SPS logo    

SPS' Digest

Issue 08, 5-Jul-2004

[Current issue] [Archives] [Search] [Email alert] [Submit article]

In this issue, 78 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 (4) / Biomedical applications (2) / Clinical applications (17) / Eukaryotic Cells And Tissues (2) / Prokaryotes (1) / Protein Characterization (1) / Protein-protein interaction (4) / PTMs (8) / Quantitation (1) / Review (3) / Methodology (19) / Meeting (1) / Other (7) /

Bioinformatics

High-throughput automated post-processing of separation data
Jonathan G. Shackman, Christopher J. Watson and Robert T. Kennedy
Journal of Chromatography A (2004) 1040(2): 273-282

ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels
Brian D. Halligan, Victor Ruotti, Weihong Jin, Scott Laffoon, Simon N. Twigger, and Edward A. Dratz
Nucl. Acids. Res. (2004) 32(Web Server issue): W638-W644

GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates
Klaus Karl Lohmann and Claus-W. von der Lieth
Nucl. Acids. Res. (2004) 32(Web Server issue): W261-W266

ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry
Richard D. LeDuc, Gregory K. Taylor, Yong-Bin Kim, Thomas E. Januszyk, Lee H. Bynum, Joseph V. Sola, John S. Garavelli, and Neil L. Kelleher
Nucl. Acids. Res. (2004) 32(Web Server issue): W340-W345

TANDEM: matching proteins with tandem mass spectra
Robertson Craig and Ronald C. Beavis
Bioinformatics (2004) 20(9): 1466-1467

Using Proteomics to Mine Genome Sequences
Jonathan W. Arthur and Marc R. Wilkins
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 393-402

Identification of Phosphorylation Sites in Protein Kinase A Substrates Using Artificial Neural Networks and Mass Spectrometry
Majbrit Hjerrild, Allan Stensballe, Thomas E. Rasmussen, Christine B. Kofoed, Nikolaj Blom, Thomas Sicheritz-Ponten, Martin R. Larsen, S ren Brunak, Ole N. Jensen, and Steen Gammeltoft
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 426-433

Simple Method for Three-Dimensional Representation of 2-DE Spots Using a Spreadsheet Program
Martin H. Maurer
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 665-666

SILVER helps assign peptides to tandem mass spectra using intensity-based scoring
Francis D. Gibbons, Joshua E. Elias, Steven P. Gygi and Frederick P. Roth
Journal of The American Society for Mass Spectrometry (2004) 15(6): 910-912

Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, and David Meeuwis
Nucl. Acids. Res. (2004) 32(Web Server issue): W365-W371

PrediSi: prediction of signal peptides and their cleavage positions
Karsten Hiller, Andreas Grote, Maurice Scheer, Richard Munch, and Dieter Jahn
Nucl. Acids. Res. (2004) 32(Web Server issue): W375-W379

[Back to TOP]

Biological applications

Global Analysis of the Membrane Subproteome of Pseudomonas aeruginosa Using Liquid Chromatography-Tandem Mass Spectrometry
Josip Blonder, Michael B. Goshe, Wenzhong Xiao, David G. Camp II, Mark Wingerd, Ronald W. Davis, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 434-444

Expanded Coverage of the Human Heart Mitochondrial Proteome Using Multidimensional Liquid Chromatography Coupled with Tandem Mass Spectrometry
Sara P. Gaucher, Steven W. Taylor, Eoin Fahy, Bing Zhang, # Dale E. Warnock, Soumitra S. Ghosh, and Bradford W. Gibson
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 495-505

Shotgun Proteomics of Methanococcus jannaschii and Insights into Methanogenesis
Wenhong Zhu, Claudia I. Reich, Gary J. Olsen, Carol S. Giometti, and John R. Yates III
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 538-548

Proteome Analysis of Lipid Rafts in Jurkat Cells Characterizes a Raft Subset That Is Involved in NF-B Activation
Xiaolin Tu, Aaron Huang, David Bae, Ndaisha Slaughter, Julian Whitelegge, Timothy Crother, Perry E. Bickel, and Andre Nel
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 445-454

[Back to TOP]

Biomedical applications

Investigation of Doxorubicin Resistance in MCF-7 Breast Cancer Cells Using Shot-Gun Comparative Proteomics with Proteolytic 18O Labeling
Kristy J. Brown and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 455-462

Two-dimensional electrophoresis protein profiling and identification in rat bronchoalveolar lavage fluid following allergen and endotoxin challenge
Luca Signor, Bruno Tigani, Nicolau Beckmann, Rocco Falchetto, Markus Stoeckli
PROTEOMICS (2004) 4(7): 2101-2110

[Back to TOP]

Clinical applications

High-resolution serum proteomic features for ovarian cancer detection.
Conrads TP, Fusaro VA, Ross S, Johann D, Rajapakse V, Hitt BA, Steinberg SM, Kohn EC, Fishman DA, Whitely G, Barrett JC, Liotta LA, Petricoin III EF, Veenstra TD.
Endocr Relat Cancer. (2004) 11(2): 163-78

Proteomic approaches in endometriosis research
Anne E. Poliness, Martin G. Healey, Shaun P. Brennecke, Eric K. Moses
PROTEOMICS (2004) 4(7): 1897-1902

Applications of proteomic methodologies to human pregnancy research: A growing gestation approaching delivery?
Renu Shankar, Fiona Cullinane, Shaun Patrick Brennecke, Eric Keith Moses
PROTEOMICS (2004) 4(7): 1909-1917

Two-dimensional electrophoresis protein profiling and identification in rat bronchoalveolar lavage fluid following allergen and endotoxin challenge
Luca Signor, Bruno Tigani, Nicolau Beckmann, Rocco Falchetto, Markus Stoeckli
PROTEOMICS (2004) 4(7): 2101-2110

Proteomic profiling of proteins decreased in hepatocellular carcinoma from patients infected with hepatitis C virus
Yuichiro Yokoyama, Yasuhiro Kuramitsu, Motonari Takashima, Norio Iizuka, Toshifusa Toda, Shuji Terai, Isao Sakaida, Masaaki Oka, Kazuyuki Nakamura, Kiwamu Okita
PROTEOMICS (2004) 4(7): 2111-2116

Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients
Debora Dumont, Jean-Paul Noben, Jef Raus, Piet Stinissen, Johan Robben
PROTEOMICS (2004) 4(7): 2117-2124

A proteomic analysis of changes in prothrombin and plasma proteins associated with the G20210A mutation
Cecilia Gelfi, Agnese Viganò, Marilena Ripamonti, Robin Wait, Shajna Begum, Eugenia Biguzzi, Giancarlo Castaman, Elena Maria Faioni
PROTEOMICS (2004) 4(7): 2151-2159

New antigenic candidates in multiple sclerosis: Identification by serological proteome analysis
Lionel Almeras, Didier Lefranc, Hervé Drobecq, Jérome de Seze, Sylvain Dubucquoi, Patrick Vermersch, Lionel Prin
PROTEOMICS (2004) 4(7): 2184-2194

The Barrett's Antigen Anterior Gradient-2 Silences the p53 Transcriptional Response to DNA Damage
Elizabeth Pohler, Ashley L. Craig, James Cotton, Laura Lawrie, John F.Dillon, Pete Ross, Neil Kernohan, and Ted R. Hupp
Mol Cell Proteomics (2004) 3(6): 534-547

Proteomic Analysis of Human Tears: Defensin Expression after Ocular Surface Surgery
L. Zhou, L. Q. Huang, R. W. Beuerman, M. E. Grigg, S. F. Y. Li, F. T. Chew, # L. Ang, M. E. Stern, and D. Tan
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 410-416

Proteomic Analysis of SARS Associated Coronavirus Using Two-Dimensional Liquid Chromatography Mass Spectrometry and One-Dimensional Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis Followed by Mass Spectroemtric Analysis
Rong Zeng, Hong-Qiang Ruan, Xiao-Sheng Jiang, Hu Zhou, Lv Shi, Lei Zhang, Quan-Hu Sheng, Qiang Tu, Qi-Chang Xia, and Jia-Rui Wu
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 549-555

Proteomic Analysis of Ductal Carcinoma of the Breast Using Laser Capture Microdissection, LC-MS, and 16O/18O Isotopic Labeling
Li Zang, Darryl Palmer Toy, William S. Hancock, Dennis C. Sgroi, and Barry L. Karger
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 604-612

Proteome and Transcriptome Analysis of Retinoic Acid-Induced Differentiation of Human Acute Promyelocytic Leukemia Cells, NB4
Daojing Wang, # Ronald Jensen, Gurmil Gendeh, Katherine Williams, and Maria G. Pallavicini
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 627-635

Protein Expression Profiling of Endometrial Malignancies Reveals a New Tumor Marker: Chaperonin 10
Eric C. C. Yang, Jingzhong Guo, Georg Diehl, Leroi DeSouza, Mary Joe Rodrigues, Alexander D. Romaschin, Terence J. Colgan, and K. W. Michael Siu
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 636-643

Capillary electrophoresis and mass spectrometry for screening of metabolic disorders in newborns
Petr ?enk, Libor Kozák, Franti?ek Foret
ELECTROPHORESIS (2004) 25(10-11): 1447-1456

Proteomics/genomics and signaling in lymphocytes
Bernd Wollscheid, Julian D Watts and Ruedi Aebersold
Current Opinion in Immunology (2004) 16(3): 337-344

Glycoproteomics of cerebrospinal fluid in neurodegenerative disease
Carina Sihlbom, Pia Davidsson, Mark R. Emmett, Alan G. Marshall and Carol L. Nilsson
International Journal of Mass Spectrometry (2004) 234(1-3): 145-152

[Back to TOP]

Eukaryotic Cells And Tissues

Comparative Proteomics of Cannabis sativa Plant Tissues
Tri J. Raharjo, Ivy Widjaja, Sittiruk Roytrakul, and Robert Verpoorte
J Biomol Tech (2004) 15(2): 97-106

Proteomics in the chicken: tools for understanding immune responses to avian diseases.
Burgess SC.
Poult Sci. (2004) 83(4): 552-73

[Back to TOP]

Prokaryotes

Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements
M. Mohiuddin Kabir, Kazuyuki Shimizu
Appl Microbiol Biotechnol (2004) 65(1): 84-96

[Back to TOP]

Protein Characterization

Industrial-scale proteomics: From liters of plasma to chemically synthesized proteins
Keith Rose, Lydie Bougueleret, Thierry Baussant, Günter Böhm, Paolo Botti, Jacques Colinge, Isabelle Cusin, Hubert Gaertner, Anne Gleizes, Manfred Heller, Silvia Jimenez, Andrew Johnson, Martin Kussmann, Laure Menin, Christoph Menzel, Frederic Ranno, Patricia Rodriguez-Tomé, John Rogers, Cedric Saudrais, Matteo Villain, Diana Wetmore, Amos Bairoch, Denis Hochstrasser
PROTEOMICS (2004) 4(7): 2125-2150

[Back to TOP]

Protein-protein interaction

Development of a Protein Chip: A MS-Based Method for Quantitation of Protein Expression and Modification Levels Using an Immunoaffinity Approach
Erin N. Warren, Phillip J. Elms, Carol E. Parker, and Christoph H. Borchers
ANALYTICAL CHEMISTRY Early Edition: published 06/11/2004

Toward a General Chemical Method for Rapidly Mapping Multi-Protein Complexes
Carilee Denison and Thomas Kodadek
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 417-425

Development of an LC-MALDI method for the analysis of protein complexes
Yuejun Zhen, Nafei Xu, Bonnie Richardson, Robert Becklin, Justin R. Savage, Kelly Blake and John M. Peltier
Journal of The American Society for Mass Spectrometry (2004) 15(6): 803-822

Protein interaction networks from yeast to human
Peer Bork, Lars J Jensen, Christian von Mering, Arun K Ramani, Insuk Lee and Edward M Marcotte
Current Opinion in Structural Biology (2004) 14(3): 292-299

[Back to TOP]

PTMs

Localization of the O-Glycosylated Sites in Peptides by Fixed-Charge Derivatization with a Phosphonium Group
Xavier Czeszak, Willy Morelle, Guy Ricart, Daniel Tétaert, and Jérôme Lemoine
ANALYTICAL CHEMISTRY Early Edition: published 06/11/2004

Analysis of Protein Phosphorylation by Hypothesis-Driven Multiple-Stage Mass Spectrometry
Emmanuel J. Chang, Vincent Archambault, Derek T. McLachlin, Brian T. Chait
ANALYTICAL CHEMISTRY Early Edition: published 06/11/2004

Selective Isolation at the Femtomole Level of Phosphopeptides from Proteolytic Digests Using 2D-NanoLC-ESI-MS/MS and Titanium Oxide Precolumns
Martijn W. H. Pinkse, Pauliina M. Uitto, Martijn J. Hilhorst, Bert Ooms, and Albert J. R. Heck
ANALYTICAL CHEMISTRY Early Edition: published 06/18/2004

Predicting N-terminal myristoylation sites in plant proteins
Sheila Podell and Michael Gribskov
BMC Genomics (2004) 5(1): 37

A New Strategy for Identification of N-Glycosylated Proteins and Unambiguous Assignment of Their Glycosylation Sites Using HILIC Enrichment and Partial Deglycosylation
Per Hägglund, Jakob Bunkenborg, Felix Elortza, Ole N rregaard Jensen, and Peter Roepstorff
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 556-566

Lectin Affinity as an Approach to the Proteomic Analysis of Membrane Glycoproteins
Dhiman Ghosh, Oleg Krokhin, Mihaela Antonovici, Werner Ens, Ronald C. Beavis, and John A. Wilkins
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/11/2004

An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins
Adrian D. Hegeman, Amy C. Harms, Michael R. Sussman, Anne E. Bunner and Jeffrey F. Harper
Journal of The American Society for Mass Spectrometry (2004) 15(5): 647-653

Glycoprotein profiling by electrospray mass spectrometry
Hui Jiang, Heather Desaire, Vladimir Y. Butnev and George R. Bousfield
Journal of The American Society for Mass Spectrometry (2004) 15(5): 750-758

[Back to TOP]

Quantitation

Quantitative Analysis of Tryptic Protein Mixtures Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Charlotte Hagman, Margareta Ramström, Per Håkansson, and Jonas Bergquist
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 587-594

[Back to TOP]

Review

Proteomics and cancer: Running before we can walk?
Erika Check
Nature (2004) 429(6991): 496-497

Quantification in Proteomics through Stable Isotope Coding: A Review
Samir Julka and Fred Regnier
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 350-363

Industrial-scale proteomics: From liters of plasma to chemically synthesized proteins
Keith Rose, Lydie Bougueleret, Thierry Baussant, Günter Böhm, Paolo Botti, Jacques Colinge, Isabelle Cusin, Hubert Gaertner, Anne Gleizes, Manfred Heller, Silvia Jimenez, Andrew Johnson, Martin Kussmann, Laure Menin, Christoph Menzel, Frederic Ranno, Patricia Rodriguez-Tomé, John Rogers, Cedric Saudrais, Matteo Villain, Diana Wetmore, Amos Bairoch, Denis Hochstrasser
PROTEOMICS (2004) 4(7): 2125-2150

[Back to TOP]

Methodology

Divinyl Sulfone as a Postdigestion Modifier for Enhancing the a1 Ion in MS/MS and Postsource Decay: Potential Applications in Proteomics
Emily S. Boja, Edward A. Sokoloski, and Henry M. Fales
ANALYTICAL CHEMISTRY Early Edition: published 06/04/2004

Electrosonic Spray Ionization. A Gentle Technique for Generating Folded Proteins and Protein Complexes in the Gas Phase and for Studying Ion-Molecule Reactions at Atmospheric Pressure
Zoltán Takáts, Justin M. Wiseman, Bogdan Gologan, and R. Graham Cooks
ANALYTICAL CHEMISTRY Early Edition: published 06/04/2004

A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics
Hongbin Liu, Rovshan G. Sadygov, and John R. Yates, III
ANALYTICAL CHEMISTRY Early Edition: published 06/04/2004

Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy
Oh P, Li Y, Yu J, Durr E, Krasinska KM, Carver LA, Testa JE, Schnitzer JE.
Nature (2004) 429(6991): 629-635

Characterization of Protein Glycosylation Using Chip-based Infusion Nanoelectrospray Linear Ion Trap Tandem Mass Spectrometry
Sheng Zhang, and Dirk Chelius
J Biomol Tech (2004) 15(2): 120-133

Improved 2D Nano-LC/MS for Proteomics Applications: A Comparative Analysis Using Yeast Proteome
E. Nägele, M. Vollmer, and P. Hörth
J Biomol Tech (2004) 15(2): 134-143

Boosting accuracy of automated classification of fluorescence microscope images for location proteomics
Huang K, Murphy RF
BMC Bioinformatics (2004) 5(1): 78

Enrichment of Cysteine-Containing Peptides from Tryptic Digests Using a Quaternary Amine Tag
Diya Ren, Samir Julka, Halina D. Inerowicz, and Fred E. Regnier
ANALYTICAL CHEMISTRY Early Edition: published 06/18/2004

Using Proteomics to Mine Genome Sequences
Jonathan W. Arthur and Marc R. Wilkins
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 393-402

Sequential Peptide Affinity (SPA) System for the Identification of Mammalian and Bacterial Protein Complexes
Mahel Zeghouf, Joyce Li, Gareth Butland, Anna Borkowska, Veronica Canadien, Dawn Richards, Bryan Beattie, Andrew Emili, and Jack F. Greenblatt
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 463-468

Novel Linear Quadrupole Ion Trap/FT Mass Spectrometer: Performance Characterization and Use in the Comparative Analysis of Histone H3 Post-translational Modifications
John E. P. Syka, # Jarrod A. Marto, # Dina L. Bai, Stevan Horning, Michael W. Senko, Jae C. Schwartz, Beatrix Ueberheide, Benjamin Garcia, Scott Busby, Tara Muratore, Jeffrey Shabanowitz, and Donald F. Hunt
JOURNAL OF PROTEOME RESEARCH (2004) 3(3): 621-626

Multidimensional Protein Profiling Technology and Its Application to Human Plasma Proteome
Kiyonaga Fujii, Tomoyo Nakano, Takeshi Kawamura, Fumihiko Usui, Rong Wang, and Toshihide Nishimura
JOURNAL OF PROTEOME RESEARCH Early Edition: published 06/11/2004

Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues
Jesper V. Olsen, Shao-En Ong, and Matthias Mann
Mol Cell Proteomics (2004) 3(6): 608-614

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
Jacques Colinge, Alexandre Masselot, Isabelle Cusin, Eve Mahé, Anne Niknejad, Ghislaine Argoud-Puy, Samia Reffas, Nassima Bederr, Anne Gleizes, Pierre-Antoine Rey, Lydie Bougueleret
PROTEOMICS (2004) 4(7): 1977-1984

De novo sequencing, peptide composition analysis, and composition-based sequencing: a new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry
Bernhard Spengler
Journal of The American Society for Mass Spectrometry (2004) 15(5): 703-714

Strategies for automating top-down protein analysis with Q-FTICR MS
Steven M. Patrie, Dana E. Robinson, Fanyu Meng, Yi Du and Neil L. Kelleher
International Journal of Mass Spectrometry (2004) 234(1-3): 175-184

High pressure MALDI-FTMS: implications for proteomics
Bogdan A. Budnik, Susanne C. Moyer, Jason L. Pittman, Vera B. Ivleva, Ulf Sommer, Catherine E. Costello and Peter B. O'Connor
International Journal of Mass Spectrometry (2004) 234(1-3): 203-212

Optimized sample-processing time and peptide recovery for the mass spectrometric analysis of protein digests
Doris E. Terry, Edward Umstot and Dominic M. Desiderio
Journal of The American Society for Mass Spectrometry (2004) 15(6): 784-794

Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate-polyacrylamide gels and polyvinyldifluoride membranes
Charlotte Svaerke Jorgensen, Mitchell Jagd, Birgitte Kjaer Sorensen, Jim McGuire, Vibeke Barkholt, Peter Hojrup and Gunnar Houen
Analytical Biochemistry (2004) 330(1): 87-97

[Back to TOP]

Meeting

Integrative functional genomics
Martha L Bulyk
Genome Biology (2004) 5(7): 331-333

[Back to TOP]

Other

PubCrawler: keeping up comfortably with PubMed and GenBank
Karsten Hokamp and Kenneth H. Wolfe
Nucl. Acids. Res. (2004) 32(Web Server issue): W16-W19

Current awareness on comparative and functional genomics
Comparative and Functional Genomics (2004) 5(4): 373-380

Plant bioinformatics: from genome to phenome
David Edwards and Jacqueline Batley
Trends in Biotechnology (2004) 22(5): 232-237

Pitfalls in Proteomics 1
G. Lubec and D. Pollak
Amino Acids (2004) 26(3): 215

Editorial: A case of scientific fraud
Geoffrey J. Laurent, Bertold J. Radola
ELECTROPHORESIS (2004) 25(12): NA

The Need for Guidelines in Publication of Peptide and Protein Identification Data: Working Group On Publication Guidelines For Peptide And Protein Identification Data
Steven Carr, Ruedi Aebersold, Michael Baldwin, Al Burlingame, Karl Clauser, and Alexey Nesvizhskii
Mol Cell Proteomics (2004) 3(6): 531-533

The morality of problem selection in proteomics
Adam J. Liska
PROTEOMICS (2004) 4(7): 1929-1931

[Home]
[About the Society] [Statutes] [Membership] [Committee]
[Career & Employment] [Links]
[News & Events] [SPS' Digest] [Jokeomics]
[Support & Award]