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SPS' Digest

Issue 15, 27-Jan-2005

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Quick jumps to articles in: Bioinformatics (23) / Biological applications (23) / Biomedical and clinical applications (19) / Eukaryotic Cells And Tissues (1) / Prokaryotes (4) / Protein Array (5) / Protein Characterization - PTMs (12) / Protein-protein interaction (4) / Quantitation (4) / Review (22) / Methodology (34) / Meeting (1) / Other (8) /

In this issue, 158 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 (23) / Biological applications (23) / Biomedical and clinical applications (19) / Eukaryotic Cells And Tissues (1) / Prokaryotes (4) / Protein Array (5) / Protein Characterization - PTMs (12) / Protein-protein interaction (4) / Quantitation (4) / Review (22) / Methodology (34) / Meeting (1) / Other (8) /

Bioinformatics

Proteomic Pattern Classification Using Bio-markers for Prostate Cancer Diagnosis
Jung-Ja Kim, Young-Ho Kim, Yonggwan Won
Lecture Notes in Computer Science (2004) 3314: 631

Performance of a genetic algorithm for mass spectrometry proteomics
Jeffries NO.
BMC Bioinformatics (2004) 5(1): 180

Differential Proteomics via Probabilistic Peptide Identification Scores
Jacques Colinge, Diego Chiappe, Sophie Lagache, Marc Moniatte, and Lydie Bougueleret
ANALYTICAL CHEMISTRY (2005) 77(2): 596-606

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.
Aubourg S, Brunaud V, Bruyere C, Cock M, Cooke R, Cottet A, Couloux A, Dehais P, Deleage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlne G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Riviere S, Rombauts S, Rouze P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M, Lecharny A.
Nucl Acids Res (2005) 33 Database Issue: D641-D646

AMPDB: the Arabidopsis Mitochondrial Protein Database.
Heazlewood JL, Millar AH.
Nucl Acids Res (2005) 33 Database Issue: D605-10.

Organelle DB: a cross-species database of protein localization and function.
Wiwatwattana N, Kumar A.
Nucl Acids Res (2005) 33 Database Issue: D598-604.

The European Bioinformatics Institute's data resources: towards systems biology.
Brooksbank C, Cameron G, Thornton J.
Nucl Acids Res (2005) 33 Database Issue: D46-53.

The UCSC Proteome Browser.
Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ.
Nucl Acids Res (2005) 33 Database Issue: D454-8.

EcoCyc: a comprehensive database resource for Escherichia coli.
Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD.
Nucl Acids Res (2005) 33 Database Issue: D334-D337

Comparative and Functional Genomics: A Special section of articles from the 7th Annual Bio-Ontologies Meeting ?Ontologies and Bio-Images?
Comparative and Functional Genomics (2004) 5(6-7): 497

Biomedical informatics and granularity
Anand Kumar, Barry Smith, Daniel D. Novotny
Comparative and Functional Genomics (2004) 5(6-7): 501-508

PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling
Ari Frank and Pavel Pevzner
ANALYTICAL CHEMISTRY Early Edition: published 01/14/2005

PRIME: A graphical interface for integrating genomic/proteomic databases
Axel Facius, Claudia Englbrecht, Fabian Birzele, Andreas Groscurth, Benjamin Schmid, Steffi Wanka, Werner Mewes
PROTEOMICS (2005) 5(1): 76-80

Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics
Natasha A. Karp, Julian L. Griffin, Kathryn S. Lilley
PROTEOMICS (2005) 5(1): 81-90

Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource.
Lefkowitz EJ, Upton C, Changayil SS, Buck C, Traktman P, Buller RM.
Nucl Acids Res (2005) 33 Database Issue: D311-D316

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, McLaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.
Nucl Acids Res (2005) 33 Database Issue: D297-D302

PFD: a database for the investigation of protein folding kinetics and stability.
Fulton KF, Devlin GL, Jodun RA, Silvestri L, Bottomley SP, Fersht AR, Buckle AM.
Nucl Acids Res (2005) 33 Database Issue: D279-D283

SPD--a web-based secreted protein database.
Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J.
Nucl Acids Res (2005) 33 Database Issue: D169-73.

PSORTdb: a protein subcellular localization database for bacteria.
Rey S, Acab M, Gardy JL, Laird MR, Defays K, Lambert C, Brinkman FS.
Nucl Acids Res (2005) 33 Database Issue: D164-8.

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.
Lu P, Szafron D, Greiner R, Wishart DS, Fyshe A, Pearcy B, Poulin B, Eisner R, Ngo D, Lamb N.
Nucl Acids Res (2005) 33 Database Issue: D147-53.

Modeling and analysis of heterogeneous regulation in biological networks.
Gat-Viks I, Tanay A, Shamir R
J Comput Biol (2004) 11(6): 1034-49

Robust estimation of protein expression ratios with lysate microarray technology.
Mircean C, Shmulevich I, Cogdell D, Choi W, Jia Y, Tabus I, Hamilton SR, Zhang W
Bioinformatics Early Edition: published 12-Jan-2005

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.
Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R
Genome Biol (2005) 6(1): R9. Epub 2004 Dec 10

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Biological applications

A matrix-assisted laser desorption/ionization mass spectrometry study of the non-enzymatic glycation products of human globins in diabetes
A. Lapolla, M. Tubaro, D. Fedele, R. Reitano, N. C. Aricň, E. Ragazzi, R. Seraglia, S. Vogliardi, P. Traldi
Rapid Communications in Mass Spectrometry (2005) 19(2): 162-168

S-nitroso proteome of Mycobacterium tuberculosis: Enzymes of intermediary metabolism and antioxidant defense.
Rhee KY, Erdjument-Bromage H, Tempst P, Nathan CF.
Proc Natl Acad Sci U S A Early Edition: published 30-Dec-2004

Proteomics of Bovine Mitochondrial RNA-Binding Proteins: HES1/KNP-I Is a New Mitochondrial Resident Protein
Mikhail V Ponamarev, Yi-Min She, Li Zhang, and Brian H Robinson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/21/2005

Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae
Maya R. Said, Thomas J. Begley, Alan V. Oppenheim, Douglas A. Lauffenburger, and Leona D. Samson
PNAS (2004) 101(52): 18006-18011

Mass spectrometry and database search in the analysis of proteins from the fungus Pleurotus ostreatus
Maja Matis, Marija ?akelj-Mavri?, Jasna Peter-Katalini?
PROTEOMICS (2005) 5(1): 67-75

Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex
Pedro R. Cutillas, Juerg Biber, Joanne Marks, Richard Jacob, Bruno Stieger, Rainer Cramer, Michael Waterfield, Alma L. Burlingame, Robert J. Unwin
PROTEOMICS (2005) 5(1): 101-112

Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells
Petr Man, Petr Novák, Marek Cebecauer, Ondrej Horváth, Anna Fi?erová, Vladimír Havlí?ek, Karel Bezou?ka
PROTEOMICS (2005) 5(1): 113-122

Cell wall proteins in apoplastic fluids of Arabidopsis thaliana rosettes: Identification by mass spectrometry and bioinformatics
Georges Boudart, Elisabeth Jamet, Michel Rossignol, Claude Lafitte, Gisčle Borderies, Alain Jauneau, Marie-Thérčse Esquerré-Tugayé, Rafael Pont-Lezica
PROTEOMICS (2005) 5(1): 212-221

The Holm Oak leaf proteome: Analytical and biological variability in the protein expression level assessed by 2-DE and protein identification tandem mass spectrometry de novo sequencing and sequence similarity searching
Inmaculada Jorge, Rafael M. Navarro, Christof Lenz, David Ariza, Carlos Porras, Jesús Jorrín
PROTEOMICS (2005) 5(1): 222-234

Proteomic analysis of salt stress-responsive proteins in rice root
Shunping Yan, Zhangcheng Tang, Weiai Su, Weining Sun
PROTEOMICS (2005) 5(1): 235-244

Profiling of abundant proteins associated with dichlorodiphenyltrichloroethane resistance in Drosophila melanogaster
Joao H. F. Pedra, Reginaldo A. Festucci-Buselli, Weilin Sun, William M. Muir, Michael E. Scharf, Barry R. Pittendrigh
PROTEOMICS (2005) 5(1): 258-269

Novel isoforms of Pru av 1 with diverging immunoglobulin E binding properties identified by a synergistic combination of molecular biology and proteomics
Andreas Reuter, Donatella Fortunato, Lorenza Perono Garoffo, Lorenzo Napolitano, Stephan Scheurer, Maria G. Giuffrida, Stefan Vieths, Amedeo Conti
PROTEOMICS (2005) 5(1): 282-289

Using Models of the Myocyte for Functional Interpretation of Cardiac Proteomic Data.
Winslow RL, Cortassa S, Greenstein JL.
J Physiol Early Edition: published 20-Dec-2004

Proteomic analysis of nipple aspirate fluid using SELDI-TOF-MS.
Sauter ER, Shan S, Hewett JE, Speckman P, Du Bois GC.
Int J Cancer Early Edition: published 17-Dec-2004

Proteomic analysis of human natural killer cells: insights on new potential NK immune functions.
Hanna J, Fitchett J, Rowe T, Daniels M, Heller M, Gonen-Gross T, Manaster E, Cho SY, Labarre MJ, Mandelboim O.
Mol Immunol (2005) 42(4): 425-31

Proteomic analysis of phosphotyrosyl proteins in morphine-dependent rat brains.
Kim SY, Chudapongse N, Lee SM, Levin MC, Oh JT, Park HJ, Ho IK
Brain Res Mol Brain Res (2005) 133(1): 58-70

Quantitative proteomic analysis of fibroblast nuclear proteins after stimulation with mitogen activated protein kinase inhibiting heparan sulfate.
Malmstrom J, Marchese J, Juhasz P, Pukac L, Karnovsky M, Marko-Varga G, Westergren-Thorsson G
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 333-42

Proteomics analysis of human cerebrospinal fluid.
Yuan X, Desiderio DM
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 179-89

Use of targeted glycoproteomics to identify serum glycoproteins that correlate with liver cancer in woodchucks and humans.
Block TM, Comunale MA, Lowman M, Steel LF, Romano PR, Fimmel C, Tennant BC, London WT, Evans AA, Blumberg BS, Dwek RA, Mattu TS, Mehta AS
Proc Natl Acad Sci U S A (2005) 102(3): 779-84. Epub 2005 Jan 10

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.
Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR 3rd, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE.
Science (2005) 307(5706): 82-6

First proteomic analysis of Legionella pneumophila based on its developing genome sequence.
Lebeau I, Lammertyn E, De Buck E, Maes L, Geukens N, Van Mellaert L, Arckens L, Anne J, Clerens S.
Res Microbiol (2005) 156(1): 119-29

Nucleolar proteome dynamics.
Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M.
Nature (2005) 433(7021): 77-83

Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples
Karin Björhall, Tasso Miliotis, Pia Davidsson
PROTEOMICS (2005) 5(1): 307-317

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Biomedical and clinical applications

Mass mapping of cancer cell lysates using two-dimensional liquid separations, electrospray-time of flight-mass spectrometry, and automated data processing
Nathan S. Buchanan, Rick L. Hamler, Peter E. Leopold, Fred R. Miller, David M. Lubman
ELECTROPHORESIS (2005) 26(1): 248-256

Two-dimensional electrophoresis protein profiling as an analytical tool for human acute leukemia classification
Jiu-Wei Cui, Jie Wang, Kun He, Bao-Feng Jin, Hong-Xia Wang, Wei Li, Li-Hua Kang, Mei-Ru Hu, Hui-Yan Li, Ming Yu, Bei-fen Shen, Guan-Jun Wang, Xue-Min Zhang
ELECTROPHORESIS (2005) 26(1): 268-279

Proteomic Comparison of Two-Dimensional Gel Electrophoresis Profiles from Human Lung Squamous Carcinoma and Normal Bronchial Epithelial Tissues.
Li C, Zhan X, Li M, Wu X, Li F, Li J, Xiao Z, Chen Z, Feng X, Chen P, Xie J, Liang S.
Genomics Proteomics Bioinformatics (2003) 1(1): 58-67

Purification and proteomic analysis of outer membrane vesicles from a clinical isolate of Leptospira interrogans serovar Copenhageni
Jarlath E. Nally, Julian P. Whitelegge, Rodrigo Aguilera, Martha M. Pereira, David R. Blanco, Michael A. Lovett
PROTEOMICS (2005) 5(1): 144-152

Eye lens proteomics: from global approach to detailed information about phakinin and gamma E and F crystallin genes
Wolfgang Hoehenwarter, Nalin M. Kumar, Maik Wacker, Ursula Zimny-Arndt, Joachim Klose, Peter R. Jungblut
PROTEOMICS (2005) 5(1): 245-257

Proteomic analysis of the proliferative and secretory phases of the human endometrium: Protein identification and differential protein expression
Leroi DeSouza, Georg Diehl, Eric C.C. Yang, Jingzhong Guo, Mary Joe Rodrigues, Alexander D. Romaschin, Terence J. Colgan, K.W. Michael Siu
PROTEOMICS (2005) 5(1): 270-281

The impact of blood contamination on the proteome of cerebrospinal fluid
Jin-Sam You, Valentina Gelfanova, Michael D. Knierman, Frank A. Witzmann, Mu Wang, John E. Hale
PROTEOMICS (2005) 5(1): 290-296

Transcriptomic and proteomic responses of human renal HEK293 cells to uranium toxicity
Odette Prat, Frédéric Berenguer, Véronique Malard, Emmanuelle Tavan, Nicole Sage, Gérard Steinmetz, Eric Quemeneur
PROTEOMICS (2005) 5(1): 297-306

Partial hepatectomy induced liver proteome changes in mice
Christoph W. Strey, Mike S. Winters, Maciej M. Markiewski, John D. Lambris
PROTEOMICS (2005) 5(1): 318-325

Extraction and proteomic analysis of proteins from normal and multiple sclerosis postmortem brain.
Newcombe J, Eriksson B, Ottervald J, Yang Y, Franzen B
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 191-202

A proteomic approach to tumour target identification using phage display, affinity purification and mass spectrometry.
Geuijen CA, Bijl N, Smit RC, Cox F, Throsby M, Visser TJ, Jongeneelen MA, Bakker AB, Kruisbeek AM, Goudsmit J, de Kruif J.
Eur J Cancer (2005) 41(1): 178-187

Proteomic analyzes of copper metabolism in an in vitro model of Wilson disease using surface enhanced laser desorption/ionization-time of flight-mass spectrometry.
Roelofsen H, Balgobind R, Vonk RJ
J Cell Biochem (2004) 93(4): 732-740

Proteome analysis of skin distinguishes acute guttate from chronic plaque psoriasis.
Carlen LM, Sanchez F, Bergman AC, Becker S, Hirschberg D, Franzen B, Coffey J, Jornvall H, Auer G, Alaiya AA, Stahle M
J Invest Dermatol (2005) 124(1): 63-9

Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases.
Paradis V, Degos F, Dargere D, Pham N, Belghiti J, Degott C, Janeau JL, Bezeaud A, Delforge D, Cubizolles M, Laurendeau I, Bedossa P.
Hepatology (2004) 41(1): 40-47

Candidate-Based Proteomics in the Search for Biomarkers of Cardiovascular Disease.
Anderson NL.
J Physiol Early Edition: published 20-Dec-2004

Detection of prostate cancer using serum proteomics pattern in a histologically confirmed population Li J, White N, Zhang Z, Rosenzweig J, Mangold LA, Partin AW, Chan DW, Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD. J Urol 2004;171:1782-7.
Carroll PR.
Urol Oncol (2004) 22(6): 497-8

Different proteome pattern of epidermal growth factor receptor-positive colorectal cancer cell lines that are responsive and nonresponsive to C225 antibody treatment.
Skvortsov S, Sarg B, Loeffler-Ragg J, Skvortsova I, Lindner H, Werner Ott H, Lukas P, Illmensee K, Zwierzina H.
Mol Cancer Ther (2004) 3(12): 1551-8

Differential expression profiling of serum proteins and metabolites for biomarker discovery
Sushmita Mimi Roy, Markus Anderle, Hua Lin and Christopher H. Becker
International Journal of Mass Spectrometry (2004) 238(2): 163-171

Search of plasma markers for colorectal cancer by matrix-assisted laser desorption/ionization mass spectrometry
R. Seraglia, E. Ragazzi, S. Vogliardi, G. Allegri, S. Pucciarelli, M. Agostini, M. Lise, D. Nitti, E.D. Urso, P. Traldi
Journal of Mass Spectrometry (2005) 40(1): 123-126

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Eukaryotic Cells And Tissues

Comparative proteomic analysis of mammalian animal tissues and body fluids: bovine proteome database.
D'Ambrosio C, Arena S, Talamo F, Ledda L, Renzone G, Ferrara L, Scaloni A
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 157-68

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Prokaryotes

Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation
Andreas Tebbe, Christian Klein, Birgit Bisle, Frank Siedler, Beatrix Scheffer, Carolina Garcia-Rizo, Jan Wolfertz, Volker Hickmann, Friedhelm Pfeiffer, Dieter Oesterhelt
PROTEOMICS (2005) 5(1): 168-179

The membrane proteome of Halobacterium salinarum
Christian Klein, Carolina Garcia-Rizo, Birgit Bisle, Beatrix Scheffer, Hans Zischka, Friedhelm Pfeiffer, Frank Siedler, Dieter Oesterhelt
PROTEOMICS (2005) 5(1): 180-197

Differential protein expression by Porphyromonas gingivalis in response to secreted epithelial cell components
Yi Zhang, Tiansong Wang, Weibin Chen, Özlem Yilmaz, Yoonsuk Park, Il-Young Jung, Murray Hackett, Richard J. Lamont
PROTEOMICS (2005) 5(1): 198-211

Heat Shock Proteome Analysis of Wild-Type Corynebacterium glutamicum ATCC 13032 and a Spontaneous Mutant Lacking GroEL1, a Dispensable Chaperone.
Barreiro C, Gonzalez-Lavado E, Brand S, Tauch A, Martin JF
J Bacteriol (2005) 187(3): 884-9

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Protein Array

A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics
Amal S. Essader, Benjamin J. Cargile, Jonathan L. Bundy, James L. Stephenson Jr.
PROTEOMICS (2005) 5(1): 24-34

High-throughput and multiplexed protein array technology: protein-DNA and protein-protein interactions.
Sakanyan V
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 77-95

Proteomic analysis of mantle cell lymphoma by protein microarray.
Ghobrial IM, McCormick DJ, Kaufmann SH, Leontovich AA, Loegering DA, Dai NT, Krajnik KL, Stenson MJ, Melhem MF, Novak AJ, Ansell SM, Witzig TE
Blood Early Edition: published 13-Jan-2005

Identification of protein pattern in kidney cancer using ProteinChip(R) arrays and bioinformatics.
Junker K, Gneist J, Melle C, Driesch D, Schubert J, Claussen U, Von Eggeling F
Int J Mol Med (2005) 15(2): 285-90

Profiling the humoral immune response to infection by using proteome microarrays: High-throughput vaccine and diagnostic antigen discovery.
Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL
Proc Natl Acad Sci U S A (2005) 102(3): 547-52. Epub 2005 Jan 12

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Protein Characterization / PTMs

On-line counting of cysteine residues in peptides during electrospray ionization by electrogenerated tags and their application to protein identification
Loďc Dayon, Christophe Roussel, Michel Prudent, Niels Lion, Hubert H. Girault
ELECTROPHORESIS (2005) 26(1): 238-247

Top-down analysis of protein isoprenylation by electrospray ionization hybrid quadrupole time-of-flight tandem mass spectrometry; the mouse T? protein
Hidetoshi Kassai, Yoshinori Satomi, Yoshitaka Fukada, Toshifumi Takao
Rapid Communications in Mass Spectrometry (2005) 19(2): 269-274

High-Throughput Method for N-Terminal Sequencing of Proteins by MALDI Mass Spectrometry
Minoru Yamaguchi, Takashi Nakazawa, Hiroki Kuyama, Takashi Obama, Eiji Ando, Taka-aki Okamura, Norikazu Ueyama, and Shigemi Norioka
ANALYTICAL CHEMISTRY (2005) 77(2): 645-651

Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications
Lianna Johnson, Sahana Mollah, Benjamin A. Garcia, Tara L. Muratore, Jeffrey Shabanowitz, Donald F. Hunt, and Steven E. Jacobsen
Nucl Acids Res (2004) 32(22): 6511-6518

Detection and localization of protein modifications by high resolution tandem mass spectrometry
Fanyu Meng, Andrew J. Forbes, Leah M. Miller, Neil L. Kelleher
Mass Spectrometry Reviews (2005) 24(2): 126-134

Activation of large lons in FT-ICR mass spectrometry
Julia Laskin, Jean H. Futrell
Mass Spectrometry Reviews (2005) 24(2): 135-167

Proteomics by FTICR mass spectrometry: Top down and bottom up
Bogdan Bogdanov, Richard D. Smith
Mass Spectrometry Reviews (2005) 24(2): 168-200

Protein Glycosylation Analyzed by Normal-Phase Nano-Liquid Chromatography-Mass Spectrometry of Glycopeptides
Manfred Wuhrer, Carolien A. M. Koeleman, Cornelis H. Hokke, and André M. Deelder
ANALYTICAL CHEMISTRY Early Edition: published 12/24/2004

Phosphoproteomic analysis using immobilized metal ion affinity chromatography on the basis of cellulose powder
Isabel Feuerstein, Sandra Morandell, Guenther Stecher, Christian W. Huck, Taras Stasyk, Hong-Lei Huang, David Teis, Lukas A. Huber, Guenther K. Bonn
PROTEOMICS (2005) 5(1): 46-54

Phosphoprotein profiling of erythropoietin receptor- dependent pathways using different proteomic strategies
Sandra Körbel, Tom Büchse, Holger Prietzsch, Tilo Sasse, Michael Schümann, Eberhard Krause, Josef Brock, Thomas Bittorf
PROTEOMICS (2005) 5(1): 91-100

A proteomic approach to characterize protein shedding
Mamoun Ahram, Joshua N. Adkins, Deanna L. Auberry, David S. Wunschel, David L. Springer
PROTEOMICS (2005) 5(1): 123-131

Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination.
Esteban Warren MR, Parker CE, Mocanu V, Klapper D, Borchers CH
Rapid Commun Mass Spectrom (2005) 19(4): 429-437 [Epub ahead of print]

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Protein-protein interaction

Chemical Cross-Linking and High-Performance Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Protein Interaction Analysis: Application to a Calmodulin/Target Peptide Complex
Stefan Kalkhof, Christian Ihling, Karl Mechtler, and Andrea Sinz
ANALYTICAL CHEMISTRY (2005) 77(2): 495-503

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 (2005) 77(1): 311-318

A modified tandem affinity purification tag technique for the purification of protein complexes in mammalian cells
Robert Drakas, Marco Prisco, Renato Baserga
PROTEOMICS (2005) 5(1): 132-137

Detecting protein-protein interaction in live yeast by flow cytometry.
Dye BT, Schell K, Miller DJ, Ahlquist P
Cytometry A Early Edition: published 13-Jan-2005

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Quantitation

Targeted Comparative Proteomics by Liquid Chromatography-Tandem Fourier Ion Cyclotron Resonance Mass Spectrometry
Christophe Masselon, Ljiljana Pa a-Toli , Nikola Toli , Gordon A. Anderson, Bogdan Bogdanov, Andrey N. Vilkov, Yufeng Shen, Rui Zhao, Wei-Jun Qian, Mary S. Lipton, David G. Camp, II, and Richard D. Smith
ANALYTICAL CHEMISTRY (2005) 77(2): 400-406

Detection of Local Polarity of -Lactalbumin by N-Terminal Specific Labeling with a New Tailor-made Fluorescent Probe
Su-Ying Dong, Hui-Min Ma, Xue-Jun Duan, Xin-Qi Chen, and Jun Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/21/2005

A novel strategy for quantitative proteomics using isotope-coded protein labels
Alexander Schmidt, Josef Kellermann, Friedrich Lottspeich
PROTEOMICS (2005) 5(1): 4-15

18O-labeling quantitative proteomics using an ion trap mass spectrometer
Jun Sakai, Shinich Kojima, Kazunori Yanagi, Masaharu Kanaoka
PROTEOMICS (2005) 5(1): 16-23

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Review

Proteomics of Halophilic archaea.
Joo WA, Kim CW
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 237-50

Proteomics analysis of human cerebrospinal fluid.
Yuan X, Desiderio DM
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 179-89

The role of electron capture dissociation in biomolecular analysis
Helen J. Cooper, Kristina Hĺkansson, Alan G. Marshall
Mass Spectrometry Reviews (2005) 24(2): 201-222

Proteomic patterns: their potential for disease diagnosis.
Xiao Z, Prieto D, Conrads TP, Veenstra TD, Issaq HJ
Mol Cell Endocrinol (2005) 230(1-2): 95-106

Gels and more gels: probing toxicity.
Witzmann FA, Bai F, Hong SM, Liu S, Pedrick N, Ringham H, Tan J
Curr Opin Mol Ther (2004) 6(6): 608-15

Genomic and proteomic profiling for biomarkers and signature profiles of toxicity.
Merrick BA, Bruno ME
Curr Opin Mol Ther (2004) 6(6): 600-7

Prefractionation techniques in proteome analysis: The mining tools of the third millennium.
Righetti PG, Castagna A, Antonioli P, Boschetti E
Electrophoresis (2005) 26(2): 297-319 [Epub ahead of print]

Asthma, the ugly duckling of lung disease proteomics?
Houtman R, van den Worm E
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 285-94

Methods of comparative proteomic profiling for disease diagnostics.
Steel LF, Haab BB, Hanash SM
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 275-84

Proteomics of breast carcinoma.
Somiari RI, Somiari S, Russell S, Shriver CD
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 215-25

Revealing urologic diseases by proteomic techniques.
Lee SW, Lee KI, Kim JY
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 203-13

Proteomics of bronchoalveolar lavage fluid.
Wattiez R, Falmagne P
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 169-78

Role of chromatographic techniques in proteomic analysis.
Neverova I, Van Eyk JE
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 51-63

Strategies for revealing lower abundance proteins in two-dimensional protein maps.
Ahmed N, Rice GE
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 39-50

Peptidomics, current status.
Soloviev M, Finch P
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 11-24

Defining mitogen-activated protein kinase pathways with mass spectrometry-based approaches.
Powell DW, Pierce WM, McLeish KR.
Mass Spectrom Rev Early Edition: published 23-Dec-2004

Mapping protein-protein interactions by bioinformatics and cross-linking.
Friedhoff P.
Anal Bioanal Chem Early Edition: published 22-Dec-2004

Proteomic approaches in the search for disease biomarkers.
Vlahou A, Fountoulakis M.
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 814(1): 11-9

Combination of two-dimensional electrophoresis and shotgun peptide sequencing in comparative proteomics.
Kubota K, Kosaka T, Ichikawa K
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 3-9

Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery.
Berger AB, Vitorino PM, Bogyo M
Am J Pharmacogenomics (2004) 4(6): 371-81

Integrated transcriptome and proteome data: the challenges ahead.
Hack CJ
Brief Funct Genomic Proteomic (2004) 3(3): 212-9

Current chemical tagging strategies for proteome analysis by mass spectrometry
Alexander Leitner and Wolfgang Lindner
J Chromatogr B (2004) 813(1-2): 1-26

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Methodology

Preparative-scale fractionation by isoelectric trapping under nondenaturing conditions: Separation of egg white protein isoforms on a modified Gradiflow unit
Clemens C. Möller, Denise Thomas, Derek Van Dyk, Dennis Rylatt, Marian Sheehan
ELECTROPHORESIS (2005) 26(1): 35-46

New azo dyes as colored isoelectric point markers for isoelectric focusing in acidic pH region
Miroslava ?tastná, Martin Trávní?ek, Karel ?lais
ELECTROPHORESIS (2005) 26(1): 53-59

Functional characterization of two-dimensional gel-separated proteins using sequential staining
Jian Wu, Nataliya J. Lenchik, Michael J. Pabst, Solomon S. Solomon, James Shull, Ivan C. Gerling
ELECTROPHORESIS (2005) 26(1): 225-237

Integrated Capillary Isoelectric Focusing/Nano-reversed Phase Liquid Chromatography Coupled with ESI-MS for Characterization of Intact Yeast Proteins
Yueju Wang, Brian M. Balgley, Paul A. Rudnick, Erin L. Evans, Cheng S. Lee
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/07/2005

Beyond Quantitative Proteomics: Signal Enhancement of the a1 Ion as a Mass Tag for Peptide Sequencing Using Dimethyl Labeling
Jue-Liang Hsu, Sheng-Yu Huang, Jen-Taie Shiea, Wen-Ying Huang, and Shu-Hui Chen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/24/2004

Applications of a matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer. l. Metastable decay and collision-induced dissociation for sequencing peptides
Suzanne Ackloo, Alexandre Loboda
Rapid Communications in Mass Spectrometry (2005) 19(2): 213-220

Oxidized carbon nanotubes as matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of biomolecules
Shi-fang Ren, Yin-long Guo
Rapid Communications in Mass Spectrometry (2005) 19(2): 255-260

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 (2005) 77(1): 47-56

Instrumental Parameters in the MALDI-TOF Mass Spectrometric Analysis of Quaternary Protein Structures
Martin Zehl and Günter Allmaier
ANALYTICAL CHEMISTRY (2005) 77(1): 103-110

Charge Ratio Analysis Method: Approach for the Deconvolution of Electrospray Mass Spectra
Simin D. Maleknia and Kevin M. Downard
ANALYTICAL CHEMISTRY (2005) 77(1): 111-119

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 (2005) 77(1): 259-265

Hand-Held Microanalytical Instrument for Chip-Based Electrophoretic Separations of Proteins
Ronald F. Renzi, James Stamps, Brent A. Horn, Scott Ferko, Victoria A. VanderNoot, Jay A. A. West, Robert Crocker, Boyd Wiedenman, Daniel Yee, and Julia A. Fruetel
ANALYTICAL CHEMISTRY (2005) 77(2): 435-441

Microfluidic Chip for Peptide Analysis with an Integrated HPLC Column, Sample Enrichment Column, and Nanoelectrospray Tip
Hongfeng Yin, Kevin Killeen, Reid Brennen, Dan Sobek, Mark Werlich, and Tom van de Goor
ANALYTICAL CHEMISTRY (2005) 77(2): 527-533

Digital Microfluidics with In-Line Sample Purification for Proteomics Analyses with MALDI-MS
Aaron R. Wheeler, Hyejin Moon, Christopher A. Bird, Rachel R. Ogorzalek Loo, Chang-Jin "C.J." Kim, Joseph A. Loo, and Robin L. Garrell
ANALYTICAL CHEMISTRY (2005) 77(2): 534-540

Tissue-print and print-phoresis as platform technologies for the molecular analysis of human surgical specimens: mapping tumor invasion of the prostate capsule.
Gaston SM, Soares MA, Siddiqui MM, Vu D, Lee JM, Goldner DL, Brice MJ, Shih JC, Upton MP, Perides G, Baptista J, Lavin PT, Bloch BN, Genega EM, Rubin MA, Lenkinski RE.
Nat Med Early Edition: published 26-Dec-2004

Protocol for the Thermodynamic Analysis of Some Proteins Using an H/D Exchange- and Mass Spectrometry-Based Technique
Susie Y. Dai, Myles W. Gardner, and Michael C. Fitzgerald
ANALYTICAL CHEMISTRY (2005) 77(2): 693-697

A subcellular prefractionation protocol for minute amounts of mammalian cell cultures and tissue
Isabelle Guillemin, Michael Becker, Kornelia Ociepka, Eckhard Friauf, Hans Gerd Nothwang
PROTEOMICS (2005) 5(1): 35-45

Peptide mass fingerprinting by matrix-assisted laser desorption ionization mass spectrometry of proteins detected by immunostaining on nitrocellulose
Genevičve Dufresne-Martin, Jean-François Lemay, Pierre Lavigne, Klaus Klarskov
PROTEOMICS (2005) 5(1): 55-66

Accurate mass measurement in nano-electrospray ionization mass spectrometry by alternate switching of high voltage between sample and reference sprayers.
Satomi Y, Kudo Y, Sasaki K, Hase T, Takao T
Rapid Commun Mass Spectrom (2005) 19(4): 540-546 [Epub ahead of print]

Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples
Karin Björhall, Tasso Miliotis, Pia Davidsson
PROTEOMICS (2005) 5(1): 307-317

Effectiveness and limitation of two-dimensional gel electrophoresis in bacterial membrane protein proteomics and perspectives.
Bunai K, Yamane K
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 227-36

Immunoproteomics.
Hess JL, Blazer L, Romer T, Faber L, Buller RM, Boyle MD
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 65-75

Geometrical distortions in two-dimensional gels: applicable correction methods.
Aittokallio T, Salmi J, Nyman TA, Nevalainen OS
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 815(1-2): 25-37

Activity Staining of Glutathione Peroxidase after Two-dimensional Gel Electrophoresis.
Kho CW, Park SG, Lee do H, Cho S, Oh GT, Kang S, Park BC
Mol Cells (2004) 18(3): 369-73

Targeted comparative proteomics by liquid chromatography-tandem fourier ion cyclotron resonance mass spectrometry.
Masselon C, Pasa-Tolic L, Tolic N, Anderson GA, Bogdanov B, Vilkov AN, Shen Y, Zhao R, Qian WJ, Lipton MS, Camp DG 2nd, Smith RD
Anal Chem (2005) 77(2): 400-6

Application of metal-chelate affinity chromatography to the study of the phosphoproteome.
Imam-Sghiouar N, Joubert-Caron R, Caron M
Amino Acids Early Edition: published 13-Jan-2005

Utilisation of proteomics datasets generated via multidimensional protein identification technology (MudPIT).
Washburn MP
Brief Funct Genomic Proteomic (2004) 3(3): 280-6

Quantitation of binding, recovery and desalting efficiency of peptides and proteins in solid phase extraction micropipette tips.
Palmblad M, Vogel JS
J Chromatogr B Analyt Technol Biomed Life Sci (2005) 814(2): 309-13

Improved protein identification using automated high mass measurement accuracy MALDI FT-ICR MS peptide mass fingerprinting
David M. Horna, Eric C. Petersa, Heath Klocka, Andrew Meyersb and Ansgar Brocka
International Journal of Mass Spectrometry (2004) 238(2): 189-196

Electrochemical oxidation and cleavage of proteins with on-line mass spectrometric detection: Development of an instrumental alternative to enzymatic protein digestion
Hjalmar P. Permentiera and Andries P. Bruins
Journal of the American Society for Mass Spectrometry (2004) 15(12): 1707-1716

Generation of mass tags by the inherent electrochemistry of electrospray for protein mass spectrometry
Christophe Roussel, Loďc Dayon, Niels Lion, Tatiana C. Rohner, Jacques Josserand, Joël S. Rossier, Henrik Jensena and Hubert H. Girault
Journal of the American Society for Mass Spectrometry (2004) 15(12): 1767-1779

Ion soft-landing into liquids: Protein identification, separation, and purification with retention of biological activity
Bogdan Gologan, Zoltán Takáts, Jormarie Alvarez, Justin M. Wiseman, Nari Talaty, Zheng Ouyang and R. Graham Cooks
Journal of the American Society for Mass Spectrometry (2004) 15(12): 1874-1884

Implications of column peak capacity on the separation of complex peptide mixtures in single- and two-dimensional high-performance liquid chromatography
Martin Gilar, , Amy E. Daly, Marianna Kele, Uwe D. Neue and John C. Gebler
J Chromatogr A (2004) 1061(2): 180-192

On peptide de novo sequencing: a new approach.
Bruni R, Gianfranceschi G, Koch G.
J Pept Sci Early Edition: published 1-Nov-2004

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Meeting

Meetings: Proteomics 1/2005
PROTEOMICS (2005) 5(1): 326-327

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Other

Protein open-access liquid chromatography/mass spectrometry
Wendy L. White, Craig D. Wagner, John T. Hall, Erin E. Chaney, Bindu George, Karen Hofmann, Luke A. D. Miller, Jon D. Williams
Rapid Communications in Mass Spectrometry (2005) 19(2): 241-249

Preconcentration of Proteins on Microfluidic Devices Using Porous Silica Membranes
Robert S. Foote, Julia Khandurina, Stephen C. Jacobson, and J. Michael Ramsey
ANALYTICAL CHEMISTRY (2005) 77(1): 57-63

Comparison of the Thermodynamic Properties of Particulate and Monolithic Columns of Molecularly Imprinted Copolymers
Hyunjung Kim and Georges Guiochon
ANALYTICAL CHEMISTRY (2005) 77(1): 93-102

Evaluation of "Shotgun" Proteomics for Identification of Biological Threat Agents in Complex Environmental Matrixes: Experimental Simulations
Nathan C. VerBerkmoes, W. Judson Hervey, Manesh Shah, Miriam Land, Frank W. Larimer, Gary J. Van Berkel, and Douglas E. Goeringer
ANALYTICAL CHEMISTRY Early Edition: published 01/07/2005

Chip with Twin Anchors for Reduced Ion Suppression and Improved Mass Accuracy in MALDI-TOF Mass Spectrometry
Johan Sjödahl, Martin Kempka, Karin Hermansson, Anders Thorsén, and Johan Roeraade
ANALYTICAL CHEMISTRY Early Edition: published 01/07/2005

Surface Plasmon Resonance/Mass Spectrometry Interface
Jens Grote, Nico Dankbar, Erk Gedig, and Simone Koenig
ANALYTICAL CHEMISTRY Early Edition: published 01/14/2005

Product News: Proteomics 1/2005
PROTEOMICS (2005) 5(1): 328-331

Current literature in mass spectrometry.
J Mass Spectrom (2004) 39(12): 1582-1587

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