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SPS' Digest

Issue 05, 2-Apr-2004

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In this issue, 114 articles have been selected from:
Disclaimer: The selection and categorisation reflect the views and understandings of contributors (i.e. SPS members).

Quick jumps to articles in: Bioinformatics (11) / Biological applications (17) / Biomedical applications (18) / Clinical applications (14) / Eukaryotic Cells And Tissues (3) / Prokaryotes (4) / Protein Array (3) / Protein Characterization (8) / Protein-protein interaction (4) / PTMs (12) / Quantitation (3) / Review (5) / Methodology (29) / Books (1) / Meeting (3) / Other (2) /

Bioinformatics

Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data
Daniel C. Chamrad, Gerhard Ko"rting, Kai Stu"hler, Helmut E. Meyer, Joachim Klose, Martin Blu"ggel
PROTEOMICS (2004) 4(3): 619-628

Sweet Substitute: A software tool for in silico fragmentation of peptide-linked N-glycans
Stefan Clerens, Wim Van den Ende, Peter Verhaert, Lieve Geenen, Lutgarde Arckens
PROTEOMICS (2004) 4(3): 629-632

Database search post-processing by neural network: Advanced facilities for identification of components in protein mixtures using mass spectrometric peptide mapping
Petr G. Lokhov, Olga V. Tikhonova, Sergei A. Moshkovskii, Eugene I. Goufman, Marina V. Serebriakova, Boris I. Maksimov, Ilya Yu. Toropyguine, Victor G. Zgoda, Vadim M. Govorun, Alexander I. Archakov
PROTEOMICS (2004) 4(3): 633-642

A map of WW domain family interactions
Hai Hu, John Columbus, Yi Zhang, Dongying Wu, Lubing Lian, Song Yang, Jennifer Goodwin, Christine Luczak, Mark Carter, Lin Chen, Michael James, Roger Davis, Marius Sudol, John Rodwell, Juan J. Herrero
PROTEOMICS (2004) 4(3): 643-655

Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture
Kris Laukens, Peter Deckers, Eddy Esmans, Harry Van Onckelen, Erwin Witters
PROTEOMICS (2004) 4(3): 720-727

The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches
Bianca Habermann, Jeffrey Oegema, Shamil Sunyaev, and Andrej Shevchenko
Mol Cell Proteomics (2004) 3(3): 238-249

Predicting subcellular localization of proteins using machine-learned classifiers
Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner
Bioinformatics (2004) 20(4): 547-556

Statistical Models for Protein Validation Using Tandem Mass Spectral Data and Protein Amino Acid Sequence Databases
Rovshan G. Sadygov, Hongbin Liu, and John R. Yates
ANALYTICAL CHEMISTRY (2004) 76(6): 1664-1671

Improving large-scale proteomics by clustering of mass spectrometry data
Ilan Beer, Eilon Barnea, Tamar Ziv, Arie Admon
PROTEOMICS (2004) 4(4): 950-960

A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST
Jane Razumovskaya, Victor Olman, Dong Xu, Edward C. Uberbacher, Nathan C. VerBerkmoes, Robert L. Hettich, Ying Xu
PROTEOMICS (2004) 4(4): 961-969

Artificial Neural Network Analysis for Evaluation of Peptide MS/MS Spectra in Proteomics
Tomasz B czek, Adam Buci ski, Alexander R. Ivanov, and Roman Kaliszan
ANALYTICAL CHEMISTRY (2004) 76(6): 1726-1732

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Biological applications

Extensive analysis of the human platelet proteome by two-dimensional gel electrophoresis and mass spectrometry
Angel Garci'a, Sripadi Prabhakar, Chris J. Brock, Andrew C. Pearce, Raymond A. Dwek, Steve P. Watson, Holger F. Hebestreit, Nicole Zitzmann
PROTEOMICS (2004) 4(3): 656-668

Cell wall proteomics of the green alga Haematococcus pluvialis (Chlorophyceae)
Sheng-Bing Wang, Qiang Hu, Milton Sommerfeld, Feng Chen
PROTEOMICS (2004) 4(3): 692-708

Differential protein expression assessed by two-dimensional gel electrophoresis for two wheat varieties grown at four nitrogen levels
Nasser Bahrman, Jacques Le Gouis, Luc Negroni, Laurence Amilhat, Philippe Leroy, Anne-Lyse Laine', Odile Jaminon
PROTEOMICS (2004) 4(3): 709-719

Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry
Kristian Sass Bak-Jensen, Sabrina Laugesen, Peter Roepstorff, Birte Svensson
PROTEOMICS (2004) 4(3): 728-742

Comparative proteome analysis of thalamus in MK-801-treated rats
Linda Paulson, Peter Martin, Carol L. Nilsson, Elisabeth Ljung, Ann Westman-Brinkmalm, Kaj Blennow, Pia Davidsson
PROTEOMICS (2004) 4(3): 819-825

Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis
Tina Guldberg Klen?, Lise R?nnedal Leonardsen, Helle ?rsted Kjeldal, Steen M?ller Laursen, Ole N?rregaard Jensen, Dorrit Baunsgaard
PROTEOMICS (2004) 4(3): 868-880

Synergistic Computational and Experimental Proteomics Approaches for More Accurate Detection of Active Serine Hydrolases in Yeast
Susan M. Baxter, Jonathan S. Rosenblum, Stacy Knutson, Melanie R. Nelson, Jennifer S. Montimurro, Jeannine A. Di Gennaro, Jeffrey A. Speir, Jonathan J. Burbaum, and Jacquelyn S. Fetrow
Mol Cell Proteomics (2004) 3(3): 209-225

A Proteome Analysis of the Subcutaneous Gel in Avian Hatchlings
Lynn McLean, Mary K. Doherty, D. Charles Deeming, and Robert J. Beynon
Mol Cell Proteomics (2004) 3(3): 250-256

Proteomic Characterization of Protein Phosphatase Complexes of the Mammalian Nucleus
Hue T. Tran, Annegret Ulke, Nick Morrice, Christine J. Johannes, and Greg B. G. Moorhead
Mol Cell Proteomics (2004) 3(3): 257-265

Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli
Jaya K. Kumar, Stanley Tabor, and Charles C. Richardson
PNAS (2004) 101(11): 3759-3764

The modal distribution of protein isoelectric points reflects amino acid properties rather than sequence evolution
Georg F. Weiller, Gilles Caraux, Nicole Sylvester
PROTEOMICS (2004) 4(4): 943-949

Transforming growth factor-?1-regulated proteins in human endothelial cells identified by two-dimensional gel electrophoresis and mass spectrometry
Marta Lomnytska, Vasyl Lukiyanchuk, Ulf Hellman, Serhiy Souchelnytskyi
PROTEOMICS (2004) 4(4): 995-1006

Proteome analysis of adipogenesis
Gavin I. Welsh, Matthew R. Griffiths, Kenneth J. Webster, Martin J. Page, Jeremy M. Tavare'
PROTEOMICS (2004) 4(4): 1042-1051

Serum Peptide Profiling by Magnetic Particle-Assisted, Automated Sample Processing and MALDI-TOF Mass Spectrometry
Josep Villanueva, John Philip, David Entenberg, Carlos A. Chaparro, Meena K. Tanwar, # Eric C. Holland, # and Paul Tempst
ANALYTICAL CHEMISTRY (2004) 76(6): 1560-1570

High-Throughput Comprehensive Analysis of Human Plasma Proteins: A Step toward Population Proteomics
Dobrin Nedelkov, Kemmons A. Tubbs, Eric E. Niederkofler, Urban A. Kiernan, and Randall W. Nelson
ANALYTICAL CHEMISTRY (2004) 76(6): 1733-1737

Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast
Johannes Graumann, Leslie A. Dunipace, Jae Hong Seol, W. Hayes McDonald, John R. Yates, III, Barbara J. Wold, and Raymond J. Deshaies
Mol Cell Proteomics (2004) 3(3): 226-237

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Biomedical applications

A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification
Rick L. Hamler, Kan Zhu, Nathan S. Buchanan, Paweena Kreunin, Maureen T. Kachman, Fred R. Miller, David M. Lubman
PROTEOMICS (2004) 4(3): 562-577

Preparation of human heart for laser microdissection and proteomics
Ayesha I. De Souza, Emma McGregor, Michael J. Dunn, Marlene L. Rose
PROTEOMICS (2004) 4(3): 578-586

Proteomic analysis of lymph
Lee V. Leak, Lance A. Liotta, Henry Krutzsch, Michael Jones, Vincent A. Fusaroa, Sally J. Ross, Yingming Zhao, Emanuel F. Petricoin III
PROTEOMICS (2004) 4(3): 753-765

Ovarian cancer detection by logical analysis of proteomic data
Gabriela Alexe, Sorin Alexe, Lance A. Liotta, Emanuel Petricoin, Michael Reiss, Peter L. Hammer
PROTEOMICS (2004) 4(3): 766-783

Proteomic analysis of selected prognostic factors of breast cancer
Kylie Roberts, Kiron Bhatia, Peter Stanton, Roger Lord
PROTEOMICS (2004) 4(3): 784-792

Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry
David B. Friedman, Salisha Hill, Jeffrey W. Keller, Nipun B. Merchant, Shawn E. Levy, Robert J. Coffey, Richard M. Caprioli
PROTEOMICS (2004) 4(3): 793-811

Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status
Mary Ann Comunale, Taj S. Mattu, Melissa A. Lowman, Alison A. Evans, W. Thomas London, O. John Semmes, Michael Ward, Richard Drake, Patrick R. Romano, Laura F. Steel, Timothy M. Block, Anand Mehta
PROTEOMICS (2004) 4(3): 826-838

Proteomic analysis of mouse jejunal epithelium and its response to infection with the intestinal nematode, Trichinella spiralis
Alan D. Pemberton, Pamela A. Knight, Steven H. Wright, Hugh R. P. Miller
PROTEOMICS (2004) 4(4): 1101-1108

Identification of human whole saliva protein components using proteomics
Rui Vitorino, Maria Joa~o C. Lobo, Anto'nio J. Ferrer-Correira, Joshua R. Dubin, Kenneth B. Tomer, Pedro M. Domingues, Francisco M. L. Amado
PROTEOMICS (2004) 4(4): 1109-1115

Quantitative profiling of LNCaP prostate cancer cells using isotope-coded affinity tags and mass spectrometry
Katie L. Meehan, Marianne D. Sadar
PROTEOMICS (2004) 4(4): 1116-1134

Proteomic analysis of cholangiocarcinoma cell line
Chantragan Srisomsap, Phannee Sawangareetrakul, Pantipa Subhasitanont, Tasanee Panichakul, Siriporn Keeratichamroen, Kriengsak Lirdprapamongkol, Daranee Chokchaichamnankit, Stitaya Sirisinha, Jisnuson Svasti
PROTEOMICS (2004) 4(4): 1135-1144

Proteomic determination of metabolic enzymes of the amnion cell: Basis for a possible diagnostic tool?
Ji-eun Oh, Michael Fountoulakis, Jean-Franc,ois Juranville, Margit Rosner, Markus Hengstschlaeger, Gert Lubec
PROTEOMICS (2004) 4(4): 1145-1158

Characterization of the human urinary proteome: A method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots
Rembert Pieper, Christine L. Gatlin, Andrew M. McGrath, Anthony J. Makusky, Madhu Mondal, Michael Seonarain, Erin Field, Courtney R. Schatz, Marla A. Estock, Nasir Ahmed, Norman G. Anderson, Sandra Steiner
PROTEOMICS (2004) 4(4): 1159-1174

Identification of novel and downregulated biomarkers for alcoholism by surface enhanced laser desorption/ionization-mass spectrometry
Fumio Nomura, Takeshi Tomonaga, Kazuyuki Sogawa, Tatsuya Ohashi, Masahiko Nezu, Masahiko Sunaga, Naoki Kondo, Masaomi Iyo, Hideaki Shimada, Takenori Ochiai
PROTEOMICS (2004) 4(4): 1187-1194

Identification of circulating antibodies to tumor-associated proteins for combined use as markers of non-small cell lung cancer
Li Zhong, Xuejun Peng, Giovanna E. Hidalgo, Dennis E. Doherty, Arnold J. Stromberg, Edward A. Hirschowitz
PROTEOMICS (2004) 4(4): 1216-1225

Proteome analysis of hepatocellular carcinoma cell strains, MHCC97-H and MHCC97-L, with different metastasis potentials
Shi-Jian Ding, Yan Li, Xiao-Xia Shao, Hu Zhou, Rong Zeng, Zhao-You Tang, Qi-Chang Xia
PROTEOMICS (2004) 4(4): 982-994

Mass spectrometric analysis of Plasmodium falciparum erythrocyte membrane protein-1 variants expressed by placental malaria parasites
Michal Fried, Jason P. Wendler, Theonest K. Mutabingwa, Patrick E. Duffy
PROTEOMICS (2004) 4(4): 1086-1093

SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer
Emanuel F Petricoin and Lance A Liotta
Current Opinion in Biotechnology (2004) 15(1): 24-30

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Clinical applications

Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards
Eric Kuhn, Jiang Wu, Johann Karl, Hua Liao, Werner Zolg, Brad Guild
PROTEOMICS (2004) 4(4): 1175-1186

Immunoproteomics: Mass Spectrometry-based Methods to Study the Targets of the Immune Response
A. W. Purcell and J. J. Gorman
Mol Cell Proteomics (2004) 3(3): 193-208

A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification
Rick L. Hamler, Kan Zhu, Nathan S. Buchanan, Paweena Kreunin, Maureen T. Kachman, Fred R. Miller, David M. Lubman
PROTEOMICS (2004) 4(3): 562-577

Preparation of human heart for laser microdissection and proteomics
Ayesha I. De Souza, Emma McGregor, Michael J. Dunn, Marlene L. Rose
PROTEOMICS (2004) 4(3): 578-586

Identification and characterization of phosphorylated proteins in the human pituitary
Francesco Giorgianni, Sarka Beranova-Giorgianni, Dominic M. Desiderio
PROTEOMICS (2004) 4(3): 587-598

Extensive analysis of the human platelet proteome by two-dimensional gel electrophoresis and mass spectrometry
Angel Garci'a, Sripadi Prabhakar, Chris J. Brock, Andrew C. Pearce, Raymond A. Dwek, Steve P. Watson, Holger F. Hebestreit, Nicole Zitzmann
PROTEOMICS (2004) 4(3): 656-668

Proteomic analysis of lymph
Lee V. Leak, Lance A. Liotta, Henry Krutzsch, Michael Jones, Vincent A. Fusaroa, Sally J. Ross, Yingming Zhao, Emanuel F. Petricoin III
PROTEOMICS (2004) 4(3): 753-765

Ovarian cancer detection by logical analysis of proteomic data
Gabriela Alexe, Sorin Alexe, Lance A. Liotta, Emanuel Petricoin, Michael Reiss, Peter L. Hammer
PROTEOMICS (2004) 4(3): 766-783

Proteomic analysis of selected prognostic factors of breast cancer
Kylie Roberts, Kiron Bhatia, Peter Stanton, Roger Lord
PROTEOMICS (2004) 4(3): 784-792

Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry
David B. Friedman, Salisha Hill, Jeffrey W. Keller, Nipun B. Merchant, Shawn E. Levy, Robert J. Coffey, Richard M. Caprioli
PROTEOMICS (2004) 4(3): 793-811

Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status
Mary Ann Comunale, Taj S. Mattu, Melissa A. Lowman, Alison A. Evans, W. Thomas London, O. John Semmes, Michael Ward, Richard Drake, Patrick R. Romano, Laura F. Steel, Timothy M. Block, Anand Mehta
PROTEOMICS (2004) 4(3): 826-838

Effect of collagen substrates on proteomic modulation of breast cancer cells
Simona Fontana, Ida Pucci-Minafra, Michel Becchi, Anne-Marie Freyria, Salvatore Minafra
PROTEOMICS (2004) 4(3): 849-860

Proteomics of methylene blue photo-treated plasma before and after removal of the dye by an absorbent filter
David Crettaz, Luc Sensebe, Dinh-Hao Vu, Philippe Schneider, Franc,ois Depasse, Willy-Vincent Bienvenut, Manfredo Quadroni, Jean-Daniel Tissot
PROTEOMICS (2004) 4(3): 881-891

Search for serum protein-binding disaccharides and disaccharide-binding serum proteins by affinity capillary electrophoresis
Atsushi Taga, Yuka Yamamoto, Rie Maruyama, Susumu Honda
ELECTROPHORESIS (2004) 25(6): 876-881

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Eukaryotic Cells And Tissues

Protein profiling and identification of modulators regulated by the E7 oncogene in the C33A cell line by proteomics and genomics
Kyung-Ae Lee, Jung-Hyun Shim, Chang Won Kho, Sung Goo Park, Byoung Chul Park, Jae-Wha Kim, Jong-Seok Lim, Yong-Kyung Choe, Sang-Gi Paik, Do-Young Yoon
PROTEOMICS (2004) 4(3): 839-848

Effect of collagen substrates on proteomic modulation of breast cancer cells
Simona Fontana, Ida Pucci-Minafra, Michel Becchi, Anne-Marie Freyria, Salvatore Minafra
PROTEOMICS (2004) 4(3): 849-860

Proteomic analysis of hyperoxia-induced responses in the human choriocarcinoma cell line JEG-3
Henrik Vorum, Morten ?stergaard, Philip Hensechke, Jan J. Enghild, Mahtab Riazati, Gregory E. Rice
PROTEOMICS (2004) 4(3): 861-867

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Prokaryotes

Identification of chromosomally encoded membranal polypeptides of Bacillus anthracis by a proteomic analysis: Prevalence of proteins containing S-layer homology domains
Theodor Chitlaru, Naomi Ariel, Anat Zvi, Menahem Lion, Baruch Velan, Avigdor Shafferman, Eytan Elhanany
PROTEOMICS (2004) 4(3): 677-691

Proteomic analysis of the human pathogen Trypanosoma cruzi
Jaime Paba, Jaime M. Santana, Antonio R. L. Teixeira, Wagner Fontes, Marcelo V. Sousa, Carlos A. O. Ricart
PROTEOMICS (2004) 4(4): 1052-1059

Two-dimensional reference map of Agrobacterium tumefaciens proteins
Ran Rosen, Ayelet Sacher, Nelia Shechter, Do"rte Becher, Knut Bu"ttner, Dvora Biran, Michael Hecker, Eliora Z. Ron
PROTEOMICS (2004) 4(4): 1061-1073

Differential proteomic analysis of Aeromonas salmonicida outer membrane proteins in response to low iron and in vivo growth conditions
Roger O. Ebanks, Andrew Dacanay, Michel Goguen, Devanand M. Pinto, Neil W. Ross
PROTEOMICS (2004) 4(4): 1074-1085

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Protein Array

About thiol derivatization and resolution of basic proteins in two-dimensional electrophoresis
Sylvie Luche, He'le`ne Diemer, Chistophe Tastet, Mireille Chevallet, Alain Van Dorsselaer, Emmanuelle Leize-Wagner, Thierry Rabilloud
PROTEOMICS (2004) 4(3): 551-561

Photoaptamer arrays applied to multiplexed proteomic analysis
Chris Bock, Mike Coleman, Brian Collins, Jody Davis, Glenn Foulds, Larry Gold, Chad Greef, Jim Heil, Joseph S. Heilig, Brian Hicke, Michele Nelson Hurst, Gregory M. Husar, Darcey Miller, Rachel Ostroff, Helen Petach, Dan Schneider, Barry Vant-Hull, Sheela Waugh, Allison Weiss, Sheri K. Wilcox, Dominic Zichi
PROTEOMICS (2004) 4(3): 609-618

Probing Protein-Carbohydrate Interactions with Microarrays of Synthetic Oligosaccharides
Daniel M. Ratner, Eddie W. Adams, Jing Su, Barry R. O'Keefe, Milan Mrksich, Peter H. Seeberger
ChemBioChem (2004) 5(3): 379-383

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Protein Characterization

About the mechanism of interference of silver staining with peptide mass spectrometry
Sophie Richert, Sylvie Luche, Mireille Chevallet, Alain Van Dorsselaer, Emmanuelle Leize-Wagner, Thierry Rabilloud
PROTEOMICS (2004) 4(4): 909-916

The modal distribution of protein isoelectric points reflects amino acid properties rather than sequence evolution
Georg F. Weiller, Gilles Caraux, Nicole Sylvester
PROTEOMICS (2004) 4(4): 943-949

Protein kinase A phosphorylation characterized by tandem Fourier transform ion cyclotron resonance mass spectrometry
Michael J. Chalmers, Kristina Ha*kansson, Robert Johnson, Richard Smith, Jianwei Shen, Mark R. Emmett, Alan G. Marshall
PROTEOMICS (2004) 4(4): 970-981

>From The Cover: Water in protein structure prediction
Garegin A. Papoian, Johan Ulander, Michael P. Eastwood, Zaida Luthey-Schulten, and Peter G. Wolynes
PNAS (2004) 101(10): 3352-3357

Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain
John Karanicolas and Charles L. Brooks, III
PNAS (2004) 101(10): 3432-3437

Screening protein refolding using surface plasmon resonance
Daniel B. Jones, Matthew H. Hutchinson, Anton P. J. Middelberg
PROTEOMICS (2004) 4(4): 1007-1013

Influence of Basic Residue Content on Fragment Ion Peak Intensities in Low-Energy Collision-Induced Dissociation Spectra of Peptides
David L. Tabb, Yingying Huang, Vicki H. Wysocki, and John R. Yates, III
ANALYTICAL CHEMISTRY (2004) 76(5): 1243-1248

Trace Labeling of Proteins with Stable Isotopes To Identify Fragments in Complex Mixtures
Juan Zou, A. Neil Turner, and Richard G. Phelps
ANALYTICAL CHEMISTRY (2004) 76(5): 1445-1452

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Protein-protein interaction

Use of Magnetic Nanoparticles as Nanosensors to Probe for Molecular Interactions
J. Manuel Perez, Lee Josephson, Ralph Weissleder
ChemBioChem (2004) 5(3): 261-264

Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast
Johannes Graumann, Leslie A. Dunipace, Jae Hong Seol, W. Hayes McDonald, John R. Yates, III, Barbara J. Wold, and Raymond J. Deshaies
Mol Cell Proteomics (2004) 3(3): 226-237

Functional and topological characterization of protein interaction networks
Soon-Hyung Yook, Zolta'n N. Oltvai, Albert-La'szlo' Baraba'si
PROTEOMICS (2004) 4(4): 928-942

Radiolytic Modification of Acidic Amino Acid Residues in Peptides: Probes for Examining Protein-Protein Interactions
Guozhong Xu and Mark R. Chance
ANALYTICAL CHEMISTRY (2004) 76(5): 1213-1221

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PTMs

Effect of chromatographic conditions on resolution in high-performance ion-exchange chromatography of proteins on macroporous anion-exchange resin
Yoshio Kato, Koji Nakamura, Takashi Kitamura, Teruhiko Tsuda, Masazumi Hasegawa and Hiroo Sasaki
Journal of Chromatography A (2004) 1031(1-2): 101-105

The Q-Trap mass spectrometer, a novel tool in the study of protein glycosylation
K. Sandra, B. Devreese, J. Van Beeumen, I. Stals and M. Claeyssens
Journal of The American Society for Mass Spectrometry (2004) 15(3): 413-423

Identification and characterization of phosphorylated proteins in the human pituitary
Francesco Giorgianni, Sarka Beranova-Giorgianni, Dominic M. Desiderio
PROTEOMICS (2004) 4(3): 587-598

Proteomic analysis of ?-casein micro-heterogeneity
John W. Holland, Hilton C. Deeth, Paul F. Alewood
PROTEOMICS (2004) 4(3): 743-752

Proline-Directed Random-Coil Chemical Shift Values as a Tool for the NMR Assignment of the Tau Phosphorylation Sites
Guy Lippens, Jean-Michel Wieruszeski, Arnaud Leroy, Caroline Smet, Alain Sillen, Luc Bue'e, Isabelle Landrieu
ChemBioChem (2004) 5(3): 256

Expanding the Diversity of Unnatural Cell-Surface Sialic Acids
Sarah J. Luchansky, Scarlett Goon, Carolyn R. Bertozzi
ChemBioChem (2004) 5(3): 371-374

Targeted analysis and discovery of posttranslational modifications in proteins from methanogenic archaea by top-down MS
Andrew J. Forbes, Steven M. Patrie, Gregory K. Taylor, Yong-Bin Kim, Lihua Jiang, and Neil L. Kelleher
PNAS (2004) 101(9): 2678-2683

Metal Ligand Affinity Pipettes and Bioreactive Alkaline Phosphatase Probes: Tools for Characterization of Phosphorylated Proteins and Peptides
Allan L. Bieber, Kemmons A. Tubbs, and Randall W. Nelson
Mol Cell Proteomics (2004) 3(3): 266-272

Identification of Phosphoproteins and Their Phosphorylation Sites in the WEHI-231 B Lymphoma Cell Line
Hongjun Shu, She Chen, Qun Bi, Marc Mumby, and Deirdre L. Brekken
Mol Cell Proteomics (2004) 3(3): 279-286

Identification of apoptotic tyrosine-phosphorylated proteins after etoposide or retinoic acid treatment
Ruta Navakauskiene, Grazina Treigyte, Arunas Gineitis, Karl-Eric Magnusson
PROTEOMICS (2004) 4(4): 1029-1041

Contributions of commercial sorbents to the selectivity in immobilized metal affinity chromatography with Cu(II)
Diya Ren, Natalia A. Penner, Benjamin E. Slentz, Halina D. Inerowicz, Marina Rybalko and Fred E. Regnier
Journal of Chromatography A (2004) 1031(1-2): 87-92

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Quantitation

Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling
Tao He, Kim Alving, Brian Feild, James Norton, Elizabeth G. Joseloff, Scott D. Patterson and Bruno Domon
Journal of The American Society for Mass Spectrometry (2004) 15(3): 363-373

Isotope-coded Affinity Tag Approach to Identify and Quantify Oxidant-sensitive Protein Thiols
Mahadevan Sethuraman, Mark E. McComb, Tyler Heibeck, Catherine E. Costello, and Richard A. Cohen
Mol Cell Proteomics (2004) 3(3): 273-278

Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics
Gert Van den Bergh and Lutgarde Arckens
Current Opinion in Biotechnology (2004) 15(1): 38-43

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Review

Proteomics in living cells
Stephen W. Michnick
Drug Discovery Today (2004) 9(6): 262-267

Immunoproteomics: Mass Spectrometry-based Methods to Study the Targets of the Immune Response
A. W. Purcell and J. J. Gorman
Mol Cell Proteomics (2004) 3(3): 193-208

Water and proteins: A love-hate relationship
Yaakov Levy and Jose N. Onuchic
PNAS (2004) 101(10): 3325-3326

Membrane proteins: A new method enters the fold
James U. Bowie
PNAS (2004) 101(12): 3995-3996

Evolution and evolvability of proteins in the laboratory
Michael W. Deem
PNAS (2004) 101(12): 3997-3998

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Methodology

MALDI post-source decay and LIFT-TOF/TOF investigation of alpha-cyano-4-hydroxycinnamic acid cluster interferences
Hendrik Neubert, John M. Halket, Mireia Fernandez Ocana and Raj K. P. Patel
Journal of The American Society for Mass Spectrometry (2004) 15(3): 336-343

A novel nib-like design for microfabricated nanospray tips
Severine Le Gac, Cecile Cren-Olive, Christian Rolando and Steve Arscott
Journal of The American Society for Mass Spectrometry (2004) 15(3): 409-412

Targeted analysis and discovery of posttranslational modifications in proteins from methanogenic archaea by top-down MS
Andrew J. Forbes, Steven M. Patrie, Gregory K. Taylor, Yong-Bin Kim, Lihua Jiang, and Neil L. Kelleher
PNAS (2004) 101(9): 2678-2683

About thiol derivatization and resolution of basic proteins in two-dimensional electrophoresis
Sylvie Luche, He'le`ne Diemer, Chistophe Tastet, Mireille Chevallet, Alain Van Dorsselaer, Emmanuelle Leize-Wagner, Thierry Rabilloud
PROTEOMICS (2004) 4(3): 551-561

Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies
Kris Gevaert, Bart Ghesquie`re, An Staes, Lennart Martens, Jozef Van Damme, Gre'goire R. Thomas, Joe"l Vandekerckhove
PROTEOMICS (2004) 4(4): 897-908

Nonredundant mass spectrometry: A strategy to integrate mass spectrometry acquisition and analysis
Alexander Scherl, Patrice Francois, Ve'ronique Converset, Manuela Bento, Jennifer A. Burgess, Jean-Charles Sanchez, Denis F. Hochstrasser, Jacques Schrenzel, Garry L. Corthals
PROTEOMICS (2004) 4(4): 917-927

Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins
Stefanie Wienkoop, Mirko Glinski, Nobuo Tanaka, Vladimir Tolstikov, Oliver Fiehn, Wolfram Weckwerth
Rapid Communications in Mass Spectrometry (2004) 18(6): 617-628

A complete peptide mapping of membrane proteins: a novel surfactant aiding the enzymatic digestion of bacteriorhodopsin
Ying-Qing Yu, Martin Gilar, John C. Gebler
Rapid Communications in Mass Spectrometry (2004) 18(6): 711-715

Improved Ruthenium II tris (bathophenantroline disulfonate) staining and destaining protocol for a better signal-to-background ratio and improved baseline resolution
Andreas Lamanda, Alain Zahn, Daniel Ro"der, Hanno Langen
PROTEOMICS (2004) 4(3): 599-608

Determination of the stoichiometry of protein complexes using liquid chromatography with fluorescence and mass spectrometric detection of fluorescently labeled proteolytic peptides
Elisabeth O. Hochleitner, Peter Sondermann, Friedrich Lottspeich
PROTEOMICS (2004) 4(3): 669-676

Profiling the activity of G proteins in patient-derived tissues by rapid affinity-capture of signal transduction proteins (GRASP)
David M. Berman, Ie-Ming Shih, Lorri-Anne Burke, Timothy D. Veenstra, Yingming Zhao, Thomas P. Conrads, Sung Won Kwon, Van Hoang, Li-Rong Yu, Ming Zhou, Robert J. Kurman, Emanuel F. Petricoin, Lance A. Liotta
PROTEOMICS (2004) 4(3): 812-818

Proteomics of methylene blue photo-treated plasma before and after removal of the dye by an absorbent filter
David Crettaz, Luc Sensebe, Dinh-Hao Vu, Philippe Schneider, Franc,ois Depasse, Willy-Vincent Bienvenut, Manfredo Quadroni, Jean-Daniel Tissot
PROTEOMICS (2004) 4(3): 881-891

About the mechanism of interference of silver staining with peptide mass spectrometry
Sophie Richert, Sylvie Luche, Mireille Chevallet, Alain Van Dorsselaer, Emmanuelle Leize-Wagner, Thierry Rabilloud
PROTEOMICS (2004) 4(4): 909-916

A combination of proteomics, principal component analysis and transcriptomics is a powerful tool for the identification of biomarkers for macrophage maturation in the U937 cell line
Kitty C. M. Verhoeckx, Sabina Bijlsma, Els M. de Groene, Renger F. Witkamp, Jan van der Greef, Richard J. T. Rodenburg
PROTEOMICS (2004) 4(4): 1014-1028

Mycobacterial proteome extraction: Comparison of disruption methods
Mark D. Lanigan, Jill A. Vaughan, Brian J. Shiell, Gary J. Beddome, Wojtek P. Michalski
PROTEOMICS (2004) 4(4): 1094-1100

Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry
Oleg Chertov, Arya Biragyn, Larry W. Kwak, John T. Simpson, Tatiana Boronina, Van M. Hoang, DaRue A. Prieto, Thomas P. Conrads, Timothy D. Veenstra, Robert J. Fisher
PROTEOMICS (2004) 4(4): 1195-1203

Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast
Johannes Graumann, Leslie A. Dunipace, Jae Hong Seol, W. Hayes McDonald, John R. Yates, III, Barbara J. Wold, and Raymond J. Deshaies
Mol Cell Proteomics (2004) 3(3): 226-237

One- and Two-Dimensional Miniaturized Electrophoresis of Proteins with Native Fluorescence Detection
Chanan Sluszny and Edward S. Yeung
ANALYTICAL CHEMISTRY (2004) 76(5): 1359-1365

Influence of Basic Residue Content on Fragment Ion Peak Intensities in Low-Energy Collision-Induced Dissociation Spectra of Peptides
David L. Tabb, Yingying Huang, Vicki H. Wysocki, and John R. Yates, III
ANALYTICAL CHEMISTRY (2004) 76(5): 1243-1248

Trace Labeling of Proteins with Stable Isotopes To Identify Fragments in Complex Mixtures
Juan Zou, A. Neil Turner, and Richard G. Phelps
ANALYTICAL CHEMISTRY (2004) 76(5): 1445-1452

Enzymatic Tissue Digestion as an Alternative Sample Preparation Approach for Quantitative Analysis Using Liquid Chromatography-Tandem Mass Spectrometry
Chongwoo Yu, Lara D. Penn, John Hollembaek, Wenlin Li, and Lucinda H. Cohen
ANALYTICAL CHEMISTRY (2004) 76(6): 1761-1767

Potential of silica monolithic columns in peptide separations
Li Xiong, Roujian Zhang and Fred E. Regnier
Journal of Chromatography A (2004) 1030(1-2): 187-194

Gas phase derivatization in peptide analysis I: the utility of trimethyl borate in identifying phosphorylation sites
Scott Gronert, Renee Huang and Kathy H. Li
International Journal of Mass Spectrometry (2004) 231(2-3): 179-187

Electron-capture dissociation tandem mass spectrometry
Roman A Zubarev
Current Opinion in Biotechnology (2004) 15(1): 12-16

The molecular scanner: concept and developments
Pierre-Alain Binz, Markus Muller, Christine Hoogland, Catherine Zimmermann, Carla Pasquarello, Garry Corthals, Jean-Charles Sanchez, Denis F Hochstrasser and Ron D Appel
Current Opinion in Biotechnology (2004) 15(1): 17-23

Enhanced Ionization of Phosphorylated Peptides during MALDI TOF Mass Spectrometry
Xiaofeng Yang, Huaping Wu, Tomoyoshi Kobayashi, R. John Solaro, and Richard B. van Breemen
ANALYTICAL CHEMISTRY (2004) 76(5): 1532-1536

Why the move to microfluidics for protein analysis?
Niels Lion, Frederic Reymond, Hubert H Girault and Joel S Rossier
Current Opinion in Biotechnology (2004) 15(1): 31-37

Field-enhanced sample injection for high-sensitivity analysis of peptides and proteins in capillary electrophoresis-mass spectrometry
Maria Rowena N. Monton and Shigeru Terabe
Journal of Chromatography A (2004) 1032(1-2): 203-211

Mutant rat trypsin selectively cleaves tyrosyl peptide bonds
Gabor Pal, Andras Patthy, Jozsef Antal and Laszlo Graf
Analytical Biochemistry (2004) 326(2): 190-199

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Books

Book Review: Methods in Molecular Biology, Vol. 228: Membrane Protein Protocols: Expression, Purification and Characterization. Edited by Barry S. Selinsky
Reinhard Grisshammer
ChemBioChem (2004) 5(3): 388-389

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Meeting

Meetings: Proteomics 3/2004
PROTEOMICS (2004) 4(3): 892

Meetings: Proteomics 4/2004
PROTEOMICS (2004) 4(4): 1229

Calendar
Mol Cell Proteomics (2004) 3(3): 287-288

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Other

One- and Two-Dimensional Miniaturized Electrophoresis of Proteins with Native Fluorescence Detection
Chanan Sluszny and Edward S. Yeung
ANALYTICAL CHEMISTRY (2004) 76(5): 1359-1365

Protein dynamics and the immunological evolution of molecular recognition
Ralph Jimenez, Georgina Salazar, Jun Yin, Taiha Joo, and Floyd E. Romesberg
PNAS (2004) 101(11): 3803-3808

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