SPS' Digest

Issue 07, 4-Jun-2004

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In this issue, 78 articles have been selected from:

ANALYTICAL CHEMISTRY, Early Edition, 05/07/2004->05/21/2004 (3 articles)
ANALYTICAL CHEMISTRY, Volume 76, Issues 9+10+11, 2004 (8 articles)
Analytical Biochemistry, Volume 327, Issue 2, 2004 (1 article)
Analytical Biochemistry, Volume 328, Issue 2, 2004 (1 article)
BIOCHEMISTRY, Volume 43, Issue 17, 2004 (3 articles)
Bioinformatics, Volume 20, Issues 7+8, 2004 (7 articles)
ChemBioChem, Volume 5, Issues 5+6, 2004 (7 articles)
Current Opinion in Structural Biology, Volume 14, Issue 2, 2004 (1 article)
Drug Discovery Today: TARGETS, Volume 3, Issues 2+2S, 2004 (10 articles)
ELECTROPHORESIS, Volume 25, Issue 9, 2004 (1 article)
Genome Biology, Volume 5, Issue 5, 2004 (1 article)
JOURNAL OF PROTEOME RESEARCH, Early Edition, 04/30/2004->05/28/2004 (11 articles)
Journal of Chromatography A, Volume 1037, Issue 1-2, 2004 (1 article)
Journal of Mass Spectrometry, Volume 39, Issue 5, 2004 (1 article)
Journal of The American Society for Mass Spectrometry, Volume 15, Issue 5, 2004 (4 articles)
Mass Spectrometry Reviews, Volume 23, Issue 4, 2004 (2 articles)
Mol Cell Proteomics, Volume 3, Issue 5, 2004 (2 articles)
Nature Biotechnology, Volume 22, Issue 5, 2004 (1 article)
Nucl. Acids. Res., Volume 32, Issue 8, 2004 (1 article)
PNAS, Volume 101, Issue 18, 2004 (1 article)
PROTEOMICS, Volume 4, Issue 6, 2004 (8 articles)
Rapid Communications in Mass Spectrometry, Volume 18, Issue 12, 2004 (3 articles)

Disclaimer: The selection and categorisation reflect the views and understandings of contributors (i.e. SPS members).

Quick jumps to articles in: Bioinformatics (13) / Biological applications (5) / Biomedical applications (2) / Prokaryotes (1) / Protein Array (1) / Protein Characterization (21) / Protein-protein interaction (2) / PTMs (15) / Quantitation (6) / Review (8) / Methodology (6) / Books (1) / Meeting (1) / Other (2) /

Bioinformatics

PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
Peter V. Hornbeck, Indy Chabra, Jon M. Kornhauser, Elzbieta Skrzypek, Bin Zhang
PROTEOMICS (2004) 4(6): 1551-1561

Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity
Jacques Colinge and Alexandre Masselot
Drug Discovery Today: TARGETS (2004) 3(2S): 50-55

Analysis of large-scale MS data sets: the dramas and the delights
Keiryn L. Bennett, Jan C. Br?nd, Dan B. Kristensen, Alexandre V. Podtelejnikov and Jacek R. Wisniewski
Drug Discovery Today: TARGETS (2004) 3(2S): 43-49

Measuring the similarity of protein structures by means of the universal similarity metric
N. Krasnogor and D. A. Pelta
Bioinformatics (2004) 20(7): 1015-1021

Rapid 3D protein structure database searching using information retrieval techniques
Zeyar Aung and Kian-Lee Tan
Bioinformatics (2004) 20(7): 1045-1052

Statistically rigorous automated protein annotation
Werner G. Krebs and Philip E. Bourne
Bioinformatics (2004) 20(7): 1066-1073

NvAssign: protein NMR spectral assignment with NMRView
Nigel I. Kirby, Eugene F. DeRose, Robert E. London, and Geoffrey A. Mueller
Bioinformatics (2004) 20(7): 1201-1203

Probabilistic inference of molecular networks from noisy data sources
Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S. Bader, Kevin P. White, and Andrey Rzhetsky
Bioinformatics (2004) 20(8): 1205-1213

Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition
Yu-Dong Cai and Andrew J. Doig
Bioinformatics (2004) 20(8): 1292-1300

eF-site and PDBjViewer: database and viewer for protein functional sites
Kengo Kinoshita and Haruki Nakamura
Bioinformatics (2004) 20(8): 1329-1330

On Invariants of a 2-D Proteome Map Derived from Neighborhood Graphs
Milan Randi , Nella Ler , Dejan Plav i , and Subhash C. Basak
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

Predicting transmembrane beta-barrels in proteomes
Henry R. Bigelow, Donald S. Petrey, Jinfeng Liu, Dariusz Przybylski, and Burkhard Rost
Nucl. Acids. Res. (2004) 32(8): 2566-2577

A Tool To Visualize and Evaluate Data Obtained by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry
Xiao-jun Li, Patrick G. A. Pedrioli, Jimmy Eng, Dan Martin, Eugene C. Yi, Ruedi Aebersold
ANALYTICAL CHEMISTRY Early Edition: published 05/21/2004

Biological applications

Conformational Dynamics of the GdmHCl-Induced Molten Globule State of Creatine Kinase Monitored by Hydrogen Exchange and Mass Spectrometry
Hortense Mazon, Olivier Marcillat, Eric Forest, David L. Smith, and Christian Vial
BIOCHEMISTRY (2004) 43(17): 5045-5054

Characterization of the Human Salivary Basic Proline-Rich Protein Complex by a Proteomic Approach
Irene Messana, Tiziana Cabras, Rosanna Inzitari, Alessandro Lupi, Chiara Olmi, Maria Benedetta Fadda, Massimo Cordaro, Massimo Castagnola
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

Application of proteomics technologies in the investigation of the brain
Michael Fountoulakis
Mass Spectrometry Reviews (2004) 23(4): 231-258

Comparison of Multiplexed Techniques for Detection of Bacterial and Viral Proteins
Rupa S. Rao, Steven R. Visuri, Mary T. McBride, Dennis L. Matthews, and Matthew A. Coleman
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/07/2004

Membrane protease proteomics: Isotope-coded affinity tag MS identification of undescribed MT1-matrix metalloproteinase substrates
Eric M. Tam, Charlotte J. Morrison, Yi I. Wu, M. Sharon Stack, and Christopher M. Overall
PNAS (2004) 101(18): 6917-6922

Biomedical applications

Analyzing Alkaline Proteins in Human Colon Crypt Proteome
Xin-Ming Li, Bhavinkumar B. Patel, Elena L. Blagoi, Steven H. Seehozer, Tao Zhang, Shirish Damle, Zhenqiang Gao, Anthony T. Yeung
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/07/2004

Characterization of major histocompatibility complex-associated peptides from a small volume of whole blood
Leann M. Hopkins, Michael Schall, Joseph F. Leykam and John A. Gerlach
Analytical Biochemistry (2004) 328(2): 155-161

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Prokaryotes

Analysis of Altered Protein Expression Patterns of Chlamydia pneumoniae by an Integrated Proteome-Works System
Sanghamitra Mukhopadhyay, Richard D. Miller, and James T. Summersgill
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/28/2004

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Protein Array

Two-Dimensional Multiarray Formation of Hepatocyte Spheroids on a Microfabricated PEG-Brush Surface
Hidenori Otsuka, Akihiro Hirano, Yukio Nagasaki, Teruo Okano, Yasuhiro Horiike, Kazunori Kataoka
ChemBioChem (2004) 5(6): 850-855

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Protein Characterization

Fragmentation of biotinylated cyclic peptides
Michael E. Lassman, Nadia Kulagina, Chris Rowe Taitt
Rapid Communications in Mass Spectrometry (2004) 18(12): 1277-1285

An unusual cleavage reaction of a peptide observed during dithiotreitol and tris(2-carboxyethyl)phosphine reduction: application to sequencing of HpTx2 spider toxin using nanospray tandem mass spectrometry
Christian Legros, Marie-Louise Célérier, Catherine Guette
Rapid Communications in Mass Spectrometry (2004) 18(12): 1317-1323

Analytical characterization of a facile porous polymer monolithic trypsin microreactor enabling peptide mass mapping using mass spectrometry
Anders K. Palm, Milos V. Novotny
Rapid Communications in Mass Spectrometry (2004) 18(12): 1374-1382

Protein Characterization by On-Line Capillary Isoelectric Focusing, Reversed-Phase Liquid Chromatography, and Mass Spectrometry
Feng Zhou and Murray V. Johnston
ANALYTICAL CHEMISTRY (2004) 76(10): 2734-2740

Molecular-Level Description of Proteins from Saccharomyces cerevisiae Using Quadrupole FT Hybrid Mass Spectrometry for Top Down Proteomics
Fanyu Meng, Yi Du, Leah M. Miller, Steven M. Patrie, Dana E. Robinson, and Neil L. Kelleher
ANALYTICAL CHEMISTRY (2004) 76(10): 2852-2858

Impact of Ion Trap Tandem Mass Spectra Variability on the Identification of Peptides
John D. Venable and John R. Yates, III
ANALYTICAL CHEMISTRY (2004) 76(10): 2928-2937

MALDI MS Peptide Mapping Performance by In-Gel Digestion on a Probe with Prestructured Sample Supports
Tina Guldberg Klen , Christian Maal v Andreasen, Lise R nnedal Leonardsen, Thomas Nylandsted Krogh, Marianne Vind S rensen, and Ole N rregaard Jensen
ANALYTICAL CHEMISTRY Early Edition: published 05/07/2004

Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides
Zhongqi Zhang
ANALYTICAL CHEMISTRY Early Edition: published 05/21/2004

Structural Characterization of the Fibrillar Form of the Yeast Saccharomyces cerevisiae Prion Ure2p
Luc Bousset, Virginie Redeker, Paulette Decottignies, Steven Dubois, Pierre Le Mare'chal, and Ronald Melki
BIOCHEMISTRY (2004) 43(17): 5022-5032

A Monomeric Human Apolipoprotein E Carboxyl-Terminal Domain
Daping Fan, Qianqian Li, Leslie Korando, W. Gray Jerome, and Jianjun Wang
BIOCHEMISTRY (2004) 43(17): 5055-5064

Improved Molecular Weight-Based Processing of Intact Proteins for Interrogation by Quadrupole-Enhanced FT MS/MS
Yi Du, Fanyu Meng, Steven M. Patrie, Leah M. Miller, and Neil L. Kelleher
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

Statistical and Mechanistic Approaches to Understanding the Gas-Phase Fragmentation Behavior of Methionine Sulfoxide Containing Peptides
Gavin E. Reid, Kade D. Roberts, Eugene A. Kapp, and Richard J. Simpson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/30/2004

Paraffin-wax-coated plates as matrix-assisted laser desorption/ionization sample support for high-throughput identification of proteins by peptide mass fingerprinting
Nilesh S. Tannu, Jian Wu, Vamshi K. Rao, Himanshu S. Gadgil, Michael J. Pabst, Ivan C. Gerling and Rajendra Raghow
Analytical Biochemistry (2004) 327(2): 222-232

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

Determination of the isoelectric point of proteins by capillary isoelectric focusing
Pier Giorgio Righetti
Journal of Chromatography A (2004) 1037(1-2): 491-499

Factors that contribute to the complexity of protein digests
E'va Hunyadi-Gulya's and Katalin F. Medzihradszky
Drug Discovery Today: TARGETS (2004) 3(2S): 3-10

COFRADIC^(TM): the Hubble telescope of proteomics
Kris Gevaert and Joe"l Vandekerckhove
Drug Discovery Today: TARGETS (2004) 3(2S): 16-22

Q TRAP^(TM) mass spectrometer technology for proteomics applications
James W. Hager
Drug Discovery Today: TARGETS (2004) 3(2S): 31-36

Characterization of the Human Salivary Basic Proline-Rich Protein Complex by a Proteomic Approach
Irene Messana, Tiziana Cabras, Rosanna Inzitari, Alessandro Lupi, Chiara Olmi, Maria Benedetta Fadda, Massimo Cordaro, Massimo Castagnola
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

Proteolysis and Mass Spectrometric Analysis of an Integral Membrane: Aquaporin 0
Jun Han and Kevin L. Schey
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

Insights from Modeling Three-Dimensional Structures of the Human Potassium and Sodium Channels
Kuo-Chen Chou
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

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Protein-protein interaction

Identification of protein associations in organelles, using mass spectrometry-based proteomics
Dale E. Warnock, Eoin Fahy, Steven W. Taylor
Mass Spectrometry Reviews (2004) 23(4): 259-280

Unraveling the human interactome: lessons from the yeast
J. Daniel Navarro and Akhilesh Pandey
Drug Discovery Today: TARGETS (2004) 3(2): 79-84

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PTMs

The RESID Database of Protein Modifications as a resource and annotation tool
John S. Garavelli
PROTEOMICS (2004) 4(6): 1527-1533

Annotation of post-translational modifications in the Swiss-Prot knowledge base
Nathalie Farriol-Mathis, John S. Garavelli, Brigitte Boeckmann, Séverine Duvaud, Elisabeth Gasteiger, Alain Gateau, Anne-Lise Veuthey, Amos Bairoch
PROTEOMICS (2004) 4(6): 1537-1550

Selective Detection of Glycopeptides on Ion Trap Mass Spectrometers
Barbara Sullivan, Theresa A. Addona, and Steven A. Carr
ANALYTICAL CHEMISTRY (2004) 76(11): 3112-3118

Robust Phosphoproteomic Profiling of Tyrosine Phosphorylation Sites from Human T Cells Using Immobilized Metal Affinity Chromatography and Tandem Mass Spectrometry
Laurence M. Brill, Arthur R. Salomon, Scott B. Ficarro, Mridul Mukherji, Michelle Stettler-Gill, and Eric C. Peters
ANALYTICAL CHEMISTRY (2004) 76(10): 2763-2772

The Phosphorylation Site Database: A guide to the serine-, threonine-, and/or tyrosine-phosphorylated proteins in prokaryotic organisms
Susannah M. Wurgler-Murphy, Douglas M. King, Peter J. Kennelly
PROTEOMICS (2004) 4(6): 1562-1570

A Chemically Designed Enzymatic Cleavage Site for Phosphoproteome Analysis
Jianhe Peng
ChemBioChem (2004) 5(6): 768-770

Functional Evaluation of Carbohydrate-Centred Glycoclusters by Enzyme-Linked Lectin Assay: Ligands for Concanavalin A
Maja Köhn, Juan M. Benito, Carmen Ortiz Mellet, Thisbe K. Lindhorst, José M. García Fernández
ChemBioChem (2004) 5(6): 771-777

O-Sulfonation of Serine and Threonine: Mass Spectrometric Detection and Characterization of a New Posttranslational Modification in Diverse Proteins Throughout the Eukaryotes
K. F. Medzihradszky, Z. Darula, E. Perlson, M. Fainzilber, R. J. Chalkley, H. Ball, D. Greenbaum, M. Bogyo, D. R. Tyson, R. A. Bradshaw, and A. L. Burlingame
Mol Cell Proteomics (2004) 3(5): 429-440

Improved Detection of Hydrophilic Phosphopeptides Using Graphite Powder Microcolumns and Mass Spectrometry: Evidence for in Vivo Doubly Phosphorylated Dynamin I and Dynamin III
Martin R. Larsen, Mark E. Graham, Phillip J. Robinson, and Peter Roepstorff
Mol Cell Proteomics (2004) 3(5): 456-465

Unimod: Protein modifications for mass spectrometry
David M. Creasy, John S. Cottrell
PROTEOMICS (2004) 4(6): 1534-1536

New Approach for Analysis of the Phosphotyrosine Proteome and Its Application to the Chicken B Cell Line, DT40
Melissa D. Zolodz, Karl V. Wood, Fred E. Regnier, and Robert L. Geahlen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/07/2004

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

Fragmentation of protonated ions of peptides containing cysteine, cysteine sulfinic acid, and cysteine sulfonic acid
Yinsheng Wang, Shetty Vivekananda, Lijie Men and Qibin Zhang
Journal of The American Society for Mass Spectrometry (2004) 15(5): 697-702

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

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Quantitation

Absolute Quantification of Proteins in Solutions and in Polyacrylamide Gels by Mass Spectrometry
Jan Havli and Andrej Shevchenko
ANALYTICAL CHEMISTRY (2004) 76(11): 3029-3036

Probing the Proteolytic Stability of ?-Peptides Containing ?-Fluoro- and ?-Hydroxy-?-Amino Acids
David F. Hook, Franc,ois Gessier, Christian Noti, Peter Kast, Dieter Seebach
ChemBioChem (2004) 5(5): 691-706

Evaluation of the Molecular Interactions of Fluorinated Amino Acids with Native Polypeptides
Christian Ja"ckel, Wolfgang Seufert, Sven Thust, Beate Koksch
ChemBioChem (2004) 5(5): 717-720

Global Differential Non-Gel Proteomics by Quantitative and Stable Labeling of Tryptic Peptides with Oxygen-18
An Staes, Hans Demol, Jozef Van Damme, Lennart Martens, Kris Gevaert
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/07/2004

Quantitative proteomics by metabolic labeling with stable isotopes
Jeroen Krijgsveld and Albert J.R. Heck
Drug Discovery Today: TARGETS (2004) 3(2S): 11-15

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Review

Moonlighting proteins: complications and implications for proteomics research
Constance J. Jeffery
Drug Discovery Today: TARGETS (2004) 3(2): 71-78

Proteomics: the `omic' technology hole in drug discovery and development?
Stephen Naylor
Drug Discovery Today: TARGETS (2004) 3(2S): 1-2

PRISM: a new strategy to analyze the mammalian proteome
Thomas Kislinger, Brian Cox and Andrew Emili
Drug Discovery Today: TARGETS (2004) 3(2S): 37-42

Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity
Jacques Colinge and Alexandre Masselot
Drug Discovery Today: TARGETS (2004) 3(2S): 50-55

Advances in the prediction of protein targeting signals
Gisbert Schneider, Uli Fechner
PROTEOMICS (2004) 4(6): 1571-1580

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
Nikolaj Blom, Thomas Sicheritz-Pontén, Ramneek Gupta, Steen Gammeltoft, Søren Brunak
PROTEOMICS (2004) 4(6): 1633-1649

Data standards for 'omic' science
John Quackenbush
Nature Biotechnology (2004) 22(5): 613-614

Has the yo-yo stopped? An assessment of human protein-coding gene number
Christopher Southan
PROTEOMICS (2004) 4(6): 1712-1726

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Methodology

Use of Polymer-Modified MALDI-MS Probes To Improve Analyses of Protein Digests and DNA
Yingda Xu, Merlin L. Bruening, and J. Throck Watson
ANALYTICAL CHEMISTRY (2004) 76(11): 3106-3111

Crystallographic Evidence for Isomeric Chromophores in 3-Fluorotyrosyl-Green Fluorescent Protein
Jae Hyun Bae, Prajna Paramita Pal, Luis Moroder, Robert Huber, Nediljko Budisa
ChemBioChem (2004) 5(5): 720-722

Blue silver: A very sensitive colloidal Coomassie G-250 staining for proteome analysis
Giovanni Candiano, Maurizio Bruschi, Luca Musante, Laura Santucci, Gian Marco Ghiggeri, Barbara Carnemolla, Paola Orecchia, Luciano Zardi, Pier Giorgio Righetti
ELECTROPHORESIS (2004) 25(9): 1327-1333

High-sensitivity mass spectrometry for imaging subunit interactions: hydrogen/deuterium exchange
Jason Lanman and Peter E Prevelige Jr
Current Opinion in Structural Biology (2004) 14(2): 181-188

Multistep Microreactions with Proteins Using Electrocapture Technology
Juan Astorga-Wells, Tomas Bergman, and Hans Jo"rnvall
ANALYTICAL CHEMISTRY (2004) 76(9): 2425-2429

Improved Molecular Weight-Based Processing of Intact Proteins for Interrogation by Quadrupole-Enhanced FT MS/MS
Yi Du, Fanyu Meng, Steven M. Patrie, Leah M. Miller, and Neil L. Kelleher
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/21/2004

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Books

Book Review: The Expanding Role of Mass Spectrometry in Biotechnology. By Gary Siuzdak
Mathias Schäfer
ChemBioChem (2004) 5(6): 887

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Meeting

A European focus on proteomics
Christian MT Spahn, Hans Lehrach, Peter R Jungblut
Genome Biology (2004) 5(5): 322

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Other

Current literature in mass spectrometry
Journal of Mass Spectrometry (2004) 39(5): 565-576

Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides
Zhongqi Zhang
ANALYTICAL CHEMISTRY Early Edition: published 05/21/2004

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