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SPS' DigestIssue 57, 12-Dec-2008 |
A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry
Melanie Osl, Stephan Dreiseitl, Bernhard Pfeifer, Klaus Weinberger, Helmut Klocker, Georg Bartsch, Georg Schafer, Bernhard Tilg, Armin Graber, and Christian Baumgartner
Bioinformatics (2008) 24(24): 2908-2914
Physical protein-protein interactions predicted from microarrays
Ta-tsen Soong, Kazimierz O. Wrzeszczynski, and Burkhard Rost
Bioinformatics (2008) 24(22): 2608-2614
Protein Expression Profile of the Mouse Metaphase-II Oocyte
Minyue Ma, Xuejiang Guo, Fuqiang Wang, Chun Zhao, Zichuan Liu, Zhonghua Shi, Yufeng Wang, Ping Zhang, Kemei Zhang, Ningling Wang, Min Lin, Zuomin Zhou, Jiayin Liu, Qingzhang Li, Liu Wang, Ran Huo, Jiahao Sha, and Qi Zhou
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4821-4830
High Quality Catalog of Proteotypic Peptides from Human Heart
Kelli G. Kline, Barbara Frewen, Michael R. Bristow, Michael J. MacCoss, and Christine C. Wu
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5055-5061
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
Simon Rogers, Mark Girolami, Walter Kolch, Katrina M. Waters, Tao Liu, Brian Thrall, and H. Steven Wiley
Bioinformatics (2008) 24(24): 2894-2900
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry
Dihui Lu, Richard Z. Liu, Victoria Izumi, David Fenstermacher, Eric B. Haura, John Koomen, and Steven A. Eschrich
Bioinformatics (2008) 24(23): 2801-2802
A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications
Jayson A. Falkner, Jarret W. Falkner, Anastasia K. Yocum, and Philip C. Andrews
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4614-4622
ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics
Benjamin Mann, Milan Madera, Quanhu Sheng, Haixu Tang, Yehia Mechref, Milos V. Novotny
Rapid Communications in Mass Spectrometry (2008) 22(23): 3823-3834
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis
Daehee Hwang, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, and Ruedi Aebersold
Bioinformatics (2008) 24(22): 2641-2642
DOCKGROUND protein-protein docking decoy set
Shiyong Liu, Ying Gao, and Ilya A. Vakser
Bioinformatics (2008) 24(22): 2634-2635
Improving classification performance with discretization on biomedical datasets
Lustgarten JL, Gopalakrishnan V, Grover H, Visweswaran S.
AMIA Annu Symp Proc (2008) : 445-9.
Peptizer, a Tool for Assessing False Positive Peptide Identifications and
Manually Validating Selected Results
Mol Cell Proteomics (2008) 7(12): 2364-2372
Using a novel resource to decrease proteomic biomarker identification time
Lustgarten JL, Visweswaran S, Grover H, Kimmel CP, Ryberg HL, Bowser RP, Gopalakrishnan V, Hogan W.
AMIA Annu Symp Proc (2008) : 1033.
VirHostNet: a knowledge base for the management and the analysis of virus-host interaction networks
Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, Andre P, Lotteau V, Rabourdin-Combe C
Nucl Acids Res Early Edition: published 2008 Nov 4
Adaptive Discriminant Function Analysis and Reranking of MS/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics
Ying Ding, Hyungwon Choi, and Alexey I. Nesvizhskii
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4878-4889
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
Alves G, Ogurtsov AY, Yu YK.
BMC Genomics (2008) 9(1): 505
Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS Instruments
Aleksey V. Tolmachev, Matthew E. Monroe, Samuel O. Purvine, Ronald J. Moore, Navdeep Jaitly, Joshua N. Adkins, Gordon A. Anderson, and Richard D. Smith
ANALYTICAL CHEMISTRY (2008) 80(22): 8514-8525
The Impact of Peptide Abundance and Dynamic Range on Stable-Isotope-Based Quantitative Proteomic Analyses
Corey E. Bakalarski, Joshua E. Elias, Judit Villén, Wilhelm Haas, Scott A. Gerber, Patrick A. Everley, and Steven P. Gygi
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4756-4765
A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry
Quanhu Sheng, Yehia Mechref, Yixue Li, Milos V. Novotny, Haixu Tang
Rapid Communications in Mass Spectrometry (2008) 22(22): 3561-3569
A toolkit for capturing and sharing FuGE experiments
Khalid Belhajjame, Andrew R. Jones, and Norman W. Paton
Bioinformatics (2008) 24(22): 2647-2649
An in silico method for detecting overlapping functional modules from biological networks
Maraziotis IA, Dimitrakopoulou K, Bezerianos A
BMC Syst Biol (2008) 2(1): 93
G2Cdb: the Genes to Cognition database
Croning MD, Marshall MC, McLaren P, Armstrong JD, Grant SG
Nucl Acids Res Early Edition: published 2008 Nov 4
GOSLING: a rule-based protein annotator using BLAST and GO
Craig E. Jones, Julian Schwerdt, Tessa Arwen Bretag, Ute Baumann, and Alfred L. Brown
Bioinformatics (2008) 24(22): 2628-2629
MSX-3D: a tool to validate 3D protein models using mass spectrometry
Michael Heymann, David Paramelle, Gilles Subra, Eric Forest, Jean Martinez, Christophe Geourjon, and Gilbert Deleage
Bioinformatics (2008) 24(23): 2782-2783
Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors
Sheila J. Barton, John C. Whittaker
Mass Spectrometry Reviews (2009) 28(1): 177-187
Proteomics researchers now agree on some aspects of data sharing
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4612-4612
The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches
Eizadora T. Yu, Arie Hawkins, Irwin D. Kuntz, Larry A. Rahn, Andrew Rothfuss, Kenneth Sale, Malin M. Young, Christine L. Yang, Carmen M. Pancerella, and Daniele Fabris
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4848-4857
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions
Seesandra V. Rajagopala, Johannes Goll, N.D. Deve Gowda, Kumar C. Sunil, Bjorn Titz, Arnab Mukherjee, Sharmila S. Mary, Naresh Raviswaran, Chetan S. Poojari, Srinivas Ramachandra, Svetlana Shtivelband, Stephen M. Blazie, Julia Hofmann, and Peter Uetz
Bioinformatics (2008) 24(22): 2622-2627
Comparative Proteomic Analysis Provides New Insights into the Fiber Elongating Process in Cotton
Yi-Wei Yang, Shao-Min Bian, Yuan Yao, and Jin-Yuan Liu
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4623-4637
Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome
Gu J, Hilser VJ.
Structure (2008) 16(11): 1627-37
Sys-BodyFluid: a systematical database for human body fluid proteome research
Li SJ, Peng M, Li H, Liu BS, Wang C, Wu JR, Li YX, Zeng R
Nucl Acids Res Early Edition: published 2008 Oct 31
Human Protein Reference Database--2009 update
Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A
Nucl Acids Res Early Edition: published 2008 Nov 6
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
Hakan Viklund, Andreas Bernsel, Marcin Skwark, and Arne Elofsson
Bioinformatics (2008) 24(24): 2928-2929
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
Elmer A. Ferna;ndez, Maria R. Girotti, Juan A. Lopez del Olmo, Andrea S. Llera, Osvaldo L. Podhajcer, Rodolfo J. C. Cantet, and Monica Balzarini
Bioinformatics (2008) 24(23): 2706-2712
Laboratory information management system for membrane protein structure initiative - from gene to crystal
Troshin PV, Morris C, Prince SM, Papiz MZ.
Mol Membr Biol (2008) 25(8): 639-52
ExDom: an integrated database for comparative analysis of the structures of protein domains in eukaryotes
Bhasi A, Philip P, Manikandan V, Senapathy P
Nucl Acids Res Early Edition: published 2008 Nov 4
A data-mining approach to biomarker identification from protein profiles discrete stationary wavelet transform
Montazery-Kordy H, Miran-Baygi MH, Moradi MH
J Zhejiang Univ Sci B (2008) 9(11): 863-70
MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments
Daniel B. Martin, Ted Holzman, Damon May, Amelia Peterson, Ashley Eastham, Jimmy Eng, and Martin McIntosh
Mol Cell Proteomics (2008) 7(11): 2270-2278
TESE: generating specific protein structure test set ensembles
Francesco Sirocco and Silvio C. E. Tosatto
Bioinformatics (2008) 24(22): 2632-2633
Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems
Gabriele Cavallaro, Leonardo Decaria, and Antonio Rosato
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4946-4954
Prediction of kinase-specific phosphorylation sites using conditional random fields
Thanh Hai Dang, Koenraad Van Leemput, Alain Verschoren, and Kris Laukens
Bioinformatics (2008) 24(24): 2857-2864
mspire: mass spectrometry proteomics in Ruby
John T. Prince and Edward M. Marcotte
Bioinformatics (2008) 24(23): 2796-2797
Quantitative Proteome-Property Relationships (QPPRs). Part 1: Finding biomarkers of organic drugs with mean Markov connectivity indices of spiral networks of blood mass spectra
Cruz-Monteagudo M, Munteanu CR, Borges F, Cordeiro MN, Uriarte E, González-DÃaz H.
Bioorg Med Chem (2008) 16(22): 9684-93
NOPdb: Nucleolar Proteome Database--2008 update
Ahmad Y, Boisvert FM, Gregor P, Cobley A, Lamond AI
Nucl Acids Res Early Edition: published 2008 Nov 4
The Rate of False Positive Sequence Matches of Peptides Profiled by MALDI MS and Identified by MS/MS
Marcel P. Stoop, Robert-Jan A. N. Lamers, Peter C. Burgers, Peter A. E. Sillevis Smitt, Rogier Q. Hintzen, and Theo M. Luider
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4841-4847
Annotating proteins with generalized functional linkages
Llewellyn R, Eisenberg DS.
Proc Natl Acad Sci U S A Early Edition: published 12-Nov-2008
Impact of rpoS Deletion on the Proteome of Escherichia coli Grown Planktonically and as Biofilm
Anthony Collet, Pascal Cosette, Christophe Beloin, Jean-Marc Ghigo, Christophe Rihouey, Patrice Lerouge, Guy-Alain Junter, and Thierry Jouenne
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4659-4669
Methylene blue-mediated photodynamic therapy induces apoptosis in HeLa cell
Lu Y, Jiao R, Chen X, Zhong J, Ji J, Shen P
J Cell Biochem (2008) 105(6): 1451-60
Proteomic Analysis of Oxidative Stress-Responsive Proteins in Human Pneumocytes: Insight into the Regulation of DJ-1 Expression
Xunbao Duan, Steven G. Kelsen, and Salim Merali
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4955-4961
Comparative Proteomics Study Reveals That Bacterial CpG Motifs Induce Tumor
Cell Autophagy in Vitro and in Vivo
Mol Cell Proteomics (2008) 7(12): 2311-2322
Proteomics Identification of Nuclear Ran GTPase as an Inhibitor of Human VRK1 and VRK2 (Vaccinia-related Kinase) Activities
Marta Sanz-Garcia, Inmaculada Lopez-Sanchez, and Pedro A. Lazo
Mol Cell Proteomics (2008) 7(11): 2199-2214
Proteomic map of Trypanosoma cruzi CL Brener: the reference strain of the genome project
Sodré CL, Chapeaurouge AD, Kalume DE, de Mendonça Lima L, Perales J, Fernandes O.
Arch Microbiol Early Edition: published 11-Nov-2008
Lamin A Ser404 Is a Nuclear Target of Akt Phosphorylation in C2C12 Cells
Vittoria Cenni, Jessika Bertacchini, Francesca Beretti, Giovanna Lattanzi, Alberto Bavelloni, Massimo Riccio, Maria Ruzzene, Oriano Marin, Giorgio Arrigoni, Veena Parnaik, Manfred Wehnert, Nadir M. Maraldi, Anto de Pol, Lucio Cocco, and Sandra Marmiroli
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4727-4735
Rapid characterization of binding specificity and cross-reactivity of antibodies using recombinant human protein arrays
Kijanka G, Ipcho S, Baars S, Chen H, Hadley K, Beveridge A, Gould E, Murphy D.
J Immunol Methods Early Edition: published 6-Nov-2008
Establishing substantial equivalence: proteomics
Lovegrove A, Salt L, Shewry PR.
Methods Mol Biol (2009) 478: 273-88
Body Cooling Causes Normalization of Cardiac Protein Expression and Function in a Rat Heatstroke Model
Bor-Chih Cheng, Ching-Ping Chang, Yeou-Guang Tsay, Ting-Feng Wu, Chiung-Yueh Hsu, and Mao-Tsun Lin
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4935-4945
Root proteomic responses to heat stress in two Agrostis grass species contrasting in heat tolerance
Xu C, Huang B.
J Exp Bot (2008) 59(15): 4183-94
Ankylosing spondylitis monocytes show upregulation of proteins involved in inflammation and the Ubiquitin Proteasome pathway
Wright CA, Edelmann M, Digleria K, Kollnberger S, Kramer H, McGowan S, McHugh K, Taylor S, Kessler BM, Bowness P.
Ann Rheum Dis Early Edition: published 24-Oct-2008
Toponomics Analysis of Functional Interactions of the Ubiquitin Ligase PAM
(Protein Associated with Myc) during Spinal Nociceptive Processing
Mol Cell Proteomics (2008) 7(12): 2475-2485
The Viral Inhibitor of Apoptosis vFLIP/K13 Protects Endothelial Cells Superoxide-induced Cell Death
Thurau M, Marquardt G, Gonin-Laurent N, Weinlander K, Naschberger E, Jochmann R, Alkharsah KR, Schulz TF, Thome M, Neipel F, Sturzl M
J Virol Early Edition: published 2008 Nov 5
Revealing the Dynamics of the 20 S Proteasome Phosphoproteome: A Combined CID and Electron Transfer Dissociation Approach
Haojie Lu, Chenggong Zong, Yueju Wang, Glen W. Young, Ning Deng, Pete Souda, Xiaohai Li, Julian Whitelegge, Oliver Drews, Peng-Yuan Yang, and Peipei Ping
Mol Cell Proteomics (2008) 7(11): 2073-2089
Functions of defense-related proteins and dehydrogenases in resistance response induced by salicylic acid in sweet cherry fruits at different maturity stages
Zhulong Chan, Qing Wang, Xiangbin Xu, Xianghong Meng, Guozheng Qin, Boqiang Li, Shiping Tian
PROTEOMICS (2008) 8(22): 4791-4807
A proteomic analysis of the aphid Macrosiphum euphorbiae under heat and radiation stress
Nguyen TT, Michaud D, Cloutier C.
Insect Biochem Mol Biol Early Edition: published 1-Nov-2008
Shotgun Proteomics of the Haloarchaeon Haloferax volcanii
P. Aaron Kirkland, Matthew A. Humbard, Charles J. Daniels, and Julie A. Maupin-Furlow
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5033-5039
Proteome Analysis of Potato under Salt Stress
Keyvan Aghaei, Ali Akbar Ehsanpour, and Setsuko Komatsu
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4858-4868
Proteomic Analysis of the Hyaloid Vascular System Regression during Ocular Development
Elena Albè, Jin-Hong Chang, Nathalie F. Azar, Alexander R. Ivanov, and Dimitri T. Azar
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4904-4913
Proteomic analysis of somatic embryogenesis in Valencia sweet orange sinensis Osbeck)
Pan Z, Guan R, Zhu S, Deng X
Plant Cell Rep Early Edition: published 2008 Nov 7
Global Topology Analysis of Pancreatic Zymogen Granule Membrane Proteins
Xuequn Chen, Peter J. Ulintz, Eric S. Simon, John A. Williams, and Philip
Mol Cell Proteomics (2008) 7(12): 2323-2336
Abnormal Expression of TIMP-2, SOD, Vimentin and PAI Proteins in Cloned Bovine Placentae
Kim HR, Naruse K, Lee HR, Han RX, Park CS, Jin DI.
Reprod Domest Anim Early Edition: published 22-Oct-2008
Proteomic Analysis of Left Ventricular Remodeling in an Experimental Model of Heart Failure
Caroline Cieniewski-Bernard, Paul Mulder, Jean-Paul Henry, Hervé Drobecq, Emilie Dubois, Gwënaël Pottiez, Christian Thuillez, Philippe Amouyel, Vincent Richard, and Florence Pinet
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5004-5016
Identification of the proteome of the midgut of silkworm, Bombyx mori L. by multidimensional liquid chromatography LTQ-Orbitrap mass spectrometry
Yao HP, Xiang XW, Chen L, Guo AQ, He FQ, Lan LP, Lu XM, Wu XF.
Biosci Rep Early Edition: published 14-Nov-2008
Distinction between Human Cytochrome P450 (CYP) Isoforms and Identification of New Phosphorylation Sites by Mass Spectrometry
Gorden Redlich, Ulrich M. Zanger, Stephan Riedmaier, Nicolai Bache, Anders B. M. Giessing, Martin Eisenacher, Christian Stephan, Helmut E. Meyer, Ole N. Jensen, and Katrin Marcus
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4678-4688
Translational responses of NR2B overexpression in the cerebral cortex of transgenic mice: A liquid chromatography-based proteomic approach
Gu F, Wen Y, Fan H, Hu J, Hu Y, Zhao Z.
Brain Res Early Edition: published 30-Oct-2008
Profiling the Phospho-status of the BKCa Channel {alpha} Subunit in Rat Brain Reveals Unexpected Patterns and Complexity
Jiusheng Yan, Jesper V. Olsen, Kang-Sik Park, Weiyan Li, Wolfgang Bildl, Uwe Schulte, Richard W. Aldrich, Bernd Fakler, and James S. Trimmer
Mol Cell Proteomics (2008) 7(11): 2188-2198
Alteration of S-nitrosothiol homeostasis and targets for protein S-nitrosation in human hepatocytes
Laura M. López-Sánchez, Fernando J. Corrales, Raúl González, Gustavo Ferrín, Juan R. Muñoz-Castañeda, Isidora Ranchal, Ana B. Hidalgo, Javier Briceño, Pedro López-Cillero, Miguel A. Gómez, Manuel De La Mata, Jordi Muntané, Antonio Rodríguez-Ariza
PROTEOMICS (2008) 8(22): 4709-4720
Enhanced Capacity of Antigen Presentation of HBc-VLP-Pulsed RAW264.7 Cells Revealed by Proteomics Analysis
Fu Yang, Fang Wang, Yingjun Guo, Qi Zhou, Yue Wang, Yixuan Yin, and Shuhan Sun
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4898-4903
Integration of the barley genetic and seed proteome maps for chromosome 1H, 2H, 3H, 5H and 7H
Finnie C, Bagge M, Steenholdt T, Ostergaard O, Bak-Jensen KS, Backes G, Jensen A, Giese H, Larsen J, Roepstorff P, Svensson B.
Funct Integr Genomics Early Edition: published 14-Nov-2008
Proteomic Comparison between Two Marine Snail Ecotypes Reveals Details about the Biochemistry of Adaptation
Mónica Martínez-Fernández, Ana M. Rodríguez-Piñeiro, Eliandre Oliveira, María Páez de la Cadena, and Emilio Rolán-Alvarez
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4926-4934
A Fluorescent Two-hybrid Assay for Direct Visualization of Protein Interactions in Living Cells
Kourosh Zolghadr, Oliver Mortusewicz, Ulrich Rothbauer, Regina Kleinhans, Heike Goehler, Erich E. Wanker, M. Cristina Cardoso, and Heinrich Leonhardt
Mol Cell Proteomics (2008) 7(11): 2279-2287
Riboproteomic analysis of polypeptides interacting with the internal ribosome-entry site element of foot-and-mouth disease viral RNA
Almudena Pacheco, Sandrine Reigadas, Encarnación Martínez-Salas
PROTEOMICS (2008) 8(22): 4782-4790
Proteomic analysis of the porcine platelet proteome and alterations induced by thrombin activation
Gloria Esteso, MarÃa Isabel Mora, Juan José Garrido, Fernando Corrales and Ãngela Moreno
Journal of Proteomics (2008) 71(5): 547-560
The Proteomic Response of Saccharomyces cerevisiae in Very High Glucose Conditions with Amino Acid Supplementation
Trong Khoa Pham and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4766-4774
PTP? has a critical role in signaling transduction pathways and phosphoprotein network topology in red cells
Lucia De Franceschi, Andrea Biondani, Franco Carta, Franco Turrini, Carlo Laudanna, Renzo Deana, Anna Maria Brunati, Loris Turretta, Achille Iolascon, Silverio Perrotta, Ari Elson, Cristina Bulato, Carlo Brugnara
PROTEOMICS (2008) 8(22): 4695-4708
A Proteomics Analysis of Yeast Mot1p Protein-Protein Associations: Insights into Mechanism
Diana R. Arnett, Jennifer L. Jennings, David L. Tabb, Andrew J. Link, and P. Anthony Weil
Mol Cell Proteomics (2008) 7(11): 2090-2106
Proteomics Analysis Identifies Phosphorylation-dependent {alpha}-Synuclein Protein Interactions
Melinda A. McFarland, Christopher E. Ellis, Sanford P. Markey, and Robert L. Nussbaum
Mol Cell Proteomics (2008) 7(11): 2123-2137
Functional genes and proteins of Trichinella spp
Nagano I, Wu Z, Takahashi Y
Parasitol Res Early Edition: published 2008 Nov 6
Discovery, Identification, and Characterization of Candidate Pharmacodynamic Markers of Methionine Aminopeptidase-2 Inhibition
Scott E. Warder, Lora A. Tucker, Shaun M. McLoughlin, Tamara J. Strelitzer, Joseph L. Meuth, Qian Zhang, George S. Sheppard, Paul L. Richardson, Rick Lesniewski, Steven K. Davidsen, Randy L. Bell, John C. Rogers, and Jieyi Wang
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4807-4820
Fish Authentication by MALDI-TOF Mass Spectrometry
Mazzeo MF, Giulio BD, Guerriero G, Ciarcia G, Malorni A, Russo GL, Siciliano RA.
J Agric Food Chem Early Edition: published 14-Nov-2008
Protein complex analysis of native brain potassium channels by proteomics
Sandoz G, Lesage F.
Methods Mol Biol (2009) 491: 113-23
Proteome analysis of Legionella vacuoles purified by magnetic reveals secretory and endosomal GTPases
Urwyler S, Nyfeler Y, Ragaz C, Lee H, Muller L, Aebersold R, Hilbi H
Traffic Early Edition: published 2008 Oct 29
Proteomic changes during intestinal cell maturation in vivo
Jinsook Chang, Mark R. Chance, Courtney Nicholas, Naseem Ahmed, Sandra Guilmeau, Marta Flandez, Donghai Wang, Do-Sun Byun, Shannon Nasser, Joseph M. Albanese, Georgia A. Corner, Barbara G. Heerdt, Andrew J. Wilson, Leonard H. Augenlicht and John M. Mariadason
Journal of Proteomics (2008) 71(5): 530-546
Ordered Organelle Degradation during Starvation-induced Autophagy
Anders Riis Kristensen, Soren Schandorff, Maria Hoyer-Hansen, Maria
Mol Cell Proteomics (2008) 7(12): 2419-2428
Complementary methods to assist subcellular fractionation in organellar proteomics
Daniel J Gauthier and Claude Lazure
Expert Review of Proteomics (2008) 5(4): 603-617
Proteomic studies in biomedically and industrially relevant fungi
Carberry S, Doyle S.
Cytotechnology (2007) 53(1-3): 95-100
Proteomics study of the hepatitis C virus replication complex
Chang K, Wang T, Luo G.
Methods Mol Biol (2009) 510: 185-93
Using enrichment index for quality control of secretory protein sample and identification of secretory proteins
Chen Y, Gu B, Wu S, Sun W, Ma S, Liu Y, Gao Y.
J Mass Spectrom Early Edition: published 10-Nov-2008
Lamellar Bodies of Human Epidermis: Proteomics Characterization by High Throughput Mass Spectrometry and Possible Involvement of CLIP-170 in their Trafficking/Secretion
Anne-Aurelie Raymond, Anne Gonzalez de Peredo, Alexandre Stella, Akemi Ishida-Yamamoto, David Bouyssie, Guy Serre, Bernard Monsarrat, and Michel Simon
Mol Cell Proteomics (2008) 7(11): 2151-2175
Proteins modulation in human skeletal muscle in the early phase of adaptation to hypobaric hypoxia
Agnese Viganò, Marilena Ripamonti, Sara De Palma, Daniele Capitanio, Michele Vasso, Robin Wait, Carsten Lundby, Paolo Cerretelli, Cecilia Gelfi
PROTEOMICS (2008) 8(22): 4668-4679
Biochemical characterization of membrane fractions in murine sperm: Identification of three distinct sub-types of membrane rafts
Asano A, Selvaraj V, Buttke DE, Nelson JL, Green KM, Evans JE, Travis AJ.
J Cell Physiol Early Edition: published 12-Nov-2008
Molecular targets of TBBPA in zebrafish analysed through integration of and proteomic approaches
De Wit M, Keil D, Remmerie N, van der Ven K, van den Brandhof EJ, Knapen D, Witters E, De Coen W
Chemosphere (2008) 74(1): 96-105
Identification of Structural and Functional O-Linked N-Acetylglucosamine-bearing Proteins in Xenopus laevis Oocyte
Vanessa Dehennaut, Marie-Christine Slomianny, Adeline Page, Anne-Sophie Vercoutter-Edouart, Catherine Jessus, Jean-Claude Michalski, Jean-Pierre Vilain, Jean-Francois Bodart, and Tony Lefebvre
Mol Cell Proteomics (2008) 7(11): 2229-2245
A comparative proteomic analysis for capsaicin-induced apoptosis between human hepatocarcinoma (HepG2) and human neuroblastoma (SK-N-SH) cells
Yu Mi Baek, Hye Jin Hwang, Sang Woo Kim, Hee Sun Hwang, Sung Hak Lee, Jung Ae Kim, Jong Won Yun
PROTEOMICS (2008) 8(22): 4748-4767
The Ubiquitin-Proteasome System Is a Key Component of the SUMO-2/3 Cycle
Joost Schimmel, Katja M. Larsen, Ivan Matic, Martijn van Hagen, Jurgen Cox, Matthias Mann, Jens S. Andersen, and Alfred C. O. Vertegaal
Mol Cell Proteomics (2008) 7(11): 2107-2122
Characterization of the Human COP9 Signalosome Complex Using Affinity Purification and Mass Spectrometry
Lei Fang, Xiaorong Wang, Kosj Yamoah, Phang-lang Chen, Zhen-Qiang Pan, and Lan Huang
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4914-4925
Immune-related proteins induced in the hemolymph after aseptic and differ in honey bee worker larvae and adults
Randolt K, Gimple O, Geissendorfer J, Reinders J, Prusko C, Mueller MJ, Albert S, Tautz J, Beier H
Arch Insect Biochem Physiol (2008) 69(4): 155-67
Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer
Guoan Zhang, David Fenyö, and Thomas A. Neubert
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4715-4726
Comparative Phosphoproteomics of Zebrafish Fyn/Yes Morpholino Knockdown Embryos
Simone Lemeer, Chris Jopling, Joost Gouw, Shabaz Mohammed, Albert J. R. Heck, Monique Slijper, and Jeroen den Hertog
Mol Cell Proteomics (2008) 7(11): 2176-2187
Subnuclear compartmentalization and function of actin and nuclear Myosin plants
Cruz JR, Moreno Diaz de la Espina S
Chromosoma Early Edition: published 2008 Nov 4
An insight into the salivary transcriptome and proteome of the soft tick and vector of epizootic bovine abortion, Ornithodoros coriaceus☆
Ivo M.B. Francischetti, Zhaojing Meng, Ben J. Mans, Nanda Gudderra, Mark Hall, Timothy D. Veenstra, Van M. Pham, Michail Kotsyfakis and José M.C. Ribeiro
Journal of Proteomics (2008) 71(5): 493-512
Lessons learned from lipid raft proteomics
Leonard J Foster
Expert Review of Proteomics (2008) 5(4): 541-543
Interaction proteomics of the HMGA chromatin architectural factors
Riccardo Sgarra, Cristina Furlan, Salvina Zammitti, Alessandra Lo Sardo, Elisa Maurizio, Julie Di Bernardo, Vincenzo Giancotti, Guidalberto Manfioletti
PROTEOMICS (2008) 8(22): 4721-4732
Expression of differential antennal proteins in males and females of an crop pest, Sesamia nonagrioides
Acin P, Carrascal M, Abian J, Guerrero A, Quero C
Insect Biochem Mol Biol Early Edition: published 2008 Oct 14
Proteomic analysis of protein deposits on worn daily wear silicone contact lenses
Zhao Z, Wei X, Aliwarga Y, Carnt NA, Garrett Q, Willcox MD
Mol Vis (2008) 14: 2016-24
Analysis of the human testis proteome by mass spectrometry and bioinformatics
Xuejiang Guo, Ping Zhang, Ran Huo, Zuomin Zhou, Jiahao Sha
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1651-1657
Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines
Weiwei Wang, Bo Meng, Xiaomeng Ge, Shuhui Song, Yue Yang, Xiaomin Yu, Liguo Wang, Songnian Hu, Siqi Liu, Jun Yu
PROTEOMICS (2008) 8(22): 4808-4821
Estrogen Regulation of Proteins in the Rat Ventromedial Nucleus of the Hypothalamus
Bing Mo, Eduardo Callegari, Martin Telefont, and Kenneth J. Renner
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5040-5048
Targeted Peptidecentric Proteomics Reveals Caspase-7 as a Substrate of the
Caspase-1 Inflammasomes
Mol Cell Proteomics (2008) 7(12): 2350-2363
High Quality Catalog of Proteotypic Peptides from Human Heart
Kelli G. Kline, Barbara Frewen, Michael R. Bristow, Michael J. MacCoss, and Christine C. Wu
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5055-5061
Influence of clotting time on the protein composition of serum samples based on LC-MS data
Govorukhina NI, de Vries M, Reijmers TH, Horvatovich P, van der Zee AG, Bischoff R.
J Chromatogr B Early Edition: published 1-Nov-2008
Proteins modulation in human skeletal muscle in the early phase of adaptation to hypobaric hypoxia
Agnese Viganò, Marilena Ripamonti, Sara De Palma, Daniele Capitanio, Michele Vasso, Robin Wait, Carsten Lundby, Paolo Cerretelli, Cecilia Gelfi
PROTEOMICS (2008) 8(22): 4668-4679
The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile
Kon OL, Yip TT, Ho MF, Chan WH, Wong WK, Tan SY, Ng WH, Kam SY, Eng AK, Ho P, Viner R, Ong HS, Kumarasinghe MP.
BMC Med Genomics (2008) 1(1): 54
Mass spectrometry for structural characterization of therapeutic antibodies
Zhongqi Zhang, Hai Pan, Xiaoyu Chen
Mass Spectrometry Reviews (2009) 28(1): 147-176
Proteomic analysis of conditioned media from glucose responsive and glucose non-responsive phenotypes reveals a panel of secreted proteins associated with beta cell dysfunction
Paul Dowling, William Shields, Sweta Rani, Paula Meleady, Michael Henry, Per Jeppesen, Lorraine O'Driscoll, Martin Clynes
ELECTROPHORESIS (2008) 29(20): 4141-4149
Enhanced Capacity of Antigen Presentation of HBc-VLP-Pulsed RAW264.7 Cells Revealed by Proteomics Analysis
Fu Yang, Fang Wang, Yingjun Guo, Qi Zhou, Yue Wang, Yixuan Yin, and Shuhan Sun
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4898-4903
Brief Alteration of NMDA or GABAA Receptor-mediated Neurotransmission Has
Long Term Effects on the Developing Cerebral Cortex
Mol Cell Proteomics (2008) 7(12): 2293-2310
Current status and future prospects in the search for protein biomarkers of immunosenescence
Steve Wilson and Dawn J Mazzatti
Expert Review of Proteomics (2008) 5(4): 561-569
A data-mining approach to biomarker identification from protein profiles discrete stationary wavelet transform
Montazery-Kordy H, Miran-Baygi MH, Moradi MH
J Zhejiang Univ Sci B (2008) 9(11): 863-70
A recombinant chimeric antigen toward a standardized serodiagnosis of Taenia solium neurocysticercosis
Young-An Bae, Yeon-Tack Jeong, Joon-Yong Chung, Seon-Hee Kim, Jagadish Mahanta, Zheng Feng, Chom-Kyu Chong, Tong-Soo Kim, Yoon Kong
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1596-1610
New Guidelines for Clinical Proteomics Manuscripts
Julio E. Celis, Steven A. Carr, and Ralph A. Bradshaw
Mol Cell Proteomics (2008) 7(11): 2071-2072
Proteomic profiling of urine identifies specific fragments of SERPINA1 albumin as biomarkers of preeclampsia
Buhimschi IA, Zhao G, Funai EF, Harris N, Sasson IE, Bernstein IM, Saade GR, Buhimschi CS
Am J Obstet Gynecol (2008) 199(5): 551.e1-16
Quantitative Proteome-Property Relationships (QPPRs). Part 1: Finding biomarkers of organic drugs with mean Markov connectivity indices of spiral networks of blood mass spectra
Cruz-Monteagudo M, Munteanu CR, Borges F, Cordeiro MN, Uriarte E, González-DÃaz H.
Bioorg Med Chem (2008) 16(22): 9684-93
Chitinase 3-Like-1 (CHI3L1): a putative disease marker at the interface of proteomics and glycomics
Coffman FD.
Crit Rev Clin Lab Sci (2008) 45(6): 531-62
Aldehyde dehydrogenase 1A1 and gelsolin identified as novel invasion-modulating factors in conditioned medium of pancreatic cancer cells
Naomi Walsh, Paul Dowling, Norma O'Donovan, Michael Henry, Paula Meleady and Martin Clynes
Journal of Proteomics (2008) 71(5): 561-571
Proteomics blood testing to distinguish chronic rhinosinusitis subtypes
Das S, Maeso PA, Becker AM, Prosser JD, Adam BL, Kountakis SE
Laryngoscope (2008) 118(12): 2231-4
Mass spectrometry analysis of the influenza virus
Kevin M. Downard, Bethny Morrissey, Alexander B. Schwahn
Mass Spectrometry Reviews (2009) 28(1): 35-49
Application of proteomic techniques to the study of urine and renal tissue
Annalisa Vilasi, Pedro R. Cutillas, Robert J. Unwin
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1564-1574
Advances in ovarian cancer proteomics: the quest for biomarkers and improved therapeutic interventions
Andrea Jurisicova, Igor Jurisica, and Thomas Kislinger
Expert Review of Proteomics (2008) 5(4): 551-560
Body Cooling Causes Normalization of Cardiac Protein Expression and Function in a Rat Heatstroke Model
Bor-Chih Cheng, Ching-Ping Chang, Yeou-Guang Tsay, Ting-Feng Wu, Chiung-Yueh Hsu, and Mao-Tsun Lin
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4935-4945
Transketolase and 2',3'-Cyclic-nucleotide 3'-Phosphodiesterase Type I
Isoforms Are Specifically Recognized by IgG Autoantibodies in Multiple
Mol Cell Proteomics (2008) 7(12): 2337-2349
Differential Proteome Expression Associated with Urokinase Plasminogen Activator Receptor (uPAR) Suppression in Malignant Epithelial Cancer
Rohit G. Saldanha, Ning Xu, Mark P. Molloy, Duncan A. Veal, and Mark S. Baker
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4792-4806
2D Difference Gel Electrophoresis of Prepubertal and Pubertal Rat Mammary Gland Proteomes
Helen Kim, Mark B. Cope, Richie Herring, Gloria Robinson, Landon Wilson, Grier P. Page, and Stephen Barnes
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4638-4650
Profiling humoral immune responses to P. falciparum infection with protein microarrays
Denise L. Doolan, Yunxiang Mu, Berkay Unal, Suman Sundaresh, Siddiqua Hirst, Conrad Valdez, Arlo Randall, Douglas Molina, Xiaowu Liang, Daniel A. Freilich, J. Aggrey Oloo, Peter L. Blair, Joao C. Aguiar, Pierre Baldi, D. Huw Davies, Philip L. Felgner
PROTEOMICS (2008) 8(22): 4680-4694
Overexpression of cell surface cytokeratin 8 in multidrug-resistant MCF-7/MX cells enhances cell adhesion to the extracellular matrix
Liu F, Chen Z, Wang J, Shao X, Cui Z, Yang C, Zhu Z, Xiong D.
Neoplasia (2008) 10(11): 1275-84
Proteomic Analyses Associate Cystatin B with Restricted HIV-1 Replication in Placental Macrophages
Luciano-Montalvo C, Ciborowski P, Duan F, Gendelman HE, Meléndez LM.
Placenta (2008) 29(12): 1016-23
Proteomic Analysis of Oxidative Stress-Responsive Proteins in Human Pneumocytes: Insight into the Regulation of DJ-1 Expression
Xunbao Duan, Steven G. Kelsen, and Salim Merali
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4955-4961
Proteomic analysis of membrane rafts of melanoma cells identifies protein patterns characteristic of the tumor progression stage
Frédérique Baruthio, Manfredo Quadroni, Curzio Rüegg, Agnese Mariotti
PROTEOMICS (2008) 8(22): 4733-4747
Identification of metastasis-related proteins and their clinical triple-negative human breast cancer
Sun B, Zhang S, Zhang D, Li Y, Zhao X, Luo Y, Guo Y
Clin Cancer Res (2008) 14(21): 7050-9
A unified sample preparation protocol for proteomic and genomic profiling of cervical swabs to identify biomarkers for cervical cancer screening
Janet S. Rader, James P. Malone, Julia Gross, Petra Gilmore, Rebecca A. Brooks, Loan Nguyen, Dan L. Crimmins, Sheng Feng, Jason D. Wright, Nicholas Taylor, Israel Zighelboim, Margo C. Funk, Phyllis C. Huettner, Jack H. Ladenson, David Gius, R. Reid Townsend
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1658-1669
Proteomic analysis of the nuclear matrix in the early stages of rat liver carcinogenesis: Identification of differentially expressed and MAR-binding proteins
Barboro P, D'Arrigo C, Repaci E, Bagnasco L, Orecchia P, Carnemolla B, Patrone E, Balbi C.
Exp Cell Res Early Edition: published 28-Oct-2008
Analysis of the expression protein profiles of lung squamous carcinoma shot-gun proteomics strategy
Nan Y, Yang S, Tian Y, Zhang W, Zhou B, Bu L, Huo S
Med Oncol Early Edition: published 2008 Nov 6
An approach to remove alpha amylase for proteomic analysis of low abundance biomarkers in human saliva
Omer Deutsch, Yoram Fleissig, Batia Zaks, Guy Krief, Doron J. Aframian, Aaron Palmon
ELECTROPHORESIS (2008) 29(20): 4150-4157
Comparative Proteomics Study Reveals That Bacterial CpG Motifs Induce Tumor
Cell Autophagy in Vitro and in Vivo
Mol Cell Proteomics (2008) 7(12): 2311-2322
Proteomic Analysis of Endothelial Cell Autoantigens Recognized by Anti-Dengue Virus Nonstructural Protein 1 Antibodies
Cheng HJ, Lin CF, Lei HY, Liu HS, Yeh TM, Luo YH, Lin YS.
Exp Biol Med (Maywood) Early Edition: published 7-Nov-2008
Proteomic studies of B16 lines: Involvement of Annexin A1 in melanoma dissemination
Rondepierre F, Bouchon B, Papon J, Bonnet-Duquennoy M, Kintossou R, Moins N, Maublant J, Madelmont JC, D'Incan M, Degoul F.
Biochim Biophys Acta (2009) 1794(1): 61-9
Differential Membrane Proteomics Using 18O-Labeling To Identify Biomarkers for Cholangiocarcinoma
Troels Zakarias Kristiansen, H. C. Harsha, Mads Grønborg, Anirban Maitra, and Akhilesh Pandey
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4670-4677
A proteomic analysis of IVF follicular fluid in women
Estes SJ, Ye B, Qiu W, Cramer D, Hornstein MD, Missmer SA
Fertil Steril Early Edition: published 2008 Nov 1
How does the mammary gland proteome change during puberty?
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4611-4611
Proteomic Changes associated with Diabetes in the BB-DP rat
Johnson DT, Harris RA, French S, Aponte A, Balaban RS
Am J Physiol Endocrinol Metab Early Edition: published 2008 Nov 4
Multiplex analysis of cytokines as biomarkers that differentiate benign and malignant thyroid diseases
Faina Linkov, Robert L. Ferris, Zoya Yurkovetsky, Adele Marrangoni, Lyudmila Velikokhatnaya, William Gooding, Brian Nolan, Matthew Winans, Eric R. Siegel, Anna Lokshin, Brendan C. Stack Jr.
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1575-1585
Proteomics: new technologies and clinical applications
Latterich M, Abramovitz M, Leyland-Jones B
Eur J Cancer (2008) 44(18): 2737-41
Multiplex Detection of Protease Activity with Quantum Dot Nanosensors Prepared by Intein-Mediated Specific Bioconjugation
Zuyong Xia, Yun Xing, Min-Kyung So, Ai Leen Koh, Robert Sinclair, and Jianghong Rao
ANALYTICAL CHEMISTRY (2008) 80(22): 8649-8655
Proteomic Analysis of Calcium Oxalate Monohydrate Crystal-Induced Cytotoxicity in Distal Renal Tubular Cells
Visith Thongboonkerd, Theptida Semangoen, Supachok Sinchaikul, and Shui-Tein Chen
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4689-4700
Proteome Analysis of Multidrug Resistance of Human Oral Squamous Carcinoma Cells Using CD147 Silencing
Ye-Hong Kuang, Xiang Chen, Juan Su, Li-Sha Wu, Ji Li, Jing Chang, Ying Qiu, Zhe-Sheng Chen, and Takuro Kanekura
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4784-4791
Proteomic analysis of the neuroprotective mechanisms of acupuncture treatment in a Parkinson's disease mouse model
Songhee Jeon, Youn Jung Kim, Seung-Tae Kim, Woongjoon Moon, Younbyoung Chae, Minjeong Kang, Mi-Young Chung, Hyangsook Lee, Mi-Sook Hong, Joo-Ho Chung, Tong H. Joh, Hyejung Lee, Hi-Joon Park
PROTEOMICS (2008) 8(22): 4822-4832
A comparative proteomic analysis for capsaicin-induced apoptosis between human hepatocarcinoma (HepG2) and human neuroblastoma (SK-N-SH) cells
Yu Mi Baek, Hye Jin Hwang, Sang Woo Kim, Hee Sun Hwang, Sung Hak Lee, Jung Ae Kim, Jong Won Yun
PROTEOMICS (2008) 8(22): 4748-4767
Growth hormone-dependent changes in the rat lung proteome during lung throughout the period of alveolarization (day 4-14 postnatally)
Beyea JA, Olson DM, Harvey S
Mol Cell Biochem Early Edition: published 2008 Nov 5
Proteomic identification of differentially-expressed proteins in squamous cervical cancer
Zhu X, Lv J, Yu L, Zhu X, Wu J, Zou S, Jiang S.
Gynecol Oncol Early Edition: published 11-Nov-2008
Proneurotensin/neuromedin N secreted from small cell lung carcinoma cell lines as a potential tumor marker
Shun-ichiro Ogura, Kumi Kaneko, Shoji Miyajima, Keiichi Ohshima, Ken Yamaguchi, Tohru Mochizuki
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1620-1627
Age-dependent gene expression profile and protein expression in a transgenic rat model of Huntington's disease
Huu Phuc Nguyen, Silke Metzger, Carsten Holzmann, Dirk Koczan, Hans-Jürgen Thiesen, Stephan von Hörsten, Olaf Riess, Michael Bonin
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1638-1650
Using a novel resource to decrease proteomic biomarker identification time
Lustgarten JL, Visweswaran S, Grover H, Kimmel CP, Ryberg HL, Bowser RP, Gopalakrishnan V, Hogan W.
AMIA Annu Symp Proc (2008) : 1033.
Proteomic Analysis of Left Ventricular Remodeling in an Experimental Model of Heart Failure
Caroline Cieniewski-Bernard, Paul Mulder, Jean-Paul Henry, Hervé Drobecq, Emilie Dubois, Gwënaël Pottiez, Christian Thuillez, Philippe Amouyel, Vincent Richard, and Florence Pinet
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5004-5016
Novel MMP-9 Substrates in Cancer Cells Revealed by a Label-free Quantitative Proteomics Approach
Danmei Xu, Naoko Suenaga, Mariola J. Edelmann, Rafael Fridman, Ruth J. Muschel, and Benedikt M. Kessler
Mol Cell Proteomics (2008) 7(11): 2215-2228
Activated Epidermal Growth Factor Receptor as a Novel Target in Pancreatic Cancer Therapy
H. C. Harsha, Antonio Jimeno, Henrik Molina, Anca B. Mihalas, Michael G. Goggins, Ralph H. Hruban, Richard D. Schulick, Ullas Kamath, Anirban Maitra, Manuel Hidalgo, and Akhilesh Pandey
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4651-4658
Identification of differentially displayed proteins in cerebrospinal Parkinson's disease patients: A proteomic approach
Sinha A, Srivastava N, Singh S, Singh AK, Bhushan S, Shukla R, Singh MP
Clin Chim Acta Early Edition: published 2008 Oct 2
Altered plasma proteome during an early phase of peritonitis-induced sepsis
Thongboonkerd V, Chiangjong W, Mares J, Moravec J, Tuma Z, Karvunidis T, Sinchaikul S, Chen ST, Opatrný K, Matejovic M.
Clin Sci (Lond) Early Edition: published 13-Nov-2008
Differential expression of ceruloplasmin isoforms in the cerebrospinal fluid of amyotrophic lateral sclerosis patients
Antonio Conti, Sandro Iannaccone, Barbara Sferrazza, Lucia De Monte, Stefano Cappa, Diego Franciotta, Stefano Olivieri, Massimo Alessio
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1628-1637
Hepatitis C virus infection protein network
de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, Le Breton M, Pellet J, Davoust N, Mangeot PE, Chaboud A, Penin F, Jacob Y, Vidalain PO, Vidal M, Andre P, Rabourdin-Combe C, Lotteau V
Mol Syst Biol (2008) 4: 230
Proteome analysis of human foetal, aged and advanced nuclear cataract lenses
Peter G. Hains, Roger J. W. Truscott
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1611-1619
Analysis of the Differential Host-Cell Nuclear Proteome Induced by Attenuated and Virulent Hemorrhagic Arenavirus Infection
Bowick GC, Spratt HM, Hogg AE, Endsley JJ, Wiktorowicz JE, Kurosky A, Luxon BA, Gorenstein DG, Herzog NK.
J Virol Early Edition: published 12-Nov-2008
Overexpression and elevated plasma level of tumor-associated antigen 90K/Mac-2 binding protein in colorectal carcinoma
Chih-Ching Wu, Yu-Shan Huang, Li-Yu Lee, Ying Liang, Rei-Ping Tang, Yu-Sun Chang, Ling-Ling Hsieh, Jau-Song Yu
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1586-1595
Studying Protein Phosphorylation in Low MW CSF Fractions with capLC−ICPMS and nanoLC−CHIP-ITMS for Identification of Phosphoproteins
Jenny Ellis, Rudolf Grimm, Joseph F. Clark, Gail Pyne-Gaithman, Steve Wilbur, and Joseph A. Caruso
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4736-4742
Immunization against Clostridium perfringens cells elicits protection against Clostridium tetani in mouse model: identification of cross-reactive proteins using proteomic methodologies
Alam SI, Bansod S, Singh L.
BMC Microbiol (2008) 8(1): 194
Sys-BodyFluid: a systematical database for human body fluid proteome research
Li SJ, Peng M, Li H, Liu BS, Wang C, Wu JR, Li YX, Zeng R
Nucl Acids Res Early Edition: published 2008 Oct 31
Proteomic analysis identifies proteins that continue to grow hepatic stem-like cells without differentiation
Saheki T, Ito H, Sekiguchi A, Nishina A, Sugiyama T, Izumi T, Kojima I.
Cytotechnology (2008) 57(2): 137-43
Protein Expression Profile of the Mouse Metaphase-II Oocyte
Minyue Ma, Xuejiang Guo, Fuqiang Wang, Chun Zhao, Zichuan Liu, Zhonghua Shi, Yufeng Wang, Ping Zhang, Kemei Zhang, Ningling Wang, Min Lin, Zuomin Zhou, Jiayin Liu, Qingzhang Li, Liu Wang, Ran Huo, Jiahao Sha, and Qi Zhou
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4821-4830
Evidence for Insertional RNA Editing in Humans
Zougman A, Ziółkowski P, Mann M, Wiśniewski JR.
Curr Biol (2008) 18(22): 1760-5
Proteomics analysis of A375 human malignant melanoma cells in response to arbutin treatment
Nawarak J, Huang-Liu R, Kao SH, Liao HH, Sinchaikul S, Chen ST, Cheng SL.
Biochim Biophys Acta Early Edition: published 18-Oct-2008
Proteomic analysis of the membrane palmitoylated protein-4 (MPP4)-associated protein complex in the retina
Förster JR, Lochnit G, Stöhr H.
Exp Eye Res Early Edition: published 9-Oct-2008
The cold-shock response in mammalian cells: investigating the HeLa cell cold-shock proteome
Underhill MF, Smales CM.
Cytotechnology (2007) 53(1-3): 47-53
Axonal regeneration in the organotypically cultured monkey retina: Biological aspects, dependence on substrates and age-related proteomic profiling
Rose K, Schröer U, Volk GF, Schlatt S, König S, Feigenspan A, Thanos S.
Restor Neurol Neurosci (2008) 26(4-5): 249-66
Proteomic profiling of recombinant cells from large-scale mammalian cell culture processes
Meleady P.
Cytotechnology (2007) 53(1-3): 23-31
Human normal tear proteome
Chu CY, Poon CW, Pong CF, Pang CP, Wang CC.
Graefes Arch Clin Exp Ophthalmol Early Edition: published 25-Oct-2008
Impact of rpoS Deletion on the Proteome of Escherichia coli Grown Planktonically and as Biofilm
Anthony Collet, Pascal Cosette, Christophe Beloin, Jean-Marc Ghigo, Christophe Rihouey, Patrice Lerouge, Guy-Alain Junter, and Thierry Jouenne
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4659-4669
Immunization against Clostridium perfringens cells elicits protection against Clostridium tetani in mouse model: identification of cross-reactive proteins using proteomic methodologies
Alam SI, Bansod S, Singh L.
BMC Microbiol (2008) 8(1): 194
Identification of proteins from membrane preparations by a combination of MALDI TOF-TOF and LC-coupled linear ion trap MS analysis of an Antarctic bacterium Pseudomonas syringae Lz4W, a strain with unsequenced genome
Medicharla V. Jagannadham
ELECTROPHORESIS (2008) 29(21): 4341-4350
Catabolic pathways and cellular responses of Pseudomonas putida P8 on benzoate with a proteomics approach
Cao B, Loh KC
Biotechnol Bioeng (2008) 101(6): 1297-312
Molecular approaches in bioremediation
Wood TK.
Curr Opin Biotechnol (2008) 19(6): 572-578
Different Residues in Channel Turret Determining the Selectivity of ADWX-1 Inhibitor Peptide between Kv1.1 and Kv1.3 Channels
Shi-Jin Yin, Ling Jiang, Hong Yi, Song Han, Dai-Wen Yang, Mai-Li Liu, Hui Liu, Zhi-Jian Cao, Ying-Liang Wu, and Wen-Xin Li
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4890-4897
Matrix-Assisted Laser Desorption/Ionization-Ion Mobility Separation-Mass Spectrometry Imaging of Vinblastine in Whole Body Tissue Sections
Paul J. Trim, Claire M. Henson, Jennie L. Avery, Andrew McEwen, Marten F. Snel, Emmanuelle Claude, Peter S. Marshall, Andrew West, Alessandra P. Princivalle, and Malcolm R. Clench
ANALYTICAL CHEMISTRY (2008) 80(22): 8628-8634
Estrogen Regulation of Proteins in the Rat Ventromedial Nucleus of the Hypothalamus
Bing Mo, Eduardo Callegari, Martin Telefont, and Kenneth J. Renner
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5040-5048
Identification of rat urinary glycoproteome captured by three lectins using gel and LC-based proteomics
Pyong-Gon Moon, Hyun-Ho Hwang, Yong Chool Boo, Joseph Kwon, Je-Yoel Cho, Moon-Chang Baek
ELECTROPHORESIS (2008) 29(21): 4324-4331
Optimal Conditions for Protein Array Deposition Using Continuous Flow
Sriram Natarajan, Andrew Hatch, David G. Myszka, and Bruce K. Gale
ANALYTICAL CHEMISTRY (2008) 80(22): 8561-8567
Quantitative Serum Proteomics from Surface Plasmon Resonance Imaging
Christopher Lausted, Zhiyuan Hu, and Leroy Hood
Mol Cell Proteomics (2008) 7(12): 2464-2474
Physical protein-protein interactions predicted from microarrays
Ta-tsen Soong, Kazimierz O. Wrzeszczynski, and Burkhard Rost
Bioinformatics (2008) 24(22): 2608-2614
Rapid characterization of binding specificity and cross-reactivity of antibodies using recombinant human protein arrays
Kijanka G, Ipcho S, Baars S, Chen H, Hadley K, Beveridge A, Gould E, Murphy D.
J Immunol Methods Early Edition: published 6-Nov-2008
Microarray-Based Study of Carbohydrate−Protein Binding by Gold Nanoparticle Probes
Jingqing Gao, Dianjun Liu, and Zhenxin Wang
ANALYTICAL CHEMISTRY (2008) 80(22): 8822-8827
In Vivo Interactome of Helicobacter pylori Urease Revealed by Tandem
Affinity Purification
Mol Cell Proteomics (2008) 7(12): 2429-2441
Unrestrictive Identification of Multiple Post-translational Modifications
from Tandem Mass Spectrometry Using an Error-tolerant Algorithm Based on an
Mol Cell Proteomics (2008) 7(12): 2452-2463
Microarray-Based Study of Carbohydrate−Protein Binding by Gold Nanoparticle Probes
Jingqing Gao, Dianjun Liu, and Zhenxin Wang
ANALYTICAL CHEMISTRY (2008) 80(22): 8822-8827
Structural proteomics by NMR spectroscopy
Joon Shin, Woonghee Lee, and Weontae Lee
Expert Review of Proteomics (2008) 5(4): 589-601
Analysis of the Human Casein Phosphoproteome by 2-D Electrophoresis and MALDI-TOF/TOF MS Reveals New Phosphoforms
Aaron G. Poth, Hilton C. Deeth, Paul F. Alewood, and John W. Holland
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5017-5027
Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy
Pragya Singh, Scott A. Shaffer, Alexander Scherl, Carol Holman, Richard A. Pfuetzner, Theodore J. Larson Freeman, Samuel I. Miller, Patricia Hernandez, Ron D. Appel, and David R. Goodlett
ANALYTICAL CHEMISTRY (2008) 80(22): 8799-8806
Quantitative Analysis of Brain Nuclear Phosphoproteins Identifies Developmentally Regulated Phosphorylation Events
Lujian Liao, Daniel B. McClatchy, Sung Kyu Park, Tao Xu, Bingwen Lu, and John R. Yates III
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4743-4755
Distinction between Human Cytochrome P450 (CYP) Isoforms and Identification of New Phosphorylation Sites by Mass Spectrometry
Gorden Redlich, Ulrich M. Zanger, Stephan Riedmaier, Nicolai Bache, Anders B. M. Giessing, Martin Eisenacher, Christian Stephan, Helmut E. Meyer, Ole N. Jensen, and Katrin Marcus
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4678-4688
De novo sequencing of peptides secreted by the skin glands of the Caucasian Green Frog Rana ridibunda
Tatiana Yu. Samgina, Konstantin A. Artemenko, Vladimir A. Gorshkov, Sergey V. Ogourtsov, Roman A. Zubarev, Albert T. Lebedev
Rapid Communications in Mass Spectrometry (2008) 22(22): 3517-3525
Investigations into charge heterogeneity of wool intermediate filament proteins
Louise N. Paton, Juliet A. Gerrard and Warren G. Bryson
Journal of Proteomics (2008) 71(5): 513-529
ExDom: an integrated database for comparative analysis of the structures of protein domains in eukaryotes
Bhasi A, Philip P, Manikandan V, Senapathy P
Nucl Acids Res Early Edition: published 2008 Nov 4
Identification of Structural and Functional O-Linked N-Acetylglucosamine-bearing Proteins in Xenopus laevis Oocyte
Vanessa Dehennaut, Marie-Christine Slomianny, Adeline Page, Anne-Sophie Vercoutter-Edouart, Catherine Jessus, Jean-Claude Michalski, Jean-Pierre Vilain, Jean-Francois Bodart, and Tony Lefebvre
Mol Cell Proteomics (2008) 7(11): 2229-2245
PTP? has a critical role in signaling transduction pathways and phosphoprotein network topology in red cells
Lucia De Franceschi, Andrea Biondani, Franco Carta, Franco Turrini, Carlo Laudanna, Renzo Deana, Anna Maria Brunati, Loris Turretta, Achille Iolascon, Silverio Perrotta, Ari Elson, Cristina Bulato, Carlo Brugnara
PROTEOMICS (2008) 8(22): 4695-4708
Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks
Carsten Jers, Boumediene Soufi, Christophe Grangeasse, Josef Deutscher, and Ivan Mijakovic
Expert Review of Proteomics (2008) 5(4): 619-627
Profiling the Phospho-status of the BKCa Channel {alpha} Subunit in Rat Brain Reveals Unexpected Patterns and Complexity
Jiusheng Yan, Jesper V. Olsen, Kang-Sik Park, Weiyan Li, Wolfgang Bildl, Uwe Schulte, Richard W. Aldrich, Bernd Fakler, and James S. Trimmer
Mol Cell Proteomics (2008) 7(11): 2188-2198
Discovery, Identification, and Characterization of Candidate Pharmacodynamic Markers of Methionine Aminopeptidase-2 Inhibition
Scott E. Warder, Lora A. Tucker, Shaun M. McLoughlin, Tamara J. Strelitzer, Joseph L. Meuth, Qian Zhang, George S. Sheppard, Paul L. Richardson, Rick Lesniewski, Steven K. Davidsen, Randy L. Bell, John C. Rogers, and Jieyi Wang
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4807-4820
Application of proteomics to the characterization of beta-lactoglobulin variants by capillary electrophoresis-mass spectrometry and nano-liquid chromatography-mass spectrometry-mass spectrometry
Vallejo-Cordoba B, Gonzalez-Cordova AF, Olguin-Arredondo HA
J Capill Electrophor Microchip Technol (2008) 10(5-6): 87-92
Identification of the rapamycin-sensitive phosphorylation sites within the Ser/Thr-rich domain of the yeast Npr1 protein kinase
Stefan Gander, Debora Bonenfant, Patrick Altermatt, Dietmar E. Martin, Simon Hauri, Suzette Moes, Michael N. Hall, Paul Jenoe
Rapid Communications in Mass Spectrometry (2008) 22(23): 3743-3753
Is asparagine deamidation in the porcine odorant-binding protein related to the odor molecules binding?
Mamone G, D'Auria S.
Protein Pept Lett (2008) 15(9): 895-9
Redox proteomics: basic principles and future perspectives for the protein oxidation in plants
Rinalducci S, Murgiano L, Zolla L
J Exp Bot (2008) 59(14): 3781-801
Differential Proteomic Screen To Evidence Proteins Ubiquitinated upon Mitotic Exit in Cell-Free Extract of Xenopus laevis Embryos
Franck Bazile, Jean-Philippe Gagné, Geneviève Mercier, Ken Sin Lo, Aude Pascal, Julian Vasilescu, Daniel Figeys, Guy G. Poirier, Jacek Z. Kubiak, and Franck Chesnel
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4701-4714
A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry
Quanhu Sheng, Yehia Mechref, Yixue Li, Milos V. Novotny, Haixu Tang
Rapid Communications in Mass Spectrometry (2008) 22(22): 3561-3569
Two dimensional gel electrophoresis of apolipoprotein C-III and MALDI-TOF MS are complementary techniques for the study of combined defects in N- and mucin type O-glycan biosynthesis
Arnaud Bruneel, Willy Morelle, Yoann Carre, Florence Habarou, Damien Dupont, Aurélie Hesbert, Geneviève Durand, Jean Claude Michalski, Valérie Drouin-Garraud, Nathalie Seta
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(12): 1670-1674
The Tandem PDZ Protein Syntenin Interacts with the Aminoacyl tRNA Synthetase Complex in a Lysyl-tRNA Synthetase-Dependent Manner
Kris Meerschaert, Eline Remue, Ariane De Ganck, An Staes, Ciska Boucherie, Kris Gevaert, Joël Vandekerckhove, Lawrence Kleiman, and Jan Gettemans
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4962-4973
A Comparative Study of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) versus SCX-IMAC-Based Methods for Phosphopeptide Isolation/Enrichment
Chee Sian Gan, Tiannan Guo, Huoming Zhang, Sai Kiang Lim, and Siu Kwan Sze
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4869-4877
Fragmentations of (M-H)- anions of underivatised peptides. Part 2: Characteristic cleavages of Ser and Cys and of disulfides and other post-translational modifications, together with some unusual internal proces
Daniel Bilusich, John. H. Bowie
Mass Spectrometry Reviews (2009) 28(1): 20-34
Proteomics Analysis Identifies Phosphorylation-dependent {alpha}-Synuclein Protein Interactions
Melinda A. McFarland, Christopher E. Ellis, Sanford P. Markey, and Robert L. Nussbaum
Mol Cell Proteomics (2008) 7(11): 2123-2137
Comparative Phosphoproteomics of Zebrafish Fyn/Yes Morpholino Knockdown Embryos
Simone Lemeer, Chris Jopling, Joost Gouw, Shabaz Mohammed, Albert J. R. Heck, Monique Slijper, and Jeroen den Hertog
Mol Cell Proteomics (2008) 7(11): 2176-2187
Alteration of S-nitrosothiol homeostasis and targets for protein S-nitrosation in human hepatocytes
Laura M. López-Sánchez, Fernando J. Corrales, Raúl González, Gustavo Ferrín, Juan R. Muñoz-Castañeda, Isidora Ranchal, Ana B. Hidalgo, Javier Briceño, Pedro López-Cillero, Miguel A. Gómez, Manuel De La Mata, Jordi Muntané, Antonio Rodríguez-Ariza
PROTEOMICS (2008) 8(22): 4709-4720
Grp94 is Tyr-phosphorylated by Fyn in the lumen of the endoplasmic reticulum and translocates to Golgi in differentiating myoblasts
Frasson M, Vitadello M, Brunati AM, La Rocca N, Tibaldi E, Pinna LA, Gorza L, Donella-Deana A.
Biochim Biophys Acta Early Edition: published 22-Oct-2008
Targeted identification of phosphorylated peptides by off-line HPLC-MALDI-MS/MS using LC retention time prediction
Vincent C. Chen, Chi-Chi Chou, Hsin-Yu Hsieh, Hélène Perreault, Kay-Hooi Khoo
Journal of Mass Spectrometry (2008) 43(12): 1649-1658
Factors That Contribute to the Misidentification of Tyrosine Nitration by
Shotgun Proteomics
Mol Cell Proteomics (2008) 7(12): 2442-2451
Separation of multiphosphorylated peptide isomers by CZE
Marika V. Muetzelburg, Ralf Hoffmann
ELECTROPHORESIS (2008) 29(21): 4381-4385
Lamin A Ser404 Is a Nuclear Target of Akt Phosphorylation in C2C12 Cells
Vittoria Cenni, Jessika Bertacchini, Francesca Beretti, Giovanna Lattanzi, Alberto Bavelloni, Massimo Riccio, Maria Ruzzene, Oriano Marin, Giorgio Arrigoni, Veena Parnaik, Manfred Wehnert, Nadir M. Maraldi, Anto de Pol, Lucio Cocco, and Sandra Marmiroli
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4727-4735
Online immobilized metal affinity chromatography/mass spectrometric analysis of changes elicited by cCMP in the murine brain phosphoproteome
S. Ding, A. E. Bond, F. Lemière, R. Tuytten, E. L. Esmans, A. G. Brenton, E. Dudley, R. P. Newton
Rapid Communications in Mass Spectrometry (2008) 22(24): 4129-4138
Studying Protein Phosphorylation in Low MW CSF Fractions with capLC−ICPMS and nanoLC−CHIP-ITMS for Identification of Phosphoproteins
Jenny Ellis, Rudolf Grimm, Joseph F. Clark, Gail Pyne-Gaithman, Steve Wilbur, and Joseph A. Caruso
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4736-4742
A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications
Jayson A. Falkner, Jarret W. Falkner, Anastasia K. Yocum, and Philip C. Andrews
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4614-4622
Comparative Proteomic Analysis Provides New Insights into the Fiber Elongating Process in Cotton
Yi-Wei Yang, Shao-Min Bian, Yuan Yao, and Jin-Yuan Liu
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4623-4637
Revealing the Dynamics of the 20 S Proteasome Phosphoproteome: A Combined CID and Electron Transfer Dissociation Approach
Haojie Lu, Chenggong Zong, Yueju Wang, Glen W. Young, Ning Deng, Pete Souda, Xiaohai Li, Julian Whitelegge, Oliver Drews, Peng-Yuan Yang, and Peipei Ping
Mol Cell Proteomics (2008) 7(11): 2073-2089
Prediction of kinase-specific phosphorylation sites using conditional random fields
Thanh Hai Dang, Koenraad Van Leemput, Alain Verschoren, and Kris Laukens
Bioinformatics (2008) 24(24): 2857-2864
Annotating proteins with generalized functional linkages
Llewellyn R, Eisenberg DS.
Proc Natl Acad Sci U S A (2008) 105(46): 17700-5
The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches
Eizadora T. Yu, Arie Hawkins, Irwin D. Kuntz, Larry A. Rahn, Andrew Rothfuss, Kenneth Sale, Malin M. Young, Christine L. Yang, Carmen M. Pancerella, and Daniele Fabris
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4848-4857
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions
Seesandra V. Rajagopala, Johannes Goll, N.D. Deve Gowda, Kumar C. Sunil, Bjorn Titz, Arnab Mukherjee, Sharmila S. Mary, Naresh Raviswaran, Chetan S. Poojari, Srinivas Ramachandra, Svetlana Shtivelband, Stephen M. Blazie, Julia Hofmann, and Peter Uetz
Bioinformatics (2008) 24(22): 2622-2627
Proteomic analysis of the membrane palmitoylated protein-4 (MPP4)-associated protein complex in the retina
Förster JR, Lochnit G, Stöhr H.
Exp Eye Res Early Edition: published 9-Oct-2008
Riboproteomic analysis of polypeptides interacting with the internal ribosome-entry site element of foot-and-mouth disease viral RNA
Almudena Pacheco, Sandrine Reigadas, Encarnación Martínez-Salas
PROTEOMICS (2008) 8(22): 4782-4790
Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes
Gagne JP, Isabelle M, Lo KS, Bourassa S, Hendzel MJ, Dawson VL, Dawson TM, Poirier GG
Nucl Acids Res Early Edition: published 2008 Nov 3
DOCKGROUND protein-protein docking decoy set
Shiyong Liu, Ying Gao, and Ilya A. Vakser
Bioinformatics (2008) 24(22): 2634-2635
Interaction proteomics of the HMGA chromatin architectural factors
Riccardo Sgarra, Cristina Furlan, Salvina Zammitti, Alessandra Lo Sardo, Elisa Maurizio, Julie Di Bernardo, Vincenzo Giancotti, Guidalberto Manfioletti
PROTEOMICS (2008) 8(22): 4721-4732
A Proteomics Analysis of Yeast Mot1p Protein-Protein Associations: Insights into Mechanism
Diana R. Arnett, Jennifer L. Jennings, David L. Tabb, Andrew J. Link, and P. Anthony Weil
Mol Cell Proteomics (2008) 7(11): 2090-2106
A Fluorescent Two-hybrid Assay for Direct Visualization of Protein Interactions in Living Cells
Kourosh Zolghadr, Oliver Mortusewicz, Ulrich Rothbauer, Regina Kleinhans, Heike Goehler, Erich E. Wanker, M. Cristina Cardoso, and Heinrich Leonhardt
Mol Cell Proteomics (2008) 7(11): 2279-2287
An in silico method for detecting overlapping functional modules from biological networks
Maraziotis IA, Dimitrakopoulou K, Bezerianos A
BMC Syst Biol (2008) 2(1): 93
Proteomics analysis of A375 human malignant melanoma cells in response to arbutin treatment
Nawarak J, Huang-Liu R, Kao SH, Liao HH, Sinchaikul S, Chen ST, Cheng SL.
Biochim Biophys Acta Early Edition: published 18-Oct-2008
The Tandem PDZ Protein Syntenin Interacts with the Aminoacyl tRNA Synthetase Complex in a Lysyl-tRNA Synthetase-Dependent Manner
Kris Meerschaert, Eline Remue, Ariane De Ganck, An Staes, Ciska Boucherie, Kris Gevaert, Joël Vandekerckhove, Lawrence Kleiman, and Jan Gettemans
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4962-4973
The Prediction of Protein-Protein Interaction Networks in Rice
He F, Zhang Y, Chen H, Zhang Z, Peng YL
BMC Genomics (2008) 9(1): 519
Thermal activation of the co-chaperonins GroES and gp31 probed by mass spectrometry
Rimco B. J. Geels, Stephane Calmat, Albert J. R. Heck, Saskia M. van der Vies, Ron M. A. Heeren
Rapid Communications in Mass Spectrometry (2008) 22(22): 3633-3641
Quantitative proteomics by fluorescent labeling of cysteine residues using a set of two cyanine-based or three rhodamine-based dyes
Daniela Volke, Ralf Hoffmann
ELECTROPHORESIS (2008) 29(22): 4516-4526
Investigating the Quantitative Nature of MALDI-TOF MS
Emilia Szajli, Tamas Feher, and Katalin F. Medzihradszky
Mol Cell Proteomics (2008) 7(12): 2410-2418
Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates
Paul J. Boersema, Thin Thin Aye, Toon A. B. van Veen, Albert J. R. Heck, Shabaz Mohammed
PROTEOMICS (2008) 8(22): 4624-4632
Quantitative Analysis of Brain Nuclear Phosphoproteins Identifies Developmentally Regulated Phosphorylation Events
Lujian Liao, Daniel B. McClatchy, Sung Kyu Park, Tao Xu, Bingwen Lu, and John R. Yates III
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4743-4755
Sensitive fluorescent staining for proteomic analysis of proteins in 1-D and 2-D SDS-PAGE and its comparison with SYPRO Ruby by PMF
Wei-Tao Cong, Sun-Young Hwang, Li-Tai Jin, Jung-Kap Choi
ELECTROPHORESIS (2008) 29(21): 4304-4315
Magnetic Electrochemical Immunoassays with Quantum Dot Labels for Detection of Phosphorylated Acetylcholinesterase in Plasma
Hua Wang, Jun Wang, Charles Timchalk, and Yuehe Lin
ANALYTICAL CHEMISTRY (2008) 80(22): 8477-8484
Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer
Guoan Zhang, David Fenyö, and Thomas A. Neubert
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4715-4726
Differential Membrane Proteomics Using 18O-Labeling To Identify Biomarkers for Cholangiocarcinoma
Troels Zakarias Kristiansen, H. C. Harsha, Mads Grønborg, Anirban Maitra, and Akhilesh Pandey
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4670-4677
The use of proteome similarity for the qualitative and quantitative profiling of reperfused myocardium
Vissers JP, Pons S, Hulin A, Tissier R, Berdeaux A, Connolly JB, Langridge JI, Geromanos SJ, Ghaleh B.
J Chromatogr B Early Edition: published 1-Nov-2008
Quantitative assessment of the structural bias in protein-protein interaction assays
Åsa K. Björklund, Sara Light, Linnea Hedin, Arne Elofsson
PROTEOMICS (2008) 8(22): 4657-4667
Hybridization of Pulsed-Q Dissociation and Collision-Activated Dissociation in Linear Ion Trap Mass Spectrometer for iTRAQ Quantitation
Tiannan Guo, Chee Sian Gan, Huoming Zhang, Yi Zhu, Oi Lian Kon, and Siu Kwan Sze
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4831-4840
The Proteomic Response of Saccharomyces cerevisiae in Very High Glucose Conditions with Amino Acid Supplementation
Trong Khoa Pham and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4766-4774
Significance Analysis of Spectral Count Data in Label-free Shotgun
Proteomics
Mol Cell Proteomics (2008) 7(12): 2373-2385
2D Difference Gel Electrophoresis of Prepubertal and Pubertal Rat Mammary Gland Proteomes
Helen Kim, Mark B. Cope, Richie Herring, Gloria Robinson, Landon Wilson, Grier P. Page, and Stephen Barnes
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4638-4650
ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics
Benjamin Mann, Milan Madera, Quanhu Sheng, Haixu Tang, Yehia Mechref, Milos V. Novotny
Rapid Communications in Mass Spectrometry (2008) 22(23): 3823-3834
Characterization of the Human COP9 Signalosome Complex Using Affinity Purification and Mass Spectrometry
Lei Fang, Xiaorong Wang, Kosj Yamoah, Phang-lang Chen, Zhen-Qiang Pan, and Lan Huang
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4914-4925
Label-free Quantitative Analysis of One-dimensional PAGE LC/MS/MS Proteome:
Application on Angiotensin II-Stimulated Smooth Muscle Cells Secretome
Mol Cell Proteomics (2008) 7(12): 2399-2409
Stable isotope ratio analysis as a tool to discriminate between rainbow trout (O. mykiss) fed diets based on plant or fish-meal proteins
J. M. Moreno-Rojas, F. Tulli, M. Messina, E. Tibaldi, C. Guillou
Rapid Communications in Mass Spectrometry (2008) 22(23): 3706-3710
MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments
Daniel B. Martin, Ted Holzman, Damon May, Amelia Peterson, Ashley Eastham, Jimmy Eng, and Martin McIntosh
Mol Cell Proteomics (2008) 7(11): 2270-2278
A Combination of Immobilised pH Gradients Improves Membrane Proteomics
J. M. Chick, P. A. Haynes, B. Bjellqvist, and M. S. Baker
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4974-4981
The Impact of Peptide Abundance and Dynamic Range on Stable-Isotope-Based Quantitative Proteomic Analyses
Corey E. Bakalarski, Joshua E. Elias, Judit Villén, Wilhelm Haas, Scott A. Gerber, Patrick A. Everley, and Steven P. Gygi
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4756-4765
Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks
Alain Dupuis, Jacques-Antoine Hennekinne, Jérôme Garin, Virginie Brun
PROTEOMICS (2008) 8(22): 4633-4636
Advances in ovarian cancer proteomics: the quest for biomarkers and improved therapeutic interventions
Andrea Jurisicova, Igor Jurisica, and Thomas Kislinger
Expert Review of Proteomics (2008) 5(4): 551-560
Proteomes and transcriptomes of Apicomplexa - Where's the message?
Wastling JM, Xia D, Sohal A, Chaussepied M, Pain A, Langsley G.
Int J Parasitol Early Edition: published 1-Nov-2008
Molecular approaches in bioremediation
Wood TK.
Curr Opin Biotechnol (2008) 19(6): 572-578
Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: An update of recent developments
Mischak H, Coon JJ, Novak J, Weissinger EM, Schanstra JP, Dominiczak AF.
Mass Spectrom Rev Early Edition: published 30-Oct-2008
Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis
Mikkel Nissum and Aude L Foucher
Expert Review of Proteomics (2008) 5(4): 571-587
Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks
Carsten Jers, Boumediene Soufi, Christophe Grangeasse, Josef Deutscher, and Ivan Mijakovic
Expert Review of Proteomics (2008) 5(4): 619-627
Human normal tear proteome
Chu CY, Poon CW, Pong CF, Pang CP, Wang CC.
Graefes Arch Clin Exp Ophthalmol Early Edition: published 25-Oct-2008
Proteomics: new technologies and clinical applications
Latterich M, Abramovitz M, Leyland-Jones B
Eur J Cancer (2008) 44(18): 2737-41
The challenge of lipid rafts
Pike LJ.
J Lipid Res Early Edition: published 27-Oct-2008
Science, marketing and wishful thinking in quantitative proteomics
Murray Hackett
PROTEOMICS (2008) 8(22): 4618-4623
Structural proteomics by NMR spectroscopy
Joon Shin, Woonghee Lee, and Weontae Lee
Expert Review of Proteomics (2008) 5(4): 589-601
Proteomic studies in biomedically and industrially relevant fungi
Carberry S, Doyle S.
Cytotechnology (2007) 53(1-3): 95-100
Neutrophil proteome: lessons from different standpoints
Morris CF, Castro MS, Fontes W.
Protein Pept Lett (2008) 15(9): 995-1001
Proteomics researchers now agree on some aspects of data sharing
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4612-4612
Discovery of novel vaccine candidates and drug targets against visceral leishmaniasis using proteomics and transcriptomics
Kumari S, Kumar A, Samant M, Singh N, Dube A.
Curr Drug Targets (2008) 9(11): 938-47
High-Throughput Protein Production (HTPP): A Review of Enabling Expedite Protein Production
Koehn J, Hunt I
Methods Mol Biol (2009) 498: 1-18
Proteomics of the lysosome
Lubke T, Lobel P, Sleat DE
Biochim Biophys Acta Early Edition: published 2008 Oct 15
How does the mammary gland proteome change during puberty?
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 4611-4611
Mass spectrometry and illicit drug testing: analytical challenges of the anti-doping laboratories
Francesco Botre
Expert Review of Proteomics (2008) 5(4): 535-539
Current status and future prospects in the search for protein biomarkers of immunosenescence
Steve Wilson and Dawn J Mazzatti
Expert Review of Proteomics (2008) 5(4): 561-569
Redox proteomics: basic principles and future perspectives for the protein oxidation in plants
Rinalducci S, Murgiano L, Zolla L
J Exp Bot (2008) 59(14): 3781-801
Lessons learned from lipid raft proteomics
Leonard J Foster
Expert Review of Proteomics (2008) 5(4): 541-543
Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors
Sheila J. Barton, John C. Whittaker
Mass Spectrometry Reviews (2009) 28(1): 177-187
Complementary methods to assist subcellular fractionation in organellar proteomics
Daniel J Gauthier and Claude Lazure
Expert Review of Proteomics (2008) 5(4): 603-617
Laboratory information management system for membrane protein structure initiative - from gene to crystal
Troshin PV, Morris C, Prince SM, Papiz MZ.
Mol Membr Biol (2008) 25(8): 639-52
Negative ion production from peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Junjie Gao, Carolyn J. Cassady
Rapid Communications in Mass Spectrometry (2008) 22(24): 4066-4072
In-Capillary Protein Enrichment and Removal of Nonbuffering Salts Using Capillary Electrophoresis with Discontinuous Buffers
Christina J. Booker and Ken K.-C. Yeung
ANALYTICAL CHEMISTRY (2008) 80(22): 8598-8604
Alternating current-assisted on-plate proteolysis for MALDI-TOF MS peptide mapping
Sheng Wang, Bangguo Wei, Pengyuan Yang, Gang Chen
PROTEOMICS (2008) 8(22): 4637-4641
De novo sequencing of peptides secreted by the skin glands of the Caucasian Green Frog Rana ridibunda
Tatiana Yu. Samgina, Konstantin A. Artemenko, Vladimir A. Gorshkov, Sergey V. Ogourtsov, Roman A. Zubarev, Albert T. Lebedev
Rapid Communications in Mass Spectrometry (2008) 22(22): 3517-3525
Searching biomarker candidates in serum using multidimensional native chromatography I. Enhanced separation method
Kreusch S, Schulze M, Cumme GA, Ditze G, Moore T, Rhode H.
J Chromatogr B (2008) 875(2): 567-72
Significance Analysis of Spectral Count Data in Label-free Shotgun
Proteomics
Mol Cell Proteomics (2008) 7(12): 2373-2385
Detergent-Based but Gel-Free Method Allows Identification of Several Hundred Membrane Proteins in Single LC-MS Runs
Nagarjuna Nagaraj, Aiping Lu, Matthias Mann, and Jacek R. Wiśniewski
JOURNAL OF PROTEOME RESEARCH (2008) 7(11): 5028-5032
An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures
Alexander Schmidt, Nils Gehlenborg, Bernd Bodenmiller, Lukas N. Mueller, Dave Campbell, Markus Mueller, Ruedi Aebersold, and Bruno Domon
Mol Cell Proteomics (2008) 7(11): 2138-2150
Establishing substantial equivalence: proteomics
Lovegrove A, Salt L, Shewry PR.
Methods Mol Biol (2009) 478: 273-88
Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements
William Burkitt, Gavin O'Connor
Rapid Communications in Mass Spectrometry (2008) 22(23): 3893-3901
Influence of clotting time on the protein composition of serum samples based on LC-MS data
Govorukhina NI, de Vries M, Reijmers TH, Horvatovich P, van der Zee AG, Bischoff R.
J Chromatogr B Early Edition: published 1-Nov-2008
An approach to remove alpha amylase for proteomic analysis of low abundance biomarkers in human saliva
Omer Deutsch, Yoram Fleissig, Batia Zaks, Guy Krief, Doron J. Aframian, Aaron Palmon
ELECTROPHORESIS (2008) 29(20): 4150-4157
Multiplex detection and identification of proteins on a PVDF membrane blocked with a synthetic polymer-based reagent
Hiroshi Kawasaki, Akiko Okayama, Yuko Iwafune, Shota Yahagi, Noriaki Arakawa, Hisashi Hirano
ELECTROPHORESIS (2008) 29(21): 4377-4380
Matrix-Assisted Laser Desorption/Ionization-Ion Mobility Separation-Mass Spectrometry Imaging of Vinblastine in Whole Body Tissue Sections
Paul J. Trim, Claire M. Henson, Jennie L. Avery, Andrew McEwen, Marten F. Snel, Emmanuelle Claude, Peter S. Marshall, Andrew West, Alessandra P. Princivalle, and Malcolm R. Clench
ANALYTICAL CHEMISTRY (2008) 80(22): 8628-8634
Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to rapidly screen for albuminuria
Jentaie Shiea, Yi-Tzu Cho, Yen-Hsiu Lin, Chin-Wen Chang, Li-Hua Lo, Yi-Chern Lee, Hung-Lung Ke, Wen-Jeng Wu, Deng-Chyang Wu
Rapid Communications in Mass Spectrometry (2008) 22(23): 3754-3760
High-throughput protein expression using cell-free system
Sitaraman K, Chatterjee DK
Methods Mol Biol (2009) 498: 229-44
Sensitive fluorescent staining for proteomic analysis of proteins in 1-D and 2-D SDS-PAGE and its comparison with SYPRO Ruby by PMF
Wei-Tao Cong, Sun-Young Hwang, Li-Tai Jin, Jung-Kap Choi
ELECTROPHORESIS (2008) 29(21): 4304-4315
Mass spectrometry and illicit drug testing: analytical challenges of the anti-doping laboratories
Francesco Botre
Expert Review of Proteomics (2008) 5(4): 535-539
Comparing the applicability of CGE-on-the-chip and SDS-PAGE for fast pre-screening of mouse serum samples prior to proteomics analysis
Tom Grunert, Martina Marchetti-Deschmann, Ingrid Miller, Mathias Müller, Günter Allmaier
ELECTROPHORESIS (2008) 29(21): 4332-4340
Detection of recombinant growth hormone in human plasma by a 2-D PAGE method
Maxie Kohler, Klaus Püschel, Dimitri Sakharov, Alexander Tonevitskiy, Wilhelm Schänzer, Mario Thevis
ELECTROPHORESIS (2008) 29(22): 4495-4502
Improvement of bacterial two-hybrid vectors for detection of fusion proteins and transfer to pBAD-tandem affinity purification, calmodulin binding peptide, or 6-histidine tag vectors
Aurélia Battesti, Emmanuelle Bouveret
PROTEOMICS (2008) 8(22): 4768-4771
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