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SPS' Digest

Issue 12, 3-Nov-2004

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Quick jumps to articles in: Bioinformatics (15) / Biological applications (13) / Biomedical and clinical applications (32) / Eukaryotic Cells And Tissues (8) / Prokaryotes (1) / Pharmacology and Toxicology (3) / Protein Characterization - PTMs (10) / Protein-protein interaction (2) / Quantitation (2) / Review (15) / Methodology (15) / Other (3) /

In this issue, 115 articles have been selected from:
Disclaimer: The selection and categorisation reflect the views and understandings of contributors (i.e. SPS members).

Quick jumps to articles in: Bioinformatics (15) / Biological applications (13) / Biomedical and clinical applications (32) / Eukaryotic Cells And Tissues (8) / Prokaryotes (1) / Pharmacology and Toxicology (3) / Protein Characterization - PTMs (10) / Protein-protein interaction (2) / Quantitation (2) / Review (15) / Methodology (15) / Other (3) /

Bioinformatics

De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation
Zhongqi Zhang
ANALYTICAL CHEMISTRY (2004) 76(21): 6374-6383

Processing of Data Generated by 2-Dimensional Gel Electrophoresis for Statistical Analysis: Missing Data, Normalization, and Statistics
Jinsook Chang, Holly Van Remmen, # Walter F. Ward, Arlan Richardson, # and John Cornell #
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/15/2004

Proteins associated with diseases show enhanced sequence correlation between charged residues
Ruxandra I. Dima and D. Thirumalai
Bioinformatics (2004) 20(15): 2345-2354

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins
Aleksey A. Porollo, Rafal Adamczak, and Jaroslaw Meller
Bioinformatics (2004) 20(15): 2460-2462

HPID: The Human Protein Interaction Database
Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong, and Jong Park
Bioinformatics (2004) 20(15): 2466-2470

The SRS 3D module: integrating structures, sequences and features
Sean I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, and Karsten Fries
Bioinformatics (2004) 20(15): 2476-2478

The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries
Daniel Fischer, Jakub Pas, and Leszek Rychlewski
Bioinformatics (2004) 20(15): 2482-2484

Proteomic informatics.
Russell SA, Old W, Resing KA, Hunter L.
Int Rev Neurobiol (2004) 61: 127-57

Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry
Dragan Radulovic, Salomeh Jelveh, Soyoung Ryu, T. Guy Hamilton, Eric Foss, Yongyi Mao, and Andrew Emili
Mol Cell Proteomics (2004) 3(10): 984-997

Experimental Peptide Identification Repository (EPIR): An Integrated Peptide-Centric Platform for Validation and Mining of Tandem Mass Spectrometry Data
Dan Bach Kristensen, Jan Christian Brond, Peter Aagaard Nielsen, Jens Roswald Andersen, Ole Tang Sorensen, Vibeke Jorgensen, Kenneth Budin, Jesper Matthiesen, Peter Veno, Hans Mikael Jespersen, Christian H. Ahrens, Soeren Schandorff, Peder Thusgaard Ruhoff, Jacek R. Wisniewski, Keiryn L. Bennett, and Alexandre V. Podtelejnikov
Mol Cell Proteomics (2004) 3(10): 1023-1038

A Dataset of Human Liver Proteins Identified by Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry
Wei Yan, Hookeun Lee, Eric W. Deutsch, Catherine A. Lazaro, Weiliang Tang, Eric Chen, Nelson Fausto, Michael G. Katze, and Ruedi Aebersold
Mol Cell Proteomics (2004) 3(10): 1039-1041

Open Source System for Analyzing, Validating, and Storing Protein Identification Data
Robertson Craig, John P. Cortens, and Ronald C. Beavis
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Open Mass Spectrometry Search Algorithm
Lewis Y. Geer, Sanford P. Markey, Jeffrey A. Kowalak, Lukas Wagner, Ming Xu, Dawn M. Maynard, Xiaoyu Yang, Wenyao Shi, and Stephen H. Bryant
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 958-964

The Statistical Significance of Protein Identification Results as a Function of the Number of Protein Sequences Searched
Jan Eriksson and David Fenyö
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 979-982

DBParser: Web-Based Software for Shotgun Proteomic Data Analyses
Xiaoyu Yang, Vijay Dondeti, Rebecca Dezube, Dawn M. Maynard, Lewis Y. Geer, Jonathan Epstein, Xiongfong Chen, Sanford P. Markey, and Jeffrey A. Kowalak
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1002-1008

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Biological applications

Structural Modifications Enable Conserved Peptides to Fit into MHC Molecules thus Inducing Protection against Malaria
Manuel Elkin Patarroyo, Gladys Cifuentes, Luis Eduardo Vargas, Jaiver Rosas
ChemBioChem (2004) 5(11): 1588-1593

Expression proteomics identifies biochemical adaptations and defense responses in transgenic plants with perturbed polyamine metabolism.
Franceschetti M, Perry B, Thompson B, Hanfrey C, Michael AJ.
FEBS Lett (2004) 576(3): 477-80

Molecular mechanisms in clathrin-mediated membrane budding revealed through subcellular proteomics.
Ritter B, Blondeau F, Denisov AY, Gehring K, McPherson PS.
Biochem Soc Trans (2004) 32(Pt 5): 769-73

Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells
Qiang Tian, Serguei B. Stepaniants, Mao Mao, Lee Weng, Megan C. Feetham, Michelle J. Doyle, Eugene C. Yi, Hongyue Dai, Vesteinn Thorsson, Jimmy Eng, David Goodlett, Joel P. Berger, Bert Gunter, Peter S. Linseley, Roland B. Stoughton, Ruedi Aebersold, Steven J. Collins, William A. Hanlon, and Leroy E. Hood
Mol Cell Proteomics (2004) 3(10): 960-969

A Dataset of Human Liver Proteins Identified by Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry
Wei Yan, Hookeun Lee, Eric W. Deutsch, Catherine A. Lazaro, Weiliang Tang, Eric Chen, Nelson Fausto, Michael G. Katze, and Ruedi Aebersold
Mol Cell Proteomics (2004) 3(10): 1039-1041

Proteomics-application to the brain.
Marcus K, Schmidt O, Schaefer H, Hamacher M, van Hall A, Meyer HE.
Int Rev Neurobiol (2004) 61: 285-311

The Schistosoma mansoni soluble proteome: a comparison across four life-cycle stages.
Curwen RS, Ashton PD, Johnston DA, Wilson RA.
Mol Biochem Parasitol (2004) 138(1): 57-66

Global Investigation of p53-induced Apoptosis Through Quantitative Proteomic Profiling Using Comparative Amino Acid-coded Tagging
Sheng Gu, Zhihe Liu, Songqin Pan, Zeyu Jiang, Huimei Lu, Or Amit, E. Morton Bradbury, Chien-An A. Hu, and Xian Chen
Mol Cell Proteomics (2004) 3(10): 998-1008

Biology of the Cold Adapted Archaeon, Methanococcoides burtonii Determined by Proteomics Using Liquid Chromatography-Tandem Mass Spectrometry
Amber Goodchild, Mark Raftery, Neil F. W. Saunders, Ricardo Cavicchioli
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Proteome Analysis of Tobacco Bright Yellow-2 (BY-2) Cell Culture Plastids as a Model for Undifferentiated Heterotrophic Plastids
Sacha Baginsky, Asim Siddique, and Wilhelm Gruissem
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Membrane proteome analysis of the green-sulfur bacterium Chlorobium tepidum
Michalis Aivaliotis, Carsten Corvey, Irene Tsirogianni, Michael Karas, Georgios Tsiotis
ELECTROPHORESIS (2004) 25(20): 3468-3474

Proteomics and Leukocytes: An Approach to Understanding Potential Molecular Mechanisms of Inflammatory Responses
Xiangdong Wang, Hong Zhao, and Roland Andersson
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 921-929

Two-Dimensional Liquid Chromatography Study of the Human Whole Saliva Proteome
Phillip A. Wilmarth, Michael A. Riviere, D. Leif Rustvold, Jeffrey D. Lauten, Theresa E. Madden, and Larry L. David
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1017-1023

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Biomedical and clinical applications

Proteome Analysis of Gastric Cancer Metastasis by Two-Dimensional Gel Electrophoresis and Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry for Identification of Metastasis-Related Proteins
Jie Chen, Thilo Kähne, Christoph Röcken, Tobias Götze, Jun Yu, Joseph J. Y. Sung, Minhu Chen, # Pinjin Hu, # Peter Malfertheiner, and Matthias P. A. Ebert
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1009-1016

Proteomic analysis of human acute leukemia cells: insight into their classification.
Cui JW, Wang J, He K, Jin BF, Wang HX, Li W, Kang LH, Hu MR, Li HY, Yu M, Shen BF, Wang GJ, Zhang XM.
Clin Cancer Res (2004) 10(20): 6887-96

Application of Mycobacterial Proteomics to Vaccine Design: Improved Protection by Mycobacterium bovis BCG Prime-Rv3407 DNA Boost Vaccination against Tuberculosis.
Mollenkopf HJ, Grode L, Mattow J, Stein M, Mann P, Knapp B, Ulmer J, Kaufmann SH.
Infect Immun (2004) 72(11): 6471-9

Proteomics: a novel tool to unravel the patho-physiology of uraemia.
Weissinger EM, Kaiser T, Meert N, De Smet R, Walden M, Mischak H, Vanholder RC.
Nephrol Dial Transplant Early Edition: published 19-Oct-2004

Identification of hypoxia-regulated proteins in head and neck cancer by proteomic and tissue array profiling.
Chen Y, Shi G, Xia W, Kong C, Zhao S, Gaw AF, Chen EY, Yang GP, Giaccia AJ, Le QT, Koong AC.
Cancer Res (2004) 64(20): 7302-10

Proteomic analysis of plasma from patients during an acute coronary syndrome.
Mateos-Caceres PJ, Garcia-Mendez A, Lopez Farre A, Macaya C, Nunez A, Gomez J, Alonso-Orgaz S, Carrasco C, Burgos ME, de Andres R, Granizo JJ, Farre J, Rico LA.
J Am Coll Cardiol (2004) 44(8): 1578-83

Comparative analysis of the proteome of left ventricular heart of arteriosclerosis in rat.
Huang ZY, Yang PY, Radwan Almofti M, Yu YL, Rui YC, Yang PY.
Life Sci (2004) 75(26): 3103-15

Proteomics and Leukocytes: An Approach to Understanding Potential Molecular Mechanisms of Inflammatory Responses
Xiangdong Wang, Hong Zhao, and Roland Andersson
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 921-929

Two-Dimensional Liquid Chromatography Study of the Human Whole Saliva Proteome
Phillip A. Wilmarth, Michael A. Riviere, D. Leif Rustvold, Jeffrey D. Lauten, Theresa E. Madden, and Larry L. David
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1017-1023

Comprehensive Proteomic Analysis of Human Pancreatic Juice
Mads Gr nborg, Jakob Bunkenborg, Troels Zakarias Kristiansen, Ole N rregaard Jensen, Charles J. Yeo, Ralph H. Hruban, Anirban Maitra, Michael G. Goggins, and Akhilesh Pandey
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1042-1055

Evaluation of Metabolic Labeling for Comparative Proteomics in Breast Cancer Cells
Marion L. Gehrmann, Yetrib Hathout, and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1063-1068

From genomes to vaccines via the proteome.
Wilson RA, Curwen RS, Braschi S, Hall SL, Coulson PS, Ashton PD.
Mem Inst Oswaldo Cruz (2004) 99: 45-50.

Proteomics in cancer screening and management in gynecologic cancer.
Hu W, Wu W, Kobayashi R, Kavanagh JJ.
Curr Oncol Rep (2004) 6(6): 456-62

Proteomic approaches in drug discovery and development.
Soares HD, Williams SA, Snyder PJ, Gao F, Stiger T, Rohlff C, Herath A, Sunderland T, Putnam K, White WF.
Int Rev Neurobiol (2004) 61: 97-126

Proteomic analysis of blood level of proteins before and after operation in patients with esophageal squamous cell carcinoma at high-incidence area in Henan Province.
An JY, Fan ZM, Zhuang ZH, Qin YR, Gao SS, Li JL, Wang LD.
World J Gastroenterol (2004) 10(22): 3365-8

Differential analysis of two-dimension gel electrophoresis profiles from the normal-metaplasia-dysplasia-carcinoma tissue of human bronchial epithelium.
Wu X, Xiao Z, Chen Z, Li C, Li J, Feng X, Yi H, Liang S, Chen P.
Pathol Int (2004) 54(10): 765-73

Influence of Huntington's Disease on the Human and Mouse Proteome.
Zabel C, Klose J.
Int Rev Neurobiol (2004) 61: 241-83

Proteome analysis of prostate cancer.
Kuruma H, Egawa S, Oh-Ishi M, Kodera Y, Maeda T.
Prostate Cancer Prostatic Dis Early Edition: published 12-Oct-2004

Proteomics studies of traumatic brain injury.
Wang KK, Ottens A, Haskins W, Cheng Liu M, Kobeissy F, Denslow N, Chen S, Hayes RL.
Int Rev Neurobiol (2004) 61: 215-40

Proteomic patterns for early cancer detection.
Veenstra TD, Prieto DA, Conrads TP.
Drug Discov Today (2004) 9(20): 889-97

Proteomics and alcoholism.
Witzmann FA, Strother WN.
Int Rev Neurobiol (2004) 61: 189-214

Proteomics analysis in Alzheimer's disease: new insights into mechanisms of neurodegeneration.
Butterfield DA, Boyd-Kimball D.
Int Rev Neurobiol (2004) 61: 159-88

Proteomic fingerprinting of human immunodeficiency virus type 1associated dementia from patient monocyte-derived macrophages: A case study.
Wojna V, Carlson K, Luo X, Mayo R, Mel Ez L, Kraiselburd E, Gendelman H.
J Neurovirol (2004) 10(Supplement 1): 74-81

Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.
Imafuku Y, Omenn GS, Hanash S.
Dis Markers (2004) 20(3): 149-53

A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays.
Zangar RC, Varnum SM, Covington CY, Smith RD.
Dis Markers (2004) 20(3): 135-48

Advancement of biomarker discovery and validation through the HUPO plasma proteome project.
Omenn GS.
Dis Markers (2004) 20(3): 131-4

Combined proteomic approach with SELDI-TOF-MS and peptide mass fingerprinting identified the rapid increase of monomeric transthyretin in rat cerebrospinal fluid after transient focal cerebral ischemia.
Suzuyama K, Shiraishi T, Oishi T, Ueda S, Okamoto H, Furuta M, Mineta T, Tabuchi K.
Brain Res Mol Brain Res (2004) 129(1-2): 44-53

Proteomics in diagnostic pathology: profiling and imaging proteins directly in tissue sections.
Chaurand P, Sanders ME, Jensen RA, Caprioli RM.
Am J Pathol (2004) 165(4): 1057-68

Proteomics techniques for cystic fibrosis research.
Roxo-Rosa M, Davezac N, Bensalem N, Majumder M, Heda GD, Simas A, Penque D, Amaral MD, Lukacs GL, Edelman A.
J Cyst Fibros (2004) 3(Suppl 2): 85-9

Proteome Analysis of NIH3T3 Cells Transformed by Activated G12: Regulation of Leukemia-Associated Protein SET
Rashmi N. Kumar, Rangasudhakar Radhakrishnan, Ji Hee Ha, and N. Dhanasekaran
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Analyzing Alkaline Proteins in Human Colon Crypt Proteome [J. Proteome Res. 2004, 4, 821-833],
Xin-Ming Li, Bhavinkumar B. Patel, Maketa D. Patterson, Steven H. Seeholzer, Shirish Damle, Zhenqiang Gao, Anthony T. Yeung
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Identification of Gastric Cancer Patients by Serum Protein Profiling
Matthias P. A. Ebert, Jörn Meuer, Jan C. Wiemer, Hans-Ulrich Schulz, Ulrich Traugott, Peter Malfertheiner, and Christoph Röcken
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

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Eukaryotic Cells And Tissues

Transcriptomic and proteomic analysis of liver and muscle alterations caused by surgical stress in rat.
Lopez-Hellin J, Gonzalo R, Tejeda M, Carrascal M, Vila MR, Abian J, Garcia-Arumi E.
Clin Sci (Lond) Early Edition: published 25-Oct-2004

Proteomic Analysis of the Arabidopsis Nucleolus Suggests Novel Nucleolar Functions.
Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M, Lamond AI, Brown JW, Shaw PJ.
Mol Biol Cell Early Edition: published 20-Oct-2004

Proteomics in platelet science.
Perrotta PL, Bahou WF.
Curr Hematol Rep (2004) 3(6): 462-9

Quantitative amino acid and proteomic analysis: Very low excretion of polypeptides >750 Da in normal urine.
Norden AG, Sharratt P, Cutillas PR, Cramer R, Gardner SC, Unwin RJ.
Kidney Int (2004) 66(5): 1994-2003

Comparative proteomic analysis of human whole saliva.
Huang CM.
Arch Oral Biol (2004) 49(12): 951-62

Proteomic analysis of mitochondrial proteins.
Lopez MF, Melov S, Johnson F, Nagulko N, Golenko E, Kuzdzal S, Ackloo S, Mikulskis A.
Int Rev Neurobiol (2004) 61: 31-48

Transcriptome and proteome expression in activated human CD4 and CD8 T-lymphocytes.
Stentz FB, Kitabchi AE.
Biochem Biophys Res Commun (2004) 324(2): 692-6

Proteomic analysis of the drosophila larval hemolymph clot.
Karlsson C, Korayem AM, Scherfer C, Loseva O, Dushay MS, Theopold U.
J Biol Chem Early Edition: published 4-Oct-2004

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Prokaryotes

Analysis of TNT (2,4,6-Trinitrotoluene)-Inducible Cellular Responses and Stress Shock Proteome in Stenotrophomonas sp. OK-5.
Ho EM, Chang HW, Kim SI, Kahng HY, Oh KH.
Curr Microbiol (2004) 49(5): 346-52

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Pharmacology and Toxicology

Genomics, proteomics and metabonomics in toxicology: hopefully not 'fashionomics'.
Pognan F.
Pharmacogenomics (2004) 5(7): 879-93

Recent advances in neuroproteomics and potential application to studies of drug addiction.
Williams K, Wu T, Colangelo C, Nairn AC.
Neuropharmacology (2004) 47(Suppl 1): 148-66

Proteomic approaches in brain research and neuropharmacology.
Vercauteren FG, Bergeron JJ, Vandesande F, Arckens L, Quirion R.
Eur J Pharmacol (2004) 500(1-3): 385-398

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Protein Characterization / PTMs

Laser Desorption and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry of 29-kDa Au:SR Cluster Compounds
T. Gregory Schaaff
ANALYTICAL CHEMISTRY (2004) 76(21): 6187-6196

Preparative Linear Ion Trap Mass Spectrometer for Separation and Collection of Purified Proteins and Peptides in Arrays Using Ion Soft Landing
Thomas A. Blake, Zheng Ouyang, Justin M. Wiseman, Zoltán Takáts, Andrew J. Guymon, Sameer Kothari, and R. Graham Cooks
ANALYTICAL CHEMISTRY (2004) 76(21): 6293-6305

Determination of Ligand-Protein Dissociation Constants by Electrospray Mass Spectrometry-Based Diffusion Measurements
Sonya M. Clark and Lars Konermann
ANALYTICAL CHEMISTRY Early Edition: published 10/29/2004

Off-line capillary electrophoresis/fully automated nanoelectrospray chip quadrupole time-of-flight mass spectrometry and tandem mass spectrometry for glycoconjugate analysis
Laura Bindila, Reinaldo Almeida, Alistair Sterling, Mark Allen, Jasna Peter-Katalini?, Alina Zamfir
Journal of Mass Spectrometry (2004) 39(10): 1190-1201

Using LC-MS with de novo software to fully characterize the multiple methylations of lysine residues in a recombinant fragment of an outer membrane protein from a virulent strain of Rickettsia prowazekii.
Chao CC, Wu SL, Ching WM.
Biochim Biophys Acta (2004) 1702(2): 145-52

Derivatization of phosphorylated peptides with S- and N-nucleophiles for enhanced ionization efficiency in matrix-assisted laser desorption/ionization mass spectrometry
Clementine Klemm, Stephan Schröder, Matthias Glückmann, Michael Beyermann, Eberhard Krause
Rapid Communications in Mass Spectrometry (2004) 18(22): 2697-2705

Structural Characterization of N-Glycopeptides by Matrix-Dependent Selective Fragmentation of MALDI-TOF/TOF Tandem Mass Spectrometry
Masaki Kurogochi and Shin-Ichiro Nishimura
ANALYTICAL CHEMISTRY (2004) 76(20): 6097-6101

Hydrophilic Affinity Isolation and MALDI Multiple-Stage Tandem Mass Spectrometry of Glycopeptides for Glycoproteomics
Yoshinao Wada, Michiko Tajiri, and Shumi Yoshida
ANALYTICAL CHEMISTRY Early Edition: published 10/15/2004

Definition and Characterization of a "Trypsinosome" from Specific Peptide Characteristics by Nano-HPLC-MS/MS and in Silico Analysis of Complex Protein Mixtures
Thierry Le Bihan, Mark D. Robinson, Ian I. Stewart, and Daniel Figeys
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Two-Dimensional Mass Spectra Generated from the Analysis of 15N-Labeled and Unlabeled Peptides for Efficient Protein Identification and de novo Peptide Sequencing
Hongying Zhong, Sandra L. Marcus, and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

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Protein-protein interaction

Optimal docking area: A new method for predicting protein-protein interaction sites.
Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R.
Proteins Early Edition: published 19-Oct-2004

GPCR-interacting proteins (GIPs): nature and functions.
Bockaert J, Roussignol G, Becamel C, Gavarini S, Joubert L, Dumuis A, Fagni L, Marin P.
Biochem Soc Trans (2004) 32(Pt 5): 851-5

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Quantitation

Quantitative proteome analysis in benign thyroid nodular disease using the fluorescent ruthenium II tris(bathophenanthroline disulfonate) stain.
Berger K, Wissmann D, Ihling C, Kalkhof S, Beck-Sickinger A, Sinz A, Paschke R, Fuhrer D.
Mol Cell Endocrinol (2004) 227(1-2): 21-30

N-Terminal Isotope Tagging Strategy for Quantitative Proteomics: Results-Driven Analysis of Protein Abundance Changes
Francesca Zappacosta and Roland S. Annan
ANALYTICAL CHEMISTRY Early Edition: published 10/15/2004

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Review

Molecular Therapeutic Target for Type-2 Diabetes
Kuo-Chen Chou
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/22/2004

Chemistry meets Biology: Chemical Approaches to the Study of Biology
Kristian Strømgaard
ChemBioChem (2004) 5(11): 1601-1603

Proteomics for hepatocellular carcinoma marker discovery.
Chignard N, Beretta L.
Gastroenterology (2004) 127(5 Suppl 2): S120-5

Heart disease, clinical proteomics and mass spectrometry.
Stanley BA, Gundry RL, Cotter RJ, Van Eyk JE.
Dis Markers (2004) 20(3): 167-78

Update on diabetes mellitus.
Korc M.
Dis Markers (2004) 20(3): 161-5

The use of laser capture microscopy in proteomics research--a review.
Kunz GM Jr, Chan DW.
Dis Markers (2004) 20(3): 155-60

Ion activation methods for tandem mass spectrometry
Lekha Sleno, Dietrich A. Volmer
Journal of Mass Spectrometry (2004) 39(10): 1091-1112

Proteomics.
de Hoog CL, Mann M.
Annu Rev Genomics Hum Genet (2004) 5: 267-93

The use of proteomics for the assessment of clinical samples in research.
Aldred S, Grant MM, Griffiths HR.
Clin Biochem (2004) 37(11): 943-52

Comparative proteomics analysis of human pituitary adenomas: Current status and future perspectives.
Zhan X, Desiderio DM.
Mass Spectrom Rev Early Edition: published 19-Oct-2004

Mass spectrometry in aging research.
Schoneich C.
Mass Spectrom Rev Early Edition: published 19-Oct-2004

Membrane trafficking in plants: new discoveries and approaches.
Carter CJ, Bednarek SY, Raikhel NV.
Curr Opin Plant Biol (2004) 7(6): 701-7

Proteomics of the Drosophila immune response.
Engstrom Y, Loseva O, Theopold U.
Trends Biotechnol (2004) 22(11): 600-5

Mitochondriomics or what makes us breathe.
Reichert AS, Neupert W.
Trends Genet (2004) 20(11): 555-62

MHC-bound antigens and proteomics for novel target discovery.
Shoshan SH, Admon A.
Pharmacogenomics (2004) 5(7): 845-59

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Methodology

Characterization of the 70S Ribosome from Rhodopseudomonas palustris Using an Integrated "Top-Down" and "Bottom-Up" Mass Spectrometric Approach
Michael Brad Strader, Nathan C. VerBerkmoes, David L. Tabb, Heather M. Connelly, John W. Barton, Barry D. Bruce, Dale A. Pelletier, Brian H. Davison, Robert L. Hettich, Frank W. Larimer, and Gregory B. Hurst
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 965-978

Integrated Protein Microchip Assay with Dual Fluorescent- and MALDI Read-Out
D. Finnskog, A. Ressine, T. Laurell, and G. Marko-Varga
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 988-994

Magnetic Cell Separation Using Antibody Binding with Protein A Expressed on Bacterial Magnetic Particles
Motoki Kuhara, Haruko Takeyama, Tsuyoshi Tanaka, and Tadashi Matsunaga
ANALYTICAL CHEMISTRY (2004) 76(21): 6207-6213

Automating proteome analysis: improvements in throughput, quality and accuracy of protein identification by peptide mass fingerprinting.
Canelle L, Pionneau C, Marie A, Bousquet J, Bigeard J, Lutomski D, Kadri T, Caron M, Joubert-Caron R.
Rapid Commun Mass Spectrom (2004) 18(23): 2785-2794

Utility of Dry Gel from Two-dimensional Electrophoresis for Peptide Mass Fingerprinting Analysis of Silkworm Proteins.
Zhang P, Yamamoto K, Wang Y, Banno Y, Fujii H, Miake F, Kashige N, Aso Y.
Biosci Biotechnol Biochem (2004) 68(10): 2148-54

Evaluation of Metabolic Labeling for Comparative Proteomics in Breast Cancer Cells
Marion L. Gehrmann, Yetrib Hathout, and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1063-1068

Characterization of Low Abundant Membrane Proteins Using the Protein Sequence Tag Technology
Thorsten Prinz, Jörg Müller, Karsten Kuhn, Jürgen Schäfer, Andrew Thompson, Josef Schwarz, and Christian Hamon
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1073-1081

Potential for False Positive Identifications from Large Databases through Tandem Mass Spectrometry
Benjamin J. Cargile, Jonathan L. Bundy, and James L. Stephenson, Jr.
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 1082-1085

Isotope-Coded Affinity Tag (ICAT) Approach to Redox Proteomics: Identification and Quantitation of Oxidant-Sensitive Cysteine Thiols in Complex Protein Mixtures
Mahadevan Sethuraman, Mark E. McComb, Hua Huang, Sequin Huang, Catherine E. Costello, and Richard A. Cohen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 10/15/2004

Ion activation methods for tandem mass spectrometry.
Sleno L, Volmer DA.
J Mass Spectrom (2004) 39(10): 1091-1112

Diagnostic protein discovery using proteolytic peptide targeting and identification
John M. Koomen, Haitao Zhao, Donghui Li, James Abbruzzese, Keith Baggerly, Ryuji Kobayashi
Rapid Communications in Mass Spectrometry (2004) 18(21): 2537-2548

Increased Identification of Peptides by Enhanced Data Processing of High-Resolution MALDI TOF/TOF Mass Spectra Prior to Database Searching
Tomas Rejtar, Hsuan-shen Chen, Victor Andreev, Eugene Moskovets, and Barry L. Karger
ANALYTICAL CHEMISTRY (2004) 76(20): 6017-6028

Differential Mass Spectrometry: A Label-Free LC-MS Method for Finding Significant Differences in Complex Peptide and Protein Mixtures
Matthew C. Wiener, Jeffrey R. Sachs, Ekaterina G. Deyanova, and Nathan A. Yates
ANALYTICAL CHEMISTRY (2004) 76(20): 6085-6096

Nano-scale Proteomics Approach Using Two-dimensional Fibrin Zymography Combined with Fluorescent SYPRO Ruby Dye.
Choi NS, Yoo KH, Yoon KS, Maeng PJ, Kim SH.
J Biochem Mol Biol (2004) 37(3): 298-303

Capillary isoelectric focusing-mass spectrometry for shotgun approach in proteomics
Henricus F. Storms, Robert van der Heijden, Ubbo R. Tjaden, Jan van der Greef
ELECTROPHORESIS (2004) 25(20): 3461-3467

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Other

A Profound State of Ignorance
William S. Hancock
JOURNAL OF PROTEOME RESEARCH (2004) 3(5): 909

Gel-based Proteomics: What Does MCP Expect?
Julio E. Celis
Mol Cell Proteomics (2004) 3(10): 949

Bacterial Identification by Protein Mass Mapping Combined with an Experimentally Derived Protein Mass Database
Lidan Tao, Xinlei Yu, A. Peter Snyder, and Liang Li
ANALYTICAL CHEMISTRY Early Edition: published 10/22/2004

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