags W, Walther M, Masree M, Kratzel M, Noe CR, Lachmann B
Electrophoresis Early Edition: published 30-May-2005

Selective Identification and Quantitative Analysis of Methionine Containing Peptides by Charge Derivatization and Tandem Mass Spectrometry
Reid GE, Roberts KD, Simpson RJ, O'hair RA
J Am Soc Mass Spectrom Early Edition: published 26-May-2005

Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry
Anne K. Callesen, Shabaz Mohammed, Jakob Bunkenborg, Torben A. Kruse, S�ren Cold, Ole Mogensen, Rene dePont Christensen, Werner Vach, Per E. J�rgensen, Ole N. Jensen
Rapid Communications in Mass Spectrometry (2005) 19(12): 1578-1586

High-Sensitivity Analysis of Human Plasma Proteome by Immobilized Isoelectric Focusing Fractionation Coupled to Mass Spectrometry Identification
Cheng-Jian Tu, Jie Dai, Su-Jun Li, Quan-Hu Sheng, Wen-Jun Deng, Qi-Chang Xia, and Rong Zeng
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

The Sentinel Within: Exploiting the Immune System for Cancer Biomarkers
Karen S. Anderson and Joshua LaBaer
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Direct Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometric Identification of Proteins on Membrane Detected by Western Blotting and Lectin Blotting
Iwao Ohtsu, Tsuyoshi Nakanisi, Masaru Furuta, Eiji Ando, and Osamu Nishimura
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Proteomic Analysis of Erythrocyte Membranes by Soft Immobiline Gels Combined with Differential Protein Extraction
Maurizio Bruschi, Claudio Seppi, Simona Arena, Luca Musante, Laura Santucci, Cesare Balduini, Andrea Scaloni, Marina Lanciotti, Pier Giorgio Righetti, and Giovanni Candiano
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/24/2005

Solution phase isoelectric fractionation in the multi-compartment electrolyser: A divide and conquer strategy for the analysis of complex proteomes
Smejkal GB, Lazarev A
Brief Funct Genomic Proteomic (2005) 4(1): 76-81

Enrichment of low-abundant serum proteins by albumin/immunoglobulin G immunoaffinity depletion under partly denaturing conditions
Huang HL, Stasyk T, Morandell S, Mogg M, Schreiber M, Feuerstein I, Huck CW, Stecher G, Bonn GK, Huber LA
Electrophoresis Early Edition: published 21-Jun-2005

Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry
Michael L. Nielsen, Mikhail M. Savitski, and Roman A. Zubarev
Mol Cell Proteomics (2005) 4(6): 835-845

Preparation of protein extracts from recalcitrant plant tissues: An evaluation of different methods for two-dimensional gel electrophoresis analysis
Sebastien Christian Carpentier, Erwin Witters, Kris Laukens, Peter Deckers, Rony Swennen, Bart Panis
PROTEOMICS (2005) 5(10): 2497-2507

A robust, streamlined, and reproducible method for proteomic analysis of serum by delipidation, albumin and IgG depletion, and two-dimensional gel electrophoresis
Qin Fu, Christopher P. Garnham, Steven T. Elliott, Diane E. Bovenkamp, Jennifer E. Van Eyk
PROTEOMICS (2005) 5(10): 2656-2664

Method optimisation for peptide profiling of microdissected breast carcinoma tissue by matrix-assisted laser desorption/ionisation-time of flight and matrix-assisted laser desorption/ionisation-time of flight/time of flight-mass spectrometry
Arzu Umar, Johannes C. H. Dalebout, A. Mieke Timmermans, John A. Foekens, Theo M. Luider
PROTEOMICS (2005) 5(10): 2680-2688

Kinetic characterization of sequencing grade modified trypsin
Erin J. Finehout, Jason R. Cantor, Kelvin H. Lee
PROTEOMICS (2005) 5(9): 2319-2321

Acrylamide-agarose copolymers: Improved resolution of high molecular mass proteins in two-dimensional gel electrophoresis
Paola Roncada, Marina Cretich, Riccardo Fortin, Susanna Agosti, Lucia De Franceschi, Gian Franco Greppi, Francesco Turrini, Franco Carta, Stefano Turri, Marinella Levi, Marcella Chiari
PROTEOMICS (2005) 5(9): 2331-2339

Protein sequence tags: A novel solution for comparative proteomics
Karsten Kuhn, Thorsten Prinz, J�rgen Sch�fer, Christian Baumann, Marco Sch�rfke, Stefan Kienle, Josef Schwarz, Sandra Steiner, Christian Hamon
PROTEOMICS (2005) 5(9): 2364-2368

De novo sequence analysis of N-terminal sulfonated peptides after in-gel guanidination
Kjell Sergeant, Bart Samyn, Griet Debyser, Jozef Van Beeumen
PROTEOMICS (2005) 5(9): 2369-2380

Two-stage affinity purification for inducibly phosphorylated membrane proteins
Matthew J. Peirce, Shajna Begum, Jeremy Saklatvala, Andrew P. Cope, Robin Wait
PROTEOMICS (2005) 5(9): 2417-2421

Comparison of protein and peptide prefractionation methods for the shotgun proteomic analysis of Synechocystis sp. PCC 6803
Chee Sian Gan, Kenneth F. Reardon, Phillip C. Wright
PROTEOMICS (2005) 5(9): 2468-2478

A ?de-streaking? method for two-dimensional electrophoresis using the reducing agent tris(2-carboxyethyl)-phosphine hydrochloride and alkylating agent vinylpyridine
Fengju Bai, Sheng Liu, Frank A. Witzmann
PROTEOMICS (2005) 5(9): 2479

?LANESPECTOR?, a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography - tandem mass spectrometry analysis: Application to Listeria monocytogenes membrane proteins
Dirk Wehmh�ner, Guido Dieterich, Elmar Fischer, Maja Baumg�rtner, J�rgen Wehland, Lothar J�nsch
ELECTROPHORESIS (2005) 26(12): 2450-2460

Comparison of protein solubilization methods suitable for proteomic analysis of soybean seed proteins
Natarajan S, Xu C, Caperna TJ, Garrett WM
Anal Biochem Early Edition: published 10-Jun-2005

Analytical and Preanalytical Biases in Serum Proteomic Pattern Analysis for Breast Cancer Diagnosis
Karsan A, Eigl BJ, Flibotte S, Gelmon K, Switzer P, Hassell P, Harrison D, Law J, Hayes M, Stillwell M, Xiao Z, Conrads TP, Veenstra T
Clin Chem Early Edition: published 10-Jun-2005

Novel application of layered expression scanning for proteomic profiling of plucked hair follicles
Traicoff JL, Baibakov G, Biesecker G, Richardson F, Ramesh A, Galperin MM, Iwata KK, Knezevic V
Dermatology (2005) 210(4): 273-8

Molecular Weight Assessment of Proteins in Total Proteome Profiles Using 1D-PAGE and LC/MS/MS
Ahmad R, Nguyen DH, Wingerd MA, Church GM, Steffen MA
Proteome Sci (2005) 3(1): 6

Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis
Churchward MA, Butt RH, Lang JC, Hsu KK, Coorssen JR
Proteome Sci (2005) 3(1): 5

Evaluation of two-dimensional electrophoresis and liquid chromatography - tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples
Schad M, Lipton MS, Giavalisco P, Smith RD, Kehr J
Electrophoresis Early Edition: published 21-Jun-2005

"LANESPECTOR", a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography - tandem mass spectrometry analysis: Application to Listeria monocytogenes membrane proteins
Wehmhoner D, Dieterich G, Fischer E, Baumgartner M, Wehland J, Jansch L
Electrophoresis (2005) 26(12): 2450-2460

Use of selective extraction and fast chromatographic separation combined with electrophoretic methods for mapping of membrane proteins
Josic D, Brown MK, Huang F, Callanan H, Rucevic M, Nicoletti A, Clifton J, Hixson DC
Electrophoresis Early Edition: published 20-Jun-2005

Books

Book Reviews: Proteomics Today: Protein Assessment and Biomarkers using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology. By Hamdan Mahmoud and Righetti Pier Giorgio
Jean-Daniel Tissot
PROTEOMICS (2005) 5(10): 2703

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Meeting

Peptide - Fourth Australian Conference. From discovery to therapeutics - The New Millennium
Craik D
IDrugs (2001) 4(11): 1263-5

Business & Science of Proteomics - Third Annual Event. Next-generation technologies for high-throughput proteomics
Farr-Jones S
IDrugs (2001) 4(11): 1235-6

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Other

Afamin Is a Novel Human Vitamin E-Binding Glycoprotein Characterization and In Vitro Expression
Lidija Jerkovic, Andreas F. Voegele, Sabine Chwatal, Florian Kronenberg, Catherine M. Radcliffe, Mark R. Wormald, Eva M. Lobentanz, Benjie Ezeh, Patricia Eller, Norbert Dejori, Benjamin Dieplinger, Friedrich Lottspeich, Wolfgang Sattler, # Manfred Uhr, Karl Mechtler, Raymond A. Dwek, Pauline M. Rudd, Gottfried Baier, and Hans Dieplinger
JOURNAL OF PROTEOME RESEARCH (2005) 4(3): 889-899

Protein length in eukaryotic and prokaryotic proteomes
Luciano Brocchieri and Samuel Karlin
Nucl. Acids Res. (2005) 33(10): 3390-3400

Metabolic Labeling of Proteins for Proteomics
Robert J. Beynon and Julie M. Pratt
Mol Cell Proteomics (2005) 4(7): 857-872

So, You Want to Look for Biomarkers (Introduction to the Special Biomarkers Issue)
Joshua LaBaer
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/01/2005

Gene products with evolutionary functions
Werner Arber
PROTEOMICS (2005) 5(9): 2280-2284

United States National Heart, Lung, and Blood Institute Proteomics Initiative
Margaret Schachte
PROTEOMICS (2005) 5(9): 2285

Design, construction, and characterization of a large synthetic human antibody phage display library
Michela Silacci, Simon Brack, Giulia Schirru, Jessica M�rlind, Anna Ettorre, Adrian Merlo, Francesca Viti, Dario Neri
PROTEOMICS (2005) 5(9): 2340-2350

HUPO Brain Proteome Project Pilot Studies: Bioinformatics at Work
Stephan C, Reidegeld K, Meyer HE, Hamacher M
Proteomics Early Edition: published 13-Jun-2005

Industrial process proteomics: Alfalfa protein patterns during wet fractionation processing
Incamps A, Hely-Joly F, Chagvardieff P, Rambourg JC, Dedieu A, Linares E, Quemeneur E
Biotechnol Bioeng Early Edition: published 9-Jun-2005

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