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SPS' Digest

Issue 21, 28-Jul-2005

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Quick jumps to articles in: Bioinformatics (11) / Biological applications (16) / Biomedical and clinical applications (22) / Eukaryotic Cells And Tissues (9) / Prokaryotes (5) / Pharmacology and Toxicology (3) / Protein Array (1) / Protein Characterization - PTMs (1) / Protein-protein interaction (2) / Quantitation (9) / Review (33) / Methodology (23) / Meeting (2) / Other (3) /

In this issue, 139 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 (16) / Biomedical and clinical applications (22) / Eukaryotic Cells And Tissues (9) / Prokaryotes (5) / Pharmacology and Toxicology (3) / Protein Array (1) / Protein Characterization - PTMs (1) / Protein-protein interaction (2) / Quantitation (9) / Review (33) / Methodology (23) / Meeting (2) / Other (3) /

Bioinformatics

Nh3D: A reference dataset of non-homologous protein structures
Thiruv B, Quon GT, Saldanha SA, Steipe B
BMC Structural Biology (2005) 5(1): 12

Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information
James W Cooper, Aaron Kershenbaum
BMC Bioinformatics (2005) 6(1): 143

Algorithms for alignment of mass spectrometry proteomic data
Neal Jeffries
Bioinformatics (2005) 21(14): 3066-3073

PMUT: a web-based tool for the annotation of pathological mutations on proteins
Carles Ferrer-Costa, Josep Lluis Gelpi, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, and Modesto Orozco
Bioinformatics (2005) 21(14): 3176-3178

Proteomic mass spectra classification using decision tree based ensemble methods
Pierre Geurts, Marianne Fillet, Dominique de Seny, Marie-Alice Meuwis, Michel Malaise, Marie-Paule Merville, and Louis Wehenkel
Bioinformatics (2005) 21(14): 3138-3145

Post-genomics of microsporidia, with emphasis on a model of minimal eukaryotic proteome: a review
Texier C, Brosson D, El Alaoui H, Metenier G, Vivares CP
Folia Parasitol (Praha) (2005) 52(1-2): 15-22

Processing methods for differential analysis of LC/MS profile data
Katajamaa M Mk, Oresic M Mo
BMC Bioinformatics (2005) 6(1): 179

Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)
Hong H, Dragan Y, Epstein J, Teitel C, Chen B, Xie Q, Fang H, Shi L, Perkins R, Tong W
BMC Bioinformatics (2005) 6(Suppl 2): S5

DEPD: a novel database for differentially expressed protein
He QY, Cao J, Liu XH, Li MX, Liu YS, Xie JY, Liang SP
Bioinformatics Early Edition: published 14-Jul-2005

InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra
Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V
Anal Chem (2005) 77(14): 4626-4639

Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines
Wang J, Sung WK, Krishnan A, Li KB
BMC Bioinformatics (2005) 6(1): 174

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Biological applications

Proteome analysis of rat pancreas induced by pancreatectomy
Jun-Seop Shin, Jae-Jeong Lee, Eun-Ju Lee, Yeon-Hee Kim, Kwon-Seok Chae and Chan-Wha Kim
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics (2005) 1749(1): 23-32

Proteomic analysis of complexes formed by human topoisomerase I
Alicja Czubaty, Agnieszka Girstun, Barbara Kowalska-Loth, Agata M. Trzcinska, Elzbieta Purta, Alicja Winczura, Wojciech Grajkowski and Krzysztof Staron
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics (2005) 1749(1): 133-141

Proteome Analysis of Separated Male and Female Gametocytes Reveals Novel Sex-Specific Plasmodium Biology
Shahid M. Khan, Blandine Franke-Fayard Gunnar R. Mair, Edwin Lasonder, Chris J. Janse, Matthias Mann and Andrew P. Waters
Cell (2005) 121(5): 675-687

Immunogenic membrane-associated proteins of Mycobacterium tuberculosis revealed by proteomics
Sinha S, Kosalai K, Arora S, Namane A, Sharma P, Gaikwad AN, Brodin P, Cole ST
Microbiology (2005) 151(Pt 7): 2411-9

Proteomic identification of differentially expressed proteins in the aging murine olfactory system and transcriptional analysis of the associated genes
Poon HF, Vaishnav RA, Butterfield DA, Getchell ML, Getchell TV
J Neurochem (2005) 94(2): 380-92

Proteomics analysis provides insight into caloric restriction mediated oxidation and expression of brain proteins associated with age-related impaired cellular processes: Mitochondrial dysfunction, glutamate dysregulation and impaired protein synthesis
Poon HF, Shepherd HM, Reed TT, Calabrese V, Stella AM, Pennisi G, Cai J, Pierce WM, Klein JB, Butterfield DA
Neurobiol Aging Early Edition: published 1-Jul-2005

Farnesyltransferase inhibitor SCH66336 induces rapid phosphorylation of eukaryotic translation elongation factor 2 in head and neck squamous cell carcinoma cells
Ren H, Tai SK, Khuri F, Chu Z, Mao L
Cancer Res (2005) 65(13): 5841-7

Two-dimensional electrophoresis and mass spectrometry for the identification of species-specific Trichinella antigens
Dea-Ayuela MA, Bolas-Fernandez F
Vet Parasitol Early Edition: published 30-Jun-2005

Proteomics of gluten: mapping of the 1Bx7 glutenin subunit in Chinese Spring cultivar by matrix-assisted laser desorption/ionization
Alberghina G, Cozzolino R, Fisichella S, Garozzo D, Savarino A
Rapid Commun Mass Spectrom (2005) 19(14): 2069-2074

A scalable, GFP-based pipeline for membrane protein overexpression screening and purification
Drew D, Slotboom DJ, Friso G, Reda T, Genevaux P, Rapp M, Meindl-Beinker NM, Lambert W, Lerch M, Daley DO, Van Wijk KJ, Hirst J, Kunji E, De Gier JW
Protein Sci Early Edition: published 29-Jun-2005

The Trypanosoma cruzi Proteome
Atwood JA 3rd, Weatherly DB, Minning TA, Bundy B, Cavola C, Opperdoes FR, Orlando R, Tarleton RL
Science (2005) 309(5733): 473-6

Functional and Structural Analysis of Bacillus Proteome
Sinchaikul, S.; Sookkheo, B.; Topanurak, S.; Pan, Fu-Ming i.n.i.t.s..; Phutrakul, S.; Chen, Shui-Tein
Current Proteomics (2005) 2(2): 109-145

Proteome analysis of serovars Typhimurium and Pullorum of Salmonella enterica subspecies I
Encheva V, Wait R, Gharbia SE, Begum S, Shah HN
BMC Microbiol (2005) 5(1): 42

Characterization of the secreted proteome of rat hepatocytes cultured in collagen sandwiches
Farkas D, Bhat VB, Mandapati S, Wishnok JS, Tannenbaum SR
Chem Res Toxicol (2005) 18(7): 1132-9

The Platelet Microparticle Proteome
Benjamin A. Garcia, David M. Smalley, HyungJun Cho, Jeffrey Shabanowitz, Klaus Ley, and Donald F. Hunt
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/22/2005

Dietary Effects of Copper and Iron Deficiency on Rat Intestine: A Differential Display Proteome Analysis
Alessandra Tosco, Rosa Anna Siciliano, Giuseppina Cacace, Maria Fiorella Mazzeo, Roberta Capone, Antonio Malorni, Arturo Leone, and Liberato Marzullo
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/22/2005

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Biomedical and clinical applications

The Discovery of Stannin in Rat Dorsal Root Ganglia Using an Integrated Proteohistological Approach: Potential Role in Inflammatory Hyperalgesia
Belkowski, Stanley M.; Colburn, Raymond W.; Stone, Dennis J.; Van Besien, Christopher R.; Polkovitch, Deborah; Andrade-Gordon, Patricia; D'Andrea, Michael R
Clinical Proteomics (2004) 1(3-4): 249-258

Antiproliferative Heparan Sulfate Inhibiting Hyaluronan and Transforming Growth Factor-beta Expression in Human Lung Fibroblast Cells: A Possible Antifibrotic Therapy?
Larsen, Kristoffer; Malmstrom, Johan; Tufvesson, Ellen; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla
Clinical Proteomics (2004) 1(3-4): 271-284

Comparison of Protein Expression Patterns Between Hepatocellular Carcinoma Cell Lines and a Hepatoblastoma Cell Line
Pang, Ronald T. K.; Poon, Terence C. W.; Wong, Nathalie; Lai, Paul B. S.; Wong, Navy L. Y; Chan, Charles M. L.; Yu, Jasmine W. S.; Chan, Anthony T. C.; Sung, Joseph J. Y
Clinical Proteomics (2004) 1(3-4): 313-332

In-Depth Analysis of the Human CSF Proteome Using Protein Prefractionation
Maccarrone, Giuseppina; Birg, Isabel; Malisch, Eva; Rosenhagen, Marcus C.; Ditzen, Claudia; Chakel, John A.; Mandel, Friedrich; Reimann, Andreas; Doertbudak, Can-Carlo; Haegler, Katrin; Holsboer, Florian; Turck, Christoph W
Clinical Proteomics (2004) 1(3-4): 333-364

Serum Proteomic Pattern for Predicting Recurrence of Undifferentiated Nasopharyngeal Carcinoma After Radiotherapy: A Potential Surrogate Marker
Poon, Terence C. W.; Chow, Shuk Man; Ma, Brigette B. Y.; Hui, Edwin P.; Chan, Anthony T. C
Clinical Proteomics (2004) 1(3-4): 365-374

Proteomic but not enzyme-linked immunosorbent assay technology detects amniotic fluid monomeric calgranulins from their complexed calprotectin form
Buhimschi IA, Buhimschi CS, Weiner CP, Kimura T, Hamar BD, Sfakianaki AK, Norwitz ER, Funai EF, Ratner E
Clin Diagn Lab Immunol (2005) 12(7): 837-44

Unique distribution of apolipoproteins on small, dense LDL in patients with the metabolic syndrome and type 2 diabetes: a proteomic study
Davidsson P, Hulthe J, Fagerberg B, Olsson BM, Hallberg C, Dahllof B, Camejo G
J Lipid Res Early Edition: published 1-Jul-2005

The role of proteomics in investigating psychiatric disorders
Pennington K, Cotter D, Dunn MJ
Br J Psychiatry (2005) 187: 4-6.

The emergence of genomic and proteomic biomarkers in heart transplantation
Mehra MR
J Heart Lung Transplant (2005) 24(7 Suppl): S213-8

Identification of urinary protein pattern in Type 1 diabetic adolescents with early diabetic nephropathy by a novel combined proteome analysis
Meier M, Kaiser T, Herrmann A, Knueppel S, Hillmann M, Koester P, Danne T, Haller H, Fliser D, Mischak H
J Diabetes Complications (2005) 19(4): 223-32

Novel strategies for the early detection and prevention of lung cancer
Wardwell NR, Massion PP
Semin Oncol (2005) 32(3): 259-68

The nutritional phenotype in the age of metabolomics
Zeisel SH, Freake HC, Bauman DE, Bier DM, Burrin DG, German JB, Klein S, Marquis GS, Milner JA, Pelto GH, Rasmussen KM
J Nutr (2005) 135(7): 1613-6

Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy
Miyamae T, Malehorn DE, Lemster B, Mori M, Imagawa T, Yokota S, Bigbee WL, Welsh M, Klarskov K, Nishomoto N, Vallejo AN, Hirsch R
Arthritis Res Ther (2005) 7(4): R746-55

Protein Fingerprints of Anti-cancer Effects of Cyclin-dependent Kinase Inhibition: Identification of Candidate Biomarkers Using 2-D Liquid Phase Separation Coupled to Mass Spectrometry
Skalnikova H, Halada P, Dzubak P, Hajduch M, Kovarova H
Technol Cancer Res Treat (2005) 4(4): 447-54

Two-dimensional electrophoresis database of fluorescence-labeled proteins of colon cancer cells
Mori Y, Kondo T, Yamada T, Tsuchida A, Aoki T, Hirohashi S
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 9-Jul-2005

High molecular mass proteome of androgen-independent prostate cancer
Ratliff TL
J Urol (2005) 174(2): 787

Identification and Characterization of Plant Allergens Using Proteomic Approaches
Law, A.; Gupta, N.; Louie, M.; Poddar, R.; Ray, A.; Chakravarti, D. N
Current Proteomics (2005) 2(2): 147-164

A proteomics analysis of cellular proteins associated with HBV genotype-specific HBX: potential in identification of early diagnostic markers for HCC
Tan TL, Chen WN
J Clin Virol (2005) 33(4): 293-8

Analysis of candidate genes through a proteomics-based approach in primary cell lines from malignant melanomas and their metastases
Carta F, Demuro PP, Zanini C, Santona A, Castiglia D, D'atri S, Ascierto PA, Napolitano M, Cossu A, Tadolini B, Turrini F, Manca A, Sini MC, Palmieri G, Rozzo AC
Melanoma Res (2005) 15(4): 235-244

Breast carcinomas fulfill the Warburg hypothesis and provide metabolic markers of cancer prognosis
Isidoro A, Casado E, Redondo A, Acebo P, Espinosa E, Alonso AM, Cejas P, Hardisson D, Fresno Vara JA, Belda-Iniesta C, Gonzalez-Baron M, Cuezva JM
Carcinogenesis Early Edition: published 20-Jul-2005

Rapid detection of fetal aneuploidy using proteomics approaches on amniotic fluid supernatant
Wang TH, Chang YL, Peng HH, Wang ST, Lu HW, Teng SH, Chang SD, Wang HS
Prenat Diagn (2005) 25(7): 559-566

Application of serum SELDI proteomic patterns in diagnosis of lung cancer
Yang SY, Xiao XY, Zhang WG, Zhang LJ, Zhang W, Zhou B, Chen G, He DC
BMC Cancer (2005) 5(1): 83

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Eukaryotic Cells And Tissues

Three-Dimensional Visualization of Protein Expression in Mouse Brain Structures Using Imaging Mass Spectrometry
Anna C. Crecelius, D. Shannon Cornett, Richard M. Caprioli, Betsy Williams, Benoit M. Dawant and Bobby Bodenheimer
Journal of the American Society for Mass Spectrometry (2005) 16(7): 1093-1099

Proteomics takes stem cell analyses to another level
Levchenko A
Nat Biotechnol (2005) 23(7): 828-30

Proteomic analysis of rhoptry organelles reveals many novel constituents for host-parasite interactions in toxoplasma gondii
Bradley PJ, Ward C, Cheng SJ, Alexander DL, Coller S, Coombs GH, Dunn JD, Ferguson DJ, Sanderson SJ, Wastling JM, Boothroyd JC
J Biol Chem Early Edition: published 7-Jul-2005

The opportunistic pathogen toxoplasma gondll deploys a diverse legion of invasion and survival proteins
Zhou XW, Kafsack BF, Cole RN, Beckett P, Shen RF, Carruthers VB
J Biol Chem Early Edition: published 7-Jul-2005

Proteomic approach to identify changes in protein expression modified by 17beta-estradiol in bovine vascular smooth muscle cells
Molero L, Garcia-Mendez A, Alonso Orgaz S, Carrasco C, Macaya C, Lopez Farre AJ
Clin Sci (Lond) Early Edition: published 21-Jul-2005

Proteomic analysis of a eukaryotic cilium
Pazour GJ, Agrin N, Leszyk J, Witman GB
J Cell Biol (2005) 170(1): 103-13

Profiling excretory/secretory proteins of Trichinella spiralis muscle larvae by two-dimensional gel electrophoresis and mass spectrometry
Robinson MW, Gare DC, Connolly B
Vet Parasitol Early Edition: published 28-Jun-2005

A two-dimensional electrophoresis reference map of human ovary
Wang L, Zhu YF, Guo XJ, Huo R, Ma X, Lin M, Zhou ZM, Sha JH
J Mol Med Early Edition: published 15-Jul-2005

Developmental changes in the neuronal protein composition: a study by high resolution 2D-gel electrophoresis
Chatterjee M, Chatterjee D
Mol Cell Biochem (2005) 272(1-2): 201-7

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Prokaryotes

Proteomic analysis of Bacillus anthracis Sterne vegetative cells
Anthony W. Francis, Christy E. Ruggiero, Andrew T. Koppisch, Jingao Dong, Jian Song, Thomas Brettin and Srinivas Iyer
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics (2005) 1748(2): 191-200

Bacterial response to eukaryotic cells Analysis of differentially expressed proteins using nano liquid chromatography-electrospray ionization tandem mass spectrometry
C. Alpert, W. Engst, A. Guehler, T. Oelschlaeger and M. Blaut
J Chromatogr A (2005) 1082(1): 25-32

Identification of inducible protein complexes in the phenol degrader Pseudomonas sp. strain phDV1 by blue native gel electrophoresis and mass spectrometry
Tsirogianni E, Aivaliotis M, Papasotiriou DG, Karas M, Tsiotis G
Amino Acids Early Edition: published 12-Jul-2005

From genomics via proteomics to cellular physiology of the Gram-positive model organism Bacillus subtilis
Volker U, Hecker M
Cell Microbiol (2005) 7(8): 1077-85

Proteomics meets microbiology: technical advances in the global mapping of protein expression and function
Phillips CI, Bogyo M
Cell Microbiol (2005) 7(8): 1061-76

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Pharmacology and Toxicology

New Targets for an Old Drug: II. Hypoxanthine-Guanine Amidophosphoribosyltransferase As a New Pharmacodynamic Target of Methotrexate
Slon-Usakiewicz, Jacek J.; Pasternak, Andrew; Reid, Neil; Toledo-Sherman, Leticia M
Clinical Proteomics (2004) 1(3-4): 227-234

Toxicoproteomics: Applications in Drug Development
Gupta, N.; Law, A.; Poddar, R.; Louie, M.; Ray, A.; Chakravarti, D. N
Current Proteomics (2005) 2(2): 97-101

Effect of JP-8 jet fuel exposure on protein expression in human keratinocyte cells in culture
Witzmann FA, Monteiro-Riviere NA, Inman AO, Kimpel MA, Pedrick NM, Ringham HN, Riviere JE
Toxicol Lett Early Edition: published 11-Jul-2005

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Protein Array

Antibody-Based Tissue Profiling As a Tool for Clinical Proteomics
Kampf, Caroline; Andersson, Ann-Catrin; Wester, Kenneth; Bjorling, Erik; Uhlen, Mathias; Ponten, Fredrik
Clinical Proteomics (2004) 1(3-4): 285-300

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Protein Characterization / PTMs

Phosphorylation and subcellular localization of transmissible gastroenteritis virus nucleocapsid protein in infected cells
Calvo E, Escors D, Lopez JA, Gonzalez JM, Alvarez A, Arza E, Enjuanes L
J Gen Virol (2005) 86(Pt 8): 2255-67

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Protein-protein interaction

High-Affinity Chelator Thiols for Switchable and Oriented Immobilization of Histidine-Tagged Proteins: A Generic Platform for Protein Chip Technologies
Tinazli A, Tang J, Valiokas R, Picuric S, Lata S, Piehler J, Liedberg B, Tampe R
Chemistry Early Edition: published 30-Jun-2005

Functional Proteomics Using Direct Protein Inactivation
Eustace, B. K.; Jay, D. G
Current Proteomics (2005) 2(2): 103-107

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Quantitation

Simultaneous Quantification and Identification Using 18O Labeling with an Ion Trap Mass Spectrometer and the Analysis Software Application "ZoomQuant"
Wayne A. Hicks, Brian D. Halligan, Ronit Y. Slyper, Simon N. Twigger, Andrew S. Greene and Michael Olivier
Journal of the American Society for Mass Spectrometry (2005) 16(6): 916-925

Development of Competitive ELISA for Neosporosis by Employing Immunoproteomics
Shin, Yong-seung; Lee, Eung-goo; Shin, Gee-wook; Kim, Young-rim; Lee, Eun-young; Kim, Jae-hoon; Jang, Hwan; Kim, Dae-yong; Kim, Yong-hwan; Kim, Gon-sup; Suh, Myung-deuk; Jung, Tae-sung
Clinical Proteomics (2004) 1(3-4): 235-248

Technical Evaluation of MALDI-TOF Mass Spectrometry for Quantitative Proteomic Profiling: Matrix Formulation and Application
Pang, Ronald T. K.; Johnson, Philip J.; Chan, Charles M. L.; Kong, Ebenezer K. C.; Chan, Anthony T. C.; Sung, Joseph J. Y.; Poon, Terence C. W
Clinical Proteomics (2004) 1(3-4): 259-270

Selective Identification and Quantitative Analysis of Methionine Containing Peptides by Charge Derivatization and Tandem Mass Spectrometry
Gavin E. Reid, Kade D. Roberts, Richard J. Simpson and Richard A.J. O-Hair
Journal of the American Society for Mass Spectrometry (2005) 16(7): 1131-1150

An Automated Method for the Analysis of Stable Isotope Labeling Data in Proteomics
Xiang Zhang, Wade Hines, Jiri Adamec, John M. Asara, Stephen Naylor and Fred E. Regnier
Journal of the American Society for Mass Spectrometry (2005) 16(7): 1181-1191

Mass Tagging Approach for Mitochondrial Thiol Proteins
Kevin Marley, Duane T. Mooney, Gretchen Clark-Scannell, Tony T.-H. Tong, Jeffrey Watson, Tory M. Hagen, Jan F. Stevens, and Claudia S. Maier
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/15/2005

Evaluation of Clinical Colon Carcinoma Using Activity-Based Proteomic Profiling
Zhang, Melissa C.; Wu, Jiangyue; Ardlie, Kristin G.; Lin, Emme C. K
Clinical Proteomics (2004) 1(3-4): 301-312

Relative quantification of erythropoietin receptor-dependent phosphoproteins using in-gel (18)O-labeling and tandem mass spectrometry
Korbel S, Schumann M, Bittorf T, Krause E
Rapid Commun Mass Spectrom (2005) 19(16): 2259-2271

Quantitative Analysis of Membrane Proteins from Breast Cancer Cell Lines BT474 and MCF7 Using Multistep Solid Phase Mass Tagging and 2D LC/MS
Yang Shi, Rong Xiang, Csaba Horváth, and James A. Wilkins
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/22/2005

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Review

Prospective highlights of functional skin proteomics
Chun-Ming Huang, Craig A. Elmets, Kent R. van Kampen, Tivanka S. DeSilva, Stephen Barnes, Helen Kim, De-chu C. Tang
Mass Spectrometry Reviews (2005) 24(5): 647-660

Mass spectrometry in aging research
Christian Schöneich
Mass Spectrometry Reviews (2005) 24(5): 701-718

The continuing evolution of shotgun proteomics
Selene K. Swanson and Michael P. Washburn
Drug Discovery Today (2005) 10(10): 719-725

Proteomic approaches in the analysis of hypertension
Naaby-Hansen S, Warnasuriya GD, Hastie C, Gallney P, Cramer R
Methods Mol Med (2004) 108: 275-96

From proteins to proteomics
Bradshaw RA, Burlingame AL
IUBMB Life (2005) 57(4-5): 267-72

Modern approaches to age-old questions about thyroid tumors
Diehl S, Umbricht CB, Dackiw AP, Zeiger MA
Thyroid (2005) 15(6): 575-82

Identification and Mapping of Protein-Protein Interactions by a Combination of Cross-Linking, Cleavage, and Proteomics
Trakselis MA, Alley SC, Ishmael FT
Bioconjug Chem (2005) 16(4): 741-750

Helicobacter pylori: current status and future prospects
O'Mahony R, Vaira D, Holton J, Basset C
Sci Prog (2004) 87(Pt 4): 269-96

Molecular markers of early pancreatic cancer
Goggins M
J Clin Oncol (2005) 23(20): 4524-31

Use of high-throughput arrays for profiling differentially expressed proteins in normal and malignant tissues
Hudelist G, Singer CF, Kubista E, Czerwenka K
Anticancer Drugs (2005) 16(7): 683-689

Complementary gene and protein expression studies and integrative approaches in toxicogenomics
Merrick BA, Madenspacher JH
Toxicol Appl Pharmacol Early Edition: published 28-Jun-2005

Applying proteomics to drug discovery
Stubberfield CR, Page MJ
Expert Opin Investig Drugs (1999) 8(1): 65-70

Limitations of current proteomics technologies
Garbis S, Lubec G, Fountoulakis M
J Chromatogr A (2005) 1077(1): 1-18

Comparison of the specificity and sensitivity of traditional methods for assessment of nephrotoxicity in the rat with metabonomic and proteomic methodologies
Gibbs A
J Appl Toxicol (2005) 25(4): 277-295

Genomic and proteomic approaches for Chagas' disease: critical analysis of diagnostic methods
Huete-Perez JA, Flores-Obando RE, Ghedin E, Caffrey CR
Expert Rev Mol Diagn (2005) 5(4): 521-530

Proteomics in clinical laboratory diagnosis
Shoshan SH, Admon A
Adv Clin Chem (2005) 39: 159-84

Population proteomics: addressing protein diversity in humans
Dobrin Nedelkov
Expert Review of Proteomics (2005) 2(3): 315-324

Tissue microarrays: bridging the gap between research and the clinic
Till Braunschweig, Joon-Yong Chung, Stephen M Hewitt
Expert Review of Proteomics (2005) 2(3): 325-336

Morphoproteomics: exposing protein circuitries in tumors to identify potential therapeutic targets in cancer patients
Robert E Brown
Expert Review of Proteomics (2005) 2(3): 337-348

Proteomic analysis of renal diseases: unraveling the pathophysiology and biomarker discovery
Visith Thongboonkerd
Expert Review of Proteomics (2005) 2(3): 349-366

Use of proteomics to define targets of T-cell immunity
Nicholas A Williamson, Anthony W Purcell
Expert Review of Proteomics (2005) 2(3): 367-380

Mass spectrometry-based peptide quantification: applications and limitations
Stephanie Putz, Joerg Reinders, Yvonne Reinders, Albert Sickmann
Expert Review of Proteomics (2005) 2(3): 381-392

Rarity gives a charm: evaluation of trace proteins in plasma and serum
Julia Tait Lathrop, Timothy K Hayes, Kevin Carrick, David J Hammond
Expert Review of Proteomics (2005) 2(3): 393-406

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry
Rainer Cramer, Johan Gobom, Eckhard Nordhoff
Expert Review of Proteomics (2005) 2(3): 407-420

Ribosome display: next-generation display technologies for production of antibodies in vitro
Mingyue He, Farid Khan
Expert Review of Proteomics (2005) 2(3): 421-430

Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics
Yufeng Shen, Richard D Smith
Expert Review of Proteomics (2005) 2(3): 431-447

Vectorial proteomics
Vener AV, Stralfors P
IUBMB Life (2005) 57(6): 433-40

Advances and applications of de novo designed affinity ligands in proteomics
Roque AC, Lowe CR
Biotechnol Adv Early Edition: published 7-Jul-2005

Post-genomics of microsporidia, with emphasis on a model of minimal eukaryotic proteome: a review
Texier C, Brosson D, El Alaoui H, Metenier G, Vivares CP
Folia Parasitol (Praha) (2005) 52(1-2): 15-22

Imaging Biomarkers in Drug Development: An Overview of Opportunities and Open Issues
Sudeep Chandra, Craig Muir, Matt Silva, and Steven Carr
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/22/2005

Place of Pattern in Proteomic Biomarker Discovery
Michael A. Gillette, D. R. Mani, and Steven A. Carr
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/22/2005

Discovery of Biomarker Candidates within Disease by Protein Profiling: Principles and Concepts
György Marko-Varga, Henrik Lindberg, Claes-Göran Löfdahl, Per Jönsson, Lennart Hansson, Magnus Dahlbäck, Eva Lindquist, Leif Johansson, # Martyn Foster, and Thomas E. Fehniger
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/22/2005

Mass spectrometry in metabolome analysis
Silas G. Villas-Bôas, Sandrine Mas, Mats Åkesson, Jørn Smedsgaard, Jens Nielsen
Mass Spectrometry Reviews (2005) 24(5): 613-646

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Methodology

Protein fragmentation via liquid chromatography-quadrupole time-of-flight mass spectrometry: The use of limited sequence information in structural characterization
Robert W. Johnson,Jr., Tanveer F. Ahmed, Laura J. Miesbauer, Rohinton Edalji, Richard Smith, John Harlan, Sarah Dorwin, Karl Walter and Tom Holzman
Analytical Biochemistry (2005) 341(1): 22-32

Solid-phase capture and release of arginine peptides by selective tagging and boronate affinity chromatography - Dedicated to the memory of Csaba Horváth
A. Foettinger, A. Leitner and W. Lindner
J Chromatogr A (2005) 1079(1-2): 187-196

Evaluation of multidimensional (ion-exchange/reversed-phase) protein separations using linear and step gradients in the first dimension
Kevin M. Millea, Ignatius J. Kass, Steven A. Cohen, Ira S. Krull, John C. Gebler and Scott J. Berger
J Chromatogr A (2005) 1079(1-2): 287-298

Fast on-column protein digestion with subsequent peptide mapping using tandem mass spectrometry with information dependent acquisition
Martin Hedström, Maria Andersson, Igor Yu. Galaev and Bo Mattiasson
J Chromatogr A (2005) 1080(2): 117-123

Comparison of protein solubilization methods suitable for proteomic analysis of soybean seed proteins
Savithiry Natarajan, Chenping Xu, Thomas J. Caperna and Wesley M. Garrett
Analytical Biochemistry (2005) 342(2): 214-220

Models of protein modification in Tris-glycine and neutral pH Bis-Tris gels during electrophoresis: Effect of gel pH
John P. Hachmann and Joseph W. Amshey
Analytical Biochemistry (2005) 342(2): 237-245

An agarose-acrylamide composite native gel system suitable for separating ultra-large protein complexes
Man-Hee Suh, Ping Ye, Ajit B. Datta, Mincheng Zhang and Jianhua Fu
Analytical Biochemistry (2005) 343(1): 166-175

Protein identification using sequential ion/ion reactions and tandem mass spectrometry
Joshua J. Coon, Beatrix Ueberheide, John E. P. Syka, Deanna D. Dryhurst, Juan Ausio, Jeffrey Shabanowitz, and Donald F. Hunt
PNAS (2005) 102(27): 9463-9468

Proteomic analysis of human bladder tissue using SELDI approach following microdissection techniques
Krieg RC, Gaisa NT, Paweletz CP, Knuechel R
Methods Mol Biol (2005) 293: 255-67

Laser capture microdissection and colorectal cancer proteomics
Lawrie LC, Curran S
Methods Mol Biol (2005) 293: 245-53

Porous Anodic Alumina Membrane as a Sample Support for MALDI-TOF MS Analysis of Salt-Containing Proteins
Wang Y, Xia X, Guo Y
J Am Soc Mass Spectrom Early Edition: published 13-Jul-2005

Influences of Sample Processing on Low-Molecular-Weight Proteome Identified by Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry
Banks RE, Stanley AJ, Cairns DA, Barrett JH, Clarke P, Thompson D, Selby PJ
Clin Chem Early Edition: published 7-Jul-2005

A hybrid LC-Gel-MS method for proteomics research and its application to protease functional pathway mapping
Wu S, Tang XT, Siems WF, Bruce JE
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 30-Jun-2005

Microfluidic systems and proteomics: Applications of the electrocapture technology to protein and peptide analysis
Astorga-Wells J, Vollmer S, Bergman T, Jornvall H
Anal Biochem Early Edition: published 30-Jun-2005

Effects of Tryptic Peptide Esterification in MALDI Mass Spectrometry
Kim TY, Brun YV, Reilly JP
Anal Chem (2005) 77(13): 4185-93

Electrospray diagnostics by fourier analysis of current oscillations and fast imaging
Parvin L, Galicia MC, Gauntt JM, Carney LM, Nguyen AB, Park E, Heffernan L, Vertes A
Anal Chem (2005) 77(13): 3908-15

Characterization of proteins from Spirulina platensis microalga using capillary electrophoresis-ion trap-mass spectrometry and capillary electrophoresis-time of flight-mass spectrometry
Carolina Simó, Miguel Herrero, Christian Neusüß, Matthias Pelzing, Ernst Kenndler, Coral Barbas, Elena Ibáñez, Alejandro Cifuentes
ELECTROPHORESIS (2005) 26(13): 2674-2683

Prefractionation of Proteome by Liquid Isoelectric Focusing Prior to Two-Dimensional Liquid Chromatography Mass Spectrometric Identification
Rong-Xia Li, Hu Zhou, Su-Jun Li, Quan-Hu Sheng, Qi-Chang Xia, and Rong Zeng
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/15/2005

Functional RNAs as Tools in Proteomics
Vaish, N. K.; Zinnen, S
Current Proteomics (2005) 2(2): 165-178

Complex proteome prefractionation using microscale solution isoelectrofocusing
Hsin-Yao Tang, David W Speicher
Expert Review of Proteomics (2005) 2(3): 295-306

A tandem orthogonal proteolysis strategy for high-content chemical proteomics
Speers AE, Cravatt BF
J Am Chem Soc (2005) 127(28): 10018-9

Mapping of Phosphorylation Sites by a Multi-Protease Approach with Specific Phosphopeptide Enrichment and NanoLC-MS/MS Analysis
Andreas Schlosser, Jens T. Vanselow, and Achim Kramer
ANALYTICAL CHEMISTRY Early Edition: published 07/15/2005

Toward a Global Analysis of the Human Pituitary Proteome by Multiple Gel-Based Technology
Yingxin Zhao, Francesco Giorgianni, Dominic M. Desiderio, Bing Fang, and Sarka Beranova-Giorgianni
ANALYTICAL CHEMISTRY Early Edition: published 07/15/2005

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Meeting

Second Proteomics Standards Initiative Spring Workshop (Meeting Report)
Sandra Orchard, Henning Hermjakob, Chris F Taylor, Frank Potthast, Phil Jones, Weimin Zhu, Randall K Julian Jr, Rolf Apweiler
Expert Review of Proteomics (2005) 2(3): 287-289

Keystone symposia: Proteomics and Bioinformatics and Systems and Biology (Meeting Report)
Anne-Claude Gavin
Expert Review of Proteomics (2005) 2(3): 291-293

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Other

Building Integrated Approaches for the Proteomics of Complex, Dynamic Systems: NIH Programs in Technology and Infrastructure Development
Douglas M. Sheeley, Joseph J. Breen, and Susan E. Old
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/15/2005

What have we learned from proteomic studies of serum? (Editorial)
Thomas P Conrads, Timothy D Veenstra
Expert Review of Proteomics (2005) 2(3): 279-281

Use and misuse of p-values in designed and observational studies: guide for researchers and reviewers
Ludwig DA
Aviat Space Environ Med (2005) 76(7): 675-80

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