SPS' Digest

Issue 17, 7-Apr-2005

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Quick jumps to articles in: Bioinformatics (15) / Biological applications (35) / Biomedical and clinical applications (49) / Eukaryotic Cells And Tissues (7) / Prokaryotes (10) / Pharmacology and Toxicology (2) / Protein Array (5) / Protein Characterization - PTMs (14) / Protein-protein interaction (1) / Quantitation (9) / Review (26) / Methodology (33) / Books (1) / Meeting (2) / Other (7) /

In this issue, 214 articles have been selected from:

Am J Obstet Gynecol, Volume 192, Issue 3, 2005 (1 article)
Am J Transplant, Volume 5, Issue 4, 2005 (1 article)
Anal Chem, Volume 77, Issues 3+6+7, 2005 (5 articles)
Analytical Biochemistry , Volume 338, Issue 2, 2005 (1 article)
Analytical Biochemistry, Volume 338, Issue 1, 2005 (2 articles)
Arthritis Rheum, Volume 52, Issue 3, 2005 (1 article)
BMC Biochem, Volume 6, Issue 1, 2005 (1 article)
Biochem Biophys Res Commun, Volume 330, Issues 1+2, 2005 (2 articles)
Biochem Soc Trans, Volume 33, Issue Pt 2, 2005 (1 article)
Bioinformatics, Early Edition, 3-Mar-2005->15-Mar-2005 (2 articles)
Bioinformatics, Volume 21, Issue 5, 2005 (2 articles)
Biomarkers, Volume 9, Issue 3, 2004 (1 article)
Brain Pathol, Volume 15, Issue 1, 2005 (1 article)
Brain Res Mol Brain Res, Volume 134, Issue 1, 2005 (1 article)
Cancer Invest, Volume 23, Issue 1, 2005 (1 article)
Curr Opin Drug Discov Devel, Volume 8, Issue 2, 2005 (1 article)
Curr Opin Struct Biotechnol, Volume 16, Issue 1, 2005 (1 article)
Drug Discovery Today, Volume 10, Issue 5, 2005 (1 article)
Electrophoresis, Early Edition, 14-Mar-2005->17-Mar-2005 (2 articles)
Electrophoresis, Volume 26, Issue 6, 2005 (4 articles)
FASEB J, Early Edition, 3-Mar-2005 (1 article)
Int Angiol, Volume 23, Issue 3, 2004 (1 article)
Int J Biochem Cell Biol, Volume 37, Issues 5+6, 2005 (2 articles)
Int J Oncol, Volume 26, Issue 4, 2005 (1 article)
International Journal of Mass Spectrometry, Volume 242, Issue 2-3, 2005 (1 article)
J Am Soc Mass Spectrom, Volume 16, Issue 4, 2005 (2 articles)
J Biol Chem, Early Edition, 29-Mar-2005 (2 articles)
J Cell Biochem, Early Edition, 9-Mar-2005 (1 article)
J Chromatogr A, Volume 1065, Issue 1, 2005 (1 article)
J Chromatogr B, Volume 819, Issue 1, 2005 (1 article)
J Histochem Cytochem, Volume 53, Issue 3, 2005 (1 article)
J Mass Spectrom, Volume 40, Issue 3, 2005 (4 articles)
J Mol Cell Cardiol, Volume 38, Issue 3, 2005 (1 article)
J Mol Neurosci, Volume 25, Issue 1, 2005 (1 article)
J Pathol, Early Edition, 16-Mar-2005 (1 article)
J Pediatr Surg, Volume 40, Issue 2, 2005 (1 article)
J Proteome Res, Early Edition, 02/11/2005->04/01/2005 (22 articles)
J Proteome Res, Volume 4, Issue 1, 2005 (11 articles)
Journal of the American Society for Mass Spectrometry, Volume 16, Issue 3, 2005 (1 article)
Mass Spectrom Rev, Early Edition, 3-Mar-2005 (1 article)
Mass Spectrom Rev, Volume 24, Issue 3, 2005 (3 articles)
Mol Carcinog, Early Edition, 24-Mar-2005 (1 article)
Mol Cell Proteomics, Volume 4, Issues 3+4, 2005 (28 articles)
Nat Biotechnol, Early Edition, 13-Mar-2005 (1 article)
Nat Biotechnol, Volume 23, Issue 3, 2005 (2 articles)
Nat Methods, Early Edition, 23-Mar-2005 (1 article)
Nat Methods, Volume 1, Issues 1+2+3, 2004 (3 articles)
Nat Methods, Volume 2, Issue 3, 2005 (1 article)
Nat Rev Drug Discov, Early Edition, 24-Mar-2005 (1 article)
Neurochem Res, Volume 30, Issue 1, 2005 (1 article)
Neuroscience, Volume 132, Issue 2, 2005 (1 article)
Pac Symp Biocomput, Volume , 2005 (2 articles)
Plant Cell Physiol, Early Edition, 15-Mar-2005 (1 article)
Plant Physiology and Biochemistry, Volume 42, Issue 12, 2004 (11 articles)
Proc Natl Acad Sci U S A, Early Edition, 23-Mar-2005->28-Mar-2005 (2 articles)
Proteomics, Volume 5, Issues 4+5, 2005 (62 articles)
Radiat Res, Volume 163, Issue 3, 2005 (1 article)
Rapid Commun Mass Spectrom, Volume 19, Issues 6+8, 2005 (2 articles)
Trends Parasitol, Volume 21, Issue 4, 2005 (1 article)

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

Quick jumps to articles in: Bioinformatics (15) / Biological applications (35) / Biomedical and clinical applications (49) / Eukaryotic Cells And Tissues (7) / Prokaryotes (10) / Pharmacology and Toxicology (2) / Protein Array (5) / Protein Characterization - PTMs (14) / Protein-protein interaction (1) / Quantitation (9) / Review (26) / Methodology (33) / Books (1) / Meeting (2) / Other (7) /

Bioinformatics

A graph-theoretic approach for the separation of b and y ions in tandem mass spectra
Bo Yan, Chongle Pan, Victor N. Olman, Robert L. Hettich, and Ying Xu
Bioinformatics (2005) 21(5): 563-574

A simple tool for drawing proteolytic peptide maps
Robert J. Beynon
Bioinformatics (2005) 21(5): 674-675

A novel approach for clustering proteomics data using Bayesian Fast Fourier Transform
Bensmail H, Golek J, Moody MM, Semmes OJ, Haoudi A
Bioinformatics Early Edition: published 15-Mar-2005

The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools
Michel Schneider, Michael Tognolli and Amos Bairoch
Plant Physiology and Biochemistry (2004) 42(12): 1013-1021

Plant membrane proteome databases
Rainer Schwacke, Ulf-Ingo Flu"gge and Reinhard Kunze
Plant Physiology and Biochemistry (2004) 42(12): 1023-1034

Experiments in Searching Small Proteins in Unannotated Large Eukaryotic Genomes
Jacques Colinge, Isabelle Cusin, Samia Reffas, Eve Mahé, Anne Niknejad, Pierre-Antoine Rey, Hassan Mattou, Marc Moniatte, and Lydie Bougueleret
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 167-174

ZoomQuant: An application for the quantitation of stable isotope labeled peptides
Brian D. Halligan Ronit Y. Slyper, Simon N. Twigger, Wayne Hicks, Michael Olivier and Andrew S. Greene
Journal of the American Society for Mass Spectrometry (2005) 16(3): 302-306

Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm
Brian C. Searle, Surendra Dasari, Phillip A. Wilmarth, Mark Turner, Larry L. David, and Srinivasa R. Nagalla
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

The development of an algorithm for the mass spectral interpretation of phosphoproteins
Yupeng Zhao, Yen-Han Lin
PROTEOMICS (2005) 5(4): 843-845

A proteomic tool for protein identification from tandem mass spectral data
Yupeng Zhao, Yen-Han Lin
PROTEOMICS (2005) 5(4): 853-855

Effect of training datasets on support vector machine prediction of protein-protein interactions
Siaw Ling Lo, Cong Zhong Cai, Yu Zong Chen, Maxey C. M. Chung
PROTEOMICS (2005) 5(4): 876-884

Genome-scale protein function prediction in yeast Saccharomyces cerevisiae through integrating multiple sources of high-throughput data
Chen Y, Xu D
Pac Symp Biocomput (2005) : 471-82.

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments
Orchard S, Montecchi-Palazzi L, Hermjakob H, Apweiler R
Pac Symp Biocomput (2005) : 186-96.

Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome
Wei-Jun Qian, Tao Liu, Matthew E. Monroe, Eric F. Strittmatter, Jon M. Jacobs, Lars J. Kangas, Konstantinos Petritis, David G. Camp II, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 53-62

Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined
Falkner J, Andrews P
Bioinformatics Early Edition: published 3-Mar-2005

Biological applications

Analysis of leukocyte membrane protein interactions using protein microarrays
Letarte M, Voulgaraki D, Hatherley D, Foster-Cuevas M, Saunders NJ, Barclay N
BMC Biochem (2005) 6(1): 2

Coregulator Interactions with the Thyroid Hormone Receptor
Jamie M. R. Moore and R. Kiplin Guy
Mol Cell Proteomics (2005) 4(4): 475-482

Measurement of the Uncomplexed Fraction of Tissue Inhibitor of Metalloproteinases-1 in the Prognostic Evaluation of Primary Breast Cancer Patients
Sidse Ornbjerg Wurtz, Ib Jarle Christensen, Anne-Sofie Schrohl, Henning Mouridsen, Ulrik Lademann, Vibeke Jensen, and Nils Brunner
Mol Cell Proteomics (2005) 4(4): 483-491

Identification of Extracellular and Intracellular Signaling Components of the Mammary Adipose Tissue and Its Interstitial Fluid in High Risk Breast Cancer Patients: Toward Dissecting The Molecular Circuitry of Epithelial-Adipocyte Stromal Cell Interactions
Julio E. Celis, Jose M. A. Moreira, Teresa Cabezon, Pavel Gromov, Esbern Friis, Fritz Rank, and Irina Gromova
Mol Cell Proteomics (2005) 4(4): 492-522

Down-regulation of the Tumor Suppressor Protein 14-3-3{sigma} Is a Sporadic Event in Cancer of the Breast
Jose M. A. Moreira, Gita Ohlsson, Fritz E. Rank, and Julio E. Celis
Mol Cell Proteomics (2005) 4(4): 555-569

Proteomic Analysis Identifies Novel Proteins of the Maurer's Clefts, a Secretory Compartment Delivering Plasmodium falciparum Proteins to the Surface of Its Host Cell
Laetitia Vincensini, Sophie Richert, Thierry Blisnick, Alain Van Dorsselaer, Emmanuelle Leize-Wagner, Thierry Rabilloud, and Catherine Braun Breton
Mol Cell Proteomics (2005) 4(4): 582-593

Proteomic Profiling of Pancreatic Cancer for Biomarker Discovery
Ru Chen, Sheng Pan, Teresa A. Brentnall, and Ruedi Aebersold
Mol Cell Proteomics (2005) 4(4): 523-533

Heat shock proteins and other components of cellular machinery for protein synthesis are up-regulated in vascular endothelial cell growth factor-activated human endothelial cells
Zofia Pawlowska, Patrycja Baranska, Hanna Jerczynska, Wiktor Koziolkiewicz, Czeslaw S. Cierniewski
PROTEOMICS (2005) 5(5): 1217-1227

Proteomic Mapping of Brain Plasma Membrane Proteins
Peter Aa. Nielsen, Jesper V. Olsen, Alexandre V. Podtelejnikov, Jens R. Andersen, Matthias Mann, and Jacek R. Wisniewski
Mol Cell Proteomics (2005) 4(4): 402-408

Proteomics analysis of growth hormone isoforms in the human pituitary
Xianquan Zhan, Francesco Giorgianni, Dominic M. Desiderio
PROTEOMICS (2005) 5(5): 1228-1241

Analysis of phosphatase and tensin homolog tumor suppressor interacting proteins by in vitro and in silico proteomics
David K. Crockett, G. Chris Fillmore, Kojo S. J. Elenitoba-Johnson, Megan S. Lim
PROTEOMICS (2005) 5(5): 1250-1262

Large-scale identification of proteins expressed in mouse embryonic stem cells
Kohji Nagano, Masato Taoka, Yoshio Yamauchi, Chiharu Itagaki, Takashi Shinkawa, Kazuto Nunomura, Nobuko Okamura, Nobuhiro Takahashi, Tomonori Izumi, Toshiaki Isobe
PROTEOMICS (2005) 5(5): 1346-1361

Proteomic changes in rat serum, polymorphonuclear and mononuclear leukocytes after chronic nicotine administration
Chiara Piubelli, Daniela Cecconi, Hubert Astner, Fabrizio Caldara, Michela Tessari, Lucia Carboni, Mahmoud Hamdan, Pier Giorgio Righetti, Enrico Domenici
PROTEOMICS (2005) 5(5): 1382-1394

Proteomics of ischemia/reperfusion injury in rabbit myocardium reveals alterations to proteins of essential functional systems
Melanie Y. White, Stuart J. Cordwell, Hugh C. K. McCarron, Ananth M. Prasan, George Craft, Brett D. Hambly, Richmond W. Jeremy
PROTEOMICS (2005) 5(5): 1395-1410

Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry
Brittain SM, Ficarro SB, Brock A, Peters EC
Nat Biotechnol Early Edition: published 13-Mar-2005

Serum proteomics profiling-a young technology begins to mature
Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA
Nat Biotechnol (2005) 23(3): 291-292

Quantitative proteomic analysis of mitochondrial proteins: relevance to Lewy body formation and Parkinson's disease
Jin J, Meredith GE, Chen L, Zhou Y, Xu J, Shie FS, Lockhart P, Zhang J
Brain Res Mol Brain Res (2005) 134(1): 119-38

Deciphering genetic variations of proteome responses to water deficit in maize leaves
Fre'de'rique Riccardi, Pascale Gazeau, Marie-Pierre Jacquemot, Delphine Vincent and Michel Zivy
Plant Physiology and Biochemistry (2004) 42(12): 1003-1011

The rat brain hippocampus proteome
Fountoulakis M, Tsangaris GT, Maris A, Lubec G
J Chromatogr B (2005) 819(1): 115-29

Characterization of a novel microperoxidase from Marinobacter hydrocarbonoclasticus by electrospray ionization tandem mass spectrometry
Alessandra Di Tullio, Lorenzo Caputi, Francesco Malatesta, Samantha Reale, Francesco De Angelis
Journal of Mass Spectrometry (2005) 40(3): 325-330

Mass spectrometric determination of selenenylsulfide linkages in rat selenoprotein P
Shuguang Ma, Kristina E. Hill, Raymond F. Burk, Richard M. Caprioli
Journal of Mass Spectrometry (2005) 40(3): 400-404

Purification and initial characterization of a novel protein with factor Xa activity from Lonomia obliqua caterpillar spicules
S. Lilla, R. Pereira, S. Hyslop, J. L. Donato, B. F. Le Bonniec, G. de Nucci
Journal of Mass Spectrometry (2005) 40(3): 405-412

Proteins of calcified endoskeleton: II Partial amino acid sequences of endoskeletal proteins and the characterization of proteinaceous organic matrix of spicules from the alcyonarian, Synularia polydactyla
M. Azizur Rahman, Yeishin Isa, Tsuyoshi Uehara
PROTEOMICS (2005) 5(4): 885-893

A transcriptomic and proteomic analysis of the effect of CpG-ODN on human THP-1 monocytic leukemia cells
Cheng-Chin Kuo, Chu-Wei Kuo, Chi-Ming Liang, Shu-Mei Liang
PROTEOMICS (2005) 5(4): 894-906

Global protein expression analysis in apicomplexan parasites: Current status
Sabina I. Belli, Robert A. Walker, Sarah A. Flowers
PROTEOMICS (2005) 5(4): 918-924

Rice proteome analysis: A step toward functional analysis of the rice genome
Setsuko Komatsu, Naoki Tanaka
PROTEOMICS (2005) 5(4): 938-949

Proteome analysis of sugar beet leaves under drought stress
Mohsen Hajheidari, Mohammad Abdollahian-Noghabi, Hossein Askari, Manzar Heidari, Seyed Y. Sadeghian, Eric S. Ober, Ghasem Hosseini Salekdeh
PROTEOMICS (2005) 5(4): 950-960

Proteomic changes in rice leaves during development of field-grown rice plants
Caifeng Zhao, Jingqiang Wang, Mengliang Cao, Kang Zhao, Jianmin Shao, Tingting Lei, Jianning Yin, Gradford G Hill, Ningzhi Xu, Siqi Liu
PROTEOMICS (2005) 5(4): 961-972

?-Phenylethyl isothiocyanate mediated apoptosis: A proteomic investigation of early apoptotic protein changes
Jason Chun Hong Neo, Peter Rose, Choon Nam Ong, Maxey C. M. Chung
PROTEOMICS (2005) 5(4): 1075-1082

Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database
Yutaka Yoshida, Kenji Miyazaki, Junichi Kamiie, Masao Sato, Seiji Okuizumi, Akihisa Kenmochi, Ken'ichi Kamijo, Takuji Nabetani, Akira Tsugita, Bo Xu, Ying Zhang, Eishin Yaoita, Tetsuo Osawa, Tadashi Yamamoto
PROTEOMICS (2005) 5(4): 1083-1096

Effect of thyroxine on abnormal pancreatic proteomes of the hypothyroid rdw rat
Mamoru Satoh, Eri Haruta-Satoh, Akira Omori, Masamichi Oh-Ishi, Yoshio Kodera, Sen-Ichi Furudate, Tadakazu Maeda
PROTEOMICS (2005) 5(4): 1113-1124

Proteomic-Based Identification of Cleaved Urinary beta2-microglobulin as a Potential Marker for Acute Tubular Injury in Renal Allografts
Schaub S, Wilkins JA, Antonovici M, Krokhin O, Weiler T, Rush D, Nickerson P
Am J Transplant (2005) 5(4): 729-38

Protein Expression Profiling of the Drosophila Fragile X Mutant Brain Reveals Up-regulation of Monoamine Synthesis
Yong Q. Zhang, David B. Friedman, Zhe Wang, Elvin Woodruff, III, Luyuan Pan, Janis O'Donnell, and Kendal Broadie
Mol Cell Proteomics (2005) 4(3): 278-290

Identification of Dynamic Proteome Changes Upon Ligand Activation of Trk-Receptors Using Two-dimensional Fluorescence Difference Gel Electrophoresis and Mass Spectrometry
Barbara Sitek, Ognjan Apostolov, Kai Stuhler, Kathy Pfeiffer, Helmut E. Meyer, Angelika Eggert, and Alexander Schramm
Mol Cell Proteomics (2005) 4(3): 291-299

The human mitochondrial proteome: oxidative stress, protein modifications and oxidative phosphorylation
Gibson BW
Int J Biochem Cell Biol (2005) 37(5): 927-34

Biomedical and clinical applications

Identification of the heterogeneous nuclear ribonucleoprotein A2/B1 as the antigen for the gastrointestinal cancer specific monoclonal antibody MG7
Chi-ho Lee, John Hon-kei Lum, Belinda Pik-yuen Cheung, Man-sau Wong, Yoki Kwok-chu Butt, Ming F. Tam, Wing Y. Chan, Chit Chow, Pak-kwan Hui, Francis S. L. Kwok, Samuel Chun-lap Lo, D. M. Fan
PROTEOMICS (2005) 5(4): 1160-1166

Proteomic biomarkers that predict the clinical success of rescue cerclage
Weiner CP, Lee KY, Buhimschi CS, Christner R, Buhimschi IA
Am J Obstet Gynecol (2005) 192(3): 710-8

Proteomic analysis of neurofibrillary tangles in Alzheimer disease identifies GAPDH as a detergent-insoluble paired helical filament tau binding protein
Wang Q, Woltjer RL, Cimino PJ, Pan C, Montine KS, Zhang J, Montine TJ
FASEB J Early Edition: published 3-Mar-2005

Alterations in the heart mitochondrial proteome in a desmin null heart failure model
Fountoulakis M, Soumaka E, Rapti K, Mavroidis M, Tsangaris G, Maris A, Weisleder N, Capetanaki Y
J Mol Cell Cardiol (2005) 38(3): 461-74

Proteome alterations in gamma-irradiated human T-lymphocyte leukemia cells
Szkanderova S, Vavrova J, Hernychova L, Neubauerova V, Lenco J, Stulik J
Radiat Res (2005) 163(3): 307-15

Biomarkers: Mining the Biofluid Proteome
Timothy D. Veenstra, Thomas P. Conrads, Brian L. Hood, Anthony M. Avellino, Richard G. Ellenbogen, and Richard S. Morrison
Mol Cell Proteomics (2005) 4(4): 409-418

Antibody-based Proteomics for Human Tissue Profiling
Mathias Uhlen and Fredrik Ponten
Mol Cell Proteomics (2005) 4(4): 384-393

Tissue Profiling by Mass Spectrometry: A Review of Methodology and Applications
Robert L. Caldwell and Richard M. Caprioli
Mol Cell Proteomics (2005) 4(4): 394-401

Unraveling the Pathogenesis of Type 1 Diabetes with Proteomics: Present And Future Directions
Thomas Sparre, Martin R. Larsen, Peter E. Heding, Allan E. Karlsen, Ole N. Jensen, and Flemming Pociot
Mol Cell Proteomics (2005) 4(4): 441-457

Integrating Global Proteomic and Genomic Expression Profiles Generated from Islet {alpha} Cells: Opportunities and Challenges to Deriving Reliable Biological Inferences
Marlena Maziarz, Clement Chung, Daniel J. Drucker, and Andrew Emili
Mol Cell Proteomics (2005) 4(4): 458-474

Renal and urinary proteomics: Current applications and challenges
Visith Thongboonkerd, Prida Malasit
PROTEOMICS (2005) 5(4): 1033-1042

Proteomic analysis of human pleural effusion
Yu-Chang Tyan, Hsin-Yi Wu, Wu-Chou Su, Pang-Wei Chen, Pao-Chi Liao
PROTEOMICS (2005) 5(4): 1062-1074

Human FK506 Binding Protein 65 Is Associated with Colorectal Cancer
Sanne Harder Olesen, Lise Lotte Christensen, Flemming Brandt Sorensen,Teresa Cabezon, Soren Laurberg, Torben Falck Orntoft, and Karin Birkenkamp-Demtroder
Mol Cell Proteomics (2005) 4(4): 534-544

Clinical-scale high-throughput human plasma proteome analysis: Lung adenocarcinoma
Kiyonaga Fujii, Tomoyo Nakano, Mitsuhiro Kanazawa, Shingo Akimoto, Takashi Hirano, Harubumi Kato, Toshihide Nishimura
PROTEOMICS (2005) 5(4): 1150-1159

Loss of Expression of the Adipocyte-type Fatty Acid-binding Protein (A-FABP) Is Associated with Progression of Human Urothelial Carcinomas
Gita Ohlsson, Jose M. A. Moreira, Pavel Gromov, Guido Sauter, and Julio E. Celis
Mol Cell Proteomics (2005) 4(4): 570-581

Differential protein expression in human gliomas and molecular insights
Vaibhav C. Chumbalkar, Chanumolu Subhashini, Vishnu M. Dhople, Curam S. Sundaram, Medicharla V. Jagannadham, Kafnam N. Kumar, Pasumarti N. B. S. Srinivas, Ravinutala Mythili, Mulla K. Rao, Mahesh J. Kulkarni, Sridevi Hegde, Alangar S. Hegde, Cini Samual, Vani Santosh, Lalji Singh, Ravi Sirdeshmukh
PROTEOMICS (2005) 5(4): 1167-1177

Changes in the proteomic profile during differentiation and maturation of human monocyte-derived dendritic cells stimulated with granulocyte macrophage colony stimulating factor/interleukin-4 and lipopolysaccharide
Sandra Rodrigues Pereira, Vitor Marcel Fa�a, Glauce Gaspar Gomes, Roger Chammas, Aparecida Maria Fontes, Dimas Tadeu Covas, Lewis Joel Greene
PROTEOMICS (2005) 5(5): 1186-1198

Lipoproteomics II: Mapping of proteins in high-density lipoprotein using two-dimensional gel electrophoresis and mass spectrometry
Helen Karlsson, Per Leanderson, Christer Tagesson, Mats Lindahl
PROTEOMICS (2005) 5(5): 1431-1445

Pressure overload and neurohumoral activation differentially affect the myocardial proteome
Peter Schott, Silke S. Singer, Harald K�gler, Daniel Neddermeier, Kirsten Leineweber, Otto-Erich Brodde, Vera Regitz-Zagrosek, Bernhard Schmidt, Hassan Dihazi, Gerd Hasenfuss
PROTEOMICS (2005) 5(5): 1372-1381

Cytokine profile and proteome analysis in bronchoalveolar lavage of patients with sarcoidosis, pulmonary fibrosis associated with systemic sclerosis and idiopathic pulmonary fibrosis
Paola Rottoli, Barbara Magi, Maria Grazia Perari, Sabrina Liberatori, Nikolaos Nikiforakis, Elena Bargagli, Riccardo Cianti, Luca Bini, Vitaliano Pallini
PROTEOMICS (2005) 5(5): 1423-1430

Proteomic analysis of differential protein expression in human atherosclerotic plaque progression
Donners MM, Verluyten MJ, Bouwman FG, Mariman EC, Devreese B, Vanrobaeys F, van Beeumen J, van den Akker LH, Daemen MJ, Heeneman S
J Pathol Early Edition: published 16-Mar-2005

Biomarker profiling of plasma from acute coronary syndrome patients. Application of ProteinChip Array analysis
Florian-Kujawski M, Hussain W, Chyna B, Kahn S, Hoppensteadt D, Leya F, Fareed J
Int Angiol (2004) 23(3): 246-54

A Distinctive Molecular Signature of Multiple Sclerosis Derived from MALDI-TOF/MS and Serum Proteomic Pattern Analysis: Detection of Three Biomarkers
Avasarala JR, Wall MR, Wolfe GM
J Mol Neurosci (2005) 25(1): 119-26

A proteomics approach to identify changes in protein profiles in pre-cancerous colon
Drew JE, Rucklidge GJ, Duncan G, Lufty A, Farquharson AJ, Reid MD, Russell WR, Morrice PC, Arthur JR, Duthie GG
Biochem Biophys Res Commun (2005) 330(1): 81-7

Proteomic fingerprinting for the diagnosis of human African trypanosomiasis
Agranoff D, Stich A, Abel P, Krishna S
Trends Parasitol (2005) 21(4): 154-7

Gene and protein expression profiling of the microvascular compartment in experimental autoimmune encephalomyelitis in C57Bl/6 and SJL mice
Alt C, Duvefelt K, Franzen B, Yang Y, Engelhardt B
Brain Pathol (2005) 15(1): 1-16

Proteomic analysis of interleukin 6-induced differentiation in mouse myeloid leukemia cells
Xia Q, Wang HX, Wang J, Zhang JY, Liu BY, Li AL, Lv M, Hu MR, Yu M, Feng JN, Yang SC, Zhang XM, Shen BF
Int J Biochem Cell Biol (2005) 37(6): 1197-207

S100A8 Chemotactic Protein Is Abundantly Increased, but Only a Minor Contributor to LPS-Induced, Steroid Resistant Neutrophilic Lung Inflammation in Vivo
Steven Bozinovski, # Maddalena Cross, # Ross Vlahos, # Jessica E. Jones, # Kenneth Hsuu, Philippe A. Tessier, Eric C. Reynolds, David A. Hume, # John A. Hamilton, # Carolyn L. Geczy, and Gary P. Anderson #
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 136-145

Proteomic identification of proteins specifically oxidized by intracerebral injection of amyloid beta-peptide (1-42) into rat brain: Implications for Alzheimer's disease
Boyd-Kimball D, Sultana R, Fai Poon H, Lynn BC, Casamenti F, Pepeu G, Klein JB, Butterfield DA
Neuroscience (2005) 132(2): 313-24

Proteomic Analysis of Serum Cytokine Levels in Response to Highly Active Antiretroviral Therapy (HAART)
Karen I. Relucio, Hans T. Beernink, Donna Chen, Raymond Kim, and Mark Holodniy #
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

Identification of the Thrombin Light Chain A as the Single Best Mass for Differentiation of Gastric Cancer Patients from Individuals with Dyspepsia by Proteome Analysis
Matthias P. A. Ebert, Stephanie Lamer, Jörn Meuer, Peter Malfertheiner, Thomas Buschmann, Christoph Röcken, and Volker Seibert
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

Proteins in human brain cortex are modified by oxidation, glycoxidation and lipoxidation: Effects of Alzheimer's disease and identification of lipoxidation targets
Pamplona R, Dalfo E, Ayala V, Bellmunt MJ, Prat J, Ferrer I, Portero-Otin M
J Biol Chem Early Edition: published 29-Mar-2005

Proteomics-based identification of DEAD-box protein 48 as a novel autoantigen, a prospective serum marker for pancreatic cancer
Xia Q, Kong XT, Zhang GA, Hou XJ, Qiang H, Zhong RQ
Biochem Biophys Res Commun (2005) 330(2): 526-32

Proteomic detection of prostate-specific antigen using a serum fractionation procedure: potential implication for new low-abundance cancer biomarkers detection
Je'ro^me Solassol, Philippe Marin, Edith Demettre, Philippe Rouanet, Joe"l Bockaert, Thierry Maudelonde and Alain Mange'
Analytical Biochemistry (2005) 338(1): 26-31

Biochemical and immunological studies of nucleocapsid proteins of severe acute respiratory syndrome and 229E human coronaviruses
Tswen-Kei Tang, Mark P.-J. Wu, Shui-Tsung Chen, Ming-Hon Hou, Ming-Hsiang Hong, Fu-Ming Pan, Hui-Ming Yu, Jenn-Han Chen, Chen-Wen Yao, Andrew H.-J. Wang
PROTEOMICS (2005) 5(4): 925-937

Proteomic profiling of hepatic ER-associated proteins in an animal model of insulin resistance and metabolic dyslipidemia
Morand JP, Macri J, Adeli K
J Biol Chem Early Edition: published 9-Mar-2005

Serological protein profiling of neuroblastoma by ProteinChip SELDI-TOF technology
He QY, Zhu R, Ren Y, Tam PK, Chiu JF
J Cell Biochem Early Edition: published 9-Mar-2005

Quantitative proteomic analysis of mitochondria from primary neuron cultures treated with amyloid beta peptide
Lovell MA, Xiong S, Markesbery WR, Lynn BC
Neurochem Res (2005) 30(1): 113-22

Proteome-based identification of molecular markers predicting chemosensitivity to each category of anticancer agents in human gliomas
Iwadate Y, Sakaida T, Saegusa T, Hiwasa T, Takiguchi M, Fujimoto S, Yamaura A
Int J Oncol (2005) 26(4): 993-8

A serum proteomic approach to gauging the state of remission in Wegener's granulomatosis
Stone JH, Rajapakse VN, Hoffman GS, Specks U, Merkel PA, Spiera RF, Davis JC, St Clair EW, McCune J, Ross S, Hitt BA, Veenstra TD, Conrads TP, Liotta LA, Petricoin EF 3rd
Arthritis Rheum (2005) 52(3): 902-10

Profiling of nuclear extract proteins from human neuroblastoma cell lines: The search for fingerprints
Escobar MA, Hoelz DJ, Sandoval JA, Hickey RJ, Grosfeld JL, Malkas LH
J Pediatr Surg (2005) 40(2): 349-58

Proteome Analysis of Maternal Serum Samples for Trisomy 21 Pregnancies Using ProteinChip Arrays and Bioinformatics
Busch A, Michel S, Hoppe C, Driesch D, Claussen U, von Eggeling F
J Histochem Cytochem (2005) 53(3): 341-3

A proteome analysis of conditioned media from human neonatal fibroblasts used in the maintenance of human embryonic stem cells
Andrew B. J. Prowse, Leon R. McQuade, Katherine J. Bryant, Derek D. Van Dyk, Bernard E. Tuch, Peter P. Gray
PROTEOMICS (2005) 5(4): 978-989

A differential proteome in tumors suppressed by an adenovirus-based skin patch vaccine encoding human carcinoembryonic antigen
Chun-Ming Huang, Zhongkai Shi, Tivanka S. DeSilva, Masato Yamamoto, Kent R. Van Kampen, Craig A. Elmets, De-chu C. Tang
PROTEOMICS (2005) 5(4): 1013-1023

Proteomic profiling for cancer progression: Differential display analysis for the expression of intracellular proteins between regressive and progressive cancer cell lines
Eiko Hayashi, Yasuhiro Kuramitsu, Futoshi Okada, Masanori Fujimoto, Xiulian Zhang, Masanobu Kobayashi, Norio Iizuka, Yoshiya Ueyama, Kazuyuki Nakamura
PROTEOMICS (2005) 5(4): 1024-1032

Proteomic analysis of livers of patients with primary hepatolithiasis
Takuji Nabetani, Yo Tabuse, Akira Tsugita, Junichi Shoda
PROTEOMICS (2005) 5(4): 1043-1061

High molecular mass proteome of androgen-independent prostate cancer
Hidetoshi Kuruma, Shin Egawa, Masamichi Oh-Ishi, Yoshio Kodera, Mamoru Satoh, Weigiang Chen, Hiroshi Okusa, Kazumasa Matsumoto, Tadakazu Maeda, Shiro Baba
PROTEOMICS (2005) 5(4): 1097-1112

Proteomic analysis of hepatitis B virus-associated hepatocellular carcinoma: Identification of potential tumor markers
Chen Li, Ye-Xiong Tan, Hu Zhou, Shi-Jian Ding, Su-Jun Li, Dan-jun Ma, Xiao-bo Man, Yi Hong, Lei Zhang, Long Li, Qi-Chang Xia, Jia-Rui Wu, Hong-Yang Wang, Rong Zeng
PROTEOMICS (2005) 5(4): 1125-1139

Different techniques for urinary protein analysis of normal and lung cancer patients
Payungsak Tantipaiboonwong, Supachok Sinchaikul, Supawadee Sriyam, Suree Phutrakul, Shui-Tein Chen
PROTEOMICS (2005) 5(4): 1140-1149

Eukaryotic Cells And Tissues

Protein expression patterns in zebrafish skeletal muscle: initial characterization and the effects of hypoxic exposure
Charles A. Bosworth IV, Chau-Wen Chou, Richard B. Cole, Bernard B. Rees
PROTEOMICS (2005) 5(5): 1362-1371

A Proteomic Approach to Apoplastic Proteins Involved in Cell Wall Regeneration in Protoplasts of Arabidopsis Suspension Cultured Cells
Kwon HK, Yokoyama R, Nishitani K
Plant Cell Physiol Early Edition: published 15-Mar-2005

Phosphoproteomic Analysis of Synaptosomes from Human Cerebral Cortex
Joseph A. DeGiorgis, Howard Jaffe, Jorge E. Moreira, Carlos G. Carlotti Jr., Harish C. Pant, and Ayse Dosemeci
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

The amniotic fluid cell proteome
George Tsangaris, Rachel Weitzd�rfer, Daniela Pollak, Gert Lubec, Michael Fountoulakis
ELECTROPHORESIS (2005) 26(6): 1168-1173

Proteomic Characterization of A Triton-Insoluble Fraction from Chloroplasts Defines A Novel Group of Proteins Associated with Macromolecular Structures
Brett S. Phinney and Jay J. Thelen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

Organelle Proteomics of Rat Synaptic Proteins: Correlation-Profiling by Isotope-Coded Affinity Tagging in Conjunction with Liquid Chromatography-Tandem Mass Spectrometry to Reveal Post-synaptic Density Specific Proteins
Ka wan Li, Martin P. Hornshaw, Jan van Minnen, Karl-Heinz Smalla, Eckart D. Gundelfinger, and August B. Smit
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/01/2005

Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway
Albrecht Gruhler, Jesper V. Olsen, Shabaz Mohammed, Peter Mortensen, Nils J. Faergeman, Matthias Mann, and Ole N. Jensen
Mol Cell Proteomics (2005) 4(3): 310-327

Prokaryotes

An efficient proteomics based strategy for the functional characterization of a novel halophilic enzyme from Halobacterium salinarum
Jiyeon Choi, Won-A Joo, Soo-Jin Park, So-Hee Lee, Chan-Wha Kim
PROTEOMICS (2005) 5(4): 907-917

Proteomics of Shewanella oneidensis MR-1 biofilm reveals differentially expressed proteins, including AggA and RibB
Kris De Vriendt, Sofie Theunissen, Wesley Carpentier, Lina De Smet, Bart Devreese, Jozef Van Beeumen
PROTEOMICS (2005) 5(5): 1308-1316

Mapping the membrane proteome of Corynebacterium glutamicum
Daniela Schluesener, Frank Fischer, Jochen Kruip, Matthias R�gner, Ansgar Poetsch
PROTEOMICS (2005) 5(5): 1317-1330

Subproteomes of soluble and structure-bound Helicobacter pylori proteins analyzed by two-dimensional gel electrophoresis and mass spectrometry
Steffen Backert, Terry Kwok, Monika Schmid, Matthias Selbach, Stefan Moese, Richard M. Peek Jr., Wolfgang K�nig, Thomas F. Meyer, Peter R. Jungblut
PROTEOMICS (2005) 5(5): 1331-1345

Proteomic analysis of Lyme disease: Global protein comparison of three strains of Borrelia burgdorferi
Jon M. Jacobs, Xiaohua Yang, Benjamin J. Luft, John J. Dunn, David G. Camp II, Richard D. Smith
PROTEOMICS (2005) 5(5): 1446-1453

Proteome of Methanosarcina acetivorans Part I: An Expanded View of the Biology of the Cell
Qingbo Li, Lingyun Li, Tomas Rejtar, Barry L. Karger, and James G. Ferry
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 112-128

Proteome of Methanosarcina acetivorans Part II: Comparison of Protein Levels in Acetate- and Methanol-Grown Cells
Qingbo Li, Lingyun Li , Tomas Rejtar , Barry L. Karger, and James G. Ferry
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 129-135

The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages
Kwan T, Liu J, Dubow M, Gros P, Pelletier J
Proc Natl Acad Sci U S A Early Edition: published 23-Mar-2005

Cold Adaptation of the Antarctic Archaeon, Methanococcoides burtonii Assessed by Proteomics Using ICAT
Amber Goodchild, Mark Raftery, Neil F. W. Saunders, Michael Guilhaus, and Ricardo Cavicchioli
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/25/2005

Predicted Roles for Hypothetical Proteins in the Low-Temperature Expressed Proteome of the Antarctic Archaeon Methanococcoides burtonii
Neil F. W. Saunders, Amber Goodchild, Mark Raftery, Michael Guilhaus, Paul M. G. Curmi, and Ricardo Cavicchioli
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/25/2005

Pharmacology and Toxicology

Mass Spectrometry-based Expression Profiling of Clinical Prostate Cancer
Michael E. Wright, David K. Han, and Ruedi Aebersold
Mol Cell Proteomics (2005) 4(4): 545-554

Phosphoproteome and transcriptome analysis of the neuronal response to a CDK5 inhibitor
Frank Gillardon, Peter Steinlein, Erich B�rger, Tobias Hildebrandt, Christopher Gerner
PROTEOMICS (2005) 5(5): 1299-1307

Protein Array

Use of Reverse Phase Protein Microarrays and Reference Standard Development for Molecular Network Analysis of Metastatic Ovarian Carcinoma
Katherine M. Sheehan, Valerie S. Calvert, Elaine W. Kay, Yiling Lu, David Fishman, Virginia Espina, Joy Aquino, Runa Speer, Robyn Araujo, Gordon B. Mills, Lance A. Liotta, Emanuel F. Petricoin, III, and Julia D. Wulfkuhle
Mol Cell Proteomics (2005) 4(4): 346-355

Antibody Arrays in Cancer Research
Brian B. Haab
Mol Cell Proteomics (2005) 4(4): 377-383

Protein chip-based microarray profiling of oxidized low density lipoprotein-treated cells
Sergiy Sukhanov, Patrick Delafontaine
PROTEOMICS (2005) 5(5): 1274-1280

Microarrays based on affinity-tagged single-chain Fv antibodies: Sensitive detection of analyte in complex proteomes
Christer Wingren, Cornelia Steinhauer, Johan Ingvarsson, Erik Persson, Katrin Larsson, Carl A. K. Borrebaeck
PROTEOMICS (2005) 5(5): 1281-1291

Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays
Dhaval N. Gosalia, Cleo M. Salisbury, Dustin J. Maly, Jonathan A. Ellman, Scott L. Diamond
PROTEOMICS (2005) 5(5): 1292-1298

Protein Characterization / PTMs

Protein identification from product ion spectra of peptides validated by correlation between measured and predicted elution times in liquid chromatography/mass spectrometry
Takao Kawakami, Keita Tateishi, Yuko Yamano, Takashi Ishikawa, Kazuyuki Kuroki, Toshihide Nishimura
PROTEOMICS (2005) 5(4): 856-864

Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra
David Goldberg, Mark Sutton-Smith, James Paulson, Anne Dell
PROTEOMICS (2005) 5(4): 865-875

Analysis of O-glycosylation site occupancy in bovine ?-casein glycoforms separated by two-dimensional gel electrophoresis
John W. Holland, Hilton C. Deeth, Paul F. Alewood
PROTEOMICS (2005) 5(4): 990-1002

Identification of post-translational modifications that occur during sperm maturation using difference in two-dimensional gel electrophoresis
Mark A. Baker, Roxanne Witherdin, Louise Hetherington, Kelly Cunningham-Smith, R. John Aitken
PROTEOMICS (2005) 5(4): 1003-1012

C-terminal sequencing by mass spectrometry: Application to gelatine-derived proline-rich peptides
Mireia Fernandez Oca�a, Jackie Jarvis, Richard Parker, Peter M. Bramley, John M. Halket, Raj K. P. Patel, Hendrik Neubert
PROTEOMICS (2005) 5(5): 1209-1216

Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome
Tao Liu, Wei-Jun Qian, Wan-Nan U. Chen, Jon M. Jacobs, Ronald J. Moore, David J. Anderson, Marina A. Gritsenko, Matthew E. Monroe, Brian D. Thrall, David G. Camp II, Richard D. Smith
PROTEOMICS (2005) 5(5): 1263-1273

Identifying and quantifying in vivo methylation sites by heavy methyl SILAC
Ong SE, Mittler G, Mann M
Nat Methods (2004) 1(2): 119-126

Protein Identification in Complex Mixtures
Jan Eriksson and David Fenyö
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

Mapping Sites of Protein Phosphorylation by Mass Spectrometry Utilizing a Chemical-Enzymatic Approach: Characterization of Products from -S1Casein Phosphopeptides
Daniel J. McCormick, ^, Michael W. Holmes, Benjamin J. Madden
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

Phosphotyrosine Signaling Networks in Epidermal Growth Factor Receptor Overexpressing Squamous Carcinoma Cells
April Thelemann, Filippo Petti, Graeme Griffin, Ken Iwata, Tony Hunt, Tina Settinari, David Fenyo, Neil Gibson, and John D. Haley
Mol Cell Proteomics (2005) 4(4): 356-376

Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis
Liu Z, Schey KL
J Am Soc Mass Spectrom (2005) 16(4): 482-90

Improved mass accuracy for tandem mass spectrometry
Kaiser NK, Anderson GA, Bruce JE
J Am Soc Mass Spectrom (2005) 16(4): 463-70

Complementary Structural Information from a Tryptic N-Linked Glycopeptide via Electron Transfer Ion/Ion Reactions and Collision-Induced Dissociation
Jason M. Hogan, Sharon J. Pitteri, Paul A. Chrisman, and Scott A. McLuckey
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

A Proteomic Strategy for Gaining Insights into Protein Sumoylation in Yeast
Carilee Denison, Adam D. Rudner, Scott A. Gerber, Corey E. Bakalarski,Danesh Moazed, and Steven P. Gygi
Mol Cell Proteomics (2005) 4(3): 246-254

Protein-protein interaction

Single-step Strep-tag� purification for the isolation and identification of protein complexes from mammalian cells
Melissa R. Junttila, Susanna Saarinen, Thomas Schmidt, Juergen Kast, Jukka Westermarck
PROTEOMICS (2005) 5(5): 1199-1203

Quantitation

Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling
Mark P. Molloy, Sam Donohoe, Erin E. Brzezinski, Greg W. Kilby, Tracy I. Stevenson, J. David Baker, David R. Goodlett, Douglas A. Gage
PROTEOMICS (2005) 5(5): 1204-1208

Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics
Jonas S. Almeida, Romesh Stanislaus, Ed Krug, John M. Arthur
PROTEOMICS (2005) 5(5): 1242-1249

Stable isotope methods for high-precision proteomics
Luke V. Schneider and Michael P. Hall
Drug Discovery Today (2005) 10(5): 353-363

Quantitative Profiling of the Detergent-Resistant Membrane Proteome of Iota-b Toxin Induced Vero Cells
Josip Blonder, Martha L. Hale, King C. Chan, Li-Rong Yu, Thomas P. Conrads, Ming Zhou, Michel R. Popoff, Haleem J. Issaq, Timothy D. Veenstra
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

ZoomQuant: An application for the quantitation of stable isotope labeled peptides
Brian D. Halligan Ronit Y. Slyper, Simon N. Twigger, Wayne Hicks, Michael Olivier and Andrew S. Greene
Journal of the American Society for Mass Spectrometry (2005) 16(3): 302-306

Novel Approach for Peptide Quantitation and Sequencing Based on 15N and 13C Metabolic Labeling
Ambrosius P. L. Snijders, Marjon G. J. de Vos, and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

Proteolytic 18O Labeling by Peptidyl-Lys Metalloendopeptidase for Comparative Proteomics
K. C. Sekhar Rao, Ryan T. Carruth, and Masaru Miyagi
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

Metabolic Labeling of Human Primary Retinal Pigment Epithelial Cells for Accurate Comparative Proteomics
Yetrib Hathout, Jessica Flippin, Chenguang Fan, Pinghu Liu, and Karl Csaky
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/25/2005

Quantitative Proteome Analysis Using Differential Stable Isotopic Labeling and Microbore LC-MALDI MS and MS/MS
Chengjie Ji and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/01/2005

Review

Mass Spectrometric Contributions to the Practice of Phosphorylation Site Mapping through 2003: A Literature Review
Kelly M. Loyet, John T. Stults, and David Arnott
Mol Cell Proteomics (2005) 4(3): 235-245

Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery
Kolch W, Neususs C, Pelzing M, Mischak H
Mass Spectrom Rev Early Edition: published 3-Mar-2005

Immunoaffinity CE for proteomics studies
Guzman NA, Phillips TM
Anal Chem (2005) 77(3): 61A-67A

Advances in the analysis of proteins and peptides by capillary electrophoresis with matrix-assisted laser desorption/ionization and electrospray-mass spectrometry detection
Stutz H
Electrophoresis Early Edition: published 17-Mar-2005

Combining capillary electrophoresis with mass spectrometry for applications in proteomics
Simpson DC, Smith RD
Electrophoresis Early Edition: published 14-Mar-2005

Role of biomarkers in monitoring exposures to chemicals: present position, future prospects
Watson WP, Mutti A
Biomarkers (2004) 9(3): 211-42

Dys-regulation of clusterin in human hepatoma is not associated with tumorigenesis but is secondary to cell response to external tresses
Hsieh SY, Chen WY, Shih TC, Yeh JY, Jeng JT
Mol Carcinog Early Edition: published 24-Mar-2005

Innovation: How molecular profiling could revolutionize drug discovery
Stoughton RB, Friend SH
Nat Rev Drug Discov Early Edition: published 24-Mar-2005

Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book
Sadygov RG, Cociorva D, Yates JR
Nat Methods (2004) 1(3): 195-202

Using proteomics to identify potential therapeutic targets in platelets
Maguire PB, Foy M, Fitzgerald DJ
Biochem Soc Trans (2005) 33(Pt 2): 409-12

Protein microarrays: applications and future challenges
Stoll D, Templin MF, Bachmann J, Joos TO
Curr Opin Drug Discov Devel (2005) 8(2): 239-52

Developing an understanding of proteomics: an introduction to biological mass spectrometry
Koomen J, Hawke D, Kobayashi R
Cancer Invest (2005) 23(1): 47-59

Mass spectrometry for high throughput quantitative proteomics in plant research: lessons from thylakoid membranes
Julian P. Whitelegge
Plant Physiology and Biochemistry (2004) 42(12): 919-927

Deciphering the plant phosphoproteome: tools and strategies for a challenging task
Sabrina Laugesen, Alexis Bergoin and Michel Rossignol
Plant Physiology and Biochemistry (2004) 42(12): 929-936

Plant membrane proteomics
Genevie`ve Ephritikhinea, Myriam Ferro and Norbert Rolland
Plant Physiology and Biochemistry (2004) 42(12): 943-962

Plastid proteomics
Klaas J. van Wijk
Plant Physiology and Biochemistry (2004) 42(12): 963-977

Digging deeper into the plant cell wall proteome
Sang-Jik Lee, Ramu S. Saravanan, Cynthia M.B. Damasceno, Hisayo Yamane, Byung-Dong Kim and Jocelyn K.C. Rose
Plant Physiology and Biochemistry (2004) 42(12): 979-988

Chlamydomonas reinhardtii proteomics
Einar J. Staubera and Michael Hippler
Plant Physiology and Biochemistry (2004) 42(12): 989-1001

Respiratory chain supercomplexes in plant mitochondria
Holger Eubel, Jesco Heinemeyer, Stephanie Sunderhaus and Hans-Peter Braun
Plant Physiology and Biochemistry (2004) 42(12): 937-942

Stable isotope methods for high-precision proteomics
Luke V. Schneider and Michael P. Hall
Drug Discovery Today (2005) 10(5): 353-363

Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry
Jennifer Listgarten and Andrew Emili
Mol Cell Proteomics (2005) 4(4): 419-434

Annotating the Human Proteome
Sandra Orchard, Henning Hermjakob, and Rolf Apweiler
Mol Cell Proteomics (2005) 4(4): 435-440

Chromatographic media for bioseparation
Alois Jungbauer
J Chromatogr A (2005) 1065(1): 3-12

Biochemical applications of mass spectrometry in pharmaceutical drug discovery
Kieran F. Geoghegan, Michele A. Kelly
Mass Spectrometry Reviews (2005) 24(3): 347-366

Shotgun lipidomics: Electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples
Xianlin Han, Richard W. Gross
Mass Spectrometry Reviews (2005) 24(3): 367-412

Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry
Hong Wang, Sam Hanash
Mass Spectrometry Reviews (2005) 24(3): 413-426

Methodology

A new application of microwave technology to proteomics
Hsueh-Fen Juan, Shing-Chuan Chang, Hsuan-Cheng Huang, Shui-Tein Chen
PROTEOMICS (2005) 5(4): 840-842

Tryptic transpeptidation products observed in proteome analysis by liquid chromatography-tandem mass spectrometry
Heike Schaefer, Daniel C. Chamrad, Katrin Marcus, Kai A. Reidegeld, Martin Bl�ggel, Helmut E. Meyer
PROTEOMICS (2005) 5(4): 846-852

Effective depletion of albumin using a new peptide-based affinity medium
Thierry Baussant, Lydie Bougueleret, Andrew Johnson, John Rogers, Laure Menin, Martin Hall, Per-Mikael �berg, Keith Rose
PROTEOMICS (2005) 5(4): 973-977

Proteomic study of human hepatocellular carcinoma using two-dimensional difference gel electrophoresis with saturation cysteine dye
Kazuyasu Fujii, Tadashi Kondo, Hideki Yokoo, Tesshi Yamada, Keiji Iwatsuki, Setsuo Hirohashi
PROTEOMICS (2005) 5(5): 1411-1422

Integrated Microfluidic Device for Mass Spectrometry-Based Proteomics and Its Application to Biomarker Discovery Programs
Fortier MH, Bonneil E, Goodley P, Thibault P
Anal Chem (2005) 77(6): 1631-1640

Blending Protein Separation and Peptide Analysis through Real-Time Proteolytic Digestion
Slysz GW, Schriemer DC
Anal Chem (2005) 77(6): 1572-9

In vivo protein biotinylation for identification of organ-specific antigens accessible from the vasculature
Rybak JN, Ettorre A, Kaissling B, Giavazzi R, Neri D, Elia G
Nat Methods Early Edition: published 23-Mar-2005

A new method for C-terminal sequence analysis in the proteomic era
Samyn B, Sergeant K, Castanheira P, Faro C, Van Beeumen J
Nat Methods (2005) 2(3): 193-200

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR
Nat Methods (2004) 1(1): 39-45

Investigation of Cu-, Zn- and Fe-containing human brain proteins using isotopic-enriched tracers by LA-ICP-MS and MALDI-FT-ICR-MS
J. Susanne Becker, Miroslav Zoriy, Carola Pickhardt, Michael Przybylski and J. Sabine Becker
International Journal of Mass Spectrometry (2005) 242(2-3): 135-144

Detection of myofibrillar proteins using a step gradient minigel with an ambiguous interface
Sy-Ping Chena, b, Joen-Rong Sheua, c, Ching-Yuan Laid, Tzu-Yung Linb, George Hsiaoc and Tsorng-Harn Fong
Analytical Biochemistry (2005) 338(2): 270-277

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, Don L. DeVoe, and Cheng S. Lee
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 36-42

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 (2005) 4(1): 71-74

Enhancing TOF/TOF-based de Novo Sequencing Capability for High Throughput Protein Identification with Amino Acid-Coded Mass Tagging
Wenqing Shui, Yinkun Liu, Huizhi Fan, Huimin Bao, Shufang Liang, Pengyuan Yang, and Xian Chen
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 83-90

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 (2005) 4(1): 101-108

Use of Lysozyme as a Standard for Evaluating the Effectiveness of a Proteomics Process
Leah S. Riter, Barry D. Hodge, Karen M. Gooding, and Randall K. Julian, Jr
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 153-160

Protein Staining Influences the Quality of Mass Spectra Obtained by Peptide Mass Fingerprinting after Separation on 2-D Gels. A Comparison of Staining with Coomassie Brilliant Blue and Sypro Ruby
Boel Lanne and Oleg Panfilov
JOURNAL OF PROTEOME RESEARCH (2005) 4(1): 175-179

Reproducibility of Tryptic Digestion Investigated by Quantitative Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Charlotte Hagman, Margareta Ramström, Maria Jansson, Peter James, Jonas Bergquist
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

Depletion of High-Abundant Proteins in Body Fluids Prior to Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Margareta Ramström, Charlotte Hagman, Jennifer K. Mitchell, Per Håkansson, and Jonas Bergquist
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

P-Mod: An Algorithm and Software To Map Modifications To Peptide Sequences Using Tandem MS Data
Beau T. Hansen, Sean W. Davey, Amy-Joan L. Ham, and Daniel C. Liebler
JOURNAL OF PROTEOME RESEARCH Early Edition: published 02/11/2005

An algorithm for interpretation of low-energy collision-induced dissociation product ion spectra for de novo sequencing of peptides
Zhong H, Li L
Rapid Commun Mass Spectrom (2005) 19(8): 1084-1096

Quantitative proteomic analysis by accurate mass retention time pairs
Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li GZ, McKenna T, Nold MJ, Richardson K, Young P, Geromanos S
Anal Chem (2005) 77(7): 2187-200

Coumarin Tags for Analysis of Peptides by MALDI-TOF MS and MS/MS. 2. Alexa Fluor 350 Tag for Increased Peptide and Protein Identification by LC-MALDI-TOF/TOF MS
Pashkova A, Chen HS, Rejtar T, Zang X, Giese R, Andreev V, Moskovets E, Karger BL
Anal Chem (2005) 77(7): 2085-96

High-resolution functional proteomics by active-site peptide profiling
Okerberg ES, Wu J, Zhang B, Samii B, Blackford K, Winn DT, Shreder KR, Burbaum JJ, Patricelli MP
Proc Natl Acad Sci U S A Early Edition: published 28-Mar-2005

High-efficiency staining of proteins on different blot membranes
C.R. Yonan, P.T. Duong and F.N. Chang
Analytical Biochemistry (2005) 338(1): 159-161

Site-specific labeling of proteins with small molecules in live cells
Irwin Chen and Alice Y Ting
Curr Opin Struct Biotechnol (2005) 16(1): 35-40

Two-stage Off-GelTM isoelectric focusing: Protein followed by peptide fractionation and application to proteome analysis of human plasma
Manfred Heller, Philippe E. Michel, Patrick Morier, David Crettaz, Christian Wenz, Jean-Daniel Tissot, Fr�d�ric Reymond, Joel S. Rossier
ELECTROPHORESIS (2005) 26(6): 1174-1188

Nanoliter Sample Handling Combined with Microspot MALDI-MS for Detection of Gel-Separated Phosphoproteins
Jacek Stupak, Huaizhi Liu, Zhengping Wang, Brenda J. Brix, Larry Fliegel, and Liang Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/04/2005

Two-dimensional Blue Native/sodium dodecyl sulfate gel electrophoresis for analysis of multimeric proteins in platelets
Dirk Claeys, K�thi Geering, Beat J. Meyer
ELECTROPHORESIS (2005) 26(6): 1189-1199

Solubilization of cellular membrane proteins from Streptococcus mutans for two-dimensional gel electrophoresis
Kheir Zuobi-Hasona, Paula J. Crowley, Adnan Hasona, Arnold S. Bleiweis, L. Jeannine Brady
ELECTROPHORESIS (2005) 26(6): 1200-1205

SCAPE: A New Tool for the Selective CApture of PEptides in Protein Identification
Lazaro Betancourt, Jeovanis Gil, Vladimir Besada, Luis J. González, Jorge Fernández-de-Cossio, Liudy García, Rolando Pajón, Aniel Sanchez, Félix Alvarez, and Gabriel Padrón
JOURNAL OF PROTEOME RESEARCH Early Edition: published 03/25/2005

Evaluation of Protein Depletion Methods for the Analysis of Total-, Phospho- and Glycoproteins in Lumbar Cerebrospinal Fluid
Yuko Ogata, M. Cristine Charlesworth, and David C. Muddiman
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/01/2005

Double Standards in Quantitative Proteomics: Direct Comparative Assessment of Difference in Gel Electrophoresis and Metabolic Stable Isotope Labeling
Annemieke Kolkman, Eef H. C. Dirksen, Monique Slijper, and Albert J. R. Heck
Mol Cell Proteomics (2005) 4(3): 255-266

Books

Current literature in mass spectrometry
John Wiley & Sons, Ltd
Journal of Mass Spectrometry (2005) 40(3): 416-427

Meeting

Meetings Diary: Proteomics 4/2005
PROTEOMICS (2005) 5(4): 1178-1180

Meetings Diary: Proteomics 5/2005
PROTEOMICS (2005) 5(5): 1455-1457

Other

Editorial: Proteomics 4/2005
Richard J. Simpson, Akira Tsugita, Young-Ki Paik
PROTEOMICS (2005) 5(4): 831-839

Product News: Proteomics 4/2005
PROTEOMICS (2005) 5(4): 1181-1183

Editorial: Proteomics of Disease
Julio E. Celis and Murray Korc
Mol Cell Proteomics (2005) 4(4): 345

Calendar
Mol Cell Proteomics (2005) 4(4): 594-595

Toward data standards for proteomics
Ravichandran V, Sriram RD
Nat Biotechnol (2005) 23(3): 373-376

Hardware-accelerated protein identification for mass spectrometry
Anish T. Alex, Michel Dumontier, Jonathan S. Rose, Christopher W. V. Hogue
Rapid Communications in Mass Spectrometry (2005) 19(6): 833-837

Focus on plant proteomics
He'le`ne Barbier-Brygoo and Jacques Joyard
Plant Physiology and Biochemistry (2004) 42(12): 913-917

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SPS' Digest

Issue 17, 7-Apr-2005

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Bioinformatics

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Biological applications

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Biomedical and clinical applications

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Eukaryotic Cells And Tissues

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Prokaryotes

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Pharmacology and Toxicology

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Protein Array

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Protein Characterization / PTMs

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Protein-protein interaction

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Quantitation

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Review

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Methodology

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