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SPS' DigestIssue 50, 11-Apr-2008 |
A multivariate spot filtering model for two-dimensional gel electrophoresis
Morten Beck Rye, Bjørn K. Alsberg
ELECTROPHORESIS (2008) 29(6): 1369-1381
Machine learning methods for predictive proteomics
Annalisa Barla, Giuseppe Jurman, Samantha Riccadonna, Stefano Merler, Marco Chierici, and Cesare Furlanello
Brief Bioinform (2008) 9(2): 119-128
The myth of automated, high-throughput two-dimensional gel analysis
Brittan N. Clark, Howard B. Gutstein
PROTEOMICS (2008) 8(6): 1197-1203
Approaches to dimensionality reduction in proteomic biomarker studies
Melanie Hilario and Alexandros Kalousis
Brief Bioinform (2008) 9(2): 102-118
An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications
Kai A. Reidegeld, Martin Eisenacher, Michael Kohl, Daniel Chamrad, Gerhard Körting, Martin Blüggel, Helmut E. Meyer, Christian Stephan
PROTEOMICS (2008) 8(6): 1129-1137
Multivariate Data Analysis of Two-Dimensional Gel Electrophoresis Protein Patterns from Few Samples
Kristina Nedenskov Jensen, Flemming Jessen, and Bo M. Jørgensen
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1288-1296
SPIKE - a database, visualization and analysis tool of cellular signaling pathways
Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R, Assa J, Shiloh Y, Shamir R.
BMC Bioinformatics (2008) 9(1): 110
Web-based tools for protein classification
Paliakasis CD, Michalopoulos I, Kossida S.
Methods Mol Biol (2007) 428: 349-68
iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data
D'Ascenzo M, Choe L, Lee KH.
Brief Funct Genomic Proteomic Early Edition: published 13-Feb-2008
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline
Andrew W. Dowsey, Michael J. Dunn, and Guang-Zhong Yang
Bioinformatics (2008) 24(7): 950-957
A quantitative analysis software tool for mass spectrometry-based proteomics
Park SK, Venable JD, Xu T, Yates JR 3rd.
Nat Methods (2008) 5(4): 319-22
Systematic interpretation of cyclic nucleotide binding studies using KinetXBase
Sonja Schweinsberg, Daniela Moll, Nicole C. G. Burghardt, Claudia Hahnefeld, Frank Schwede, Bastian Zimmermann, Stephan Drewianka, Lars Werner, Frank Kleinjung, Hans-Gottfried Genieser, Johannes Schuchhardt, Friedrich W. Herberg
PROTEOMICS (2008) 8(6): 1212-1220
A Noise Model for Mass Spectrometry Based Proteomics
Du P, Stolovitzky G, Horvatovich P, Bischoff R, Lim J, Suits F.
Bioinformatics Early Edition: published 18-Mar-2008
MitoP2, an integrated database for mitochondrial proteins
Prokisch H, Ahting U.
Methods Mol Biol (2007) 372: 573-86
Prediction of Membrane Protein Types in a Hybrid Space
Peilin Jia, Ziliang Qian, Kaiyan Feng, Wencong Lu, Yixue Li, and Yudong Cai
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1131-1137
Exon level integration of proteomics and microarray data
Bitton DA, Okoniewski MJ, Connolly Y, Miller CJ.
BMC Bioinformatics (2008) 9(1): 118
Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods
Villmann T, Schleif FM, Kostrzewa M, Walch A, Hammer B.
Brief Bioinform Early Edition: published 11-Mar-2008
Algorithms and tools for analysis and management of mass spectrometry data
Pierangelo Veltri
Brief Bioinform (2008) 9(2): 144-155
Directional and quantitative phosphorylation networks
Jørgensen C, Linding R.
Brief Funct Genomic Proteomic (2008) 7(1): 17-26
Complexities and algorithms for glycan sequencing using tandem mass spectrometry
Shan B, Ma B, Zhang K, Lajoie G.
J Bioinform Comput Biol (2008) 6(1): 77-91
Computational proteomics: management and analysis of proteomics data
Cannataro M.
Brief Bioinform (2008) 9(2): 97-101
A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis
Morten Beck Rye, Ellen M. Færgestad, Bjørn K. Alsberg
ELECTROPHORESIS (2008) 29(6): 1359-1368
Treatment of missing values for multivariate statistical analysis of gel-based proteomics data
Romina Pedreschi, Maarten L. A. T. M. Hertog, Sebastien C. Carpentier, Jeroen Lammertyn, Johan Robben, Jean-Paul Noben, Bart Panis, Rony Swennen, Bart M. Nicolaï
PROTEOMICS (2008) 8(7): 1371-1383
Pattern recognition approaches for classifying proteomic mass spectra of biofluids
Somorjai RL.
Methods Mol Biol (2007) 428: 383-96
OpenMS - An open-source software framework for mass spectrometry
Sturm M, Bertsch A, Groepl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O.
BMC Bioinformatics (2008) 9(1): 163
Using flowViz to visualize flow cytometry data
D. Sarkar, N. Le Meur, and R. Gentleman
Bioinformatics (2008) 24(6): 878-879
Automated extraction of meaningful pathways from quantitative proteomics data
Noirel J, Ow SY, Sanguinetti G, Jaramillo A, Wright PC.
Brief Funct Genomic Proteomic Early Edition: published 7-Mar-2008
Identification of cross-linked peptides from large sequence databases
Rinner O, Seebacher J, Walzthoeni T, Mueller L, Beck M, Schmidt A, Mueller M, Aebersold R.
Nat Methods (2008) 5(4): 315-8
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks
Liu G, Neelamegham S.
Bioinformatics Early Edition: published 28-Feb-2008
Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
Chou KC, Shen HB.
Nat Protoc (2008) 3(2): 153-162
DeconMSn: A software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Mayampurath AM, Jaitly N, Purvine SO, Monroe ME, Auberry KJ, Adkins JN, Smith RD.
Bioinformatics Early Edition: published 26-Feb-2008
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
Michael Mueller, Juan Antonio Vizcaíno, Philip Jones, Richard Côté, David Thorneycroft, Rolf Apweiler, Henning Hermjakob, Lennart Martens
PROTEOMICS (2008) 8(6): 1138-1148
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes
Zhang GL, Khan AM, Srinivasan KN, Heiny A, Lee K, Kwoh CK, August JT, Brusic V.
BMC Bioinformatics (2008) 9(Suppl 1): S19
The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world
Sandra Orchard and Henning Hermjakob
Brief Bioinform (2008) 9(2): 166-173
Automated image alignment for 2-D gel electrophoresis in a high-throughput proteomics pipeline
Dowsey AW, Dunn MJ, Yang GZ.
Bioinformatics (2008) 24(7): 950-7
An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons
Martin Irmler, Daniela Hartl, Thorsten Schmidt, Johannes Schuchhardt, Christiane Lach, Helmut E. Meyer, Martin Hrabé de Angelis, Joachim Klose, Johannes Beckers
PROTEOMICS (2008) 8(6): 1165-1169
Analysis of the human kinome using methods including fold recognition reveals two novel kinases
Briedis KM, Starr A, Bourne PE.
PLoS ONE (2008) 3(2): e1597
GOTreePlus: An Interactive Gene Ontology Browser for Proteomics Projects
Lee B, Brown K, Hathout Y, Seo J.
Bioinformatics Early Edition: published 21-Feb-2008
Finding the significant markers: statistical analysis of proteomic data
Carpentier SC, Panis B, Swennen R, Lammertyn J.
Methods Mol Biol (2007) 428: 327-48
Design and analysis of quantitative differential proteomics investigations using lc-ms technology
Bukhman YV, Dharsee M, Ewing R, Chu P, Topaloglou T, LE Bihan T, Goh T, Duewel H, Stewart II, Wisniewski JR, Ng NF.
J Bioinform Comput Biol (2008) 6(1): 107-23
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
Andrei Zinovyev, Eric Viara, Laurence Calzone, and Emmanuel Barillot
Bioinformatics (2008) 24(6): 876-877
Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome
Kyung-Hoon Kwon, Gun Wook Park, Jin Young Kim, Sang Kwang Lee, Jeong Hwa Lee, Young Hye Kim, Se-Young Kim, Young Mok Park, Jong Shin Yoo
PROTEOMICS (2008) 8(6): 1149-1161
Information quality in proteomics
David A. Stead, Norman W. Paton, Paolo Missier, Suzanne M. Embury, Cornelia Hedeler, Binling Jin, Alistair J. P. Brown, and Alun Preece
Brief Bioinform (2008) 9(2): 174-188
An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis
Morten Beck Rye, Ellen M. Færgestad, Harald Martens, Jens Petter Wold, Bjørn K. Alsberg
ELECTROPHORESIS (2008) 29(6): 1382-1393
BrainProfileDB - a platform for integration of functional genomics data
Johannes Schuchhardt, Alexander Glintschert, Daniela Hartl, Martin Irmler, Johannes Beckers, Christian Stephan, Katrin Marcus, Joachim Klose, Helmut E. Meyer, Arif Malik
PROTEOMICS (2008) 8(6): 1162-1164
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, and Richard D. Smith
Bioinformatics (2008) 24(7): 1021-1023
Proteomic analysis of the venom of Heterometrus longimanus (Asian black scorpion)
Scott Bringans, Soren Eriksen, Tulene Kendrick, P. Gopalakrishnakone, Andreja Livk, Robert Lock, Richard Lipscombe
PROTEOMICS (2008) 8(5): 1081-1096
Structure of the Cytosolic Part of the Subunit b-Dimer of Escherichia coli FoF1-ATP Synthase
Hornung T, Volkov OA, Zaida TM, Delannoy S, Wise JG, Vogel PD.
Biophys J Early Edition: published 7-Mar-2008
The candidate MAP kinase phosphorylation substrate DPL-1 (DP) promotes expression of the MAP kinase phosphatase LIP-1 in C. elegans germ cells
Lin B, Reinke V.
Dev Biol (2008) 316(1): 50-61
Changes in the Proteome of Functional and Regressing Corpus Luteum During Pregnancy and Lactation in the Rat
González-Fernández R, MartÃnez-Galisteo E, Gaytán F, Bárcena JA, Sánchez-Criado JE.
Biol Reprod Early Edition: published 19-Mar-2008
Identification of new tyrosine phosphorylated proteins in rat brain mitochondria
Lewandrowski U, Sickmann A, Cesaro L, Brunati AM, Toninello A, Salvi M.
FEBS Lett (2008) 582(7): 1104-10
Myocardial adaptation of energy metabolism to elevated preload depends on calcineurin activity : A proteomic approach
Schott P, Asif AR, Gräf C, Toischer K, Hasenfuss G, Kögler H.
Basic Res Cardiol Early Edition: published 15-Feb-2008
Proteomic analysis of the response to high-salinity stress in Physcomitrella patens
Wang X, Yang P, Gao Q, Liu X, Kuang T, Shen S, He Y.
Planta Early Edition: published 20-Mar-2008
Self-proteolysis regulation in the Bothrops jararaca venom: The metallopeptidases and their intrinsic peptidic inhibitor
Marques-Porto R, Lebrun I, Pimenta DC.
Comp Biochem Physiol C Toxicol Pharmacol (2008) 147(4): 424-33
Determining the protein repertoire of Cryptosporidium parvum sporozoites
Sanya J. Sanderson, Dong Xia, Helena Prieto, John Yates, Mark Heiges, Jessica C. Kissinger, Elizabeth Bromley, Kalpana Lal, Robert E. Sinden, Fiona Tomley, Jonathan M. Wastling
PROTEOMICS (2008) 8(7): 1398-1414
Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state
Muela A, Seco C, Camafeita E, Arana I, Orruño M, López JA, Barcina I.
FEMS Microbiol Ecol (2008) 64(1): 28-36
Transcriptome and proteome analysis of early embryonic mouse brain development
Daniela Hartl, Martin Irmler, Irmgard Römer, Michael T. Mader, Lei Mao, Claus Zabel, Martin Hrabé de Angelis, Johannes Beckers, Joachim Klose
PROTEOMICS (2008) 8(6): 1257-1265
Proteomic Analysis of Diaminochlorotriazine Adducts in Wister Rat Pituitary Glands and LbetaT2 Rat Pituitary Cells
Dooley GP, Reardon KF, Prenni JE, Tjalkens RB, Legare ME, Foradori CD, Tessari JE, Hanneman WH.
Chem Res Toxicol Early Edition: published 28-Mar-2008
Proteomic Analysis of Mouse Brain Microsomes: Identification and Bioinformatic Characterization of Endoplasmic Reticulum Proteins in the Mammalian Central Nervous System
Stanley M. Stevens Jr., R. Scott Duncan, Peter Koulen, and Laszlo Prokai
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1046-1054
Toward an Understanding of the Molecular Mechanism for Successful Blood Feeding by Coupling Proteomics Analysis with Pharmacological Testing of Horsefly Salivary Glands
Xueqing Xu, Hailong Yang, Dongying Ma, Jing Wu, Yipeng Wang, Yuzhu Song, Xu Wang, Yi Lu, Junxing Yang, and Ren Lai
Mol Cell Proteomics (2008) 7(3): 582-590
Effects of Coronary Prestenting Platelet Inhibition on Coronary Poststenting Inflammation
Sacristán D, López-Farré AJ, Zamorano-León JJ, Azcona L, Fernández-Ortiz A, Romero J, Farré J, Macaya C.
J Cardiovasc Pharmacol (2008) 51(3): 286-292
Proteomic investigation on chronic bladder irritation in the rat
Tyagi P, Chen X, Hayashi Y, Yoshimura N, Chancellor MB, de Miguel F.
Urology (2008) 71(3): 536-40
E3 ubiquitin ligase SIAH1 mediates ubiquitination and degradation of TRB3
Zhou Y, Li L, Liu Q, Xing G, Kuai X, Sun J, Yin X, Wang J, Zhang L, He F.
Cell Signal (2008) 20(5): 942-8
Proteomic Identification of Differentially Expressed Proteins in Arabidopsis Mutant ntm1-D with Disturbed Cell Division
Lee KH, Kim YS, Park CM, Kim HJ.
Mol Cells (2008) 25(1): 70-7
Long term anoxia in rainbow trout investigated by 2-DE and MS/MS
Tune Wulff, Flemming Jessen, Peter Roepstorff, Else K. Hoffmann
PROTEOMICS (2008) 8(5): 1009-1018
"Proteotyping": Population Proteomics of Human Leukocytes Using Top Down Mass Spectrometry
Roth MJ, Parks BA, Ferguson JT, Ii MT, Kelleher NL.
Anal Chem Early Edition: published 20-Mar-2008
The amyloplast proteome of potato tuber
Stensballe A, Hald S, Bauw G, Blennow A, Welinder KG.
FEBS J (2008) 275(8): 1723-41
Proteomic analysis of selenium embryotoxicity in cultured postimplantation rat embryos
Usami M, Mitsunaga K, Nakazawa K, Doi O.
Birth Defects Res B Dev Reprod Toxicol Early Edition: published 20-Mar-2008
Asparagine Deamidation and the Role of Higher Order Protein Structure
Jenny Rivers, Lucy McDonald, Ian J. Edwards, and Robert J. Beynon
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 921-927
Identification by 2-D DIGE of apoplastic proteins regulated by oligogalacturonides in Arabidopsis thaliana
Manuela Casasoli, Sara Spadoni, Kathryn S. Lilley, Felice Cervone, Giulia De Lorenzo, Benedetta Mattei
PROTEOMICS (2008) 8(5): 1042-1054
Proteomics analysis of immunoprecipitated proteins associated with the oncogenic kinase cot
Wu B, Wilmouth RC.
Mol Cells (2008) 25(1): 43-9
FHIT interaction with ferredoxin reductase triggers generation of reactive oxygen species and apoptosis of cancer cells
Trapasso F, Pichiorri F, Gaspari M, Palumbo T, Aqeilan RI, Gaudio E, Okumura H, Iuliano R, Di Leva G, Fabbri M, Birk DE, Raso C, Green-Church K, Spagnoli LG, Venuta S, Huebner K, Croce CM.
J Biol Chem Early Edition: published 3-Mar-2008
Proteomic 2-D DIGE Profiling of APP23 Transgenic Mice Brain from Pre-plaque and Plaque Phenotypes
Guerreiro N, Staufenbiel M, Gomez-Mancilla B.
J Alzheimers Dis (2008) 13(1): 17-30
The Tale of Two Domains: Proteomics and Genomics Analysis of SMYD2, A New Histone Methyltransferase
Mohamed Abu-Farha, Jean-Philippe Lambert, Ashraf S. Al-Madhoun, Fred Elisma, Ilona S. Skerjanc, and Daniel Figeys
Mol Cell Proteomics (2008) 7(3): 560-572
Outer membrane Modifications of Pseudomonas fluorescens MF37 in Response to Hyperosmolarity
Muriel Guyard-Nicodème, Alexis Bazire, Gaëlle Hémery, Thierry Meylheuc, Daniel Mollé, Nicole Orange, Laurène Fito-Boncompte, Marc Feuilloley, Dominique Haras, Alain Dufour, and Sylvie Chevalier
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1218-1225
Comprehensive and quantitative proteome profiling of the mouse liver and plasma
Lai KK, Kolippakkam D, Beretta L.
Hepatology (2008) 47(3): 1043-51
Protein profiling of hemocytes from the terrestrial crustacean Armadillidium vulgare(,)
Herbinière J, Grève P, Strub JM, Thiersé D, Raimond M, van Dorsselaer A, Martin G, Braquart-Varnier C.
Dev Comp Immunol (2008) 32(8): 875-82
Hsf1 Activation Inhibits Rapamycin Resistance and TOR Signaling in Yeast Revealed by Combined Proteomic and Genetic Analysis
Bandhakavi S, Xie H, O'Callaghan B, Sakurai H, Kim DH, Griffin TJ.
PLoS ONE (2008) 3(2): e1598
Systematic gene expression profiling of mouse model series reveals coexpressed genes
Marion Horsch, Sandra Schädler, Valerie Gailus-Durner, Helmut Fuchs, Helmut Meyer, Martin Hrabé de Angelis, Johannes Beckers
PROTEOMICS (2008) 8(6): 1248-1256
Leukemia inhibitory factor induces an antiapoptotic response in oligodendrocytes through Akt-phosphorylation and up-regulation of 14-3-3
Helena Slaets, Debora Dumont, Joris Vanderlocht, Jean-Paul Noben, Pierre Leprince, Johan Robben, Jerome Hendriks, Piet Stinissen, Niels Hellings
PROTEOMICS (2008) 8(6): 1237-1247
Dematin and adducin provide a novel link between the spectrin cytoskeleton and human erythrocyte membrane by directly interacting with glucose transporter-1
Khan AA, Hanada T, Mohseni M, Jeong JJ, Zeng L, Gaetani M, Li D, Reed BC, Speicher DW, Chishti AH.
J Biol Chem Early Edition: published 19-Mar-2008
Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility
Peddinti D, Nanduri B, Kaya A, Feugang JM, Burgess SC, Memili E.
BMC Syst Biol (2008) 2(1): 19
Proteomic profiling reveals that Th2-inducing dendritic cells stimulated with helminth antigens have a ?limited maturation? phenotype
Stéphanie Ferret-Bernard, Rachel Sally Curwen, Adrian Paul Mountford
PROTEOMICS (2008) 8(5): 980-993
Proteomics in Caenorhabditis elegans
Audhya A, Desai A.
Brief Funct Genomic Proteomic Early Edition: published 27-Mar-2008
Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus
Marcus Bode, Martin Irmler, Manuela Friedenberger, Caroline May, Klaus Jung, Christian Stephan, Helmut E. Meyer, Christiane Lach, Reyk Hillert, Andreas Krusche, Johannes Beckers, Katrin Marcus, Walter Schubert
PROTEOMICS (2008) 8(6): 1170-1178
Proteomic profiling of aging in the mouse heart: Altered expression of mitochondrial proteins
Chakravarti B, Oseguera M, Dalal N, Fathy P, Mallik B, Raval A, Chakravarti DN.
Arch Biochem Biophys Early Edition: published 10-Feb-2008
Tumor suppressor PTEN mediates a negative regulation of E3 ubiquitin-protein ligase Nedd4
Ahn Y, Hwang CY, Lee SR, Kwon KS, Lee C.
Biochem J Early Edition: published 29-Feb-2008
Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile
Sunia A. Trauger, Ewa Kalisak, Jaroslaw Kalisiak, Hirotoshi Morita, Michael V. Weinberg, Angeli Lal Menon, Farris L. Poole II, Michael W. W. Adams, and Gary Siuzdak
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1027-1035
Identification of aphid salivary proteins: a proteomic investigation of Myzus persicae
Harmel N, Létocart E, Cherqui A, Giordanengo P, Mazzucchelli G, Guillonneau F, De Pauw E, Haubruge E, Francis F.
Insect Mol Biol (2008) 17(2): 165-74
Proteomic analysis of pathogenic and attenuated Alcelaphine herpesvirus-1
Dry I, Haig DM, Inglis NF, Imrie L, Stewart JP, Russell GC.
J Virol Early Edition: published 19-Mar-2008
Proteomic Approach To Identify Champagne Wine Proteins as Modified by Botrytis cinerea Infection
Clara Cilindre, Sandrine Jégou, Agnès Hovasse, Christine Schaeffer, Antonio J. Castro, Christophe Clément, Alain Van Dorsselaer, Philippe Jeandet, and Richard Marchal
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1199-1208
Genome Comparison and Proteomic Characterization of Thermus thermophilus Bacteriophages P23-45 and P74-26: Siphoviruses with Triplex-forming Sequences and the Longest Known Tails
Minakhin L, Goel M, Berdygulova Z, Ramanculov E, Florens L, Glazko G, Karamychev VN, Slesarev AI, Kozyavkin SA, Khromov I, Ackermann HW, Washburn M, Mushegian A, Severinov K.
J Mol Biol (2008) 378(2): 468-80
Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3
Neuman BW, Joseph JS, Saikatendu KS, Serrano P, Chatterjee A, Johnson MA, Liao L, Klaus JP, Yates JR 3rd, Wüthrich K, Stevens RC, Buchmeier MJ, Kuhn P.
J Virol Early Edition: published 26-Mar-2008
Unfolded protein response and cell death after depletion of brefeldin A-inhibited guanine nucleotide-exchange protein GBF1
Citterio C, Vichi A, Pacheco-Rodriguez G, Aponte AM, Moss J, Vaughan M.
Proc Natl Acad Sci U S A (2008) 105(8): 2877-82
Adapting Proteostasis for Disease Intervention
Balch WE, Morimoto RI, Dillin A, Kelly JW.
Science (2008) 319(5865): 916-919
Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change
Rembert Pieper, Shih-Ting Huang, David J. Clark, Jeffrey M. Robinson, Prashanth P. Parmar, Hamid Alami, Christine L. Bunai, Robert D. Perry, Robert D. Fleischmann, Scott N. Peterson
PROTEOMICS (2008) 8(7): 1442-1458
Defining the Regulated Secreted Proteome of Rodent Adipocytes upon the Induction of Insulin Resistance
Jae-Min Lim, Dan Sherling, Chin Fen Teo, Dorothy B. Hausman, Dawei Lin, and Lance Wells
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1251-1263
Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli
Baars L, Wagner S, Wickström D, Klepsch M, Ytterberg AJ, van Wijk KJ, de Gier JW.
J Bacteriol Early Edition: published 22-Feb-2008
Quantitative Proteomics Analysis Demonstrates Post-transcriptional Regulation of Embryonic Stem Cell Differentiation to Hematopoiesis
Andrew J. K. Williamson, Duncan L. Smith, David Blinco, Richard D. Unwin, Stella Pearson, Claire Wilson, Crispin Miller, Lee Lancashire, Georges Lacaud, Valerie Kouskoff, and Anthony D. Whetton
Mol Cell Proteomics (2008) 7(3): 459-472
Protein expression profile in the amygdala of rats with methamphetamine-induced behavioral sensitization
Iwazaki T, McGregor IS, Matsumoto I.
Neurosci Lett (2008) 435(2): 113-9
Exploration of the normal human bronchoalveolar lavage fluid proteome
Jinzhi Chen, Soyoung Ryu, Sina A. Gharib, David R. Goodlett, Lynn M. Schnapp
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 585-595
Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes
Mohan A, Sullivan WJ Jr, Radivojac P, Dunker AK, Uversky VN.
Mol Biosyst (2008) 4(4): 328-40
ISG20L2, a Novel Vertebrate Nucleolar Exoribonuclease Involved in Ribosome Biogenesis
Yohann Coute, Karine Kindbeiter, Stephane Belin, Regis Dieckmann, Laurent Duret, Laurent Bezin, Jean-Charles Sanchez, and Jean-Jacques Diaz
Mol Cell Proteomics (2008) 7(3): 546-559
The mTOR target 4E-BP1 contributes to differential protein expression during normoxia and hypoxia through changes in mRNA translation efficiency
Michaël G. Magagnin, Twan van den Beucken, Kjell Sergeant, Philippe Lambin, Marianne Koritzinsky, Bart Devreese, Bradly G. Wouters
PROTEOMICS (2008) 8(5): 1019-1028
Proteomic Analysis of Nuclear Factors Binding to an Intronic Enhancer in the Myelin Proteolipid Protein Gene
Dobretsova A, Johnson JW, Jones RC, Edmondson RD, Wight PA.
J Neurochem Early Edition: published 7-Feb-2008
Proteomic identification of differentially expressed genes in mouse neural stem cells and neurons differentiated from embryonic stem cells in vitro
Akama K, Tatsuno R, Otsu M, Horikoshi T, Nakayama T, Nakamura M, Toda T, Inoue N.
Biochim Biophys Acta Early Edition: published 15-Feb-2008
Dissection of the insulin signaling pathway via quantitative phosphoproteomics
Krüger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M.
Proc Natl Acad Sci U S A (2008) 105(7): 2451-6
Protein Networks Supporting AP-3 Function in Targeting Lysosomal Membrane Proteins
Anitei M, Baust T, Czupalla C, Parshyna I, Bourel L, Thiele C, Krause E, Hoflack B.
Mol Biol Cell Early Edition: published 20-Feb-2008
Proteome analysis of ventral midbrain in MPTP-treated normal and L1cam transgenic mice
Madeleine Diedrich, Lei Mao, Christian Bernreuther, Claus Zabel, Grit Nebrich, Ralf Kleene, Joachim Klose
PROTEOMICS (2008) 8(6): 1266-1275
SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation
Karel Mikulík, Petra Pale?ková, Jürgen Felsberg, Jan Bobek, Jarmila Zídková, Petr Halada
PROTEOMICS (2008) 8(7): 1429-1441
Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions
Nathan P. Manes, Ryan D. Estep, Heather M. Mottaz, Ronald J. Moore, Therese R. W. Clauss, Matthew E. Monroe, Xiuxia Du, Joshua N. Adkins, Scott W. Wong, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 960-968
Atbf1 is required for the Pit1 gene early activation
Qi Y, Ranish JA, Zhu X, Krones A, Zhang J, Aebersold R, Rose DW, Rosenfeld MG, Carrière C.
Proc Natl Acad Sci U S A (2008) 105(7): 2481-6
Proteomic analysis of the EhV-86 virion
Allen MJ, Howard JA, Lilley KS, Wilson WH.
Proteome Science (2008) 6(1): 11
Differential liquid phase proteomic analysis of the effect of selenium supplementation in LNCaP cells
Roveri A, Vitale MP, Serain E, Zaccarin M, Mauri P, Di Silvestre D, De Palma A, Gion M, Toppo S, Maiorino M, Ursini F.
J Chromatogr B (2008) 865(1-2): 63-73
ClpL is essential for induction of thermotolerance and is potentially part of the HrcA regulon in Lactobacillus gasseri
Aki Suokko, Marjo Poutanen, Kirsi Savijoki, Nisse Kalkkinen, Pekka Varmanen
PROTEOMICS (2008) 8(5): 1029-1041
Toward a Confocal Subcellular Atlas of the Human Proteome
Laurent Barbe, Emma Lundberg, Per Oksvold, Anna Stenius, Erland Lewin,Erik Bjorling, Anna Asplund, Fredrik Ponten, Hjalmar Brismar, Mathias Uhlen, and Helene Andersson-Svahn
Mol Cell Proteomics (2008) 7(3): 499-508
Proteomics Analysis of Host Cells Infected with Infectious Bursal Disease Virus
Xiaojuan Zheng, Lianlian Hong, Lixue Shi, Junqing Guo, Zhen Sun, and Jiyong Zhou
Mol Cell Proteomics (2008) 7(3): 612-625
Rapid Isolation and Identification of Bacteriophage T4-Encoded Modifications of Escherichia coli RNA Polymerase: A Generic Method to Study Bacteriophage/Host Interactions
Lars F. Westblade, Leonid Minakhin, Konstantin Kuznedelov, Alan J. Tackett, Emmanuel J. Chang, Rachel A. Mooney, Irina Vvedenskaya, Qing Jun Wang, David Fenyö, Michael P. Rout, Robert Landick, Brian T. Chait, Konstantin Severinov, and Seth A. Darst
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1244-1250
Nano Scale Proteomics Revealed the Presence of Regulatory Proteins Including Three FT-like proteins in Phloem and Xylem Saps from Rice
Aki T, Shigyo M, Nakano R, Yoneyama T, Yanagisawa S.
Plant Cell Physiol Early Edition: published 27-Mar-2008
Systematic Investigation of the Hemolymph Proteome of Manduca sexta at the Fifth Instar Larvae Stage Using One- and Two-Dimensional Proteomics Platforms
Takako Furusawa, Randeep Rakwal, Hyung Wook Nam, Misato Hirano, Junko Shibato, Yu Sam Kim, Yoko Ogawa, Yasukazu Yoshida, Karl J. Kramer, Yoshiaki Kouzuma, Ganesh Kumar Agrawal, and Masami Yonekura
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 938-959
PEDF from mouse mesenchymal stem cell secretome attracts fibroblasts
Sarojini H, Estrada R, Lu H, Dekova S, Lee MJ, Gray RD, Wang E.
J Cell Biochem Early Edition: published 17-Mar-2008
Proteomic scale high-sensitivity analyses of GPI membrane anchors
Mehlert A, Ferguson MA.
Glycoconj J Early Edition: published 11-Mar-2008
Regional differences in porcine adipocytes isolated from skeletal muscle and adipose tissues as identified by a proteomic approach
Gondret F, Guitton N, Guillerm-Regost C, Louveau I.
J Anim Sci Early Edition: published 29-Feb-2008
Identification of extracellular-regulated kinase 1/2 and p38MAPK as regulators of human sperm motility and acrosome reaction and as predictors of poor spermatozoa quality
Almog T, Lazar S, Reiss N, Etkovitz N, Milch E, Rahamim N, Dobkin-Bekman M, Rotem R, Kalina M, Ramon J, Raziel A, Breitbart H, Seger R, Naor Z.
J Biol Chem Early Edition: published 27-Mar-2008
Shedding light on the role of Vitreoscilla hemoglobin on cellular catabolic regulation by proteomic analysis
Isarankura-Na-Ayudhya C, Panpumthong P, Tangkosakul T, Boonpangrak S, Prachayasittikul V.
Int J Biol Sci (2008) 4(2): 71-80
Comparative Analysis of the Venom Proteomes of Vipera ammodytes ammodytes and Vipera ammodytes meridionalis
Dessislava Georgieva, Michaela Risch, Anna Kardas, Friedrich Buck, Martin von Bergen, and Christian Betzel
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 866-886
Developmental Fate Determination and Marker Discovery in Hematopoietic Stem Cell Biology Using Proteomic Fingerprinting
Elaine Spooncer, Nathalie Brouard, Susie K. Nilsson, Brenda Williams, Mira C. Liu, Richard D. Unwin, David Blinco, Ewa Jaworska, Paul J. Simmons, and Anthony D. Whetton
Mol Cell Proteomics (2008) 7(3): 573-581
Profiling the metabolic proteome of bovine mammary tissue
Amanda J. Beddek, Pisana Rawson, Lifeng Peng, Russell Snell, Klaus Lehnert, Hamish E. Ward, T. William Jordan
PROTEOMICS (2008) 8(7): 1502-1515
Investigation of the human tear film proteome using multiple proteomic approaches
Green-Church KB, Nichols KK, Kleinholz NM, Zhang L, Nichols JJ.
Mol Vis (2008) 14: 456-70.
BetaA, the major beta globin in definitive red blood cells, is present from the onset of primitive erythropoiesis in chicken
Alev C, McIntyre BA, Nagai H, Shin M, Shinmyozu K, Jakt LM, Sheng G.
Dev Dyn (2008) 237(4): 1193-1197
Proteomic analysis of the secretome of Leishmania donovani
Silverman JM, Chan SK, Robinson DP, Dwyer DM, Nandan D, Foster LJ, Reiner NE.
Genome Biol (2008) 9(2): R35
Morphogenetic lung defects of JSAP1-deficient embryos proceeds via the disruptions of the normal expressions of cytoskeletal and chaperone proteins
Hye-Yeong Ha, Jung-Bin Kim, Ik-Hyun Cho, Hyo-Jin Joo, Kyoung-Shim Kim, Kang-Woo Lee, Hongjai Sunwoo, Joo-Young Im, Ja-Kyeong Lee, Jang-Hee Hong, Pyung-Lim Han
PROTEOMICS (2008) 8(5): 1071-1080
Protein encoded by the AxinFu allele effectively downregulates Wnt signaling but exerts a dominant negative effect on c-Jun N-terminal kinase signaling
Lu Z, Liu W, Huang H, He Y, Han Y, Wang Y, Li Q, Ruan K, Ye Z, Low BC, Meng A, Lin SC.
J Biol Chem Early Edition: published 3-Mar-2008
Mitochondrial Complexes in Trypanosoma brucei: A Novel Complex and a Unique Oxidoreductase Complex
Aswini K. Panigrahi, Alena Zikova, Rachel A. Dalley, Nathalie Acestor,Yuko Ogata, Atashi Anupama, Peter J. Myler, and Kenneth D. Stuart
Mol Cell Proteomics (2008) 7(3): 534-545
Multiple proteins and biological processes up-regulated during maxillary expansion in rats
Ma J, Wu Y, Zhang W, Smales RJ, Huang Y, Pan Y, Wang L.
BMC Musculoskelet Disord (2008) 9(1): 37
New ways to identify novel bacterial antigens for vaccine development
Movahedi AR, Hampson DJ.
Vet Microbiol Early Edition: published 10-Mar-2008
Assessing quantitative post-mortem changes in the gray matter of the human frontal cortex proteome by 2-D DIGE
Anna Crecelius, Andrea Götz, Thomas Arzberger, Thomas Fröhlich, Georg J. Arnold, Isidro Ferrer, Hans A. Kretzschmar
PROTEOMICS (2008) 8(6): 1276-1291
Integrin-linked kinase localizes to the centrosome and regulates mitotic spindle organization
Fielding AB, Dobreva I, McDonald PC, Foster LJ, Dedhar S.
J Cell Biol (2008) 180(4): 681-9
Proteomic analysis on a high salt tolerance introgression strain of Triticum aestivum/Thinopyrum ponticum
Meng-Cheng Wang, Zhen-Ying Peng, Cui-Ling Li, Fei Li, Chun Liu, Guang-Min Xia
PROTEOMICS (2008) 8(7): 1470-1489
Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation
Richard S. Lee, Flavio Monigatti, Mohini Lutchman, Thomas Patterson, Bogdan Budnik, Judith A. J. Steen, Michael R. Freeman, Hanno Steen
PROTEOMICS (2008) 8(5): 1097-1112
Upregulation of annexin A2 in H(2)O(2)-induced premature senescence as evidenced by 2D-DIGE proteome analysis
Chrétien A, Delaive E, Dieu M, Demazy C, Ninane N, Raes M, Toussaint O.
Exp Gerontol (2008) 43(4): 353-9
Genetic and proteomic analysis of the MHC class I repertoire from four ovine haplotypes
Ballingall KT, Miltiadou D, Chai ZW, McLean K, Rocchi M, Yaga R, McKeever DJ.
Immunogenetics Early Edition: published 13-Feb-2008
Proteasome subunit proteins and neuropathology in tauopathies and synucleinopathies: Consequences for proteomic analyses
Mohamed Zouambia, David F. Fischer, Barbara Hobo, Rob A. I. De Vos, Elly M. Hol, Ian M. Varndell, Paul W. Sheppard, Fred W. Van Leeuwen
PROTEOMICS (2008) 8(6): 1221-1236
Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression
Behan A, Byrne C, Dunn MJ, Cagney G, Cotter DR.
Mol Psychiatry Early Edition: published 12-Feb-2008
Proteomics-based identification of autoantibody against heat shock protein 70 as a diagnostic marker in esophageal squamous cell carcinoma
Fujita Y, Nakanishi T, Miyamoto Y, Hiramatsu M, Mabuchi H, Miyamoto A, Shimizu A, Takubo T, Tanigawa N.
Cancer Lett Early Edition: published 9-Mar-2008
Detection and identification of NAP-2 as a biomarker in hepatitis B-related hepatocellular carcinoma by proteomic approach
Min H, Qin J, Zhai R, Wei X, Wang Q, Rong M, Jiang Z, Huang Y, Zhang Z.
Proteome Science (2008) 6(1): 10
Discovering novel targets for autoantibodies in dilated cardiomyopathy
Christina Buse, Frank Altmann, Barbara Amann, Stefanie M. Hauck, Cordula Poulsen Nautrup, Marius Ueffing, Manfred Stangassinger, Cornelia A. Deeg
ELECTROPHORESIS (2008) 29(6): 1325-1332
Cytotoxicity and Proteomics Analyses of OSU03013 in Lung Cancer
Tan YH, Lee KH, Lin T, Sun YC, Hsieh-Li HM, Juan HF, Wang YC.
Clin Cancer Res (2008) 14(6): 1823-1830
Increased RhoGDI2 and peroxiredoxin 5 levels in asthmatic murine model of beta2-adrenoceptor desensitization: A proteomics approach
Liu H, Zhou LF, Zhang Q, Qian FH, Yin KS, Huang M, Zhang XL.
Chin Med J (Engl) (2008) 121(4): 355-62
Marked Defects in the Expression and Glycosylation of {alpha}2-HS Glycoprotein/Fetuin-A in Plasma from Neonates with Intrauterine Growth Restriction: Proteomics Screening and Potential Clinical Implications
Panagiotis M. Karamessinis, Ariadne Malamitsi-Puchner, Theodora Boutsikou, Manousos Makridakis, Konstantinos Vougas, Michael Fountoulakis, Antonia Vlahou, and George Chrousos
Mol Cell Proteomics (2008) 7(3): 591-599
Epitope discovery in West Nile virus infection: Identification and immune recognition of viral epitopes
McMurtrey CP, Lelic A, Piazza P, Chakrabarti AK, Yablonsky EJ, Wahl A, Bardet W, Eckerd A, Cook RL, Hess R, Buchli R, Loeb M, Rinaldo CR, Bramson J, Hildebrand WH.
Proc Natl Acad Sci U S A (2008) 105(8): 2981-6
Plasma biomarkers in pediatric patients undergoing cardiopulmonary bypass
Lull ME, Carkaci-Salli N, Freeman WM, Myers JL, Midgley FM, Thomas NJ, Kimatian SJ, Vrana KE, Undar A.
Pediatr Res Early Edition: published 27-Feb-2008
Proteomic analysis of early urinary biomarkers of renal changes in type 2 diabetic patients
Elisa Bellei, Elena Rossi, Leonardo Lucchi, Simona Uggeri, Alberto Albertazzi, Aldo Tomasi, Anna Iannone
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 478-491
Mass spectrometry is only one piece of the puzzle in clinical proteomics
James N. McGuire, Julie Overgaard, and Flemming Pociot
Brief Funct Genomic Proteomic (2008) 7(1): 74-83
Autocrine induction of invasion and metastasis by tumor-associated trypsin inhibitor in human colon cancer cells
Gouyer V, Fontaine D, Dumont P, de Wever O, Fontayne-Devaud H, Leteurtre E, Truant S, Delacour D, Drobecq H, Kerckaert JP, de Launoit Y, Bracke M, Gespach C, Desseyn JL, Huet G.
Oncogene Early Edition: published 3-Mar-2008
Pfetin as a prognostic biomarker of gastrointestinal stromal tumors revealed by proteomics
Suehara Y, Kondo T, Seki K, Shibata T, Fujii K, Gotoh M, Hasegawa T, Shimada Y, Sasako M, Shimoda T, Kurosawa H, Beppu Y, Kawai A, Hirohashi S.
Clin Cancer Res (2008) 14(6): 1707-17
Proteomics Analysis of Cells in Whole Saliva from Oral Cancer Patients via Value-added Three-dimensional Peptide Fractionation and Tandem Mass Spectrometry
Hongwei Xie, Getiria Onsongo, Jonathan Popko, Ebbing P. de Jong, Jing Cao, John V. Carlis, Robert J. Griffin, Nelson L. Rhodus, and Timothy J. Griffin
Mol Cell Proteomics (2008) 7(3): 486-498
Evaluation of Colon Cancer-Specific Antigen 2 as a Potential Serum Marker for Colorectal Cancer
Leman ES, Schoen RE, Magheli A, Sokoll LJ, Chan DW, Getzenberg RH.
Clin Cancer Res (2008) 14(5): 1349-1354
Oxidized proteins in plasma of patients with heart failure: Role in endothelial damage
Banfi C, Brioschi M, Barcella S, Veglia F, Biglioli P, Tremoli E, Agostoni P.
Eur J Heart Fail (2008) 10(3): 244-51
An immunoproteomic approach for identification of clinical biomarkers of Whipple's disease
Malgorzata Kowalczewska, Florence Fenollar, Claude Villard, Saïd Azza, Maurice Roux, Didier Raoult
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 504-516
Probing the urinary proteome of severe acute pancreatitis
Flint RS, Phillips AR, Farrant GJ, McKay D, Buchanan CM, Cooper GS, Windsor JA.
HPB (Oxford) (2007) 9(6): 447-55
Application of proteome analysis to the assessment of prognosis and response prediction in clinical oncology
Röcken C, Ketterlinus R, Ebert MP.
Curr Cancer Drug Targets (2008) 8(2): 141-5
Male gender is associated with excessive IL-6 expression following severe injury
Sperry JL, Friese RS, Frankel HL, West MA, Cuschieri J, Moore EE, Harbrecht BG, Peitzman AB, Billiar TR, Maier RV, Remick DG, Minei JP.
J Trauma (2008) 64(3): 572-8; discussion 578-9
Decreased adhesiveness, resistance to anoikis and suppression of GRP94 are integral to the survival of circulating tumor cells in prostate cancer
Howard EW, Leung SC, Yuen HF, Chua CW, Lee DT, Chan KW, Wang X, Wong YC.
Clin Exp Metastasis Early Edition: published 14-Mar-2008
Proteomic studies reveal coordinated changes in T cell expression patterns upon HIV-1 infection
Ringrose J, Jeeninga RE, Berkhout B, Speijer D.
J Virol Early Edition: published 20-Feb-2008
Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses
Anthony O. Gramolini, Thomas Kislinger, Rasoul Alikhani-Koopaei, Vincent Fong, Natalie J. Thompson, Ruth Isserlin, Parveen Sharma, Gavin Y. Oudit, Maria G. Trivieri, Ailis Fagan, Anitha Kannan, Desmond G. Higgins, Hendrik Huedig, George Hess, Sara Arab, Jonathan G. Seidman, Christine E. Seidman, Brendan Frey, Marc Perry, Peter H. Backx, Peter P. Liu, David H. MacLennan, and Andrew Emili
Mol Cell Proteomics (2008) 7(3): 519-533
Decorin Transfection Induces Proteomic and Phenotypic Modulation in Breast Cancer Cells 8701-BC
Pucci-Minafra I, Cancemi P, Cara GD, Minafra L, Feo S, Forlino A, Tira ME, Tenni R, Martini D, Ruggeri A, Minafra S.
Connect Tissue Res (2008) 49(1): 30-41
Proteomic identification and early validation of complement 1 inhibitor and pigment epithelium-derived factor: Two novel biomarkers of Alzheimer's disease in human plasma
Paul Cutler, Emma L. Akuffo, Wanda M. Bodnar, Deborah M. Briggs, John B. Davis, Christine M. Debouck, Steven M. Fox, Rachel A. Gibson, Darren A. Gormley, Joanna D. Holbrook, A. Jacqueline Hunter, Emma E. Kinsey, Rabinder Prinjha, Jill C. Richardson, Allen D. Roses, Marjorie A. Smith, Nikos Tsokanas, David R. Willé, Wen Wu, John W. Yates, Israel S. Gloger
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 467-477
Proteomic identification of FHL1 as the protein mutated in human reducing body myopathy
Schessl J, Zou Y, McGrath MJ, Cowling BS, Maiti B, Chin SS, Sewry C, Battini R, Hu Y, Cottle DL, Rosenblatt M, Spruce L, Ganguly A, Kirschner J, Judkins AR, Golden JA, Goebel HH, Muntoni F, Flanigan KM, Mitchell CA, Bönnemann CG.
J Clin Invest (2008) 118(3): 904-12
N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics
Soltermann A, Ossola R, Kilgus-Hawelski S, von Eckardstein A, Suter T, Aebersold R, Moch H.
Cancer Early Edition: published 7-Mar-2008
Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression
Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, Veenstra TD, Gutkind JS.
Clin Cancer Res (2008) 14(4): 1002-14
Oligomeric beta-amyloid(1-42) induces the expression of Alzheimer disease-relevant proteins in cholinergic SN56.B5.G4 cells as revealed by proteomic analysis
Joerchel S, Raap M, Bigl M, Eschrich K, Schliebs R.
Int J Dev Neurosci Early Edition: published 19-Jan-2008
Rictor and integrin-linked kinase interact and regulate Akt phosphorylation and cancer cell survival
McDonald PC, Oloumi A, Mills J, Dobreva I, Maidan M, Gray V, Wederell ED, Bally MB, Foster LJ, Dedhar S.
Cancer Res (2008) 68(6): 1618-24
Changes in the Proteome of Functional and Regressing Corpus Luteum During Pregnancy and Lactation in the Rat
González-Fernández R, MartÃnez-Galisteo E, Gaytán F, Bárcena JA, Sánchez-Criado JE.
Biol Reprod Early Edition: published 19-Mar-2008
Annexin A4: A novel molecular marker for gastric cancer with Helicobacter pylori infection using proteomics approach
Li-Ling Lin, Chiung-Nien Chen, Wei-Chou Lin, Po-Huang Lee, King-Jen Chang, Yo-Ping Lai, Jin-Town Wang, Hsueh-Fen Juan
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 619-634
N-Methyl-D-aspartate receptor antagonist MK-801 attenuates morphine tolerance and associated glial fibrillary acid protein up-regulation: a proteomic approach
Wen ZH, Wu GJ, Hsu LC, Chen WF, Chen JY, Shui HA, Chou AK, Wong CS.
Acta Anaesthesiol Scand (2008) 52(4): 499-508
Anaplasma phagocytophilum MSP2 (P44)-18 predominates and is modified into multiple isoforms in human myeloid cells
Sarkar M, Troese MJ, Kearns SA, Yang T, Reneer DV, Carlyon JA.
Infect Immun Early Edition: published 19-Feb-2008
Proteomic analysis of pericardial effusion: Characteristics of tuberculosis-related proteins
Yen-Wen Liu, Ming-Hui Yang, Ping-Yen Liu, Cheng-Han Lee, Pao-Chi Liao, Yu-Chang Tyan
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 458-466
Serum proteome analysis for profiling protein markers associated with carcinogenesis and lymph node metastasis in nasopharyngeal carcinoma
Liao Q, Zhao L, Chen X, Deng Y, Ding Y.
Clin Exp Metastasis Early Edition: published 21-Mar-2008
A Sequence-specific Exopeptidase Activity Test (SSEAT) for "Functional" Biomarker Discovery
Josep Villanueva, Arpi Nazarian, Kevin Lawlor, San San Yi, Richard J. Robbins, and Paul Tempst
Mol Cell Proteomics (2008) 7(3): 509-518
Spiking of serum specimens with exogenous reporter peptides for mass spectrometry based protease profiling as diagnostic tool
Findeisen P, Peccerella T, Post S, Wenz F, Neumaier M.
Rapid Commun Mass Spectrom (2008) 22(8): 1223-1229
Identification of proteomic differences in asthenozoospermic sperm samples
MartÃnez-Heredia J, de Mateo S, Vidal-Taboada JM, Ballescà JL, Oliva R.
Hum Reprod (2008) 23(4): 783-91
Renal mitochondrial damage and protein modification in type-2 diabetes
Kartha GK, Moshal KS, Sen U, Joshua IG, Tyagi N, Steed MM, Tyagi SC.
Acta Diabetol Early Edition: published 22-Feb-2008
Immunochemical and proteomic technologies as tools for unravelling toxins involved in envenoming by accidental contact with Lonomia obliqua caterpillars
Ricci-Silva ME, Valente RH, León IR, Tambourgi DV, Ramos OH, Perales J, Chudzinski-Tavassi AM.
Toxicon Early Edition: published 3-Feb-2008
A mass spectrometric strategy for profiling glycoproteinoses, Pompe disease, and sialic acid storage diseases
Valegh Faid, Jean-Claude Michalski, Willy Morelle
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 528-542
Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes
Stentz FB, Kitabchi AE.
Genomics Proteomics Bioinformatics (2007) 5(3-4): 216-35
Detection of papillary thyroid carcinoma with serum protein profile analysis
Moretz WH 3rd, Gourin CG, Terris DJ, Xia ZS, Liu Z, Weinberger PM, Chin E, Adam BL.
Arch Otolaryngol Head Neck Surg (2008) 134(2): 198-202
Proteomic analysis of aqueous humor from patients with myopia
Duan X, Lu Q, Xue P, Zhang H, Dong Z, Yang F, Wang N.
Mol Vis (2008) 14: 370-7.
CSF Multianalyte Profile Distinguishes Alzheimer and Parkinson Diseases
Zhang J, Sokal I, Peskind ER, Quinn JF, Jankovic J, Kenney C, Chung KA, Millard SP, Nutt JG, Montine TJ.
Am J Clin Pathol (2008) 129(4): 526-9
Proteomic identification of malignant transformation-related proteins in esophageal squamous cell carcinoma
Qi YJ, He QY, Ma YF, Du YW, Liu GC, Li YJ, Tsao GS, Ngai SM, Chiu JF.
J Cell Biochem Early Edition: published 4-Mar-2008
Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets
Han MH, Hwang SI, Roy DB, Lundgren DH, Price JV, Ousman SS, Fernald GH, Gerlitz B, Robinson WH, Baranzini SE, Grinnell BW, Raine CS, Sobel RA, Han DK, Steinman L.
Nature (2008) 451(7182): 1076-81
MALDI/SELDI Protein Profiling of Serum for the Identiflcation of Cancer Biomarkers
Cazares LH, Diaz JI, Drake RR, Semmes OJ.
Methods Mol Biol (2007) 428: 125-40
Humoral Response Profiling Reveals Pathways to Prostate Cancer Progression
Barry S. Taylor, Manoj Pal, Jianjun Yu, Bharathi Laxman, Shanker Kalyana-Sundaram, Rong Zhao, Anjana Menon, John T. Wei, Alexey I. Nesvizhskii, Debashis Ghosh, Gilbert S. Omenn, David M. Lubman, Arul M. Chinnaiyan, and Arun Sreekumar
Mol Cell Proteomics (2008) 7(3): 600-611
Biological Pathways Contributing to Organ-Specific Phenotype of Brain Metastatic Cells
Berta Martín, Ramón Aragüés, Rebeca Sanz, Baldo Oliva, Susana Boluda, Antonio Martínez, and Angels Sierra
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 908-920
Proteomic Profiling of Endothelial Cells in Human Lung Cancer
Hye-Jeong Park, Byung-Gyu Kim, Seung-Jin Lee, Sun-Hee Heo, Jae-Young Kim, Tae-Hwan Kwon, Eung-Bae Lee, Hyun-Mo Ryoo, and Je-Yoel Cho
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1138-1150
Chronic treatment with red wine polyphenol compounds mediates neuroprotection in a rat model of ischemic cerebral stroke
Ritz MF, Ratajczak P, Curin Y, Cam E, Mendelowitsch A, Pinet F, Andriantsitohaina R.
J Nutr (2008) 138(3): 519-25
Comparative Proteomics Analysis of Cerebrospinal Fluid of Patients with Guillain-Barré Syndrome
Yang YR, Liu SL, Qin ZY, Liu FJ, Qin YJ, Bai SM, Chen ZY.
Cell Mol Neurobiol Early Edition: published 15-Mar-2008
Identification of Target Antigens of Anti-fibroblast Antibodies in Pulmonary Arterial Hypertension
Terrier B, Tamby MC, Camoin L, Guilpain P, Broussard C, Bussone G, Yaici A, Hotellier F, Simmoneau G, Guillevin L, Humbert M, Mouthon L.
Am J Respir Crit Care Med Early Edition: published 14-Feb-2008
Discovery and validation of urinary biomarkers for prostate cancer
Dan Theodorescu, Eric Schiffer, Hartwig W. Bauer, Friedrich Douwes, Frank Eichhorn, Reinhard Polley, Thomas Schmidt, Wolfgang Schöfer, Petra Zürbig, David M. Good, Joshua J. Coon, Harald Mischak
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 556-570
Serum autoantibody to sideroflexin 3 as a novel tumor marker for oral squamous cell carcinoma
Ryuichi Murase, Yasuhito Abe, Takashi Takeuchi, Motowo Nabeta, Yoshinori Imai, Yoshiaki Kamei, Lisa Kagawa-Miki, Norifumi Ueda, Tomoki Sumida, Hiroyuki Hamakawa, Katusmi Kito
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 517-527
Redox proteomic identification of 4-Hydroxy-2-nonenal-modified brain proteins in amnestic mild cognitive impairment: Insight into the role of lipid peroxidation in the progression and pathogenesis of Alzheimer's disease
Reed T, Perluigi M, Sultana R, Pierce WM, Klein JB, Turner DM, Coccia R, Markesbery WR, Butterfield DA.
Neurobiol Dis (2008) 30(1): 107-20
Genomics and proteomics in renal cell carcinoma: diagnosis, prognosis, and treatment selection
Jones J, Pantuck AJ.
Curr Urol Rep (2008) 9(1): 9-14
The Hippocampal Proteomic Analysis of Senescence-Accelerated Mouse: Implications of Uchl3 and Mitofilin in Cognitive Disorder and Mitochondria Dysfunction in SAMP8
Wang Q, Liu Y, Zou X, Wang Q, An M, Guan X, He J, Tong Y, Ji J.
Neurochem Res Early Edition: published 29-Feb-2008
Differential expression of proteins from cultured endothelial cells exposed to uremic versus normal serum
Carbó C, Arderiu G, Escolar G, Fusté B, Cases A, Carrascal M, Abián J, DÃaz-Ricart M.
Am J Kidney Dis (2008) 51(4): 603-12
Identification of triosephosphate isomerase as an anti-drug resistance agent in human gastric cancer cells using functional proteomic analysis
Wang X, Lu Y, Yang J, Shi Y, Lan M, Liu Z, Zhai H, Fan D.
J Cancer Res Clin Oncol Early Edition: published 29-Feb-2008
Biomarkers in acute and chronic kidney disease
Nickolas TL, Barasch J, Devarajan P.
Curr Opin Nephrol Hypertens (2008) 17(2): 127-132
Up-regulation of NG2 proteoglycan and interferon-induced transmembrane proteins 1 and 3 in mouse astrocytoma: A membrane proteomics approach
Seyfried NT, Huysentruyt LC, Atwood JA 3rd, Xia Q, Seyfried TN, Orlando R.
Cancer Lett Early Edition: published 15-Feb-2008
Proteome analysis of X-ray irradiated human erythroleukemia cells
Eleuterio E, Di Giuseppe F, Sulpizio M, di Giacomo V, Rapino M, Cataldi A, Di Ilio C, Angelucci S.
Biochim Biophys Acta (2008) 1784(4): 611-20
Proteomics cataloging analysis of human expressed prostatic secretions reveals rich source of biomarker candidates
Runsheng Li, Yan Guo, Bang Ming Han, Xiaowei Yan, Angelita G. Utleg, Wei Li, Lan Chun Tu, Jian Wang, Leroy Hood, Shujie Xia, Biaoyang Lin
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 543-555
New ways to identify novel bacterial antigens for vaccine development
Movahedi AR, Hampson DJ.
Vet Microbiol Early Edition: published 10-Mar-2008
The proteome of red cell membranes and vesicles during storage in blood bank conditions
Bosman GJ, Lasonder E, Luten M, Roerdinkholder-Stoelwinder B, Novotný VM, Bos H, De Grip WJ.
Transfusion Early Edition: published 12-Mar-2008
Identification of L-plastin autoantibody in plasma of patients with non-Hodgkin's lymphoma using a proteomics-based analysis
Ueda K, Nakanishi T, Shimizu A, Takubo T, Matsuura N.
Ann Clin Biochem (2008) 45(1): 65-69
Cardioprotection by N-Acetylglucosamine Linkage to Cellular Proteins
Jones SP, Zachara NE, Ngoh GA, Hill BG, Teshima Y, Bhatnagar A, Hart GW, Marbán E.
Circulation (2008) 117(9): 1172-82
Proteome analysis of human substantia nigra in Parkinson's disease
Werner CJ, Heyny-von Haussen R, Mall G, Wolf S.
Proteome Science (2008) 6(1): 8
Serological proteome analysis to identify systemic candidiasis patients in the intensive care unit: Analytical, diagnostic and prognostic validation of anti-Candida enolase antibodies on quantitative clinical platforms
Aida Pitarch, Antonio Jiménez, César Nombela, Concha Gil
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 596-618
A Serum Biomarker Profile Associated with High Bone Turnover and Bone Mineral Density in Postmenopausal Women
Bhattacharyya S, Siegel ER, Achenbach SJ, Khosla S, Suva LJ.
J Bone Miner Res Early Edition: published 26-Feb-2008
A pilot study of GC/MS-based serum metabolic profiling of acute rejection in renal transplantation
Mao YY, Bai JQ, Chen JH, Shou ZF, He Q, Wu JY, Chen Y, Cheng YY.
Transpl Immunol (2008) 19(1): 74-80
Investigation of the human tear film proteome using multiple proteomic approaches
Green-Church KB, Nichols KK, Kleinholz NM, Zhang L, Nichols JJ.
Mol Vis (2008) 14: 456-70.
Potential Applications of Global Protein Expression Analysis (Proteomics) in Morbid Obesity and Bariatric Surgery
Brandacher G, Golderer G, Kienzl K, Werner ER, Margreiter R, Weiss HG.
Obes Surg Early Edition: published 11-Mar-2008
Identification of plasma membrane autoantigens in autoimmune hepatitis type 1 using a proteomics tool
Tahiri F, Le Naour F, Huguet S, Lai-Kuen R, Samuel D, Johanet C, Saubamea B, Tricottet V, Duclos-Vallee JC, Ballot E.
Hepatology (2008) 47(3): 937-948
Endogenous Morphine in SH-SY5Y Cells and the Mouse Cerebellum
Muller A, Glattard E, Taleb O, Kemmel V, Laux A, Miehe M, Delalande F, Roussel G, Van Dorsselaer A, Metz-Boutigue MH, Aunis D, Goumon Y.
PLoS ONE (2008) 3(2): e1641
Abnormal cytoskeletal protein expression in cultured skin fibroblasts from type 1 diabetes mellitus patients with nephropathy: A proteomic approach
Renato Millioni, Elisabetta Iori, Lucia Puricelli, Giorgio Arrigoni, Monica Vedovato, Roberto Trevisan, Peter James, Antonio Tiengo, Paolo Tessari
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 492-503
Overview and introduction to clinical proteomics
Paik YK, Kim H, Lee EY, Kwon MS, Cho SY.
Methods Mol Biol (2007) 428: 1-32
Mapping of the Serum Proteome of Hepatocellular Carcinoma Induced by Targeted Overexpression of Epidermal Growth Factor to Liver Cells of Transgenic Mice
Giuseppe Gazzana and Jürgen Borlak
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 928-937
Mitochondrial proteomics of the retinal pigment epithelium at progressive stages of age-related macular degeneration
Nordgaard CL, Karunadharma PP, Feng X, Olsen TW, Ferrington DA.
Invest Ophthalmol Vis Sci Early Edition: published 14-Mar-2008
iTRAQ-Facilitated Proteomic Analysis of Human Prostate Cancer Cells Identifies Proteins Associated with Progression
Adam Glen, Chee S. Gan, Freddie C. Hamdy, Colby L. Eaton, Simon S. Cross, James W. F. Catto, Phillip C. Wright, and Ishtiaq Rehman
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 897-907
Mass spectrometry-based proteomic analyses of contact lens deposition
Green-Church KB, Nichols JJ.
Mol Vis (2008) 14: 291-7.
Proteomic investigation on chronic bladder irritation in the rat
Tyagi P, Chen X, Hayashi Y, Yoshimura N, Chancellor MB, de Miguel F.
Urology (2008) 71(3): 536-40
Comparative proteomic analysis of low stage and high stage endometrioid ovarian adenocarcinomas
Hyeyeung Kim, Rong Wu, Kathleen R. Cho, Dafydd G. Thomas, Gabrielle Gossner, J. Rebecca Liu, Thomas J. Giordano, Kerby A. Shedden, David E. Misek, David M. Lubman
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(4): 571-584
Discovery and validation of protein abundance differences between follicular thyroid neoplasms
Netea-Maier RT, Hunsucker SW, Hoevenaars BM, Helmke SM, Slootweg PJ, Hermus AR, Haugen BR, Duncan MW.
Cancer Res (2008) 68(5): 1572-80
Proteome analysis of soybean hypocotyl and root under salt stress
Aghaei K, Ehsanpour AA, Shah AH, Komatsu S.
Amino Acids Early Edition: published 9-Feb-2008
Mitochondrial proteomics of the retinal pigment epithelium at progressive stages of age-related macular degeneration
Nordgaard CL, Karunadharma PP, Feng X, Olsen TW, Ferrington DA.
Invest Ophthalmol Vis Sci Early Edition: published 14-Mar-2008
Proteomic Analysis of Fructophilic Properties of Osmotolerant Candida magnoliae
Yu JH, Lee DH, Park YC, Lee MG, Kim DO, Ryu YW, Seo JH.
J Microbiol Biotechnol (2008) 18(2): 248-54
Gpx3-dependent Responses Against Oxidative Stress in Saccharomyces cerevisiae
Kho CW, Lee PY, Bae KH, Kang S, Cho S, Lee do H, Sun CH, Yi GS, Park BC, Park SG.
J Microbiol Biotechnol (2008) 18(2): 270-82
Quantitative 2-D gel electrophoresis-based expression proteomics of albumin and IgG immunodepleted plasma
Seferovic MD, Krughkov V, Pinto D, Han VK, Gupta MB.
J Chromatogr B (2008) 865(1-2): 147-152
Regional differences in porcine adipocytes isolated from skeletal muscle and adipose tissues as identified by a proteomic approach
Gondret F, Guitton N, Guillerm-Regost C, Louveau I.
J Anim Sci Early Edition: published 29-Feb-2008
Protein expression profile in the amygdala of rats with methamphetamine-induced behavioral sensitization
Iwazaki T, McGregor IS, Matsumoto I.
Neurosci Lett (2008) 435(2): 113-9
Protein profiling of human plasma samples by two-dimensional electrophoresis
Cho SY, Lee EY, Kim HY, Kang MJ, Lee HJ, Kim H, Paik YK.
Methods Mol Biol (2007) 428: 57-76
Proteomic profiling of aging in the mouse heart: Altered expression of mitochondrial proteins
Chakravarti B, Oseguera M, Dalal N, Fathy P, Mallik B, Raval A, Chakravarti DN.
Arch Biochem Biophys Early Edition: published 10-Feb-2008
Characterization of human mesenchymal stem cell secretome at early steps of adipocyte and osteoblast differentiation
Chiellini C, Cochet O, Negroni L, Samson M, Poggi M, Ailhaud G, Alessi MC, Dani C, Amri EZ.
BMC Mol Biol (2008) 9(1): 26
Cold stress changes the concanavalin A-positive glycosylation pattern of proteins expressed in the basal parts of rice leaf sheaths
Komatsu S, Yamada E, Furukawa K.
Amino Acids Early Edition: published 16-Feb-2008
Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state
Muela A, Seco C, Camafeita E, Arana I, Orruño M, López JA, Barcina I.
FEMS Microbiol Ecol (2008) 64(1): 28-36
Identification of new regional marker proteins to map mouse brain by 2-D difference gel electrophoresis screening
Jacobs S, Van de Plas B, Van der Gucht E, Clerens S, Cnops L, Van den Bergh G, Arckens L.
Electrophoresis (2008) 29(7): 1518-24
Two-dimensional gel electrophoresis in platelet proteomics research
GarcÃa A.
Methods Mol Med (2007) 139: 339-54
Proteomic Analysis of Highly Purified Peroxisomes from Etiolated Soybean Cotyledons
Arai Y, Hayashi M, Nishimura M.
Plant Cell Physiol Early Edition: published 15-Feb-2008
The Encysted Dormant Embryo Proteome of Artemia sinica
Zhou Q, Wu C, Dong B, Liu F, Xiang J.
Mar Biotechnol (NY) Early Edition: published 19-Feb-2008
Renal Regional Proteomes in Young Dahl Salt-Sensitive Rats
Tian Z, Greene AS, Usa K, Matus IR, Bauwens J, Pietrusz JL, Cowley AW Jr, Liang M.
Hypertension (2008) 51(4): 899-904
Identification of aphid salivary proteins: a proteomic investigation of Myzus persicae
Harmel N, Létocart E, Cherqui A, Giordanengo P, Mazzucchelli G, Guillonneau F, De Pauw E, Haubruge E, Francis F.
Insect Mol Biol (2008) 17(2): 165-74
Proteomic profiling of endorepellin angiostatic activity on human endothelial cells
Zoeller JJ, Iozzo RV.
Proteome Science (2008) 6(1): 7
Specimen collection and handling: standardization of blood sample collection
Tammen H.
Methods Mol Biol (2007) 428: 35-42
Analysis of the extracellular matrix and secreted vesicle proteomes by mass spectrometry
Xiao Z, Conrads TP, Beck GR, Veenstra TD.
Methods Mol Biol (2007) 428: 231-44
Proteome Changes in Leaves of Brassica napus L. as a Result of Sclerotinia sclerotiorum Challenge
Liang Y, Srivastava S, Rahman MH, Strelkov SE, Kav NN.
J Agric Food Chem (2008) 56(6): 1963-76
Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags
Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC.
Anal Chem Early Edition: published 1-Mar-2008
Cytosolic ascorbate peroxidase 2 (cAPX 2) is involved in the soybean response to flooding
Shi F, Yamamoto R, Shimamura S, Hiraga S, Nakayama N, Nakamura T, Yukawa K, Hachinohe M, Matsumoto H, Komatsu S.
Phytochemistry (2008) 69(6): 1295-303
Neurofibromin interacts with CRMP-2 and CRMP-4 in rat brain
Lin YL, Hsueh YP.
Biochem Biophys Res Commun (2008) 369(2): 747-52
The candidate MAP kinase phosphorylation substrate DPL-1 (DP) promotes expression of the MAP kinase phosphatase LIP-1 in C. elegans germ cells
Lin B, Reinke V.
Dev Biol (2008) 316(1): 50-61
The human sperm proteome: the potential for new biomarkers of male fertility and a transformation in our understanding of the spermatozoon as a machine
Barratt CL.
Hum Reprod Early Edition: published 27-Feb-2008
The proteome of red cell membranes and vesicles during storage in blood bank conditions
Bosman GJ, Lasonder E, Luten M, Roerdinkholder-Stoelwinder B, Novotný VM, Bos H, De Grip WJ.
Transfusion Early Edition: published 12-Mar-2008
Proteomic Analysis of Nuclear Factors Binding to an Intronic Enhancer in the Myelin Proteolipid Protein Gene
Dobretsova A, Johnson JW, Jones RC, Edmondson RD, Wight PA.
J Neurochem Early Edition: published 7-Feb-2008
Proteomic analysis of the secretome of Leishmania donovani
Silverman JM, Chan SK, Robinson DP, Dwyer DM, Nandan D, Foster LJ, Reiner NE.
Genome Biol (2008) 9(2): R35
Comprehensive and quantitative proteome profiling of the mouse liver and plasma
Lai KK, Kolippakkam D, Beretta L.
Hepatology (2008) 47(3): 1043-51
Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry
Pounds JG, Flora JW, Adkins JN, Lee KM, Rana GS, Sengupta T, Smith RD, McKinney WJ.
J Chromatogr B (2008) 864(1-2): 95-101
Urine sample preparation and protein profiling by two-dimensional electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectroscopy
Zerefos PG, Vlahou A.
Methods Mol Biol (2007) 428: 141-58
Proteomic analysis of heat-stable proteins in Escherichia coli
Kwon S, Jung Y, Lim D.
BMB Rep (2008) 41(2): 108-11
Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Flavobacterium columnare
Liu GY, Nie P, Zhang J, Li N.
J Fish Dis (2008) 31(4): 269-76
Proteomic Analysis to Investigate Regulatory Networks in Staphylococcus aureus
Engelmann S, Hecker M.
Methods Mol Biol (2007) 431: 25-46
In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea
Andrade AE, Silva LP, Pereira JL, Noronha EF, Reis FB Jr, Bloch C Jr, Dos Santos MF, Domont GB, Franco OL, Mehta A.
FEMS Microbiol Lett (2008) 281(2): 167-74
Composition of the surface proteome of Anaplasma marginale and its role in protective immunity induced by outer membrane immunization
Noh SM, Brayton KA, Brown WC, Norimine J, Munske GR, Davitt CM, Palmer GH.
Infect Immun Early Edition: published 3-Mar-2008
Downregulation of Tsx and OmpW and Upregulation of OmpX Are Required for Iron Homeostasis in Escherichia coli
Xiang-min Lin, Li-na Wu, Hui Li, San-ying Wang, and Xuan-xian Peng
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1235-1243
Protein abundance profiling of the Escherichia coli cytosol
Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D.
BMC Genomics (2008) 9(1): 102
Proteomics Characterization of Outer Membrane Vesicles from the Extraintestinal Pathogenic Escherichia coli {Delta}tolR IHE3034 Mutant
Francesco Berlanda Scorza, Francesco Doro, Manuel Jose Rodriguez-Ortega, Maria Stella, Sabrina Liberatori, Anna Rita Taddei, Laura Serino, Danilo Gomes Moriel, Barbara Nesta, Maria Rita Fontana, Angela Spagnuolo, Mariagrazia Pizza, Nathalie Norais, and Guido Grandi
Mol Cell Proteomics (2008) 7(3): 473-485
Shedding light on the role of Vitreoscilla hemoglobin on cellular catabolic regulation by proteomic analysis
Isarankura-Na-Ayudhya C, Panpumthong P, Tangkosakul T, Boonpangrak S, Prachayasittikul V.
Int J Biol Sci (2008) 4(2): 71-80
Genomic and Proteomic Analysis of phiEco32, a Novel Escherichia coli Bacteriophage
Savalia D, Westblade LF, Goel M, Florens L, Kemp P, Akulenko N, Pavlova O, Padovan JC, Chait BT, Washburn MP, Ackermann HW, Mushegian A, Gabisonia T, Molineux I, Severinov K.
J Mol Biol (2008) 377(3): 774-89
Shedding & shaving: Disclosure of proteomic expressions on a bacterial face
Harold Tjalsma, Lambert Lambooy, Peter W. Hermans, Dorine W. Swinkels
PROTEOMICS (2008) 8(7): 1415-1428
Outer-membrane proteomic maps and surface-exposed proteins of Legionella pneumophila using cellular fractionation and fluorescent labelling
Khemiri A, Galland A, Vaudry D, Chan Tchi Song P, Vaudry H, Jouenne T, Cosette P.
Anal Bioanal Chem (2008) 390(7): 1861-71
Proteomic analysis to characterize differential mouse strain sensitivity to cadmium-induced forelimb teratogenesis
Chen H, Boontheung P, Ogorzalek Loo RR, Xie Y, Loo JA, Rao JY, Collins MD.
Birth Defects Res A Clin Mol Teratol Early Edition: published 26-Feb-2008
Striatal Proteomic Analysis Suggests that First L-Dopa Dose Equates to Chronic Exposure
Scholz B, Svensson M, Alm H, Sköld K, Fälth M, Kultima K, Guigoni C, Doudnikoff E, Li Q, Crossman AR, Bezard E, Andrén PE.
PLoS ONE (2008) 3(2): e1589
Proteomic assessment of sulfur mustard-induced protein adducts and other protein modifications in human epidermal keratinocytes
Mol MA, van den Berg RM, Benschop HP.
Toxicol Appl Pharmacol Early Edition: published 15-Feb-2008
Mitochondrial protein thiol modifications in acetaminophen hepatotoxicity: Effect on HMG-CoA synthase
Andringa KK, Bajt ML, Jaeschke H, Bailey SM.
Toxicol Lett (2008) 177(3): 188-97
Protective effects of soy-isoflavones in cardiovascular disease. Identification of molecular targets
Wenzel U, Fuchs D, Daniel H.
Hamostaseologie (2008) 28(1): 85-88
The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research
Merrick BA.
Brief Funct Genomic Proteomic (2008) 7(1): 35-49
Proteomic analysis of methamphetamine-induced reinforcement processes within the mesolimbic dopamine system
Yang MH, Kim S, Jung MS, Shim JH, Ryu NK, Yook YJ, Jang CG, Bahk YY, Kim KW, Park JH.
Addict Biol Early Edition: published 14-Feb-2008
Mobile phone radiation might alter protein expression in human skin
Karinen A, Heinavaara S, Nylund R, Leszczynski D.
BMC Genomics (2008) 9(1): 77
The Proteomic Response of Mycobacterium smegmatis to Anti-Tuberculosis Drugs Suggests Targeted Pathways
Rong Wang and Edward M. Marcotte
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 855-865
Immunochemical and proteomic technologies as tools for unravelling toxins involved in envenoming by accidental contact with Lonomia obliqua caterpillars
Ricci-Silva ME, Valente RH, León IR, Tambourgi DV, Ramos OH, Perales J, Chudzinski-Tavassi AM.
Toxicon Early Edition: published 3-Feb-2008
Proteomic Analysis of Cervical Cancer Cells Treated with Adenovirus-Mediated MDA-7
Wei L, Wang Z, Cui T, Yi F, Bu Y, Ding S, Ma Y, Song F.
Cancer Biol Ther Early Edition: published 2-Jan-2007
The heavy metal cadmium induces valosin-containing protein (VCP)-mediated aggresome formation
Song C, Xiao Z, Nagashima K, Li CC, Lockett SJ, Dai RM, Cho EH, Conrads TP, Veenstra TD, Colburn NH, Wang Q, Wang JM.
Toxicol Appl Pharmacol Early Edition: published 8-Jan-2008
Proteomic analysis of lithium-induced nephrogenic diabetes insipidus: Mechanisms for aquaporin 2 down-regulation and cellular proliferation
Nielsen J, Hoffert JD, Knepper MA, Agre P, Nielsen S, Fenton RA.
Proc Natl Acad Sci U S A (2008) 105(9): 3634-9
Aldosterone: From biosynthesis to non-genomic action onto the proteome
Zöllner S, Hwang KH, Wilzewski B, Carapito C, Leize-Wagner E, Van Dorsselaer A, Bernhardt R.
Steroids Early Edition: published 6-Jan-2008
Gpx3-dependent Responses Against Oxidative Stress in Saccharomyces cerevisiae
Kho CW, Lee PY, Bae KH, Kang S, Cho S, Lee do H, Sun CH, Yi GS, Park BC, Park SG.
J Microbiol Biotechnol (2008) 18(2): 270-82
Quantifying changes in the thiol redox proteome upon oxidative stress in vivo
Leichert LI, Gehrke F, Gudiseva HV, Blackwell T, Ilbert M, Walker AK, Strahler JR, Andrews PC, Jakob U.
Proc Natl Acad Sci U S A Early Edition: published 14-Feb-2008
Chronic treatment with red wine polyphenol compounds mediates neuroprotection in a rat model of ischemic cerebral stroke
Ritz MF, Ratajczak P, Curin Y, Cam E, Mendelowitsch A, Pinet F, Andriantsitohaina R.
J Nutr (2008) 138(3): 519-25
Serum proteomic analysis during nicotine self-administration, extinction and relapse in rats
Cecconi D, Tessari M, Willé DR, Zoli M, Domenici E, Righetti PG, Carboni L.
Electrophoresis (2008) 29(7): 1525-33
Modulation of proteomic profile in H295R adrenocortical cell line induced by mitotane
Stigliano A, Cerquetti L, Borro M, Gentile G, Bucci B, Misiti S, Piergrossi P, Brunetti E, Simmaco M, Toscano V.
Endocr Relat Cancer (2008) 15(1): 1-10
Specific capture of uranyl protein targets by metal affinity chromatography
Basset C, Dedieu A, Guérin P, Quéméneur E, Meyer D, Vidaud C.
J Chromatogr A (2008) 1185(2): 233-40
The effects of anthrax lethal factor on the macrophage proteome: Potential activity on nitric oxide synthases
Kim J, Park H, Chang M, Han SH, Chung H, Lee JS, Park JS, Yoon MY.
Arch Biochem Biophys (2008) 472(1): 58-64
Proteome analysis of aflatoxin B1-induced hepatocarcinogenesis in tree shrew (Tupaia belangeri chinensis) and functional identification of candidate protein peroxiredoxin II
Yuan Li, Xue Qin, Jiefeng Cui, Zhi Dai, Xiaonan Kang, Haiying Yue, Yu Zhang, Jianjia Su, Ji Cao, Chao Ou, Chun Yang, Xiaoxian Duan, Huifen Yue, Yinkun Liu
PROTEOMICS (2008) 8(7): 1490-1501
Role of the Electrophilic Lipid Peroxidation Product 4-Hydroxynonenal in the Development and Maintenance of Obesity in Mice
Singh SP, Niemczyk M, Saini D, Awasthi YC, Zimniak L, Zimniak P.
Biochemistry (2008) 47(12): 3900-11
Role of TGF-beta1-independent changes in protein neosynthesis, p38alpha(MAPK), and cdc42 in hydrogen peroxide-induced senescence-like morphogenesis
Chrétien A, Dierick JF, Delaive E, Larsen MR, Dieu M, Raes M, Deroanne CF, Roepstorff P, Toussaint O.
Free Radic Biol Med Early Edition: published 12-Feb-2008
Proteomic profiling of endorepellin angiostatic activity on human endothelial cells
Zoeller JJ, Iozzo RV.
Proteome Science (2008) 6(1): 7
Proteome analysis of X-ray irradiated human erythroleukemia cells
Eleuterio E, Di Giuseppe F, Sulpizio M, di Giacomo V, Rapino M, Cataldi A, Di Ilio C, Angelucci S.
Biochim Biophys Acta (2008) 1784(4): 611-20
Oligomeric beta-amyloid(1-42) induces the expression of Alzheimer disease-relevant proteins in cholinergic SN56.B5.G4 cells as revealed by proteomic analysis
Joerchel S, Raap M, Bigl M, Eschrich K, Schliebs R.
Int J Dev Neurosci Early Edition: published 19-Jan-2008
Proteomic analysis of selenium embryotoxicity in cultured postimplantation rat embryos
Usami M, Mitsunaga K, Nakazawa K, Doi O.
Birth Defects Res B Dev Reprod Toxicol Early Edition: published 20-Mar-2008
Albumin Is the Main Nucleophilic Target of Human Plasma: A Protective Role Against Pro-atherogenic Electrophilic Reactive Carbonyl Species?
Aldini G, Vistoli G, Regazzoni L, Gamberoni L, Facino RM, Yamaguchi S, Uchida K, Carini M.
Chem Res Toxicol Early Edition: published 7-Mar-2008
The proteomic analysis of cisplatin resistance in breast cancer cells
Smith L, Welham KJ, Watson MB, Drew PJ, Lind MJ, Cawkwell L.
Oncol Res (2007) 16(11): 497-506
Proteomics and diagnostics: Let's Get Specific, again
Zichi D, Eaton B, Singer B, Gold L.
Curr Opin Chem Biol (2008) 12(1): 78-85
Modified Silver Nanoparticle as a Hydrophobic Affinity Probe for Analysis of Peptides and Proteins in Biological Samples by Using Liquid-Liquid Microextraction Coupled to AP-MALDI-Ion Trap and MALDI-TOF Mass Spectrometry
Kamlesh Shrivas and Hui-Fen Wu
ANALYTICAL CHEMISTRY (2008) 80(7): 2583-2589
ENSAM: Europium Nanoparticles for Signal Enhancement of Antibody Microarrays on Nanoporous Silicon
Kerstin Järås, Asilah Ahmad Tajudin, Anton Ressine, Tero Soukka, György Marko-Varga, Anders Bjartell, Johan Malm, Thomas Laurell, and Hans Lilja
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1308-1314
Light-induced immobilisation of biomolecules as an attractive alternative to micro-droplet dispensing-based arraying technologies
Meg Duroux, Esben Skovsen, Maria Teresa Neves-Petersen, Laurent Duroux, Leonid Gurevich, Steffen B. Petersen
PROTEOMICS (2008) 8(5): 1113
Protein kinase substrate identification on functional protein arrays
Meng L, Michaud GA, Merkel JS, Zhou F, Huang J, Mattoon DR, Schweitzer B.
BMC Biotechnol (2008) 8(1): 22
Dissecting cancer serum protein profiles using antibody arrays
Sanchez-Carbayo M.
Methods Mol Biol (2007) 428: 263-88
Detergent-free biotin switch combined with liquid chromatography/tandem mass spectrometry in the analysis of S-nitrosylated proteins
Han P, Chen C.
Rapid Commun Mass Spectrom (2008) 22(8): 1137-1145
Tandem Immunoprecipitation of Phosphotyrosine-Mass Spectrometry (TIPY-MS) Indicates C19ORF19 Becomes Tyrosine-Phosphorylated and Associated with Activated Epidermal Growth Factor Receptor
Jiefei Tong, Paul Taylor, Eleonora Jovceva, Jonathan R. St-Germain, Lily L. Jin, Ana Nikolic, Xiaoping Gu, Zhi Hua Li, Suzanne Trudel, and Michael F. Moran
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1067-1077
Comparative glycomics of connective tissue glycosaminoglycans
Alicia M. Hitchcock, Karen E. Yates, Catherine E. Costello, Joseph Zaia
PROTEOMICS (2008) 8(7): 1384-1397
Enhanced Protein Digestion through the Confinement of Nanozeolite-Assembled Microchip Reactors
Ji Ji, Yahong Zhang, Xiaoqin Zhou, Jilie Kong, Yi Tang, and Baohong Liu
ANALYTICAL CHEMISTRY (2008) 80(7): 2457-2463
Rictor and integrin-linked kinase interact and regulate Akt phosphorylation and cancer cell survival
McDonald PC, Oloumi A, Mills J, Dobreva I, Maidan M, Gray V, Wederell ED, Bally MB, Foster LJ, Dedhar S.
Cancer Res (2008) 68(6): 1618-24
Enrichment of Phosphopeptides by Fe3+-Immobilized Magnetic Nanoparticles for Phosphoproteome Analysis of the Plasma Membrane of Mouse Liver
Feng Tan, Yangjun Zhang, Wei Mi, Jinglan Wang, Junying Wei, Yun Cai, and Xiaohong Qian
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1078-1087
A two-matrix system for MALDI MS analysis of serine phosphorylated peptides concentrated by Fe3O4/Al2O3 magnetic nanoparticles
CHENG-TAI CHEN, YU-CHIE CHEN
Journal of Mass Spectrometry (2008) 43(4): 538-541
Complexities and algorithms for glycan sequencing using tandem mass spectrometry
Shan B, Ma B, Zhang K, Lajoie G.
J Bioinform Comput Biol (2008) 6(1): 77-91
Redox proteomic identification of 4-Hydroxy-2-nonenal-modified brain proteins in amnestic mild cognitive impairment: Insight into the role of lipid peroxidation in the progression and pathogenesis of Alzheimer's disease
Reed T, Perluigi M, Sultana R, Pierce WM, Klein JB, Turner DM, Coccia R, Markesbery WR, Butterfield DA.
Neurobiol Dis (2008) 30(1): 107-20
Low-scale phosphoproteome analyses identify the mTOR effector p70 S6 kinase 1 as a specific biomarker of the dual-HER1/HER2 tyrosine kinase inhibitor lapatinib (Tykerb(R)) in human breast carcinoma cells
Vazquez-Martin A, Oliveras-Ferraros C, Colomer R, Brunet J, Menendez JA.
Ann Oncol Early Edition: published 17-Feb-2008
Proteomic analysis of S-nitrosylated proteins in Arabidopsis thaliana undergoing hypersensitive response
Maria C. Romero-Puertas, Natascia Campostrini, Alessandro Mattè, Pier Giorgio Righetti, Michele Perazzolli, Lello Zolla, Peter Roepstorff, Massimo Delledonne
PROTEOMICS (2008) 8(7): 1459-1469
Phosphoproteome Analysis of Fission Yeast
Joshua T. Wilson-Grady, Judit Villén, and Steven P. Gygi
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1088-1097
A Targeted Proteomic Analysis of the Ubiquitin-Like Modifier Nedd8 and Associated Proteins
Jeffrey Jones, Kenneth Wu, Yingying Yang, Cortnie Guerrero, Nadinath Nillegoda, Zhen-Qiang Pan, and Lan Huang
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1274-1287
Profiling of Human Serum Glycans Associated with Liver Cancer and Cirrhosis by IMS−MS
D. Isailovic, R. T. Kurulugama, M. D. Plasencia, S. T. Stokes, Z. Kyselova, R. Goldman, Y. Mechref, M. V. Novotny, and D. E. Clemmer
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1109-1117
Detection of Multiphosphorylated Peptides in LC-MS/MS Analysis under Low pH Conditions
Choi H, Lee HS, Park ZY.
Anal Chem Early Edition: published 18-Mar-2008
Detection of carbonyl-modified proteins in interfibrillar rat mitochondria using N?-aminooxymethylcarbonylhydrazino-D-biotin as an aldehyde/keto-reactive probe in combination with Western blot analysis and tandem mass spectrometry
Woon-Gye Chung, Cristobal L. Miranda, Claudia S. Maier
ELECTROPHORESIS (2008) 29(6): 1317-1324
Efficient Identification of Phosphorylation by Mass Spectrometric Phosphopeptide Fingerprinting
Eileen M. Woo, David Fenyo, Benjamin H. Kwok, Hironori Funabiki, and Brian T. Chait
ANALYTICAL CHEMISTRY (2008) 80(7): 2419-2425
Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data
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The origin and control of ex vivo oxidative peptide modifications prior to mass spectrometry analysis
Jennifer M. Froelich, Gavin E. Reid
PROTEOMICS (2008) 8(7): 1334-1345
Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry
Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth Jr, David Jabon, Timothy McMurry, David S. Angulo, Stephen J. Kron
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Quantifying changes in the thiol redox proteome upon oxidative stress in vivo
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Proc Natl Acad Sci U S A Early Edition: published 14-Feb-2008
Analysis of the human kinome using methods including fold recognition reveals two novel kinases
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PLoS ONE (2008) 3(2): e1597
Chemical derivatization of peptides containing phosphorylated serine/threonine for efficient ionization and quantification in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Hiroki Tsumoto, Moonjin Ra, Keijiro Samejima, Ryo Taguchi, Kohfuku Kohda
Rapid Communications in Mass Spectrometry (2008) 22(7): 965-972
Combining Protein-Based IMAC, Peptide-Based IMAC, and MudPIT for Efficient Phosphoproteomic Analysis
Greg T. Cantin, Wei Yi, Bingwen Lu, Sung Kyu Park, Tao Xu, Jiing-Dwan Lee, and John R. Yates III
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1346-1351
Identification of new tyrosine phosphorylated proteins in rat brain mitochondria
Lewandrowski U, Sickmann A, Cesaro L, Brunati AM, Toninello A, Salvi M.
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Unveiling a Glycation Hot Spot in a Recombinant Humanized Monoclonal Antibody
Boyan Zhang, Yi Yang, Inn Yuk, Roger Pai, Patrick McKay, Charles Eigenbrot, Mark Dennis, Viswanatham Katta, and Kathleen Champion Francissen
ANALYTICAL CHEMISTRY (2008) 80(7): 2379-2390
Dissection of the insulin signaling pathway via quantitative phosphoproteomics
Krüger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M.
Proc Natl Acad Sci U S A (2008) 105(7): 2451-6
Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography
Guanghui Han, Mingliang Ye, Houjiang Zhou, Xinning Jiang, Shun Feng, Xiaogang Jiang, Ruijun Tian, Dafang Wan, Hanfa Zou, Jianren Gu
PROTEOMICS (2008) 8(7): 1346-1361
Proteomic assessment of sulfur mustard-induced protein adducts and other protein modifications in human epidermal keratinocytes
Mol MA, van den Berg RM, Benschop HP.
Toxicol Appl Pharmacol Early Edition: published 15-Feb-2008
NanoLC-MS/MS Analysis Provides New Insights into the Phosphorylation Pattern of Cdc25B in Vivo: Full Overlap with Sites of Phosphorylation by Chk1 and Cdk1/cycB Kinases in Vitro
Jean-Pierre Bouché, Carine Froment, Christine Dozier, Charlotte Esmenjaud-Mailhat, Matthieu Lemaire, Bernard Monsarrat, Odile Burlet-Schiltz, and Bernard Ducommun
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1264-1273
Ribosomal proteins are targets for the NEDD8 pathway
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EMBO Rep (2008) 9(3): 280-6
A Two-Dimensional Array for Simultaneous Sequencing of N- and O-Glycans and Their Glycoforms on Specific Glycosylation Sites
Yaron Tzur, Amir Markovich, and Rachel G. Lichtenstein
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1188-1198
Identification of oxidized proteins in rat plasma using avidin chromatography and tandem mass spectrometry
Hamid Mirzaei, Beatriz Baena, Coral Barbas, Fred Regnier
PROTEOMICS (2008) 8(7): 1516-1527
N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics
Soltermann A, Ossola R, Kilgus-Hawelski S, von Eckardstein A, Suter T, Aebersold R, Moch H.
Cancer Early Edition: published 7-Mar-2008
Tyrosine Phosphoproteomics and Identification of Substrates of Protein Tyrosine Phosphatase dPTP61F in Drosophila S2 Cells by Mass Spectrometry-Based Substrate Trapping Strategy
Ying-Che Chang, Shu-Yu Lin, Suh-Yuen Liang, Kuan-Ting Pan, Chi-Chi Chou, Chien-Hung Chen, Chung-Ling Liao, Kay-Hooi Khoo, and Tzu-Ching Meng
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1055-1066
High-energy collision-induced dissociation of phosphopeptides using a multi-turn tandem time-of-flight mass spectrometer ?MULTUM-TOF/TOF?
Shuichi Shimma, Hirofumi Nagao, Anastassios E. Giannakopulos, Shigeo Hayakawa, Kunio Awazu, Michisato Toyoda
Journal of Mass Spectrometry (2008) 43(4): 535-537
Analysis of TRPC3-Interacting Proteins by Tandem Mass Spectrometry
Timothy Lockwich, Jaya Pant, Anthony Makusky, Ewa Jankowska-Stephens, Jeffrey A. Kowalak, Sanford P. Markey, and Indu S. Ambudkar
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 979-989
Virion-wide Protein Interactions of Kaposi's Sarcoma-associated Herpesvirus
Rozen R, Sathish N, Li Y, Yuan Y.
J Virol Early Edition: published 5-Mar-2008
Tumor suppressor PTEN mediates a negative regulation of E3 ubiquitin-protein ligase Nedd4
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Biochem J Early Edition: published 29-Feb-2008
Integrin-linked kinase localizes to the centrosome and regulates mitotic spindle organization
Fielding AB, Dobreva I, McDonald PC, Foster LJ, Dedhar S.
J Cell Biol (2008) 180(4): 681-9
Mass Spectrometry Analysis of a Protein Kinase CK2β Subunit Interactome Isolated from Mouse Brain by Affinity Chromatography
Giorgio Arrigoni, Mario A. Pagano, Stefania Sarno, Luca Cesaro, Peter James, and Lorenzo A. Pinna
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 990-1000
E3 ubiquitin ligase SIAH1 mediates ubiquitination and degradation of TRB3
Zhou Y, Li L, Liu Q, Xing G, Kuai X, Sun J, Yin X, Wang J, Zhang L, He F.
Cell Signal (2008) 20(5): 942-8
Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset
Guo J, Wu X, Zhang DY, Lin K.
Nucl Acids Res (2008) 36(6): 2002-11
Neurofibromin interacts with CRMP-2 and CRMP-4 in rat brain
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Biochem Biophys Res Commun (2008) 369(2): 747-52
Proteomics analysis of immunoprecipitated proteins associated with the oncogenic kinase cot
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Mol Cells (2008) 25(1): 43-9
Towards multidimensional liquid chromatography separation of proteins using fluorescence and isotope-coded protein labelling for quantitative proteomics
Florian Tribl, Christiane Lohaus, Tanja Dombert, Elmar Langenfeld, Heike Piechura, Bettina Warscheid, Helmut E. Meyer, Katrin Marcus
PROTEOMICS (2008) 8(6): 1204-1211
Difference gel electrophoresis (DIGE) using CyDye DIGE fluor minimal dyes
Chakravarti B, Gallagher SR, Chakravarti DN.
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Protein Quantitation in 2-D Gels Using Fluorescence with Water Raman as an Internal Standard
Yvette L. Loethen, Giselle M. Knudsen, Brandon Davis, Ravindra Gudihal, V. Jo Davisson, and Dor Ben-Amotz
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1341-1345
Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling
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Proteome Science (2008) 6(1): 9
Directional and quantitative phosphorylation networks
Claus Jorgensen and Rune Linding
Brief Funct Genomic Proteomic (2008) 7(1): 17-26
A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen
John M. Asara, Heather R. Christofk, Lisa M. Freimark, Lewis C. Cantley
PROTEOMICS (2008) 8(5): 994-999
Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry
Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth Jr, David Jabon, Timothy McMurry, David S. Angulo, Stephen J. Kron
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Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags
Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC.
Anal Chem Early Edition: published 1-Mar-2008
Absolute SILAC for Accurate Quantitation of Proteins in Complex Mixtures Down to the Attomole Level
Stefan Hanke, Hüseyin Besir, Dieter Oesterhelt, and Matthias Mann
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1118-1130
Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics
Natasha A. Karp, Renata Feret, Denis V. Rubtsov, Kathryn S. Lilley
PROTEOMICS (2008) 8(5): 948-960
Optimizing the Difference Gel Electrophoresis (DIGE) Technology
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Protein abundance profiling of the Escherichia coli cytosol
Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D.
BMC Genomics (2008) 9(1): 102
Quantitative proteomics using stable isotope labeling with amino acids in cell culture
Harsha HC, Molina H, Pandey A.
Nat Protoc (2008) 3(3): 505-516
Activity-Based Protein Profiling: New Developments and Directions in Functional Proteomics
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Chembiochem (2008) 9(5): 667-75
Approaches to dimensionality reduction in proteomic biomarker studies
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Brief Bioinform (2008) 9(2): 102-18
Analysis of Microdissected Cells by Two-Dimensional LC-MS Approaches
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Adapting Proteostasis for Disease Intervention
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Science (2008) 319(5865): 916-919
Proteomic approaches for discovery of new targets for vaccine and therapeutics against visceral leishmaniasis
Shraddha Kumari, Awanish Kumar, Mukesh Samant, Shyam Sundar, Neeloo Singh, Anuradha Dube
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 372-386
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McGuire JN, Overgaard J, Pociot F.
Brief Funct Genomic Proteomic (2008) 7(1): 74-83
Information quality in proteomics
David A. Stead, Norman W. Paton, Paolo Missier, Suzanne M. Embury, Cornelia Hedeler, Binling Jin, Alistair J. P. Brown, and Alun Preece
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Discovery of virulence factors of pathogenic bacteria
Wu HJ, Wang AH, Jennings MP.
Curr Opin Chem Biol (2008) 12(1): 93-101
Proteomics: methodologies and applications in oncology
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Semin Radiat Oncol (2008) 18(2): 115-25
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Proteomics and diagnostics: Let's Get Specific, again
Zichi D, Eaton B, Singer B, Gold L.
Curr Opin Chem Biol (2008) 12(1): 78-85
Application of activity-based probes to the study of enzymes involved in cancer progression
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Curr Opin Genet Dev Early Edition: published 20-Feb-2008
Dissecting cancer serum protein profiles using antibody arrays
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Finding the significant markers: statistical analysis of proteomic data
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Biomarkers in acute and chronic kidney disease
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Curr Opin Nephrol Hypertens (2008) 17(2): 127-132
Human kidney glomerulus proteome and biomarker discovery of kidney diseases
Yutaka Yoshida, Masahito Miyamoto, Izumi Taguchi, Bo Xu, Ying Zhang, Eishin Yaoita, Hidehiko Fujinaka, Tadashi Yamamoto
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 420-427
From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part I 1965-1984
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J Mass Spectrom (2008) 43(4): 419-35
LC-MS-based procedures for monitoring of toxic organophosphorus compounds and verification of pesticide and nerve agent poisoning
John H, Worek F, Thiermann H.
Anal Bioanal Chem Early Edition: published 11-Mar-2008
Studying proteolysis within mitochondria
Tatsuta T, Langer T.
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Two-dimensional gel electrophoresis in platelet proteomics research
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Methods Mol Med (2007) 139: 339-54
Proteomics of yeast mitochondria
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Proteomics-driven cancer biomarker discovery: looking to the future
Simpson RJ, Bernhard OK, Greening DW, Moritz RL.
Curr Opin Chem Biol (2008) 12(1): 72-7
Proteomics in rheumatology: The beginning of a fairy tale?
Stijn Lambrecht, Kelly Tilleman, Dirk Elewaut, Dieter Deforce
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 411-419
Isolation of intact, functional mitochondria from the model plant Arabidopsis thaliana
Sweetlove LJ, Taylor NL, Leaver CJ.
Methods Mol Biol (2007) 372: 125-36
SEREX, Proteomex, AMIDA, and beyond: Serological screening technologies for target identification
Jens Rauch, Olivier Gires
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 355-371
Proteomic Analysis to Investigate Regulatory Networks in Staphylococcus aureus
Engelmann S, Hecker M.
Methods Mol Biol (2007) 431: 25-46
Proteomics and cardiovascular disease: an update
Balestrieri ML, Giovane A, Mancini FP, Napoli C.
Curr Med Chem (2008) 15(6): 555-72
Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes
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Phys Biol (2008) 5(1): 11001
Analysis of the extracellular matrix and secreted vesicle proteomes by mass spectrometry
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Fluorescence and bioluminescence procedures for functional proteomics
Anke Prinz, Gregor Reither, Mandy Diskar, Carsten Schultz
PROTEOMICS (2008) 8(6): 1179-1196
Nanofluidic Devices and Their Applications
Patrick Abgrall and Nam Trung Nguyen
ANALYTICAL CHEMISTRY (2008) 80(7): 2326-2341
Arabidopsis mitochondrial proteomics
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Proteomics and genomics: perspectives on drug and target discovery
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Curr Opin Chem Biol (2008) 12(1): 1-3
Application of proteomics in biotechnology - Microbial proteomics
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Biotechnol J Early Edition: published 4-Mar-2008
Optimizing the Difference Gel Electrophoresis (DIGE) Technology
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Proteomics in diabetic nephropathy
Hyun-Jung Kim, Hyun-Syuk Yoo, Chan-Wha Kim
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 301-311
Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins
Caterina Temporini, Enrica Calleri, Gabriella Massolini, Gabriele Caccialanza
Mass Spectrometry Reviews (2008) 27(3): 207-236
The mitochondria of cultured mammalian cells: II. Expression and visualization of exogenous proteins in fixed and live cells
Goffart S, Martinsson P, Malka F, Rojo M, Spelbrink JN.
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Difference gel electrophoresis (DIGE) using CyDye DIGE fluor minimal dyes
Chakravarti B, Gallagher SR, Chakravarti DN.
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Clinical proteomics in neurodegenerative disorders
Zetterberg H, Rüetschi U, Portelius E, Brinkmalm G, Andreasson U, Blennow K, Brinkmalm A.
Acta Neurol Scand Early Edition: published 13-Feb-2008
Specimen collection and handling: standardization of blood sample collection
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Methods Mol Biol (2007) 428: 35-42
Proteomics: technologies for protein analysis
Gomase VS, Kale KV, Tagore S, Hatture SR.
Curr Drug Metab (2008) 9(3): 213-20
Neurochemical dementia diagnostics: State of the art and research perspectives
Piotr Lewczuk, Jens Wiltfang
PROTEOMICS (2008) 8(6): 1292-1301
Web-based tools for protein classification
Paliakasis CD, Michalopoulos I, Kossida S.
Methods Mol Biol (2007) 428: 349-68
Urine sample preparation and protein profiling by two-dimensional electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectroscopy
Zerefos PG, Vlahou A.
Methods Mol Biol (2007) 428: 141-58
Proteomic methods for drug target discovery
Sleno L, Emili A.
Curr Opin Chem Biol (2008) 12(1): 46-54
Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics
Yong-Doo Park, Daeui Park, Jong Bhak, Jun-Mo Yang
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 290-300
Peptidomics: The integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis
Boonen K, Landuyt B, Baggerman G, Husson SJ, Huybrechts J, Schoofs L.
J Sep Sci (2008) 31(3): 427-445
Quantitative proteomics using stable isotope labeling with amino acids in cell culture
Harsha HC, Molina H, Pandey A.
Nat Protoc (2008) 3(3): 505-516
Proteomics and genomics: A hypothesis-free approach to the study of the role of visceral adiposity in the pathogenesis of the polycystic ovary syndrome
Héctor F. Escobar-Morreale, María Insenser, Marta Cortón, José L. San Millán, Belén Peral
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 444-455
Contributions of proteomics to understanding phagosome maturation
Rogers LD, Foster LJ.
Cell Microbiol Early Edition: published 8-Mar-2008
MALDI/SELDI Protein Profiling of Serum for the Identiflcation of Cancer Biomarkers
Cazares LH, Diaz JI, Drake RR, Semmes OJ.
Methods Mol Biol (2007) 428: 125-40
Recent development of multi-dimensional chromatography strategies in proteome research
Tang J, Gao M, Deng C, Zhang X.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 2-Feb-2008
The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research
Merrick BA.
Brief Funct Genomic Proteomic (2008) 7(1): 35-49
Analysis of laser capture microdissected cells by 2-dimensional gel electrophoresis
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Methods Mol Biol (2007) 428: 77-92
Human pathogenic streptococcal proteomics and vaccine development
Jason N. Cole, Anna Henningham, Christine M. Gillen, Vidiya Ramachandran, Mark J. Walker
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 387-410
Combining laser capture microdissection and proteomics techniques
Mustafa D, Kros JM, Luider T.
Methods Mol Biol (2007) 428: 159-78
Overview and introduction to clinical proteomics
Paik YK, Kim H, Lee EY, Kwon MS, Cho SY.
Methods Mol Biol (2007) 428: 1-32
Disease proteomics of endocrine disorders revealed by two-dimensional gel electrophoresis and mass spectrometry
Masamichi Oh-Ishi, Yoshio Kodera, Sen-ichi Furudate, Tadakazu Maeda
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 327-337
Tissue sample collection for proteomics analysis
Diaz JI, Cazares LH, Semmes OJ.
Methods Mol Biol (2007) 428: 43-54
Clinical proteomics of the cerebrospinal fluid: Towards the discovery of new biomarkers
Stéphane Roche, Audrey Gabelle, Sylvain Lehmann
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 428-436
Microproteomics: Analysis of protein diversity in small samples
Gutstein HB, Morris JS, Annangudi SP, Sweedler JV.
Mass Spectrom Rev Early Edition: published 12-Feb-2008
Proteomics of human cerebral microdialysate: From detection of biomarkers to clinical application
Martin H. Maurer, Daniel Haux, Andreas W. Unterberg, Oliver W. Sakowitz
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 437-443
Pattern recognition approaches for classifying proteomic mass spectra of biofluids
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Methods Mol Biol (2007) 428: 383-96
Physiomics
Gomase VS, Tagore S.
Curr Drug Metab (2008) 9(3): 259-62
Unraveling the molecular targets of natural products: Insights from genomic and proteomic analyses
Chi Chun Wong, Ka Wing Cheng, Qing-Yu He, Feng Chen
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 338-354
Protein profiling of human plasma samples by two-dimensional electrophoresis
Cho SY, Lee EY, Kim HY, Kang MJ, Lee HJ, Kim H, Paik YK.
Methods Mol Biol (2007) 428: 57-76
IgA nephropathy and Henoch-Schönlein purpura nephritis
Sanders JT, Wyatt RJ.
Curr Opin Pediatr (2008) 20(2): 163-170
Type 2 diabetes: Gaining insight into the disease process using proteomics
Michael Maris, Lut Overbergh, Chantal Mathieu
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(3): 312-326
Hydrophilic interaction liquid chromatography (HILIC) in proteomics
Boersema PJ, Mohammed S, Heck AJ.
Anal Bioanal Chem Early Edition: published 9-Feb-2008
Capabilities Using 2-D DIGE in Proteomics Research : The New Gold Standard for 2-D Gel Electrophoresis
Shin I, Zamfir AD, Ye B.
Methods Mol Biol (2008) 441: 19-39
Detection of carbonyl-modified proteins in interfibrillar rat mitochondria using N?-aminooxymethylcarbonylhydrazino-D-biotin as an aldehyde/keto-reactive probe in combination with Western blot analysis and tandem mass spectrometry
Woon-Gye Chung, Cristobal L. Miranda, Claudia S. Maier
ELECTROPHORESIS (2008) 29(6): 1317-1324
Coupling of Native Liquid Phase Isoelectrofocusing and Blue Native Polyacrylamide Gel Electrophoresis: A Potent Tool for Native Membrane Multiprotein Complex Separation
Gian Maria D’Amici, Anna Maria Timperio, and Lello Zolla
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1326-1340
Purification and proteomic analysis of plant plasma membranes
Alexandersson E, Gustavsson N, Bernfur K, Karlsson A, Kjellbom P, Larsson C.
Methods Mol Biol (2008) 432: 161-73
Highly efficient enrichment of phosphopeptides by magnetic nanoparticles coated with zirconium phosphonate for phosphoproteome analysis
Wei J, Zhang Y, Wang J, Tan F, Liu J, Cai Y, Qian X.
Rapid Commun Mass Spectrom (2008) 22(7): 1069-1080
Proteomic characterization of membrane protein topology
Blackler AR, Wu CC.
Methods Mol Biol (2008) 432: 185-97
Isolation and proteomic analysis of chlamydomonas centrioles
Keller LC, Marshall WF.
Methods Mol Biol (2008) 432: 289-300
Interpreting Top-Down Mass Spectra Using Spectral Alignment
Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA.
Anal Chem (2008) 80(7): 2499-2505
Spectral Index for Assessment of Differential Protein Expression in Shotgun Proteomics
Xiaoyun Fu, Sina A. Gharib, Pattie S. Green, Moira L. Aitken, David A. Frazer, David R. Park, Tomas Vaisar, and Jay W. Heinecke
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 845-854
Evaluation of Comprehensive Multidimensional Separations Using Reversed-Phase, Reversed-Phase Liquid Chromatography/Mass Spectrometry for Shotgun Proteomics
Tatsuji Nakamura, Junro Kuromitsu, and Yoshiya Oda
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1007-1011
Purification and Proteomic Analysis of 20S Proteasomes from Human Cells
Bousquet-Dubouch MP, Uttenweiler-Joseph S, Ducoux-Petit M, Matondo M, Monsarrat B, Burlet-Schiltz O.
Methods Mol Biol (2008) 432: 301-20
Hydrophilic interaction liquid chromatography (HILIC) in proteomics
Boersema PJ, Mohammed S, Heck AJ.
Anal Bioanal Chem Early Edition: published 9-Feb-2008
A two step fractionation approach for plasma proteomics using immunodepletion of abundant proteins and multi-lectin affinity chromatography: Application to the analysis of obesity, diabetes, and hypertension diseases
Dayarathna MK, Hancock WS, Hincapie M.
J Sep Sci (2008) 31(6-7): 1156-66
Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
An Staes, Petra Van Damme, Kenny Helsens, Hans Demol, Joël Vandekerckhove, Kris Gevaert
PROTEOMICS (2008) 8(7): 1362-1370
Analysis of laser capture microdissected cells by 2-dimensional gel electrophoresis
Zhang D, Koay ES.
Methods Mol Biol (2007) 428: 77-92
Reducing Sample Complexity by RP-HPLC: Beyond the Tip of the Protein Expression Iceberg
Van den Bergh G, Arckens L.
Methods Mol Biol (2008) 424: 147-56
Isolation and Fractionation of the Endoplasmic Reticulum from Castor Bean (Ricinus communis) Endosperm for Proteomic Analyses
Simon WJ, Maltman DJ, Slabas AR.
Methods Mol Biol (2008) 425: 203-15
Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes
Marelli M, Nesvizhskii AI, Aitchison JD.
Methods Mol Biol (2008) 432: 357-71
Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression
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Clin Cancer Res (2008) 14(4): 1002-14
Protein labeling and biotinylation of peptides during spot synthesis using biotin p-nitrophenyl ester (biotin-ONp)
Dirk F. H. Winkler, Patrick L. McGeer
PROTEOMICS (2008) 8(5): 961-967
Proteomic analysis of the stacked Golgi complex
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Methods Mol Biol (2008) 432: 37-49
Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments
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Rapid Communications in Mass Spectrometry (2008) 22(7): 986-992
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J Microbiol Methods (2008) 73(1): 26-32
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Methods Mol Biol (2008) 425: 187-201
Identification and Validation of Eukaryotic Aspartate and Glutamate Methylation in Proteins
Robert Sprung, Yue Chen, Kai Zhang, Dongmei Cheng, Terry Zhang, Junmin Peng, and Yingming Zhao
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1001-1006
Detection of Multiphosphorylated Peptides in LC-MS/MS Analysis under Low pH Conditions
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Methods Mol Biol (2008) 432: 175-83
Strategies to recover proteins from ocular tissues for proteomics
Nikhil Patel, Ekta Solanki, Renata Picciani, Valerie Cavett, Jennifer A. Caldwell-Busby, Sanjoy K. Bhattacharya
PROTEOMICS (2008) 8(5): 1055-1070
"Proteotyping": Population Proteomics of Human Leukocytes Using Top Down Mass Spectrometry
Roth MJ, Parks BA, Ferguson JT, Ii MT, Kelleher NL.
Anal Chem Early Edition: published 20-Mar-2008
Characterization of the Rat Liver Membrane Proteome Using Peptide Immobilized pH Gradient Isoelectric Focusing
J. M. Chick, P. A. Haynes, M. P. Molloy, B. Bjellqvist, M. S. Baker, and A. C. L. Len
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1036-1045
Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry for Protein and Peptide Profiling of Body Fluids
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Methods Mol Biol (2008) 441: 41-56
Purification and proteomics analysis of pancreatic zymogen granule membranes
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Methods Mol Biol (2008) 432: 275-87
Serum biomarker profiling by solid-phase extraction with particle-embedded micro tips and matrix-assisted laser desorption/ionization mass spectrometry
Arti Navare, Manshui Zhou, John McDonald, Fernando G. Noriega, M. Cameron Sullards, Facundo M. Fernandez
Rapid Communications in Mass Spectrometry (2008) 22(7): 997-1008
Proteome-Wide Identification of Proteins and Their Modifications with Decreased Ambiguities and Improved False Discovery Rates Using Unique Sequence Tags
Yufeng Shen, Nikola Toli , Kim K. Hixson, Samuel O. Purvine, Ljiljana Pa a-Toli , Wei-Jun Qian, Joshua N. Adkins, Ronald J. Moore, and Richard D. Smith
ANALYTICAL CHEMISTRY (2008) 80(6): 1871-1882
Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins
Yan W, Hwang D, Aebersold R.
Methods Mol Biol (2008) 432: 389-401
Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography
Guanghui Han, Mingliang Ye, Houjiang Zhou, Xinning Jiang, Shun Feng, Xiaogang Jiang, Ruijun Tian, Dafang Wan, Hanfa Zou, Jianren Gu
PROTEOMICS (2008) 8(7): 1346-1361
Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules
Rachel Haimovitz, Yoav Barak, Ely Morag, Milana Voronov-Goldman, Yuval Shoham, Raphael Lamed, Edward A. Bayer
PROTEOMICS (2008) 8(5): 968-979
Tissue sample collection for proteomics analysis
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Methods Mol Biol (2007) 428: 43-54
Preparation Methods of Human Metaphase Chromosomes for their Proteome Analysis
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Methods Mol Biol (2008) 432: 149-60
Laser Desorption/Ionization Mass Spectrometry on Porous Silica and Alumina for Peptide Mass Fingerprinting
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J Am Soc Mass Spectrom Early Edition: published 4-Mar-2008
Proteomics of cerebrospinal fluid: methods for sample processing
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Methods Mol Biol (2008) 425: 53-66
Multi-component immunoaffinity subtraction and reversed-phase chromatography of human serum
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Determination of Genuine Residents of Plant Endomembrane Organelles using Isotope Tagging and Multivariate Statistics
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Methods Mol Biol (2008) 432: 373-87
Purification and proteomic analysis of a nuclear-insoluble protein fraction
Horigome T, Furukawa K, Ishii K.
Methods Mol Biol (2008) 432: 139-48
Quantitative 2-D gel electrophoresis-based expression proteomics of albumin and IgG immunodepleted plasma
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J Chromatogr B (2008) 865(1-2): 147-152
Multiplexed proteomic sample preconcentration device using surface-patterned ion-selective membrane
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Lab Chip (2008) 8(4): 596-601
A Novel Approach Using MALDI-TOF/TOF Mass Spectrometry and Prestructured Sample Supports (AnchorChip Technology) for Proteomic Profiling and Protein Identification
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Methods Mol Biol (2008) 441: 57-70
Stain efficiency and MALDI-TOF MS compatibility of seven visible staining procedures
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Anal Bioanal Chem (2008) 390(7): 1765-73
Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling
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Proteome Science (2008) 6(1): 9
Immunoaffinity Fractionation of Plasma Proteins by Chicken IgY Antibodies
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MALDI Imaging of Formalin-Fixed Paraffin-Embedded Tissues: Application to Model Animals of Parkinson Disease for Biomarker Hunting
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JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 969-978
Isolation and enrichment of secreted proteins from filamentous fungi
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Methods Mol Biol (2008) 425: 275-85
Quantitative Gel Electrophoresis: Sources of Variation
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JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1226-1234
Proteomic approaches to identify and characterize alterations to the mitochondrial proteome in alcoholic liver disease
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Methods Mol Biol (2008) 447: 369-80
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Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data
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Purification and proteomic analysis of synaptic vesicles
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Methods Mol Biol (2008) 441: 71-90
Identification of new O-GlcNAc modified proteins using a click-chemistry-based tagging
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Purification and proteomic analysis of lysosomal integral membrane proteins
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Methods Mol Biol (2008) 432: 229-41
Towards multidimensional liquid chromatography separation of proteins using fluorescence and isotope-coded protein labelling for quantitative proteomics
Florian Tribl, Christiane Lohaus, Tanja Dombert, Elmar Langenfeld, Heike Piechura, Bettina Warscheid, Helmut E. Meyer, Katrin Marcus
PROTEOMICS (2008) 8(6): 1204-1211
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Evaluating Peptide Mass Fingerprinting-based Protein Identification
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Genomics Proteomics Bioinformatics (2007) 5(3-4): 152-7
Enriching basic and acidic rat brain proteins with ion exchange mini spin columns before two-dimensional gel electrophoresis
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Subcellular fractionation and proteomics of nuclear envelopes
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Methods Mol Biol (2008) 432: 117-37
Sample preparation procedure for cellular fungi
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Methods Mol Biol (2008) 425: 265-73
Preparation of nasal secretions for proteome analysis
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Methods Mol Biol (2008) 425: 77-87
Microscale Isoelectric Focusing in Solution : A Method for Comprehensive and Quantitative Proteome Analysis Using 1-D and 2-D DIGE Combined with MicroSol IEF Prefractionation
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Methods Mol Biol (2008) 424: 241-56
Identification of Disease Biomarkers by Profiling of Serum Proteins Using SELDI-TOF Mass Spectrometry
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The isolation of detergent-resistant lipid rafts for two-dimensional electrophoresis
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Purification and proteomic analysis of the mouse liver mitochondrial inner membrane
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Methods Mol Biol (2008) 432: 101-16
Separation of membrane proteins by two-dimensional electrophoresis using cationic rehydrated strips
Birger Wenge, Heinz Bönisch, Julia Grabitzki, Günter Lochnit, Brigitte Schmitz, Michael H. J. Ahrend
ELECTROPHORESIS (2008) 29(7): 1511-1517
Protein kinase substrate identification on functional protein arrays
Meng L, Michaud GA, Merkel JS, Zhou F, Huang J, Mattoon DR, Schweitzer B.
BMC Biotechnol (2008) 8(1): 22
Application of ion trap technology to liquid chromatography/mass spectrometry quantitation of large peptides
Petia Shipkova, Dieter M. Drexler, Robert Langish, James Smalley, Mary Ellen Salyan, Mark Sanders
Rapid Communications in Mass Spectrometry (2008) 22(9): 1359-1366
Analysis of the Oryza sativa Plasma Membrane Proteome Using Combined Protein and Peptide Fractionation Approaches in Conjunction with Mass Spectrometry
Siria H. A. Natera, Kristina L. Ford, Andrew M. Cassin, John H. Patterson, Edward J. Newbigin, and Antony Bacic
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1159-1187
Mitochondrial proteomics : analysis of a whole mitochondrial extract with two-dimensional electrophoresis
Rabilloud T.
Methods Mol Biol (2008) 432: 83-100
Mass spectrometric compatibility of Deep Purple and SYPRO Ruby total protein stains for high-throughput proteomics using large-format two-dimensional gel electrophoresis
Nock CM, Ball MS, White IR, Skehel JM, Bill L, Karuso P.
Rapid Commun Mass Spectrom (2008) 22(6): 881-886
Fractionation of proteins by heparin chromatography
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Reverse phase protein microarrays for theranostics and patient-tailored therapy
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Methods Mol Biol (2008) 441: 113-28
Prefractionation, Enrichment, Desalting and Depleting of Low Volume and Low Abundance Proteins and Peptides Using the MF10
Wasinger V, Ly L, Fitzgerald A, Walsh B.
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Fractionation of complex protein mixtures by liquid-phase isoelectric focusing
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Antibody arrays for determination of relative protein abundances
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Protein extraction from green plant tissue
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Methods Mol Biol (2008) 425: 149-52
Preparation of urine samples for proteomic analysis
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Methods Mol Biol (2008) 425: 89-99
Enrichment of membrane proteins by partitioning in detergent/polymer aqueous two-phase systems
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Methods Mol Biol (2008) 424: 403-12
Microproteomics: Analysis of protein diversity in small samples
Gutstein HB, Morris JS, Annangudi SP, Sweedler JV.
Mass Spectrom Rev Early Edition: published 12-Feb-2008
Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags
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Quantitative protein profiling by mass spectrometry using label-free proteomics
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Methods Mol Biol (2008) 439: 241-56
Cell wall fractionation for yeast and fungal proteomics
Pitarch A, Nombela C, Gil C.
Methods Mol Biol (2008) 425: 217-39
Mixed-Effects Statistical Model for Comparative LC−MS Proteomics Studies
D. S. Daly, K. K. Anderson, E. A. Panisko, S. O. Purvine, R. Fang, M. E. Monroe, and S. E. Baker
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1209-1217
Use of gas-phase fractionation to increase protein identifications : application to the peroxisome
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Methods Mol Biol (2008) 432: 217-28
Isolation of endocitic organelles by density gradient centrifugation
Araùjo M, Hube LA, Stasyk T.
Methods Mol Biol (2008) 424: 317-31
Fractionation of proteins by immobilized metal affinity chromatography
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Methods Mol Biol (2008) 424: 205-12
Gallium metal affinity capture tandem mass spectrometry for the selective detection of phosphopeptides in complex mixtures
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J Mass Spectrom Early Edition: published 11-Feb-2008
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Methods Mol Biol (2008) 424: 113-23
Global analysis of gel mobility of proteins and its use in target identification
Shirai A, Matsuyama A, Yashiroda Y, Hashimoto A, Kawamura Y, Arai R, Komatsu Y, Horinouchi S, Yoshida M.
J Biol Chem Early Edition: published 21-Feb-2008
Coimmunoprecipitation and proteomic analyses
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Methods Mol Biol (2008) 439: 291-308
Quantitation of protein in samples prepared for 2-d electrophoresis
Berkelman T.
Methods Mol Biol (2008) 424: 43-9
Spiking of serum specimens with exogenous reporter peptides for mass spectrometry based protease profiling as diagnostic tool
Findeisen P, Peccerella T, Post S, Wenz F, Neumaier M.
Rapid Commun Mass Spectrom (2008) 22(8): 1223-1229
Albumin and immunoglobulin depletion of human plasma
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Methods Mol Biol (2008) 425: 15-25
Metalloproteomics in the molecular study of cell physiology and disease
Thierse HJ, Helm S, Pankert P.
Methods Mol Biol (2008) 425: 139-47
Application of fluorescence dye saturation labeling for differential proteome analysis of 1,000 microdissected cells from pancreatic ductal adenocarcinoma precursor lesions
Sitek B, Sipos B, Klöppel G, Schmiegel W, Hahn SA, Meyer HE, Stühler K.
Methods Mol Biol (2008) 425: 1-14
Purification and Proteomic Analysis of Chloroplasts and their Sub-Organellar Compartments
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Methods Mol Biol (2008) 432: 19-36
Isolation of cytoplasmatic proteins from cultured cells for two-dimensional gel electrophoresis
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Methods Mol Biol (2008) 425: 101-12
Sequential detergent fractionation of primary neurons for proteomics studies
Simonetta Bernocco, Costanza Fondelli, Silvia Matteoni, Letizia Magnoni, Stefano Gotta, Georg C. Terstappen, Roberto Raggiaschi
PROTEOMICS (2008) 8(5): 930-938
Antigen Retrieval for Proteomic Characterization of Formalin-Fixed and Paraffin-Embedded Tissues
Haifeng Xu, Li Yang, Weijie Wang, Shan-Rong Shi, Cheng Liu, Ying Liu, Xueping Fang, Clive R. Taylor, Cheng S. Lee, and Brian M. Balgley
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1098-1108
Combining laser capture microdissection and proteomics techniques
Mustafa D, Kros JM, Luider T.
Methods Mol Biol (2007) 428: 159-78
Reducing sample complexity in proteomics by chromatofocusing with simple buffer mixtures
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Methods Mol Biol (2008) 424: 187-203
Detecting native folds in mixtures of proteins that contain disulfide bonds
Narayan M, Welker E, Zhai H, Han X, Xu G, McLafferty FW, Scheraga HA.
Nat Biotechnol (2008) 26(4): 427-9
Identification of new regional marker proteins to map mouse brain by 2-D difference gel electrophoresis screening
Jacobs S, Van de Plas B, Van der Gucht E, Clerens S, Cnops L, Van den Bergh G, Arckens L.
Electrophoresis (2008) 29(7): 1518-24
Isolation and Preparation of Chloroplasts from Arabidopsis thaliana Plants
Kubis SE, Lilley KS, Jarvis P.
Methods Mol Biol (2008) 425: 171-86
Subunit Architecture of Intact Protein Complexes from Mass Spectrometry and Homology Modeling
Taverner T, Hernández H, Sharon M, Ruotolo BT, Matak-VinkovicÌ D, Devos D, Russell RB, Robinson CV.
Acc Chem Res Early Edition: published 4-Mar-2008
Isolation of bacterial cell membranes proteins using carbonate extraction
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Methods Mol Biol (2008) 424: 397-401
Recent development of multi-dimensional chromatography strategies in proteome research
Tang J, Gao M, Deng C, Zhang X.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 2-Feb-2008
Identification of target antigens of antiendothelial cell antibodies in healthy individuals: A proteomic approach
Amélie Servettaz, Philippe Guilpain, Luc Camoin, Patrick Mayeux, Cédric Broussard, Mathieu C. Tamby, Nicolas Tamas, Srini V. Kaveri, Loïc Guillevin, Luc Mouthon
PROTEOMICS (2008) 8(5): 1000-1008
Chemical derivatization of peptides containing phosphorylated serine/threonine for efficient ionization and quantification in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Hiroki Tsumoto, Moonjin Ra, Keijiro Samejima, Ryo Taguchi, Kohfuku Kohda
Rapid Communications in Mass Spectrometry (2008) 22(7): 965-972
Free flow isoelectric focusing : a method for the separation of both hydrophilic and hydrophobic proteins of rat liver peroxisomes
Islinger M, Weber G.
Methods Mol Biol (2008) 432: 199-215
Tandem affinity purification combined with mass spectrometry to identify components of protein complexes
Kaiser P, Meierhofer D, Wang X, Huang L.
Methods Mol Biol (2008) 439: 309-26
Bioaffinity magnetic reactor for peptide digestion followed by analysis using bottom-up shotgun proteomics strategy
Korecká L, Jankovicová B, Krenková J, Hernychová L, Slováková M, Le-Nell A, ChmelÃk J, Foret F, Viovy JL, BÃlková Z.
J Sep Sci (2008) 31(3): 507-515
Online Microwave D-Cleavage LC-ESI-MS/MS of Intact Proteins: Site-Specific Cleavages at Aspartic Acid Residues and Disulfide Bonds
Nicolas J. Hauser and Franco Basile
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1012-1026
Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue : proteomic analysis of formalin-fixed tissue
Stewart NA, Veenstra TD.
Methods Mol Biol (2008) 425: 131-8
Collection of proteins secreted from yeast protoplasts in active cell wall regeneration
Pitarch A, Nombela C, Gil C.
Methods Mol Biol (2008) 425: 241-63
Reducing the Complexity of the Escherichia coli Proteome by Chromatography on Reactive Dye Columns
Cash P, Booth IR.
Methods Mol Biol (2008) 424: 167-85
Bacteria and yeast cell disruption using lytic enzymes
Salazar O.
Methods Mol Biol (2008) 424: 23-34
The Tryptophan Phosphorescence of Porcine and Mutant Bovine Odorant-Binding Proteins: A Probe for the Local Protein Structure and Dynamics
Sabato D’Auria, Maria Staiano, Antonio Varriale, Margherita Gonnelli, Anna Marabotti, Mose’ Rossi, and Giovanni B. Strambini
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1151-1158
Novel Microwave-Assisted Digestion by Trypsin-Immobilized Magnetic Nanoparticles for Proteomic Analysis
Shuang Lin, Dong Yun, Dawei Qi, Chunhui Deng, Yan Li, and Xiangmin Zhang
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 1297-1307
Assessment of organelle purity using antibodies and specific assays : the example of the chloroplast envelope
Salvi D, Rolland N, Joyard J, Ferro M.
Methods Mol Biol (2008) 432: 345-56
Analysis of Microdissected Cells by Two-Dimensional LC-MS Approaches
Li C, Yi-Hong, Tan YX, Ai JH, Zhou H, Li SJ, Zhang L, Xia QC, Wu JR, Wang HY, Zeng R.
Methods Mol Biol (2007) 428: 193-208
Free-flow electrophoresis system for plasma proteomic applications
Wildgruber R, Yi J, Nissum M, Eckerskorn C, Weber G.
Methods Mol Biol (2008) 424: 287-300
Combining MALDI-FTMS and Bioinformatics for Rapid Peptidomic Comparisons
Joshua J. Schmidt, Sean McIlwain, David Page, Andrew E. Christie, and Lingjun Li
JOURNAL OF PROTEOME RESEARCH (2008) 7(03): 887-896
Evaluation of the possible proteomic application of trypsin from Streptomyces griseus
Stosová T, Sebela M, Rehulka P, Sedo O, Havliš J, Zdráhal Z.
Anal Biochem (2008) 376(1): 94-102
Gas-Phase Proton-Transfer Chemistry Coupled with TOF Mass Spectrometry and Ion Mobility-MS for the Facile Analysis of Poly(ethylene glycols) and PEGylated Polypeptide Conjugates
Dhanashri Bagal, Heidi Zhang, and Paul D. Schnier
ANALYTICAL CHEMISTRY (2008) 80(7): 2408-2418
Isolation of mitochondria from plant cell culture
Meyer EH, Millar AH.
Methods Mol Biol (2008) 425: 163-9
Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography
Mingxia Gao, Chunhui Deng, Wenjia Yu, Yang Zhang, Pengyuan Yang, Xiangmin Zhang
PROTEOMICS (2008) 8(5): 939-947
Shedding & shaving: Disclosure of proteomic expressions on a bacterial face
Harold Tjalsma, Lambert Lambooy, Peter W. Hermans, Dorine W. Swinkels
PROTEOMICS (2008) 8(7): 1415-1428
Membrane Protein Separation and Analysis by Supercritical Fluid Chromatography-Mass Spectrometry
Xu Zhang, Mark Scalf, Michael S. Westphall, and Lloyd M. Smith
ANALYTICAL CHEMISTRY (2008) 80(7): 2590-2598
Clinical Proteomics. Von Jennifer E. Van Eyk, Michael J. Dunn (Hrsg.)
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Pharm Unserer Zeit (2008) 37(2): 177-178
6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
Sandra Orchard, Lennart Martens, Joshua Tasman, Pierre-Alain Binz, Juan Pablo Albar, Henning Hermjakob
PROTEOMICS (2008) 8(7): 1331-1333
Cardiovascular Initiative of the Human Proteome Organisation, 5th Workshop October 2007, Seoul, Korea
Sarah Warburton, Melanie Y. White, Jennifer E. Van Eyk, Robert J. Cotter, Peipei Ping, Michael J. Dunn, Thomas M. Vondriska
PROTEOMICS (2008) 8(5): 924-926
Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea
Martin Eisenacher, Tanja Hardt, Michael Hamacher, Lennart Martens, Jari Häkkinen, Fredrik Levander, Rolf Apweiler, Helmut E. Meyer, Christian Stephan
PROTEOMICS (2008) 8(7): 1326-1330
1st Central and Eastern European Proteomic Conference & 3rd Czech Proteomic Conference 29 - 31 October 2007, Prague, Czech Republic
Suresh Jivan Gadher, Karel Bezou?ka, Hana Ková?ová
PROTEOMICS (2008) 8(5): 927-929
Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes
Dunn WB.
Phys Biol (2008) 5(1): 11001
Proteome-Level Responses of Escherichia coli to Long-Chain Fatty Acids and Use of Fatty Acid Inducible Promoter in Protein Production
Han MJ, Lee JW, Lee SY, Yoo JS.
J Biomed Biotechnol (2008) 2008: 735101
Proteogenomics: needs and roles to be filled by proteomics in genome annotation
Charles Ansong, Samuel O. Purvine, Joshua N. Adkins, Mary S. Lipton, and Richard D. Smith
Brief Funct Genomic Proteomic (2008) 7(1): 50-62
Computational proteomics: management and analysis of proteomics data
Mario Cannataro
Brief Bioinform (2008) 9(2): 97-101
Proteomics: moving from a discovery to a quality assurance tool
Perrotta PL.
Transfusion (2008) 48(3): 408-10
Seven successful years of Omics research: The Human Brain Proteome Project within the National German Research Network (NGFN)
Michael Hamacher, Friedrich Herberg, Marius Ueffing, Helmut E. Meyer
PROTEOMICS (2008) 8(6): 1116-1117
Transcriptome and proteome analysis of antibody producing NS0 cells cultivated at different cell densities in perfusion culture
Krampe B, Swiderek H, Al-Rubeai M.
Biotechnol Appl Biochem Early Edition: published 27-Feb-2008
Utility of separation science in metabolomic studies
Issaq HJ, Abbott E, Veenstra TD.
J Sep Sci Early Edition: published 18-Mar-2008
Human Disease Glycomics/Proteome Initiative (HGPI)
Naoyuki Taniguchi
Mol Cell Proteomics (2008) 7(3): 626-627
Inside SMP proteomics: Six years German Human Brain Proteome Project (HBPP) - A summary
Michael Hamacher, Tanja Hardt, Andre van Hall, Christian Stephan, Katrin Marcus, Helmut E. Meyer
PROTEOMICS (2008) 8(6): 1118-1128
Proteomic and metabolomic biomarkers for III-V semiconductors: And prospects for application to nano-materials
Fowler BA, Conner EA, Yamauchi H.
Toxicol Appl Pharmacol Early Edition: published 31-Jan-2008
Information quality in proteomics
Stead DA, Paton NW, Missier P, Embury SM, Hedeler C, Jin B, Brown AJ, Preece A.
Brief Bioinform (2008) 9(2): 174-88