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SPS' DigestIssue 48, 1-Feb-2008 |
Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results
Weichaun Yu, Zengyou He, Junfeng Liu, and Hongyu Zhao
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 123-129
Clustering Millions of Tandem Mass Spectra
Ari M. Frank, Nuno Bandeira, Zhouxin Shen, Stephen Tanner, Steven P. Briggs, Richard D. Smith, and Pavel A. Pevzner
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 113-122
In Silico Tools for Predicting Peptides Binding to HLA-Class II Molecules: More Confusion than Conclusion
Uthaman Gowthaman and Javed N. Agrewala
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 154-163
Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra
Dante Mantini, Francesca Petrucci, Piero Del Boccio, Damiana Pieragostino, Marta Di Nicola, Alessandra Lugaresi, Giorgio Federici, Paolo Sacchetta, Carmine Di Ilio, and Andrea Urbani
Bioinformatics (2008) 24(1): 63-70
Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
Huang H, Jedynak BM, Bader JS.
PLoS Comput Biol (2007) 3(11): e214
Elastic image registration of 2-D gels for differential and repeatability studies
Carlos O. S. Sorzano, Ignacio Arganda-Carreras, Philippe Thévenaz, Ana Beloso, Gracia Morales, Israel Valdés, Carmen Pérez-García, Carmen Castillo, Elisa Garrido, Michael Unser
PROTEOMICS (2008) 8(1): 62-65
Prediction and Classification of Drug Toxicity Using Probabilistic Modeling of Temporal Metabolic Data: The Consortium on Metabonomic Toxicology Screening Approach
T.M.D. Ebbels, H.C. Keun, O.P. Beckonert, M.E. Bollard, J.C. Lindon, E. Holmes, J.K. Nicholson
Journal of Proteome Research (2007) 6(11): 4407-4422
X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers
Robert D. Bjornson, Nicholas J. Carriero, Christopher Colangelo, Mark Shifman, Kei-Hoi Cheung, Perry L. Miller, and Kenneth Williams
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 293-299
PhosphoBlast, a Computational Tool for Comparing Phosphoprotein Signatures among Large Datasets
Yingchun Wang and Richard L. Klemke
Mol Cell Proteomics (2008) 7(1): 145-162
Decomp from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
Böcker S, Lipták Z, Martin M, Pervukhin A.
Bioinformatics Early Edition: published 2-Jan-2008
Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling
Hyungwon Choi, Debashis Ghosh, and Alexey I. Nesvizhskii
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 286-292
Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing
Sebastian Klie, Lennart Martens, Juan Antonio Vizcaíno, Richard Côté, Phil Jones, Rolf Apweiler, Alexander Hinneburg, and Henning Hermjakob
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 182-191
Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression Data
Paul Kearney, Heather Butler, Kevin Eng, and Patrice Hugo
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 234-244
Proteomic data mining using predicted peptide chromatographic retention times
Tripet B, Renuka Jayadev M, Blow D, Nguyen C, Hodges R, Cios K.
Int J Bioinform Res Appl (2007) 3(4): 431-45
Investigating MS2/MS3 Matching Statistics: A Model For Coupling Consecutive Stage Mass Spectrometry Data For Increased Peptide Identification Confidence
Peter J. Ulintz, Bernd Bodenmiller, Philip C. Andrews, Ruedi Aebersold, and Alexey I. Nesvizhskii
Mol Cell Proteomics (2008) 7(1): 71-87
Informatics Strategies for Large-Scale Novel Cross-Linking Analysis
G.A. Anderson, N. Tolic, X. Tang, C. Zheng, J.E. Bruce
Journal of Proteome Research (2007) 6(9): 3412-3421
Deriving the Probabilities of Water Loss and Ammonia Loss for Amino Acids from Tandem Mass Spectra
Shiwei Sun, Chungong Yu, Yantao Qiao, Yu Lin, Gongjin Dong, Changning Liu, Jingfen Zhang, Zhuo Zhang, Jinjin Cai, Hong Zhang, and Dongbo Bu
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 202-208
Biomarker Discovery for Arsenic Exposure Using Functional Data. Analysis and Feature Learning of Mass Spectrometry Proteomic Data
Jaroslaw Harezlak, Michael C. Wu, Mike Wang, Armin Schwartzman, David C. Christiani, and Xihong Lin
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 217-224
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, and Predrag Radivojac
Bioinformatics (2008) 24(1): 102-109
Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics
Hyungwon Choi and Alexey I. Nesvizhskii
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 254-265
Enhanced analytical power of SDS-PAGE using machine learning algorithms
Fran Supek, Petra Peharec, Marijana Krsnik-Rasol, Tomislav ?muc
PROTEOMICS (2008) 8(1): 28-31
Network Scaling Invariants Help to Elucidate Basic Topological Principles of Proteins
A. Krishnan, A. Giuliani, J.P. Zbilut, M. Tomita
Journal of Proteome Research (2007) 6(10): 3924-3934
SwedCAD, a Database of Annotated High-Mass Accuracy MS/MS Spectra of Tryptic Peptides
M. Falth, M.M. Savitski, M.L. Nielsen, F. Kjeldsen, P.E. Andren, R.A. Zubarev
Journal of Proteome Research (2007) 6(10): 4063-4067
Statistical Analysis of Relative Labeled Mass Spectrometry Data from Complex Samples Using ANOVA
Ann L. Oberg, Douglas W. Mahoney, Jeanette E. Eckel-Passow, Christopher J. Malone, Russell D. Wolfinger, Elizabeth G. Hill, Leslie T. Cooper, Oyere K. Onuma, Craig Spiro, Terry M. Therneau, and H. Robert Bergen, III
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 225-233
Signal Detection in High-Resolution Mass Spectrometry Data
Dale F. McLerran, Ziding Feng, O. John Semmes, Lisa Cazares, and Timothy W. Randolph
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 276-285
Accurate Annotation of Peptide Modifications through Unrestrictive Database Search
Stephen Tanner, Samuel H. Payne, Surendra Dasari, Zhouxin Shen, Phillip A. Wilmarth, Larry L. David, William F. Loomis, Steven P. Briggs, and Vineet Bafna
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 170-181
Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin
Lukas Käll, John D. Storey, Michael J. MacCoss, and William Stafford Noble
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 40-44
Incorporating Sequence Information into the Scoring Function: A Hidden Markov Model for Improved Peptide Identification
Khatun J, Hamlett E, Giddings MC.
Bioinformatics Early Edition: published 10-Jan-2008
Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies
Brian C. Searle, Mark Turner, and Alexey I. Nesvizhskii
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 245-253
ToxoDB: an integrated Toxoplasma gondii database resource
Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ Jr, Wang H, Brunk BP.
Nucleic Acids Res Early Edition: published 14-Nov-2007
MPA: A multiple peak alignment algorithm to perform multiple comparisons of liquid-phase proteomic profiles
Stefano Toppo, Antonella Roveri, Maria Pia Vitale, Mattia Zaccarin, Elena Serain, Emanuele Apostolidis, Massimo Gion, Matilde Maiorino, Fulvio Ursini
PROTEOMICS (2008) 8(2): 250-253
On the Predictability of Protein Database Search Complexity and Its Relevance to Optimization of Distributed Searches
C. Deciu, J. Sun, M.A. Wall
Journal of Proteome Research (2007) 6(9): 3443-3448
Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins
Bock Axelsen J, Yan KK, Maslov S.
Biol Direct (2007) 2(1): 32
Prediction of peptides observable by mass spectrometry applied at the experimental set level
Sanders WS, Bridges SM, McCarthy FM, Nanduri B, Burgess SC.
BMC Bioinformatics (2007) 8(Suppl 7): S23
Multidimensional chromatography: Validation and efficient fishing for biomarkers and fractions containing them using the VisualCockpit software package
Gerhard A. Cumme, Stefan Kreusch, Matthias Nagel, Heidrun Rhode
PROTEOMICS (2008) 8(1): 37-41
Post alignment clustering procedure for comparative quantitative proteomics LC-MS Data
Joost C. W. de Groot, Mark W. E. J. Fiers, Roeland C. H. J. van Ham, Antoine H. P. America
PROTEOMICS (2008) 8(1): 32-36
YPED: A Web-Accessible Database System for Protein Expression Analysis
M.A. Shifman, Y. Li, C.M. Colangelo, K.L. Stone, T.L. Wu, K.-H. Cheung, P.L. Miller, K.R. Williams
Journal of Proteome Research (2007) 6(10): 4019-4024
Proteomic Parsimony through Bipartite Graph Analysis Improves Accuracy and Transparency
B. Zhang, M.C. Chambers, D.L. Tabb
Journal of Proteome Research (2007) 6(9): 3549-3557
On the Value of Knowing a z• Ion for What It Is
Jian Liu, Xiaorong Liang, and Scott A. McLuckey
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 130-137
Bioinformatics Processing of Protein and Transcript Profiles of Normal and Transformed Cell Lines Indicates Functional Impairment of Transcriptional Regulators in Buccal Carcinoma
C.A. Staab, R. Ceder, T. Jagerbrink, J.-A. Nilsson, K. Roberg, H. Jornvall, J.-O. Hoog, R.C. Grafstrom
Journal of Proteome Research (2007) 6(9): 3705-3717
Protein Information Crawler (PIC): Extensive spidering of multiple protein information resources for large protein sets
Ulrich Mayer
PROTEOMICS (2008) 8(1): 42-44
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis
Stanislaus R, Arthur JM, Rajagopalan B, Moerschell R, McGlothlen B, Almeida JS.
BMC Bioinformatics (2008) 9(1): 4
Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases
Lukas Käll, John D. Storey, Michael J. MacCoss, and William Stafford Noble
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 29-34
Pinnacle: A Fast, Automatic and Accurate Method for Detecting andQuantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data
Morris JS, Walla BC, Gutstein HB.
Bioinformatics Early Edition: published 14-Jan-2008
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M.
Genome Biol (2007) 8(11): R250
Modes of Inference for Evaluating the Confidence of Peptide Identifications
Matt Fitzgibbon, Qunhua Li, and Martin McIntosh
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 35-39
Imaging mass spectrometry of proteins and peptides: 3D volume reconstruction
Andersson M, Groseclose MR, Deutch AY, Caprioli RM.
Nat Methods (2008) 5(1): 101-8
Occurrence of Copper Proteins through the Three Domains of Life: A Bioinformatic Approach
Claudia Andreini, Lucia Banci, Ivano Bertini, and Antonio Rosato
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 209-216
OutlierD: An R package for outlier detection using quantile regression on mass spectrometry data
Cho H, Kim YJ, Jung HJ, Lee SW, Lee JW.
Bioinformatics Early Edition: published 10-Jan-2008
BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database
Faria-Campos AC, Gomes RR, Moratelli FS, Rausch-Fernandes H, Franco GR, Campos SV.
Genet Mol Res (2007) 6(4): 937-45
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry
Changyu Shen, Zhiping Wang, Ganesh Shankar, Xiang Zhang, and Lang Li
Bioinformatics (2008) 24(2): 202-208
Data Augmentation Algorithms for Detecting Conserved Domains in Protein Sequences: A Comparative Study
Chengpeng Bi
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 192-201
Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search Engine
Hua Xu, Liwen Zhang, and Michael A. Freitas
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 138-144
?Glyco-peakfinder? - de novo composition analysis of glycoconjugates
Kai Maass, René Ranzinger, Hildegard Geyer, Claus-Wilhelm von der Lieth, Rudolf Geyer
PROTEOMICS (2007) 7(24): 4435-4444
Extra Virgin Olive Oils Increase Hepatic Fat Accumulation and Hepatic Antioxidant Protein Levels in APOE-/- Mice
J.M. Arbones-Mainar, K. Ross, G.J. Rucklidge, M. Reid, G. Duncan, J.R. Arthur, G.W. Horgan, M.A. Navarro, R. Carnicer, C. Arnal, J. Osada, B. deRoos
Journal of Proteome Research (2007) 6(10): 4041-4054
Proteomic and Biochemical Studies of Calcium- and Phosphorylation-Dependent Calmodulin Complexes in Mammalian Cells
D.-J. Jang, M. Guo, D. Wang
Journal of Proteome Research (2007) 6(9): 3718-3728
Proteomic Analysis of a Membrane Skeleton Fraction from Human Liver
J. He, Y. Liu, S. He, Q. Wang, H. Pu, J. Ji
Journal of Proteome Research (2007) 6(9): 3509-3518
Proteome analysis of matrix vesicles isolated from femurs of chicken embryo
Marcin Balcerzak, Agata Malinowska, Cyril Thouverey, Anna Sekrecka, Michal Dadlez, Rene Buchet, Slawomir Pikula
PROTEOMICS (2008) 8(1): 192-205
Time-course of changes in amounts of specific proteins upon exposure to hyper-g, 2-D clinorotation, and 3-D random positioning of Arabidopsis cell cultures
Barjaktarovic Z, Nordheim A, Lamkemeyer T, Fladerer C, Madlung J, Hampp R.
J Exp Bot (2007) 58(15-16): 4357-63
Examining the Proteome of Drosophila Across Organism Lifespan
R.A. Sowell, K.E. Hersberger, T.C. Kaufman, D.E. Clemmer
Journal of Proteome Research (2007) 6(9): 3637-3647
Molecular and Proteomic Characterization of Human Mesenchymal Stem Cells Derived from Amniotic Fluid: Comparison to Bone Marrow Mesenchymal Stem Cells
Roubelakis MG, Pappa KI, Bitsika V, Zagoura D, Vlahou A, Papadaki HA, Antsaklis A, Anagnou NP.
Stem Cells Dev (2007) 16(6): 931-52
Vitellogenin cleavage products as indicators for toxic stress in zebra fish embryos: A proteomic approach
Ulrike Gündel, Dirk Benndorf, Martin von Bergen, Rolf Altenburger, Eberhard Küster
PROTEOMICS (2007) 7(24): 4541-4554
Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues
Birgit C. Bønsager, Christine Finnie, Peter Roepstorff, Birte Svensson
PROTEOMICS (2007) 7(24): 4528-4540
Immuno-proteomic approach to excitation-contraction coupling in skeletal and cardiac muscle: Molecular insights revealed by the mitsugumins
Weisleder N, Takeshima H, Ma J.
Cell Calcium (2008) 43(1): 1-8
Proteomics Approach to Identify Dehydration Responsive Nuclear Proteins from Chickpea (Cicer arietinum L.)
Aarti Pandey, Subhra Chakraborty, Asis Datta, and Niranjan Chakraborty
Mol Cell Proteomics (2008) 7(1): 88-107
"Turnover Proteome" of Human Atrial Trabeculae
F.M. Lampert, P. Matt, M. Grapow, I. Lefkovits, H.-R. Zerkowski, T. Grussenmeyer
Journal of Proteome Research (2007) 6(11): 4458-4468
Proteome Changes Induced by Knock-Down of the Deubiquitylating Enzyme HAUSP/USP7
B.M. Kessler, E. Fortunati, M. Melis, C.E.G.M. Palas, H. Clevers, M.M. Maurice
Journal of Proteome Research (2007) 6(11): 4163-4172
TOPORS Functions As A SUMO-1 E3 Ligase for Chromatin-Modifying Proteins
P. Pungaliya, D. Kulkarni, H.-J. Park, H. Marshall, H. Zheng, H. Lackland, A. Saleem, E.H. Rubin
Journal of Proteome Research (2007) 6(10): 3918-3923
Conformational diversity of the Goodpasture antigen, the noncollagenous-1 domain of the ?3 chain of collagen IV
Juan J. Calvete, Fernando Revert, Mario Blanco, Javier Cervera, Celine Tárrega, Libia Sanz, Francisco Revert-Ros, Froilán Granero, Enrique Pérez-Payá, Billy G. Hudson, Juan Saus
PROTEOMICS (2008) 8(1): 217
Proteome analysis of apoptosis signaling by S-trityl-L-cysteine, a potent reversible inhibitor of human mitotic kinesin Eg5
Frank Kozielski, Dimitrios A. Skoufias, Rose-Laure Indorato, Yasmina Saoudi, Peter R. Jungblut, Hanne K. Hustoft, Margarita Strozynski, Bernd Thiede
PROTEOMICS (2008) 8(2): 289-300
Opposite pathobiochemical fate of pyruvate kinase and adenylate kinase in aged rat skeletal muscle as revealed by proteomic DIGE analysis
Philip Doran, Kathleen O'Connell, Joan Gannon, Marcella Kavanagh, Kay Ohlendieck
PROTEOMICS (2008) 8(2): 364-377
Early manganese-toxicity response in Vigna unguiculata L. - a proteomic and transcriptomic study
Hendrik Führs, Moritz Hartwig, Laura Elisa Buitrago Molina, Dimitri Heintz, Alain Van Dorsselaer, Hans-Peter Braun, Walter J. Horst
PROTEOMICS (2008) 8(1): 149-159
PTRF-Cavin, a Conserved Cytoplasmic Protein Required for Caveola Formation and Function
Hill MM, Bastiani M, Luetterforst R, Kirkham M, Kirkham A, Nixon SJ, Walser P, Abankwa D, Oorschot VM, Martin S, Hancock JF, Parton RG.
Cell (2008) 132(1): 113-24
Identification of Potential Pluripotency Determinants for Human Embryonic Stem Cells Following Proteomic Analysis of Human and Mouse Fibroblast Conditioned Media
A.B.J. Prowse, L.R. McQuade, K.J. Bryant, H. Marcal, P.P. Gray
Journal of Proteome Research (2007) 6(9): 3796-3807
Amphibian Skin Secretomics: Application of Parallel Quadrupole Time-of-Flight Mass Spectrometry and Peptide Precursor cDNA Cloning to Rapidly Characterize the Skin Secretory Peptidome of Phyllomedusa hypochondrialis azurea: Discovery of a Novel Peptide Family, the Hyposins
A.H. Thompson, A.J. Bjourson, D.F. Orr, C. Shaw, S. McClean
Journal of Proteome Research (2007) 6(9): 3604-3613
Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome
Sharma S, Kohlstaedt LA, Damianov A, Rio DC, Black DL.
Nat Struct Mol Biol Early Edition: published 13-Jan-2008
A Quantitative Proteomic Analysis of Mitochondrial Participation in P19 Cell Neuronal Differentiation
Jermel Watkins, Siddhartha Basu, and Daniel F. Bogenhagen
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 328-338
PlyC, a novel bacteriophage lysin for compartment- dependent proteomics of group A streptococci
Thomas Köller, Daniel Nelson, Masanobu Nakata, Michael Kreutzer, Vincent A. Fischetti, Michael O. Glocker, Andreas Podbielski, Bernd Kreikemeyer
PROTEOMICS (2008) 8(1): 140-148
Proteomic Identification of the Cerebral Cavernous Malformation Signaling Complex
T.L. Hilder, M.H. Malone, S. Bencharit, J. Colicelli, T.A. Haystead, G.L. Johnson, C.C. Wu
Journal of Proteome Research (2007) 6(11): 4343-4355
Metabolic Regulatory Network Alterations in Response to Acute Cold Stress and Ginsenoside Intervention
X. Wang, M. Su, Y. Qiu, Y. Ni, T. Zhao, M. Zhou, A. Zhao, S. Yang, L. Zhao, W. Jia
Journal of Proteome Research (2007) 6(9): 3449-3455
Comparative Proteome Profiling and Functional Analysis of Chronic Myelogenous Leukemia Cell Lines
S. Fontana, R. Alessandro, M. Barranca, M. Giordano, C. Corrado, I. Zanella-Cleon, M. Becchi, E.C. Kohn, G. DeLeo
Journal of Proteome Research (2007) 6(11): 4330-4342
The role of proteomics in understanding sperm cell biology
Aitken RJ, Baker MA.
Int J Androl Early Edition: published 30-Dec-2007
Proteomics Analysis of Serum from Mutant Mice Reveals Lysosomal Proteins Selectively Transported by Each of the Two Mannose 6-Phosphate Receptors
Meiqian Qian, David E. Sleat, Haiyan Zheng, Dirk Moore, and Peter Lobel
Mol Cell Proteomics (2008) 7(1): 58-70
Identification of the surface-accessible, lineage-specific vascular proteome by two-dimensional peptide mapping
Roesli C, Mumprecht V, Neri D, Detmar M.
FASEB J Early Edition: published 7-Jan-2008
The Disruption of Hepatic Cytochrome P450 Reductase Alters Mouse Lipid Metabolism
D.M. Mutch, B. Klocke, P. Morrison, C.A. Murray, C.J. Henderson, M. Seifert, G. Williamson
Journal of Proteome Research (2007) 6(10): 3976-3984
Programmed proteome response for drought avoidance/tolerance in the root of a C3 xerophyte (wild watermelon) under water deficits
Yoshimura K, Masuda A, Kuwano M, Yokota A, Akashi K.
Plant Cell Physiol Early Edition: published 4-Jan-2008
Proteomic analysis of bovine conceptus fluids during early pregnancy
George A. Riding, Alun Jones, Michael K. Holland, Jonathan R. Hill, Sigrid A. Lehnert
PROTEOMICS (2008) 8(1): 160-177
Expression of hepatitis B virus proteins in transgenic mice alters lipid metabolism and induces oxidative stress in the liver
Yang F, Yan S, He Y, Wang F, Song S, Guo Y, Zhou Q, Wang Y, Lin Z, Yang Y, Zhang W, Sun S.
J Hepatol (2008) 48(1): 12-9
Comparative proteomics analysis of light responses in cryptochrome1-304 and Columbia wild-type 4 of Arabidopsis thaliana
Yang Y, Li Y, Li X, Guo X, Xiao X, Tang D, Liu X.
Acta Biochim Biophys Sin (Shanghai) (2008) 40(1): 27-37
CSF Proteomic Analysis Reveals Persistent Iron Deficiency-Induced Alterations in Nonhuman Primate Infants
Geguchadze RN, Coe CL, Lubach GR, Clardy TW, Beard JL, Connor JR.
J Neurochem Early Edition: published 6-Nov-2007
The HcaR regulatory protein of Photorhabdus luminescens affects the production of proteins involved in oxidative stress and toxemia
Sabina Chalabaev, Evelyne Turlin, Jean-François Charles, Abdelkader Namane, Sylvie Pagès, Alain Givaudan, Emma Brito-Fravallo, Antoine Danchin, Francis Biville
PROTEOMICS (2007) 7(24): 4499-4510
Hard (Beta-)Keratins in the Epidermis of Reptiles: Composition, Sequence, and Molecular Organization
M. Toni, L. DallaValle, L. Alibardi
Journal of Proteome Research (2007) 6(9): 3377-3392
Comparative proteomic analyses of the yeast Saccharomyces cerevisiae KNU5377 strain against menadione-induced oxidative stress
Kim I, Yun H, Jin I.
J Microbiol Biotechnol (2007) 17(2): 207-17
Survey of Differentially Expressed Proteins and Genes in Jasmonic Acid Treated Rice Seedling Shoot and Root at the Proteomics and Transcriptomics Levels
K. Cho, G.K. Agrawal, J. Shibato, Y.-H. Jung, Y.-K. Kim, B.H. Nahm, N.-S. Jwa, S. Tamogami, O. Han, K. Kohda, H. Iwahashi, R. Rakwal
Journal of Proteome Research (2007) 6(9): 3581-3603
Growth hormone action in the developing neural retina: A proteomic analysis
Marie-Laure Baudet, Zahra Hassanali, Grzegorz Sawicki, Edward O. List, John J. Kopchick, Steve Harvey
PROTEOMICS (2008) 8(2): 389-401
Proteomic analysis of a nutritional Shift-up in S. cerevisiae identifies Gvp36 as a BAR-containing protein involved in vesicular traffic and nutritional adaptation
Querin L, Sanvito R, Magni F, Busti S, Van Dorsselaer A, Alberghina L, Vanoni M.
J Biol Chem Early Edition: published 21-Dec-2007
Identification of Endogenously Presented Peptides from Chlamydia trachomatis with High Homology to Human Proteins and to a Natural Self-ligand of HLA-B27
Juan J. Cragnolini and Jose A. Lopez de Castro
Mol Cell Proteomics (2008) 7(1): 170-180
Muscle Metabolic Modulation by Chronic Hypoxia
H.R. Gosker, A.M.W.J. Schols
Journal of Proteome Research (2007) 6(9): 3400-3401
Proteomic Identification of PKC-Mediated Expression of 20E-Induced Protein in Drosophila melanogaster
Y. Sun, S. An, V.C. Henrich, X. Sun, Q. Song
Journal of Proteome Research (2007) 6(11): 4478-4488
Characterisation of the plasma membrane subproteome of bloodstream form Trypanosoma brucei
Daniel J. Bridges, Andrew R. Pitt, Orla Hanrahan, Kiva Brennan, H. Paul Voorheis, Pawel Herzyk, Harry P. de Koning, Richard J. S. Burchmore
PROTEOMICS (2008) 8(1): 83-99
Intrauterine growth restriction affects the proteomes of the small intestine, liver, and skeletal muscle in newborn pigs
Wang J, Chen L, Li D, Yin Y, Wang X, Li P, Dangott LJ, Hu W, Wu G.
J Nutr (2008) 138(1): 60-6
Motif Decomposition of the Phosphotyrosine Proteome Reveals a New N-terminal Binding Motif for SHIP2
Martin Lee Miller, Stefan Hanke, Anders Morkeberg Hinsby, Carsten Friis, Soren Brunak, Matthias Mann, and Nikolaj Blom
Mol Cell Proteomics (2008) 7(1): 181-192
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
Presser A, Elowitz MB, Kellis M, Kishony R.
Proc Natl Acad Sci U S A (2008) 105(3): 950-4
Proteome and Transcriptional Analysis of Ethanol-Grown Sulfolobus solfataricus P2 Reveals ADH2, a Potential Alcohol Dehydrogenase
P.K. Chong, A.M. Burja, H. Radianingtyas, A. Fazeli, P.C. Wright
Journal of Proteome Research (2007) 6(10): 3985-3994
The effect of serum withdrawal on the protein profile of quiescent human dermal fibroblasts in primary cell culture
Federica Boraldi, Giulia Annovi, Chiara Paolinelli-Devincenzi, Roberta Tiozzo, Daniela Quaglino
PROTEOMICS (2008) 8(1): 66-82
Functional Dissection of a HECT Ubiquitin E3 Ligase
Jin-ying Lu, Yu-yi Lin, Jiang Qian, Sheng-ce Tao, Jian Zhu, Cecile Pickart, and Heng Zhu
Mol Cell Proteomics (2008) 7(1): 35-45
The chicken egg yolk plasma and granule proteomes
Karlheinz Mann, Matthias Mann
PROTEOMICS (2008) 8(1): 178-191
Essential Dynamics of Helices Provide a Functional Classification of EF-Hand Proteins
F. Capozzi, C. Luchinat, C. Micheletti, F. Pontiggia
Journal of Proteome Research (2007) 6(11): 4245-4255
A Simple Intact Protein Analysis by MALDI-MS for Characterization of Ribosomal Proteins of Two Genome-Sequenced Lactic Acid Bacteria and Verification of Their Amino Acid Sequences
K. Teramoto, H. Sato, L. Sun, M. Torimura, H. Tao
Journal of Proteome Research (2007) 6(10): 3899-3907
Overcoming muscle atrophy in a hibernating mammal despite prolonged disuse in dormancy: Proteomic and molecular assessment
Lee K, Park JY, Yoo W, Gwag T, Lee JW, Byun MW, Choi I.
J Cell Biochem Early Edition: published 7-Jan-2008
The molecular architecture of the nuclear pore complex
Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP.
Nature (2007) 450(7170): 695-701
Antiviral Phagocytosis Is Regulated by a Novel Rab-Dependent Complex in Shrimp Penaeus japonicus
Wenlin Wu, Rongrong Zong, Jianyang Xu, and Xiaobo Zhang
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 424-431
The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum
Rogers LD, Foster LJ.
Proc Natl Acad Sci U S A (2007) 104(47): 18520-5
Identification of Proteins Involved in Microglial Endocytosis of α-Synuclein
J. Liu, Y. Zhou, Y. Wang, H. Fong, T.M. Murray, J. Zhang
Journal of Proteome Research (2007) 6(9): 3614-3627
The Tumor Suppressors p33ING1 and p33ING2 Interact with Alien in Vivo and Enhance Alien-Mediated Gene Silencing
I. Fegers, R. Kob, M. Eckey, O. Schmidt, F. Goeman, M. Papaioannou, N. Escher, F. vonEggeling, C. Melle, A. Baniahmad
Journal of Proteome Research (2007) 6(11): 4182-4188
Proteome of Murine Jejunal Brush Border Membrane Vesicles
M. Donowitz, S. Singh, F.F. Salahuddin, B.M. Hogema, Y. Chen, M. Gucek, R.N. Cole, N.C. Zachos, O. Kovbasnjuk, L.A. Lapierre, N. Broere, J. Goldenring, H. deJonge, X. Li
Journal of Proteome Research (2007) 6(10): 4068-4079
Cytoskeleton assembly at endothelial cell-cell contacts is regulated by alphaII-spectrin-VASP complexes
Benz PM, Blume C, Moebius J, Oschatz C, Schuh K, Sickmann A, Walter U, Feller SM, Renné T.
J Cell Biol (2008) 180(1): 205-19
Identification of Mouse Embryonic Stem Cell-Associated Proteins
Hossein Baharvand, Ali Fathi, Hamid Gourabi, Sepideh Mollamohammadi, and Ghasem Hosseini Salekdeh
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 412-423
Glutathione-S-transferase pi as a model protein for the characterisation of chemically reactive metabolites
Rosalind E. Jenkins, Neil R. Kitteringham, Christopher E. P. Goldring, Samantha M. J. Dowdall, Jane Hamlett, Catherine S. Lane, Jan-Simon Boerma, Nico P. E. Vermeulen, B. Kevin Park
PROTEOMICS (2008) 8(2): 301-315
A Comparative Proteomic Analysis of Human and Rat Embryonic Cerebrospinal Fluid
M.D. Zappaterra, S.N. Lisgo, S. Lindsay, S.P. Gygi, C.A. Walsh, B.A. Ballif
Journal of Proteome Research (2007) 6(9): 3537-3548
Study of Early Leaf Senescence in Arabidopsis thaliana by Quantitative Proteomics Using Reciprocal 14N/15N Labeling and Difference Gel Electrophoresis
Romano Hebeler, Silke Oeljeklaus, Kai A. Reidegeld, Martin Eisenacher,Christian Stephan, Barbara Sitek, Kai Stuhler, Helmut E. Meyer, Marcel J. G. Sturre, Paul P. Dijkwel, and Bettina Warscheid
Mol Cell Proteomics (2008) 7(1): 108-120
Proteomic analysis of the pathophysiological process involved in the antisnake venom effect of Mucuna pruriens extract
Roberto Guerranti, Ifeanyi G. Ogueli, Erica Bertocci, Chiara Muzzi, John C. Aguiyi, Riccardo Cianti, Alessandro Armini, Luca Bini, Roberto Leoncini, Enrico Marinello, Roberto Pagani
PROTEOMICS (2008) 8(2): 402-412
Human Metabolic Phenotypes Link Directly to Specific Dietary Preferences in Healthy Individuals
S. Rezzi, Z. Ramadan, F.-P.J. Martin, L.B. Fay, P. vanBladeren, J.C. Lindon, J.K. Nicholson, S. Kochhar
Journal of Proteome Research (2007) 6(11): 4469-4477
Determination of Global Protein Turnover in Stressed Mycobacterium Cells Using Hybrid-Linear Ion Trap-Fourier Transform Mass Spectrometry
Prahlad K. Rao, Bryan A. P. Roxas, and Qingbo Li
ANALYTICAL CHEMISTRY (2008) 80(2): 396-406
Alterations in Barrett's-related adenocarcinomas: A proteomic approach
Peng D, Sheta EA, Powell SM, Moskaluk CA, Washington K, Goldknopf IL, El-Rifai W.
Int J Cancer (2008) 122(6): 1303-10
A Proteome Resource of Ovarian Cancer Ascites: Integrated Proteomic and Bioinformatic Analyses To Identify Putative Biomarkers
Limor Gortzak-Uzan, Alex Ignatchenko, Andreas I. Evangelou, Mahima Agochiya, Kevin A. Brown, Peter St.Onge, Inga Kireeva, Gerold Schmitt-Ulms, Theodore J. Brown, Joan Murphy, Barry Rosen, Patricia Shaw, Igor Jurisica, and Thomas Kislinger
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 339-351
Metabolomic and Proteomic Analysis of a Clonal Insulin-Producing β-Cell Line (INS-1 832/13)
Céline Fernandez, Ulrika Fransson, Elna Hallgard, Peter Spégel, Cecilia Holm, Morten Krogh, Kristofer Wårell, Peter James, and Hindrik Mulder
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 400-411
Proteomic analysis of ampicillin-resistant oral Fusobacterium nucleatum
Al-Haroni M, Skaug N, Bakken V, Cash P.
Oral Microbiol Immunol (2008) 23(1): 36-42
Identification of Pro-MMP-7 as a Serum Marker for Renal Cell Carcinoma by Use of Proteomic Analysis
Sarkissian G, Fergelot P, Lamy PJ, Patard JJ, Culine S, Jouin P, Rioux-Leclercq N, Darbouret B.
Clin Chem Early Edition: published 17-Jan-2008
Diagnostic application of serum proteomic patterns in gastric cancer patients by ProteinChip surface-enhanced laser desorption/ionization time-of-flight mass spectrometry
Lim JY, Cho JY, Paik YH, Chang YS, Kim HG.
Int J Biol Markers (2007) 22(4): 281-6
Comparative Profiling of Serum Glycoproteome by Sequential Purification of Glycoproteins and 2-Nitrobenzensulfenyl (NBS) Stable Isotope Labeling: A New Approach for the Novel Biomarker Discovery for Cancer
K. Ueda, T. Katagiri, T. Shimada, S. Irie, T.-A. Sato, Y. Nakamura, Y. Daigo
Journal of Proteome Research (2007) 6(9): 3475-3483
Modification of the Hepatic Mitochondrial Proteome in Response to Ischemic Preconditioning following Ischemia-Reperfusion Injury of the Rat Liver
Oshima R, Nakano H, Katayama M, Sakurai J, Wu W, Koizumi S, Asano T, Watanabe T, Asakura T, Ohta T, Otsubo T.
Eur Surg Res (2007) 40(3): 247-255
Proteomic Analysis of Human Follicular Fluid Using an Alternative Bottom-Up Approach
Jörg Hanrieder, Adrien Nyakas, Tord Naessén, and Jonas Bergquist
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 443-449
Searching Urinary Tumor Markers for Bladder Cancer Using a Two-Dimensional Differential Gel Electrophoresis (2D-DIGE) Approach
E. Orenes-Pinero, M. Corton, P. Gonzalez-Peramato, F. Algaba, I. Casal, A. Serrano, M. Sanchez-Carbayo
Journal of Proteome Research (2007) 6(11): 4440-4448
Increased Striatal mRNA and Protein Levels of the Immunophilin FKBP-12 in Experimental Parkinson's Disease and Identification of FKBP-12-Binding Proteins
A. Nilsson, K. Skold, B. Sjogren, M. Svensson, J. Pierson, X. Zhang, R.M. Caprioli, J. Buijs, B. Persson, P. Svenningsson, P.E. Andren
Journal of Proteome Research (2007) 6(10): 3952-3961
Urine protein profile of IgA nephropathy patients may predict the response to ACE-inhibitor therapy
Maria Teresa Rocchetti, Marta Centra, Massimo Papale, Grazia Bortone, Carmen Palermo, Diego Centonze, Elena Ranieri, Salvatore Di Paolo, Loreto Gesualdo
PROTEOMICS (2008) 8(1): 206-216
Quantitative proteomes and in vivo secretomes of progressive and regressive UV-induced fibrosarcoma tumor cells: Mimicking tumor microenvironment using a dermis-based cell-trapped system linked to tissue chamber
Yang Shi, Craig A. Elmets, Jeffery W. Smith, Yu-Tsueng Liu, Yun-Ru Chen, Cheng-Po Huang, Wenhong Zhu, Honnavara N. Ananthaswamy, Richard L. Gallo, Chun-Ming Huang
PROTEOMICS (2007) 7(24): 4589-4600
Proteomic analyses of intermediate filaments reveals cytokeratin8 is highly acetylated - implications for colorectal epithelial homeostasis
Siân H. Leech, Caroline A. Evans, Leila Shaw, Chi H. Wong, Joanne Connolly, John R. Griffiths, Anthony D. Whetton, Bernard M. Corfe
PROTEOMICS (2008) 8(2): 279-288
Serum proteomic-based analysis for the identification of a potential serological marker for autoimmune hepatitis
Lu F, Xia Q, Ma Y, Yuan G, Yan H, Qian L, Hu M, Wang M, Lu H, Wang H, Liu B, Xue Y, Wang H, Li M, Shen B, Guo N.
Biochem Biophys Res Commun (2008) 367(2): 284-90
Proteomics-Based Strategy To Delineate the Molecular Mechanisms of the Metastasis Suppressor Gene BRMS1
J. Rivera, D. Megias, J. Bravo
Journal of Proteome Research (2007) 6(10): 4006-4018
Organellar Proteomics of Human Platelet Dense Granules Reveals That 14-3-3ζ Is a Granule Protein Related to Atherosclerosis
L. Hernandez-Ruiz, F. Valverde, M.D. Jimenez-Nunez, E. Ocana, A. Saez-Benito, J. Rodriguez-Martorell, J.-C. Bohorquez, A. Serrano, F.A. Ruiz
Journal of Proteome Research (2007) 6(11): 4449-4457
Intestinal Epithelial Cell Proteome in IL-10 Deficient Mice and IL-10 Receptor Reconstituted Epithelial Cells: Impact on Chronic Inflammation
T. Werner, A. Shkoda, D. Haller
Journal of Proteome Research (2007) 6(9): 3691-3704
Diagnosis of rheumatoid arthritis: multivariate analysis of biomarkers
Wild N, Karl J, Grunert VP, Schmitt RI, Garczarek U, Krause F, Hasler F, Van Riel PL, Bayer PM, Thun M, Mattey DL, Sharif M, Zolg W.
Biomarkers (2008) 13(1): 88-105
Protein Biomarker Identification in the CSF of Patients With CNS Lymphoma
Roy S, Josephson SA, Fridlyand J, Karch J, Kadoch C, Karrim J, Damon L, Treseler P, Kunwar S, Shuman MA, Jones T, Becker CH, Schulman H, Rubenstein JL.
J Clin Oncol (2008) 26(1): 96-105
Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform
Schiffer E, Mischak H, Theodorescu D, Vlahou A.
World J Urol Early Edition: published 4-Jan-2008
Proteomic Analysis of Peripheral Blood Mononuclear Cells: Selective Protein Processing Observed in Patients with Rheumatoid Arthritis
M. Schulz, H. Dotzlaw, S. Mikkat, M. Eggert, G. Neeck
Journal of Proteome Research (2007) 6(9): 3752-3759
Comparative proteomic and transcriptomic profiling of the human hepatocellular carcinoma
Minagawa H, Honda M, Miyazaki K, Tabuse Y, Teramoto R, Yamashita T, Nishino K, Takatori H, Ueda T, Kamijo KI, Kaneko S.
Biochem Biophys Res Commun (2008) 366(1): 186-92
Nitrated alpha-synuclein-activated microglial profiling for Parkinson's disease
Reynolds AD, Glanzer JG, Kadiu I, Ricardo-Dukelow M, Chaudhuri A, Ciborowski P, Cerny R, Gelman B, Thomas MP, Mosley RL, Gendelman HE.
J Neurochem Early Edition: published 22-Nov-2007
Myocardial ischemia/reperfusion causes VDAC phosphorylation which is reduced by cardioprotection with a p38 MAP kinase inhibitor
Hansjörg Schwertz, Justin M. Carter, Mulati Abdudureheman, Martin Russ, Ute Buerke, Axel Schlitt, Ursula Müller-Werdan, Roland Prondzinsky, Karl Werdan, Michael Buerke
PROTEOMICS (2007) 7(24): 4579-4588
Comparative Analysis of the Protein Profiles from Primary Gastric Tumors and Their Adjacent Regions: MAWBP Could Be a New Protein Candidate Involved in Gastric Cancer
J. Zhang, B. Kang, X. Tan, Z. Bai, Y. Liang, R. Xing, J. Shao, N. Xu, R. Wang, S. Liu, Y. Lu
Journal of Proteome Research (2007) 6(11): 4423-4432
Biological Variation of the Platelet Proteome in the Elderly Population and Its Implication for Biomarker Research
Wolfgang Winkler, Maria Zellner, Michael Diestinger, Rita Babeluk, Martina Marchetti, Alexandra Goll, Sonja Zehetmayer, Peter Bauer, Eduard Rappold, Ingrid Miller, Erich Roth, Gunter Allmaier, and Rudolf Oehler
Mol Cell Proteomics (2008) 7(1): 193-203
Stable and unstable angina: Identifying novel markers on circulating leukocytes
Angus Brown, Jo-Dee Lattimore, Michele McGrady, David Sullivan, Wayne Dyer, Filip Braet, Cristobal dos Remedios
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 90-98
Identification of proteins responsible for the development of adriamycin resistance in human gastric cancer cells using comparative proteomics analysis
Yang YX, Hu HD, Zhang DZ, Ren H.
J Biochem Mol Biol (2007) 40(6): 853-60
Lifetime Proteomic Profiling of an A30P α-Synuclein Drosophila Model of Parkinson's Disease
Z. Xun, R.A. Sowell, T.C. Kaufman, D.E. Clemmer
Journal of Proteome Research (2007) 6(9): 3729-3738
Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker
Michael Thierolf, Marie-Luise Hagmann, Michael Pfeffer, Nikolaos Berntenis, Norbert Wild, Markus Roeßler, Stefan Palme, Johann Karl, Heinz Bodenmüller, Josef Rüschoff, Siegbert Rossol, Gerhard Rohr, Wolfgang Rösch, Helmut Friess, Axel Eickhoff, Karl-Walter Jauch, Hanno Langen, Werner Zolg, Michael Tacke
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 11-22
Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening
Conrad DH, Goyette J, Thomas PS.
J Gen Intern Med (2008) 23(Suppl 1): 78-84
A combined transcriptome and proteome survey of malaria parasite liver stages
Tarun AS, Peng X, Dumpit RF, Ogata Y, Silva-Rivera H, Camargo N, Daly TM, Bergman LW, Kappe SH.
Proc Natl Acad Sci U S A (2008) 105(1): 305-10
Functional Proteomics Study Reveals That N-Acetylglucosaminyltransferase V Reinforces the Invasive/Metastatic Potential of Colon Cancer through Aberrant Glycosylation on Tissue Inhibitor of Metalloproteinase-
Yong-Sam Kim, Soo Young Hwang, Hye-Yeon Kang, Hosung Sohn, Sejeong Oh,Jin-Young Kim, Jong Shin Yoo, Young Hwan Kim, Cheorl-Ho Kim, Jae-Heung Jeon, Jung Mi Lee, Hyun Ah Kang, Eiji Miyoshi, Naoyuki Taniguchi, Hyang-Sook Yoo, and Jeong-Heon Ko
Mol Cell Proteomics (2008) 7(1): 1-14
Molecular pathogenesis of human prolactinomas identified by gene expression profiling, RT-qPCR, and proteomic analyses
Evans CO, Moreno CS, Zhan X, McCabe MT, Vertino PM, Desiderio DM, Oyesiku NM.
Pituitary Early Edition: published 9-Jan-2008
Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning
Zhang X, Wang B, Zhang XS, Li ZM, Guan ZZ, Jiang WQ.
BMC Cancer (2007) 7(1): 235
Use of 2-D DIGE analysis reveals altered phosphorylation in a tropomyosin mutant (Glu54Lys) linked to dilated cardiomyopathy
Chad M. Warren, Grace M. Arteaga, Sudarsan Rajan, Rafeeq P. H. Ahmed, David F. Wieczorek, R. John Solaro
PROTEOMICS (2008) 8(1): 100-105
Serum Proteome of Leprosy Patients Undergoing Erythema Nodosum Leprosum Reaction: Regulation of Expression of the Isoforms of Haptoglobin
N. Gupta, N.P. Shankernarayan, K. Dharmalingam
Journal of Proteome Research (2007) 6(9): 3669-3679
Proteomic-based approach for biomarkers discovery in early detection of invasive urothelial carcinoma
Junyu Li, Shaji Abraham, Liang Cheng, Frank A. Witzmann, Michael Koch, Jun Xie, Munazzah Rahman, Sulma I. Mohammed
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 78-89
Alterations in Cerebral Metabolomics and Proteomic Expression during Sepsis
Hinkelbein J, Feldmann RE Jr, Peterka A, Schubert C, Schelshorn D, Maurer MH, Kalenka A.
Curr Neurovasc Res (2007) 4(4): 280-8
Immunoproteomics of extracellular proteins of Chinese virulent strains of Streptococcus suis type 2
Wei Zhang, Cheng Ping Lu
PROTEOMICS (2007) 7(24): 4468-4476
Genomics and Proteomics in Venous Thromboembolism: Building a Bridge toward a Rational Personalized Medicine Framework
Lippi G, Franchini M, Montagnana M, Guidi GC.
Semin Thromb Hemost (2007) 33(8): 759-70
Apolipoprotein C-1 maintains cell survival by preventing from apoptosis in pancreatic cancer cells
Takano S, Yoshitomi H, Togawa A, Sogawa K, Shida T, Kimura F, Shimizu H, Tomonaga T, Nomura F, Miyazaki M.
Oncogene Early Edition: published 26-Nov-2007
In-Depth Proteomic Profiling of the Normal Human Kidney Glomerulus Using Two-Dimensional Protein Prefractionation in Combination with Liquid Chromatography-Tandem Mass Spectrometry
M. Miyamoto, Y. Yoshida, I. Taguchi, Y. Nagasaka, M. Tasaki, Y. Zhang, B. Xu, M. Nameta, H. Sezaki, L.M. Cuellar, T. Osawa, H. Morishita, S. Sekiyama, E. Yaoita, K. Kimura, T. Yamamoto
Journal of Proteome Research (2007) 6(9): 3680-3690
Proteomic Analysis of Peritoneal Dialysate Fluid in Patients with Different Types of Peritoneal Membranes
S. Sritippayawan, W. Chiangjong, T. Semangoen, N. Aiyasanon, P. Jaetanawanitch, S. Sinchaikul, S.-T. Chen, S. Vasuvattakul, V. Thongboonkerd
Journal of Proteome Research (2007) 6(11): 4356-4362
Specific MALDI Imaging and Profiling for Biomarker Hunting and Validation: Fragment of the 11S Proteasome Activator Complex, Reg Alpha Fragment, Is a New Potential Ovary Cancer Biomarker
R. Lemaire, S. AitMenguellet, J. Stauber, V. Marchaudon, J.-P. Lucot, P. Collinet, M.-O. Farine, D. Vinatier, R. Day, P. Ducoroy, M. Salzet, I. Fournier
Journal of Proteome Research (2007) 6(11): 4127-4134
Candidate biomarkers in renal cell carcinoma
Barbara Seliger, Sven P. Dressler, Rudolf Lichtenfels, Roland Kellner
PROTEOMICS (2007) 7(24): 4601-4612
Identification of circulating endorepellin LG3 fragment: Potential use as a serological biomarker for breast cancer
Jong Wook Chang, Un-Beom Kang, Dong Hyun Kim, Jae Kyo Yi, Jong Won Lee, Dong-Young Noh, Cheolju Lee, Myeong-Hee Yu
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 23-32
Differential Expression of Kidney Proteins in Streptozotocin-induced Diabetic Rats in Response to Hypoglycemic Fungal Polysaccharides
Hwang HJ, Baek YM, Kim SW, Kumar GS, Cho EJ, Oh JY, Yun JW.
J Microbiol Biotechnol (2007) 17(12): 2005-17
Relationship between natriuretic peptides and inflammation: proteomic evidence obtained during acute cellular cardiac allograft rejection in humans
Meirovich YF, Veinot JP, de Bold ML, Haddad H, Davies RA, Masters RG, Hendry PJ, de Bold AJ.
J Heart Lung Transplant (2008) 27(1): 31-7
Proteomic analysis of the saliva: A clue for understanding primary from secondary Sjögren's syndrome?
Baldini C, Giusti L, Bazzichi L, Lucacchini A, Bombardieri S.
Autoimmun Rev (2008) 7(3): 185-91
Effects of cathepsin B and L inhibition on postischemic protein alterations in the brain
Anagli J, Abounit K, Stemmer P, Han Y, Allred L, Weinsheimer S, Movsisyan A, Seyfried D.
Biochem Biophys Res Commun (2008) 366(1): 86-91
Proteome alterations induced in human white blood cells by consumption of Brussels sprouts: Results of a pilot intervention study
Christine Hoelzl, Olga Lorenz, Verena Haudek, Nina Gundacker, Siegfried Knasmüller, Christopher Gerner
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 108-117
Time course proteomic profile of rat acute myocardial infarction by SELDI-TOF MS analysis
Zhang G, Zhou B, Zheng Y, Feng K, Rao L, Zhang J, Xin J, Zhang B, Zhang L.
Int J Cardiol Early Edition: published 2-Jan-2008
Alpha-1-antitrypsin and complement component C7 are involved in asthma exacerbation
Tatsuji Nishioka, Kazuhiko Uchida, Kohji Meno, Takashi Ishii, Takeshi Aoki, Yoshiko Imada, Yuka Makino, Kenji Hirata, Yuri Matsumoto, Tadao Arinami, Emiko Noguchi
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 46-54
Increased expression of a disintegrin and metalloproteinase thrombospondin 1 in thrombosed hemodialysis grafts
Misra S, Lee N, Fu AA, Raghavakaimal S, Mandrekar J, Bjarnason H, McKusick MA, Iruela-Arispe L, Mukhopadhyay D.
J Vasc Interv Radiol (2008) 19(1): 111-9
Effect of UV Radiation on the Neonatal Skin Immune System- Implications for Melanoma
Muller HK, Malley RC, McGee HM, Scott DK, Wozniak T, Woods GM.
Photochem Photobiol (2008) 84(1): 47-54
Differential expression of ribosomal proteins in a human metastasis model identified by coupling 2-d liquid chromatography and mass spectrometry
Kreunin P, Yoo C, Urquidi V, Lubman DM, Goodison S.
Cancer Genomics Proteomics (2007) 4(5): 329-40
Proteomic analysis of dog tears for potential cancer markers
de Freitas Campos C, Cole N, Dyk DV, Walsh BJ, Diakos P, Almeida D, Torrecilhas A, Laus JL, Willcox MD.
Res Vet Sci Early Edition: published 27-Dec-2007
Proteomic profile determination of autosomal aneuploidies by mass spectrometry on amniotic fluids
Mange A, Desmetz C, Bellet V, Molinari N, Maudelonde T, Solassol J.
Proteome Science (2008) 6(1): 1
Comparison of human platelet membrane-cytoskeletal proteins with the plasma proteome: Towards understanding the platelet-plasma nexus
David W. Greening, Kristen M. Glenister, Eugene A. Kapp, Robert L. Moritz, Rosemary L. Sparrow, Garry W. Lynch, Richard J. Simpson
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 63-77
Chemical Proteomics Identifies Unanticipated Targets of Clinical Kinase Inhibitors
Peters EC, Gray NS.
ACS Chem Biol (2007) 2(10): 661-664
Detection of protein alterations in male breast cancer using two dimensional gel electrophoresis and mass spectrometry: The involvement of several pathways in tumorigenesis
Chahed K, Kabbage M, Hamrita B, Guillier CL, Trimeche M, Remadi S, Ehret-Sabatier L, Chouchane L.
Clin Chim Acta (2008) 388(1-2): 106-14
Proteomic Analysis of Peritoneal Fluid in Women with Endometriosis
S. Ferrero, D.J. Gillott, V. Remorgida, P. Anserini, K.-Y. Leung, N. Ragni, J.G. Grudzinskas
Journal of Proteome Research (2007) 6(9): 3402-3411
Observation of peptide differences between cancer and control in gastric juice
Wei-Chao Chang, Ping-I Hsu, Yuan-Yan Chen, Michael Hsiao, Pei-Jung Lu, Chung-Hsuan Chen
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 55-62
Cerebrospinal Fluid Proteomic Profiling of HIV-1-Infected Patients with Cognitive Impairment
W. Rozek, M. Ricardo-Dukelow, S. Holloway, H.E. Gendelman, V. Wojna, L.M. Melendez, P. Ciborowski
Journal of Proteome Research (2007) 6(11): 4189-4199
Integrated Analysis of the Cerebrospinal Fluid Peptidome and Proteome
Alexandre Zougman, Bartosz Pilch, Alexandre Podtelejnikov, Michael Kiehntopf, Claudia Schnabel, Chanchal Kumar, and Matthias Mann
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 386-399
Differential cerebro spinal fluid proteome investigation of Leber hereditary optic neuropathy (LHON) and multiple sclerosis
D'Aguanno S, Barassi A, Lupisella S, d'eril GM, Del Boccio P, Pieragostino D, Pallotti F, Carelli V, Valentino ML, Liguori R, Avoni P, Bernardini S, Gambi D, Urbani A, Federici G.
J Neuroimmunol (2008) 193(1-2): 156-60
Expression profiles in surgically-induced carotid stenosis: A combined transcriptomic and proteomic investigation
Forte A, Finicelli M, De Luca P, Quarto C, Onorati F, Santè P, Renzulli A, Galderisi U, Berrino L, De Feo M, Rossi F, Cotrufo M, Cascino A, Cipollaro M.
J Cell Mol Med Early Edition: published 25-Dec-2007
On the search for glycated lipoprotein ApoA-I in the plasma of diabetic and nephropathic patients
Annunziata Lapolla, Maura Brioschi, Cristina Banfi, Elena Tremoli, Luciana Bonfante, Simone Cristoni, Roberta Seraglia, Pietro Traldi
Journal of Mass Spectrometry (2008) 43(1): 74-81
Identification of collapsin response mediator protein-2 as a potential marker of colorectal carcinoma by comparative analysis of cancer cell secretomes
Chih-Ching Wu, Hua-Chien Chen, Su-Jen Chen, Hao-Ping Liu, Yi-Yueh Hsieh, Chia-Jung Yu, Reiping Tang, Ling-Ling Hsieh, Jau-Song Yu, Yu-Sun Chang
PROTEOMICS (2008) 8(2): 316-332
Identification of Poly-ADP-Ribosylated Mitochondrial Proteins after Traumatic Brain Injury
Lai Y, Chen Y, Watkins SC, Nathaniel PD, Guo F, Kochanek PM, Jenkins LW, Szabó C, Clark RS.
J Neurochem Early Edition: published 6-Nov-2007
Proteomic Approach for Caudal Trauma-Induced Acute Phase Proteins Reveals That Creatine Kinase Is a Key Acute Phase Protein in Amphioxus Humoral Fluid
Y.-y. Gao, D.-f. Zhang, H. Li, R. Liu, Z.-h. Zhuang, Q.-f. Li, S.-y. Wang, X.-x. Peng
Journal of Proteome Research (2007) 6(11): 4321-4329
Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer
J.R. Whiteaker, H. Zhang, L. Zhao, P. Wang, K.S. Kelly-Spratt, R.G. Ivey, B.D. Piening, L. Feng, E. Kasarda, K.E. Gurley, J.K. Eng, L.A. Chodosh, C.J. Kemp, M.W. McIntosh, A.G. Paulovich
Journal of Proteome Research (2007) 6(10): 3962-3975
Proteomic characterization of differentially expressed proteins in breast cancer: Expression of hnRNP H1, RKIP and GRP78 is strongly associated with HER-2/neu status
Daohai Zhang, Lee Kian Tai, Lee Lee Wong, Thomas C. Putti, Sunil K. Sethi, Ming Teh, Evelyn S. C. Koay
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(1): 99-107
Correspondence between clinical improvement and proteomic changes of the salivary peptide complex in a child with primary Sjögren syndrome
Rigante D, Inzitari R, Carone M, Fanali C, Stabile A, Cabras T, Capoluongo E, Gaspari S, Barone G, Castagnola M.
Rheumatol Int Early Edition: published 12-Jan-2008
Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues
Birgit C. Bønsager, Christine Finnie, Peter Roepstorff, Birte Svensson
PROTEOMICS (2007) 7(24): 4528-4540
Myocardial ischemia/reperfusion causes VDAC phosphorylation which is reduced by cardioprotection with a p38 MAP kinase inhibitor
Hansjörg Schwertz, Justin M. Carter, Mulati Abdudureheman, Martin Russ, Ute Buerke, Axel Schlitt, Ursula Müller-Werdan, Roland Prondzinsky, Karl Werdan, Michael Buerke
PROTEOMICS (2007) 7(24): 4579-4588
Proteomic analysis of the saliva: A clue for understanding primary from secondary Sjögren's syndrome?
Baldini C, Giusti L, Bazzichi L, Lucacchini A, Bombardieri S.
Autoimmun Rev (2008) 7(3): 185-91
Mass spectrometry based proteomic analysis of human stem cells: a brief review
Choi MY, An YJ, Kim SH, Roh SH, Ju HK, Hong SS, Park JH, Cho KJ, Choi DW, Kwon SW.
Exp Mol Med (2007) 39(6): 690-5
A combined transcriptome and proteome survey of malaria parasite liver stages
Tarun AS, Peng X, Dumpit RF, Ogata Y, Silva-Rivera H, Camargo N, Daly TM, Bergman LW, Kappe SH.
Proc Natl Acad Sci U S A (2008) 105(1): 305-10
Removal of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endosperm
Li G, Nallamilli BR, Tan F, Peng Z.
Electrophoresis (2008) 29(3): 604-617
Cytoskeleton assembly at endothelial cell-cell contacts is regulated by alphaII-spectrin-VASP complexes
Benz PM, Blume C, Moebius J, Oschatz C, Schuh K, Sickmann A, Walter U, Feller SM, Renné T.
J Cell Biol (2008) 180(1): 205-19
The state of proteome profiling in the fungal genus Aspergillus
Kim Y, Nandakumar MP, Marten MR.
Brief Funct Genomic Proteomic Early Edition: published 10-Jan-2008
Differential cerebro spinal fluid proteome investigation of Leber hereditary optic neuropathy (LHON) and multiple sclerosis
D'Aguanno S, Barassi A, Lupisella S, d'eril GM, Del Boccio P, Pieragostino D, Pallotti F, Carelli V, Valentino ML, Liguori R, Avoni P, Bernardini S, Gambi D, Urbani A, Federici G.
J Neuroimmunol (2008) 193(1-2): 156-60
Nuclear Proteomics and Directed Differentiation of Embryonic Stem Cells
Barthelery M, Salli U, Vrana KE.
Stem Cells Dev (2007) 16(6): 905-19
Mass spectrometry-based survey of age-associated protein carbonylation in rat brain mitochondria
Laszlo Prokai, Liang-Jun Yan, José L. Vera-Serrano, Stanley M. Stevens Jr, Michael J. Forster
Journal of Mass Spectrometry (2007) 42(12): 1583-1589
Proteomics of the Amniotic Fluid in Assessment of the Placenta. Relevance for Preterm Birth
Buhimschi IA, Buhimschi CS.
Placenta Early Edition: published 10-Jan-2008
Proteomic analysis of human lens epithelial cells exposed to microwaves
Li HW, Yao K, Jin HY, Sun LX, Lu DQ, Yu YB.
Jpn J Ophthalmol (2007) 51(6): 412-6
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
Presser A, Elowitz MB, Kellis M, Kishony R.
Proc Natl Acad Sci U S A (2008) 105(3): 950-4
The human red blood cell proteome and interactome
Goodman SR, Kurdia A, Ammann L, Kakhniashvili D, Daescu O.
Exp Biol Med (Maywood) (2007) 232(11): 1391-408
Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks
Mao L, Zabel C, Herrmann M, Nolden T, Mertes F, Magnol L, Chabert C, Hartl D, Herault Y, Delabar JM, Manke T, Himmelbauer H, Klose J.
PLoS ONE (2007) 2(11): e1218
Proteomic analysis of pancreas derived from adult cloned pig
Chae JI, Cho YK, Cho SK, Kim JH, Han YM, Koo DB, Lee KK.
Biochem Biophys Res Commun (2008) 366(2): 379-87
Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa)
Feng Tan, Guosheng Li, Brahmananda Reddy Chitteti, Zhaohua Peng
PROTEOMICS (2007) 7(24): 4511-4527
CSF Proteomic Analysis Reveals Persistent Iron Deficiency-Induced Alterations in Nonhuman Primate Infants
Geguchadze RN, Coe CL, Lubach GR, Clardy TW, Beard JL, Connor JR.
J Neurochem Early Edition: published 6-Nov-2007
Age-related subproteomic analysis of mouse liver and kidney peroxisomes
Mi J, Garcia-Arcos I, Alvarez R, Cristobal S.
Proteome Science (2007) 5(1): 19
Milk fat globule membrane components--a proteomic approach
Cavaletto M, Giuffrida MG, Conti A.
Adv Exp Med Biol (2008) 606: 129-41
Proteomic analysis of dog tears for potential cancer markers
de Freitas Campos C, Cole N, Dyk DV, Walsh BJ, Diakos P, Almeida D, Torrecilhas A, Laus JL, Willcox MD.
Res Vet Sci Early Edition: published 27-Dec-2007
N{varepsilon}-Formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function
Wisniewski JR, Zougman A, Mann M.
Nucleic Acids Res Early Edition: published 1-Dec-2007
A large-scale proteomic analysis of human embryonic stem cells
Schulz TC, Swistowska AM, Liu Y, Swistowski A, Palmarini G, Brimble SN, Sherrer E, Robins AJ, Rao MS, Zeng X.
BMC Genomics (2007) 8(1): 478
Identification by a differential proteomic approach of the induced stress and redox proteins by resveratrol in the normal and diabetic rat hearts
Dekkers DH, Bezstarosti K, Gurusamy N, Luijk K, Verhoeven AJ, Rijkers EJ, Demmers JA, Lamers JM, Maulik N, Das DK.
J Cell Mol Med Early Edition: published 11-Jan-2008
The significance of biochemical and molecular sample integrity in brain proteomics and peptidomics: Stathmin 2-20 and peptides as sample quality indicators
Karl Sköld, Marcus Svensson, Mathias Norrman, Benita Sjögren, Per Svenningsson, Per E. Andrén
PROTEOMICS (2007) 7(24): 4445-4456
Differential proteomic analysis of HeLa cells treated with Honokiol using a quantitative proteomic strategy
Ling B, Liang SF, Xu YH, Zhao XY, Tang MH, Liu XY, Zhao X, Huang CH, Chen LJ, Wei YQ.
Amino Acids Early Edition: published 21-Dec-2007
Proteomic identification of tyrosine nitration targets in kidney of spontaneously hypertensive rats
Raymond Tyther, Ahmad Ahmeda, Edward Johns, David Sheehan
PROTEOMICS (2007) 7(24): 4555-4564
Comparative proteomic analyses of the yeast Saccharomyces cerevisiae KNU5377 strain against menadione-induced oxidative stress
Kim I, Yun H, Jin I.
J Microbiol Biotechnol (2007) 17(2): 207-17
Contribution of solid-phase hexapeptide ligand libraries to the repertoire of human bile proteins
Guerrier L, Claverol S, Finzi L, Paye F, Fortis F, Boschetti E, Housset C.
J Chromatogr A (2007) 1176(1-2): 192-205
Expression analysis of highly polymorphic mucin proteins (Sm PoMuc) from the parasite Schistosoma mansoni
Roger E, Gourbal B, Grunau C, Pierce RJ, Galinier R, Mitta G.
Mol Biochem Parasitol (2008) 157(2): 217-27
Proteomic analysis of human omental adipose tissue in the polycystic ovary syndrome using two-dimensional difference gel electrophoresis and mass spectrometry
Cortón M, Botella-Carretero JI, López JA, Camafeita E, Millán JL, Escobar-Morreale HF, Peral B.
Hum Reprod Early Edition: published 22-Dec-2007
Limitations to the comparative proteomic analysis of thrombopoietin producing Chinese hamster ovary cells treated with sodium butyrate
Baik JY, Joo EJ, Kim YH, Lee GM.
J Biotechnol Early Edition: published 24-Nov-2007
Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence
Rodrigues ML, Nakayasu ES, Oliveira DL, Nimrichter L, Nosanchuk JD, Almeida IC, Casadevall A.
Eukaryot Cell (2008) 7(1): 58-67
Human protein atlas and the use of microarray technologies
Hober S, Uhlén M.
Curr Opin Biotechnol Early Edition: published 8-Jan-2008
Dataset of the plasma membrane proteome of nasopharyngeal carcinoma cell line HNE1 for uncovering protein function
Zhang L, Jia X, Liu X, Sheng T, Cao R, He Q, Liu Z, Peng X, Xiong J, Zhang P, Shi N, Liang S.
Acta Biochim Biophys Sin (Shanghai) (2008) 40(1): 55-70
Identification of membrane-associated proteins from Campylobacter jejuni strains using complementary proteomics technologies
Stuart J. Cordwell, Alice C. L. Len, Rachel G. Touma, Nichollas E. Scott, Linda Falconer, David Jones, Angela Connolly, Ben Crossett, Steven P. Djordjevic
PROTEOMICS (2008) 8(1): 122-139
Protein expression diversity amongst serovars of Salmonella enterica
Encheva V, Wait R, Begum S, Gharbia SE, Shah HN.
Microbiology (2007) 153(Pt 12): 4183-93
Proteomic analysis of the proteins regulated by HrpB from the plant pathogenic bacterium Burkholderia glumae
Yongsung Kang, Jinwoo Kim, Suhyun Kim, Hongsup Kim, Jae Yun Lim, Minkyun Kim, Jangyul Kwak, Jae Sun Moon, Ingyu Hwang
PROTEOMICS (2008) 8(1): 106-121
A proteomic approach to iron and copper homeostasis in cyanobacteria
Cerda BD, Castielli O, Durán RV, Navarro JA, Hervás M, Rosa MA.
Brief Funct Genomic Proteomic (2007) 6(4): 322-9
Role of group A Streptococcus HtrA in the maturation of SpeB protease
Jason N. Cole, John A. Aquilina, Peter G. Hains, Anna Henningham, Kadaba S. Sriprakash, Michael G. Caparon, Victor Nizet, Malak Kotb, Stuart J. Cordwell, Steven P. Djordjevic, Mark J. Walker
PROTEOMICS (2007) 7(24): 4488-4498
Proteomic analysis of ampicillin-resistant oral Fusobacterium nucleatum
Al-Haroni M, Skaug N, Bakken V, Cash P.
Oral Microbiol Immunol (2008) 23(1): 36-42
Proteomic Analysis to Identify the Role of LuxS/AI-2 Mediated Protein Expression in Escherichia coli O157:H7
Soni K, Jesudhasan P, Cepeda M, Williams B, Hume M, Russell WK, Jayaraman A, Pillai SD.
Foodborne Pathog Dis (2007) 4(4): 463-71
Proteome analysis of Streptococcus suis serotype 2
Hong-Bo Jing, Jing Yuan, Jie Wang, Yuan Yuan, Li Zhu, Xian-Kai Liu, Yu-Ling Zheng, Kai-Hua Wei, Xue-Min Zhang, Hong-Ran Geng, Qing Duan, Shu-Zhang Feng, Rui-Fu Yang, Wu-Chun Cao, Heng-Liang Wang, Yong-Qiang Jiang
PROTEOMICS (2008) 8(2): 333-349
Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10
Nicolai Juul, Evy Timmerman, Kris Gevaert, Gunna Christiansen, Svend Birkelund
PROTEOMICS (2007) 7(24): 4477-4487
Identification and Antibody-Therapeutic Targeting of Chloramphenicol-Resistant Outer Membrane Proteins in Escherichia coli
H. Li, X.-m. Lin, S.-y. Wang, X.-x. Peng
Journal of Proteome Research (2007) 6(9): 3628-3636
Characterization of the Extracellular Polymeric Substances Produced by Escherichia coli Using Infrared Spectroscopic, Proteomic, and Aggregation Studies
Eboigbodin KE, Biggs CA.
Biomacromolecules Early Edition: published 11-Jan-2008
Interaction proteome analysis of Xanthomonas Hrp proteins
Jang M, Park BC, Lee do H, Bae KH, Cho S, Park HS, Lee BR, Parki SG.
J Microbiol Biotechnol (2007) 17(2): 359-63
Immunoproteomics of extracellular proteins of Chinese virulent strains of Streptococcus suis type 2
Wei Zhang, Cheng Ping Lu
PROTEOMICS (2007) 7(24): 4468-4476
Analysis of Host-Inducing Proteome Changes in Bifidobacterium longum NCC2705 Grown in Vivo
Jing Yuan, Bin Wang, Zhongke Sun, Xin Bo, Xitong Yuan, Xiang He, Hongqing Zhao, Xinying Du, Fang Wang, Zheng Jiang, Ling Zhang, Leili Jia, Yufei Wang, KaiHua Wei, Jie Wang, Xuemin Zhang, Yansong Sun, Liuyu Huang, and Ming Zeng
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 375-385
Proteomic Analysis of Cell Envelope from Staphylococcus xylosus C2a, a Coagulase-Negative Staphylococcus
S. Planchon, C. Chambon, M. Desvaux, I. Chafsey, S. Leroy, R. Talon, M. Hebraud
Journal of Proteome Research (2007) 6(9): 3566-3580
Identification of enzymes and regulatory proteins in Escherichia coli that are oxidized under nitrogen, carbon, or phosphate starvation
Noda Y, Berlett BS, Stadtman ER, Aponte A, Morgan M, Shen RF.
Proc Natl Acad Sci U S A (2007) 104(47): 18456-60
The HcaR regulatory protein of Photorhabdus luminescens affects the production of proteins involved in oxidative stress and toxemia
Sabina Chalabaev, Evelyne Turlin, Jean-François Charles, Abdelkader Namane, Sylvie Pagès, Alain Givaudan, Emma Brito-Fravallo, Antoine Danchin, Francis Biville
PROTEOMICS (2007) 7(24): 4499-4510
Vitellogenin cleavage products as indicators for toxic stress in zebra fish embryos: A proteomic approach
Ulrike Gündel, Dirk Benndorf, Martin von Bergen, Rolf Altenburger, Eberhard Küster
PROTEOMICS (2007) 7(24): 4541-4554
Human protein atlas and the use of microarray technologies
Hober S, Uhlén M.
Curr Opin Biotechnol Early Edition: published 8-Jan-2008
Genomic and proteomic analysis of the effects of cannabinoids on normal human astrocytes
Bindukumar B, Mahajan SD, Reynolds JL, Hu Z, Sykes DE, Aalinkeel R, Schwartz SA.
Brain Res Early Edition: published 1-Nov-2007
Subcellular Proteome Analysis of Camptothecin Analogue NSC606985-Treated Acute Myeloid Leukemic Cells
Y. Yu, L.-S. Wang, S.-M. Shen, L. Xia, L. Zhang, Y.-S. Zhu, G.-Q. Chen
Journal of Proteome Research (2007) 6(9): 3808-3818
Protein Damage by Reactive Electrophiles: Targets and Consequences
Liebler DC.
Chem Res Toxicol (2008) 21(1): 117-28
Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis
Ashwin A. Dihal, Hester van der Woude, Peter J. M. Hendriksen, Halima Charif, Lennard J. Dekker, Linda IJsselstijn, Vincent C. J. de Boer, Gerrit M. Alink, Peter C. Burgers, Ivonne M. C. M. Rietjens, Ruud A. Woutersen, Rob H. Stierum
PROTEOMICS (2008) 8(1): 45-61
Diagnostic application of serum proteomic patterns in gastric cancer patients by ProteinChip surface-enhanced laser desorption/ionization time-of-flight mass spectrometry
Lim JY, Cho JY, Paik YH, Chang YS, Kim HG.
Int J Biol Markers (2007) 22(4): 281-6
Protein Expression Profiling of Breast Cancer Cells by Dissociable Antibody Microarray (DAMA) Staining
X. Cynthia Song, Guanyuan Fu, Xufen Yang, Zhong Jiang, Yingjian Wang, and G. Wayne Zhou
Mol Cell Proteomics (2008) 7(1): 163-169
Proteomic Profiling of Secreted Proteins from CHO Cells Using Surface-Enhanced Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Kumar N, Maurya P, Gammell P, Dowling P, Clynes M, Meleady P.
Biotechnol Prog Early Edition: published 29-Dec-2007
Experimental Approach for Assessing the Outcome Accuracy of Antibody Microarray Experiments
Q. Gu, T.M. Sivanandam, J. Haymore
Journal of Proteome Research (2007) 6(11): 4210-4217
Design of Recombinant Antibody Microarrays for Cell Surface Membrane Proteomics
Linda Dexlin, Johan Ingvarsson, Björn Frendéus, Carl A. K. Borrebaeck, and Christer Wingren
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 319-327
Serum proteome profiling of metastatic breast cancer using recombinant antibody microarrays
Carlsson A, Wingren C, Ingvarsson J, Ellmark P, Baldertorp B, Fernö M, Olsson H, Borrebaeck CA.
Eur J Cancer Early Edition: published 31-Dec-2007
Antibody microarray analysis of directly labelled complex proteomes
Wingren C, Borrebaeck CA.
Curr Opin Biotechnol Early Edition: published 8-Jan-2008
Development of a Highly Sensitive, High-Throughput, Mass Spectrometry-Based Assay for Rat Procollagen Type-I N-Terminal Propeptide (PINP) To Measure Bone Formation Activity
B. Han, M. Copeland, A.G. Geiser, L.V. Hale, A. Harvey, Y.L. Ma, C.S. Powers, M. Sato, J. You, J.E. Hale
Journal of Proteome Research (2007) 6(11): 4218-4229
Simultaneous Analysis of Circulating Human Cytokines Using a High-Sensitivity Cytokine Biochip Array
S. Pete FitzGerald, R. Ivan McConnell, and Allen Huxley
JOURNAL OF PROTEOME RESEARCH (2008) 7(01): 450-455
Design of Recombinant Antibody Microarrays for Serum Protein Profiling: Targeting of Complement Proteins
J. Ingvarsson, A. Larsson, A.G. Sjoholm, L. Truedsson, B. Jansson, C.A.K. Borrebaeck, C. Wingren
Journal of Proteome Research (2007) 6(9): 3527-3536
Detection and identification of plasma proteins that bind GlialCAM using ProteinChipTM Arrays, SELDI-TOF MS, and nano-LC MS/MS
Linda Favre-Kontula, Pascale Sattonnet-Roche, Edith Magnenat, Amanda E. I. Proudfoot, Ursula Boschert, Ioannis Xenarios, Francis Vilbois, Bruno Antonsson
PROTEOMICS (2008) 8(2): 378-388
Identification of Ubiquitin Target Proteins Using Cell-Based Arrays
T. Zhou, B. Liang, G.-Y. Su, W.-L. Gong, H.-Y. Li, L.-F. Tian, K. He, J. Zhao, J.-H. Man, T. Li, W.-H. Li, Z.-Y. Zhang, C.-H. Wang, A.-L. Li, H. Liu, X. Pan, P.-J. Zhang, B.-F. Jin, X.-M. Zhang
Journal of Proteome Research (2007) 6(11): 4397-4406
Proteome analysis of differentiating human myoblasts by dialysis-assisted two-dimensional gel electrophoresis (DAGE)
Florence Gonnet, Belaid Bouazza, Gaël Armel Millot, Simin Ziaei, Luis Garcia, Gillian S. Butler-Browne, Vincent Mouly, Jeanine Tortajada, Olivier Danos, Fédor Svinartchouk
PROTEOMICS (2008) 8(2): 264-278
Phosphoproteomic analysis of Leishmania donovani pro- and amastigote stages
Miguel A. Morales, Reiko Watanabe, Christine Laurent, Pascal Lenormand, Jean-Claude Rousselle, Abdelkader Namane, Gerald F. Späth
PROTEOMICS (2008) 8(2): 350-363
Glycomics of Proteoglycan Biosynthesis in Murine Embryonic Stem Cell Differentiation
A.V. Nairn, A. Kinoshita-Toyoda, H. Toyoda, J. Xie, K. Harris, S. Dalton, M. Kulik, J.M. Pierce, T. Toida, K.W. Moremen, R.J. Linhardt
Journal of Proteome Research (2007) 6(11): 4374-4387
Metal-Chelating Plastic MALDI (pMALDI) Chips for the Enhancement of Phosphorylated-Peptide/Protein Signals
A.J. Ibanez, A. Muck, A. Svatos
Journal of Proteome Research (2007) 6(9): 3842-3848
An optimized immunohistochemical method for detection of phosphorylated mitogen-activated protein kinases
Teraishi T, Miura K, Imaki J.
J Immunol Methods (2008) 330(1-2): 34-43
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M.
Genome Biol (2007) 8(11): R250
Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa)
Feng Tan, Guosheng Li, Brahmananda Reddy Chitteti, Zhaohua Peng
PROTEOMICS (2007) 7(24): 4511-4527
Post-Translational Modification of Crystallins in Vitreous Body from Experimental Autoimmune Uveitis of Rats
S.-C. Bahk, J.-U. Jang, C.-U. Choi, S.-H. Lee, Z.-Y. Park, J.-Y. Yang, J.-D. Kim, Y.-S. Yang, H.-T. Chung
Journal of Proteome Research (2007) 6(10): 3891-3898
Signal Transduction by Growth Factor Receptors: Signaling in an Instant
Dengjel J, Akimov V, Blagoev B, Andersen JS.
Cell Cycle (2007) 6(23): 2913-6
Electrostatic Repulsion Hydrophilic Interaction Chromatography for Isocratic Separation of Charged Solutes and Selective Isolation of Phosphopeptides
Andrew J. Alpert
ANALYTICAL CHEMISTRY (2008) 80(1): 62-76
Synthesis and Evaluation of Superparamagnetic Silica Particles for Extraction of Glycopeptides in the Microtiter Plate Format
Zou Z, Ibisate M, Zhou Y, Aebersold R, Xia Y, Zhang H.
Anal Chem Early Edition: published 16-Jan-2008
Characterization of Post-Translational Modifications of Histone H2B-Variants Isolated from Arabidopsis thaliana
E. Bergmuller, P.M. Gehrig, W. Gruissem
Journal of Proteome Research (2007) 6(9): 3655-3668
N{varepsilon}-Formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function
Wisniewski JR, Zougman A, Mann M.
Nucleic Acids Res Early Edition: published 1-Dec-2007
A New Approach for Mapping Sialylated N-Glycosites in Serum Proteomes
B. Ghesquiere, L. Buyl, H. Demol, J. VanDamme, A. Staes, E. Timmerman, J. Vandekerckhove, K. Gevaert
Journal of Proteome Research (2007) 6(11): 4304-4312
Proteomic Analysis of O-GlcNAc Modifications Derived from Streptozotocin and Glucosamine Induced beta-cell Apoptosis
Park J, Kwon H, Kang Y, Kim Y.
J Biochem Mol Biol (2007) 40(6): 1058-68
Shotgun Cross-Linking Analysis for Studying Quaternary and Tertiary Protein Structures
Y.J. Lee, L.L. Lackner, J.M. Nunnari, B.S. Phinney
Journal of Proteome Research (2007) 6(10): 3908-3917
De novo sequencing of a 21-kDa cytochrome c4 from Thiocapsa roseopersicina by nanoelectrospray ionization ion-trap and Fourier-transform ion-cyclotron resonance mass spectrometry
Rui Miguel Mamede Branca, Gabriella Bodó, Csaba Bagyinka, Laszlo Prokai
Journal of Mass Spectrometry (2007) 42(12): 1569-1582
Identification of Poly-ADP-Ribosylated Mitochondrial Proteins after Traumatic Brain Injury
Lai Y, Chen Y, Watkins SC, Nathaniel PD, Guo F, Kochanek PM, Jenkins LW, Szabó C, Clark RS.
J Neurochem Early Edition: published 6-Nov-2007
Preparation of Fe3O4@ZrO2 Core-Shell Microspheres as Affinity Probes for Selective Enrichment and Direct Determination of Phosphopeptides Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
Y. Li, T. Leng, H. Lin, C. Deng, X. Xu, N. Yao, P. Yang, X. Zhang
Journal of Proteome Research (2007) 6(11): 4498-4510
Phosphorylation-regulated cleavage of the reticulon protein Nogo-B by caspase-7 at a noncanonical recognition site
Rüdiger Schweigreiter, Taras Stasyk, Igea Contarini, Silke Frauscher, Thomas Oertle, Lars Klimaschewski, Lukas A. Huber, Christine E. Bandtlow
PROTEOMICS (2007) 7(24): 4457-4467
Chemical approaches to understanding O-GlcNAc glycosylation in the brain
Rexach JE, Clark PM, Hsieh-Wilson LC.
Nat Chem Biol (2008) 4(2): 97-106
Improved Titanium Dioxide Enrichment of Phosphopeptides from HeLa Cells and High Confident Phosphopeptide Identification by Cross-Validation of MS/MS and MS/MS/MS Spectra
L.-R. Yu, Z. Zhu, K.C. Chan, H.J. Issaq, D.S. Dimitrov, T.D. Veenstra
Journal of Proteome Research (2007) 6(11): 4150-4162
Rapid characterization of covalent modifications to rat brain mitochondrial proteins after ex vivo exposure to 4-hydroxy-2-nonenal by liquid chromatography-tandem mass spectrometry using data-dependent and neutral loss-driven MS3 acquisition
Stanley M. Stevens Jr, Navin Rauniyar, Laszlo Prokai
Journal of Mass Spectrometry (2007) 42(12): 1599-1605
Automated N-Glycopeptide Identification Using a Combination of Single- and Tandem-MS
D. Goldberg, M. Bern, S. Parry, M. Sutton-Smith, M. Panico, H.R. Morris, A. Dell
Journal of Proteome Research (2007) 6(10): 3995-4005
Post-Translational Modifications in the Nuclear Region of Young, Aged, and Cataract Human Lenses
P.G. Hains, R.J.W. Truscott
Journal of Proteome Research (2007) 6(10): 3935-3943
Identification of enzymes and regulatory proteins in Escherichia coli that are oxidized under nitrogen, carbon, or phosphate starvation
Noda Y, Berlett BS, Stadtman ER, Aponte A, Morgan M, Shen RF.
Proc Natl Acad Sci U S A (2007) 104(47): 18456-60
An Automated Platform for Analysis of Phosphoproteomic Datasets: Application to Kidney Collecting Duct Phosphoproteins
J.D. Hoffert, G. Wang, T. Pisitkun, R.-F. Shen, M.A. Knepper
Journal of Proteome Research (2007) 6(9): 3501-3508
On-Line LC-MS Approach Combining Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and CID of an Isolated Charge-Reduced Species for the Trace-Level Characterization of Proteins with Post-Translational Modifications
S.-L. Wu, A.F.R. Huhmer, Z. Hao, B.L. Karger
Journal of Proteome Research (2007) 6(11): 4230-4244
Applying a Targeted Label-Free Approach Using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition
F. Yang, N. Jaitly, H. Jayachandran, Q. Luo, M.E. Monroe, X. Du, M.A. Gritsenko, R. Zhang, D.J. Anderson, S.O. Purvine, J.N. Adkins, R.J. Moore, H.M. Mottaz, S.-J. Ding, M.S. Lipton, D.G. Camp, H.R. Udseth, R.D. Smith, S. Rossie
Journal of Proteome Research (2007) 6(11): 4489-4497
?Glyco-peakfinder? - de novo composition analysis of glycoconjugates
Kai Maass, René Ranzinger, Hildegard Geyer, Claus-Wilhelm von der Lieth, Rudolf Geyer
PROTEOMICS (2007) 7(24): 4435-4444
Mass spectrometry-based survey of age-associated protein carbonylation in rat brain mitochondria
Laszlo Prokai, Liang-Jun Yan, José L. Vera-Serrano, Stanley M. Stevens Jr, Michael J. Forster
Journal of Mass Spectrometry (2007) 42(12): 1583-1589
Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry
Mirza SP, Olivier M.
Physiol Genomics Early Edition: published 27-Dec-2007
Comparative RP-HPLC for rapid identification of glycopeptides and application in off-line LC-MALDI-MS analysis
Kanie Y, Enomoto A, Goto S, Kanie O.
Carbohydr Res Early Edition: published 23-Dec-2007
Glycoproteomic characterization of butyrylcholinesterase from human plasma
Daniel Kolarich, Alfred Weber, Martin Pabst, Johannes Stadlmann, Wolfgang Teschner, Hartmut Ehrlich, Hans-Peter Schwarz, Friedrich Altmann
PROTEOMICS (2008) 8(2): 254-263
Cyanogen Bromide Peptides of the Fibrillar Collagens I, III, and V and Their Mass Spectrometric Characterization: Detection of Linear Peptides, Peptide Glycosylation, and Cross-Linking Peptides Involved in Formation of Homo- and Heterotypic Fibrils
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Large-Scale Identification and Evolution Indexing of Tyrosine Phosphorylation Sites from Murine Brain
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Proteomic Studies of PP2A-B56γ1 Phosphatase Complexes Reveal Phosphorylation-Regulated Partners in Cardiac Local Signaling
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Peptide Sequencing and Characterization of Post-Translational Modifications by Enhanced Ion-Charging and Liquid Chromatography Electron-Transfer Dissociation Tandem Mass Spectrometry
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Protein partners in the life history of activated fibroblast growth factor receptors
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Interactive Three-Dimensional Visualization and Contextual Analysis of Protein Interaction Networks
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The in Vivo Brain Interactome of the Amyloid Precursor Protein
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Statistically Inferring Protein-Protein Associations with Affinity Isolation LC-MS/MS Assays
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A phage display system designed to detect and study protein-protein interactions
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Mol Microbiol Early Edition: published 2-Jan-2008
Interaction proteome analysis of Xanthomonas Hrp proteins
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J Microbiol Biotechnol (2007) 17(2): 359-63
The molecular architecture of the nuclear pore complex
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Nature (2007) 450(7170): 695-701
Determining the architectures of macromolecular assemblies
Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A.
Nature (2007) 450(7170): 683-94
Secretome analysis of novel IgE-binding proteins from Penicillium citrinum
Li-Li Chiu, Kuang-Lun Lee, Yu-Fen Lin, Chi