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SPS' Digest

Issue 13, 30-Nov-2004

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Quick jumps to articles in: Bioinformatics (25) / Biological applications (16) / Biomedical and clinical applications (13) / Eukaryotic Cells And Tissues (1) / Prokaryotes (2) / Protein Array (3) / Protein Characterization - PTMs (16) / Protein-protein interaction (5) / Quantitation (5) / Review (18) / Methodology (23) / Meeting (3) / Other (5) /

In this issue, 133 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 (25) / Biological applications (16) / Biomedical and clinical applications (13) / Eukaryotic Cells And Tissues (1) / Prokaryotes (2) / Protein Array (3) / Protein Characterization - PTMs (16) / Protein-protein interaction (5) / Quantitation (5) / Review (18) / Methodology (23) / Meeting (3) / Other (5) /

Bioinformatics

Qualified Predictions for Proteomics Pattern Diagnostics with Confidence Machines
Zhiyuan Luo, Tony Bellotti, Alex Gammerman
Lecture Notes in Computer Science (2004) 3177: 46-51

Sequence Database Compression for Peptide Identification from Tandem Mass Spectra
Nathan Edwards, Ross Lippert
Lecture Notes in Computer Science (2004) 3240: 230-241

Using PROTEUS for Modeling Data Mining Analysis of Proteomics Experiments on the Grid
Mario Cannataro, Pietro Hiram Guzzi, Tommaso Mazza, Pierangelo Veltri
Lecture Notes in Computer Science (2004) 3292: 232-243

Transmembrane proteins in the Protein Data Bank: identification and classification
Gabor E. Tusnady, Zsuzsanna Dosztanyi, and Istvan Simon
Bioinformatics (2004) 20(17): 2964-2972

EST clustering error evaluation and correction
Ji-Ping Z. Wang, Bruce G. Lindsay, James Leebens-Mack, Liying Cui, Kerr Wall, Webb C. Miller, and Claude W. dePamphilis
Bioinformatics (2004) 20(17): 2973-2984

Protein complex prediction via cost-based clustering
A. D. King, N. Przulj, and I. Jurisica
Bioinformatics (2004) 20(17): 3013-3020

Sample classification from protein mass spectrometry, by 'peak probability contrasts'
Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Scott Soltys, Gongyi Shi, Albert Koong, and Quynh-Thu Le
Bioinformatics (2004) 20(17): 3034-3044

Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens
Glen A. Satten, Somnath Datta, Hercules Moura, Adrian R. Woolfitt, Maria da G. Carvalho, George M. Carlone, Barun K. De, Antonis Pavlopoulos, and John R. Barr
Bioinformatics (2004) 20(17): 3128-3136

Prediction of phosphorylation sites using SVMs
Jong Hun Kim, Juyoung Lee, Bermseok Oh, Kuchan Kimm, and InSong Koh
Bioinformatics (2004) 20(17): 3179-3184

Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data
Cindy Lou Chepanoske, Bonnie E. Richardson, Moritz von Rechenberg, John M. Peltier
Rapid Communications in Mass Spectrometry (2005) 19(1): 9-14

Statistical Model for Large-Scale Peptide Identification in Databases from Tandem Mass Spectra Using SEQUEST
Daniel López-Ferrer, Salvador Martínez-Bartolomé, Margarita Villar, Mónica Campillos, Fernando Martín-Maroto, and Jesús Vázquez
ANALYTICAL CHEMISTRY (2004) 76(23): 6853-6860

Shotgun Protein Sequencing by Tandem Mass Spectra Assembly
Nuno Bandeira, Haixu Tang, Vineet Bafna, and Pavel Pevzner
ANALYTICAL CHEMISTRY Early Edition: published 11/12/2004

A common open representation of mass spectrometry data and its application to proteomics research.
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.
Nat Biotechnol (2004) 22(11): 1459-1466

BioRAT: extracting biological information from full-length papers
David P. A. Corney, Bernard F. Buxton, William B. Langdon, and David T. Jones
Bioinformatics (2004) 20(17): 3206-3213

UniProt archive
Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, and Rolf Apweiler
Bioinformatics (2004) 20(17): 3236-3237

Bio-Mirror project for public bio-data distribution
Don Gilbert, Yoshihiro Ugawa, Markus Buchhorn, Tan Tin Wee, Akira Mizushima, Hyunchul Kim, Kilnam Chon, Seyeon Weon, Juncai Ma, Yoshihiro Ichiyanagi, Der-Ming Liou, Somnuk Keretho, and Suhaimi Napis
Bioinformatics (2004) 20(17): 3238-3240

POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G. Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, and Chi-Ying F. Huang
Bioinformatics (2004) 20(17): 3273-3276

Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor
Dominique Tessier, Benjamin Bardiaux, Colette Larre, and Yves Popineau
Bioinformatics (2004) 20(16): 2509-2512

Predicting allergenic proteins using wavelet transform
Kuo-Bin Li, Praveen Issac, and Arun Krishnan
Bioinformatics (2004) 20(16): 2572-2578

ICBS: a database of interactions between protein chains mediated by {beta}-sheet formation
Yimeng Dou, Pierre-Francois Baisnee, Gianluca Pollastri, Yann Pecout, James Nowick, and Pierre Baldi
Bioinformatics (2004) 20(16): 2767-2777

ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences
Eisuke Chikayama, Atsushi Kurotani, Yutaka Kuroda, and Shigeyuki Yokoyama
Bioinformatics (2004) 20(16): 2836-2838

The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions
Sandra Barth, Markus Fischer, Rolf D. Schmid, and Jurgen Pleiss
Bioinformatics (2004) 20(16): 2845-2847

CoPS: Comprehensive Peptide Signature Database
Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash, and Samir K. Brahmachari
Bioinformatics (2004) 20(16): 2886-2888

Command line tool for calculating theoretical MS spectra for given sequences
Andreas M. Boehm, Florian Grosse-Coosmann, and Albert Sickmann
Bioinformatics (2004) 20(16): 2889-2891

GFSWeb: A Web Tool for Genome-Based Identification of Proteins from Mass Spectrometric Samples
Michael S. Wisz, Melissa Kimball Suarez, Mark R. Holmes, and Morgan C. Giddings
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/19/2004

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Biological applications

Identification of antigenic proteins from Neospora caninum recognized by bovine immunoglobulins M, E, A and G using immunoproteomics
Yong-seung Shin, Eung-goo Lee, Gee-wook Shin, Young-rim Kim, Eun-young Lee, Jae-hoon Kim, Hwan Jang, Laurel J. Gershwin, Dae-yong Kim, Yong-hwan Kim, Gon-sup Kim, Myung-deuk Suh, Tae-sung Jung
PROTEOMICS (2004) 4(11): 3600-3609

Establishment of a near-standard two-dimensional human urine proteomic map
Jisun Oh, Jae-Hoon Pyo, Eun-Hyun Jo, Sun-Il Hwang, Sun-Chul Kang, Jae-Hwan Jung, Eui-Kyun Park, Shin-Yoon Kim, Je-Yong Choi, Jinkyu Lim
PROTEOMICS (2004) 4(11): 3485-3497

Two-dimensional electrophoretic analysis reveals that lipid rafts are intact at physiological temperature
Ki-Bum Kim, Sang-Il Kim, Hyo-Jung Choo, Ji-Hyun Kim, Young-Gyu Ko
PROTEOMICS (2004) 4(11): 3527-3535

Expression of genes and proteins specific for prostate cancer.
Gelmann EP, Semmes OJ.
J Urol (2004) 172(5 Pt 2): S23-6; discussion S26-7

Proteomic Profiling and Intra-amniotic Infection.
Buhimschi IA, Buhimschi CS, Christner R, Norwitz E, Weiner CP.
JAMA (2004) 292(19): 2338

AT1receptor blockade alters metabolic, functional and structural proteins after reperfused myocardial infarction: detection using proteomics.
Jugdutt BI, Sawicki G.
Mol Cell Biochem (2004) 263(1-2): 179-88

Proteomic analysis identifies immunophilin FKBP52 as a downstream target of Hoxa10 in the periimplantation mouse uterus.
Daikoku T, Tranguch S, Friedman DB, Das SK, Smith DF, Dey SK.
Mol Endocrinol Early Edition: published 4-Nov-2004

Gender-specific proteomic alterations in glycolytic and mitochondrial pathways in aging monkey hearts.
Yan L, Ge H, Li H, Lieber SC, Natividad F, Resuello RR, Kim SJ, Akeju S, Sun A, Loo K, Peppas AP, Rossi F, Lewandowski ED, Thomas AP, Vatner SF, Vatner DE.
J Mol Cell Cardiol (2004) 37(5): 921-9

Characterisation of peptides released from mitochondria: evidence for constant proteolysis and peptide efflux.
Augustin S, Nolden M, Muller S, Hardt O, Arnold I, Langer T.
J Biol Chem Early Edition: published 19-Nov-2004

Discovering disease-associated enzymes by proteome reactivity profiling.
Barglow KT, Cravatt BF.
Chem Biol (2004) 11(11): 1523-31

2D LC/MS Analysis of Membrane Proteins from Breast Cancer Cell Lines MCF7 and BT474
Rong Xiang, Yang Shi, Deborah A. Dillon, Brina Negin, James A. Wilkins,
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/12/2004

Mass spectrometric analysis of tumor necrosis factor receptor-associated factor 1 ubiquitination mediated by cellular inhibitor of apoptosis 2
Jong-Sik Lee, Un-Sook Hong, Tae H. Lee, Sungjoo Kim Yoon, Jong-Bok Yoon
PROTEOMICS (2004) 4(11): 3376-3382

Identification of caspase-3 degradome by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight analysis
Ah Young Lee, Byoung Chul Park, Mi Jang, Sayeon Cho, Do Hee Lee, Sang Chul Lee, Pyung Keun Myung, Sung Goo Park
PROTEOMICS (2004) 4(11): 3429-3436

Identification of the degradome of Isp-1, a major intracellular serine protease of Bacillus subtilis, by two-dimensional gel electrophoresis and matrix- assisted laser desorption/ionization-time of flight analysis
Ah Young Lee, Sung Goo Park, Chang Won Kho, Sun Young Park, Sayeon Cho, Sang Chul Lee, Do Hee Lee, Pyung Keun Myung, Byoung Chul Park
PROTEOMICS (2004) 4(11): 3437-3445

Proteins as biomarkers of oxidative/nitrosative stress in diseases: The contribution of redox proteomics
Isabella Dalle-Donne, Andrea Scaloni, Daniela Giustarini, Eleonora Cavarra, Gianluca Tell, Giuseppe Lungarella, Roberto Colombo, Ranieri Rossi, Aldo Milzani
Mass Spectrometry Reviews (2005) 24(1): 55-99

Proteome analysis of differential protein expression in allergen-induced asthmatic mice lung after dexamethasone treatment
Gu Seob Roh, YoungHyun Shin, Seong-Won Seo, Bo Ra Yoon, SinKoo Yeo, Sung Jin Park, Jin Won Cho, KyuBum Kwack
PROTEOMICS (2004) 4(11): 3318-3327

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Biomedical and clinical applications

Antigens secreted from Mycobacterium tuberculosis: Identification by proteomics approach and test for diagnostic marker
Young Yil Bahk, Suk Am Kim, Ji-Soo Kim, Hyung-Jin Euh, Gil-Han Bai, Sang-Nae Cho, Yu Sam Kim
PROTEOMICS (2004) 4(11): 3299-3307

The use of proteomics in the discovery of serum biomarkers from patients with severe acute respiratory syndrome
Yi Ren, Qing-Yu He, Jianqing Fan, Brian Jones, Yuan Zhou, Yi Xie, Chung-Yan Cheung, Adrian Wu, Jen-Fu Chiu, J. S. Malik Peiris, Paul Kwong Hang Tam
PROTEOMICS (2004) 4(11): 3477-3484

Quantitative profiling of plasma peptides in asthmatic mice using liquid chromatography and mass spectrometry
SinKoo Yeo, Gu Seob Roh, Dong-Hoon Kim, Jung Min Lee, Seong-Won Seo, Jin Won Cho, Chan-Wha Kim, KyuBum Kwack
PROTEOMICS (2004) 4(11): 3308-3317

Allergen-induced proteolytic cleavage of annexin-1 and activation of cytosolic phospholipase A2 in the lungs of a mouse model of asthma
Youn Wook Chung, Hae Yeun Oh, Ji Yeong Kim, Jae-Hong Kim, Ick Young Kim
PROTEOMICS (2004) 4(11): 3328-3334

Profiling proteins related to amyloid deposited brain of Tg2576 mice
Su Jeon Shin, Sung-Eun Lee, Jung Hyun Boo, Mihyang Kim, Young-Dae Yoon, Su-il Kim, Inhee Mook-Jung
PROTEOMICS (2004) 4(11): 3359-3368

Proteomic analysis distinguishes basaloid carcinoma as a distinct subtype of nonsmall cell lung carcinoma
Long Shan Li, Hyunki Kim, Hwanseok Rhee, Se Hoon Kim, Dong Hwan Shin, Kyung Young Chung, Kang-Sik Park, Young-Ki Paik, Joon Chang, Hoguen Kim
PROTEOMICS (2004) 4(11): 3394-3400

Identification of B-cell translocation gene 1 as a biomarker for monitoring the remission of acute myeloid leukemia
Jae-We Cho, Jeong Jung Kim, Sung Goo Park, Do Hee Lee, Sang Chul Lee, Hyeoung-Joon Kim, Byoung Chul Park, Sayeon Cho
PROTEOMICS (2004) 4(11): 3456-3463

Diagnosis of Pancreatic Cancer Using Serum Proteomic Profiling.
Bhattacharyya S, Siegel ER, Petersen GM, Chari ST, Suva LJ, Haun RS.
Neoplasia (2004) 6(5): 674-686

Biomarkers of ovarian tumours.
Rapkiewicz AV, Espina V, Petricoin EF 3rd, Liotta LA.
Eur J Cancer (2004) 40(17): 2604-12

Discovery of laryngeal carcinoma by serum proteomic pattern analysis.
Xiao X, Zhao X, Liu J, Guo F, Liu D, He D.
Sci China C Life Sci (2004) 47(3): 219-23

AT1receptor blockade alters metabolic, functional and structural proteins after reperfused myocardial infarction: detection using proteomics.
Jugdutt BI, Sawicki G.
Mol Cell Biochem (2004) 263(1-2): 179-88

Proteomic Fingerprints for Potential Application to Early Diagnosis of Severe Acute Respiratory Syndrome.
Kang X, Xu Y, Wu X, Liang Y, Wang C, Guo J, Wang Y, Chen M, Wu D, Wang Y, Bi S, Qiu Y, Lu P, Cheng J, Xiao B, Hu L, Gao X, Liu J, Wang Y, Song Y, Zhang L, Suo F, Chen T, Huang Z, Zhao Y, Lu H, Pan C, Tang H.
Clin Chem Early Edition: published 18-Nov-2004

Gravity-induced convective flow in microfluidic systems: Electrochemical characterization and application to enzyme-linked immunosorbent assay tests
Patrick Morier, Christine Vollet, Philippe E. Michel, Frédéric Reymond, Joël S. Rossier
ELECTROPHORESIS (2004) 25(21-22): 3761-3768

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Eukaryotic Cells And Tissues

The Vegetative Vacuole Proteome of Arabidopsis thaliana Reveals Predicted and Unexpected Proteins.
Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV.
Plant Cell Early Edition: published 11-Nov-2004

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Prokaryotes

Comparative proteome analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions.
Starck J, Kallenius G, Marklund BI, Andersson DI, Akerlund T.
Microbiology (2004) 150(Pt 11): 3821-3829

Mycobacterium tuberculosis Functional Network Analysis by Global Subcellular Protein Profiling.
Mawuenyega KG, Forst CV, Dobos KM, Belisle JT, Chen J, Bradbury EM, Bradbury AR, Chen X.
Mol Biol Cell Early Edition: published 3-Nov-2004

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Protein Array

Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips.
Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL.
Proc Natl Acad Sci U S A Early Edition: published 11-Nov-2004

Protein Microarray System for Detecting Protein-Protein Interactions Using an Anti-His-Tag Antibody and Fluorescence Scanning: Effects of the Heme Redox State on Protein-Protein Interactions of Heme-Regulated Phosphodiesterase from Escherichia coli
Yukie Sasakura, Katsuhiro Kanda, Tokiko Yoshimura-Suzuki, Takuya Matsui, Shinichi Fukuzono, Moon Hi Han, and Toru Shimizu
ANALYTICAL CHEMISTRY (2004) 76(22): 6521-6527

A Prototype Antibody Microarray Platform to Monitor Changes in Protein Tyrosine Phosphorylation
Dmitry S. Gembitsky, Kevin Lawlor, Andrew Jacovina, Mariana Yaneva, and Paul Tempst
Mol Cell Proteomics (2004) 3(11): 1102-1118

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Protein Characterization / PTMs

Identification of target proteins of N-acetylglucosaminyl-transferase V and fucosyltransferase 8 in human gastric tissues by glycomic approach
Yong-Sam Kim, Soo Young Hwang, Sejeong Oh, Hosung Sohn, Hye-Yeon Kang, Jeong-Hwa Lee, Eun-Wie Cho, Jin-Young Kim, Jong Shin Yoo, Nam-Soon Kim, Cheorl-Ho Kim, Eiji Miyoshi, Naoyuki Taniguchi, Jeong Heon Ko
PROTEOMICS (2004) 4(11): 3353-3358

Phosphoproteomics by mass spectrometry and classical protein chemistry approaches.
Salih E.
Mass Spectrom Rev Early Edition: published 10-Nov-2004

Hydrophilic Affinity Isolation and MALDI Multiple-Stage Tandem Mass Spectrometry of Glycopeptides for Glycoproteomics
Yoshinao Wada, Michiko Tajiri, and Shumi Yoshida
ANALYTICAL CHEMISTRY (2004) 76(22): 6560-6565

Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multi-lectin affinity column.
Yang Z, Hancock WS.
J Chromatogr A (2004) 1053(1-2): 79-88

A thin chip microsprayer system coupled to Fourier transform ion cyclotron resonance mass spectrometry for glycopeptide screening
Laura Bindila, Martin Froesch, Niels Lion, ?eljka Vukeli?, Joël S. Rossier, Hubert H. Girault, Jasna Peter-Katalini?, Alina D. Zamfir
Rapid Communications in Mass Spectrometry (2004) 18(23): 2913-2920

Coupling of fully automated chip electrospray to Fourier transform ion cyclotron resonance mass spectrometry for high-performance glycoscreening and sequencing
Martin Froesch, Laura M. Bindila, Gökhan Baykut, Mark Allen, Jasna Peter-Katalini?, Alina D. Zamfir
Rapid Communications in Mass Spectrometry (2004) 18(24): 3084-3092

Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites
Scott B. Ficarro, Arthur R. Salomon, Laurence M. Brill, Daniel E. Mason, Michelle Stettler-Gill, Ansgar Brock, Eric C. Peters
Rapid Communications in Mass Spectrometry (2005) 19(1): 57-71

Use of Performic Acid Oxidation To Expand the Mass Distribution of Tryptic Peptides
Rune Matthiesen, Guy Bauw, and Karen G. Welinder
ANALYTICAL CHEMISTRY (2004) 76(23): 6848-6852

Integrated Lectin Affinity Microfluidic Chip for Glycoform Separation
Xiuli Mao, Yong Luo, Zhongpeng Dai, Keyi Wang, Yuguang Du, and Bingcheng Lin
ANALYTICAL CHEMISTRY (2004) 76(23): 6941-6947

Identification of Sites of Ubiquitination in Proteins: A Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Approach
Helen J. Cooper, John K. Heath, Ellis Jaffray, Ronald T. Hay, TuKiet T. Lam, and Alan G. Marshall
ANALYTICAL CHEMISTRY (2004) 76(23): 6982-6988

Direct N-Glycan Profiling in the Presence of Tryptic Peptides on MALDI-TOF by Controlled Ion Enhancement and Suppression upon Glycan-Selective Derivatization
Yasuro Shinohara, Jun-ichi Furukawa, Kenichi Niikura, Nobuaki Miura, and Shin-Ichiro Nishimura
ANALYTICAL CHEMISTRY (2004) 76(23): 6989-6997

Protein Thiol Modifications Visualized In Vivo
Lars I. Leichert, Ursula Jakob
PLoS Biology (2004) 2(11): e333

Functional proteomic analysis of a three tier PKC{epsilon}-Ak--eNOS signaling module in cardiac protection.
Zhang J, Baines CP, Zong NC, Cardwell EM, Wang G, Vondriska TM, Ping P.
Am J Physiol Heart Circ Physiol Early Edition: published 4-Nov-2004

Analysis of Phosphorylated Peptides by Ion Mobility-Mass Spectrometry.
Ruotolo BT, Gillig KJ, Woods AS, Egan TF, Ugarov MV, Schultz JA, Russell DH.
Anal Chem (2004) 76(22): 6727-6733

Mass spectrometrical analysis of phosphoprotein enriched in astrocytes of 15 kDa in mouse hippocampi.
Shin JH, Delabar JM, Lubec G.
Amino Acids Early Edition: published 5-Nov-2004

Phosphoproteomic Analysis of the Developing Mouse Brain
Bryan A. Ballif, Judit Villen, Sean A. Beausoleil, Daniel Schwartz, and Steven P. Gygi
Mol Cell Proteomics (2004) 3(11): 1093-1101

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Protein-protein interaction

Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein-Protein Interactions
Xiaoting Tang, Gerhard R. Munske, William F. Siems, and James E. Bruce
ANALYTICAL CHEMISTRY Early Edition: published 11/26/2004

Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry
Feixia Chu, Shu-ou Shan, Demetri T. Moustakas, Frank Alber, Pascal F. Egea, Robert M. Stroud, Peter Walter, and Alma L. Burlingame
PNAS (2004) 101(47): 16454-16459

Developing Photoactive Affinity Probes for Proteomic Profiling: Hydroxamate-based Probes for Metalloproteases.
Chan EW, Chattopadhaya S, Panicker RC, Huang X, Yao SQ.
J Am Chem Soc (2004) 126(44): 14435-46

Evidence that the respiratory syncytial virus polymerase complex associates with lipid rafts in virus-infected cells: a proteomic analysis.
McDonald TP, Pitt AR, Brown G, Rixon HW, Sugrue RJ.
Virology (2004) 330(1): 147-157

Proteomics-based identification of proteins interacting with Smad3: SREBP-2 forms a complex with Smad3 and inhibits its transcriptional activity.
Grimsby S, Jaensson H, Dubrovska A, Lomnytska M, Hellman U, Souchelnytskyi S.
FEBS Lett (2004) 577(1-2): 93-100

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Quantitation

N-terminal isotope tagging strategy for quantitative proteomics: results-driven analysis of protein abundance changes.
Zappacosta F, Annan RS.
Anal Chem (2004) 76(22): 6618-27

Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability.
Lee YH, Han H, Chang SB, Lee SW.
Rapid Commun Mass Spectrom (2004) 18(24): 3019-3027

N-Terminal Isotope Tagging Strategy for Quantitative Proteomics: Results-Driven Analysis of Protein Abundance Changes
Francesca Zappacosta and Roland S. Annan
ANALYTICAL CHEMISTRY (2004) 76(22): 6618-6627

Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability
Yong Ho Lee, Hoon Han, Seok-Bok Chang, Sang-Won Lee
Rapid Communications in Mass Spectrometry (2004) 18(24): 3019-3027

Differential protein expression profile in gastrointestinal stromal tumors
B. Landuyt, H. Prenen, M. Debiec-Rychter, R. Sciot, E. A de Bruijn and A. T. van Oosterom
Amino Acids Early Edition: published 12-Nov-2004

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Review

The bag or the spindle: the cell factory at the time of systems' biology.
Danchin A.
Microb Cell Fact (2004) 3(1): 13

Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches.
Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N, Antonioli P, Astner H, Hamdan M.
J Chromatogr A (2004) 1051(1-2): 3-17

The role of liquid chromatography in proteomics.
Shi Y, Xiang R, Horvath C, Wilkins JA.
J Chromatogr A (2004) 1053(1-2): 27-36

Strategies for shotgun identification of post-translational modifications by mass spectrometry.
Cantin GT, Yates JR 3rd.
J Chromatogr A (2004) 1053(1-2): 7-14

Genomic and Proteomic Profiles of Heart Disease.
Prentice H, Webster KA.
Trends Cardiovasc Med (2004) 14(7): 282-288

The Coomassie chronicles: past, present and future perspectives in polyacrylamide gel staining
GB Smejkal
Expert Review of Proteomics (2004) 1(4): 381-387

Mass spectrometric approaches for characterizing bacterial proteomes
NC VerBerkmoes, HM Connelly, C Pan & RL Hettich
Expert Review of Proteomics (2004) 1(4): 433-447

Chip-based nanoelectrospray mass spectrometry for protein characterization
S Zhang & CK Van Pelt
Expert Review of Proteomics (2004) 1(4): 449-468

Bioinformatics in mass spectrometry data analysis for proteomics studies
S Cristoni & LR Bernardi
Expert Review of Proteomics (2004) 1(4): 469-483

What can proteomic analyses contribute to understanding the molecular biology and clinical behavior of prostate cancer?
JL Ware
Expert Review of Proteomics (2004) 1(4): 485-492

Proteomic technologies and their application to pancreatic cancer
D Vimalachandran & E Costello
Expert Review of Proteomics (2004) 1(4): 493-501

Absolute quantification strategies in proteomics based on mass spectrometry
M Bro"nstrup
Expert Review of Proteomics (2004) 1(4): 503-512

Proteomic Patterns as a Diagnostic Tool for Early-Stage Cancer: A Review of its Progress to a Clinically Relevant Tool.
Conrads TP, Hood BL, Issaq HJ, Veenstra TD.
Mol Diagn (2004) 8(2): 77-85

Biomarkers of cardiac disease.
Marian AJ, Nambi V.
Expert Rev Mol Diagn (2004) 4(6): 805-20

Current chemical tagging strategies for proteome analysis by mass spectrometry.
Leitner A, Lindner W.
J Chromatogr B Analyt Technol Biomed Life Sci (2004) 813(1-2): 1-26

New directions of miniaturization within the biomarker research area
György A. Marko-Varga, Johan Nilsson, Thomas Laurell
ELECTROPHORESIS (2004) 25(21-22): 3479-3491

Immobilized microfluidic enzymatic reactors
Jana K?enková, Franti?ek Foret
ELECTROPHORESIS (2004) 25(21-22): 3550-3563

Proteomics in aging-related research.
Gafni A.
Sci Aging Knowledge Environ (2004) 2004(45): pe41

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Methodology

Analysis of Phosphorylated Peptides by Ion Mobility-Mass Spectrometry.
Ruotolo BT, Gillig KJ, Woods AS, Egan TF, Ugarov MV, Schultz JA, Russell DH.
Anal Chem (2004) 76(22): 6727-6733

Coupling of nanoflow liquid chromatography to matrix-assisted laser desorption/ionization mass spectrometry: real-time liquid chromatography run mapping on a MALDI plate.
Nagele E, Vollmer M.
Rapid Commun Mass Spectrom (2004) 18(24): 3008-3014

Photoimmobilization of Proteins for Affinity Capture Combined with MALDI TOF MS Analysis
Dariusz J. Janecki, William C. Broshears, and James P. Reilly
ANALYTICAL CHEMISTRY (2004) 76(22): 6643-6650

Protein Biophysical Properties that Correlate with Crystallization Success in Thermotoga maritima: Maximum Clustering Strategy for Structural Genomics.
Canaves JM, Page R, Wilson IA, Stevens RC.
J Mol Biol (2004) 344(4): 977-91

Free flow electrophoresis coupled with liquid chromatography-mass spectrometry for a proteomic study of the human cell line (K562/CR3).
Wang Y, Hancock WS, Weber G, Eckerskorn C, Palmer-Toy D.
J Chromatogr A (2004) 1053(1-2): 269-78

Automating proteome analysis: improvements in throughput, quality and accuracy of protein identification by peptide mass fingerprinting
Ludovic Canelle, Cédric Pionneau, Arul Marie, Jordane Bousquet, Jean Bigeard, Didier Lutomski, Tewfik Kadri, Michel Caron, Raymonde Joubert-Caron
Rapid Communications in Mass Spectrometry (2004) 18(23): 2785-2794

Capillary electrophoresis off-line matrix-assisted laser desorption/ionisation mass spectrometry of intact and digested proteins using cationic-coated capillaries
Aida Zuberovic, Sara Ullsten, Ulf Hellman, Karin E. Markides, Jonas Bergquist
Rapid Communications in Mass Spectrometry (2004) 18(23): 2946-2952

Coupling of nanoflow liquid chromatography to matrix-assisted laser desorption/ionization mass spectrometry: real-time liquid chromatography run mapping on a MALDI plate
Edgar Nägele, Martin Vollmer
Rapid Communications in Mass Spectrometry (2004) 18(24): 3008-3014

Pressurized Electrochromatography Coupled with Electrospray Ionization Mass Spectrometry for Analysis of Peptides and Proteins
Zhen Liang, Jicheng Duan, Lihua Zhang, Weibing Zhang, Yukui Zhang, and Chao Yan
ANALYTICAL CHEMISTRY (2004) 76(23): 6935-6940

LC-MS/MS Analysis of Peptides with Methanol as Organic Modifier: Improved Limits of Detection
Francesco Giorgianni, Achille Cappiello, Sarka Beranova-Giorgianni, Pierangela Palma, Helga Trufelli, and Dominic M. Desiderio
ANALYTICAL CHEMISTRY (2004) 76(23): 7028-7038

On-Line Hollow-Fiber Flow Field-Flow Fractionation-Electrospray Ionization/Time-of-Flight Mass Spectrometry of Intact Proteins
Pierluigi Reschiglian, Andrea Zattoni, Barbara Roda, and Leonardo Cinque Daniela Parisi and Aldo Roda Fabrizio Dal Piaz Myeong Hee Moon and Byung Ryul Min
ANALYTICAL CHEMISTRY Early Edition: published 11/19/2004

High-Affinity Capture of Proteins by Diamond Nanoparticles for Mass Spectrometric Analysis
X. L. Kong, L. C. L. Huang, C.-M. Hsu, W.-H. Chen, C.-C. Han, and H.-C. Chang
ANALYTICAL CHEMISTRY Early Edition: published 11/26/2004

Fully-automated chip-based nanoelectrospray tandem mass spectrometry of gangliosides from human cerebellum.
Zamfir A, Vukelic Z, Bindila L, Peter-Katalinic J, Almeida R, Sterling A, Allen M.
J Am Soc Mass Spectrom (2004) 15(11): 1649-57

Proteomic analyses using an accurate mass and time tag strategy.
Pasa-Tolic L, Masselon C, Barry RC, Shen Y, Smith RD.
Biotechniques (2004) 37(4): 636 passim

Validation of a prefractionation method followed by two-dimensional electrophoresis - Applied to cerebrospinal fluid proteins from frontotemporal dementia patients.
Folkesson Hansson S, Puchades M, Blennow K, Sjogren M, Davidsson P.
Proteome Sci (2004) 2(1): 7

All about DIGE: quantification technology for differential-display 2D-gel proteomics
KS Lilley & DB Friedman
Expert Review of Proteomics (2004) 1(4): 401-409

Depletion and fractionation technologies in plasma proteomic analysis
SW Tam, J Pirro & D Hinerfeld
Expert Review of Proteomics (2004) 1(4): 411-420

Isotope-differentiated binding energy shift tags (IDBEST^(TM)) for improved targeted biomarker discovery and validation
MP Hall & LV Schneider
Expert Review of Proteomics (2004) 1(4): 421-431

Parallel isoelectric focusing II
Gleb V. Zilberstein, Emmanuil M. Baskin, Shmuel Bukshpan, Leonid E. Korol
ELECTROPHORESIS (2004) 25(21-22): 3643-3651

Integrated selective enrichment target - a microtechnology platform for matrix-assisted laser desorption/ionization-mass spectrometry applied on protein biomarkers in prostate diseases
Simon Ekström, Lars Wallman, Johan Malm, Charlotte Becker, Hans Lilja, Thomas Laurell, György Marko-Varga
ELECTROPHORESIS (2004) 25(21-22): 3769-3777

Autonomous protein sample processing on-chip using solid-phase microextraction, capillary force pumping, and microdispensing
Lars Wallman, Simon Ekström, György Marko-Varga, Thomas Laurell, Johan Nilsson
ELECTROPHORESIS (2004) 25(21-22): 3778-3787

Photopolymerized microtips for sample preparation in proteomic analysis
Jue-Liang Hsu, Mong-Kuan Chou, Shih-Shin Liang, Sheng-Yu Huang, Chin-Jen Wu, Fong-Ku Shi, Shu-Hui Chen
ELECTROPHORESIS (2004) 25(21-22): 3840-3847

Automated Protein Identification by the Combination of MALDI MS and MS/MS Spectra from Different Instruments
Fredrik Levander and Peter James
JOURNAL OF PROTEOME RESEARCH Early Edition: published 11/19/2004

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Meeting

HUPO 3rd Annual World Congress. Beijing, China, October 25 - 27, 2004
Mol Cell Proteomics (2004) 3(10 Suppl): S1-352.

1st Workshop for Human Diseases Glycomics/Proteome Initiative of HUPO (Meeting Report)
K Nakamura
Expert Review of Proteomics (2004) 1(4): 393-395

15th Meeting on Methods in Protein Structure Analysis (Meeting Report)
MHV Van Regenmortel
Expert Review of Proteomics (2004) 1(4): 397-399

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Other

Current literature in mass spectrometry
John Wiley & Sons, Ltd.
Journal of Mass Spectrometry (2004) 39(11): 1383-1394

Evolving protein functional diversity in new genes of Drosophila
Jianming Zhang, Antony M. Dean, Frederic Brunet, and Manyuan Long
PNAS (2004) 101(46): 16246-16250

Grant-transfer plan paves the way for European mobility
Simm B
Nature (2004) 432(7015): 261

Science searches shift up a gear as Google starts Scholar engine
DECLAN BUTLER
Nature (2004) 432(7016): 423

PowerPoint in the Classroom.
[No authors listed]
Cell Biol Educ (2004) 3(3): 155-161

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