SPS' Digest

Issue 32, 30-Jun-2006

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Quick jumps to articles in: Bioinformatics (17) / Biological applications (60) / Biomedical and clinical applications (42) / Eukaryotic Cells And Tissues (8) / Prokaryotes (14) / Pharmacology and Toxicology (2) / Protein Array (6) / Protein Characterization - PTMs (16) / Protein-protein interaction (3) / Quantitation (6) / Review (29) / Methodology (50) / Books (1) / Other (4) /

In this issue, 246 articles have been selected from:

AMIA Annu Symp Proc, Volume , 2005 (2 articles)
Acta Neurochir (Wien), Early Edition, 6-Jun-2006 (1 article)
Acta Trop, Early Edition, 19-Jun-2006 (1 article)
Am J Nephrol, Volume 26, Issue 3, 2006 (1 article)
Am J Physiol Heart Circ Physiol, Early Edition, 16-Jun-2006 (1 article)
Am J Vet Res, Volume 67, Issue 6, 2006 (1 article)
Amino Acids, Volume 30, Issue 4, 2006 (1 article)
Anal Bioanal Chem, Early Edition, 22-Jun-2006 (1 article)
Anal Biochem, Early Edition, 11-May-2006 (1 article)
Anal Chem, Volume 78, Issues 11+12, 2006 (6 articles)
Ann Bot (Lond), Early Edition, 1-Jun-2006 (1 article)
Ann Oncol, Volume 17, Issue Suppl 7, 2006 (1 article)
Arch Biochem Biophys, Early Edition, 24-May-2006 (1 article)
BMC Bioinformatics, Volume 7, Issue 1, 2006 (1 article)
Biochem Biophys Res Commun, Early Edition, 19-May-2006 (1 article)
Biochem Pharmacol, Early Edition, 27-Apr-2006 (1 article)
Biochim Biophys Acta, Early Edition, 20-Apr-2006 (1 article)
Bioinformatics, Early Edition, 9-Jun-2006 (1 article)
Bioinformatics, Volume 22, Issues 12+13, 2006 (3 articles)
Biol Reprod, Early Edition, 31-May-2006 (1 article)
Biomarkers, Volume 11, Issue 3, 2006 (1 article)
Biomed Chromatogr, Volume 20, Issue 6-7, 2006 (1 article)
Bioorg Med Chem, Early Edition, 17-Jun-2006 (1 article)
Biotechniques, Volume 40, Issue 6, 2006 (2 articles)
Br J Cancer, Early Edition, 6-Jun-2006 (1 article)
Brain Res, Early Edition, 23-May-2006 (1 article)
Braz J Infect Dis, Volume 10, Issue 1, 2006 (1 article)
Brief Bioinform, Volume 7, Issue 1, 2006 (1 article)
Brief Funct Genomic Proteomic, Volume 4, Issue 4, 2006 (3 articles)
Brief Funct Genomic Proteomic, Volume 5, Issues 1+2, 2006 (9 articles)
Cancer Biol Ther, Early Edition, 2-Aug-2006 (1 article)
Cancer Res, Volume 66, Issue 11, 2006 (2 articles)
Cancer, Early Edition, 2-Jun-2006 (1 article)
Cell Res, Volume 16, Issue 6, 2006 (1 article)
Cell, Volume 125, Issue 5, 2006 (1 article)
Chem Biol Interact, Early Edition, 24-May-2006 (1 article)
Chem Commun (Camb), Volume , Issue 22, 2006 (1 article)
Clin Otolaryngol, Volume 31, Issue 3, 2006 (1 article)
Comput Biol Chem, Early Edition, 25-May-2006 (1 article)
Curr Biol, Volume 16, Issue 11, 2006 (1 article)
Curr Drug Metab, Volume 7, Issue 5, 2006 (1 article)
Curr Med Chem, Volume 13, Issue 15, 2006 (1 article)
Curr Opin Mol Ther, Volume 8, Issue 3, 2006 (3 articles)
Curr Pharm Biotechnol, Volume 7, Issue 3, 2006 (6 articles)
Cytometry A, Early Edition, 2-Jun-2006 (1 article)
DNA Cell Biol, Volume 25, Issue 6, 2006 (1 article)
Diagn Mol Pathol, Volume 15, Issue 2, 2006 (1 article)
Electrophoresis, Early Edition, 1-Jun-2006->29-May-2006 (10 articles)
Electrophoresis, Volume 27, Issue 12, 2006 (3 articles)
Endocrinology, Early Edition, 22-Jun-2006 (1 article)
Environ Health Perspect, Volume 114, Issue 6, 2006 (1 article)
Extremophiles, Early Edition, 22-Jun-2006 (1 article)
Fertil Steril, Early Edition, 31-May-2006 (1 article)
Gastroenterology, Volume 130, Issue 7, 2006 (2 articles)
Genome Biology, Volume 7, Issue 6, 2006 (3 articles)
Infect Immun, Volume 74, Issue 7, 2006 (3 articles)
Int Arch Allergy Immunol, Volume 140, Issue 4, 2006 (1 article)
Int Rev Neurobiol, Volume 73, 2006 (1 article)
Intensive Care Med, Early Edition, 2-Jun-2006 (1 article)
J Am Acad Orthop Surg, Volume 14, Issue 6, 2006 (1 article)
J Am Soc Mass Spectrom, Early Edition, 10-Jun-2006 (1 article)
J Anim Sci, Volume 84, Issue 7, 2006 (1 article)
J Antimicrob Chemother, Early Edition, 30-May-2006 (1 article)
J Bacteriol, Volume 188, Issues 12+13, 2006 (2 articles)
J Biochem (Tokyo), Volume 139, Issue 5, 2006 (1 article)
J Biomol Tech, Volume 17, Issue 2, 2006 (3 articles)
J Biotechnol, Early Edition, 17-Jun-2006 (1 article)
J Chromatogr B, Early Edition, 15-Jun-2006->30-May-2006 (2 articles)
J Korean Med Sci, Volume 21, Issue 3, 2006 (1 article)
J Mass Spectrom, Volume 41, Issue 5, 2006 (5 articles)
J Med Chem, Volume 49, Issue 12, 2006 (1 article)
J Muscle Res Cell Motil, Early Edition, 4-Jun-2006 (1 article)
J Neurochem, Early Edition, 19-Jun-2006 (1 article)
J Neurosci Methods, Early Edition, 9-Jun-2006 (1 article)
J Nutr, Volume 136, Issue 7, 2006 (1 article)
J Physiol, Early Edition, 8-Jun-2006 (1 article)
J Proteome Res, Early Edition, 06/02/2006->06/16/2006 (24 articles)
J Psychiatr Res, Early Edition, 2-Jun-2006 (1 article)
J Speech Lang Hear Res, Volume 49, Issue 3, 2006 (1 article)
J Vet Med Sci, Volume 68, Issue 5, 2006 (1 article)
Kidney Int, Early Edition, 7-Jun-2006 (1 article)
Mar Environ Res, Early Edition, 7-Apr-2006 (2 articles)
Methods Enzymol, Volume 407, 2005 (1 article)
Methods Mol Biol, Volume 322, 2006 (1 article)
Methods Mol Biol, Volume 323, 2006 (4 articles)
Methods Mol Biol, Volume 328, 2006 (8 articles)
Methods Mol Biol, Volume 333, 2006 (1 article)
Methods Mol Biol, Volume 339, 2006 (1 article)
Microbiol Mol Biol Rev, Volume 70, Issue 2, 2006 (1 article)
Microbiology, Volume 152, Issue Pt 6, 2006 (2 articles)
Mol Carcinog, Early Edition, 20-Jun-2006 (1 article)
Mol Cell Biol, Volume 26, Issue 13, 2006 (1 article)
Mol Cell Endocrinol, Early Edition, 2-Jun-2006 (1 article)
Mol Cell Proteomics, Volume 5, Issue 6, 2006 (16 articles)
Mol Syst Biol, Volume 2, 2006 (2 articles)
Mol Vis, Volume 12, 2006 (1 article)
Nat Methods, Volume 3, Issues 6+7, 2006 (2 articles)
Neurotox Res, Volume 9, Issue 4, 2006 (1 article)
Nucl Acids Res, Volume 34, Issue 10, 2006 (1 article)
Obstet Gynecol Surv, Volume 61, Issue 7, 2006 (1 article)
Oncogene, Early Edition, 29-May-2006 (2 articles)
Parasitol Res, Early Edition, 1-Jun-2006 (1 article)
Peptides, Early Edition, 17-Jun-2006 (1 article)
Plant J, Early Edition, 12-Jun-2006 (1 article)
Plant Methods, Volume 2, Issue 1, 2006 (1 article)
Plant Physiol Biochem, Early Edition, 15-May-2006 (1 article)
Proc Natl Acad Sci U S A, Early Edition, 12-Jun-2006->19-Jun-2006 (2 articles)
Proteins, Early Edition, 22-Jun-2006 (1 article)
Proteome Sci, Volume 4, Issue 1, 2006 (2 articles)
Proteomics, Volume 6, Issue 12, 2006 (22 articles)
Rapid Commun Mass Spectrom, Volume 20, Issues 11+12+14, 2006 (7 articles)
ScientificWorldJournal, Volume 6, 2006 (1 article)
Trends Microbiol, Early Edition, 15-Jun-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 (17) / Biological applications (60) / Biomedical and clinical applications (42) / Eukaryotic Cells And Tissues (8) / Prokaryotes (14) / Pharmacology and Toxicology (2) / Protein Array (6) / Protein Characterization - PTMs (16) / Protein-protein interaction (3) / Quantitation (6) / Review (29) / Methodology (50) / Books (1) / Other (4) /

Bioinformatics

The wildcat toolbox: a set of perl script utilities for use in Peptide mass spectral database searching and proteomics experiments
Haynes PA, Miller S, Radabaugh T, Galligan M, Breci L, Rohrbough J, Hickman F, Merchant N
J Biomol Tech (2006) 17(2): 97-102

An online literature mining tool for protein phosphorylation
X. Yuan, Z. Z. Hu, H. T. Wu, M. Torii, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu
Bioinformatics (2006) 22(13): 1668-1669

Predicting O-glycosylation sites in mammalian proteins by using SVMs
Li S, Liu B, Zeng R, Cai Y, Li Y
Comput Biol Chem Early Edition: published 25-May-2006

A fast coarse filtering method for peptide identification by mass spectrometry
Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, and Daniel P. Miranker
Bioinformatics (2006) 22(12): 1524-1531

Finding regions of significance in SELDI measurements for identifying protein biomarkers
Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtio, and Yudi Pawitan
Bioinformatics (2006) 22(12): 1515-1523

A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, Chen J, Goodlett D, Whiteaker J, Paulovich A, McIntosh M
Bioinformatics Early Edition: published 9-Jun-2006

Automated interpretation of subcellular patterns in fluorescence microscope images for location proteomics
Chen X, Velliste M, Murphy RF
Cytometry A Early Edition: published 2-Jun-2006

Improving the Accuracy of Protein Secondary Structure Prediction Using Structural Alignment
Montgomerie S, Sundararaj S, Gallin WJ, Wishart DS
BMC Bioinformatics (2006) 7(1): 301

Retention Prediction of Peptides Based on Uninformative Variable Elimination by Partial Least Squares
R. Put, M. Daszykowski, T. Baczek, and Y. Vander Heyden
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/16/2006

Guilt-by-association feature selection applied to simulated proteomic data
Shin H, Sheu B, Markey MK
AMIA Annu Symp Proc (2005) : 1114.

Combining functional and topological properties to identify core modules in protein interaction networks
Lubovac Z, Gamalielsson J, Olsson B
Proteins Early Edition: published 22-Jun-2006

N-glycosylation analysis using the StrOligo algorithm
Ethier M, Figeys D, Perreault H
Methods Mol Biol (2006) 328: 187-97

YPED: A Proteomics Database for Protein Expression Analysis
Shifman MA, Sun K, Colangelo CM, Cheung KH, Miller P, Williams K
AMIA Annu Symp Proc (2005) : 1111.

Transforming omics data into context: Bioinformatics on genomics and proteomics raw data
Perco P, Rapberger R, Siehs C, Lukas A, Oberbauer R, Mayer G, Mayer B
Electrophoresis Early Edition: published 1-Jun-2006

The Wildcat Toolbox: A Set of Perl Script Utilities for Use in Peptide Mass Spectral Database Searching and Proteomics Experiments
Haynes, P. A., Miller, S., Radabaugh, T., Galligan, M., Breci, L., Rohrbough, J., Hickman, F., Merchant, N
J Biomol Tech (2006) 17(2): 97-102

Using the global proteome machine for protein identification
Beavis RC
Methods Mol Biol (2006) 328: 217-28

Protein complex compositions predicted by structural similarity
Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS
Nucl Acids Res (2006) 34(10): 2943-52

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Biological applications

Alcohol Dehydrogenase Restricts the Ability of the Pathogen Candida albicans To Form a Biofilm on Catheter Surfaces through an Ethanol-Based Mechanism
Mukherjee PK, Mohamed S, Chandra J, Kuhn D, Liu S, Antar OS, Munyon R, Mitchell AP, Andes D, Chance MR, Rouabhia M, Ghannoum MA
Infect Immun (2006) 74(7): 3804-16

Proteomic analysis of sperm regions that mediate sperm-egg interactions
Kathryn K. Stein, Jowell C. Go, William S. Lane, Paul Primakoff, Diana G. Myles
PROTEOMICS (2006) 6(12): 3533-3543

Subcellular pH and predicted pH-dependent features of proteins
Pedro Chan, Josip Lovri?, Jim Warwicker
PROTEOMICS (2006) 6(12): 3494-3501

Comparative two-dimensional gel electrophoresis maps for promastigotes of Leishmania amazonensis and Leishmania major
Brobey RK, Mei FC, Cheng X, Soong L
Braz J Infect Dis (2006) 10(1): 1-6

Characterization of the Drosophila Lipid Droplet Subproteome
Mathias Beller, Dietmar Riedel, Lothar Jansch, Guido Dieterich, JurgenWehland, Herbert Jackle, and Ronald P. Kuhnlein
Mol Cell Proteomics (2006) 5(6): 1082-1094

Compatibility in the Biomphalaria glabrata/Echinostoma caproni model: Potential involvement of proteins from hemocytes revealed by a proteomic approach
Bouchut A, Sautiere PE, Coustau C, Mitta G
Acta Trop Early Edition: published 19-Jun-2006

The characterization of stem cell proteomes
Vodicka P, Skalnikova H, Kovarova H
Curr Opin Mol Ther (2006) 8(3): 232-9

A proteomic study on human osteoblastic cells proliferation and differentiation
Adriano Spreafico, Bruno Frediani, Caterina Capperucci, Francesca Chellini, Alessandro Paffetti, Chiara D'Ambrosio, Giulia Bernardini, Roberta Mini, Giulia Collodel, Andrea Scaloni, Roberto Marcolongo, Annalisa Santucci
PROTEOMICS (2006) 6(12): 3520-3532

Machine learning in bioinformatics
Larranaga P, Calvo B, Santana R, Bielza C, Galdiano J, Inza I, Lozano JA, Armananzas R, Santafe G, Perez A, Robles V
Brief Bioinform (2006) 7(1): 86-112

Proteomic profiling of fibroblasts reveals a modulating effect of extracellular calumenin on the organization of the actin cytoskeleton
Morten �stergaard, Gry A.W. Hansen, Henrik Vorum, Bent Honor�
PROTEOMICS (2006) 6(12): 3509-3519

Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS
Bong-Kwan Phee, Dong Ho Shin, Jin-Hwan Cho, Seong-Hee Kim, Jeong-Il Kim, Youn-Hyung Lee, Jong-Seong Jeon, Seong Hee Bhoo, Tae-Ryong Hahn
PROTEOMICS (2006) 6(12): 3671-3680

Molecular organization of peroxisomal enzymes: Protein-protein interactions in the membrane and in the matrix
Makkar RS, Contreras MA, Paintlia AS, Smith BT, Haq E, Singh I
Arch Biochem Biophys Early Edition: published 24-May-2006

Identification of new Golgi complex specific proteins by direct organelle proteomic analysis
Maarit S. Takatalo, Petri Kouvonen, Garry Corthals, Tuula A. Nyman, Ragna H. R�nnholm
PROTEOMICS (2006) 6(12): 3502-3508

Proteomic analysis of rice leaf, stem and root tissues during growth course
Yuzo Nozu, Akira Tsugita, Kenichi Kamijo
PROTEOMICS (2006) 6(12): 3665-3670

Inflammatory Response in White Adipose Tissue in the Non-Obese Hormone-Sensitive Lipase Null Mouse Model
Ola Hansson, Kristoffer Ström, Nuray Güner, Nils Wierup, Frank Sundler, Peter Höglund, and Cecilia Holm
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/02/2006

Proteome analysis of yeast response to various nutrient limitations
Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn MM, Pronk JT, Slijper M, Heck AJ
Mol Syst Biol (2006) 2: 2006.0026

Mass spectrometric profiling - A diagnostic tool in fish?
Provan F, Bjornstad A, Pampanin DM, Lyng E, Fontanillas R, Andersen OK, Koppe W, Bamber S
Mar Environ Res Early Edition: published 7-Apr-2006

Proteomic analysis of the eukaryotic parasite Encephalitozoon cuniculi (microsporidia): a reference map for proteins expressed in late sporogonial stages
Damien Brosson, Lauriane Kuhn, Fr�d�ric Delbac, J�r�me Garin, Christian P. Vivar�s, Catherine Texier
PROTEOMICS (2006) 6(12): 3625-3635

Differential display proteomic analysis of Picea meyeri pollen germination and pollen-tube growth after inhibition of actin polymerization by latrunculin B
Chen Y, Chen T, Shen S, Zheng M, Guo Y, Lin J, Baluska F, Samaj J
Plant J Early Edition: published 12-Jun-2006

Proteomic profiling of rat thyroarytenoid muscle
Welham NV, Marriott G, Bless DM
J Speech Lang Hear Res (2006) 49(3): 671-85

Quantitative proteomics identifies a change in glial glutamate metabolism at the time of female puberty
Roth CL, McCormack AL, Lomniczi A, Mungenast AE, Ojeda SR
Mol Cell Endocrinol Early Edition: published 2-Jun-2006

Application of a suite of biomarkers in Posidonia oceanica (L.) delile to assess the ecotoxicological impact on the coastal environment
Bucalossi D, Leonzio C, Casini S, Fossi MC, Marsili L, Ancora S, Wang W, Scali M
Mar Environ Res Early Edition: published 7-Apr-2006

PU.1 Is Degraded in Differentiation of Erythrocytes Through a Proteasome-Dependent Pathway
Konishi Y, Tominaga A
DNA Cell Biol (2006) 25(6): 340-5

Proteomic Identification of AP2{gamma} as a Rat Placental Lactogen II Trophoblast Cell-specific Enhancer Binding Protein
Ozturk A, Donald LJ, Li L, Duckworth HW, Duckworth ML
Endocrinology Early Edition: published 22-Jun-2006

Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics
Alyssa M. Redding, Aindrila Mukhopadhyay, Dominique C. Joyner, Terry C. Hazen, and Jay D. Keasling
Brief Funct Genomic Proteomic (2006) 5(2): 133-143

The Dynamic Alterations of H2AX Complex during DNA Repair Detected by a Proteomic Approach Reveal the Critical Roles of Ca2+/Calmodulin in the Ionizing Radiation-induced Cell Cycle Arrest
Yu-Chun Du, Sheng Gu, Jianhong Zhou, Tianyi Wang, Hong Cai, Mark A. MacInnes, E. Morton Bradbury, and Xian Chen
Mol Cell Proteomics (2006) 5(6): 1033-1044

Warm Ischemia-induced Alterations in Oxidative and Inflammatory Proteins in Hepatic Kupffer Cells in Rats
Jan Hirsch, Kirk C. Hansen, SooJinNa Choi, Joonhwa Noh, Ryutaro Hirose, John P. Roberts, Michael A. Matthay, Alma L. Burlingame, Jacquelyn J. Maher, and Claus U. Niemann
Mol Cell Proteomics (2006) 5(6): 979-986

Changes in Enzymes Associated with Energy Metabolism during the Early Post Mortem Period in Longissimus Thoracis Bovine Muscle Analyzed by Proteomics
Xiaohong Jia, Kjell I. Hildrum, Frank Westad, Eiliv Kummen, Laila Aass, # and Kristin Hollung
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125
Papa R, Glagla S, Danchin A, Schweder T, Marino G, Duilio A
Extremophiles Early Edition: published 22-Jun-2006

Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains
Bernhard Granvogl, Veronika Reisinger, Lutz Andreas Eichacker
PROTEOMICS (2006) 6(12): 3681-3695

Role of proteins in resistance mechanism of Pseudomonas fluorescens against heavy metal induced stress with proteomics approach
Sharma S, Luthra PM, Singh Y, Sirdeshmukh R, Gade WN
J Biotechnol Early Edition: published 17-Jun-2006

Proteomics reveals elevated levels of PR 10 proteins in saline-tolerant peanut (Arachis hypogaea) calli
Jain S, Srivastava S, Sarin NB, Kav NN
Plant Physiol Biochem Early Edition: published 15-May-2006

Proteomic Identification of Desmoglein 2 and Activated Leukocyte Cell Adhesion Molecule as Substrates of ADAM17 and ADAM10 by Difference Gel Electrophoresis
Bech-Serra JJ, Santiago-Josefat B, Esselens C, Saftig P, Baselga J, Arribas J, Canals F
Mol Cell Biol (2006) 26(13): 5086-95

Proteomic dissection of potential signal recognition particle dependence in protein secretion by Bacillus subtilis
Geeske Zanen, Haike Antelmann, Rob Meima, Jan D.H. Jongbloed, Marc Kolkman, Michael Hecker, Jan Maarten van Dijl, Wim J. Quax
PROTEOMICS (2006) 6(12): 3636-3648

Proteome Profiling of Populus euphratica Oliv. Upon Heat Stress
Ferreira S, Hjerno K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Pais MS
Ann Bot (Lond) Early Edition: published 1-Jun-2006

Systems Toxicology: Integrated Genomic, Proteomic and Metabonomic Analysis of Methapyrilene Induced Hepatotoxicity in the Rat
Andrew Craig, James Sidaway, Elaine Holmes, Terry Orton, David Jackson, Rachel Rowlinson, Janice Nickson, Robert Tonge, Ian Wilson, and Jeremy Nicholson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/16/2006

The phosphate-starvation response of Bacillus licheniformis
Le Thi Hoi, Birgit Voigt, Britta J�rgen, Armin Ehrenreich, Gerhard Gottschalk, Stefan Evers, J�rg Feesche, Karl-Heinz Maurer, Michael Hecker, Thomas Schweder
PROTEOMICS (2006) 6(12): 3582-3601

Proteomic analysis of Tityus discrepans scorpion venom and amino acid sequence of novel toxins
Cesar V. F. Batista, Gina D'Suze, Froylan G�mez-Lagunas, Fernando Z. Zamudio, Sergio Encarnaci�n, Carlos Sevcik, Lourival D. Possani
PROTEOMICS (2006) 6(12): 3718-3727

Secreted proteins and genes in fetal and neonatal pig adipose tissue and stromal-vascular cells
Hausman GJ, Poulos SP, Richardson RL, Barb CR, Andacht T, Kirk HC, Mynatt RL
J Anim Sci (2006) 84(7): 1666-81

Proteomic characterization of acid stress response in Synechocystis sp. PCC 6803
Dominic Kurian, Kanchan Phadwal, Pirkko M�enp��
PROTEOMICS (2006) 6(12): 3614-3624

Circadian orchestration of the hepatic proteome
Reddy AB, Karp NA, Maywood ES, Sage EA, Deery M, O'neill JS, Wong GK, Chesham J, Odell M, Lilley KS, Kyriacou CP, Hastings MH
Curr Biol (2006) 16(11): 1107-15

Transcriptomics, proteomics and interactomics: unique approaches to track the insights of bioremediation
Singh Om V., Nagaraj Nagathihalli S
Brief Funct Genomic Proteomic (2006) 4(4): 355-362

Proteome Profiling in the Rat Harderian Gland
Jae-Won Yang, Leila Afjehi-Sadat, Ellen Gelpi, Markus Kunze, Harald Höger, Jan Fleckner, Johannes Berger, and Gert Lubec
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/09/2006

A combined proteomic and transcriptomic approach to the study of stage differentiation in Leishmania infantum
Fran�ois McNicoll, Jolyne Drummelsmith, Michaela M�ller, �ric Madore, Nathalie Boilard, Marc Ouellette, Barbara Papadopoulou
PROTEOMICS (2006) 6(12): 3567-3581

PPAR and PPAR Regulation of Liver and Adipose Proteins in Obese and Dyslipidemic Rodents
Boel Lanne, Björn Dahllöf, Charlotta Lindahl, Kerstin Ebefors, Ida Kanmert, Helena von Bahr, Tasso Miliotis, Ann-Christin Nyström, Gunnel Arnerup, Ivar Paulsons, Santy Kerb, and Nick Oakes
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
de Godoy L, Olsen J, de Souza G, Li G, Mortensen P, Mann M
Genome Biology (2006) 7(6): R50

Exploring how the organelles are organized
Eisenstein M
Nat Methods (2006) 3(6): 420-1

Proteomic exploration of the Wnt/beta-catenin pathway
Tian Q
Curr Opin Mol Ther (2006) 8(3): 191-7

Maternal nutrient restriction affects properties of skeletal muscle in offspring
Zhu MJ, Ford SP, Means WJ, Hess BW, Nathanielsz PW, Du M
J Physiol Early Edition: published 8-Jun-2006

Relative and Absolute Quantification of Postsynaptic Density Proteome Isolated from Rat Forebrain and Cerebellum
Dongmei Cheng, Casper C. Hoogenraad, John Rush, Elizabeth Ramm, Max A.Schlager, Duc M. Duong, Ping Xu, Sameera R. Wijayawardana, John Hanfelt, Terunaga Nakagawa, Morgan Sheng, and Junmin Peng
Mol Cell Proteomics (2006) 5(6): 1158-1170

Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins
Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Alaluf I, Swerdlin N, Perzov N, Danon T, Liron Y, Raveh T, Carpenter AE, Lahav G, Alon U
Nat Methods (2006) 3(7): 525-31

Extracellular Matrix Proteome of Chickpea (Cicer arietinum L.) Illustrates Pathway Abundance, Novel Protein Functions and Evolutionary Perspect
Deepti Bhushan, Aarti Pandey, Arnab Chattopadhyay, Mani Kant Choudhary, Subhra Chakraborty, Asis Datta, and Niranjan Chakraborty
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/16/2006

Multivariate analysis of protein profiles of metal hyperaccumulator Thlaspi caerulescens accessions
Marjo H. Tuomainen, Naoise Nunan, Satu J. Lehesranta, Arja I. Tervahauta, Viivi H. Hassinen, Henk Schat, Kaisa M. Koistinen, Seppo Auriola, Jim McNicol, Sirpa O. K�renlampi
PROTEOMICS (2006) 6(12): 3696-3706

Simultaneous quantification of CTN986 and its deglycosylation products in rat serum using liquid chromatography/tandem mass spectrometry
Jifen Guo, Yimin Zhao, Ling Zhao, Weiqiang Zhang, Aijun Zhang, Bin Xu
Rapid Communications in Mass Spectrometry (2006) 20(11): 1701-1708

Identification of AGE-modified proteins in SH-SY5Y and OLN-93 cells
Langer KA, Poon HF, Munch G, Lynn CB, Arendt T, Butterfield DA
Neurotox Res (2006) 9(4): 255-268

Impact of the accessory gene regulatory system (Agr) on extracellular proteins, codY expression and amino acid metabolism in Staphylococcus epidermidis
Christoph F. Batzilla, Shwan Rachid, Susanne Engelmann, Michael Hecker, J�rg Hacker, Wilma Ziebuhr
PROTEOMICS (2006) 6(12): 3602-3613

Proteomics and its role in nutrition research
Wang J, Li D, Dangott LJ, Wu G
J Nutr (2006) 136(7): 1759-62

Proteomic analysis of experimentally induced azole resistance in Candida glabrata
Rogers PD, Vermitsky JP, Edlind TD, Hilliard GM
J Antimicrob Chemother Early Edition: published 30-May-2006

Toward the Complete Yeast Mitochondrial Proteome: Multidimensional Separation Techniques for Mitochondrial Proteomics
Joerg Reinders, René P. Zahedi, Nikolaus Pfanner, Chris Meisinger, and Albert Sickmann
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/09/2006

Increases in pig major acute-phase protein in wasting pigs brought to the abattoir
Yamane H, Kanouchi H, Arimizu G, Obi T, Oka T
J Vet Med Sci (2006) 68(5): 511-3

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Biomedical and clinical applications

Calpain product of WT-CRMP2 reduces the amount of surface NR2B NMDA receptor subunit
Bretin S, Rogemond V, Marin P, Maus M, Torrens Y, Honnorat J, Glowinski J, Premont J, Gauchy C
J Neurochem Early Edition: published 19-Jun-2006

Proteome-level display by 2-dimensional chromatography of extracellular matrix-dependent modulation of the phenotype of bladder cancer cells
Hurst RE, Kyker KD, Dozmorov MG, Takemori N, Singh A, Matsumoto H, Saban R, Betgovargez E, Simonian MH
Proteome Sci (2006) 4(1): 13

Serum Proteome to Predict Virologic Response in Patients With Hepatitis C Treated by Pegylated Interferon Plus Ribavirin
Paradis V, Asselah T, Dargere D, Ripault MP, Martinot M, Boyer N, Valla D, Marcellin P, Bedossa P
Gastroenterology (2006) 130(7): 2189-2197

Investigating the structural properties of amyloid-like fibrils formed in vitro from ?2-microglobulin using limited proteolysis and electrospray ionisation mass spectrometry
Sarah L. Myers, Neil H. Thomson, Sheena E. Radford, Alison E. Ashcroft
Rapid Communications in Mass Spectrometry (2006) 20(11): 1628-1636

Heat Shock Protects Cardiac Cells From Doxorubicin-Induced Toxicity By Activating p38MAPK and Phosphorylation of Small Heat Shock Protein 27
Venkatakrishnan CD, Tewari AK, Moldovan L, Cardounel AJ, Zweier JL, Kuppusamy P, Ilangovan G
Am J Physiol Heart Circ Physiol Early Edition: published 16-Jun-2006

Proteomic signature of human embryonic stem cells
Hossein Baharvand, Mohsen Hajheidari, Saeid Kazemi Ashtiani, Ghasem Hosseini Salekdeh
PROTEOMICS (2006) 6(12): 3544-3549

Proteomic analysis of differential protein expression in atherosclerosis
Sung HJ, Ryang YS, Jang SW, Lee CW, Han KH, Ko J
Biomarkers (2006) 11(3): 279-90

Label-free Semiquantitative Peptide Feature Profiling of Human Breast Cancer and Breast Disease Sera via Two-dimensional Liquid Chromatography-Mass Spectrometry
Qinhua Cindy Ru, Luwang Andy Zhu, Jordan Silberman, and Craig D. Shriver
Mol Cell Proteomics (2006) 5(6): 1095-1104

A proteomic analysis reveals the loss of expression of the cell death regulatory gene GRIM-19 in human renal cell carcinomas
Alchanati I, Nallar SC, Sun P, Gao L, Hu J, Stein A, Yakirevich E, Konforty D, Alroy I, Zhao X, Reddy SP, Resnick MB, Kalvakolanu DV
Oncogene Early Edition: published 29-May-2006

Identification of Cellular Factors Associated with the 3'-Nontranslated Region of the Hepatitis C Virus Genome
Dylan Harris, Zhengbin Zhang, Binay Chaubey, and Virendra N. Pandey
Mol Cell Proteomics (2006) 5(6): 1006-1018

Cleavage of endoplasmic reticulum proteins in hepatocellular carcinoma: detection of generated fragments in patient sera
Chignard N, Shang S, Wang H, Marrero J, Brechot C, Hanash S, Beretta L
Gastroenterology (2006) 130(7): 2010-22

A proteomic analysis of liver mitochondria during acute endotoxemia
Crouser ED, Julian MW, Huff JE, Mandich DV, Green-Church KB
Intensive Care Med Early Edition: published 2-Jun-2006

Altered Levels of Acute Phase Proteins in the Plasma of Patients with Schizophrenia
Yang Y, Wan C, Li H, Zhu H, La Y, Xi Z, Chen Y, Jiang L, Feng G, He L
Anal Chem (2006) 78(11): 3571-3576

Coordination of nuclear- and mitochondrial-DNA encoded proteins in cancer and normal colon tissues
Mazzanti R, Giulivi C
Biochim Biophys Acta Early Edition: published 20-Apr-2006

Biomarker and drug-target discovery using proteomics in a new rat model of sepsis-induced acute renal failure
Holly MK, Dear JW, Hu X, Schechter AN, Gladwin MT, Hewitt SM, Yuen PS, Star RA
Kidney Int Early Edition: published 7-Jun-2006

Identification of serum biomarkers for colon cancer by proteomic analysis
Ward DG, Suggett N, Cheng Y, Wei W, Johnson H, Billingham LJ, Ismail T, Wakelam MJ, Johnson PJ, Martin A
Br J Cancer Early Edition: published 6-Jun-2006

From Gene Expression Analysis to Tissue Microarrays: A Rational Approach to Identify Therapeutic and Diagnostic Targets in Lymphoid Malignancies
Sara Ek, Ulrika Andreasson, Sophia Hober, Caroline Kampf, Fredrik Ponten, Mathias Uhlen, Hartmut Merz, and Carl A. K. Borrebaeck
Mol Cell Proteomics (2006) 5(6): 1072-1081

Proteomics of acute myeloid leukaemia: cytogenetic risk groups differ specifically in their proteome, interactome and post-translational protein modifications
Balkhi MY, Trivedi AK, Geletu M, Christopeit M, Bohlander SK, Behre HM, Behre G
Oncogene Early Edition: published 29-May-2006

Protein expression profile in the striatum of acute methamphetamine-treated rats
Iwazaki T, McGregor IS, Matsumoto I
Brain Res Early Edition: published 23-May-2006

Serum proteome profiles identifies parathyroid hormone physiologic response
Agasanur K. Prahalad, Robert J. Hickey, Jeffrey Huang, Derek J. Hoelz, Lacey Dobrolecki, Sreemala Murthy, Therry Winata, Janet M. Hock
PROTEOMICS (2006) 6(12): 3482-3493

Sampling and analytical strategies for biomarker discovery using mass spectrometry
Conrads TP, Hood BL, Veenstra TD
Biotechniques (2006) 40(6): 799-805

Quantitative and qualitative differences in protein expression between papillary thyroid carcinoma and normal thyroid tissue
Brown LM, Helmke SM, Hunsucker SW, Netea-Maier RT, Chiang SA, Heinz DE, Shroyer KR, Duncan MW, Haugen BR
Mol Carcinog Early Edition: published 20-Jun-2006

Salicylate modulates oxidative stress in the rat colon: A proteomic approach
Drew JE, Padidar S, Horgan G, Duthie GG, Russell WR, Reid M, Duncan G, Rucklidge GJ
Biochem Pharmacol Early Edition: published 27-Apr-2006

Proteomic Analysis of Colorectal Cancer Reveals Alterations in Metabolic Pathways: Mechanism of Tumorigenesis
Xuezhi Bi, Qingsong Lin, Tet Wei Foo, Shashikant Joshi, Tao You, Han-Ming Shen, Choon Nam Ong, Peh Yean Cheah, Kong Weng Eu, and Choy-Leong Hew
Mol Cell Proteomics (2006) 5(6): 1119-1130

Proteomic Analysis of Mitochondria-to-Nucleus Retrograde Response in Human Cancer
Kulawiec M, Arnouk H, Desouki MM, Kazim L, Still I, Singh KK
Cancer Biol Ther Early Edition: published 2-Aug-2006

SAP Deficiency Results in a Striking Alteration of the Protein Profile in Activated CD4 T Cells
Cris Kamperschroer , Susan L. Swain , Thomas Grussenmeyer, and Ivan Lefkovits
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/16/2006

Periplaneta americana Arginine Kinase as a Major Cockroach Allergen among Thai Patients with Major Cockroach Allergies
Sookrung N, Chaicumpa W, Tungtrongchitr A, Vichyanond P, Bunnag C, Ramasoota P, Tongtawe P, Sakolvaree Y, Tapchaisri P
Environ Health Perspect (2006) 114(6): 875-80

Urinary oxytocin as a non-invasive biomarker for neurohypophyseal hormone secretion
Polito AB 3rd, Goldstein DL, Sanchez L, Cool DR, Morris M
Peptides Early Edition: published 17-Jun-2006

2-Dimensional gel electrophoresis and MALDI-MS of cystic cervical metastasis from head and neck squamous cell carcinoma
Beer HL, Jenkins RE, Gutowska-Owsiak D, Pazmany L, Birchall MA, Kitteringham NR
Clin Otolaryngol (2006) 31(3): 246

Analysis of potential diagnostic biomarkers in cerebrospinal fluid of idiopathic normal pressure hydrocephalus by proteomics
Li X, Miyajima M, Mineki R, Taka H, Murayama K, Arai H
Acta Neurochir (Wien) Early Edition: published 6-Jun-2006

Proteomic profiling of lipid droplet proteins in hepatoma cell lines expressing hepatitis C virus core protein
Sato S, Fukasawa M, Yamakawa Y, Natsume T, Suzuki T, Shoji I, Aizaki H, Miyamura T, Nishijima M
J Biochem (Tokyo) (2006) 139(5): 921-30

Investigation of differentially expressed proteins in rat gastrocnemius muscle during denervation-reinnervation
Sun H, Liu J, Ding F, Wang X, Liu M, Gu X
J Muscle Res Cell Motil Early Edition: published 4-Jun-2006

Use of proteomic analysis of endometriosis to identify different protein expression in patients with endometriosis versus normal controls
Zhang H, Niu Y, Feng J, Guo H, Ye X, Cui H
Fertil Steril Early Edition: published 31-May-2006

Proteomic analysis of opsins and thyroid hormone-induced retinal development using isotope-coded affinity tags (ICAT) and mass spectrometry
Allison WT, Veldhoen KM, Hawryshyn CW
Mol Vis (2006) 12: 655-72.

Proteomics: applications to the study of rheumatoid arthritis and osteoarthritis
Gobezie R, Millett PJ, Sarracino DS, Evans C, Thornhill TS
J Am Acad Orthop Surg (2006) 14(6): 325-32

Production and Proteomic Characterization of Pharmaceutical-Grade Dermatophagoides pteronyssinus and Dermatophagoides farinae Extracts for Allergy Vaccines
Batard T, Hrabina A, Bi XZ, Chabre H, Lemoine P, Couret MN, Faccenda D, Villet B, Harzic P, Andre F, Goh SY, Andre C, Chew FT, Moingeon P
Int Arch Allergy Immunol (2006) 140(4): 295-305

Changes of the cortex proteome and Apolipoprotein E in transgenic mouse models of Alzheimer's Disease
Carrette O, Burgess JA, Burkhard PR, Lang C, Cote M, Rodrigo N, Hochstrasser DF, Sanchez JC
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 15-Jun-2006

Urinary Proteome of Steroid-Sensitive and Steroid-Resistant Idiopathic Nephrotic Syndrome of Childhood
Woroniecki RP, Orlova TN, Mendelev N, Shatat IF, Hailpern SM, Kaskel FJ, Goligorsky MS, O'riordan E
Am J Nephrol (2006) 26(3): 258-267

Nonribosomal cyclic peptides: specific markers of fungal infections
Alexandr Jegorov, Marian Hajduch, Miroslav Sulc, Vladimir Havlicek
Journal of Mass Spectrometry (2006) 41(5): 563-576

Comparative proteomic analysis with postmortem prefrontal cortex tissues of suicide victims versus controls
Schlicht K, Buttner A, Siedler F, Scheffer B, Zill P, Eisenmenger W, Ackenheil M, Bondy B
J Psychiatr Res Early Edition: published 2-Jun-2006

Identification of Brain Cell Death Associated Proteins in Human Post-mortem Cerebrospinal Fluid
Jennifer A. Burgess, # Pierre Lescuyer, # Alexandre Hainard, Pierre R. Burkhard, Natacha Turck, Philippe Michel, Joël S. Rossier, Frédéric Reymond, Denis F. Hochstrasser, and Jean-Charles Sanchez
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Disease-specific Proteins from Rheumatoid Arthritis Patients
Kim CW, Cho EH, Lee YJ, Kim YH, Hah YS, Kim DR
J Korean Med Sci (2006) 21(3): 478-84

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Eukaryotic Cells And Tissues

Unravelling the proteome of formalin-fixed paraffin-embedded tissue
Brian L. Hood, Thomas P. Conrads, and Timothy D. Veenstra
Brief Funct Genomic Proteomic (2006) 5(2): 169-175

Large-scale identification of cytosolic mouse brain proteins by chromatographic prefractionation
Shin JH, Krapfenbauer K, Lubec G
Electrophoresis Early Edition: published 1-Jun-2006

Studying fertilization in cell-free extracts: Focusing on membrane/lipid raft functions and proteomics
Sato K, Yoshino K, Tokmakov AA, Iwasaki T, Yonezawa K, Fukami Y
Methods Mol Biol (2006) 322: 395-411

A Novel Fixative Improves Opportunities of Nucleic Acids and Proteomic Analysis in Human Archive's Tissues
Stanta G, Mucelli SP, Petrera F, Bonin S, Bussolati G
Diagn Mol Pathol (2006) 15(2): 115-123

Characterization of proteome of human cerebrospinal fluid
Xu J, Chen J, Peskind ER, Jin J, Eng J, Pan C, Montine TJ, Goodlett DR, Zhang J
Int Rev Neurobiol (2006) 73: 29-98

Enhanced sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS/MS
Roger G. Biringer, Heidi Amato, Michael G. Harrington, Alfred N. Fonteh, James N. Riggins, and Andreas F. R. Huhmer
Brief Funct Genomic Proteomic (2006) 5(2): 144-153

Proteomic analysis of cartilage- and bone-associated samples
Lammi MJ, Hayrinen J, Mahonen A
Electrophoresis Early Edition: published 1-Jun-2006

Proteomic Analysis on the Alteration of Protein Expression in the Placental Villous Tissue of Early Pregnancy Loss
Liu AX, Jin F, Zhang WW, Zhou TH, Zhou CY, Yao WM, Qian YL, Huang HF
Biol Reprod Early Edition: published 31-May-2006

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Prokaryotes

MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome
Samyn B, Sergeant K, Memmi S, Debyser G, Devreese B, Van Beeumen J
Electrophoresis Early Edition: published 1-Jun-2006

Identification, Recombinant Expression, Immunolocalization in Macrophages, and T-Cell Responsiveness of the Major Extracellular Proteins of Francisella tularensis
Lee BY, Horwitz MA, Clemens DL
Infect Immun (2006) 74(7): 4002-13

Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter
Rueichi R. Gan, Eugene C. Yi, Yulun Chiu, Hookeun Lee, Yu-chieh P. Kao, Timothy H. Wu, Ruedi Aebersold, David R. Goodlett, and Wailap Victor Ng
Mol Cell Proteomics (2006) 5(6): 987-997

Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34
Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B, Mergeay M, Taghavi S, van der Lelie D, Vallaeys T
Microbiology (2006) 152(Pt 6): 1765-76

Shotgun proteomics of cyanobacteria--applications of experimental and data-mining techniques
Martin E. Barrios-Llerena, Poh Kuan Chong, Chee Sian Gan, Ambrosius P. L. Snijders, Kenneth F. Reardon, and Phillip C. Wright
Brief Funct Genomic Proteomic (2006) 5(2): 121-132

A Proteome Reference Map and Proteomic Analysis of Bifidobacterium longum NCC2705
Jing Yuan, Li Zhu, Xiankai Liu, Ting Li, Ying Zhang, Tianyi Ying, Bin Wang, Junjun Wang, Hua Dong, Erling Feng, Qiang Li, Jie Wang, Hongxia Wang, Kaihua Wei, Xuemin Zhang, Cuifeng Huang, Peitang Huang, Liuyu Huang, Ming Zeng, and Hengliang Wang
Mol Cell Proteomics (2006) 5(6): 1105-1118

Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO
Brook L. Nunn, Scott A. Shaffer, Alexander Scherl, Byron Gallis, Manhong Wu, Samuel I. Miller, and David R. Goodlett
Brief Funct Genomic Proteomic (2006) 5(2): 154-168

In vivo proteomic analysis of the intracellular bacterial pathogen, Francisella tularensis, isolated from mouse spleen
Twine SM, Mykytczuk NC, Petit MD, Shen H, Sjostedt A, Wayne Conlan J, Kelly JF
Biochem Biophys Res Commun Early Edition: published 19-May-2006

Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress
Steven D. Brown, Melissa R. Thompson, Nathan C. VerBerkmoes, Karuna Chourey, Manesh Shah, Jizhong Zhou, Robert L. Hettich, and Dorothea K. Thompson
Mol Cell Proteomics (2006) 5(6): 1054-1071

Protein-Protein Interactions among Helicobacter pylori Cag Proteins
Busler VJ, Torres VJ, McClain MS, Tirado O, Friedman DB, Cover TL
J Bacteriol (2006) 188(13): 4787-800

Comparative Proteome Analysis of Laboratory Grown Brucella abortus 2308 and Brucella melitensis 16M
Michel Eschenbrenner, Troy A. Horn, Mary Ann Wagner, Cesar V. Mujer, Tabbi L. Miller-Scandle, and Vito G. DelVecchio
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/09/2006

Proteomic Analysis of Campylobacter jejuni 11168 Biofilms Reveals a Role for the Motility Complex in Biofilm Formation
Kalmokoff M, Lanthier P, Tremblay TL, Foss M, Lau PC, Sanders G, Austin J, Kelly J, Szymanski CM
J Bacteriol (2006) 188(12): 4312-20

Serologic Proteome Analysis of Borrelia burgdorferi Membrane-Associated Proteins
Nowalk AJ, Gilmore RD Jr, Carroll JA
Infect Immun (2006) 74(7): 3864-73

The proteome of Mannheimia succiniciproducens, a capnophilic rumen bacterium
Jeong Wook Lee, Sang Yup Lee, Hyohak Song, Jong-Shin Yoo
PROTEOMICS (2006) 6(12): 3550-3566

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Pharmacology and Toxicology

Phenotypic anchoring of arsenic and cadmium toxicity in three hepatic-related cell systems reveals compound- and cell-specific selective up-regulation of stress protein expression: Implications for fingerprint profiling of cytotoxicity
Gottschalg E, Moore NE, Ryan AK, Travis LC, Waller RC, Pratt S, Atmaca M, Kind CN, Fry JR
Chem Biol Interact Early Edition: published 24-May-2006

An automated and fully validated LC-MS/MS procedure for the simultaneous determination of 11 opioids used in palliative care, with 5 of their metabolites
F. Musshoff, J. Trafkowski, U. Kuepper, B. Madea
Journal of Mass Spectrometry (2006) 41(5): 633-640

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Protein Array

In-Gel Isoelectric Focusing of Peptides as a Tool for Improved Protein Identification
Jeroen Krijgsveld, Sharon Gauci, Wilma Dormeyer, and Albert J. R. Heck
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/09/2006

An ELISA-based procedure for assaying proteins in digests of human leukocytes and cell lines, using specifically selected peptides and appropriate antibodies
Braitbard O, Bishara-Shieban J, Glickstein H, Kott-Gutkowski M, Pace U, Rund DG, Stein WD
Proteome Sci (2006) 4(1): 14

Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting
Sun H, Chattopadhaya S, Wang J, Yao SQ
Anal Bioanal Chem Early Edition: published 22-Jun-2006

Activity-based proteomics: enzymatic activity profiling in complex proteomes
Schmidinger H, Hermetter A, Birner-Gruenberger R
Amino Acids (2006) 30(4): 333-50

Comparison of Ovalbumin Quantification Using Forward-Phase Protein Microarrays and Suspension Arrays
L. Wang, K. D. Cole, Hua-Jun He, D. K. Hancock, A. K. Gaigalas, and Y. Zong
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Analytical platforms for activity-based protein profiling - exploiting the versatility of chemistry for functional proteomics
Sieber SA, Cravatt BF
Chem Commun (Camb) (2006) (22): 2311-9.

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Protein Characterization / PTMs

Phospho-proteomic analysis of cellular signaling
de Graauw M, Hensbergen P, van de Water B
Electrophoresis Early Edition: published 1-Jun-2006

A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases
Adrian D. Hegeman, Miguel Rodriguez, Byung Woo Han, Yuichi Uno, George N. Phillips Jr., Estelle M. Hrabak, John C. Cushman, Jeff F. Harper, Alice C. Harmon, Michael R. Sussman
PROTEOMICS (2006) 6(12): 3649-3664

Absolute Quantification of Multisite Phosphorylation by Selective Reaction Monitoring Mass Spectrometry: Determination of Inhibitory Phosphorylation Status of Cyclin-Dependent Kinases
Viveka Mayya, Karim Rezual, Linfeng Wu, Michael B. Fong, and David K. Han
Mol Cell Proteomics (2006) 5(6): 1146-1157

Algal toxins as guidance to identify phosphoproteins with key roles in apoptotic cell death
Solstad T, Fladmark KE
Curr Pharm Biotechnol (2006) 7(3): 209-15

Glycoproteomic Survey of Mammillaria gracillis Tissues Grown in Vitro
Biljana Balen, Marijana Krsnik-Rasol, Alina D. Zamfir, Jadranka Milo evi , Sergey Y. Vakhrushev, and Jasna Peter-Katalini
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Profiling of Glycans in Serum for the Discovery of Potential Biomarkers for Ovarian Cancer
Hyun Joo An, Suzanne Miyamoto, Katherine S. Lancaster, Crystal Kirmiz, Bensheng Li, Kit S. Lam, Gary S. Leiserowitz, and Carlito B. Lebrilla
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/02/2006

Characterizing phosphoproteins and phosphoproteomes using mass spectrometry
Goshe Michael B
Brief Funct Genomic Proteomic (2006) 4(4): 363-376

Bacterial glycoproteomics
Hitchen PG, Dell A
Microbiology (2006) 152(Pt 6): 1575-80

A Tagging-via-Substrate Technology for Genome-Wide Detection and Identification of Farnesylated Proteins
Chan Kim S, Kho Y, Barma D, Falck J, Zhao Y
Methods Enzymol (2005) 407: 629-37

Predicting O-glycosylation sites in mammalian proteins by using SVMs
Li S, Liu B, Zeng R, Cai Y, Li Y
Comput Biol Chem Early Edition: published 25-May-2006

Ultrasensitive Detection and Characterization of Posttranslational Modifications Using Surface-Enhanced Raman Spectroscopy
Sundararajan N, Mao D, Chan S, Koo TW, Su X, Sun L, Zhang J, Sung KB, Yamakawa M, Gafken PR, Randolph T, McLerran D, Feng Z, Berlin AA, Roth MB
Anal Chem (2006) 78(11): 3543-3550

Global analysis of protein palmitoylation in yeast
Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR 3rd, Davis NG
Cell (2006) 125(5): 1003-13

A Proteomic Screen Identified Stress-Induced Chaperone Proteins as Targets of Akt Phosphorylation in Mesangial Cells
Michelle T. Barati, Madhavi J. Rane, Jon B. Klein, and Kenneth R. McLeish
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/16/2006

Determination of the phosphorylation level and deamidation susceptibility of equine ?-casein
Jean-Michel Girardet, Laurent Miclo, Sabrina Florent, Daniel Moll�, Jean-Luc Gaillard
PROTEOMICS (2006) 6(12): 3707-3717

An online literature mining tool for protein phosphorylation
X. Yuan, Z. Z. Hu, H. T. Wu, M. Torii, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu
Bioinformatics (2006) 22(13): 1668-1669

Phosphoproteomic analysis of Her2/neu signaling and inhibition
Bose R, Molina H, Patterson AS, Bitok JK, Periaswamy B, Bader JS, Pandey A, Cole PA
Proc Natl Acad Sci U S A Early Edition: published 19-Jun-2006

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Protein-protein interaction

The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour
Pocklington AJ, Cumiskey M, Armstrong JD, Grant SG
Mol Syst Biol (2006) 2: 2006.0023

What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
Ekman D, Light S, Björklund Å, Elofsson A
Genome Biology (2006) 7(6): R45

Towards an understanding of kinesin-1 dependent transport pathways through the study of protein-protein interactions
Gindhart Joseph G
Brief Funct Genomic Proteomic (2006) 5(1): 74-86

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Quantitation

Quantitative Multiplexed C-Reactive Protein Mass Spectrometric Immunoassay
Urban A. Kiernan, Riccardo Addobbati, Dobrin Nedelkov, and Randall W. Nelson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/02/2006

Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics
Alyssa M. Redding, Aindrila Mukhopadhyay, Dominique C. Joyner, Terry C. Hazen, and Jay D. Keasling
Brief Funct Genomic Proteomic (2006) 5(2): 133-143

Absolute quantification of Atlantic salmon and rainbow trout vitellogenin by the ?signature peptide? approach using electrospray ionization QqToF tandem mass spectrometry
Alejandro M. Cohen, Atef A. H. Mansour, Joseph H. Banoub
Journal of Mass Spectrometry (2006) 41(5): 646-658

Shotgun proteomics using the iTRAQ isobaric tags
Kunal Aggarwal, Leila H. Choe, and Kelvin H. Lee
Brief Funct Genomic Proteomic (2006) 5(2): 112-120

Systematic Characterization of Nuclear Proteome during Apoptosis: A Quantitative Proteomic Study by Differential Extraction and Stable Isotope Labeling
Sun-Il Hwang, Deborah H. Lundgren, Viveka Mayya, Karim Rezaul, Ann E. Cowan, Jimmy K. Eng, and David K. Han
Mol Cell Proteomics (2006) 5(6): 1131-1145

Quantitative Analysis of Mitochondrial Protein Expression in Methylmalonic Acidemia by Two-Dimensional Difference Gel Electrophoresis
Eva Richard, Lucia Monteoliva, Silvia Juarez, Belén Pérez, Lourdes R. Desviat, Magdalena Ugarte, and Juan Pablo Albar
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

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Review

The nucleolus: reviewing oldies to have new understandings
Lo SJ, Lee CC, Lai HJ
Cell Res (2006) 16(6): 530-8

The characterization of stem cell proteomes
Vodicka P, Skalnikova H, Kovarova H
Curr Opin Mol Ther (2006) 8(3): 232-9

The Escherichia coli Proteome: Past, Present, and Future Prospects
Han MJ, Lee SY
Microbiol Mol Biol Rev (2006) 70(2): 362-439

Clinical Proteomics: A Novel Diagnostic Tool for the New Biology of Preterm Labor, Part I: Proteomics Tools
Buhimschi CS, Weiner CP, Buhimschi IA
Obstet Gynecol Surv (2006) 61(7): 481-486

Neuroproteomics - the tasks lying ahead
Becker M, Schindler J, Nothwang HG
Electrophoresis Early Edition: published 1-Jun-2006

Clinical proteomics: new trends for protein microarrays
Becker KF, Metzger V, Hipp S, Hofler H
Curr Med Chem (2006) 13(15): 1831-7

Developments in mass spectrometry for the analysis of complex protein mixtures
Gurusahai Khalsa-Moyers and William Hayes McDonald
Brief Funct Genomic Proteomic (2006) 5(2): 98-111

The subcellular localization of the mammalian proteome comes a fraction closer
Jeremy C Simpson and Rainer Pepperkok
Genome Biology (2006) 7(6): 213

A systems approach to model metastatic progression
Taylor BS, Varambally S, Chinnaiyan AM
Cancer Res (2006) 66(11): 5537-9

Proteomic and computational methods in systems modeling of cellular signaling
Kleppe R, Kjarland E, Selheim F
Curr Pharm Biotechnol (2006) 7(3): 135-45

Dependence of molecular properties on proteomic family for marketed oral drugs
Vieth M, Sutherland JJ
J Med Chem (2006) 49(12): 3451-3

Bacterial glycoproteomics
Hitchen PG, Dell A
Microbiology (2006) 152(Pt 6): 1575-80

Shotgun proteomics using the iTRAQ isobaric tags
Kunal Aggarwal, Leila H. Choe, and Kelvin H. Lee
Brief Funct Genomic Proteomic (2006) 5(2): 112-120

Mass spectrometry of RNA: linking the genome to the proteome
Meng Zhaojing, Limbach Patrick A
Brief Funct Genomic Proteomic (2006) 5(1): 87-95

From bio-molecular and technology innovations to clinical practice: focus on ovarian cancer
Legge F, Ferrandina G, Scambia G
Ann Oncol (2006) 17(Suppl 7): vii46-vii48

Proteomic-based biomarker discovery with emphasis on cerebrospinal fluid and multiple sclerosis
Berven FS, Flikka K, Berle M, Vedeler C, Ulvik RJ
Curr Pharm Biotechnol (2006) 7(3): 147-58

Proteomics of p53 in Diagnostics and Therapy of Acute Myeloid Leukemia
Nensen N, Haaland I, D'Santos C, Van Belle W, Gjertsen BT
Curr Pharm Biotechnol (2006) 7(3): 199-207

Phospho-proteomic analysis of cellular signaling
de Graauw M, Hensbergen P, van de Water B
Electrophoresis Early Edition: published 1-Jun-2006

Proteomics and laser microdissection
McGregor E, De Souza A
Methods Mol Biol (2006) 333: 291-304

Proteomic exploration of the Wnt/beta-catenin pathway
Tian Q
Curr Opin Mol Ther (2006) 8(3): 191-7

Assessment of the catabolic effects of interleukin-1beta on proteoglycan metabolism in equine cartilage cocultured with synoviocytes
Gregg AJ, Fortier LA, Mohammed HO, Mayr KG, Miller BJ, Haupt JL
Am J Vet Res (2006) 67(6): 957-62

Sampling and analytical strategies for biomarker discovery using mass spectrometry
Conrads TP, Hood BL, Veenstra TD
Biotechniques (2006) 40(6): 799-805

Proteomics Approaches to Elucidate Oncogenic Tyrosine Kinase Signaling in Myeloid Malignancies
Oveland E, Fladmark KE, Wergeland L, Gjertsen BT, Hovland R
Curr Pharm Biotechnol (2006) 7(3): 185-198

A human protein atlas based on antibody proteomics
Persson A, Hober S, Uhlen M
Curr Opin Mol Ther (2006) 8(3): 185-90

Mass spectrometry technologies for proteomics
Canas Benito, Lopez-Ferrer Daniel, Ramos-Fernandez Antonio, Camafeita Emilio, Calvo Enrique
Brief Funct Genomic Proteomic (2006) 4(4): 295-320

Differential mitochondrial protein expression profiling in neurodegenerative diseases
Gillardon F
Electrophoresis Early Edition: published 1-Jun-2006

Proteomic Strategies for Individualizing Therapy of Acute Myeloid Leukemia (AML)
Sj holt G, Bedringaas SL, D skeland AP, Gjertsen BT
Curr Pharm Biotechnol (2006) 7(3): 159-170

The role of mass spectrometry in biomarker discovery and measurement
Ackermann BL, Hale JE, Duffin KL
Curr Drug Metab (2006) 7(5): 525-39

Cancer proteomics and its application to discovery of therapy response markers in human cancer
Smith L, Lind MJ, Welham KJ, Cawkwell L
Cancer Early Edition: published 2-Jun-2006

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Methodology

Top-down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry
Satoko Akashi, Koichi Suzuki, Akihiro Arai, Naoyuki Yamada, Ei-Ichiro Suzuki, Kazuo Hirayama, Shin Nakamura, Yoshifumi Nishimura
Rapid Communications in Mass Spectrometry (2006) 20(12): 1932-1938

Solid-Phase Extraction and Elution on Diamond (SPEED): A Fast and General Platform for Proteome Analysis with Mass Spectrometry
Wei-Hao Chen, Sheng-Chung Lee, Sahadevan Sabu, Huei-Chun Fang, Shu-Chien Chung, Chau-Chung Han, and Huan-Cheng Chang
ANALYTICAL CHEMISTRY (2006) 78(12): 4228-4234

Purification and fractionation of membranes for proteomic analyses
Marmagne A, Salvi D, Rolland N, Ephritikhine G, Joyard J, Barbier-Brygoo H
Methods Mol Biol (2006) 323: 403-20

Protein isolation and second-dimension electrophoretic separation
Schlesier B, Mock HP
Methods Mol Biol (2006) 323: 381-91

N-terminal H3/D3-acetylation for improved high-throughput peptide sequencing by matrix-assisted laser desorption/ionization mass spectrometry with a time-of-flight/time-of-flight analyzer
Marek J. Noga, Arndt Asperger, Jerzy Silberring
Rapid Communications in Mass Spectrometry (2006) 20(12): 1823-1827

A Novel Fixative Improves Opportunities of Nucleic Acids and Proteomic Analysis in Human Archive's Tissues
Stanta G, Mucelli SP, Petrera F, Bonin S, Bussolati G
Diagn Mol Pathol (2006) 15(2): 115-123

Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes
Lawson EL, Clifton JG, Huang F, Li X, Hixson DC, Josic D
Electrophoresis Early Edition: published 1-Jun-2006

Enhancing Electrospray Ionization Efficiency of Peptides by Derivatization
Hamid Mirzaei and Fred Regnier
ANALYTICAL CHEMISTRY (2006) 78(12): 4175-4183

A universal and rapid protocol for protein extraction from recalcitrant plant tissues for proteomic analysis
Wang W, Vignani R, Scali M, Cresti M
Electrophoresis Early Edition: published 29-May-2006

Synthesis and evaluation of fluorogenic reagents for simultaneous detection of peptides and proteins by HPLC in two different samples
Saimaru H, Yasui E, Takamura N, Imai K
Biomed Chromatogr (2006) 20(6-7): 576-584

Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT)
Dieterich DC, Link AJ, Graumann J, Tirrell DA, Schuman EM
Proc Natl Acad Sci U S A Early Edition: published 12-Jun-2006

Two-dimensional difference gel electrophoresis
Wu TL
Methods Mol Biol (2006) 328: 71-95

Protein separations
Chow AW
Methods Mol Biol (2006) 339: 145-58

Quality Control Metrics for LC-MS Feature Detection Tools Demonstrated on Saccharomyces cerevisiae Proteomic Profiles
Brian D. Piening, Pei Wang, Chaitanya S. Bangur, Jeffrey Whiteaker, Heidi Zhang, Li-Chia Feng, John F. Keane, Jimmy K. Eng, Hua Tang, Amol Prakash, Martin W. McIntosh, and Amanda Paulovich
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/02/2006

Unravelling the proteome of formalin-fixed paraffin-embedded tissue
Brian L. Hood, Thomas P. Conrads, and Timothy D. Veenstra
Brief Funct Genomic Proteomic (2006) 5(2): 169-175

Multiplexed Two-Dimensional Liquid Chromatography for MALDI and Nanoelectrospray Ionization Mass Spectrometry in Proteomics
Haruna Saito, Yoshiya Oda, Toshitaka Sato, Junro Kuromitsu, and Yasushi Ishihama
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Interdomain Conformational Changes in Akt Activation Revealed by Chemical Cross-linking and Tandem Mass Spectrometry
Bill X. Huang and Hee-Yong Kim
Mol Cell Proteomics (2006) 5(6): 1045-1053

Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling
Simpson DC, Ahn S, Pasa-Tolic L, Bogdanov B, Mottaz HM, Vilkov AN, Anderson GA, Lipton MS, Smith RD
Electrophoresis Early Edition: published 29-May-2006

Ultra-fast tandem mass spectrometry scanning combined with monolithic column liquid chromatography increases throughput in proteomic analysis
Batycka M, Inglis NF, Cook K, Adam A, Fraser-Pitt D, Smith DG, Main L, Lubben A, Kessler BM
Rapid Commun Mass Spectrom (2006) 20(14): 2074-2080

Enhanced detection of sulfo-peptides as onium salts in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Masaaki Ueki, Miyuki Yamaguchi
Rapid Communications in Mass Spectrometry (2006) 20(11): 1615-1620

Increased Protein Yields from Escherichia coli Using Pressure-Cycling Technology
Smejkal GB, Robinson MH, Lawrence NP, Tao F, Saravis CA, Schumacher RT
J Biomol Tech (2006) 17(2): 173-5

Phosphopeptides enrichment using on-line two-dimensional strong cation exchange followed by reversed-phase liquid chromatography/mass spectrometry
Lim KB, Kassel DB
Anal Biochem Early Edition: published 11-May-2006

Chemical proteomics profiling of proteasome activity
Verdoes M, Berkers CR, Florea BI, van Swieten PF, Overkleeft HS, Ovaa H
Methods Mol Biol (2006) 328: 51-69

Capillary electrophoresis for the analysis of glycoprotein pharmaceuticals
Satoru Kamoda, Kazuaki Kakehi
ELECTROPHORESIS (2006) 27(12): 2495-2504

Prefractionation by Digitonin Extraction Increases Representation of the Cytosolic and Intracellular Proteome of Leishmania infantum
Aude L. Foucher, Barbara Papadopoulou, and Marc Ouellette
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

Proteomic analysis by multidimensional protein identification technology
Florens L, Washburn MP
Methods Mol Biol (2006) 328: 159-75

Advancing proteomics with ion/ion chemistry
Good DM, Coon JJ
Biotechniques (2006) 40(6): 783-9

Proteome-level display by 2-dimensional chromatography of extracellular matrix-dependent modulation of the phenotype of bladder cancer cells
Hurst R, Kyker K, Dozmorov M, Takemori N, Singh A, Matsumoto H, Saban R, Betgovargez E, Simonian M
Proteome Sci (2006) 4: 13

pH Dependency of the Carboxyl Oxygen Exchange Reaction Catalyzed by Lysyl Endopeptidase and Trypsin
Dagmar Hajkova, K. C. Sekhar Rao, and Masaru Miyagi
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/02/2006

Derivatisation of arginine residues with malondialdehyde for the analysis of peptides and protein digests by LC-ESI-MS/MS
Alexandra Foettinger, Alexander Leitner, Wolfgang Lindner
Journal of Mass Spectrometry (2006) 41(5): 623-632

Comparative studies on the analysis of urinary trypsin inhibitor (ulinastatin) preparations
Yu-ki Matsuno, Hitomi Nakamura, Kazuaki Kakehi
ELECTROPHORESIS (2006) 27(12): 2486-2494

Material-Enhanced Laser Desorption/Ionization (MELDI)-A New Protein Profiling Tool Utilizing Specific Carrier Materials for Time of Flight Mass Spectrometric Analysis
Feuerstein I, Najam-Ul-Haq M, Rainer M, Trojer L, Bakry R, Aprilita NH, Stecher G, Huck CW, Bonn GK, Klocker H, Bartsch G, Guttman A
J Am Soc Mass Spectrom Early Edition: published 10-Jun-2006

N-Terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: A mass spectrometry technique for N-terminus identification
Chacon A, Masterson DS, Yin H, Liebler DC, Porter NA
Bioorg Med Chem Early Edition: published 17-Jun-2006

On-chip protein synthesis for making microarrays
Ramachandran N, Hainsworth E, Demirkan G, LaBaer J
Methods Mol Biol (2006) 328: 1-14

Continuous-Flow pI-Based Sorting of Proteins and Peptides in a Microfluidic Chip Using Diffusion Potential
Song YA, Hsu S, Stevens AL, Han J
Anal Chem (2006) 78(11): 3528-36

Use of surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) to study protein expression in a rat model of cocaine withdrawal
Geng T, Seitz PK, Thomas ML, Xu B, Soman KV, Kurosky A, Luxon BA, Cunningham KA
J Neurosci Methods Early Edition: published 9-Jun-2006

Implementation of Ion/Ion Reactions in a Quadrupole/Time-of-Flight Tandem Mass Spectrometer
Yu Xia, Paul A. Chrisman, David E. Erickson, Jian Liu, Xiaorong Liang, Frank A. Londry, Min J. Yang, and Scott A. McLuckey
ANALYTICAL CHEMISTRY (2006) 78(12): 4146-4154

Evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls
Feiz L, Irshad M, Pont-Lezica RF, Canut H, Jamet E
Plant Methods (2006) 2(1): 10

Studying the Protein Organization of the Postsynaptic Density by a Novel Solid Phase- and Chemical Cross-linking-based Technology
Szu-Heng Liu, Huei-Hsuan Cheng, San-Yuan Huang, Pei-Chun Yiu, and Yen-Chung Chang
Mol Cell Proteomics (2006) 5(6): 1019-1032

SwePep, a Database Designed for Endogenous Peptides and Mass Spectrometry
Maria Falth, Karl Skold, Mathias Norrman, Marcus Svensson, David Fenyo, and Per E. Andren
Mol Cell Proteomics (2006) 5(6): 998-1005

Isotope-coded affinity tags for protein quantification
Colangelo CM, Williams KR
Methods Mol Biol (2006) 328: 151-8

Isolation of nuclear proteins
Calikowski TT, Meier I
Methods Mol Biol (2006) 323: 393-402

Protein microsequencing
Paradela A, Albar JP
Methods Mol Biol (2006) 323: 421-9

Efficient High-Throughput Discovery of Large Peptidic Hormones and Biomarkers
Steven W. Taylor, Nancy L. Andon, James M. Bilakovics, Carolyn Lowe, Michael R. Hanley, Richard Pittner, and Soumitra S. Ghosh
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/09/2006

High-throughput affinity mass spectrometry
Kiernan UA, Nedelkov D, Niederkofler EE, Tubbs KA, Nelson RW
Methods Mol Biol (2006) 328: 141-50

Development of capillary electrophoresis methods for quantitative determination of taurine in vehicle system and biological media
Dayse. L. P. da Silva, Hans H. R�ttinger, Yahia Mrestani, Walter F. Baum, Reinhard H. H. Neubert
ELECTROPHORESIS (2006) 27(12): 2330-2337

An improved procedure for Percoll gradient separation of sporogonial stages in Encephalitozoon cuniculi (Microsporidia)
Taupin V, Metenier G, Vivares CP, Prensier G
Parasitol Res Early Edition: published 1-Jun-2006

Capillary electrophoresis of peptides and proteins with plug of Pluronic gel
Sedlakova P, Svobodova J, Miksik I
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 30-May-2006

Resampling and deconvolution of linear time-of-flight records for enhanced protein profiling
Dariya I. Malyarenko, William E. Cooke, Eugene R. Tracy, Richard R. Drake, Susanna Shin, O. John Semmes, Maciek Sasinowski, Dennis M. Manos
Rapid Communications in Mass Spectrometry (2006) 20(11): 1670-1678

Protein Separation and Characterization by np-RP-HPLC Followed by Intact MALDI-TOF Mass Spectrometry and Peptide Mass Mapping Analyses
Claire Dauly, David H. Perlman, Catherine E. Costello, and Mark E. McComb
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/23/2006

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Books

Handbook of Isoelectric Focusing and Proteomics. By David Garfin and Satinder Ahuja (Eds.)
Marco Monopoli
PROTEOMICS (2006) 6(12): 3728

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Other

Capturing cellular machines by systematic screens of protein complexes
Gagneur J, David L, Steinmetz LM
Trends Microbiol Early Edition: published 15-Jun-2006

Current literature in mass spectrometry
John Wiley & Sons, Ltd
Journal of Mass Spectrometry (2006) 41(5): 693-704

Serum Proteomic Profiling by Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry for Cancer Diagnosis: Next Steps
Diamandis EP
Cancer Res (2006) 66(11): 5540-1

Lipid mediator informatics and proteomics in inflammation resolution
Lu Y, Hong S, Gotlinger K, Serhan CN
ScientificWorldJournal (2006) 6: 589-614.

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