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SPS' Digest

Issue 22, 1-Sep-2005

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Quick jumps to articles in: Bioinformatics (36) / Biological applications (47) / Biomedical and clinical applications (72) / Eukaryotic Cells And Tissues (12) / Prokaryotes (10) / Pharmacology and Toxicology (4) / Protein Array (7) / Protein Characterization - PTMs (23) / Protein-protein interaction (5) / Quantitation (9) / Review (24) / Methodology (48) / Books (2) / Meeting (5) / Other (12) /

In this issue, 301 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 (36) / Biological applications (47) / Biomedical and clinical applications (72) / Eukaryotic Cells And Tissues (12) / Prokaryotes (10) / Pharmacology and Toxicology (4) / Protein Array (7) / Protein Characterization - PTMs (23) / Protein-protein interaction (5) / Quantitation (9) / Review (24) / Methodology (48) / Books (2) / Meeting (5) / Other (12) /

Bioinformatics

Modeling Biological Variability in 2-D Gel Proteomic Carcinogenesis Experiments
Craig Rowell, Mark Carpenter, and Coral A. Lamartiniere
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/19/2005

STEM: A Software Tool for Large-Scale Proteomic Data Analyses
Takashi Shinkawa, Masato Taoka, Yoshio Yamauchi, Tohru Ichimura, Hiroyuki Kaji, Nobuhiro Takahashi, and Toshiaki Isobe
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/26/2005

New Data Base-independent, Sequence Tag-based Scoring of Peptide MS/MS Data Validates Mowse Scores, Recovers Below Threshold Data, Singles Out Modified Peptides, and Assesses the Quality of MS/MS Techniques
Mikhail M. Savitski, Michael L. Nielsen, and Roman A. Zubarev
Mol Cell Proteomics (2005) 4(8): 1180-1188

Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer: I. How Much of the Data is Theoretically Interpretable by Search Engines?
Robert J. Chalkley, Peter R. Baker, Kirk C. Hansen, Katalin F. Medzihradszky, Nadia P. Allen, Michael Rexach, and Alma L. Burlingame
Mol Cell Proteomics (2005) 4(8): 1189-1193

Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer: II. New Developments in Protein Prospector Allow for Reliable and Comprehensive Automatic Analysis of Large Datasets
Robert J. Chalkley, Peter R. Baker, Lan Huang, Kirk C. Hansen, Nadia P. Allen, Michael Rexach, and Alma L. Burlingame
Mol Cell Proteomics (2005) 4(8): 1194-1204

Localization, Annotation, and Comparison of the Escherichia coli K-12 Proteome under Two States of Growth
Ana Lopez-Campistrous, Paul Semchuk, Lorne Burke, Taunja Palmer-Stone,Stephen J. Brokx, Gordon Broderick, Drell Bottorff, Sandra Bolch, Joel H. Weiner, and Michael J. Ellison
Mol Cell Proteomics (2005) 4(8): 1205-1209

Sociomics! Using the IssueCrawler to map, monitor and engage with the global proteomics research network
Ruth McNally
PROTEOMICS (2005) 5(12): 3010-3016

A novel strategy using MASCOT Distiller for analysis of cleavable isotope-coded affinity tag data to quantify protein changes in plasma
Kit-Yi Leung, Pierre Lescuyer, James Campbell, Helen L. Byers, Laure Allard, Jean-Charles Sanchez, Malcolm A. Ward
PROTEOMICS (2005) 5(12): 3040-3044

SPS' Digest: The Swiss Proteomics Society selection of proteomics articles
Christine Hoogland, Niels Lion, Patricia M. Palagi, Jean-Charles Sanchez, Jean-Daniel Tissot
PROTEOMICS (2005) 5(12): 3045-3047

Web-based data warehouse on gene expression in human colorectal cancer
Emil Sagynaliev, Ralf Steinert, Gerd Nestler, Hans Lippert, Manfred Knoch, Marc-André Reymond
PROTEOMICS (2005) 5(12): 3066-3078

Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data
Yu J, Chen XW
Bioinformatics (2005) 21(Suppl 1): i487-i494

Automated interpretation of MS/MS spectra of oligosaccharides
Tang H, Mechref Y, Novotny MV
Bioinformatics (2005) 21(Suppl 1): i431-i439

In silico identification of functional regions in proteins
Nimrod G, Glaser F, Steinberg D, Ben-Tal N, Pupko T
Bioinformatics (2005) 21(Suppl 1): i328-i337

Beyond the clause: extraction of phosphorylation information from medline abstracts
M. Narayanaswamy, K. E. Ravikumar and K. Vijay-Shanker
Bioinformatics (2005) 21(Suppl 1): i319-i327

Bias, Randomization, and Ovarian Proteomic Data: A Reply to "Producers and Consumers"
Keith Baggerly, Kevin Coombes, Jeffrey Morris
Cancer Informatics (2005) 1(1): 9-14

Understanding the Characteristics of Mass Spectrometry Data Through the Use of Simulation
Kevin Coombes, John Koomen, Keith Baggerley, Jeffrey Morris, Ryuji Kobayashi
Cancer Informatics (2005) 1(1): 41-52

Robust Accurate Identification of Peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics
Alves G, Yu YK
Bioinformatics Early Edition: published 16-Aug-2005

Objective clustering of proteins based on subcellular location patterns
Chen X, Murphy RF
J Biomed Biotechnol (2005) 2005(2): 87-95

Functional clustering algorithm for high-dimensional proteomics data
Bensmail H, Aruna B, Semmes OJ, Haoudi A
J Biomed Biotechnol (2005) 2005(2): 80-6

Data standards for proteomics: mitochondrial two-dimensional polyacrylamide gel electrophoresis data as a model system
Ravichandran V, Vasquez GB, Srivastava S, Verma M, Petricoin E, Lubell J, Sriram RD, Barker PE, Gilliland GL
Mitochondrion (2004) 3(6): 327-36

DBToolkit: processing protein databases for peptide-centric proteomics
Lennart Martens, Joel Vandekerckhove, and Kris Gevaert
Bioinformatics (2005) 21(17): 3584-3585

Guidelines for the Routine Application of the Peptide Hits Technique
Ji Gao, Mark S. Friedrichs, Ashok R. Dongre and Gregory J. Opiteck
Journal of the American Society for Mass Spectrometry (2005) 16(8): 1231-1238

MS2Grouper: Group Assessment and Synthetic Replacement of Duplicate Proteomic Tandem Mass Spectra
David L. Tabb, Melissa R. Thompson, Gurusahai Khalsa-Moyers, Nathan C. VerBerkmoes and W. Hayes McDonald
Journal of the American Society for Mass Spectrometry (2005) 16(8): 1250-1261

Identification of Protein Fragments as Pattern Features in MALDI-MS Analyses of Serum
Lisa J. Zimmerman, Gregory R. Wernke, Richard M. Caprioli, and Daniel C. Liebler
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

Parallel Tandem: A Program for Parallel Processing of Tandem Mass Spectra Using PVM or MPI and X!Tandem
Dexter T. Duncan, Robertson Craig, and Andrew J. Link
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

AUDENS: A Tool for Automated Peptide de Novo Sequencing
Jonas Grossmann, Franz F. Roos, Mark Cieliebak, Zsuzsanna Lipták, Lucas K. Mathis, Matthias Müller, Wilhelm Gruissem, and Sacha Baginsky
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

Automated PreScan Function for Scanning Fluorescently Stained 2D-PAGE Gels
Peter Bäck, Sofia Bengtsson, and Peter James
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences
Ruan J, Wang K, Yang J, Kurgan LA, Cios K
Artif Intell Med Early Edition: published 1-Aug-2005

COPASAAR - A database tool for comparative proteomic analysis of single amino acid repeats
Depledge DP, Dalby AR
BMC Bioinformatics (2005) 6(1): 196

Evaluation of sequest result filter-Xcorr and Unified Score
Sun W, Li FX, Gaol YH, Zheng DX
Chin Med Sci J (2005) 20(2): 99-103

Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
Ari Frank, Stephen Tanner, Vineet Bafna, and Pavel Pevzner
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1287-1295

Large Scale Analysis of MASCOT Results Using a Mass Accuracy-Based THreshold (MATH) Effectively Improves Data Interpretation
Paul A. Rudnick, Yueju Wang, Erin Evans, Cheng S. Lee, and Brian M. Balgley
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1353-1360

Decoding two-dimensional polyacrylamide gel electrophoresis complex maps by autocovariance function: A simplified approach useful for proteomics
Maria Chiara Pietrogrande, Nicola Marchetti, Azzurra Tosi, Francesco Dondi, Pier Giorgio Righetti
ELECTROPHORESIS (2005) 26(14): 2739-2748

Predicting membrane protein type by functional domain composition and pseudo-amino acid composition
Cai YD, Chou KC
J Theor Biol Early Edition: published 22-Jul-2005

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments
Robert Moulder, Jan-Jonas Filén, Jussi Salmi, Mikko Katajamaa, Olli S. Nevalainen, Matej Oresic, Tero Aittokallio, Riitta Lahesmaa, Tuula A. Nyman
PROTEOMICS (2005) 5(11): 2748-2760

Improving feature detection and analysis of surface-enhanced laser desorption/ionization-time of flight mass spectra
Scott M. Carlson, Amir Najmi, John C. Whitin, Harvey J. Cohen
PROTEOMICS (2005) 5(11): 2778-2788

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Biological applications

Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes
Chanda I, Pan A, Dutta C
J Mol Evol Early Edition: published 21-Jul-2005

Repression of phase-variable cup gene expression by H-NS-like proteins in Pseudomonas aeruginosa
Vallet-Gely I, Donovan KE, Fang R, Joung JK, Dove SL
Proc Natl Acad Sci U S A Early Edition: published 25-Jul-2005

The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, Deboy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM
Proc Natl Acad Sci U S A Early Edition: published 25-Jul-2005

Investigating diversity in human plasma proteins
Nedelkov D, Kiernan UA, Niederkofler EE, Tubbs KA, Nelson RW
Proc Natl Acad Sci U S A Early Edition: published 25-Jul-2005

Proteomic identification of putative plasmodesmatal proteins from Chara corallina
Christine R. Faulkner, Leila M. Blackman, Stuart J. Cordwell, Robyn L. Overall
PROTEOMICS (2005) 5(11): 2866-2875

Proteomic analysis of kidney in fluoride-treated rat
Xu H, Hu LS, Chang M, Jing L, Zhang XY, Li GS
Toxicol Lett Early Edition: published 22-Jul-2005

Proteomic analysis of protein expression profiles during Caenorhabditis elegans development using two-dimensional difference gel electrophoresis
Yo Tabuse, Takuji Nabetani, Akira Tsugita
PROTEOMICS (2005) 5(11): 2876-2891

Structure-function relationships in mitochondrial complex I of the strictly aerobic yeast Yarrowia lipolytica
Brandt U, Abdrakhmanova A, Zickermann V, Galkin A, Drose S, Zwicker K, Kerscher S
Biochem Soc Trans (2005) 33(Pt 4): 840-4

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis
Hong-Lin Chan, Severine Gharbi, Piers R. Gaffney, Rainer Cramer, Michael D. Waterfield, John F. Timms
PROTEOMICS (2005) 5(11): 2908-2926

Site-specific detection of S-nitrosylated PKB alpha/Akt1 from rat soleus muscle using CapLC-Q-TOF(micro) mass spectrometry
Lu XM, Lu M, Tompkins RG, Fischman AJ
J Mass Spectrom Early Edition: published 22-Jul-2005

Protein profiling and identification of modulators regulated by human papillomavirus 16 E7 oncogene in HaCaT keratinocytes by proteomics
Lee KA, Kang JW, Shim JH, Won Kho C, Goo Park S, Gu Lee H, Paik SG, Lim JS, Yoon DY
Gynecol Oncol Early Edition: published 19-Jul-2005

Strategies to avoid the mis-identification of anatoxin-a using mass spectrometry in the forensic investigation of acute neurotoxic poisoning
Furey A, Crowley J, Hamilton B, Lehane M, James KJ
J Chromatogr A (2005) 1082(1): 91-7

Correcting Common Errors in Identifying Cancer-Specific Serum Peptide Signatures
Josep Villanueva, John Philip, Carlos A. Chaparro, Yongbiao Li, Ricardo Toledo-Crow, Lin DeNoyer, Martin Fleisher, Richard J. Robbins, and Paul Tempst
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1060-1072

Proteomic Analysis of Erythrocyte Membranes by Soft Immobiline Gels Combined with Differential Protein Extraction
Maurizio Bruschi, Claudio Seppi, Simona Arena, Luca Musante, Laura Santucci, Cesare Balduini, Andrea Scaloni, Marina Lanciotti, Pier Giorgio Righetti, and Giovanni Candiano
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1304-1309

Application of Two-Dimensional Difference Gel Electrophoresis to Studying Bone Marrow Macrophages and Their in Vivo Responses to Ionizing Radiation
Changwei Chen, Michael T. Boylan, Caroline A. Evans, Antony D. Whetton, and Eric G. Wright
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1371-1380

Metabolic Activation-related CD147-CD98 Complex
Daosong Xu and Martin E. Hemler
Mol Cell Proteomics (2005) 4(8): 1061-1071

Proteome Analysis of the Rice Etioplast: Metabolic and Regulatory Networks and Novel Protein Functions
Anne von Zychlinski, Torsten Kleffmann, Nandini Krishnamurthy, Kimmen Sjolander, Sacha Baginsky, and Wilhelm Gruissem
Mol Cell Proteomics (2005) 4(8): 1072-1084

Differential Impact of Environmental Stresses on the Pea Mitochondrial Proteome
Nicolas L. Taylor, Joshua L. Heazlewood, David A. Day, and A. Harvey Millar
Mol Cell Proteomics (2005) 4(8): 1122-1133

Non-stoichiometric Relationship between Clathrin Heavy and Light Chains Revealed by Quantitative Comparative Proteomics of Clathrin-coated Vesicles from Brain and Liver
Martine Girard, Patrick D. Allaire, Peter S. McPherson, and Francois Blondeau
Mol Cell Proteomics (2005) 4(8): 1145-1154

Carbonylation of milk powder proteins as a consequence of processing conditions
François Fenaille, Véronique Parisod, Jean-Claude Tabet, Philippe A. Guy
PROTEOMICS (2005) 5(12): 3097-3104

Novel Src Homology 3 Domain-binding Motifs Identified from Proteomic Screen of a Pro-rich Region
Christina Y. H. Jia, Jing Nie, Chenggang Wu, Chengjun Li, and Shawn S.-C. Li
Mol Cell Proteomics (2005) 4(8): 1155-1166

Cooperative evolution in protein complexes of yeast from comparative analyses of its interaction network
Massimo Vergassola, Alessandro Vespignani, Bernard Dujon
PROTEOMICS (2005) 5(12): 3116-3119

Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics
Dwayne A. Elias, Matthew E. Monroe, Matthew J. Marshall, Margaret F. Romine, Alexander S. Belieav, James K. Fredrickson, Gordon A. Anderson, Richard D. Smith, Mary S. Lipton
PROTEOMICS (2005) 5(12): 3120-3130

The N-terminal fragment of gelsolin inhibits the interaction of DNase I with isolated actin, but not with the cofilin-actin complex
Deepak Chhabra, Neil J. Nosworthy, Cristobal G. dos Remedios
PROTEOMICS (2005) 5(12): 3131-3136

Proteomic analysis on the expression of outer membrane proteins of Vibrio alginolyticus at different sodium concentrations
Changxin Xu, Sanying Wang, Haixia Ren, Xiangmin Lin, Lina Wu, Xuanxian Peng
PROTEOMICS (2005) 5(12): 3142-3152

Analysis of secreted proteins from Aspergillus flavus
Martha L. Medina, Paul A. Haynes, Linda Breci, Wilson A. Francisco
PROTEOMICS (2005) 5(12): 3153-3161

The human platelet proteome mapped by peptide-centric proteomics: A functional protein profile
Lennart Martens, Petra Van Damme, Jozef Van Damme, An Staes, Evy Timmerman, Bart Ghesquière, Grégoire R. Thomas, Joël Vandekerckhove, Kris Gevaert
PROTEOMICS (2005) 5(12): 3193-3204

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM
Proteomics (2005) 5(13): 3226-3245

Phosphorylation of numb family proteins: Possible involvement of Ca2+/calmodulin-dependent protein kinases
Tokumitsu H, Hatano N, Inuzuka H, Sueyoshi Y, Yokokura S, Ichimura T, Nozaki N, Kobayashi R
J Biol Chem Early Edition: published 16-Aug-2005

Mapping the platelet proteome: a report of the ISTH Platelet Physiology Subcommittee
Watson SP, Bahou WF, Fitzgerald D, Ouwehand W, Rao AK, Leavitt AD
J Thromb Haemost (2005) 3(9): 2098-101

Targets of microRNA regulation in the Drosophila oocyte proteome
Nakahara K, Kim K, Sciulli C, Dowd SR, Minden JS, Carthew RW
Proc Natl Acad Sci U S A Early Edition: published 12-Aug-2005

Cell cycle: proteomics gives it a spin
Vincent Archambault
Expert Review of Proteomics (2005) 2(4): 615-625

Analysis of proteins dominantly expressed in hepatic stellate cells of activated phenotype
Kawada N
Methods Mol Med (2005) 117: 371-80

The protein composition of honeybee venom reconsidered by a proteomic approach
Peiren N, Vanrobaeys F, de Graaf DC, Devreese B, Van Beeumen J, Jacobs FJ
Biochim Biophys Acta Early Edition: published 17-Aug-2005

Functional proteomics: a promising approach to find novel components of the circadian system
Wagner V, Gessner G, Mittag M
Chronobiol Int (2005) 22(3): 403-15

Comparative Proteomics of Symbiotic and Aposymbiotic Juvenile Soft Corals
Barneah O, Benayahu Y, Weis VM
Mar Biotechnol (NY) Early Edition: published 21-Jul-2005

Proteome Profiling for Assessing Diversity: Analysis of Individual Heads of Drosophila melanogaster Using LC-Ion Mobility-MS
John A. Taraszka, Xinfeng Gao, Stephen J. Valentine, Renã A. Sowell, Stormy L. Koeniger, David F. Miller, Thomas C. Kaufman, and David E. Clemmer
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1238-1247

Inventory of the Proteins in Neisseria meningitidis Serogroup B Strain MC58
Giuseppina Mignogna, Alessandra Giorgi, Paola Stefanelli, Arianna Neri, Gianni Colotti, Bruno Maras, and M. Eugenia Schininà
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1361-1370

Quantitative Analysis of Membrane Proteins from Breast Cancer Cell Lines BT474 and MCF7 Using Multistep Solid Phase Mass Tagging and 2D LC/MS
Yang Shi, Rong Xiang, Csaba Horváth, and James A. Wilkins
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1427-1433

Proteomic exploration of pancreatic islets in mice null for the {alpha}2A adrenergic receptor
Hu X, Friedman D, Hill S, Caprioli R, Nicholson W, Powers AC, Hunter L, Limbird LE
J Mol Endocrinol (2005) 35(1): 73-88

Characterization of Vacuolar Membrane Proteins Changed in Rice Root Treated with Gibberellin
Hirosato Konishi, Masayoshi Maeshima, and Setsuko Komatsu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/29/2005

Uncovering the Unfoldome: Enriching Cell Extracts for Unstructured Proteins by Acid Treatment
Marc S. Cortese, Jason P. Baird, Vladimir N. Uversky, and A. Keith Dunker
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/29/2005

Investigation of the Mouse Serum Proteome
Brian L. Hood, Ming Zhou, King C. Chan, David A. Lucas, Grace J. Kim, Haleem J. Issaq, Timothy D. Veenstra, and Thomas P. Conrads
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/29/2005

Capacitation-dependent concentration of lipid rafts in the apical ridge head area of porcine sperm cells
van Gestel RA, Brewis IA, Ashton PR, Helms JB, Brouwers JF, Gadella BM
Mol Hum Reprod Early Edition: published 28-Jul-2005

Proteomic Analysis of Steady-State Nuclear Hormone Receptor Coactivator Complexes
Jung SY, Malovannaya A, Wei J, O'malley BW, Qin J
Mol Endocrinol Early Edition: published 28-Jul-2005

Proteomic comparison of two fractions derived from the transsynaptic scaffold
Phillips GR, Florens L, Tanaka H, Khaing ZZ, Fidler L, Yates JR 3rd, Colman DR
J Neurosci Res Early Edition: published 26-Jul-2005

Hematopoietic prostaglandin D(2) synthase in the chicken Harderian gland
Scott TR, Messersmith AR, McCrary WJ, Herlong JL, Burgess SC
Vet Immunol Immunopathol Early Edition: published 23-Jul-2005

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Biomedical and clinical applications

Correlation-associated peptide networks of human cerebrospinal fluid
Jens Lamerz, Hartmut Selle, Leonardo Scapozza, Reto Crameri, Peter Schulz-Knappe, Thomas Mohring, Markus Kellmann, Valeri Khamenia, Hans-Dieter Zucht
PROTEOMICS (2005) 5(11): 2789-2798

Increased lungkine and chitinase levels in allergic airway inflammation: A proteomics approach
Jing Zhao, Hua Zhu, Chui Hong Wong, Ka Yin Leung, W.S. Fred Wong
PROTEOMICS (2005) 5(11): 2799-2807

Genistein blocks homocysteine-induced alterations in the proteome of human endothelial cells
Dagmar Fuchs, Petra Erhard, Gerald Rimbach, Hannelore Daniel, Uwe Wenzel
PROTEOMICS (2005) 5(11): 2808-2818

Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus
Kaveh Shakib, Jill T. Norman, Leon G. Fine, Larry R. Brown, Jasminka Godovac-Zimmermann
PROTEOMICS (2005) 5(11): 2819-2838

Serum proteomic fingerprinting discriminates between clinical stages and predicts disease progression in melanoma patients
Mian S, Ugurel S, Parkinson E, Schlenzka I, Dryden I, Lancashire L, Ball G, Creaser C, Rees R, Schadendorf D
J Clin Oncol (2005) 23(22): 5088-93

Proteomic analysis of slow- and fast-twitch skeletal muscles
Nobuaki Okumura, Akiko Hashida-Okumura, Kanako Kita, Masami Matsubae, Toshiya Matsubara, Toshifumi Takao, Katsuya Nagai
PROTEOMICS (2005) 5(11): 2896-2906

Mass profiling-directed isolation and identification of a stage-specific serologic protein biomarker of advanced prostate cancer
Ying Wai Lam, James A. Mobley, James E. Evans, James F. Carmody, Shuk-Mei Ho
PROTEOMICS (2005) 5(11): 2927-2938

Proteomic signatures for histological types of lung cancer
Masahiro Seike, Tadashi Kondo, Kazuyasu Fujii, Tetsuya Okano, Tesshi Yamada, Yoshihiro Matsuno, Akihiko Gemma, Shoji Kudoh, Setsuo Hirohashi
PROTEOMICS (2005) 5(11): 2939-2948

A pilot proteomic study of amyloid precursor interactors in Alzheimer's disease
Cottrell BA, Galvan V, Banwait S, Gorostiza O, Lombardo CR, Williams T, Schilling B, Peel A, Gibson B, Koo EH, Link CD, Bredesen DE
Ann Neurol (2005) 58(2): 277-289

Redox proteomics analysis of oxidatively modified proteins in G93A-SOD1 transgenic mice-a model of familial amyotrophic lateral sclerosis
Poon HF, Hensley K, Thongboonkerd V, Merchant ML, Lynn BC, Pierce WM, Klein JB, Calabrese V, Butterfield DA
Free Radic Biol Med (2005) 39(4): 453-62

Diagnostic proteomics: back to basics?
Master SR
Clin Chem (2005) 51(8): 1333-4

Influence of hormone replacement therapy on proteomic pattern in serum of postmenopausal women
Gericke B, Koebnick C, Reimann M, Forterre S, Franz Zunft HJ, Schweigert FJ
Maturitas (2005) 51(4): 334-42

Identification of human nasal mucous proteins using proteomics
Begoña Casado, Lewis K. Pannell, Paolo Iadarola, James N. Baraniuk
PROTEOMICS (2005) 5(11): 2949-2959

Comparative proteomic analysis of esophageal squamous cell carcinoma
Yijun Qi, Jen-Fu Chiu, Lidong Wang, Dora L. W. Kwong, Qing-Yu He
PROTEOMICS (2005) 5(11): 2960-2971

Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorption/ionization-mass spectrometry profiling with mass spectrometric protein identification
Dietrich Merkel, Wolfgang Rist, Peter Seither, Andreas Weith, Martin C. Lenter
PROTEOMICS (2005) 5(11): 2972-2980

A two-dimensional electrophoretic map of human mitochondrial proteins from immortalized lymphoblastoid cell lines: A prerequisite to study mitochondrial disorders in patients
Jing Xie, Sandra Techritz, Sophie Haebel, Anke Horn, Heidemarie Neitzel, Joachim Klose, Markus Schuelke
PROTEOMICS (2005) 5(11): 2981-2999

Utilizing Human Blood Plasma for Proteomic Biomarker Discovery
Jon M. Jacobs, Joshua N. Adkins, Wei-Jun Qian, Tao Liu, Yufeng Shen, David G. Camp II, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1073-1085

Clinical Cancer Proteomics: Promises and Pitfalls
Ayodele Alaiya, Mai Al-Mohanna, and Stig Linder
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1213-1222

Proteomic Profiling of Human Pleural Effusion Using Two-Dimensional Nano Liquid Chromatography Tandem Mass Spectrometry
Yu-Chang Tyan, Hsin-Yi Wu, Wu-Wei Lai, Wu-Chou Su, and Pao-Chi Liao
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1274-1286

An Immunoproteomic Approach for Identification of Clinical Biomarkers for Monitoring Disease: Application to Cystic Fibrosis
Susanne K. Pedersen, Andrew J. Sloane, Sindhu S. Prasad, Lucille T. Sebastian, Robyn A. Lindner, Michael Hsu, Michael Robinson, Peter T. Bye, Ron P. Weinberger, and Jenny L. Harry
Mol Cell Proteomics (2005) 4(8): 1052-1060

Identification and Analysis of Multivalent Proteolytically Resistant Peptides from Gluten: Implications for Celiac Sprue
Lu Shan, Shuo-Wang Qiao, Helene Arentz-Hansen, Øyvind Molberg, Gary M. Gray, Ludvig M. Sollid, and Chaitan Khosla #
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/19/2005

Primary Cell Cultures Arising from Normal Kidney and Renal Cell Carcinoma Retain the Proteomic Profile of Corresponding Tissues
Roberto A. Perego, Cristina Bianchi, Matteo Corizzato, Barbara Eroini, Barbara Torsello, Cristina Valsecchi, Andrea Di Fonzo, Nicoletta Cordani, Paolo Favini, Stefano Ferrero, Marina Pitto, Cecilia Sarto, Fulvio Magni, Francesco Rocco, and Paolo Mocarelli
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/26/2005

Genetic Association, Post-translational Modification, and Protein-Protein Interactions in Type 2 Diabetes Mellitus
Amitabh Sharma, Sreenivas Chavali, Anubha Mahajan, Rubina Tabassum, Vijaya Banerjee, Nikhil Tandon, and Dwaipayan Bharadwaj
Mol Cell Proteomics (2005) 4(8): 1029-1037

Large Scale Protein Identification in Intracellular Aquaporin-2 Vesicles from Renal Inner Medullary Collecting Duct
Maria Barile, Trairak Pisitkun, Ming-Jiun Yu, Chung-Lin Chou, Michael J. Verbalis, Rong-Fong Shen, and Mark A. Knepper
Mol Cell Proteomics (2005) 4(8): 1095-1106

Proteomic characterization of human normal articular chondrocytes: A novel tool for the study of osteoarthritis and other rheumatic diseases
Cristina Ruiz-Romero, María J. López-Armada, Francisco J. Blanco
PROTEOMICS (2005) 5(12): 3048-3059

Truncated cystatin C in cerebrospiral fluid: Technical artefact or biological process?
Odile Carrette, Pierre R. Burkhard, Severine Hughes, Denis F. Hochstrasser, Jean-Charles Sanchez
PROTEOMICS (2005) 5(12): 3060-3065

Cryodetector mass spectrometry profiling of plasma samples for HELLP diagnosis: An exploratory study
Cornelia Koy, Juliane C. Heitner, Ralf Woisch, Michael Kreutzer, Pablo Serrano-Fernandez, Rüdiger Gohlke, Toralf Reimer, Michael O. Glocker
PROTEOMICS (2005) 5(12): 3079-3087

Proteomic analysis of urinary protein markers for accurate prediction of diabetic kidney disorder
Jain S, Rajput A, Kumar Y, Uppuluri N, Arvind AS, Tatu U
J Assoc Physicians India (2005) 53: 513-20.

Genomics and proteomics of Type 2 diabetes in Indians
Mohan V, Balasubramanyam M, Radha V
J Assoc Physicians India (2005) 53: 507-9.

Proteome profiling of interleukin-12 treated human T helper cells
Arsi T. Rosengren, Tuula A. Nyman, Riitta Lahesmaa
PROTEOMICS (2005) 5(12): 3137-3141

Cancer cell-secreted proteomes as a basis for searching potential tumor markers: Nasopharyngeal carcinoma as a model
Chih-Ching Wu, Kun-Yi Chien, Ngan-Ming Tsang, Kai-Ping Chang, Sheng-Po Hao, Chuang-Hui Tsao, Yu-Sun Chang, Jau-Song Yu
PROTEOMICS (2005) 5(12): 3173-3182

Proteomic identification of differentially-expressed genes in human gastric carcinomas
Ryuichi Nishigaki, Mitsuhiko Osaki, Masaharu Hiratsuka, Tosifusa Toda, Kaori Murakami, Kuan-Teh Jeang, Hisao Ito, Toshiaki Inoue, Mitsuo Oshimura
PROTEOMICS (2005) 5(12): 3205-3213

Proteomic analysis of differently expressed proteins in a mouse model for allergic asthma
Jeong HS, Rhim TY, Ahn MH, Yoon PO, Kim SH, Chung IY, Uh ST, Kim SI, Park CS
J Korean Med Sci (2005) 20(4): 579-85

Use of Proteomic Methods to Identify Serum Biomarkers Associated with Rat Liver Toxicity or Hypertrophy
Amacher DE, Adler R, Herath A, Townsend RR
Clin Chem Early Edition: published 11-Aug-2005

Proteomic identification of proteins specifically oxidized in Caenorhabditis elegans expressing human Abeta(1-42): Implications for Alzheimer's disease
Boyd-Kimball D, Poon HF, Lynn BC, Cai J, Pierce Jr WM, Klein JB, Ferguson J, Link CD, Butterfield DA
Neurobiol Aging Early Edition: published 10-Aug-2005

New insights into viral structure and virus-cell interactions through proteomics
Oliver K Bernhard, Russell J Diefenbach, Anthony L Cunningham
Expert Review of Proteomics (2005) 2(4): 577-588

Current progress in proteomic study of hepatitis C virus-related human hepatocellular carcinoma
Yasuhiro Kuramitsu, Kazuyuki Nakamura
Expert Review of Proteomics (2005) 2(4): 589-601

Proteomic identification of biomarkers of traumatic brain injury
Kevin KW Wang, Andrew K Ottens, Ming Cheng Liu, Stephen B Lewis, Colleen Meegan, Monika W Oli, Frank C Tortella, Ronald L Hayes
Expert Review of Proteomics (2005) 2(4): 603-614

Proteomic and Metabolomic Analyses of Atherosclerotic Vessels From Apolipoprotein E-Deficient Mice Reveal Alterations in Inflammation, Oxidative Stress, and Energy Metabolism
Mayr M, Chung YL, Mayr U, Yin X, Ly L, Troy H, Fredericks S, Hu Y, Griffiths JR, Xu Q
Arterioscler Thromb Vasc Biol Early Edition: published 25-Aug-2005

Two-dimensional electrophoresis and mass spectrometric identification of mitochondrial proteins from an SH-SY5Y neuroblastoma cell line
Scheffler NK, Miller SW, Carroll AK, Anderson C, Davis RE, Ghosh SS, Gibson BW
Mitochondrion (2001) 1(2): 161-79

A genomic and proteomic study of the spectrum of nonalcoholic fatty liver disease
Younossi ZM, Baranova A, Ziegler K, Del Giacco L, Schlauch K, Born TL, Elariny H, Gorreta F, Vanmeter A, Younoszai A, Ong JP, Goodman Z, Chandhoke V
Hepatology (2005) 42(3): 665-674

Proteomic analysis of apoptotic pathways reveals prognostic factors in follicular lymphoma
Gulmann C, Espina V, Petricoin E 3rd, Longo DL, Santi M, Knutsen T, Raffeld M, Jaffe ES, Liotta LA, Feldman AL
Clin Cancer Res (2005) 11(16): 5847-55

Gefitinib-responsive EGFR-positive colorectal cancers have different proteome profiles from non-responsive cell lines
Loeffler-Ragg J, Skvortsov S, Sarg B, Skvortsova I, Witsch-Baumgartner M, Mueller D, Lindner H, Zwierzina H
Eur J Cancer Early Edition: published 19-Aug-2005

Multidimensional Protein Identification Technology (MudPIT): Technical Overview of a Profiling Method Optimized for the Comprehensive Proteomic Investigation of Normal and Diseased Heart Tissue
Thomas Kislinger, Anthony O. Gramolini, David H. MacLennan and Andrew Emili
Journal of the American Society for Mass Spectrometry (2005) 16(8): 1207-1220

Two-dimensional electrophoresis database of fluorescence-labeled proteins of colon cancer cells
Yasuharu Mori, Tadashi Kondo, Tesshi Yamada, Akihiko Tsuchida, Tetsuya Aoki and Setsuo Hirohashi
J Chromatogr B (2005) 823(2): 82-97

Characterization of Pepsinogen C as a Potential Biomarker for Gastric Cancer Using a Histo-Proteomic Approach
Christian Melle, Günther Ernst, Bettina Schimmel, Annett Bleul, Roland Kaufmann, Merten Hommann, Konrad K. Richter, Wolfgang Daffner, Utz Settmacher, Uwe Claussen, and Ferdinand von Eggeling
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

High-Resolution Serum Proteomic Profiling of Alzheimer Disease Samples Reveals Disease-Specific, Carrier-Protein-Bound Mass Signatures
Lopez MF, Mikulskis A, Kuzdzal S, Bennett DA, Kelly J, Golenko E, Dicesare J, Denoyer E, Patton WF, Ediger R, Sapp L, Ziegert T, Lynch C, Kramer S, Whiteley GR, Wall MR, Mannion DP, Della Cioppa G, Rakitan JS, Wolfe GM
Clin Chem Early Edition: published 4-Aug-2005

Proteomic analysis of vitreous from diabetic macular edema
Ouchi M, West K, Crabb JW, Kinoshita S, Kamei M
Exp Eye Res (2005) 81(2): 176-82

Proteomic Patterns and Prediction of Glomerulosclerosis and Its Mechanisms
Xu BJ, Shyr Y, Liang X, Ma LJ, Donnert EM, Roberts JD, Zhang X, Kon V, Brown NJ, Caprioli RM, Fogo AB
J Am Soc Nephrol Early Edition: published 3-Aug-2005

Combined Proteomics and Pathways Analysis of Collecting Duct Reveals a Protein Regulatory Network Activated in Vasopressin Escape
Hoorn EJ, Hoffert JD, Knepper MA
J Am Soc Nephrol Early Edition: published 3-Aug-2005

The proteomics of neurodegeneration
Johnson MD, Yu LR, Conrads TP, Kinoshita Y, Uo T, McBee JK, Veenstra TD, Morrison RS
Am J Pharmacogenomics (2005) 5(4): 259-70

The Marriage of Proteomics and Biomarkers
Joshua LaBaerSteven A. Carr
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1043

So, You Want to Look for Biomarkers (Introduction to the Special Biomarkers Issue)
Joshua LaBaer
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1053-1059

Proteomics in the Forefront of Cancer Biomarker Discovery
Sudhir Srivastava and Rashmi-Gopal Srivastava
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1098-1103

Identification of proteins of human colorectal carcinoma cell line SW480 by two-dimensional electrophoresis and MALDI-TOF mass spectrometry
Zhang YT, Geng YP, Zhou L, Lai BC, Si LS, Wang YL
World J Gastroenterol (2005) 11(30): 4679-84

Protein expression profiling identifies maspin and stathmin as potential biomarkers of adenoid cystic carcinoma of the salivary glands
Nakashima D, Uzawa K, Kasamatsu A, Koike H, Endo Y, Saito K, Hashitani S, Numata T, Urade M, Tanzawa H
Int J Cancer Early Edition: published 10-Aug-2005

Proteome profiling of corneal epithelium and identification of marker proteins for keratoconus, a pilot study
Nielsen K, Vorum H, Fagerholm P, Birkenkamp-Demtroder K, Honore B, Ehlers N, Orntoft TF
Exp Eye Res Early Edition: published 2-Aug-2005

Perspective: A Program to Improve Protein Biomarker Discovery for Cancer
Ruedi Aebersold, Leigh Anderson, Richard Caprioli, Brian Druker, Leland Hartwell, and Richard Smith
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1104-1109

The Sentinel Within: Exploiting the Immune System for Cancer Biomarkers
Karen S. Anderson and Joshua LaBaer
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1123-1133

Imaging Biomarkers in Drug Development: An Overview of Opportunities and Open Issues
Sudeep Chandra, Craig Muir, Matt Silva, and Steven Carr
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1134-1137

MALDI Mass Spectrometry for Direct Tissue Analysis: A New Tool for Biomarker Discovery
Michelle L. Reyzer and Richard M. Caprioli
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1138-1142

Place of Pattern in Proteomic Biomarker Discovery
Michael A. Gillette, D. R. Mani, and Steven A. Carr
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1143-1154

Proteomic Maps of the Cancer-Associated Infectious Agents
Sudhir Srivastava, Mukesh Verma, and Rashmi Gopal-Srivastava
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1171-1180

Quest for Novel Cardiovascular Biomarkers by Proteomic Analysis
Fernando Vivanco, Jose L. Martín-Ventura, Mari Carmen Duran, Maria G. Barderas, Luis Blanco-Colio, Verónica M. Dardé, Sebastián Mas, Olivier Meilhac, Jean B. Michel, Jose Tuñón, and Jesús Egido
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1181-1191

Evaluation of Biomarker Discovery Approaches to Detect Protein Biomarkers of Acute Renal Allograft Rejection
Hans Voshol, Nathalie Brendlen, Dieter Müller, Bruno Inverardi, Angélique Augustin, Charles Pally, Grazyna Wieczorek, Randall E. Morris, Friedrich Raulf, and Jan van Oostrum
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1192-1199

Discovery of Biomarker Candidates within Disease by Protein Profiling: Principles and Concepts
György Marko-Varga, Henrik Lindberg, Claes-Göran Löfdahl, Per Jönsson, Lennart Hansson, Magnus Dahlbäck, Eva Lindquist, Leif Johansson, Martyn Foster, and Thomas E. Fehniger
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1200-1212

Global Phosphoproteome of HT-29 Human Colon Adenocarcinoma Cells
Ji-Eun Kim, Steven R. Tannenbaum, and Forest M. White
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1339-1346

Capillary electrophoresis coupled to mass spectrometry for clinical diagnostic purposes
Danilo Fliser, Stefan Wittke, Harald Mischak
ELECTROPHORESIS (2005) 26(14): 2708-2716

Stem cell proteomes: A profile of human mesenchymal stem cells derived from umbilical cord blood
Robert E. Feldmann Jr., Karen Bieback, Martin H. Maurer, Armin Kalenka, Heinrich F. Bürgers, Benjamin Gross, Christian Hunzinger, Harald Klüter, Wolfgang Kuschinsky, Hermann Eichler
ELECTROPHORESIS (2005) 26(14): 2749-2758

Column chromatographic prefractionation leads to the detection of 543 different gene products in human fetal brain
Joo-Ho Shin, Kurt Krapfenbauer, Gert Lubec
ELECTROPHORESIS (2005) 26(14): 2759-2778

Pilot study of capillary electrophoresis coupled to mass spectrometry as a tool to define potential prostate cancer biomarkers in urine
Dan Theodorescu, Danilo Fliser, Stefan Wittke, Harald Mischak, Ronald Krebs, Michael Walden, Mark Ross, Elke Eltze, Olaf Bettendorf, Christian Wulfing, Axel Semjonow
ELECTROPHORESIS (2005) 26(14): 2797-2808

Direct targeting of human plasma for matrix-assisted laser desorption/ionization and analysis of plasma proteins by time of flight-mass spectrometry
Ya Jin, Takashi Manabe
ELECTROPHORESIS (2005) 26(14): 2823-2834

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Eukaryotic Cells And Tissues

A proteomics study of in vitro cyst germination and appressoria formation in Phytophthora infestans
Tine Ebstrup, Gerhard Saalbach, Helge Egsgaard
PROTEOMICS (2005) 5(11): 2839-2848

Probing heat-stable water-soluble proteins from barley to malt and beer
Ludivine Perrocheau, Hélène Rogniaux, Patrick Boivin, Didier Marion
PROTEOMICS (2005) 5(11): 2849-2858

Characterization of wheat gliadin proteins by combined two-dimensional gel electrophoresis and tandem mass spectrometry
Gianfranco Mamone, Francesco Addeo, Lina Chianese, Aldo Di Luccia, Alessandra De Martino, Annunziata Nappo, Annarita Formisano, Pasqualina De Vivo, Pasquale Ferranti
PROTEOMICS (2005) 5(11): 2859-2865

Proteomics: From Basic Research to Diagnostic Application. A Review of Requirements & Needs
Frank Vitzthum, Fritz Behrens, N. Leigh Anderson, and John H. Shaw
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1086-1097

A proteomic analysis of cold stress responses in rice seedlings
Suxia Cui, Fang Huang, Jie Wang, Xiao Ma, Yongsheng Cheng, Jinyuan Liu
PROTEOMICS (2005) 5(12): 3162-3172

Mouse Anterior Pituitary Gland: Analysis by Ion Trap Mass Spectrometry
Blake CA, Kakhniashvili DG, Goodman SR
Neuroendocrinology (2005) 81(4): 229-243

Analysis of the human saliva proteome
Francisco Manuel Lemos Amado, Rui Miguel Pinheiro Vitorino, Pedro Miguel Dimas Neves Domingues, Maria Joao Calheiros Lobo, Jose Alberto Ramos Duarte
Expert Review of Proteomics (2005) 2(4): 521-539

Building the mitochondrial proteome
Sandrine Da Cruz, Philippe A Parone, Jean-Claude Martinou
Expert Review of Proteomics (2005) 2(4): 541-551

Proteomics in hematologic malignancies
Michel Caron, Raymonde Joubert-Caron
Expert Review of Proteomics (2005) 2(4): 567-576

Investigating diversity in human plasma proteins
Dobrin Nedelkov, Urban A. Kiernan, Eric E. Niederkofler, Kemmons A. Tubbs, and Randall W. Nelson
PNAS (2005) 102(31): 10852-10857

Mapping the Proteome of Drosophila melanogaster: Analysis of Embryos and Adult Heads by LC-IMS-MS Methods
John A. Taraszka, Ruwan Kurulugama, Renã A. Sowell, Stephen J. Valentine, Stormy L. Koeniger, Randy J. Arnold, David F. Miller, Thomas C. Kaufman, and David E. Clemmer
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1223-1237

Evaluation of two-dimensional electrophoresis and liquid chromatography - tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples
Martina Schad, Mary S. Lipton, Patrick Giavalisco, Richard D. Smith, Julia Kehr
ELECTROPHORESIS (2005) 26(14): 2729-2738

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Prokaryotes

Proteome-wide Analysis of Chaperonin-Dependent Protein Folding in Escherichia coli
Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C, Frishman D, Hayer-Hartl M, Mann M, Hartl FU
Cell (2005) 122(2): 209-20

Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis
Fournier M, Aubert C, Dermoun Z, Durand MC, Moinier D, Dolla A
Biochimie Early Edition: published 21-Jul-2005

Bacterial response to eukaryotic cells analysis of differentially expressed proteins using nano liquid chromatography-electrospray ionization tandem mass spectrometry
Alpert C, Engst W, Guehler A, Oelschlaeger T, Blaut M
J Chromatogr A (2005) 1082(1): 25-32

Proteome response of Escherichia coli fed-batch culture to temperature downshift
Yang-Hoon Kim, Kyung Yeon Han, Kibeom Lee, Jeewon Lee
Applied Microbiology and Biotechnology Early Edition: published 06/28/2005

Isolation and characterisation of a Lactobacillus helveticus ITG LH1 peptidase-rich sub-proteome
Manso MA, Leonil J, Piot M, Gagnaire V
Int J Food Microbiol Early Edition: published 11-Aug-2005

Comparison of proteome and antigenic proteome between two Neospora caninum isolates
Shin YS, Shin GW, Kim YR, Lee EY, Yang HH, Palaksha KJ, Youn HJ, Kim JH, Kim DY, Marsh AE, Lakritz J, Jung TS
Vet Parasitol Early Edition: published 9-Aug-2005

Analysis of differential protein expression in Acidithiobacillus ferrooxidans grown under different energy resources respectively using SELDI-ProteinChip technologies
He Z, Zhong H, Hu Y, Xiao S, Xu J
J Microbiol Methods Early Edition: published 17-Aug-2005

Proteomic Analysis of Global Changes in Protein Expression during Bile Salt Exposure of Bifidobacterium longum NCIMB 8809
Sanchez B, Champomier-Verges MC, Anglade P, Baraige F, de Los Reyes-Gavilan CG, Margolles A, Zagorec M
J Bacteriol (2005) 187(16): 5799-808

Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias
Wang R, Prince JT, Marcotte EM
Genome Res (2005) 15(8): 1118-26

Proteomic Analysis of the Outer Membrane of Anabaena sp. Strain PCC 7120
Suncana Moslavac, Rolf Bredemeier, Oliver Mirus, Bernhard Granvogl, Lutz A. Eichacker, and Enrico Schleiff
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1330-1338

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Pharmacology and Toxicology

Proteomic Analysis Reveals the Participation of Energy- and Stress-Related Proteins in the Response of Pseudomonas putida DOT-T1E to Toluene
Segura A, Godoy P, van Dillewijn P, Hurtado A, Arroyo N, Santacruz S, Ramos JL
J Bacteriol (2005) 187(17): 5937-45

Research Profile: Proteomics sheds light on dioxin toxicity
Britt E. Erickson
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1049

Plasma Protein Level Changes in Waste Incineration Workers Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin
Mee Jeong Kang, Do-Youn Lee, Won-A Joo, and Chan-Wha Kim
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1248-1255

The identification of mammalian proteins crosslinked to DNA by ionizing radiation
Barker SL, Weinfeld M, Zheng J, Li L, Murray D
J Biol Chem Early Edition: published 9-Aug-2005

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Protein Array

A quantitative investigation into the losses of proteins at different stages of a two-dimensional gel electrophoresis procedure
Shaobo Zhou, Matthew J. Bailey, Michael J. Dunn, Victor R. Preedy, Peter W. Emery
PROTEOMICS (2005) 5(11): 2739-2747

Optimization of IPG strip equilibration for the basic membrane protein mABC1
Jason McDonough, Eduardo Marbán
PROTEOMICS (2005) 5(11): 2892-2895

A simplified 2-D electrophoresis protocol with the aid of an organic disulfide
Jesper J. Hedberg, Erik J. Bjerneld, Siham Cetinkaya, Jan Goscinski, Ioana Grigorescu, Daniel Haid, Ylva Laurin, Bengt Bjellqvist
PROTEOMICS (2005) 5(12): 3088-3096

Chromatofocusing fractionation and two-dimensional difference gel electrophoresis for low abundance serum proteins
Shuzhen Qin, Angeline S. Ferdinand, Jerome P. Richie, Michael P. O'Leary, Samuel C. Mok, Brian C.-S. Liu
PROTEOMICS (2005) 5(12): 3183-3192

Multiplex approaches in protein microarray technology
Birgit Kersten, Erich E Wanker, Jorg D Hoheisel, Philipp Angenendt
Expert Review of Proteomics (2005) 2(4): 499-510

An array of options: proteomics gets parallel
Dove A
Nat Methods (2005) 2(9): 709-17

High-speed separation of proteins by microchip electrophoresis using a polyethylene glycol-coated plastic chip with a sodium dodecyl sulfate-linear polyacrylamide solution
Hideya Nagata, Mari Tabuchi, Ken Hirano, Yoshinobu Baba
ELECTROPHORESIS (2005) 26(14): 2687-2691

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Protein Characterization / PTMs

Direct Identification of Ubiquitination Sites on Ubiquitin-Conjugated CHIP Using MALDI Mass Spectrometry
Dongxia Wang, # Wanping Xu, Sara C. McGrath, Cam Patterson, Len Neckers, and Robert J. Cotter
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/19/2005

Comprehensive Phosphoproteome Analysis in Rice and Identification of Phosphoproteins Responsive to Different Hormones/Stresses
Monowar Khan, Hironori Takasaki, and Setsuko Komatsu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/19/2005

Structural and functional characterization of glycosylation in an immunoglobulin G1 to Cryptococcus neoformans glucuronoxylomannan
Wang F, Nakouzi A, Alvarez M, Zaragoza O, Angeletti RH, Casadevall A
Mol Immunol Early Edition: published 18-Jul-2005

An in-gel digestion procedure that facilitates the identification of highly hydrophobic proteins by electrospray ionization-mass spectrometry analysis
Lila Castellanos-Serra, Yassel Ramos, Vivian Huerta
PROTEOMICS (2005) 5(11): 2729-2738

Oxidation of carboxyamidomethyl cysteine may add complexity to protein identification
Jesús Yagüe, Antonio Núñez, Manuel Boix, Manel Esteller, Patricia Alfonso, J. Ignacio Casal
PROTEOMICS (2005) 5(11): 2761-2768

Including mutations from conceptually translated expressed sequence tags into orthologous proteins improves the preliminary assignment of peptide mass fingerprints on non-model genomes
Jérôme Grimplet, José Walter Gaspar, Anne-Laure Gancel, François-Xavier Sauvage, Charles Romieu
PROTEOMICS (2005) 5(11): 2769-2777

Enrichment of Phosphoproteins for Proteomic Analysis Using Immobilized Fe(III)-Affinity Adsorption Chromatography
Ida Chiara Guerrera, Jelena Predic-Atkinson, Oliver Kleiner, Vukic Soskic, and Jasminka Godovac-Zimmermann
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/26/2005

Quantification of Gel-separated Proteins and Their Phosphorylation Sites by LC-MS Using Unlabeled Internal Standards: Analysis of Phosphoprotein Dynamics in a B Cell Lymphoma Cell Line
Pedro R. Cutillas, Barbara Geering, Mike D. Waterfield, and Bart Vanhaesebroeck
Mol Cell Proteomics (2005) 4(8): 1038-1051

Systematic Analysis of the Epidermal Growth Factor Receptor by Mass Spectrometry Reveals Stimulation-dependent Multisite Phosphorylation
Elisabetta Boeri Erba, Elena Bergatto, Sara Cabodi, Lorenzo Silengo, Guido Tarone, Paola Defilippi, and Ole N. Jensen
Mol Cell Proteomics (2005) 4(8): 1107-1121

Multiple Reaction Monitoring to Identify Sites of Protein Phosphorylation with High Sensitivity
Richard D. Unwin, John R. Griffiths, Michael K. Leverentz, Agnes Grallert, Iain M. Hagan, and Anthony D. Whetton
Mol Cell Proteomics (2005) 4(8): 1134-1144

Proteomic identification of oxidatively modified retinal proteins in a chronic pressure-induced rat model of glaucoma
Tezel G, Yang X, Cai J
Invest Ophthalmol Vis Sci (2005) 46(9): 3177-87

Challenges facing the development and use of protein chips to analyze the phosphoproteome
Hans TH Beernink, Steffen Nock
Expert Review of Proteomics (2005) 2(4): 487-497

Structural proteomics in drug discovery
Leslie W Tari, Martin Rosenberg, Anthony B Schryvers
Expert Review of Proteomics (2005) 2(4): 511-519

Investigating diversity in human plasma proteins
Dobrin Nedelkov, Urban A. Kiernan, Eric E. Niederkofler, Kemmons A. Tubbs, and Randall W. Nelson
PNAS (2005) 102(31): 10852-10857

LC-tandem MS in proteome characterization
Sarah R. Hart and Simon J. Gaskell
TrAC Trends in Analytical Chemistry (2005) 24(7): 566-575

Effects of growth phase and the developmentally significant bldA-specified tRNA on the membrane-associated proteome of Streptomyces coelicolor
Kim DW, Chater KF, Lee KJ, Hesketh A
Microbiology (2005) 151(Pt 8): 2707-20

Processed N-termini of mature proteins in higher eukaryotes and their major contribution to dynamic proteomics
Meinnel T, Peynot P, Giglione C
Biochimie (2005) 87(8): 701-12

Matrix-assisted laser desorption/ionisation mass spectrometry for the direct analysis of enzymatically digested kappa- iota- and hybrid iota/nu-carrageenans
Aristotelis Antonopoulos, Julie Hardouin, Patrick Favetta, William Helbert, Agnès F. Delmas, Michel Lafosse
Rapid Communications in Mass Spectrometry (2005) 19(16): 2217-2226

?De novo? sequencing of Atlantic cod vitellogenin tryptic peptides by matrix-assisted laser desorption/ionization quadrupole time-of-flight tandem mass spectrometry: similarities with haddock vitellogenin
Alejandro M. Cohen, Atef A. H. Mansour, Joseph H. Banoub
Rapid Communications in Mass Spectrometry (2005) 19(17): 2454-2460

Evaluation and improving the success rate of protein identification by peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Freek Bouwman, Dennis Suylen, Johan Renes, Edwin Mariman
Rapid Communications in Mass Spectrometry (2005) 19(17): 2465-2468

Age-dependent variations of cell response to oxidative stress: Proteomic approach to protein expression and phosphorylation
Yuri Miura, Mayumi Kano, Kazuhiko Abe, Shiro Urano, Shozo Suzuki, Tosifusa Toda
ELECTROPHORESIS (2005) 26(14): 2786-2796

Use of selective extraction and fast chromatographic separation combined with electrophoretic methods for mapping of membrane proteins
Djuro Josic, Mari Kino Brown, Feilei Huang, Helen Callanan, Marijana Ru?evi?, Alison Nicoletti, James Clifton, Douglas C. Hixson
ELECTROPHORESIS (2005) 26(14): 2809-2822

Quantitative detection of phosphoproteins by combination of two-dimensional difference gel electrophoresis and phosphospecific fluorescent staining
Taras Stasyk, Sandra Morandell, Rania Bakry, Isabel Feuerstein, Christian W. Huck, Guenther Stecher, Guenther K. Bonn, Lukas A. Huber
ELECTROPHORESIS (2005) 26(14): 2850-2854

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Protein-protein interaction

I-DIRT, A General Method for Distinguishing between Specific and Nonspecific Protein Interactions
Alan J. Tackett, Jeffrey A. DeGrasse, Matthew D. Sekedat, Marlene Oeffinger, Michael P. Rout, and Brian T. Chait
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/26/2005

Isotopically Coded Cleavable Cross-linker for Studying Protein-Protein Interaction and Protein Complexes
Evgeniy V. Petrotchenko, Vyacheslav K. Olkhovik, and Christoph H. Borchers
Mol Cell Proteomics (2005) 4(8): 1167-1179

Mass spectrometry-based approaches to protein-ligand interactions
Sonya M Schermann, Douglas A Simmons, Lars Konermann
Expert Review of Proteomics (2005) 2(4): 475-485

Analysis of protein interaction and function with a 3-dimensional MALDI-MS protein array
Gavin IM, Kukhtin A, Glesne D, Schabacker D, Chandler DP
Biotechniques (2005) 39(1): 99-107

Coupling Interaction between Thromboxane A2 Receptor and Alpha-13 Subunit of Guanine Nucleotide-Binding Protein
Kuo-Chen Chou
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/29/2005

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Quantitation

Identification and relative quantification of membrane proteins by surface biotinylation and two-dimensional peptide mapping
Simone B. Scheurer, Jascha-N. Rybak, Christoph Roesli, René A. Brunisholz, Frank Potthast, Ralph Schlapbach, Dario Neri, Giuliano Elia
PROTEOMICS (2005) 5(11): 2718-2728

Difference in Mass Analysis Using Labeled Lysines (DIMAL-K): A New, Efficient Proteomic Quantification Method Applied to the Analysis of Astrocytic Secretomes
Nicolas Delcourt, Patrick Jouin, Joel Poncet, Emmanuelle Demey, Eric Mauger, Joel Bockaert, Philippe Marin, and Nathalie Galeotti
Mol Cell Proteomics (2005) 4(8): 1085-1094

Quantitative Analysis of the Low Molecular Weight Serum Proteome Using 18O Stable Isotope Labeling in a Lung Tumor Xenograft Mouse Model
Brian L. Hood, David A. Lucas, Grace Kim, King C. Chana, Josip Blonder, Haleem J. Issaq, Timothy D. Veenstra, Thomas P. Conrads, Ingrid Pollet and Aly Karsan
Journal of the American Society for Mass Spectrometry (2005) 16(8): 1221-1230

Comprehensive Label-Free Method for the Relative Quantification of Proteins from Biological Samples
Richard E. Higgs, Michael D. Knierman, Valentina Gelfanova, Jon P. Butler, and John E. Hale
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1442-1450

Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides
Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ
Nat Methods (2005) 2(8): 587-9

Relative quantification of erythropoietin receptor-dependent phosphoproteins using in-gel 18O-labeling and tandem mass spectrometry
Sandra Körbel, Michael Schümann, Thomas Bittorf, Eberhard Krause
Rapid Communications in Mass Spectrometry (2005) 19(16): 2259-2271

Treatment methods for the determination of ?2H and ?18O of hair keratin by continuous-flow isotope-ratio mass spectrometry
Gabriel J. Bowen, Lesley Chesson, Kristine Nielson, Thure E. Cerling, James R. Ehleringer
Rapid Communications in Mass Spectrometry (2005) 19(17): 2371-2378

A novel modification reagent for proteins: monitoring by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Jing Zhang, Y.-L. Guo
Rapid Communications in Mass Spectrometry (2005) 19(17): 2461-2464

Recent advancements in differential proteomics based on stable isotope coding
Julka, Samir; Regnier, Fred. E
Briefings in Functional Genomics and Proteomics (2005) 4(2): 158-177

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Review

HUPO Brain Proteome Project Pilot Studies: Bioinformatics at Work
Christian Stephan, Kai Reidegeld, Helmut E. Meyer, Michael Hamacher
PROTEOMICS (2005) 5(11): 2716-2717

Proteomics: Analysis of Spectral Data
Harry Burke
Cancer Informatics (2005) 1(1): 15-24

The Need for Review and Understanding of SELDI/MALDI: Mass Spectrscopy Data Prior to Analysis
William Grizzle, O. John Semmes, William Bigbee, Liu Zhu, Ganjan Malik, Denise Oelschlager, Barkha Manne, Upender Manne
Cancer Informatics (2005) 1(1): 86-97

Peptidomics: a logical sequel to proteomics
Vadim T Ivanov, Oleg N Yatskin
Expert Review of Proteomics (2005) 2(4): 463-473

Mass spectrometry-based approaches to protein-ligand interactions
Sonya M Schermann, Douglas A Simmons, Lars Konermann
Expert Review of Proteomics (2005) 2(4): 475-485

Challenges facing the development and use of protein chips to analyze the phosphoproteome
Hans TH Beernink, Steffen Nock
Expert Review of Proteomics (2005) 2(4): 487-497

Multiplex approaches in protein microarray technology
Birgit Kersten, Erich E Wanker, Jorg D Hoheisel, Philipp Angenendt
Expert Review of Proteomics (2005) 2(4): 499-510

Structural proteomics in drug discovery
Leslie W Tari, Martin Rosenberg, Anthony B Schryvers
Expert Review of Proteomics (2005) 2(4): 511-519

Analysis of the human saliva proteome
Francisco Manuel Lemos Amado, Rui Miguel Pinheiro Vitorino, Pedro Miguel Dimas Neves Domingues, Maria Joao Calheiros Lobo, Jose Alberto Ramos Duarte
Expert Review of Proteomics (2005) 2(4): 521-539

Building the mitochondrial proteome
Sandrine Da Cruz, Philippe A Parone, Jean-Claude Martinou
Expert Review of Proteomics (2005) 2(4): 541-551

Developing liquid chromatography ion mobility mass spectometry techniques
Stephen J Valentine, Xiaoyun Liu, Manolo D Plasencia, Amy E Hilderbrand, Ruwan T Kurulugama, Stormy L Koeniger, David E Clemmer
Expert Review of Proteomics (2005) 2(4): 553-565

Proteomics in hematologic malignancies
Michel Caron, Raymonde Joubert-Caron
Expert Review of Proteomics (2005) 2(4): 567-576

New insights into viral structure and virus-cell interactions through proteomics
Oliver K Bernhard, Russell J Diefenbach, Anthony L Cunningham
Expert Review of Proteomics (2005) 2(4): 577-588

Recent advances in blood-related proteomics
Lynne Thadikkaran, Michèle A. Siegenthaler, David Crettaz, Pierre-Alain Queloz, Philippe Schneider, Jean-Daniel Tissot
PROTEOMICS (2005) 5(12): 3019-3034

Current progress in proteomic study of hepatitis C virus-related human hepatocellular carcinoma
Yasuhiro Kuramitsu, Kazuyuki Nakamura
Expert Review of Proteomics (2005) 2(4): 589-601

Proteomic identification of biomarkers of traumatic brain injury
Kevin KW Wang, Andrew K Ottens, Ming Cheng Liu, Stephen B Lewis, Colleen Meegan, Monika W Oli, Frank C Tortella, Ronald L Hayes
Expert Review of Proteomics (2005) 2(4): 603-614

Cell cycle: proteomics gives it a spin
Vincent Archambault
Expert Review of Proteomics (2005) 2(4): 615-625

Mycobacterial gene cloning and expression, comparative genomics, bioinformatics and proteomics in relation to the development of new vaccines and diagnostic reagents
Mustafa AS
Med Princ Pract (2005) 14(Suppl 1): 27-34

Recent advancements in differential proteomics based on stable isotope coding
Julka S, Regnier FE
Brief Funct Genomic Proteomic (2005) 4(2): 158-77

Glycomics and mass spectrometry
Morelle W, Michalski JC
Curr Pharm Des (2005) 11(20): 2615-45

Targeted lipidomics and drug abuse research
Rapaka RS
Prostaglandins Other Lipid Mediat (2005) 77(1-4): 219-22

Standards requirements for systems biology approaches to health care: mitochondrial proteomics
Vasquez GB, Zullo SJ, Barker PE
Mitochondrion (2004) 3(4): 205-15

Lysosomal membrane proteomics and biogenesis of lysosomes
Bagshaw RD, Mahuran DJ, Callahan JW
Mol Neurobiol (2005) 32(1): 27-42

Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics
Kirkpatrick DS, Denison C, Gygi SP
Nat Cell Biol (2005) 7(8): 750-7

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Methodology

A fast method for quantitative proteomics based on a combination between two-dimensional electrophoresis and (15)N-metabolic labelling
Snijders AP, de Vos MG, Koning BD, Wright PC
Electrophoresis Early Edition: published 26-Jul-2005

Identification of human calphoglin-induced phosphoglucomutase phosphorylation in Escherichia coli
Ingi T, Mori H, Inuzuka M
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 23-Jul-2005

A method for simple identification of signature peptides derived from polyUb-K48 and K63 by MALDI-TOF MS and chemically assisted MS/MS fragmentation
Doskeland AP
Amino Acids Early Edition: published 28-Jul-2005

Isoelectric focusing in serial immobilized pH gradient gels to improve protein separation in proteomic analysis
Poznanovic S, Schwall G, Zengerling H, Cahill MA
Electrophoresis Early Edition: published 22-Jul-2005

Data-Dependent Electron Capture Dissociation FT-ICR Mass Spectrometry for Proteomic Analyses
Helen J. Cooper, Shiva Akbarzadeh, John K. Heath, and Martin Zeller
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

Ultra Fast Trypsin Digestion of Proteins by High Intensity Focused Ultrasound
D. López-Ferrer, J. L. Capelo, and J. Vázquez
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

Impact of Replicate Types on Proteomic Expression Analysis
Natasha A. Karp, Matthew Spencer, Helen Lindsay, Kevin O'Dell, and Kathryn S. Lilley
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/19/2005

Simple and Robust Two-Layer Matrix/Sample Preparation Method for MALDI MS/MS Analysis of Peptides
Jing Zheng, Nan Li, Marc Ridyard, Hui Dai, Stephen M. Robbins, and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/26/2005

Novel Approaches to Smoothing and Comparing SELDI TOF Spectra
Sreelatha Meleth, Isam-Eldin Eltoum, Liu Zhu, Denise Oelschlager, Chandrika Piyathilake, David Chhieng, William Grizzle
Cancer Informatics (2005) 1(1): 78-85

Characterising Phase Variations in MALDI-TOF Data and Correcting Them by Peak Alignment
Simon Lin, Richard Haney, Michael Campa, Michael Fitzgerald, Edward F Patz, Jr
Cancer Informatics (2005) 1(1): 32-40

Impact of Freeze-thaw Cycles and Storage Time on Plasma Samples: Used in Mass Spectrometry Based Biomarker Discoverey Projects
Breeana Mitchell, Yutaka Yasui, Christopher Li, Annette Fitzpatrick, Paul Lampe
Cancer Informatics (2005) 1(1): 25-31

A new approach in proteomics of wheat gluten: combining chymotrypsin cleavage and matrix-assisted laser desorption/ionization quadrupole ion trap reflectron tandem mass spectrometry
Salplachta J, Marchetti M, Chmelik J, Allmaier G
Rapid Commun Mass Spectrom (2005) 19(18): 2725-2728

Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes
Natasha A. Karp, Kathryn S. Lilley
PROTEOMICS (2005) 5(12): 3105-3115

Two-dimensional gel isoelectric focusing
Stastna M, Slais K
Electrophoresis Early Edition: published 15-Aug-2005

Evaluation of several two-dimensional gel electrophoresis techniques in cardiac proteomics
Li ZB, Flint PW, Boluyt MO
Electrophoresis Early Edition: published 15-Aug-2005

Toward a global analysis of the human pituitary proteome by multiple gel-based technology
Zhao Y, Giorgianni F, Desiderio DM, Fang B, Beranova-Giorgianni S
Anal Chem (2005) 77(16): 5324-31

Sample Handling for Mass Spectrometric Proteomic Investigations of Human Sera
West-Nielsen M, Hogdall EV, Marchiori E, Hogdall CK, Schou C, Heegaard NH
Anal Chem (2005) 77(16): 5114-5123

Differentiation of Phosphorylated and Unphosphorylated Peptides by High-Performance Liquid Chromatography-Electrospray Ionization-Infrared Multiphoton Dissociation in a Quadrupole Ion Trap
Matthew C. Crowe and Jennifer S. Brodbelt
ANALYTICAL CHEMISTRY (2005) 77(17): 5726-5734

On-Probe Sample Preparation without Washes for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using an Anion Exchange Medium
Seketsu Fukuzawa, Miwako Asanuma, Kazuo Tachibana, and Hiroshi Hirota
ANALYTICAL CHEMISTRY (2005) 77(17): 5750-5754

Developing liquid chromatography ion mobility mass spectometry techniques
Stephen J Valentine, Xiaoyun Liu, Manolo D Plasencia, Amy E Hilderbrand, Ruwan T Kurulugama, Stormy L Koeniger, David E Clemmer
Expert Review of Proteomics (2005) 2(4): 553-565

Tandem mass spectrometry of integral membrane proteins for top-down proteomics
Julian Whitelegge
TrAC Trends in Analytical Chemistry (2005) 24(7): 576-582

A streamlined platform for high-content functional proteomics of primary human specimens
Jessani N, Niessen S, Wei BQ, Nicolau M, Humphrey M, Ji Y, Han W, Noh DY, Yates JR, Jeffrey SS, Cravatt BF
Nat Methods (2005) 2(9): 691-697

A hybrid LC-Gel-MS method for proteomics research and its application to protease functional pathway mapping
Si Wu, Xiao-Ting Tang, William F. Siems and James E. Bruce
J Chromatogr B (2005) 822(1-2): 98-111

Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
Elias JE, Haas W, Faherty BK, Gygi SP
Nat Methods (2005) 2(9): 667-75

Valid data from large-scale proteomics studies
Chamrad D, Meyer HE
Nat Methods (2005) 2(9): 647-8

Reversed-Phase High-Performance Liquid Chromatographic Prefractionation of Immunodepleted Human Serum Proteins to Enhance Mass Spectrometry Identification of Lower-Abundant Proteins
James Martosella, Nina Zolotarjova, Hongbin Liu, Gordon Nicol, and Barry E. Boyes
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/05/2005

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes
Angela D. Norbeck, Matthew E. Monroe, Joshua N. Adkins, Kevin K. Anderson, Don S. Daly and Richard D. Smith
Journal of the American Society for Mass Spectrometry (2005) 16(8): 1239-1249

Further application of a two-step heparin affinity chromatography method using divalent cations as eluents: Purification and identification of membrane-bound heparin binding proteins from the mitochondrial fraction of HL-60 cells
Tsukimi Iida, Masaharu Kamo, Nobuyuki Uozumi, Takashi Inui and Katsuyuki Ima
J Chromatogr B (2005) 823(2): 209-212

Protein sample concentration by repeated loading onto SDS-PAGE
Hyukho Sheen and Zafer Ali-Khan
Analytical Biochemistry (2005) 343(2): 338-340

Francisella tularensis Proteome: Low Levels of ASB-14 Facilitate the Visualization of Membrane Proteins in Total Protein Extracts
Susan M. Twine, Nadia C. S. Mykytczuk, Mireille Petit, Tammy-Lynn Tremblay, J. Wayne Conlan, and John F. Kelly
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/12/2005

Proteomic analysis of protein adsorption: Serum amyloid P adsorbs to materials and promotes leukocyte adhesion
Kim JK, Scott EA, Elbert DL
J Biomed Mater Res A Early Edition: published 4-Aug-2005

Nonaqueous capillary electrophoresis in coated capillaries: An interesting alternative for proteomic applications
Assuncao NA, Deziderio LA, Paulino LG, Lupetti KO, Carrilho E
Electrophoresis Early Edition: published 4-Aug-2005

Preparation of 20-mum-i.d. Silica-Based Monolithic Columns and Their Performance for Proteomics Analyses
Luo Q, Shen Y, Hixson KK, Zhao R, Yang F, Moore RJ, Mottaz HM, Smith RD
Anal Chem (2005) 77(15): 5028-35

Continuous pH/Salt Gradient and Peptide Score for Strong Cation Exchange Chromatography in 2D-Nano-LC/MS/MS Peptide Identification for Proteomics
Winnik WM
Anal Chem (2005) 77(15): 4991-8

A Multidimensional Differential Proteomic Platform Using Dual-Phase Ion-Exchange Chromatography-Polyacrylamide Gel Electrophoresis/Reversed-Phase Liquid Chromatography Tandem Mass Spectrometry
Ottens AK, Kobeissy FH, Wolper RA, Haskins WE, Hayes RL, Denslow ND, Wang KK
Anal Chem (2005) 77(15): 4836-4845

Extravasation of plasma proteins can confound interpretation of proteomic studies of brain: A lesson from apo A-I in mesial temporal lobe epilepsy
Yang JW, Czech T, Gelpi E, Lubec G
Brain Res Mol Brain Res Early Edition: published 8-Aug-2005

Extended Range Proteomic Analysis (ERPA): A New and Sensitive LC-MS Platform for High Sequence Coverage of Complex Proteins with Extensive Post-translational Modifications-Comprehensive Analysis of Beta-Casein and Epidermal Growth Factor Receptor (EGFR)
Shiaw-Lin Wu, Jeongkwon Kim, William S. Hancock, and Barry Karger
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1155-1170

Prefractionation of Proteome by Liquid Isoelectric Focusing Prior to Two-Dimensional Liquid Chromatography Mass Spectrometric Identification
Rong-Xia Li, Hu Zhou, Su-Jun Li, Quan-Hu Sheng, Qi-Chang Xia, and Rong Zeng
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1256-1264

High-Sensitivity Analysis of Human Plasma Proteome by Immobilized Isoelectric Focusing Fractionation Coupled to Mass Spectrometry Identification
Cheng-Jian Tu, Jie Dai, Su-Jun Li, Quan-Hu Sheng, Wen-Jun Deng, Qi-Chang Xia, and Rong Zeng
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1265-1273

Application of Relative Warp Analysis to the Evaluation of Two-Dimensional Gels in Proteomics: Studying Isoelectric Point and Relative Molecular Mass Variation
Ana M. Rodríguez-Piñeiro, Antonio Carvajal-Rodríguez, Emilio Rolán-Alvarez, Francisco J. Rodríguez-Berrocal, Mónica Martínez-Fernández, and María Páez de la Cadena
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1318-1323

Direct Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometric Identification of Proteins on Membrane Detected by Western Blotting and Lectin Blotting
Iwao Ohtsu, Tsuyoshi Nakanisi, Masaru Furuta, Eiji Ando, and Osamu Nishimura
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1391-1396

Mass Tagging Approach for Mitochondrial Thiol Proteins
Kevin Marley, Duane T. Mooney, Gretchen Clark-Scannell, Tony T.-H. Tong, Jeffrey Watson, Tory M. Hagen, Jan F. Stevens, and Claudia S. Maier
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1403-1412

Increased Protein Identification Capabilities through Novel Tandem MS Calibration Strategies
Si Wu, Nathan K. Kaiser, Da Meng, Gordon A. Anderson, Kai Zhang, and James E. Bruce
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1434-1441

A novel technique to specifically analyze the secretome of cells and tissues
Hannes Zwickl, Elisabeth Traxler, Stefan Staettner, Wolfram Parzefall, Bettina Grasl-Kraupp, Josef Karner, Rolf Schulte-Hermann, Christopher Gerner
ELECTROPHORESIS (2005) 26(14): 2779-2785

Fast prototyping of hydrophobic disposable polymer support arrays for matrix-assisted laser desorption/ionization-time of flight-mass spectrometry of proteins by atmospheric molding
Alexander Muck, Petra Ne?n?rová, Iva Pichová, Ale? Svato?
ELECTROPHORESIS (2005) 26(14): 2835-2842

Enrichment of low-abundant serum proteins by albumin/immunoglobulin G immunoaffinity depletion under partly denaturing conditions
Hong-Lei Huang, Taras Stasyk, Sandra Morandell, Maurice Mogg, Martin Schreiber, Isabel Feuerstein, Christian W. Huck, Guenther Stecher, Guenther K. Bonn, Lukas A. Huber
ELECTROPHORESIS (2005) 26(14): 2843-2849

Detection and purification of glucose 6-phosphate dehydrogenase, malic enzyme, and NADP-dependent isocitrate dehydrogenase by blue native polyacrylamide gel electrophoresis
Robin Bériault, Daniel Chénier, Ranji Singh, Jeff Middaugh, Ryan Mailloux, Vasu Appanna
ELECTROPHORESIS (2005) 26(15): 2892-2897

On-line affinity selection of histidine-containing peptides using a polymeric monolithic support for capillary electrophoresis
Nora M. Vizioli, Maria Lucía Rusell, Maria Laura Carbajal, Clyde N. Carducci, Mariano Grasselli
ELECTROPHORESIS (2005) 26(15): 2942-2948

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Books

Book Reviews: Chemical Genomics. By Ferenc Darvas, Andras Guttmann, Gyorgy Dorman (Eds.)
Gerard Cagney
PROTEOMICS (2005) 5(12): 3214

Book Reviews: Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews. By Neil Woodford, Alan P. Johnson (Eds.)
Phillip Cash
PROTEOMICS (2005) 5(12): 3214-3215

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Meeting

Report on the First Congress of the Spanish Proteomics Society
Jesús Jorrín, José Antonio Bárcena, Angela Moreno, Juan J. Calvete
PROTEOMICS (2005) 5(11): 2712-2715

Meetings Diary: Proteomics 11/2005
PROTEOMICS (2005) 5(11): 3000-3002

53rd American Society for Mass Spectrometry Conference (Meeting Report)
Robert L Hettich
Expert Review of Proteomics (2005) 2(4): 459-461

Meetings: Proteomics 12/2005
PROTEOMICS (2005) 5(12): 3216-3218

Meeting News: Looking at large peptides | Proteomics study of signaling networks | Universal proteomics guidelines debated
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1050-1051

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Other

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K
Proteomics Early Edition: published 22-Jul-2005

The emerging field of lipidomics
Wenk MR
Nat Rev Drug Discov (2005) 4(7): 594-610

Data requirements for protein identification using chemically-assisted fragmentation and tandem mass spectrometry
Juhlin KD, Swift DD, Lacey MP, Correa PE, Keough TW
Eur J Mass Spectrom (2005) 11(2): 161-7

Proteomics. New database to track protein locations
Service RF
Science (2005) 309(5739): 1310

Cover Picture: Proteomics 12/2005
PROTEOMICS (2005) 5(12): published 2 Aug 2005

Contents: Proteomics 12/2005
PROTEOMICS (2005) 5(12): published 2 Aug 2005

Proteomics for Health
Patricia Palagi, Jean-Charles Sanchez, Reto Stöcklin
PROTEOMICS (2005) 5(12): 3007-3009

Report of the roundtable discussion organised by the Swiss Proteomics Society (SPS), Bern, 8th December 2004
Dimitrios Noukakis, Stephan Gadola, Reto Stöcklin
PROTEOMICS (2005) 5(12): 3017-3018

Product News: Proteomics 12/2005
PROTEOMICS (2005) 5(12): 3219-3221

Systems biology: where it's at in 2005
Lehner B, Tischler J, Fraser AG
Genome Biol (2005) 6(8): 338

Introduction to the Food and Drug Administration (FDA) Regulatory Process
Joseph L. Hackett and Steven I. Gutman
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1110-1113

Building Integrated Approaches for the Proteomics of Complex, Dynamic Systems: NIH Programs in Technology and Infrastructure Development
Douglas M. Sheeley, Joseph J. Breen, and Susan E. Old
JOURNAL OF PROTEOME RESEARCH (2005) 4(4): 1114-1122

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