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SPS' Digest

Issue 16, 4-Mar-2005

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Quick jumps to articles in: Bioinformatics (17) / Biological applications (27) / Biomedical and clinical applications (30) / Eukaryotic Cells And Tissues (7) / Prokaryotes (6) / Pharmacology and Toxicology (2) / Protein Array (1) / Protein Characterization - PTMs (14) / Protein-protein interaction (6) / Quantitation (3) / Review (26) / Methodology (35) / Meeting (1) / Other (4) /

In this issue, 172 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 (17) / Biological applications (27) / Biomedical and clinical applications (30) / Eukaryotic Cells And Tissues (7) / Prokaryotes (6) / Pharmacology and Toxicology (2) / Protein Array (1) / Protein Characterization - PTMs (14) / Protein-protein interaction (6) / Quantitation (3) / Review (26) / Methodology (35) / Meeting (1) / Other (4) /

Bioinformatics

Assessing Data Quality of Peptide Mass Spectra Obtained by Quadrupole Ion Trap Mass Spectrometry
Ming Xu , Lewis Y. Geer , Stephen H. Bryant , Jeri S. Roth , Dawn M. Maynard , and Sanford P. Markey
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/04/2005

Detection of parallel functional modules by comparative analysis of genome sequences
Li H, Pellegrini M, Eisenberg D
Nat Biotechnol (2005) 23(2): 253-60

Further steps towards data standardisation: The Proteomic Standards Initiative HUPO 3rd annual congress, Beijing 25-27th October, 2004
Sandra Orchard, Henning Hermjakob, Pierre-Alain Binz, Christine Hoogland, Chris F. Taylor, Weimin Zhu, Randall K. Julian Jr., Rolf Apweiler
PROTEOMICS (2005) 5(2): 337-339

The olfactory receptor universe - from whole genome analysis to structure and evolution
Olender T, Feldmesser E, Atarot T, Eisenstein M, Lancet D
Genet Mol Res (2004) 3(4): 545-53

Computational systems analysis of developmental toxicity: design, development and implementation of a Birth Defects Systems Manager (BDSM)
Singh AV, Knudsen KB, Knudsen TB
Reprod Toxicol (2005) 19(3): 421-39

SpecAlign - processing and alignment of mass spectra datasets
Wong JW, Cagney G, Cartwright HM
Bioinformatics Early Edition: published 2-Feb-2005

Proteios: an open source proteomics initiative
Garden P, Alm R, Hakkinen J
Bioinformatics Early Edition: published 3-Feb-2005

PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling
Ari Frank and Pavel Pevzner
ANALYTICAL CHEMISTRY (2005) 77(4): 964-973

Numerical approaches for quantitative analysis of two-dimensional maps: A review of commercial software and home-made systems
Emilio Marengo, Elisa Robotti, Francesca Antonucci, Daniela Cecconi, Natascia Campostrini, Pier Giorgio Righetti
PROTEOMICS (2005) 5(3): 654-666

Integrating gene and protein expression data: pattern analysis and profile mining
Cox B, Kislinger T, Emili A
Methods (2005) 35(3): 303-14

Informatics for protein identification by mass spectrometry
Johnson RS, Davis MT, Taylor JA, Patterson SD
Methods (2005) 35(3): 223-36

Spectral quality assessment for high-throughput tandem mass spectrometry proteomics
Purvine S, Kolker N, Kolker E
OMICS (2004) 8(3): 255-65

Experiments in Searching Small Proteins in Unannotated Large Eukaryotic Genomes
Jacques Colinge, Isabelle Cusin, Samia Reffas, Eve Mahé, Anne Niknejad, Hassan Mattou, Marc Moniatte, and Lydie Bougueleret
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/28/2005

Prediction of Peptide Retention at Different HPLC Conditions from Multiple Linear Regression Models
Tomasz B czek, Pawe Wiczling, Micha Marsza , Roman Kaliszan
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/25/2005

An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experiments
Bernhard M. Kohli, Jimmy K. Eng, Roger M. Nitsch, Uwe Konietzko
Rapid Communications in Mass Spectrometry (2005) 19(5): 589-596

Plant membrane proteome databases
Schwacke R, Flugge UI, Kunze R
Plant Physiol Biochem (2004) 42(12): 1023-34

The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools
Schneider M, Tognolli M, Bairoch A
Plant Physiol Biochem (2004) 42(12): 1013-21

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Biological applications

Unraveling Kinase Signaling Pathways with Chemical Genetic and Chemical Proteomic Approaches
Beillard E, Witte ON
Cell Cycle (2005) 4(3):

Proteomic profiling of human stem cells derived from umbilical cord blood
Zenzmaier C, Gesslbauer B, Grobuschek N, Jandrositz A, Preisegger KH, Kungl AJ
Biochem Biophys Res Commun (2005) 328(4): 968-72

Effect of chronic morphine exposure on the synaptic plasma-membrane subproteome of rats: a quantitative protein profiling study based on isotope-coded affinity tags and liquid chromatography/mass spectrometry
Laszlo Prokai, Alevtina D. Zharikova, Stanley M. Stevens Jr
Journal of Mass Spectrometry (2005) 40(2): 169-175

Human cerebrospinal fluid peptidomics
Xianglin Yuan, Dominic M. Desiderio
Journal of Mass Spectrometry (2005) 40(2): 176-181

Relative quantitation of peptides in wild-type and Cpefat/fat mouse pituitary using stable isotopic tags and mass spectrometry
Fa-Yun Che, Reeta Biswas, Lloyd D. Fricker
Journal of Mass Spectrometry (2005) 40(2): 227-237

The amniotic fluid cell proteome
Tsangaris G, Weitzdorfer R, Pollak D, Lubec G, Fountoulakis M
Electrophoresis Early Edition: published 11-Feb-2005

Proteomics of the Injured Rat Sciatic Nerve Reveals Protein Expression Dynamics During Regeneration
Connie R. Jimenez, Floor J. Stam, Ka Wan Li, Yvonne Gouwenberg, MartinP. Hornshaw, Fred De Winter, Joost Verhaagen, and August B. Smit
Mol Cell Proteomics (2005) 4(2): 120-132

High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry
Hui Zhang, Eugene C. Yi, Xiao-jun Li, Parag Mallick, Karen S. Kelly-Spratt, Christophe D. Masselon, David G. Camp, II, Richard D. Smith, Christopher J. Kemp, and Ruedi Aebersold
Mol Cell Proteomics (2005) 4(2): 144-155

Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry
Wei-Jun Qian, Jon M. Jacobs, David G. Camp II, Matthew E. Monroe, Ronald J. Moore, Marina A. Gritsenko, Steve E. Calvano, Stephen F. Lowry, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Ronald G. Tompkins, Richard D. Smith
PROTEOMICS (2005) 5(2): 572-584

Proteome analysis of human metaphase chromosomes
Uchiyama S, Kobayashi S, Takata H, Ishihara T, Hori N, Higashi T, Hayashihara K, Sone T, Higo D, Nirasawa T, Takao T, Matsunaga S, Fukui K
J Biol Chem Early Edition: published 31-Jan-2005

Application of a systems biology approach to developmental neurotoxicology
Slikker W, Xu Z, Wang C
Reprod Toxicol (2005) 19(3): 305-19

Proteomics in developmental toxicology
Barrier M, Mirkes PE
Reprod Toxicol (2005) 19(3): 291-304

Glutathione S-transferase tissue profiling by reporter peptide monitoring
M. Eugenia Schininà, Giuseppina Pitari, Tommaso Paolone, Alessandra Giorgi, Rodolfo Ippoliti, Silvestro Duprè, Bruno Maras
PROTEOMICS (2005) 5(3): 648-653

Analysis of the composition of an immunoglobulin E reactive high molecular weight protein complex of peanut extract containing Ara h 1 and Ara h 3/4
Andrea Boldt, Donatella Fortunato, Amedeo Conti, Arnd Petersen, Barbara Ballmer-Weber, Ute Lepp, Gerald Reese, Wolf-Meinhard Becker
PROTEOMICS (2005) 5(3): 675-686

Two-dimensional mapping as a tool for classification of green coffee bean species
Maria Teresa Gil-Agusti, Natascia Campostrini, Lello Zolla, Corrado Ciambella, Carlo Invernizzi, Pier Giorgio Righetti
PROTEOMICS (2005) 5(3): 710-718

Characterization of B- and C-type low molecular weight glutenin subunits by electrospray ionization mass spectrometry and matrix-assisted laser desorption/ ionization mass spectrometry
Vera Muccilli, Vincenzo Cunsolo, Rosaria Saletti, Salvatore Foti, Stefania Masci, Domenico Lafiandra
PROTEOMICS (2005) 5(3): 719-728

Changes in the tobacco leaf apoplast proteome in response to salt stress
Valeria Dani, William J. Simon, Marcello Duranti, Ron R. D. Croy
PROTEOMICS (2005) 5(3): 737-745

Water Deficits Affect Caffeate O-Methyltransferase, Lignification, and Related Enzymes in Maize Leaves. A Proteomic Investigation
Vincent D, Lapierre C, Pollet B, Cornic G, Negroni L, Zivy M
Plant Physiol Early Edition: published 22-Feb-2005

Proteome analysis of programmed cell death and defense signaling using the rice lesion mimic mutant cdr2
Tsunezuka H, Fujiwara M, Kawasaki T, Shimamoto K
Mol Plant Microbe Interact (2005) 18(1): 52-9

Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats
Dieck HT, Doring F, Fuchs D, Roth HP, Daniel H
J Nutr (2005) 135(2): 199-205

Proteomics of immune-challenged Drosophila melanogaster larvae hemolymph
de Morais Guedes S, Vitorino R, Domingues R, Tomer K, Correia AJ, Amado F, Domingues P
Biochem Biophys Res Commun (2005) 328(1): 106-15

A proteomic approach for investigation of photosynthetic apparatus in plants
Corrado Ciambella, Peter Roepstorff, Eva Mari Aro, Lello Zolla
PROTEOMICS (2005) 5(3): 746-757

Differential accumulation of Lhcb gene products in thylakoid membranes of Zea mays plants grown under contrasting light and temperature conditions
Stefano Caffarri, Sara Frigerio, Erna Olivieri, Pier Giorgio Righetti, Roberto Bassi
PROTEOMICS (2005) 5(3): 758-768

Towards royal jelly proteome
Roberta Scarselli, Elena Donadio, Maria Gabriella Giuffrida, Donatella Fortunato, Amedeo Conti, Ettore Balestreri, Romano Felicioli, Mauro Pinzauti, Anna Gloria Sabatini, Antonio Felicioli
PROTEOMICS (2005) 5(3): 769-776

Expanding the proteome two-dimensional gel electrophoresis reference map of human renal cortex by peptide mass fingerprinting
Fulvio Magni, Cecilia Sarto, Cristina Valsecchi, Stefano Casellato, Stefano Ferrero Bogetto, Silvano Bosari, Andrea Di Fonzo, Roberto A. Perego, Matteo Corizzato, Giancarlo Doro, Carmen Galbusera, Francesco Rocco, Paolo Mocarelli, Marzia Galli Kienle
PROTEOMICS (2005) 5(3): 816-825

Proteomics analysis of growth hormone isoforms in the human pituitary
Zhan X, Giorgianni F, Desiderio DM
Proteomics Early Edition: published 16-Feb-2005

Proteomic analysis of aqueous humour from patients with acute corneal rejection
Funding M, Vorum H, Honore B, Nexo E, Ehlers N
Acta Ophthalmol Scand (2005) 83(1): 31-9

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Biomedical and clinical applications

Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins
Koomen JM, Shih LN, Coombes KR, Li D, Xiao LC, Fidler IJ, Abbruzzese JL, Kobayashi R
Clin Cancer Res (2005) 11(3): 1110-8

Application of Isotope Coded Affinity Tag (ICAT) Analysis for the Identification of Differentially Expressed Proteins Following Infection of Atlantic Salmon (Salmo salar) with Infectious Hematopoietic Necrosis Virus (IHNV) or Renibacterium salmoninarum (BKD)
A. T. Booy, J. D. Haddow, L. B. Ohlund, D. B. Hardie, and R. W. Olafson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/28/2005

Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer
Baggerly KA, Morris JS, Edmonson SR, Coombes KR
J Natl Cancer Inst (2005) 97(4): 307-9

Detection of bladder cancer using a point-of-care proteomic assay
Grossman HB, Messing E, Soloway M, Tomera K, Katz G, Berger Y, Shen Y
JAMA (2005) 293(7): 810-6

Proteomic detection of prostate-specific antigen using a serum fractionation procedure: potential implication for new low-abundance cancer biomarkers detection
Solassol J, Marin P, Demettre E, Rouanet P, Bockaert J, Maudelonde T, Mange A
Anal Biochem (2005) 338(1): 26-31

Proteome-wide analysis of head and neck squamous cell carcinomas using laser-capture microdissection and tandem mass spectrometry
Baker H, Patel V, Molinolo AA, Shillitoe EJ, Ensley JF, Yoo GH, Meneses-Garcia A, Myers JN, El-Naggar AK, Gutkind JS, Hancock WS
Oral Oncol (2005) 41(2): 183-99

Proteome Changes in Ovarian Epithelial Cells Derived from Women with BRCA1 Mutations and Family Histories of Cancer
Diana M. Smith-Beckerman, Kit W. Fung, Katherine E. Williams, Nelly Auersperg, Andrew K. Godwin, and Alma L. Burlingame
Mol Cell Proteomics (2005) 4(2): 156-168

A Systematic Characterization of Mitochondrial Proteome from Human T Leukemia Cells
Karim Rezaul, Linfeng Wu, Viveka Mayya, Sun-Il Hwang, and David Han
Mol Cell Proteomics (2005) 4(2): 169-181

High Throughput Proteome Screening for Biomarker Detection
Sheng Pan, Hui Zhang, John Rush, Jimmy Eng, Ning Zhang, Dale Patterson, Michael J. Comb, and Ruedi Aebersold
Mol Cell Proteomics (2005) 4(2): 182-190

Identification of differentially expressed proteins of gamma-ray irradiated rat intestinal epithelial IEC-6 cells by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry
Zhang Bo, Su Yongping, Wang Fengchao, Ai Guoping, Wei Yongjiang
PROTEOMICS (2005) 5(2): 426-432

Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry
Pawlik TM, Fritsche H, Coombes KR, Xiao L, Krishnamurthy S, Hunt KK, Pusztai L, Chen JN, Clarke CH, Arun B, Hung MC, Kuerer HM
Breast Cancer Res Treat (2005) 89(2): 149-57

Platelet proteomics: identification of potential therapeutic targets
Maguire PB
Pathophysiol Haemost Thromb (2003) 33(5-6): 481-6

Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases
Paradis V, Degos F, Dargere D, Pham N, Belghiti J, Degott C, Janeau JL, Bezeaud A, Delforge D, Cubizolles M, Laurendeau I, Bedossa P
Hepatology (2005) 41(1): 40-7

Analyzing Mycobacterium tuberculosis proteomes for candidate vaccine epitopes
McMurry J, Sbai H, Gennaro ML, Carter EJ, Martin W, De Groot AS
Tuberculosis (Edinb) (2005) 85(1-2): 95-105

Proteomics analysis of growth hormone isoforms in the human pituitary
Zhan X, Giorgianni F, Desiderio DM
Proteomics Early Edition: published 16-Feb-2005

Proteomic identification of the involvement of the mitochondrial rieske protein in epilepsy
Junker H, Spate K, Suofu Y, Walther R, Schwarz G, Kammer W, Nordheim A, Walker LC, Runge U, Kessler C, Popa-Wagner A
Epilepsia (2005) 46(3): 339-43

Glucose-induced changes of multiple mouse islet proteins analysed by two-dimensional gel electrophoresis and mass spectrometry
Ahmed M, Bergsten P
Diabetologia Early Edition: published 24-Feb-2005

SELDI-TOF MS profiling of serum for detection of the progression of chronic hepatitis C to hepatocellular carcinoma
Schwegler EE, Cazares L, Steel LF, Adam BL, Johnson DA, Semmes OJ, Block TM, Marrero JA, Drake RR
Hepatology (2005) 41(3): 634-642

Biomarkers for melanoma
Torabian S, Kashani-Sabet M
Curr Opin Oncol (2005) 17(2): 167-71

Serum, salivary and tissue proteomics for discovery of biomarkers for head and neck cancers
Drake RR, Cazare LH, Semmes OJ, Wadsworth JT
Expert Rev Mol Diagn (2005) 5(1): 93-100

3rd HUPO Brain Proteome Project Workshop promises successful pilot studies
Christian Stephan, Michael Hamacher, Helmut E. Meyer
PROTEOMICS (2005) 5(3): 615-616

Identification of grass pollen allergens by two-dimensional gel electrophoresis and serological screening
Valeria Corti, Angela Cattaneo, Angela Bachi, Renato E. Rossi, Giorgio Monasterolo, Clara Paolucci, Samuele E. Burastero, Massimo Alessio
PROTEOMICS (2005) 5(3): 729-736

Toward Defining the Human Parotid Gland Salivary Proteome and Peptidome: Identification and Characterization Using 2D SDS-PAGE, Ultrafiltration, HPLC, and Mass Spectrometry
Hardt M, Thomas LR, Dixon SE, Newport G, Agabian N, Prakobphol A, Hall SC, Witkowska HE, Fisher SJ
Biochemistry (2005) 44(8): 2885-2899

Characterization of heat shock protein 27 phosphorylation sites in renal cell carcinoma
Lucia Tremolada, Fulvio Magni, Cristina Valsecchi, Cecilia Sarto, Paolo Mocarelli, Roberto Perego, Nicoletta Cordani, Paolo Favini, Marzia Galli Kienle, Jean-Charles Sanchez, Denis F. Hochstrasser, Garry L. Corthals
PROTEOMICS (2005) 5(3): 788-795

Blood-Brain Barrier Genomics, Proteomics, and New Transporter Discovery
Shusta EV
Neurorx (2005) 2(1): 151-161

A proteomic investigation into etoposide chemo-resistance of neuroblastoma cell lines
Andrea Urbani, Julia Poland, Sergio Bernardini, Lorenza Bellincampi, Antonino Biroccio, Martina Schnölzer, Pranav Sinha, Giorgio Federici
PROTEOMICS (2005) 5(3): 796-804

Biomarkers of Alzheimer Disease in Plasma
Irizarry MC
Neurorx (2004) 1(2): 226-234

Proteomic analysis of aqueous humour from patients with acute corneal rejection
Funding M, Vorum H, Honore B, Nexo E, Ehlers N
Acta Ophthalmol Scand (2005) 83(1): 31-9

Cow's milk allergens identification by two-dimensional immunoblotting and mass spectrometry
Natale M, Bisson C, Monti G, Peltran A, Garoffo LP, Valentini S, Fabris C, Bertino E, Coscia A, Conti A
Mol Nutr Food Res (2004) 48(5): 363-9

Analysis of the Dorsal Spinal Cord Synaptic Architecture by Combined Proteome Analysis and in Situ Hybridization
Mathias Dreger, # Joanna Mika, Annette Bieller, Ricarda Jahnel, Martin K. H. Schaefer, Eberhard Weihe, and Ferdinand Hucho
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/25/2005

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Eukaryotic Cells And Tissues

Peptidomic analysis of the larval Drosophila melanogaster central nervous system by two-dimensional capillary liquid chromatography quadrupole time-of-flight mass spectrometry
Geert Baggerman, Kurt Boonen, Peter Verleyen, Arnold De Loof, Liliane Schoofs
Journal of Mass Spectrometry (2005) 40(2): 250-260

Proteomic analysis of the wing imaginal discs of Drosophila melanogaster
Jana Alonso, Juan F. Santarén
PROTEOMICS (2005) 5(2): 474-489

Proteomic analysis of bovine skeletal muscle hypertrophy
Julien Bouley, Bruno Meunier, Christophe Chambon, Stefaan De Smet, Jean François Hocquette, Brigitte Picard
PROTEOMICS (2005) 5(2): 490-500

Analysis of the Golden Syrian Hamster Anterior Pituitary Gland Proteome by Ion Trap Mass Spectrometry
Blake CA, Kakhniashvili DG, Goodman SR
Neuroendocrinology (2005) 80(6): 355-367

A differential proteomic approach to identify proteins associated with thyroid cell transformation
Paron I, D'Ambrosio C, Scaloni A, Berlingieri MT, Pallante PL, Fusco A, Bivi N, Tell G, Damante G
J Mol Endocrinol (2005) 34(1): 199-207

gamma-Glutamylcysteine ethyl ester protection of proteins from Abeta(1-42)-mediated oxidative stress in neuronal cell culture: A proteomics approach
Boyd-Kimball D, Sultana R, Poon HF, Mohmmad-Abdul H, Lynn BC, Klein JB, Butterfield DA
J Neurosci Res Early Edition: published 25-Jan-2005

Proteomics of immune-challenged Drosophila melanogaster larvae hemolymph
de Morais Guedes S, Vitorino R, Domingues R, Tomer K, Correia AJ, Amado F, Domingues P
Biochem Biophys Res Commun (2005) 328(1): 106-15

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Prokaryotes

Proteome of Methanosarcina acetivorans Part II: Comparison of Protein Levels in Acetate- and Methanol-Grown Cells
Qingbo Li, Lingyun Li , Tomas Rejtar , Barry L. Karger, and James G. Ferry
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/28/2005

Proteome of Methanosarcina acetivorans Part I: An Expanded View of the Biology of the Cell
Qingbo Li, Lingyun Li, Tomas Rejtar, Barry L. Karger, and James G. Ferry
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/28/2005

Comparative Proteome Analysis of Saccharomyces cerevisiae Grown in Chemostat Cultures Limited for Glucose or Ethanol
Annemieke Kolkman, Maurien M. A. Olsthoorn, Carola E. M. Heeremans, Albert J. R. Heck, and Monique Slijper
Mol Cell Proteomics (2005) 4(1): 1-11

Analysis of the Listeria cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry
Enrique Calvo, M. Graciela Pucciarelli, Hélène Bierne, Pascale Cossart, Juan Pablo Albar, Francisco García-del Portillo
PROTEOMICS (2005) 5(2): 433-443

A proteomic approach to studying biogenic amine producing lactic acid bacteria
Enrica Pessione, Roberto Mazzoli, Maria Gabriella Giuffrida, Cristina Lamberti, Emilia Garcia-Moruno, Cristina Barello, Amedeo Conti, Carlo Giunta
PROTEOMICS (2005) 5(3): 687-698

Helicobacter pylori immunoproteomes in case reports of rosacea and chronic urticaria
Roberta Mini, Natale Figura, Chiara D'Ambrosio, Daniela Braconi, Giulia Bernardini, Francesca Di Simplicio, Cristina Lenzi, Ranuccio Nuti, Lorenza Trabalzini, Paola Martelli, Lucia Bovalini, Andrea Scaloni, Annalisa Santucci
PROTEOMICS (2005) 5(3): 777-787

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Pharmacology and Toxicology

Combined effects of gamma radiation and arsenite on the proteome of human TK6 lymphoblastoid cells
Tapio S, Danescu-Mayer J, Asmuss M, Posch A, Gomolka M, Hornhardt S
Mutat Res (2005) 581(1-2): 141-52

The Agony and Ecstasy of "OMIC" Technologies in Drug Development
Bilello JA
Curr Mol Med (2005) 5(1): 39-52

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Protein Array

Protein microarrays as tools for functional proteomics
Labaer J, Ramachandran N
Curr Opin Chem Biol (2005) 9(1): 14-19

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Protein Characterization / PTMs

A Universal Strategy for Proteomic Studies of SUMO and Other Ubiquitin-like Modifiers
German Rosas-Acosta, William K. Russell, Adeline Deyrieux, David H. Russell, and Van G. Wilson
Mol Cell Proteomics (2005) 4(1): 56-72

Identification of Sumoylated Proteins by Systematic Immunoprecipitation of the Budding Yeast Proteome
Dennis D. Wykoff and Erin K. O'Shea
Mol Cell Proteomics (2005) 4(1): 73-83

Characterization of Gel-separated Glycoproteins Using Two-step Proteolytic Digestion Combined with Sequential Microcolumns and Mass Spectrometry
Martin R. Larsen, Peter Hojrup, and Peter Roepstorff
Mol Cell Proteomics (2005) 4(2): 107-119

Quantification of phosphoproteins with global internal standard technology
Larry Riggs, Erin H. Seeley and Fred E. Regnier
J Chromatogr B (2005) 817(1): 89-96

Protein Glycosylation Analyzed by Normal-Phase Nano-Liquid Chromatography-Mass Spectrometry of Glycopeptides
Manfred Wuhrer, Carolien A. M. Koeleman, Cornelis H. Hokke, and André M. Deelder
ANALYTICAL CHEMISTRY (2005) 77(3): 886-894

Analysis of Keratan Sulfate Oligosaccharides by Electrospray Ionization Tandem Mass Spectrometry
Yuntao Zhang, Yutaka Kariya, Abigail H. Conrad, Elena S. Tasheva, and Gary W. Conrad
ANALYTICAL CHEMISTRY (2005) 77(3): 902-910

Sequence tag scanning: A new explorative strategy for recognition of unexpected protein alterations by nanoelectrospray ionization-tandem mass spectrometry
Mogjiborahman Salek, Vincenzo Di Bartolo, Davide Cittaro, Dario Borsotti, Junhua Wei, Oreste Acuto, Juri Rappsilber, Wolf D. Lehmann
PROTEOMICS (2005) 5(3): 667-674

Different isoforms and post-translational modifications of human salivary acidic proline-rich proteins
Rosanna Inzitari, Tiziana Cabras, Giuseppina Onnis, Chiara Olmi, Andrea Mastinu, Maria Teresa Sanna, Maria Guiseppina Pellegrini, Massimo Castagnola , Irene Messana
PROTEOMICS (2005) 5(3): 805-815

Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination
Maria R. Esteban Warren, Carol E. Parker, Viorel Mocanu, David Klapper, Christoph H. Borchers
Rapid Communications in Mass Spectrometry (2005) 19(4): 429-437

Selective detection of thiosulfate-containing peptides using tandem mass spectrometry
Mark J. Raftery
Rapid Communications in Mass Spectrometry (2005) 19(5): 674-682

Determination of sites citrullinated by peptidylarginine deiminase using 18O stable isotope labeling and mass spectrometry
Kazuishi Kubota, Tomoko Yoneyama-Takazawa, Kimihisa Ichikawa
Rapid Communications in Mass Spectrometry (2005) 19(5): 683-688

Global and site-specific detection of human integrin ?5?1 glycosylation using tandem mass spectrometry and the StrOligo algorithm
Martin Ethier, Oleg Krokhin, Werner Ens, Kenneth G. Standing, John A. Wilkins, Hélène Perreault
Rapid Communications in Mass Spectrometry (2005) 19(5): 721-727

Peptide mass fingerprinting
Thiede B, Hohenwarter W, Krah A, Mattow J, Schmid M, Schmidt F, Jungblut PR
Methods (2005) 35(3): 237-47

Mass spectrometry in proteomics
McCormack AL
Methods (2005) 35(3): 209-10

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Protein-protein interaction

Simple Protein Complex Purification and Identification Method for High-Throughput Mapping of Protein Interaction Networks
Lye Meng Markillie, Chiann-Tso Lin, Joshua N. Adkins, Deanna L. Auberry, Brian S. Hooker, Priscilla A. Moore, Ronald J. Moore, Liang Shi, Vladimir Kery
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/04/2005

In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system
Burkle L, Meyer S, Dortay H, Lehrach H, Heyl A
Funct Integr Genomics Early Edition: published 16-Feb-2005

Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry
Veraksa A, Bauer A, Artavanis-Tsakonas S
Dev Dyn Early Edition: published 9-Feb-2005

Automated Yeast Two-hybrid Screening for Nuclear Receptor-interacting Proteins
Michael Albers, Harald Kranz, Ingo Kober, Carmen Kaiser, Martin Klink,Jorg Suckow, Rainer Kern, and Manfred Koegl
Mol Cell Proteomics (2005) 4(2): 205-213

Novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in Escherichia coli by bacterial conjugation
Clarke P, Cuiv PO, O'Connell M
Nucl Acids Res (2005) 33(2): e18

Effect of training datasets on support vector machine prediction of protein-protein interactions
Lo SL, Cai CZ, Chen YZ, Chung MC
Proteomics Early Edition: published 16-Feb-2005

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Quantitation

A novel strategy for quantitative proteomics using isotope-coded protein labels (vol. 5, Issue 1, pp. 4-15)
Alexander Schmidt, Josef Kellermann, Friedrich Lottspeich
PROTEOMICS (2005) 5(3): 826

18O-labeling quantitative proteomics using an ion trap mass spectrometer (vol. 5, Issue 1, pp. 16-23)
Jun Sakai, Shinich Kojima, Kazunori Yanagi, Masaharu Kanaoka
PROTEOMICS (2005) 5(3): 826

Biomarker discovery in biological fluids
Gao J, Garulacan LA, Storm SM, Opiteck GJ, Dubaquie Y, Hefta SA, Dambach DM, Dongre AR
Methods (2005) 35(3): 291-302

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Review

An overview of lung cancer genomics and proteomics
Granville CA, Dennis PA
Am J Respir Cell Mol Biol (2005) 32(3): 169-76

Molecular and evolutionary basis of the cellular stress response
Kultz D
Annu Rev Physiol (2005) 67: 225-57

Deciphering the plant phosphoproteome: tools and strategies for a challenging task
Laugesen S, Bergoin A, Rossignol M
Plant Physiol Biochem (2004) 42(12): 929-36

Mass spectrometry for high throughput quantitative proteomics in plant research: lessons from thylakoid membranes
Whitelegge JP
Plant Physiol Biochem (2004) 42(12): 919-927

Proteomics and peptidomics in neuroscience. Experience of capabilities and limitations in a neurochemical laboratory
Linda Paulson, Rita Persson, Gösta Karlsson, Jerzy Silberring, Anna Bierczynska-Krzysik, Rolf Ekman, Ann Westman-Brinkmalm
Journal of Mass Spectrometry (2005) 40(2): 202-213

Proteomic approaches in the search for disease biomarkers
A. Vlahou and M. Fountoulakis
J Chromatogr B (2005) 814(1): 11-19

Structure specific chromatographic selection in targeted proteomics
Hamid Mirzaei and Fred Regnier
J Chromatogr B (2005) 817(1): 23-34

Multidimensional separation of peptides for effective proteomic analysis
Haleem J. Issaq, , King C. Chan, George M. Janini, Thomas P. Conrads and Timothy D. Veenstra
J Chromatogr B (2005) 817(1): 35-47

On-line multidimensional liquid chromatography and capillary electrophoresis systems for peptides and proteins
Thom Stroink, Mireya Castillo Ortiz, Auke Bult, Henk Lingeman, Gerhardus J. de Jong and Willy J.M. Underberg
J Chromatogr B (2005) 817(1): 49-66

Protein biochips: the calm before the storm
Steven Bodovitz, Thomas Joos and Jutta Bachmann
Drug Discovery Today (2005) 10(4): 283-287

Protein microarrays as tools for functional proteomics
Joshua LaBaer and Niroshan Ramachandran
Curr Opin Chem Biol (2005) 9(1): 14-19

Selective chemical labeling of proteins in living cells
Lawrence W Miller and Virginia W Cornish
Curr Opin Chem Biol (2005) 9(1): 56-61

Global strategies to integrate the proteome and metabolome
Alan Saghatelian and Benjamin F Cravatt
Curr Opin Chem Biol (2005) 9(1): 62-68

Proteomic insights into ubiquitin and ubiquitin-like proteins
Carilee Denison, Donald S Kirkpatrick and Steven P Gygi
Curr Opin Chem Biol (2005) 9(1): 69-75

Functional proteomics for the discovery of carbohydrate-related enzyme activities
Nicola L Pohl
Curr Opin Chem Biol (2005) 9(1): 76-81

Protein localization studies in the age of 'Omics'
Nancy A O'Rourke, Tobias Meyer and Grischa Chandy
Curr Opin Chem Biol (2005) 9(1): 82-87

Computational analysis of shotgun proteomics data
Michael J MacCoss
Curr Opin Chem Biol (2005) 9(1): 88-94

Bibunt centum, bibunt mille..
Pier Giorgio Righetti
PROTEOMICS (2005) 5(3): 617-619

Amphoteric, buffering chromatographic beads for proteome prefractionation. I: Theoretical model
Frédéric Fortis, Pierre Girot, Olivier Brieau, Egisto Boschetti, Annalisa Castagna, Pier Giorgio Righetti
PROTEOMICS (2005) 5(3): 620-628

Perspectives in spicing up proteomics with splicing
Jasminka Godovac-Zimmermann, Oliver Kleiner, Larry R. Brown, Andrzej K. Drukier
PROTEOMICS (2005) 5(3): 699-709

Genomics, proteomics and integrative 'omics' in hypertension research
Thongboonkerd V
Curr Opin Nephrol Hypertens (2005) 14(2): 133-9

Proteomics strategies for protein identification
Resing KA, Ahn NG
FEBS Lett (2005) 579(4): 885-9

Current two-dimensional electrophoresis technology for proteomics (vol. 4, Issue 12, pp. 3665-3685)
Angelika Görg, Walter Weiss, Michael J. Dunn
PROTEOMICS (2005) 5(3): 826-827

Will we ever understand? The undescribable diversity of the prokaryotes
Stackebrandt E
Acta Microbiol Immunol Hung (2004) 51(4): 449-62

Proteomics and genomics A chemo-centric view of proteomics and genomics
Cravatt BF, Kodadek T
Curr Opin Chem Biol (2005) 9(1): 1-3

Prefractionation techniques in proteome analysis: The mining tools of the third millennium
Pier Giorgio Righetti, Annalisa Castagna, Paolo Antonioli, Egisto Boschetti
ELECTROPHORESIS (2005) 26(2): 297-319

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Methodology

Use of Lysozyme as a Standard for Evaluating the Effectiveness of a Proteomics Process
Leah S. Riter, Barry D. Hodge, Karen M. Gooding, and Randall K. Julian, Jr
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/28/2005

Differential Detergent Fractionation for Non-electrophoretic Eukaryote Cell Proteomics
Fiona M. McCarthy, Shane C. Burgess, Bart H. J. van den Berg, G. Todd Pharr
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/28/2005

Discovery of an exceptionally potent and selective class of fatty acid amide hydrolase inhibitors enlisting proteome-wide selectivity screening: concurrent optimization of enzyme inhibitor potency and selectivity
Leung D, Du W, Hardouin C, Cheng H, Hwang I, Cravatt BF, Boger DL
Bioorg Med Chem Lett (2005) 15(5): 1423-8

The case for well-conducted experiments to validate statistical protocols for 2D gels: Different pre-processing = different lists of significant proteins
Meleth S, Deshane J, Kim H
BMC Biotechnol (2005) 5(1): 7

Subcellular imaging mass spectrometry of brain tissue
Liam A. McDonnell, Sander R. Piersma, A. F. Maarten Altelaar, Todd H. Mize, Stefan L. Luxembourg, Peter D. E. M. Verhaert, Jan van Minnen, Ron M. A. Heeren
Journal of Mass Spectrometry (2005) 40(2): 160-168

Prediction of Peptide Retention at Different HPLC Conditions from Multiple Linear Regression Models
Tomasz B czek, Pawe Wiczling, Micha Marsza , Roman Kaliszan
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/25/2005

Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry
Thomas Möhring, Markus Kellmann, Michael Jürgens, Michael Schrader
Journal of Mass Spectrometry (2005) 40(2): 214-226

Analysis of the Dorsal Spinal Cord Synaptic Architecture by Combined Proteome Analysis and in Situ Hybridization
Mathias Dreger, # Joanna Mika, Annette Bieller, Ricarda Jahnel, Martin K. H. Schaefer, Eberhard Weihe, and Ferdinand Hucho
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/25/2005

Quantitative peptidomics of mouse pituitary: comparison of different stable isotopic tags
Fa-Yun Che, Lloyd D. Fricker
Journal of Mass Spectrometry (2005) 40(2): 238-249

A Comparative Proteomic Strategy for Subcellular Proteome Research: Icat Approach Coupled with Bioinformatics Prediction to Ascertain Rat Liver Mitochondrial Proteins and Indication of Mitochondrial Localization for Catalase
Xiao-Sheng Jiang, Jie Dai, Quan-Hu Sheng, Lei Zhang, Qi-Chang Xia, Jia-Rui Wu, and Rong Zeng
Mol Cell Proteomics (2005) 4(1): 12-34

Two-dimensional Blue Native/sodium dodecyl sulfate gel electrophoresis for analysis of multimeric proteins in platelets
Claeys D, Geering K, Meyer BJ
Electrophoresis Early Edition: published 11-Feb-2005

Two-stage Off-Geltrade mark isoelectric focusing: Protein followed by peptide fractionation and application to proteome analysis of human plasma
Heller M, Michel PE, Morier P, Crettaz D, Wenz C, Tissot JD, Reymond F, Rossier JS
Electrophoresis Early Edition: published 9-Feb-2005

Systematic Comparison of a Two-dimensional Ion Trap and a Three-dimensional Ion Trap Mass Spectrometer in Proteomics
Viveka Mayya, Karim Rezaul, Yu-Sheng Cong, and David Han
Mol Cell Proteomics (2005) 4(2): 214-223

Matrix-assisted laser desorption/ionization of protein samples containing a denaturant at high concentration using a mid-infrared free-electron laser (MIR-FEL)
Yasuhide Naito, Sachiko Yoshihashi-Suzuki, Katsunori Ishii, Taizo Kanai and Kunio Awazu
International Journal of Mass Spectrometry (2005) 241(1): 49-56

Liquid ultraviolet matrix-assisted laser desorption/ionization - mass spectrometry for automated proteomic analysis
Rainer Cramer, Steve Corless
PROTEOMICS (2005) 5(2): 360-370

Increased quantitative proteome coverage with 13C/12C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme
Eugene C. Yi, Xiao-jun Li, Kelly Cooke, Hookeun Lee, Brian Raught, Andrew Page, Victoria Aneliunas, Phil Hieter, David R. Goodlett, Ruedi Aebersold
PROTEOMICS (2005) 5(2): 380-387

Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol
Keith Vosseller, Kirk C. Hansen, Robert J. Chalkley, Jonathan C. Trinidad, Lance Wells, Gerald W. Hart, Alma L. Burlingame
PROTEOMICS (2005) 5(2): 388-398

Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: Sample preparation, data analysis, and application to the analysis of complex peptide mixtures
Ekaterina Mirgorodskaya, Corina Braeuer, Paola Fucini, Hans Lehrach, Johan Gobom
PROTEOMICS (2005) 5(2): 399-408

On-line combination of capillary isoelectric focusing and capillary non-gel sieving electrophoresis using a hollow-fiber membrane interface: a novel two-dimensional separation system for proteins
Hechun Liu, Chun Yang, Qing Yang, Weibing Zhang and Yukui Zhang
J Chromatogr B (2005) 817(1): 119-126

Dynamic electric field assisted multi-dimensional liquid chromatography of biological samples
T.P. Hennessya, M. Quagliaa, O. Kornyšovab, B.A. Grimesa, D. Lubdac and K.K. Ungera
J Chromatogr B (2005) 817(1): 127-137

Database independent detection of isotopically labeled MS/MS spectrum peptide pairs
Frank Potthasta, Jiri Ocenasek, Dorothea Rutishauser, Martin Pelikan and Ralph Schlapbach
J Chromatogr B (2005) 817(2): 225-230

Chip with Twin Anchors for Reduced Ion Suppression and Improved Mass Accuracy in MALDI-TOF Mass Spectrometry
Johan Sjödahl, Martin Kempka, Karin Hermansson, Anders Thorsén, and Johan Roeraade
ANALYTICAL CHEMISTRY (2005) 77(3): 827-832

Immunoaffinity reactors for prion protein qualitative analysis
Zuzana Bílková, Annalisa Castagna, Gianluigi Zanusso, Alessia Farinazzo, Salvatore Monaco, Eugen Damoc, Michael Przybylski, Milan Bene?, Ji?í Lenfeld, Jean-Louis Viovy, Pier Giorgo Righetti
PROTEOMICS (2005) 5(3): 639-647

Immobilized trypsin systems coupled on-line to separation methods: recent developments and analytical applications
Massolini G, Calleri E
J Sep Sci (2005) 28(1): 7-21

Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect
Scherl A, Zimmermann-Ivol CG, Dio JD, Vaezzadeh AR, Binz PA, Amez-Droz M, Cochard R, Sanchez JC, Gluckmann M, Hochstrasser DF
Rapid Commun Mass Spectrom (2005) 19(5): 605-610

Surface Plasmon Resonance/Mass Spectrometry Interface
Jens Grote, Nico Dankbar, Erk Gedig, and Simone Koenig
ANALYTICAL CHEMISTRY (2005) 77(4): 1157-1162

High-Throughput Mass-Spectrometry Monitoring for Multisubstrate Enzymes: Determining the Kinetic Parameters and Catalytic Activities of Glycosyltransferases
Min Yang, Melissa Brazier, Robert Edwards, Benjamin G. Davis
ChemBioChem (2005) 6(2): 346-357

Ionization and fragmentation of N-linked glycans as silver adducts by electrospray mass spectrometry
David J. Harvey
Rapid Communications in Mass Spectrometry (2005) 19(4): 484-492

Accurate mass measurement in nano-electrospray ionization mass spectrometry by alternate switching of high voltage between sample and reference sprayers
Yoshinori Satomi, Yoichiro Kudo, Kyoko Sasaki, Toshiharu Hase, Toshifumi Takao
Rapid Communications in Mass Spectrometry (2005) 19(4): 540-546

An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experiments
Bernhard M. Kohli, Jimmy K. Eng, Roger M. Nitsch, Uwe Konietzko
Rapid Communications in Mass Spectrometry (2005) 19(5): 589-596

Isoelectric beads for proteome pre-fractionation. II: Experimental evaluation in a multicompartment electrolyzer
Frédéric Fortis, Pierre Girot, Olivier Brieau, Annalisa Castagna, Pier Giorgio Righetti, Egisto Boschetti
PROTEOMICS (2005) 5(3): 629-638

Chemical proteomics applied to target identification and drug discovery
Verhelst SH, Bogyo M
Biotechniques (2005) 38(2): 175-7

Single-step affinity purification of toxic and non-toxic proteins on a fluidics platform
Miao J, Wu W, Spielmann T, Belfort M, Derbyshire V, Belfort G
Lab Chip (2005) 5(3): 248-53

Hardware-accelerated protein identification for mass spectrometry
Alex AT, Dumontier M, Rose JS, Hogue CW
Rapid Commun Mass Spectrom (2005) 19(6): 833-837

A proteomic strategy for the identification of caspase-associating proteins
Tan EL, Panicker RC, Chen GY, Yao SQ
Chem Commun (Camb) (2005) 5: 596-8.

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Meeting

Meetings Diary: Proteomics 3/2005
PROTEOMICS (2005) 5(3): 828-830

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Other

Direct Molecular Imaging of Lymnaea stagnalis Nervous Tissue at Subcellular Spatial Resolution by Mass Spectrometry
A. F. Maarten Altelaar, Jan van Minnen, Connie R. Jiménez, Ron M. A. Heeren, and Sander R. Piersma
ANALYTICAL CHEMISTRY (2005) 77(3): 735-741

Evaluation of "Shotgun" Proteomics for Identification of Biological Threat Agents in Complex Environmental Matrixes: Experimental Simulations
Nathan C. VerBerkmoes, W. Judson Hervey, Manesh Shah, Miriam Land, Loren Hauser, Frank W. Larimer, Gary J. Van Berkel, and Douglas E. Goeringer
ANALYTICAL CHEMISTRY (2005) 77(3): 923-932

A New Chemical Probe for Proteomics of Carbohydrate-Binding Proteins
Lluis Ballell, Kirstin J. Alink, Monique Slijper, Cees Versluis, Rob M. J. Liskamp, Roland J. Pieters
ChemBioChem (2005) 6(2): 291-295

High-throughput measurement of protein stability in microtiter plates
Aucamp JP, Cosme AM, Lye GJ, Dalby PA
Biotechnol Bioeng Early Edition: published 25-Jan-2005

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