SPS' Digest

Issue 33, 3-Aug-2006

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Quick jumps to articles in: Bioinformatics (21) / Biological applications (29) / Biomedical and clinical applications (42) / Eukaryotic Cells And Tissues (13) / Prokaryotes (10) / Pharmacology and Toxicology (3) / Protein Array (2) / Protein Characterization - PTMs (16) / Protein-protein interaction (3) / Quantitation (4) / Review (23) / Methodology (28) / Meeting (1) / Other (6) /

In this issue, 192 articles have been selected from:

Acta Otolaryngol, Volume 126, Issue 8, 2006 (1 article)
Am J Med Genet C Semin Med Genet, Early Edition, 12-Jul-2006 (1 article)
Anal Bioanal Chem, Early Edition, 8-Jul-2006 (1 article)
Anal Chem, Volume 78, Issues 13+14, 2006 (14 articles)
Ann N Y Acad Sci, Volume 1067, 2006 (1 article)
Anticancer Res, Volume 26, Issue 3A, 2006 (1 article)
BMC Bioinformatics, Volume 7, Issue 1, 2006 (1 article)
BMC Microbiol, Volume 6, Issue 1, 2006 (1 article)
Biochem Biophys Res Commun, Early Edition, 21-Jun-2006->30-Jun-2006 (2 articles)
Biochemistry, Volume 45, Issue 26, 2006 (1 article)
Biochim Biophys Acta, Early Edition, 16-May-2006->19-May-2006 (2 articles)
Biochimie, Early Edition, 22-Jun-2006 (1 article)
Bioconjug Chem, Volume 17, Issue 4, 2006 (1 article)
Bioinformatics, Early Edition, 14-Jul-2006 (1 article)
Bioinformatics, Volume 22, Issue 14, 2006 (4 articles)
Biotechnol Bioeng, Early Edition, 28-Jun-2006 (1 article)
Brain Res, Early Edition, 22-Jun-2006 (1 article)
Brief Funct Genomic Proteomic, Volume 5, Issue 2, 2006 (1 article)
Cancer Epidemiol Biomarkers Prev, Volume 15, Issue 7, 2006 (1 article)
Cell Mol Biol Lett, Early Edition, 20-Jun-2006 (1 article)
Cell Mol Biol Lett, Volume 11, Issue 2, 2006 (1 article)
Cell Mol Life Sci, Early Edition, 17-Jul-2006 (1 article)
Cell Signal, Early Edition, 24-May-2006 (1 article)
Cell, Volume 126, Issue 1, 2006 (1 article)
Chem Res Toxicol, Volume 19, Issue 7, 2006 (1 article)
Circ Res, Early Edition, 20-Jul-2006 (2 articles)
Clin Cancer Res, Volume 12, Issue 14, 2006 (1 article)
Clin Chem, Early Edition, 13-Jul-2006->29-Jun-2006 (2 articles)
Comb Chem High Throughput Screen, Volume 9, Issue 6, 2006 (1 article)
Curr Microbiol, Early Edition, 10-Jul-2006 (1 article)
Curr Opin Chem Biol, Early Edition, 3-Jul-2006 (1 article)
Curr Opin Struct Biol, Early Edition, 3-Jul-2006 (1 article)
Curr Top Med Chem, Volume 6, Issue 11, 2006 (1 article)
Cytometry A, Volume 69A, Issue 7, 2006 (1 article)
Diagn Pathol, Volume 1, Issue 1, 2006 (1 article)
Drug Metabol Drug Interact, Volume 21, Issue 3-4, 2006 (1 article)
Electrophoresis, Early Edition, 21-Jul-2006->29-Jun-2006 (3 articles)
Electrophoresis, Volume 27, Issue 13, 2006 (4 articles)
Environ Sci Technol, Volume 40, Issue 12, 2006 (1 article)
Eur J Gastroenterol Hepatol, Volume 18, Issue 8, 2006 (1 article)
Exp Mol Pathol, Early Edition, 7-Jul-2006 (1 article)
Expert Opin Biol Ther, Volume 6, Issue 8, 2006 (1 article)
Expert Rev Mol Diagn, Volume 6, Issue 4, 2006 (1 article)
FEBS Lett, Early Edition, 13-Jul-2006 (1 article)
FEMS Microbiol Lett, Volume 261, Issue 1, 2006 (1 article)
Glycobiology, Early Edition, 6-Jul-2006 (1 article)
IEEE Trans Vis Comput Graph, Volume 12, Issue 4, 2006 (1 article)
Inflamm Res, Early Edition, 19-Jul-2006 (1 article)
Int J Gynecol Cancer, Volume 16, Issue 3, 2006 (3 articles)
J Am Soc Mass Spectrom, Early Edition, 27-Jun-2006 (1 article)
J Biol Chem, Early Edition, 17-Jul-2006 (1 article)
J Biosci, Volume 31, Issue 2, 2006 (1 article)
J Chromatogr A, Early Edition, 3-Jul-2006 (2 articles)
J Chromatogr B, Early Edition, 4-Jul-2006->10-Jul-2006 (2 articles)
J Clin Endocrinol Metab, Early Edition, 5-Jul-2006 (1 article)
J Dairy Res, Early Edition, 12-Jul-2006 (1 article)
J Ethnopharmacol, Early Edition, 20-May-2006 (1 article)
J Exp Bot, Early Edition, 27-Jun-2006 (1 article)
J Microbiol Methods, Early Edition, 5-Jul-2006 (1 article)
J Mol Microbiol Biotechnol, Volume 11, Issue 1-2, 2006 (1 article)
J Neural Transm, Early Edition, 13-Jul-2006 (7 articles)
J Neurosci Methods, Early Edition, 22-Jun-2006 (1 article)
J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory, Volume 109, Issue 38, 2005 (1 article)
J Physiol, Early Edition, 6-Jul-2006 (1 article)
J Proteome Res, Volume 5, Issue 7, 2006 (6 articles)
Lab Invest, Early Edition, 17-Jul-2006 (1 article)
Microbiology, Volume 152, Issue Pt 8, 2006 (1 article)
Mol Cell Biochem, Early Edition, 15-Jul-2006 (1 article)
Mol Cell Biol, Volume 26, Issue 14, 2006 (1 article)
Mol Cell Proteomics, Volume 5, Issue 7, 2006 (14 articles)
Nat Biotechnol, Volume 24, Issue 7, 2006 (1 article)
Nat Rev Mol Cell Biol, Volume 7, Issue 7, 2006 (1 article)
Neurochem Res, Early Edition, 28-Jun-2006 (1 article)
Nucl Acids Res, Volume 34, Issues Web Server issue+11, 2006 (6 articles)
Obstet Gynecol Surv, Volume 61, Issue 8, 2006 (1 article)
Oncogene, Early Edition, 26-Jun-2006 (1 article)
Oncogene, Volume 25, Issue 27, 2006 (1 article)
Pediatr Nephrol, Early Edition, 30-Jun-2006 (1 article)
Plant Cell, Early Edition, 23-Jun-2006 (1 article)
Proc Natl Acad Sci U S A, Early Edition, 17-Jul-2006->26-Jun-2006 (2 articles)
Protein Pept Lett, Volume 13, Issue 5, 2006 (1 article)
Proteome Sci, Volume 4, Issue 1, 2006 (1 article)
Proteomics, Volume 6, Issues 13+14, 2006 (46 articles)
Rev Inst Med Trop Sao Paulo, Volume 48, Issue 3, 2006 (1 article)
Stem Cells Dev, Volume 15, Issue 3, 2006 (1 article)
Stud Health Technol Inform, Volume 120, 2006 (1 article)
Transplantation, Volume 82, Issue 2, 2006 (1 article)
Vaccine, Early Edition, 12-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 (21) / Biological applications (29) / Biomedical and clinical applications (42) / Eukaryotic Cells And Tissues (13) / Prokaryotes (10) / Pharmacology and Toxicology (3) / Protein Array (2) / Protein Characterization - PTMs (16) / Protein-protein interaction (3) / Quantitation (4) / Review (23) / Methodology (28) / Meeting (1) / Other (6) /

Bioinformatics

Universal Metrics for Quality Assessment of Protein Identifications by Mass Spectrometry
David A. Stead, Alun Preece, and Alistair J. P. Brown
Mol Cell Proteomics (2006) 5(7): 1205-1211

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Bigelow H, Rost B.
Nucl Acids Res (2006) 34(Web Server issue): W186-8

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
Castrignano T, Rizzi R, Talamo IG, De Meo PD, Anselmo A, Bonizzoni P, Pesole G.
Nucl Acids Res (2006) 34(Web Server issue): W440-3

Recognition of culture state using two-dimensional gel electrophoresis with an artificial neural network
Naoki Izawa, Michimasa Kishimoto, Masaaki Konishi, Takeshi Omasa, Suteaki Shioya, Hisao Ohtake
PROTEOMICS (2006) 6(13): 3730-3738

Government and Society: PSI announces deadlines for merging data formats
JOURNAL OF PROTEOME RESEARCH (2006) 5(7): 1526

A multiplexed proteomics approach to differentiate neurite outgrowth patterns.
Liu T, D'mello V, Deng L, Hu J, Ricardo M, Pan S, Lu X, Wadsworth S, Siekierka J, Birge R, Li H.
J Neurosci Methods Early Edition: published 22-Jun-2006

KemaDom: a web server for domain prediction using kernel machine with local context.
Chen L, Wang W, Ling S, Jia C, Wang F.
Nucl Acids Res (2006) 34(Web Server issue): W158-63

On the statistical analysis of the GS-NS0 cell proteome: Imputation, clustering and variability testing.
Ahmad N, Zhang J, Brown PJ, James DC, Birch JR, Racher AJ, Smales CM.
Biochim Biophys Acta Early Edition: published 19-May-2006

Probabilistic enrichment of phosphopeptides by their mass defect.
Bruce C, Shifman MA, Miller P, Gulcicek EE.
Anal Chem (2006) 78(13): 4374-82

pTARGET: a web server for predicting protein subcellular localization.
Guda C.
Nucl Acids Res (2006) 34(Web Server issue): W210-3

Semi-supervised LC/MS alignment for differential proteomics
Bernd Fischer, Jonas Grossmann, Volker Roth, Wilhelm Gruissem, Sacha Baginsky, and Joachim M. Buhmann
Bioinformatics (2006) 22(14): 132-140

High Performance GRID Based Implementation for Genomics and Protein Analysis.
Milanesi L, Merelli I.
Stud Health Technol Inform (2006) 120: 374-80

BaCelLo: a balanced subcellular localization predictor
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, and Rita Casadio
Bioinformatics (2006) 22(14): 408-416

SUMOsp: a web server for sumoylation site prediction.
Xue Y, Zhou F, Fu C, Xu Y, Yao X.
Nucl Acids Res (2006) 34(Web Server issue): W254-7

Cluster analysis of protein array results via similarity of Gene Ontology annotation.
Wolting C, McGlade CJ, Tritchler D.
BMC Bioinformatics (2006) 7(1): 338

Improved Peptide Elution Time Prediction for Reversed-Phase Liquid Chromatography-MS by Incorporating Peptide Sequence Information
Konstantinos Petritis, Lars J. Kangas, Bo Yan, Matthew E. Monroe, Eric F. Strittmatter, Wei-Jun Qian, Joshua N. Adkins, Ronald J. Moore, Ying Xu, Mary S. Lipton, David G. Camp, II, and Richard D. Smith
ANALYTICAL CHEMISTRY (2006) 78(14): 5026-5039

Informatics-assisted Protein Profiling in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis
Thomas J. Lukas, Wei Wei Luo, Haihong Mao, Natalie Cole, and Teepu Siddique
Mol Cell Proteomics (2006) 5(7): 1233-1244

Global topological features of cancer proteins in the human interactome.
Jonsson PF, Bates PA.
Bioinformatics Early Edition: published 14-Jul-2006

A computational approach toward label-free protein quantification using predicted peptide detectability
Haixu Tang, Randy J. Arnold, Pedro Alves, Zhiyin Xun, David E. Clemmer, Milos V. Novotny, James P. Reilly, and Predrag Radivojac
Bioinformatics (2006) 22(14): 481-488

Visual analysis of gel-free proteome data.
Linsen L, Locherbach J, Berth M, Becher D, Bernhardt J.
IEEE Trans Vis Comput Graph (2006) 12(4): 497-508

Peptide sequence tag-based blind identification of post-translational modifications with point process model
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, and Liming Cai
Bioinformatics (2006) 22(14): 307-313

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Biological applications

Protein changes between dormant and dormancy-broken seeds of Prunus campanulata Maxim
Chung-Shu Lee, Ching-Te Chien, Chao-Hsiung Lin, Yi-Ying Chiu, Yuh-Shyong Yang
PROTEOMICS (2006) 6(14): 4147-4154

Endogenously Nitrated Proteins in Mouse Brain: Links to Neurodegenerative Disease.
Sacksteder CA, Qian WJ, Knyushko TV, Wang H, Chin MH, Lacan G, Melega WP, Camp DG 2nd, Smith RD, Smith DJ, Squier TC, Bigelow DJ.
Biochemistry (2006) 45(26): 8009-8022

Proteomic analysis of antigens from Leishmania infantum promastigotes
Mar�a Auxiliadora Dea-Ayuela, Sara Rama-I�iguez, Francisco Bol�s-Fern�ndez
PROTEOMICS (2006) 6(14): 4187-4194

Development and plasticity-related changes in protein expression patterns in cat visual cortex: A fluorescent two-dimensional difference gel electrophoresis approach
Gert Van den Bergh, Stefan Clerens, Bonnie L. Firestein, Kalina Burnat, Lutgarde Arckens
PROTEOMICS (2006) 6(13): 3821-3832

Protein Composition and Electron Microscopy Structure of Affinity-Purified Human Spliceosomal B Complexes Isolated under Physiological Conditions.
Deckert J, Hartmuth K, Boehringer D, Behzadnia N, Will CL, Kastner B, Stark H, Urlaub H, Luhrmann R.
Mol Cell Biol (2006) 26(14): 5528-43

Glutathione peroxidase 3 of Saccharomyces cerevisiae regulates the activity of methionine sulfoxide reductase in a redox state-dependent way.
Kho CW, Lee PY, Bae KH, Cho S, Lee ZW, Park BC, Kang S, Lee DH, Park SG.
Biochem Biophys Res Commun Early Edition: published 21-Jun-2006

Proteomic analysis of tomato fruits from two ecotypes during ripening
Mariapina Rocco, Chiara D'Ambrosio, Simona Arena, Mirelle Faurobert, Andrea Scaloni, Mauro Marra
PROTEOMICS (2006) 6(13): 3781-3791

Comparative proteome analysis of changes in the 26S proteasome during oocyte maturation in goldfish
Ryo Horiguchi, Hideo Dohra, Toshinobu Tokumoto
PROTEOMICS (2006) 6(14): 4195-4202

Endogenous Transforming Growth Factor-{beta} Receptor-mediated Smad Signaling Complexes Analyzed by Mass Spectrometry
Qilie Luo, Edward Nieves, Julia Kzhyshkowska, and Ruth Hogue Angeletti
Mol Cell Proteomics (2006) 5(7): 1245-1260

Comparative proteomics analysis of differentially expressed phosphoproteins in adult rat ventricular myocytes subjected to diazoxide preconditioning.
Li H, Xiao YB, Gao YQ, Yang TD.
Drug Metabol Drug Interact (2006) 21(3-4): 245-58

A global topology map of the Saccharomyces cerevisiae membrane proteome.
Kim H, Melen K, Osterberg M, von Heijne G.
Proc Natl Acad Sci U S A Early Edition: published 17-Jul-2006

Mass Spectrometrical Analysis of Galectin Proteins in Primary Rat Cerebellar Astrocytes.
Yang JW, Kang SU, Engidawork E, Rodrigo R, Felipo V, Lubec G.
Neurochem Res Early Edition: published 28-Jun-2006

A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis.
Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M.
Electrophoresis Early Edition: published 21-Jul-2006

Some aspects of the venom proteome of the Colubridae snake Philodryas olfersii revealed from a Duvernoy's (venom) gland transcriptome.
Ching AT, Rocha MM, Paes Leme AF, Pimenta DC, de Fatima D Furtado M, Serrano SM, Ho PL, Junqueira-de-Azevedo IL.
FEBS Lett Early Edition: published 13-Jul-2006

Unraveling age-dependent variation of the mitochondrial proteome.
Dencher NA, Goto S, Reifschneider NH, Sugawa M, Krause F.
Ann N Y Acad Sci (2006) 1067: 116-9.

Regulation of Murine Cardiac 20S Proteasomes. Role of Associating Partners.
Zong C, Gomes AV, Drews O, Li X, Young GW, Berhane B, Qiao X, French SW, Bardag-Gorce F, Ping P.
Circ Res Early Edition: published 20-Jul-2006

Mapping the Murine Cardiac 26S Proteasome Complexes.
Gomes AV, Zong C, Edmondson RD, Li X, Stefani E, Zhang J, Jones RC, Thyparambil S, Wang GW, Qiao X, Bardag-Gorce F, Ping P.
Circ Res Early Edition: published 20-Jul-2006

Identification of biofilm proteins in non-typeable Haemophilus Influenzae.
Gallaher TK, Wu S, Webster P, Aguilera R.
BMC Microbiol (2006) 6(1): 65

Maternal housekeeping proteins translated during bovine oocyte maturation and early embryo development
Lyne Massicotte, Karine Coenen, Marina Mourot, Marc-Andr� Sirard
PROTEOMICS (2006) 6(13): 3811-3820

Proteomic analysis of the acid-soluble organic matrix of the chicken calcified eggshell layer
Karlheinz Mann, Boris Ma?ek, Jesper V. Olsen
PROTEOMICS (2006) 6(13): 3801-3810

Analysis of the defence phosphoproteome of Arabidopsis thaliana using differential mass tagging
Alexandra M. E. Jones, Mark H. Bennett, John W. Mansfield, Murray Grant
PROTEOMICS (2006) 6(14): 4155-4165

Proteomic dissection of plant development
Frank Hochholdinger, Michaela Sauer, Diana Dembinsky, Nadine Hoecker, Nils Muthreich, Muhammad Saleem, Yan Liu
PROTEOMICS (2006) 6(14): 4076-4083

The proteomics of plant cell membranes.
Komatsu S, Konishi H, Hashimoto M.
J Exp Bot Early Edition: published 27-Jun-2006

Proteomic Analysis of the Eyespot of Chlamydomonas reinhardtii Provides Novel Insights into Its Components and Tactic Movements.
Schmidt M, Gessner G, Luff M, Heiland I, Wagner V, Kaminski M, Geimer S, Eitzinger N, Reissenweber T, Voytsekh O, Fiedler M, Mittag M, Kreimer G.
Plant Cell Early Edition: published 23-Jun-2006

The analysis of proteome changes in sunflower seeds induced by N+ implantation.
Guijun D, Weidong P, Gongshe L.
J Biosci (2006) 31(2): 247-53

Proteomic analysis of factors released from p21-overexpressing tumour cells
Caroline A. Currid, Darran P. O'Connor, Bey-Dih Chang, Caroline Gebus, Nathan Harris, Kenneth A. Dawson, Michael J. Dunn, Stephen R. Pennington, Igor B. Roninson, William M. Gallagher
PROTEOMICS (2006) 6(13): 3739-3753

The mTOR pathway regulates mitochondrial oxygen consumption and oxidative capacity.
Schieke SM, Phillips D, McCoy JP Jr, Aponte AM, Shen RF, Balaban RS, Finkel T.
J Biol Chem Early Edition: published 17-Jul-2006

A proteomics study of the mung bean epicotyl regulated by brassinosteroids under conditions of chilling stress.
Huang B, Chu CH, Chen SL, Juan HF, Chen YM.
Cell Mol Biol Lett (2006) 11(2): 264-78

Experimental Metabonomic Model of Dietary Variation and Stress Interactions
Yulan Wang, Elaine Holmes, Huiru Tang, John C. Lindon, Norbert Sprenger, Marco E. Turini, Gabriela Bergonzelli, Laurent B. Fay, Sunil Kochhar, and Jeremy K. Nicholson
JOURNAL OF PROTEOME RESEARCH (2006) 5(7): 1535-1542

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Biomedical and clinical applications

Proteome analysis of resting human neutrophils.
de Souza Castro M, de Sa NM, Gadelha RP, de Sousa MV, Ricart CA, Fontes B, Fontes W.
Protein Pept Lett (2006) 13(5): 481-7

Plasma proteomics of lung cancer by a linkage of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis
Tetsuya Okano, Tadashi Kondo, Tatsuhiko Kakisaka, Kiyonaga Fujii, Masayo Yamada, Harubumi Kato, Toshihide Nishimura, Akihiko Gemma, Shoji Kudoh, Setsuo Hirohashi
PROTEOMICS (2006) 6(13): 3938-3948

Protein profiling of sickle cell versus control RBC core membrane skeletons by ICAT technology and tandem mass spectrometry.
Chou J, Choudhary PK, Goodman SR.
Cell Mol Biol Lett Early Edition: published 20-Jun-2006

Schizophrenia proteomics: biomarkers on the path to laboratory medicine?
Lakhan SE.
Diagn Pathol (2006) 1(1): 11

Plasma proteomic profiling for detecting and differentiating in situ and invasive carcinomas of the uterine cervix.
Lin YW, Lai HC, Lin CY, Chiou JY, Shui HA, Chang CC, Yu MH, Chu TY.
Int J Gynecol Cancer (2006) 16(3): 1216-24

Serum proteomic features for detection of endometrial cancer.
Zhu LR, Zhang WY, Yu L, Zheng YH, Zhang JZ, Liao QP.
Int J Gynecol Cancer (2006) 16(3): 1374-8

RET oncoproteins induce tyrosine phosphorylation changes of proteins involved in RNA metabolism.
Gorla L, Cantu M, Micciche F, Patelli C, Mondellini P, Pierotti MA, Bongarzone I.
Cell Signal Early Edition: published 24-May-2006

Quantitative proteomic profiling of pancreatic cancer juice
Ru Chen, Sheng Pan, Eugene C. Yi, Samuel Donohoe, Mary P. Bronner, John D. Potter, David R. Goodlett, Ruedi Aebersold, Teresa A. Brentnall
PROTEOMICS (2006) 6(13): 3871-3879

Myeloperoxidase-Catalyzed Metabolism of Etoposide to Its Quinone and Glutathione Adduct Forms in HL60 Cells.
Fan Y, Schreiber EM, Giorgianni A, Yalowich JC, Day BW.
Chem Res Toxicol (2006) 19(7): 937-43

Proteomics in neurodegeneration - disease driven approaches.
Schulenborg T, Schmidt O, van Hall A, Meyer HE, Hamacher M, Marcus K.
J Neural Transm Early Edition: published 13-Jul-2006

Proteomic biomarkers for autoimmune disease
Wolfgang Hueber, William H. Robinson
PROTEOMICS (2006) 6(14): 4100-4105

Proteomics, Part II: The Emerging Role of Proteomics Over Genomics in Spontaneous Preterm Labor/Birth.
Buhimschi CS, Weiner CP, Buhimschi IA.
Obstet Gynecol Surv (2006) 61(8): 543-553

Differentiation of HELLP patients from healthy pregnant women by proteome analysis-On the way towards a clinical marker set.
Heitner JC, Koy C, Kreutzer M, Gerber B, Reimer T, Glocker MO.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 10-Jul-2006

Proteomic analysis of Brucella abortus cell envelope and identification of immunogenic candidate proteins for vaccine development
Joseph P. Connolly, Diego Comerci, Timothy G. Alefantis, Alexander Walz, Marian Quan, Ryan Chafin, Paul Grewal, Cesar V. Mujer, Rodolfo A. Ugalde, Vito G. DelVecchio
PROTEOMICS (2006) 6(13): 3767-3780

Proteomic analysis of estrogen response of premalignant human breast cells using a 2-D liquid separation/mass mapping technique
Jia Zhao, Kan Zhu, David M. Lubman, Fred R. Miller, Malthy P. V. Shekhar, Brigitte Gerard, Timothy J. Barder
PROTEOMICS (2006) 6(13): 3847-3861

Comparative analysis of two-dimensional electrophoresis maps (2-DE) of Helicobacter pylori from Brazilian patients with chronic gastritis and duodenal ulcer: a preliminary report.
Pereira DR, Martins D, Winck FV, Smolka MB, Nishimura NF, Rabelo-Goncalves EM, Hara NH, Marangoni S, Zeitune JM, Novello JC.
Rev Inst Med Trop Sao Paulo (2006) 48(3): 175-7

Proteomic analysis of the allograft response.
El Essawy B, Otu HH, Choy B, Zheng XX, Libermann TA, Strom TB.
Transplantation (2006) 82(2): 267-74

Proteomic Analysis of Ischemia-Reperfusion Injury upon Human Liver Transplantation Reveals the Protective Role of IQGAP1
Anouk Emadali, Beatrice Muscatelli-Groux, Frederic Delom, Sarah Jenna,Daniel Boismenu, David B. Sacks, Peter P. Metrakos, and Eric Chevet
Mol Cell Proteomics (2006) 5(7): 1300-1313

A multiplex tissue immunoblotting assay for proteomic profiling: a pilot study of the normal to tumor transition of esophageal squamous cell carcinoma.
Chung JY, Braunschweig T, Hu N, Roth M, Traicoff JL, Wang QH, Knezevic V, Taylor PR, Hewitt SM.
Cancer Epidemiol Biomarkers Prev (2006) 15(7): 1403-8

Proteomic analysis of glutamine-treated human intestinal epithelial HCT-8 cells under basal and inflammatory conditions
Sandrine Th�bault, Nicolas Deniel, Rachel Marion, Roland Charlionet, Fran�ois Tron, David Cosquer, J�r�me Leprince, Hubert Vaudry, Philippe Ducrott�, Pierre D�chelotte
PROTEOMICS (2006) 6(13): 3926-3937

Identification of differentiating neural progenitor cell markers using shotgun isobaric tagging mass spectrometry.
Salim K, Kehoe L, Minkoff MS, Bilsland JG, Munoz-Sanjuan I, Guest PC.
Stem Cells Dev (2006) 15(3): 461-70

Altered expression of serum protein in ginsenoside Re-treated diabetic rats detected by SELDI-TOF MS.
Cho WC, Yip TT, Chung WS, Lee SK, Leung AW, Cheng CH, Yue KK.
J Ethnopharmacol Early Edition: published 20-May-2006

Detection of hypopharyngeal squamous cell carcinoma using serum proteomics.
Zhou L, Cheng L, Tao L, Jia X, Lu Y, Liao P.
Acta Otolaryngol (2006) 126(8): 853-60

Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage
Carlos de Torre, Sai-Xia Ying, Peter J. Munson, G. Umberto Meduri, Anthony F. Suffredini
PROTEOMICS (2006) 6(13): 3949-3957

Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: Unlocking the proteome within
Brian L. Hood, Thomas P. Conrads, Timothy D. Veenstra
PROTEOMICS (2006) 6(14): 4106-4114

Proteomic identification of a role for the von Hippel Lindau tumour suppressor in changes in the expression of mitochondrial proteins and septin 2 in renal cell carcinoma
Rachel A. Craven, Sarah Hanrahan, Nick Totty, Patricia Harnden, Anthea J. Stanley, Eamonn R. Maher, Adrian L. Harris, William S. Trimble, Peter J. Selby, Rosamonde E. Banks
PROTEOMICS (2006) 6(13): 3880-3893

Proteomic characterization of human serum proteins associated with the fat-derived hormone adiponectin
Yu Wang, Lance Yi Xu, Karen S. L. Lam, Gang Lu, Garth J. S. Cooper, Aimin Xu
PROTEOMICS (2006) 6(13): 3862-3870

Urine proteomic profiling of pediatric nephrotic syndrome.
Khurana M, Traum AZ, Aivado M, Wells MP, Guerrero M, Grall F, Libermann TA, Schachter AD.
Pediatr Nephrol Early Edition: published 30-Jun-2006

Comparative analysis of whole saliva proteomes for the screening of biomarkers for oral lichen planus.
Yang LL, Liu XQ, Liu W, Cheng B, Li MT.
Inflamm Res Early Edition: published 19-Jul-2006

Using Capillary Electrophoresis-Selective Tandem Mass Spectrometry To Identify Pathogens in Clinical Samples
Anren Hu, Cheng-Tung Chen, Pei-Jen Tsai, and Yen-Peng Ho
ANALYTICAL CHEMISTRY (2006) 78(14): 5124-5133

Isolation of human prostatic epithelial plasma membranes for proteomics using mirror image tissue banking of radical prostatectomy specimens.
Sircar K, Gaboury L, Ouadi L, Mecteau M, Scarlata E, Saad F, Aprikian A, Tanguay S, Lapointe S, Lussier C, Miletti T, Lanoix J.
Clin Cancer Res (2006) 12(14): 4178-84

Proteomic analysis of autoantibodies in patients with hepatocellular carcinoma
Motonari Takashima, Yasuhiro Kuramitsu, Yuichiro Yokoyama, Norio Iizuka, Toshio Harada, Masanori Fujimoto, Isao Sakaida, Kiwamu Okita, Masaaki Oka, Kazuyuki Nakamura
PROTEOMICS (2006) 6(13): 3894-3900

Analysis of the in vitro synergistic effect of 5-fluorouracil and cisplatin on cervical carcinoma cells.
Yim EK, Lee SB, Lee KH, Kim CJ, Park JS.
Int J Gynecol Cancer (2006) 16(3): 1321-9

Clinical proteomics: Study of a cryogel
Daniel Robert, Stefano Barelli, David Crettaz, Pierre-Alexandre Bart, J�rg A. Schifferli, Daniel Betticher, Jean-Daniel Tissot
PROTEOMICS (2006) 6(13): 3958-3960

Molecular screening of gastric cancer by proteome analysis.
Ebert MP, Rocken C.
Eur J Gastroenterol Hepatol (2006) 18(8): 847-53

Global proteomic analysis of microdissected cirrhotic nodules reveals significant biomarkers associated with clonal expansion.
Guedj N, Dargere D, Degos F, Janneau JL, Vidaud D, Belghiti J, Bedossa P, Paradis V.
Lab Invest Early Edition: published 17-Jul-2006

Cystic fibrosis enters the proteomics scene: New answers to old questions
Mario Ollero, Franck Brouillard, Aleksander Edelman
PROTEOMICS (2006) 6(14): 4084-4099

Proteomic Identification of a Stress Protein, Mortalin/mthsp70/GRP75: Relevance To Parkinson Disease
Jinghua Jin, Christine Hulette, Yan Wang, Terry Zhang, Catherine Pan, Renu Wadhwa, and Jing Zhang
Mol Cell Proteomics (2006) 5(7): 1193-1204

Serum proteomic patterns for gastric lesions as revealed by SELDI mass spectrometry.
Liang Y, Fang M, Li J, Liu CB, Rudd JA, Kung HF, Yew DT.
Exp Mol Pathol Early Edition: published 7-Jul-2006

Calreticulin induces delayed cardioprotection through mitogen-activated protein kinases
Xiuhua Liu, Feifei Xu, Yan Fu, Fengying Liu, Sheng Sun, Xudong Wu
PROTEOMICS (2006) 6(13): 3792-3800

Proteomic analysis identifies alterations in cellular morphology and cell death pathways in mouse brain after chronic corticosterone treatment.
Skynner HA, Amos DP, Murray F, Salim K, Knowles MR, Munoz-Sanjuan I, Camargo LM, Bonnert TP, Guest PC.
Brain Res Early Edition: published 22-Jun-2006

Up-regulation of Metabotropic glutamate receptor 3 (mGluR3) in rat fibrosis and cirrhosis model of persistent hypoxic condition.
Do SH, Yun HS, Jeong WI, Jeong DH, Ki MR, Chung JY, Park SJ, Kim SB, Jeong KS.
Mol Cell Biochem Early Edition: published 15-Jul-2006

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Eukaryotic Cells And Tissues

Peptidomics and proteomics studies of transformed lymphocytes from patients mutated for the eukaryotic initiation factor 2B.
Fogli A, Malinverni C, Thadikkaran L, Combes P, Perret F, Crettaz D, Tissot JD, Boespflug-Tanguy O, Stocklin R, Bulet P.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 4-Jul-2006

An integrated map of the murine hippocampal proteome based upon five mouse strains
Daniela D. Pollak, Julius John, Harald Hoeger, Gert Lubec
ELECTROPHORESIS (2006) 27(13): 2787-2798

Proteomics of the human brain: sub-proteomes might hold the key to handle brain complexity.
Tribl F, Marcus K, Bringmann G, Meyer HE, Gerlach M, Riederer P.
J Neural Transm Early Edition: published 13-Jul-2006

Proteome analysis of Schizosaccharomyces pombe by two-dimensional gel electrophoresis and mass spectrometry
Kyung-Hoon Hwang, Christine Carapito, Susanne B�hmer, Emmanuelle Leize, Alain Van Dorsselaer, Rita Bernhardt
PROTEOMICS (2006) 6(14): 4115-4129

Construction of quantitative proteome reference maps of mouse spleen and lymph node based on two-dimensional gel electrophoresis
Yayoi Kimura, Ryo Yokoyama, Yuri Ishizu, Toshio Nishigaki, Yasuaki Murahashi, Atsushi Hijikata, Hiroshi Kitamura, Osamu Ohara
PROTEOMICS (2006) 6(13): 3833-3844

Plasma proteome analysis reveals the geographical origin and liver tumor status of Dab (Limanda limanda) from UK marine waters.
Ward DG, Wei W, Cheng Y, Billingham LJ, Martin A, Johnson PI, Lyons BP, Feist SW, Stentiford GD.
Environ Sci Technol (2006) 40(12): 4031-6

Changes in protein expression in the medial vestibular nuclei during vestibular compensation.
Paterson JM, Short D, Flatman PW, Seckl JR, Aitken A, Dutia MB.
J Physiol Early Edition: published 6-Jul-2006

Proteome analysis of cultured fibroblasts from type 1 diabetic patients and normal subjects.
Puricelli L, Iori E, Millioni R, Arrigoni G, James P, Vedovato M, Tessari P.
J Clin Endocrinol Metab Early Edition: published 5-Jul-2006

ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A, Arai R, Yashiroda Y, Shirai A, Kamata A, Sekido S, Kobayashi Y, Hashimoto A, Hamamoto M, Hiraoka Y, Horinouchi S, Yoshida M.
Nat Biotechnol (2006) 24(7): 841-7

Bovine Milk Fat Globule Membrane Proteome.
Reinhardt TA, Lippolis JD.
J Dairy Res Early Edition: published 12-Jul-2006

The proteins of human chromosome 21.
Gardiner K, Costa AC.
Am J Med Genet C Semin Med Genet Early Edition: published 12-Jul-2006

The HUPO Brain Proteome Project - No need to hurry?
Hamacher M, Marcus K, van Hall A, Meyer HE, Stephan C.
J Neural Transm Early Edition: published 13-Jul-2006

A Quest for Human and Mouse Embryonic Stem Cell-specific Proteins
Dennis Van Hoof, Robert Passier, Dorien Ward-Van Oostwaard, Martijn W.H. Pinkse, Albert J. R. Heck, Christine L. Mummery, and Jeroen Krijgsveld
Mol Cell Proteomics (2006) 5(7): 1261-1273

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Prokaryotes

Morphological changes and proteome response of Corynebacterium glutamicum to a partial depletion of FtsI.
Valbuena N, Letek M, Ramos A, Ayala J, Nakunst D, Kalinowski J, Mateos LM, Gil JA.
Microbiology (2006) 152(Pt 8): 2491-503

Proteomic analysis of Agrobacterium tumefaciens response to the vir gene inducer acetosyringone
Erh-Min Lai, Hsiao-Wei Shih, Sy-Ray Wen, Min-Wen Cheng, Hau-Hsuan Hwang, Shih-Hua Chiu
PROTEOMICS (2006) 6(14): 4130-4136

Comparative proteomic analysis between the invasive and commensal strains of Staphylococcus epidermidis.
Yang XM, Li N, Chen JM, Ou YZ, Jin H, Lu HJ, Zhu YL, Qin ZQ, Qu D, Yang PY.
FEMS Microbiol Lett (2006) 261(1): 32-40

Mass Spectrometric Identification of Proteins in Complex Post-Genomic Projects. Soluble Proteins of the Metabolically Versatile, Denitrifying 'Aromatoleum' Sp. Strain EbN1.
Hufnagel P, Rabus R.
J Mol Microbiol Biotechnol (2006) 11(1-2): 53-81

Gel-free and Gel-based Proteomics in Bacillus subtilis: A Comparative Study
Susanne Wolff, Andreas Otto, Dirk Albrecht, Jianru Stahl Zeng, Knut Buttner, Matthias Gluckmann, Michael Hecker, and Dorte Becher
Mol Cell Proteomics (2006) 5(7): 1183-1192

Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes.
Callister SJ, Nicora CD, Zeng X, Roh JH, Dominguez MA, Tavano CL, Monroe ME, Kaplan S, Donohue TJ, Smith RD, Lipton MS.
J Microbiol Methods Early Edition: published 5-Jul-2006

The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions.
Ding YH, Hixson KK, Giometti CS, Stanley A, Esteve-Nunez A, Khare T, Tollaksen SL, Zhu W, Adkins JN, Lipton MS, Smith RD, Mester T, Lovley DR.
Biochim Biophys Acta Early Edition: published 16-May-2006

Compensatory effect of the minor Streptomyces lividans type I signal peptidases on the SipY major signal peptidase deficiency as determined by extracellular proteome analysis
Marta R. Escutia, Gema Val, Arantxa Palac�n, Nick Geukens, Jozef Ann�, Rafael P. Mellado
PROTEOMICS (2006) 6(14): 4137-4146

Proteome Analysis of Cellular Response of Pseudomonas putida KT2440 to Tetracycline Stress.
Yun SH, Kim YH, Joo EJ, Choi JS, Sohn JH, Kim SI.
Curr Microbiol Early Edition: published 10-Jul-2006

Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO.
Nunn BL, Shaffer SA, Scherl A, Gallis B, Wu M, Miller SI, Goodlett DR.
Brief Funct Genomic Proteomic (2006) 5(2): 154-68

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Pharmacology and Toxicology

Novel surface polypeptides of Campylobacter jejuni as traveller's diarrhoea vaccine candidates discovered by proteomics.
Prokhorova TA, Nielsen PN, Petersen J, Kofoed T, Crawford JS, Morsczeck C, Boysen A, Schrotz-King P.
Vaccine Early Edition: published 12-Jun-2006

Identification of Proteomic Signatures of Exposure to Marine Pollutants in Mussels (Mytilus edulis)
Itxaso Apraiz, Jia Mi, and Susana Cristobal
Mol Cell Proteomics (2006) 5(7): 1274-1285

Molecular determinants of differential sensitivity to docetaxel and paclitaxel in human pediatric cancer models.
Izbicka E, Campos D, Marty J, Carrizales G, Mangold G, Tolcher A.
Anticancer Res (2006) 26(3A): 1983-8

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Protein Array

Identification of proteins bound to a thioaptamer probe on a proteomics array.
Wang H, Yang X, Bowick GC, Herzog NK, Luxon BA, Lomas LO, Gorenstein DG.
Biochem Biophys Res Commun Early Edition: published 30-Jun-2006

An affinity-based method for the purification of fluorescently-labeled biomolecules.
Nguyen T, Joshi NS, Francis MB.
Bioconjug Chem (2006) 17(4): 869-72

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Protein Characterization / PTMs

Myosin binding protein C is differentially phosphorylated upon myocardial stunning in canine and rat hearts - Evidence for novel phosphorylation sites
Chao Yuan, Yurong Guo, Rajashree Ravi, Karin Przyklenk, Nicole Shilkofski, Roberto Diez, Robert N. Cole, Anne M. Murphy
PROTEOMICS (2006) 6(14): 4176-4186

Characterization of the phosphorylation sites of Mycobacterium tuberculosis serine/threonine protein kinases, PknA, PknD, PknE, and PknH by mass spectrometry
Virginie Molle, Isabelle Zanella-Cleon, Jean-Philippe Robin, Souen Mallejac, Alain J. Cozzone, Michel Becchi
PROTEOMICS (2006) 6(13): 3754-3766

Detailed Map of Oxidative Post-Translational Modifications of Human P21Ras Using Fourier Transform Mass Spectrometry
Cheng Zhao, Mahadevan Sethuraman, Nicolas Clavreul, Parminder Kaur, Richard A. Cohen, and Peter B. O'Connor
ANALYTICAL CHEMISTRY (2006) 78(14): 5134-5142

Quantitative Proteomic Analysis of Post-translational Modifications of Human Histones
Hans Christian Beck, Eva C. Nielsen, Rune Matthiesen, Lars H. Jensen, Maxwell Sehested, Paul Finn, Morten Grauslund, Anne Maria Hansen, and Ole Norregaard Jensen
Mol Cell Proteomics (2006) 5(7): 1314-1325

Identification and Stoichiometry of Glycosylphosphatidylinositol-anchored Membrane Proteins of the Human Malaria Parasite Plasmodium falciparum
Paul R. Gilson, Thomas Nebl, Damjan Vukcevic, Robert L. Moritz, TobiasSargeant, Terence P. Speed, Louis Schofield, and Brendan S. Crabb
Mol Cell Proteomics (2006) 5(7): 1286-1299

Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes
Frank Krause
ELECTROPHORESIS (2006) 27(13): 2759-2781

Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism
de la Fuente van Bentem S, Anrather D, Roitinger E, Djamei A, Hufnagl T, Barta A, Csaszar E, Dohnal I, Lecourieux D, Hirt H
Nucleic Acids Res (2006) 34(11): 3267-78

Mapping of Protein Disulfide Bonds Using Negative Ion Fragmentation with a Broadband Precursor Selection
Mingxuan Zhang and Igor A. Kaltashov
ANALYTICAL CHEMISTRY (2006) 78(14): 4820-4829

The use of mass spectrometry for the proteomic analysis of glycosylation
Willy Morelle, K�vin Canis, Fr�d�ric Chirat, Valegh Faid, Jean-Claude Michalski
PROTEOMICS (2006) 6(14): 3993-4015

Gender-specific expression of complex-type N-glycans in schistosomes.
Wuhrer M, Koeleman CA, Fitzpatrick JM, Hoffmann KF, Deelder AM, Hokke CH.
Glycobiology Early Edition: published 6-Jul-2006

Phosphoprotein analysis: from proteins to proteomes.
Delom F, Chevet E.
Proteome Sci (2006) 4(1): 15

Identification of Phosphorylation Sites in N-Linked Glycans by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
Minako Takashiba, Yasunori Chiba, and Yoshifumi Jigami
ANALYTICAL CHEMISTRY (2006) 78(14): 5208-5213

Phosphoproteomics strategies for the functional analysis of signal transduction
Sandra Morandell, Taras Stasyk, Karin Grosstessner-Hain, Elisabeth Roitinger, Karl Mechtler, Guenther K. Bonn, Lukas A. Huber
PROTEOMICS (2006) 6(14): 4047-4056

Local Flexibility in Molecular Function Paradigm
Jag Bhalla, Geoffrey B. Storchan, Caitlin M. MacCarthy, Vladimir N. Uversky, and Olga Tcherkasskaya
Mol Cell Proteomics (2006) 5(7): 1212-1223

Glycosylation patterns of human chorionic gonadotropin revealed by liquid chromatography-mass spectrometry and bioinformatics
Hansj�rg Toll, Peter Berger, Andreas Hofmann, Andreas Hildebrandt, Herbert Oberacher, Hans Peter Lenhof, Christian G. Huber
ELECTROPHORESIS (2006) 27(13): 2734-2746

Reading protein modifications with interaction domains.
Seet BT, Dikic I, Zhou MM, Pawson T.
Nat Rev Mol Cell Biol (2006) 7(7): 473-83

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Protein-protein interaction

An Integrated Machine Learning System to Computationally Screen Protein Databases for Protein Binding Peptide Ligands
Ling Zhang, Chen Shao, Dexian Zheng, and Youhe Gao
Mol Cell Proteomics (2006) 5(7): 1224-1232

A method for rapid protease substrate evaluation and optimization.
Kozlov IA, Melnyk PC, Zhao C, Hachmann JP, Shevchenko V, Srinivasan A, Barker DL, Lebl M.
Comb Chem High Throughput Screen (2006) 9(6): 481-7

Biomolecular interaction analysis in functional proteomics.
Moll D, Prinz A, Gesellchen F, Drewianka S, Zimmermann B, Herberg FW.
J Neural Transm Early Edition: published 13-Jul-2006

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Quantitation

Quantitative Analysis of Modified Proteins and Their Positional Isomers by Tandem Mass Spectrometry: Human Histone H4.
Pesavento JJ, Mizzen CA, Kelleher NL.
Anal Chem (2006) 78(13): 4271-4280

Label-free Quantitative Proteomics Using Large Peptide Data Sets Generated by Nanoflow Liquid Chromatography and Mass Spectrometry
Masaya Ono, Miki Shitashige, Kazufumi Honda, Tomohiro Isobe, Hideya Kuwabara, Hirotaka Matsuzuki, Setsuo Hirohashi, and Tesshi Yamada
Mol Cell Proteomics (2006) 5(7): 1338-1347

Robust protein quantitation in chromatographic fractions using MALDI-MS of tryptic peptides
Renate Bublitz, Stefan Kreusch, G�nther Ditze, Margarete Schulze, Gerhard A. Cumme, Christine Fischer, Adrienne Winter, Horst Hoppe, Heidrun Rhode
PROTEOMICS (2006) 6(13): 3909-3917

Primary amine coding as a path to comparative proteomics
Fred E. Regnier, Samir Julka
PROTEOMICS (2006) 6(14): 3968-3979

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Review

Proteomic biomarkers for autoimmune disease
Wolfgang Hueber, William H. Robinson
PROTEOMICS (2006) 6(14): 4100-4105

Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity
Lianyi Han, Juan Cui, Honghuang Lin, Zhiliang Ji, Zhiwei Cao, Yixue Li, Yuzong Chen
PROTEOMICS (2006) 6(14): 4023-4037

Slide-based cytometry for cytomics-A minireview.
Tarnok A.
Cytometry A (2006) 69A(7): 555-562

The use of mass spectrometry for the proteomic analysis of glycosylation
Willy Morelle, K�vin Canis, Fr�d�ric Chirat, Valegh Faid, Jean-Claude Michalski
PROTEOMICS (2006) 6(14): 3993-4015

The purinome, a complex mix of drug and toxicity targets.
Haystead TA.
Curr Top Med Chem (2006) 6(11): 1117-27

Automation, parallelism, and robotics for proteomics
Gil Alterovitz, Jonathan Liu, Jijun Chow, Marco F. Ramoni
PROTEOMICS (2006) 6(14): 4016-4022

Cystic fibrosis enters the proteomics scene: New answers to old questions
Mario Ollero, Franck Brouillard, Aleksander Edelman
PROTEOMICS (2006) 6(14): 4084-4099

Mass spectrometry-based proteomics for the detection of plant pathogens
Neerav D. Padliya, Bret Cooper
PROTEOMICS (2006) 6(14): 4069-4075

Progress in structure prediction of alpha-helical membrane proteins.
Fleishman SJ, Ben-Tal N.
Curr Opin Struct Biol Early Edition: published 3-Jul-2006

A high efficiency cloning and expression system for proteomic analysis
Xuan Z. Ding, Ian T. Paulsen, Apurba K. Bhattacharjee, Mikeljon P. Nikolich, Gary Myers, David L. Hoover
PROTEOMICS (2006) 6(14): 4038-4046

Progress in biomarker discovery for diagnostic testing in epithelial ovarian cancer.
Gogoi R, Srinivasan S, Fishman DA.
Expert Rev Mol Diagn (2006) 6(4): 627-37

Alternative splicing: new insights from global analyses.
Blencowe BJ.
Cell (2006) 126(1): 37-47

Update and challenges on proteomics in rice
Setsuko Komatsu, Hiroyuki Yano
PROTEOMICS (2006) 6(14): 4057-4068

Protein EqualizerTM Technology: The quest for a ?democratic proteome?
Pier Giorgio Righetti, Egisto Boschetti, Lee Lomas, Attilio Citterio
PROTEOMICS (2006) 6(14): 3980-3992

Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: Unlocking the proteome within
Brian L. Hood, Thomas P. Conrads, Timothy D. Veenstra
PROTEOMICS (2006) 6(14): 4106-4114

Primary amine coding as a path to comparative proteomics
Fred E. Regnier, Samir Julka
PROTEOMICS (2006) 6(14): 3968-3979

The application of systems biology to drug discovery.
Cho CR, Labow M, Reinhardt M, van Oostrum J, Peitsch MC.
Curr Opin Chem Biol Early Edition: published 3-Jul-2006

Antibody microarray-based oncoproteomics.
Borrebaeck CA.
Expert Opin Biol Ther (2006) 6(8): 833-8

Phosphoproteomics strategies for the functional analysis of signal transduction
Sandra Morandell, Taras Stasyk, Karin Grosstessner-Hain, Elisabeth Roitinger, Karl Mechtler, Guenther K. Bonn, Lukas A. Huber
PROTEOMICS (2006) 6(14): 4047-4056

Antibody Arrays: Technical Considerations And Clinical Applications in Cancer.
Sanchez-Carbayo M.
Clin Chem Early Edition: published 29-Jun-2006

Proteomic dissection of plant development
Frank Hochholdinger, Michaela Sauer, Diana Dembinsky, Nadine Hoecker, Nils Muthreich, Muhammad Saleem, Yan Liu
PROTEOMICS (2006) 6(14): 4076-4083

Proteomics for the early detection and treatment of hepatocellular carcinoma.
Feng JT, Shang S, Beretta L.
Oncogene (2006) 25(27): 3810-7

Proteome research based on modern liquid chromatography - tandem mass spectrometry: separation, identification and quantification.
Frohlich T, Arnold GJ.
J Neural Transm Early Edition: published 13-Jul-2006

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Methodology

Proteomic analysis of low-abundant integral plasma membrane proteins based on gels.
Zhang LJ, Wang XE, Peng X, Wei YJ, Cao R, Liu Z, Xiong JX, Yin XF, Ping C, Liang S.
Cell Mol Life Sci Early Edition: published 17-Jul-2006

A simple protocol for protein extraction of recalcitrant fruit tissues suitable for 2-DE and MS analysis.
Song J, Braun G, Bevis E, Doncaster K.
Electrophoresis Early Edition: published 29-Jun-2006

Development of an effective sample preparation approach for proteomic analysis of silkworm eggs using two-dimensional gel electrophoresis and mass spectrometry.
Long XH, Zhu JW, Mo ZH, Feng S, Cheng G, Zhou XW, Zhang YZ, Yang PY.
J Chromatogr A Early Edition: published 3-Jul-2006

Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry-applications and perspectives.
Tholey A, Heinzle E.
Anal Bioanal Chem Early Edition: published 8-Jul-2006

Insights into the mechanism of microtubule stabilization by Taxol.
Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, Burd B, Angeletti R, Fiser A, Horwitz SB, Orr GA.
Proc Natl Acad Sci U S A Early Edition: published 26-Jun-2006

Efficient extraction of proteins from woody plant samples for two-dimensional electrophoresis
Cristina-Maria V�lcu, Katja Schlink
PROTEOMICS (2006) 6(14): 4166-4175

Microfluidic Analysis of Antibody Specificity in a Compact Disk Format
Cecilia Eriksson, Charlotta Agaton, Rikard Kånge, Mårten Sundberg, Peter Nilsson, Bo Ek, Mathias Uhlén, Magnus Gustafsson, and Sophia Hober
JOURNAL OF PROTEOME RESEARCH (2006) 5(7): 1568-1574

Impact of Analytical Bias in Metabonomic Studies of Human Blood Serum and Plasma.
Teahan O, Gamble S, Holmes E, Waxman J, Nicholson JK, Bevan C, Keun HC.
Anal Chem (2006) 78(13): 4307-4318

Knowledge-based proteome profiling: Considering identified proteins to evaluate separation efficiency by 2-D PAGE
Nina Gundacker, Editha Bayer, Elisabeth Traxler, Hannes Zwickl, Markus Kubicek, Johannes St�ckl, Christopher Gerner
ELECTROPHORESIS (2006) 27(13): 2712-2721

Proteomic methods applied to the analysis of immobilized biocatalysts.
Petry I, Ganesan A, Pitt A, Moore BD, Halling PJ.
Biotechnol Bioeng Early Edition: published 28-Jun-2006

ESI-MS Compatible Permanent Coating of Glass Surfaces Using Poly(ethylene glycol)-Terminated Alkoxysilanes for Capillary Zone Electrophoretic Protein Separations.
Razunguzwa TT, Warrier M, Timperman AT.
Anal Chem (2006) 78(13): 4326-33

Automated Ultra-High-Pressure Multidimensional Protein Identification Technology (UHP-MudPIT) for Improved Peptide Identification of Proteomic Samples
Akira Motoyama, John D. Venable, Cristian I. Ruse, and John R. Yates, III
ANALYTICAL CHEMISTRY (2006) 78(14): 5109-5118

Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues.
Hwang SI, Thumar J, Lundgren DH, Rezaul K, Mayya V, Wu L, Eng J, Wright ME, Han DK.
Oncogene Early Edition: published 26-Jun-2006

Protein EqualizerTM Technology: The quest for a ?democratic proteome?
Pier Giorgio Righetti, Egisto Boschetti, Lee Lomas, Attilio Citterio
PROTEOMICS (2006) 6(14): 3980-3992

Enrichment of integral membrane proteins from small amounts of brain tissue.
Schindler J, Jung S, Niedner-Schatteburg G, Friauf E, Nothwang HG.
J Neural Transm Early Edition: published 13-Jul-2006

Quantitative mass spectrometric identification of isomers applying coherent laser control.
Dela Cruz JM, Lozovoy VV, Dantus M.
J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory (2005) 109(38): 8447-50

Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics
Wilhelm Haas, Brendan K. Faherty, Scott A. Gerber, Joshua E. Elias, Sean A. Beausoleil, Corey E. Bakalarski, Xue Li, Judit Villen, and Steven P. Gygi
Mol Cell Proteomics (2006) 5(7): 1326-1337

Evaluation of two sample preparation methods for prostate proteome analysis
Helena Lexander, Ulf Hellman, Carina Palmberg, Gert Auer, Magnus Hellstr�m, Bo Franz�n, Hans J�rnvall, Lars Egevad
PROTEOMICS (2006) 6(13): 3918-3925

A high efficiency cloning and expression system for proteomic analysis
Xuan Z. Ding, Ian T. Paulsen, Apurba K. Bhattacharjee, Mikeljon P. Nikolich, Gary Myers, David L. Hoover
PROTEOMICS (2006) 6(14): 4038-4046

Side-Chain Fragmentation of Alkylated Cysteine Residues in Electron Capture Dissociation Mass Spectrometry.
Chalkley RJ, Brinkworth CS, Burlingame AL.
J Am Soc Mass Spectrom Early Edition: published 27-Jun-2006

Comparison of different separation technologies for proteome analyses: Isoform resolution as a prerequisite for the definition of protein biomarkers on the level of posttranslational modifications.
Hunzinger C, Schrattenholz A, Poznanovic S, Schwall GP, Stegmann W.
J Chromatogr A Early Edition: published 3-Jul-2006

Use of Nitrocellulose Membranes for Protein Characterization by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
Jose L. Luque-Garcia, Ge Zhou, Tung-Tien Sun, and Thomas A. Neubert
ANALYTICAL CHEMISTRY (2006) 78(14): 5102-5108

Prostatic tissue protein alterations due to delayed time to freezing
David Jackson, Rachel A. Rowlinson, Cassie K. Eaton, Janice A. Nickson, Ian D. Wilson, Jonathan D. Mills, Robert W. Wilkinson, Robert P. Tonge
PROTEOMICS (2006) 6(13): 3901-3908

Nanopore-Based Proteolytic Reactor for Sensitive and Comprehensive Proteomic Analyses
Wenqing Shui, Jie Fan, Pengyuan Yang, Chunli Liu, Jianjun Zhai, Jie Lei, Yan Yan, Dongyuan Zhao, and Xian Chen
ANALYTICAL CHEMISTRY (2006) 78(14): 4811-4819

Utility of cleavable isotope-coded affinity-tagged reagents for quantification of low-copy proteins induced by methylprednisolone using liquid chromatography/tandem mass spectrometry.
Qu J, Jusko WJ, Straubinger RM.
Anal Chem (2006) 78(13): 4543-52

A relevant in vitro eukaryotic live-cell system for the evaluation of plasmodial protein localization.
Chan M, Tan DS, Wong SH, Sim TS.
Biochimie Early Edition: published 22-Jun-2006

Effect of staining reagent on peptide mass fingerprinting from in-gel trypsin digestions: A comparison of SyproRubytrade mark and DeepPurpletrade mark.
Tannu NS, Sanchez-Brambila G, Kirby P, Andacht TM.
Electrophoresis Early Edition: published 26-Jun-2006

Monolithic Column HPLC Separation of Intact Proteins Analyzed by LC-MALDI Using On-Plate Digestion: An Approach To Integrate Protein Separation and Identification
Suping Zheng, Chul Yoo, Nathanael Delmotte, Fred R. Miller, Christian G. Huber, and David M. Lubman
ANALYTICAL CHEMISTRY (2006) 78(14): 5198-5204

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Meeting

Standards for Plasma and Serum Proteomics in Early Cancer Detection: A Needs Assessment Report from the National Institute of Standards and Technology-National Cancer Institute Standards, Methods, Assays, Reagents and Technologies Workshop, August 18-19, 2005.
Barker PE, Wagner PD, Bunk SE, Srivastava S, Omenn GS.
Clin Chem Early Edition: published 13-Jul-2006

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Other

The launch of PROTEOMICS - Clinical Applications
Michael J. Dunn
PROTEOMICS (2006) 6(13): 3729

TOOLbox: Metabolite projection analysis | 2DDB for proteomics data | Real-time peptide-spectrum matching | Integrator
JOURNAL OF PROTEOME RESEARCH (2006) 5(7): 1522-1523

Society News: Proteomics 14/2006
PROTEOMICS (2006) 6(14): 4207

Currents: Multidimensional IMS | What's in that organelle? | Variables that affect serum and plasma profiling | Which cows are on steroids? | Plastic chip for 2D protein separations | The lipid droplet subproteome
JOURNAL OF PROTEOME RESEARCH (2006) 5(7): 1521-1523

Proteomics Projects: HUPO Publications Committee and PSI discuss standards
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2006) 5(7): 1526

Reverse genetics for proteomics: From proteomic discovery to scientific content.
Bauer M, Ueffing M.
J Neural Transm Early Edition: published 13-Jul-2006

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