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SPS' Digest

Issue 31, 2-Jun-2006

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Quick jumps to articles in: Bioinformatics (18) / Biological applications (42) / Biomedical and clinical applications (39) / Eukaryotic Cells And Tissues (9) / Prokaryotes (13) / Pharmacology and Toxicology (10) / Protein Array (11) / Protein Characterization - PTMs (9) / Protein-protein interaction (4) / Quantitation (4) / Review (17) / Methodology (26) / Books (1) / Meeting (3) / Other (7) /

In this issue, 211 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 (18) / Biological applications (42) / Biomedical and clinical applications (39) / Eukaryotic Cells And Tissues (9) / Prokaryotes (13) / Pharmacology and Toxicology (10) / Protein Array (11) / Protein Characterization - PTMs (9) / Protein-protein interaction (4) / Quantitation (4) / Review (17) / Methodology (26) / Books (1) / Meeting (3) / Other (7) /

Bioinformatics

Probing Latent Biomarker Signatures and in Vivo Pathway Activity in Experimental Disease States via Statistical Total Correlation Spectroscopy (STOCSY) of Biofluids: Application to HgCl2 Toxicity
E. Holmes, O. Cloarec, and J. K. Nicholson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/12/2006

Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables
Van Belle WW, Anensen NN, Haaland II, Bruserud OO, Hogda KA, Tore Gjertsen BB
BMC Bioinformatics (2006) 7(1): 198

UniSave: the UniProtKB Sequence/Annotation Version database
Rasko Leinonen, Francesco Nardone, Weimin Zhu, and Rolf Apweiler
Bioinformatics (2006) 22(10): 1284-1285

Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins
Nie L, Wu G, Brockman FJ, Zhang W
Bioinformatics Early Edition: published 4-May-2006

FCP: functional coverage of the proteome by structures
Garcia-Serna R, Opatowski L, Mestres J
Bioinformatics Early Edition: published 16-May-2006

A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Keller A, Eng J, Zhang N, Li XJ, Aebersold R
Mol Syst Biol (2005) 1: 2005.0017

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data
Zhang Z, Sun S, Zhu X, Chang S, Liu X, Yu C, Bu D, Chen R
BMC Bioinformatics (2006) 7: 222

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ
Genome Biol (2006) 7(4): R35

ProMAT: protein microarray analysis tool
Amanda M. White, Don S. Daly, Susan M. Varnum, Kevin K. Anderson, Nikki Bollinger, and Richard C. Zangar
Bioinformatics (2006) 22(10): 1278-1279

Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data
Zhang X, Lu X, Shi Q, Xu XQ, Leung HC, Harris LN, Iglehart JD, Miron A, Liu JS, Wong WH
BMC Bioinformatics (2006) 7: 197

MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Annette Hoglund, Pierre Donnes, Torsten Blum, Hans-Werner Adolph, and Oliver Kohlbacher
Bioinformatics (2006) 22(10): 1158-1165

Convergence of the proteomic pattern in cancer
Ute Muller, Gunther Ernst, Christian Melle, Reinhard Guthke, and Ferdinand von Eggeling
Bioinformatics (2006) 22(11): 1293-1296

A statistical framework to discover true associations from multiprotein complex pull-down proteomics data sets
Shen C, Li L, Chen JY
Proteins Early Edition: published 16-May-2006

Informatics solutions for high-throughput proteomics
Topaloglou T
Drug Discov Today (2006) 11(11-12): 509-16

Constructing support vector machine ensembles for cancer classification based on proteomic profiling
Mao Y, Zhou XB, Pi DY, Sun YX
Genomics Proteomics Bioinformatics (2005) 3(4): 238-41

Issues of processing and multiple testing of SELDI-TOF MS proteomic data
Birkner MD, Hubbard AE, van der Laan MJ, Skibola CF, Hegedus CM, Smith MT
Stat Appl Genet Mol Biol (2006) 5(1): Article11

Ensemble classifier for protein fold pattern recognition
Shen HB, Chou KC
Bioinformatics Early Edition: published 3-May-2006

BIOINFORMATICS AND ITS APPLICATIONS IN PLANT BIOLOGY
Rhee SY, Dickerson J, Xu D
Annu Rev Plant Biol (2006) 57: 335-360.

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Biological applications

A comparative proteomic evaluation of culture grown vs nodule isolated Bradyrhizobium japonicum
Annamraju D. Sarma, David W. Emerich
PROTEOMICS (2006) 6(10): 3008-3028

Possible dysregulation of chaperon and metabolic proteins in cystic fibrosis bronchial tissue
Thomas Frischer, Jae-Kyung Myung, Gerald Maurer, Irmgard Eichler, Zsolt Szepfalusi, Gert Lubec
PROTEOMICS (2006) 6(11): 3381-3388

High light response of the thylakoid proteome in Arabidopsis thaliana wild type and the ascorbate deficient mutant vtc2-2; a comparative proteomics study
Giacomelli L, Rudella A, van Wijk KJ
Plant Physiol Early Edition: published 28-Apr-2006

Proteomic analysis of acidic chaperones, and stress proteins in extreme halophile Halobacterium NRC-1: A comparative proteomic approach to study heat shock response
Shukla H
Proteome Sci (2006) 4: 6

Proteins differentially expressed in response to nicotine in five rat brain regions: Identification using a 2-DE/MS-based proteomics approach
Yoon Y. Hwang, Ming D. Li
PROTEOMICS (2006) 6(10): 3138-3153

Proteomic pattern-based analyses of light responses in Arabidopsis thaliana wild-type and photoreceptor mutants
Dong Su Kim, Dae Shik Cho, Won-Man Park, Hyung Jin Na, Hong Gil Nam
PROTEOMICS (2006) 6(10): 3040-3049

Caenorhabditis elegans as a screening tool for the endothelial cell-derived putative aging-related proteins detected by proteomic analysis
Moon Kyung Ha, Jeong Soo Cho, Ok-Ryun Baik, Kwang Hoon Lee, Hyeon-Sook Koo, Kee Yang Chung
PROTEOMICS (2006) 6(11): 3339-3351

Proteomic analysis of the transition from quiescent to proliferating stages in rat liver hepatectomy model
Fuzheng Guo, Hui Nian, Hao Zhang, Lingyun Huang, Ying Tang, Xueyuan Xiao, Dacheng He
PROTEOMICS (2006) 6(10): 3075-3086

Quantitative and qualitative comparisons of Cryptosporidium faecal purification procedures for the isolation of oocysts suitable for proteomic analysis
Truong Q, Ferrari BC
Int J Parasitol Early Edition: published 31-Mar-2006

Functional proteomics of BK potassium channels: defining the acute oxygen sensor
Kemp PJ, Williams SE, Mason HS, Wootton P, Iles DE, Riccardi D, Peers C
Novartis Found Symp (2006) 272: 141-51; discussion 151-6: 214-7

Identification of phosphoproteins associated with maintenance of transformed state in temperature-sensitive Rous sarcoma-virus infected cells by proteomic analysis
Yamaoka K, Imajoh-Ohmi S, Fukuda H, Akita Y, Kurosawa K, Yamamoto Y, Sanai Y
Biochem Biophys Res Commun Early Edition: published 15-May-2006

Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes
Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ
Genes Dev (2006) 20(10): 1294-307

Changes in the rat heart proteome induced by exercise training: Increased abundance of heat shock protein hsp20
Marvin O. Boluyt, Julie L. Brevick, David S. Rogers, Michael J. Randall, Antony F. Scalia, Zhao Bo Li
PROTEOMICS (2006) 6(10): 3154-3169

Ontogenetic variations in the venom proteome of the Amazonian snake Bothrops atrox
Guercio RA, Shevchenko A, Shevchenko A, Lopez-Lozano JL, Paba J, Sousa MV, Ricart CA
Proteome Sci (2006) 4(1): 11

Genomic and Proteomic Analyses of the Agarolytic System Expressed by Saccharophagus degradans 2-40
Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM, Hutcheson SW
Appl Environ Microbiol (2006) 72(5): 3396-405

Comparative proteomic analysis of hypoxia-treated and untreated human leukemic U937 cells
Yu-Hui Han, Li Xia, Li-Ping Song, Ying Zheng, Wen-Li Chen, Lei Zhang, Ying Huang, Guo-Qiang Chen, Li-Shun Wang
PROTEOMICS (2006) 6(11): 3262-3274

Proteomic Analysis of Extracellular Proteins from Aspergillus oryzae Grown under Submerged and Solid-State Culture Conditions
Oda K, Kakizono D, Yamada O, Iefuji H, Akita O, Iwashita K
Appl Environ Microbiol (2006) 72(5): 3448-57

Proteomic analysis of protein profiles during early development of the zebrafish, Danio rerio
Tuan Leng Tay, Qingsong Lin, Teck Keong Seow, Keng Hwa Tan, Choy Leong Hew, Zhiyuan Gong
PROTEOMICS (2006) 6(10): 3176-3188

Progress in in silico functional genomics: the malaria Metabolic Pathways database
Ginsburg H
Trends Parasitol Early Edition: published 15-May-2006

Comparative proteomics of glycosomes from bloodstream form and procyclic culture form Trypanosoma brucei brucei
Claudia Colasante, Margrit Ellis, Thomas Ruppert, Frank Voncken
PROTEOMICS (2006) 6(11): 3275-3293

The Potential of Bothrops moojeni Venom in the Field of Hemostasis. Established Use and New Insights
Perchuc AM, Menin L, Stocklin R, Buhler B, Schoni R
Pathophysiol Haemost Thromb (2005) 34(4-5): 241-5

The plasma membrane proteome of Saccharomyces cerevisiae and its response to the antifungal calcofluor
Frédéric Delom, Wojciech Szponarski, Nicolas Sommerer, Jean-Christophe Boyer, Jean-Michel Bruneau, Michel Rossignol, Rémy Gibrat
PROTEOMICS (2006) 6(10): 3029-3039

Proteomic analysis of the 14-3-3 family in Arabidopsis
Brian Fuller, Stanley M. Stevens Jr., Paul C. Sehnke, Robert J. Ferl
PROTEOMICS (2006) 6(10): 3050-3059

Analysis of the effects of cryopreservation on rat hepatocytes using SELDI-TOF mass spectrometry
Terry C, Bailey M, Mitry RR, Lehec SC, Dhawan A, Hughes RD
Cell Transplant (2006) 15(1): 35-43

Identification of crystallin family proteins in vitreous body in rat endotoxin-induced uveitis: Involvement of crystallin truncation in uveitis pathogenesis
Song-Chul Bahk, Sook-Hee Lee, Jung-Un Jang, Chang-Uk Choi, Bok-Soo Lee, Soo-Cheon Chae, Hye-Jin Song, Zee-Yong Park, Yun-Sik Yang, Hun-Taeg Chung
PROTEOMICS (2006) 6(11): 3436-3444

Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics
Gupta N, Wollscheid B, Watts JD, Scheer B, Aebersold R, Defranco AL
Nat Immunol Early Edition: published 30-Apr-2006

Integral membrane proteins in the mitochondrial outer membrane of Saccharomyces cerevisiae
Burri L, Vascotto K, Gentle IE, Chan NC, Beilharz T, Stapleton DI, Ramage L, Lithgow T
FEBS J (2006) 273(7): 1507-15

Towards a lung adenocarcinoma proteome map: Studies with SP-C/c-raf transgenic mice
Heike Rütters, Petra Zürbig, Roman Halter, Jürgen Borlak
PROTEOMICS (2006) 6(10): 3127-3137

Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply
Le Lay P, Isaure MP, Sarry JE, Kuhn L, Fayard B, Le Bail JL, Bastien O, Garin J, Roby C, Bourguignon J
Biochimie Early Edition: published 24-Apr-2006

Redox proteomics in the mussel, Mytilus edulis
McDonagh B, Tyther R, Sheehan D
Mar Environ Res Early Edition: published 7-Apr-2006

Proteomic trajectory mapping of biological transformation: Application to developmental mouse retina
Hisao Haniu, Naoka Komori, Nobuaki Takemori, Anil Singh, John D. Ash, Hiroyuki Matsumoto
PROTEOMICS (2006) 6(11): 3251-3261

Following the differentiation of human pluripotent stem cells by proteomic identification of biomarkers
Hayman MW, Christie VB, Keating TS, Przyborski SA
Stem Cells Dev (2006) 15(2): 221-31

The abundance of short proteins in the mammalian proteome
Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM
PLoS Genet (2006) 2(4): e52

Proteomic analysis of rat pheochromocytoma PC12 cells
Wei Yang, Peng Liu, Yashu Liu, Qingsong Wang, Yuanpeng Tong, Jianguo Ji
PROTEOMICS (2006) 6(10): 2982-2990

Peptidomics Analysis of Neuropeptides Involved in Copulatory Behavior of the Mollusk Lymnaea stagnalis
Z. El Filali, J. Van Minnen, W. K. Liu, A. B. Smit, and K. W. Li
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/26/2006

Proteome analysis of rice uppermost internodes at the milky stage
Pingfang Yang, Yu Liang, Shihua Shen, Tingyun Kuang
PROTEOMICS (2006) 6(11): 3330-3338

Changes in liver protein abundance in inbred alcohol-preferring rats due to chronic alcohol exposure, as measured through a proteomics approach
Iveta Klouckova, Petra Hrncirova, Yehia Mechref, Randy J. Arnold, Ting-Kai Li, William J. McBride, Milos V. Novotny
PROTEOMICS (2006) 6(10): 3060-3074

Proteomic Investigation of the Effect of Salicylic Acid on Arabidopsis Seed Germination and Establishment of Early Defense Mechanisms
Rajjou L, Belghazi M, Huguet R, Robin C, Moreau A, Job C, Job D
Plant Physiol Early Edition: published 5-May-2006

Proteomic identification of potential target proteins regulated by an ASK1-mediated proteolysis pathway
Wang X, Ni W, Ge X, Zhang J, Ma H, Cao K
Cell Res (2006) 16(5): 489-98

Differential gel electrophoresis and transgenic mitochondrial calcium reporters demonstrate spatiotemporal filtering in calcium control of mitochondria
Terhzaz S, Southall TD, Lilley KS, Kean L, Allan AK, Davies SA, Dow JA
J Biol Chem Early Edition: published 2-May-2006

In search of the acute oxygen sensor: Functional proteomics and acute regulation of large-conductance, calcium-activated potassium channels by hemeoxygenase-2
Kemp PJ, Peers C, Riccardi L, Iles DE, Mason HS, Wootton P, Williams SE
Adv Exp Med Biol (2006) 580: 137-46; discussion 351-9

Analysis of the cGMP/cAMP Interactome Using a Chemical Proteomics Approach in Mammalian Heart Tissue Validates Sphingosine Kinase Type 1-interacting Protein as a Genuine and Highly Abundant AKAP
Arjen Scholten, Mee Kian Poh, Toon A. B. van Veen, Bas van Breukelen, Marc A. Vos, and Albert J. R. Heck
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/12/2006

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Biomedical and clinical applications

Proteomic analysis for the identification of proteins related to methotrexate resistance
Feng YX, Bai J, Zhang CY, Fu SB
Yi Chuan Xue Bao (2006) 33(5): 391-6

Accurate diagnosis of acute graft-versus-host disease using serum proteomic pattern analysis
Srinivasan R, Daniels J, Fusaro V, Lundqvist A, Killian JK, Geho D, Quezado M, Kleiner D, Rucker S, Espina V, Whiteley G, Liotta L, Petricoin E, Pittaluga S, Hitt B, Barrett AJ, Rosenblatt K, Childs RW
Exp Hematol (2006) 34(6): 796-801

Proteomic analysis of suction blister fluid isolated from human skin
Macdonald N, Cumberbatch M, Singh M, Moggs JG, Orphanides G, Dearman RJ, Griffiths CE, Kimber I
Clin Exp Dermatol (2006) 31(3): 445-8

Proteomic comparison of prostate cancer cell lines LNCaP-FGC and LNCaP-r reveals heatshock protein 60 as a marker for prostate malignancy
Johansson B, Pourian MR, Chuan YC, Byman I, Bergh A, Pang ST, Norstedt G, Bergman T, Pousette A
Prostate Early Edition: published 16-May-2006

The promising future of proteomics in sarcoidosis
Agostini C, Facco M
Am J Respir Crit Care Med (2006) 173(10): 1053-4

Proteomic analysis of UVC irradiation-induced damage of plasma proteins: Serum amyloid P component as a major target of photolysis
Chan HL, Gaffney PR, Waterfield MD, Anderle H, Peter Matthiessen H, Schwarz HP, Turecek PL, Timms JF
FEBS Lett Early Edition: published 6-May-2006

Proteomic analysis of liver tissues subjected to early ischemia/reperfusion injury during human orthotopic liver transplantation
Carlo Vascotto, Laura Cesaratto, Chiara D'Ambrosio, Andrea Scaloni, Claudio Avellini, Igor Paron, Umberto Baccarani, Gian Luigi Adani, Claudio Tiribelli, Franco Quadrifoglio, Gianluca Tell
PROTEOMICS (2006) 6(11): 3455-3465

Comparative Serum Glycoproteomics Using Lectin Selected Sialic Acid Glycoproteins with Mass Spectrometric Analysis: Application to Pancreatic Cancer Serum
Jia Zhao, Diane M. Simeone, David Heidt, Michelle A. Anderson, and David M. Lubman
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/26/2006

Proteomic analysis of the anterior cingulate cortex in the major psychiatric disorders: Evidence for disease-associated changes
Clare L. Beasley, Kyla Pennington, Aine Behan, Robin Wait, Michael J. Dunn, David Cotter
PROTEOMICS (2006) 6(11): 3414-3425

Proteomics for the identification of new prostate cancer biomarkers
Ornstein DK, Tyson DR
Urol Oncol (2006) 24(3): 231-6

Proteomic Analysis of Neuroblastoma Subtypes in Response to Mitogen-Activated Protein Kinase Inhibition: Profiling Multiple Targets of Cancer Kinase Signaling
Sandoval JA, Eppstein AC, Hoelz DJ, Klein PJ, Linebarger JH, Turner KE, Rescorla FJ, Hickey RJ, Malkas LH, Schmidt CM
J Surg Res Early Edition: published 29-Apr-2006

Proteomic changes in hearts of kyphoscoliosis (ky) mutant mice in the absence of structural pathology: Implication for the analysis of early human heart disease
Yanwen Hou, Marie-Catherine Le Bihan, David Vega-Avelaira, Gary R. Coulton
PROTEOMICS (2006) 6(10): 3096-3108

Proteomic Analysis of Tumor Establishment and Growth in the B16-F10 Mouse Melanoma Model
W. David Culp, Rachel Neal, Robert Massey, Lars Egevad, Pavel Pisa, and Donita Garland
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/12/2006

Strategies for examination of Alzheimer's disease amyloid precursor protein isoforms
Newton JR, Parkinson D, Clench MR
Anal Bioanal Chem Early Edition: published 18-May-2006

Proteomic analysis of soluble factors secreted by limbal fibroblasts
Shimmura S, Miyashita H, Higa K, Yoshida S, Shimazaki J, Tsubota K
Mol Vis (2006) 12: 478-84.

Proteomic analysis of anaplastic lymphoma cell lines: Identification of potential tumour markers
Daniel Cussac, Carole Pichereaux, Audrey Colomba, Florence Capilla, Frédéric Pont, Frédérique Gaits-Iacovoni, Laurence Lamant, Estelle Espinos, Odile Burlet-Schiltz, Bernard Monsarrat, Georges Delsol, Bernard Payrastre
PROTEOMICS (2006) 6(10): 3210-3222

Suppression of human selenium-binding protein 1 is a late event in colorectal carcinogenesis and is associated with poor survival
Hyunki Kim, Hyun Ju Kang, Kwon Tae You, Se Hoon Kim, Kang Young Lee, Tae Il Kim, Chul Kim, Si Young Song, Hye-Jung Kim, Cheolju Lee, Hoguen Kim
PROTEOMICS (2006) 6(11): 3466-3476

Genetics, Transcriptomics, and Proteomics of Alzheimer's Disease
Papassotiropoulos A, Fountoulakis M, Dunckley T, Stephan DA, Reiman EM
J Clin Psychiatry (2006) 67(4): 652-670

Impairment of mitochondrial anti-oxidant defence in SOD1-related motor neuron injury and amelioration by ebselen
Wood-Allum CA, Barber SC, Kirby J, Heath P, Holden H, Mead R, Higginbottom A, Allen S, Beaujeux T, Alexson SE, Ince PG, Shaw PJ
Brain Early Edition: published 15-May-2006

The human cornea proteome: bioinformatic analyses indicate import of plasma proteins into the cornea
Karring H, Thogersen IB, Klintworth GK, Moller-Pedersen T, Enghild JJ
Mol Vis (2006) 12: 451-60.

Identification of candidate antigen in Whipple's disease using a serological proteomic approach
Malgorzata Kowalczewska, Florence Fenollar, Daniel Lafitte, Didier Raoult
PROTEOMICS (2006) 6(11): 3294-3305

The proteome of central and peripheral retina with progression of age-related macular degeneration
Ethen CM, Reilly C, Feng X, Olsen TW, Ferrington DA
Invest Ophthalmol Vis Sci (2006) 47(6): 2280-90

Consequence of Gastrin-Releasing Peptide Receptor Activation in a Human Colon Cancer Cell Line: A Proteomic Approach
Tom Ruginis, Lauren Taglia, Damien Matusiak, Bao-Shiang Lee, and Richard V. Benya
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/05/2006

High glucose concentration induces elevated expression of anti-oxidant and proteolytic enzymes in cultured human retinal pigment epithelial cells
Yokoyama T, Yamane K, Minamoto A, Tsukamoto H, Yamashita H, Izumi S, Hoppe G, Sears JE, Mishima HK
Exp Eye Res Early Edition: published 10-May-2006

Lumbar Cerebrospinal Fluid Proteome in Multiple Sclerosis: Characterization by Ultrafiltration, Liquid Chromatography, and Mass Spectrometry
Jean-Paul Noben, Debora Dumont, Natalia Kwasnikowska, Peter Verhaert, Veerle Somers, Raymond Hupperts, Piet Stinissen, and Johan Robben
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/19/2006

Bisphosphonates activate nucleotide receptors signaling and induce the expression of Hsp90 in osteoblast-like cell lines
Romanello M, Bivi N, Pines A, Deganuto M, Quadrifoglio F, Moro L, Tell G
Bone Early Edition: published 11-May-2006

Proteomic analysis of recurrent spontaneous abortion: Identification of an inadequately expressed set of proteins in human follicular fluid
Yong-Soo Kim, Myung-Sun Kim, Sook-Hwan Lee, Bum-Chae Choi, Jeong-Mook Lim, Kwang Yul Cha, Kwang-Hyun Baek
PROTEOMICS (2006) 6(11): 3445-3454

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry serum protein profiling to identify nasopharyngeal carcinoma
Wing Yuen Ho D, Fan Yang Z, Yee-Hang Wong B, Lai-Wan Kwong D, Shun-Tong Sham J, Ignace Wei W, Po Wing Yuen A
Cancer Early Edition: published 17-May-2006

Identification of a plasma proteomic signature to distinguish pediatric osteosarcoma from benign osteochondroma
Yiting Li, Tu Anh Dang, Jianhe Shen, Laszlo Perlaky, John Hicks, Jeffrey Murray, William Meyer, Murali Chintagumpala, Ching C. Lau, Tsz-Kwong Man
PROTEOMICS (2006) 6(11): 3426-3435

Degradomics: Systems biology of the protease web. Pleiotropic roles of MMPs in cancer
Overall CM, Dean RA
Cancer Metastasis Rev (2006) 25(1): 69-75

Technology Insight: pharmacoproteomics for cancer-promises of patient-tailored medicine using protein microarrays
Wulfkuhle JD, Edmiston KH, Liotta LA, Petricoin EF
Nat Clin Pract Oncol (2006) 3(5): 256-68

Large-scale and high-confidence proteomic analysis of human seminal plasma
Pilch B, Mann M
Genome Biol (2006) 7(5): R40

Analysis of variabilities of serum proteomic spectra in patients with gastric cancer before and after operation
Ren H, Du N, Liu G, Hu HT, Tian W, Deng ZP, Shi JS
World J Gastroenterol (2006) 12(17): 2789-2792

Identification of proteins released by follicular lymphoma-derived cells using a mass spectrometry-based approach
Cecily P. Vaughn, David K. Crockett, Zhaosheng Lin, Megan S. Lim, Kojo S. J. Elenitoba-Johnson
PROTEOMICS (2006) 6(10): 3223-3230

Proteomic classification of pancreatic adenocarcinoma tissue using protein chip technology
Scarlett CJ, Smith RC, Saxby A, Nielsen A, Samra JS, Wilson SR, Baxter RC
Gastroenterology (2006) 130(6): 1670-8

Proteomics: A New Diagnostic Frontier
Hortin GL, Jortani SA, Ritchie JC Jr, Valdes R Jr, Chan DW
Clin Chem Early Edition: published 4-May-2006

Identification of breast cancer metastasis-associated proteins in an isogenic tumor metastasis model using two-dimensional gel electrophoresis and liquid chromatography-ion trap-mass spectrometry
Da-Qiang Li, Lei Wang, Fei Fei, Yi-Feng Hou, Jian-Min Luo, Wei-Chen, Rong Zeng, Jiong Wu, Jin-Song Lu, Gen-Hong Di, Zhou-Luo Ou, Qi-Chang Xia, Zhen-Zhou Shen, Zhi-Min Shao
PROTEOMICS (2006) 6(11): 3352-3368

Serum CYFRA 21-1 level reflects hepatocellular carcinoma metastasis: study in nude mice model and clinical patients
Li Y, Tang ZY, Tian B, Ye SL, Qin LX, Xue Q, Sun RX
J Cancer Res Clin Oncol Early Edition: published 19-May-2006

Parallel Analysis of Transcript and Translation Profiles: Identification of Metastasis-Related Signal Pathways Differentially Regulated by Drug and Genetic Modifications
Haiyan Yang, Li-Rong Yu, Ming Yi, David A. Lucas, Luanne Lukes, Mindy Lancaster, King C. Chan, Haleem J. Issaq, Robert M. Stephens, Thomas P. Conrads, Timothy D. Veenstra, and Kent W. Hunter
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/19/2006

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Eukaryotic Cells And Tissues

Subcellular proteomics reveals neuromelanin granules to be a lysosome-related organelle
Tribl F, Marcus K, Meyer HE, Bringmann G, Gerlach M, Riederer P
J Neural Transm Early Edition: published 5-May-2006

Proteomic analysis of enamel matrix using a two-dimensional protein fractionation system
Yamakoshi Y, Hu JC, Zhang H, Iwata T, Yamakoshi F, Simmer JP
Eur J Oral Sci (2006) 114(Suppl 1): 266-71

Towards second-generation proteome analysis of murine enamel-forming cells
Mangum JE, Veith PD, Reynolds EC, Hubbard MJ
Eur J Oral Sci (2006) 114(Suppl 1): 259-65

Proteomic analysis of hen egg white
Guerin-Dubiard C, Pasco M, Molle D, Desert C, Croguennec T, Nau F
J Agric Food Chem (2006) 54(11): 3901-10

The Human Muscle Proteome in Aging
Cecilia Gelfi, Agnese Vigan , Marilena Ripamonti, Alessandro Pontoglio, Shajna Begum, Maria Antonietta Pellegrino, Bruno Grassi, Roberto Bottinelli, Robin Wait, and Paolo Cerretelli
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/05/2006

A comprehensive proteomic analysis of the accessory sex gland fluid from mature Holstein bulls
Moura AA, Chapman DA, Koc H, Killian GJ
Anim Reprod Sci Early Edition: published 17-May-2006

Proteomic identification of Drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble gamma-glutamyl transpeptidase
Walker MJ, Rylett CM, Keen JN, Audsley N, Sajid M, Shirras AD, Isaac RE
Proteome Sci (2006) 4(1): 9

Characterization of the Human Salivary Proteome by Capillary Isoelectric Focusing/Nanoreversed-Phase Liquid Chromatography Coupled with ESI-Tandem MS
Tong Guo, Paul A. Rudnick, Weijie Wang, Cheng S. Lee, Don L. DeVoe, and Brian M. Balgley
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/12/2006

Constitutive and inducible stress proteins dominate the proteome of the murine inner medullary collecting duct-3 (mIMCD3) cell line
Valkova N, Kultz D
Biochim Biophys Acta Early Edition: published 19-Apr-2006

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Prokaryotes

Complete Cellulase System in the Marine Bacterium Saccharophagus degradans Strain 2-40T
Taylor LE 2nd, Henrissat B, Coutinho PM, Ekborg NA, Hutcheson SW, Weiner RM
J Bacteriol (2006) 188(11): 3849-61

Comparison of extraction procedures for proteome analysis of Streptococcus pneumoniae and a basic reference map
Vesela Encheva, Saheer E. Gharbia, Robin Wait, Shajna Begum, Haroun N. Shah
PROTEOMICS (2006) 6(11): 3306-3317

Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach
Mukhopadhyay A, He Z, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, Oeller P, Redding A, Sun J, Wall J, Wei J, Yang Z, Yen HC, Zhou J, Keasling JD
J Bacteriol (2006) 188(11): 4068-78

Proteomic analysis of Neisseria lactamica and N eisseria meningitidis outer membrane vesicle vaccine antigens
Vaughan TE, Skipp PJ, O'connor CD, Hudson MJ, Vipond R, Elmore MJ, Gorringe AR
Vaccine Early Edition: published 23-Mar-2006

Proteomic mapping of the hyperthermophilic and acidophilic archaeon Sulfolobus solfataricus P2
Barry RC, Young MJ, Stedman KM, Dratz EA
Electrophoresis Early Edition: published 24-May-2006

Different Roles of EIIABMan and EIIGlc in Regulation of Energy Metabolism, Biofilm Development, and Competence in Streptococcus mutans
Abranches J, Candella MM, Wen ZT, Baker HV, Burne RA
J Bacteriol (2006) 188(11): 3748-56

Identification of Staphylococcus aureus Proteins Recognized by the Antibody-Mediated Immune Response to a Biofilm Infection
Brady RA, Leid JG, Camper AK, Costerton JW, Shirtliff ME
Infect Immun (2006) 74(6): 3415-26

Proteomic analysis of a meningococcal outer membrane vesicle vaccine prepared from the group B strain NZ98/254
Caroline Vipond, Janet Suker, Christopher Jones, Christoph Tang, Ian M. Feavers, Jun X. Wheeler
PROTEOMICS (2006) 6(11): 3400-3413

Differential Proteomic Analysis of the Bacillus anthracis Secretome: Distinct Plasmid and Chromosome CO2-Dependent Cross Talk Mechanisms Modulate Extracellular Proteolytic Activities
Chitlaru T, Gat O, Gozlan Y, Ariel N, Shafferman A
J Bacteriol (2006) 188(10): 3551-71

Pseudomonas putida KT2440 responds specifically to chlorophenoxy herbicides and their initial metabolites
Dirk Benndorf, Markus Thiersch, Norbert Loffhagen, Christfried Kunath, Hauke Harms
PROTEOMICS (2006) 6(11): 3319-3329

Proteomic Insights into Metabolic Adaptations in Alcanivorax borkumensis Induced by Alkane Utilization
Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Golyshin PN
J Bacteriol (2006) 188(11): 3763-73

Technologies for bacterial surface proteomics
Cordwell SJ
Curr Opin Microbiol Early Edition: published 4-May-2006

Outer membrane vesicles of the VA-MENGOC-BC® vaccine against serogroup B of Neisseria meningitidis: Analysis of protein components by two-dimensional gel electrophoresis and mass spectrometry
Liliam Uli, Lila Castellanos-Serra, Lazaro Betancourt, Francisco Domínguez, Ramón Barberá, Franklin Sotolongo, Gerardo Guillén, Rolando Pajón Feyt
PROTEOMICS (2006) 6(11): 3389-3399

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Pharmacology and Toxicology

dUTP Pyrophosphatase, its appearance in extracellular compartment may serve as a potential biomarker for N-methyl-N'-nitro-N-nitrosoguanidine exposure in mammalian cells
Meiping Wu, Jing Shen, Jinbiao Zhan, Yingnian Yu
PROTEOMICS (2006) 6(10): 3001-3007

Proteomics analysis of a novel compound: Cyclic RGD in breast carcinoma cell line MCF-7
Hsueh-Fen Juan, I-Hsiu Wang, Tsui-Chin Huang, Jia-Je Li, Shui-Tein Chen, Hsuan-Cheng Huang
PROTEOMICS (2006) 6(10): 2991-3000

Analysis of differential protein expression by cisplatin treatment in cervical carcinoma cells
Yim EK, Lee KH, Kim CJ, Park JS
Int J Gynecol Cancer (2006) 16(2): 690-7

New urinary EPO drug testing method using two-dimensional gel electrophoresis
Khan A, Packer N
Clin Chim Acta Early Edition: published 17-May-2006

Proteomic analysis of rat liver phosphoproteins following treatment with protein kinase inhibitor H89 (N-(2-[p- bromocinnamylamino-]ethyl)-5-isoquinoline-sulfonamide)
Davis M, Hinerfeld D, Joseph S, Hui YH, Leszyk J, Huang NH, Rutherford-Bethard J, Tam SW
J Pharmacol Exp Ther Early Edition: published 10-May-2006

Evaluation of Toxicological Monitoring Markers Using Proteomic Analysis in Rats Exposed to Formaldehyde
Hosub Im, Eunha Oh, Joohee Mun, Jin-Young Khim, Eunil Lee, Hyung-Sik Kang, Eunmi Kim, Hyunsuk Kim, Nam-Hee Won, # Young-Hwan Kim, Woon-Won Jung, and Donggeun Sul
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/05/2006

Integrated Metabonomic Analysis of Bromobenzene-Induced Hepatotoxicity: Novel Induction of 5-Oxoprolinosis
Nigel J. Waters, Catherine J. Waterfield, R. Duncan Farrant, Elaine Holmes, and Jeremy K. Nicholson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/12/2006

Alterations in the rat serum proteome during liver injury from acetaminophen exposure
Merrick BA, Bruno ME, Madenspacher JH, Wetmore BA, Foley J, Pieper R, Zhao M, Makusky AJ, McGrath AM, Zhou JX, Taylor J, Tomer KB
J Pharmacol Exp Ther Early Edition: published 10-May-2006

Proteomics analyses of specific protein oxidation and protein expression in aged rat brain and its modulation by L-acetylcarnitine: insights into the mechanisms of action of this proposed therapeutic agent for CNS disorders associated with oxidative stress
Poon HF, Calabrese V, Calvani M, Butterfield DA
Antioxid Redox Signal (2006) 8(3-4): 381-94

Acute toxicity profile of cadmium revealed by proteomics in brain tissue of Paralichthys olivaceus: Potential role of transferrin in cadmium toxicity
Zhu JY, Huang HQ, Bao XD, Lin QM, Cai Z
Aquat Toxicol Early Edition: published 26-Apr-2006

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Protein Array

Efficient and highly reproducible capillary electrophoresis-mass spectrometry of peptides using Polybrene-poly(vinyl sulfonate)-coated capillaries
Jonatan R. Catai, Javier Sastre Torańo, Gerhardus J. de Jong, Govert W. Somsen
ELECTROPHORESIS (2006) 27(11): 2091-2099

A simple and rapid protein array based method for the simultaneous detection of biowarfare agents
Birgit Huelseweh, Ralf Ehricht, Hans-Juergen Marschall
PROTEOMICS (2006) 6(10): 2972-2981

ProMAT: protein microarray analysis tool
Amanda M. White, Don S. Daly, Susan M. Varnum, Kevin K. Anderson, Nikki Bollinger, and Richard C. Zangar
Bioinformatics (2006) 22(10): 1278-1279

Toward high sequence coverage of proteins in human breast cancer cells using on-line monolith-based HPLC-ESI-TOF MS compared to CE MS
Chul Yoo, Manoj Pal, Fred R. Miller, Timothy J. Barder, Christian Huber, David M. Lubman
ELECTROPHORESIS (2006) 27(11): 2126-2138

Convergence of the proteomic pattern in cancer
Ute Muller, Gunther Ernst, Christian Melle, Reinhard Guthke, and Ferdinand von Eggeling
Bioinformatics (2006) 22(11): 1293-1296

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays
Rongcai Jiang, Cristian Mircean, Ilya Shmulevich, David Cogdell, Yu Jia, Ioan Tabus, Kenneth Aldape, Raymond Sawaya, Janet M. Bruner, Gregory N. Fuller, Wei Zhang
PROTEOMICS (2006) 6(10): 2964-2971

ProteinChip technology is a useful method in the pathogenesis and diagnosis of endometriosis: a preliminary study
Kyama CM, T'jampens D, Mihalyi A, Simsa P, Debrock S, Waelkens E, Landuyt B, Meuleman C, Fulop V, Mwenda JM, D'Hooghe TM
Fertil Steril Early Edition: published 20-May-2006

Targeted proteomics in biomarker validation: Detection and quantification of proteins using a multi-dimensional peptide separation strategy
Dorian Immler, Simone Greven, Peter Reinemer
PROTEOMICS (2006) 6(10): 2947-2958

Proteome chips for whole-organism assays
Kung LA, Snyder M
Nat Rev Mol Cell Biol Early Edition: published 24-May-2006

Comprehensive two-dimensional separation in coupling of reversed-phase chromatography with capillary isoelectric focusing followed by MALDI-MS identification using on-target digestion for intact protein analysis
Wenjia Yu, Yan Li, Chunhui Deng, Xiangmin Zhang
ELECTROPHORESIS (2006) 27(11): 2100-2110

Development of a ?reverse capture? autoantibody microarray for studies of antigen-autoantibody profiling
Shuzhen Qin, Weiliang Qiu, Joshua R. Ehrlich, Angeline S. Ferdinand, Jerome P. Richie, Michael P. O'Leary, Mei-Ling Ting Lee, Brian C.-S. Liu
PROTEOMICS (2006) 6(10): 3199-3209

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Protein Characterization / PTMs

Comprehensive glyco-proteomic analysis of human ?1-antitrypsin and its charge isoforms
Daniel Kolarich, Alfred Weber, Peter L. Turecek, Hans-Peter Schwarz, Friedrich Altmann
PROTEOMICS (2006) 6(11): 3369-3380

Protein Arginylation in Rat Brain Cytosol: A Proteomic Analysis
Decca MB, Bosc C, Luche S, Brugiere S, Job D, Rabilloud T, Garin J, Hallak ME
Neurochem Res Early Edition: published 3-May-2006

Mass spectrometric profiling of O-linked glycans released directly from glycoproteins in gels using in-gel reductive ?-elimination
Adrian M. Taylor, Otto Holst, Jane Thomas-Oates
PROTEOMICS (2006) 6(10): 2936-2946

Identification of N-Linked Glycoproteins in Human Saliva by Glycoprotein Capture and Mass Spectrometry
Prasanna Ramachandran, Pinmannee Boontheung, Yongming Xie, Melissa Sondej, David T. Wong, and Joseph A. Loo
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/12/2006

Mass defect labeling of cysteine for improving Peptide assignment in shotgun proteomic analyses
Hernandez H, Niehauser S, Boltz SA, Gawandi V, Phillips RS, Amster IJ
Anal Chem (2006) 78(10): 3417-23

Automatic Determination of O-Glycan Structure from Fragmentation Spectra
David Goldberg, Marshall Bern, Bensheng Li, and Carlito B. Lebrilla
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/19/2006

Solid-phase chemical tools for glycobiology
Larsen K, Thygesen MB, Guillaumie F, Willats WG, Jensen KJ
Carbohydr Res Early Edition: published 19-May-2006

Protein thiol oxidation in health and disease: Techniques for measuring disulfides and related modifications in complex protein mixtures
Eaton P
Free Radic Biol Med (2006) 40(11): 1889-1899

Interpreting the protein language using proteomics
Jensen ON
Nat Rev Mol Cell Biol (2006) 7(6): 391-403

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Protein-protein interaction

Proteomic identification of glucocorticoid receptor interacting proteins
Erik Hedman, Christina Widén, Abolfazl Asadi, Ingrid Dinnetz, Wolfgang P. Schröder, Jan-Ĺke Gustafsson, Ann-Charlotte Wikström
PROTEOMICS (2006) 6(10): 3114-3126

Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations
Xiaomei Wu, Lei Zhu, Jie Guo, Da-Yong Zhang, and Kui Lin
Nucl. Acids Res. (2006) 34(7): 2137-2150

Protein interactions probed with mass spectrometry
Kaveti S, Engen JR
Methods Mol Biol (2006) 316: 179-97

Analysis of protein-protein interactions with a multi-capillary electrophoresis instrument
Kiyohito Shimura, Takuma Waki, Masaki Okada, Toshifusa Toda, Izumi Kimoto, Ken-ichi Kasai
ELECTROPHORESIS (2006) 27(10): 1886-1894

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Quantitation

Time-based analysis of silver-stained proteins in acrylamide gels
Bertram Becher, Ann-Kathrin Knöfel, Jörg Peters
ELECTROPHORESIS (2006) 27(10): 1867-1873

Quantitative Characterizations of Proteome: Dependence on the Number of Proteins Considered
Milan Randi
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/26/2006

Quantitation in two-dimensional fluorescence difference gel electrophoresis: Effect of protein fixation
Nilesh Tannu, Scott E. Hemby
ELECTROPHORESIS (2006) 27(10): 2011-2015

Mass spectrometric quantitation of C-reactive protein using labeled tryptic peptides
Aguiar M, Masse R, Gibbs BF
Anal Biochem Early Edition: published 21-Apr-2006

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Review

Proteomics in renal transplantation: opportunities and challenges
Schaub S, Wilkins JA, Nickerson P
Clin Transpl (2004) : 253-60.

Proteomics and heart disease: identifying biomarkers of clinical utility
Qin Fu, Jennifer E Van Eyk
Expert Review of Proteomics (2006) 3(2): 237-249

The Application of Proteomics for the Early Detection of Lung Cancer
Roh, Mee S
Current Proteomics (2006) 3(1): 23-31

Proteomic analysis in cancer research: potential application in clinical use
Garcia-Foncillas J, Bandres E, Zarate R, Remirez N
Clin Transl Oncol (2006) 8(4): 250-61

Yeast-based functional genomics and proteomics technologies: the first 15 years and beyond
Suter B, Auerbach D, Stagljar I
Biotechniques (2006) 40(5): 625-44

Separation Media in Affinity Chromatography of Proteins - A Critical Review
Varilova, Tereza; Madera, Milan; Pacakova, Vera; Stulik, Karel
Current Proteomics (2006) 3(1): 55-79

Biomarkers for amyotrophic lateral sclerosis
Bowser R, Cudkowicz M, Kaddurah-Daouk R
Expert Rev Mol Diagn (2006) 6(3): 387-398

The Application of DIGE-Based Proteomics to Renal Physiology
Hoorn EJ, Hoffert JD, Knepper MA
Nephron Physiol (2006) 104(1): p61-p72

Type 1 diabetes: entering the proteomic era
Wannes DHertog, Chantal Mathieu, Lut Overbergh
Expert Review of Proteomics (2006) 3(2): 223-236

Chemistry in Proteomics: An Interplay between Classical Methods in Chemical Modification of Proteins and Mass Spectrometry at the Cutting Edge
Nakazawa, Takashi
Current Proteomics (2006) 3(1): 33-54

Proteomics technology and therapeutics
Hong ML, Jiang N, Gopinath S, Chew FT
Clin Exp Pharmacol Physiol (2006) 33(5-6): 563-8

Role and challenges of proteomics in pharma and biotech: technical, scientific and commercial perspective
M Walid Qoronfleh
Expert Review of Proteomics (2006) 3(2): 179-195

Protein primary structure using orthogonal fragmentation techniques in Fourier transform mass spectrometry
Roman Zubarev
Expert Review of Proteomics (2006) 3(2): 251-261

Three Dimensional Structures of Proteins and Protein Complexes from Chemical Cross-Linking and Mass Spectrometry: A Biochemical and Computational Overview
Chakravarti, Bulbul; Lewis, Steven J.; Chakravarti, Deb N.; Raval, Alpan
Current Proteomics (2006) 3(1): 1-21

Putting proteomics on target: activity-based profiling of ubiquitin and ubiquitin-like processing enzymes
Benedikt M Kessler
Expert Review of Proteomics (2006) 3(2): 213-221

Proteomics and Genomics of Microgravity
Nichols HL, Zhang N, Wen X
Physiol Genomics Early Edition: published 16-May-2006

Mass Spectrometry and Protein Analysis
Bruno Domon and Ruedi Aebersold
Science (2006) 312(5771): 212-217

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Methodology

Specific Capture of Mammalian Cells by Cell Surface Receptor Binding to Ligand Immobilized on Gold Thin Films
Dora Peelen, Voula Kodoyianni, Jieun Lee, Ting Zheng, Michael R. Shortreed, and Lloyd M. Smith
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/26/2006

Thermostable trypsin conjugates for high-throughput proteomics: synthesis and performance evaluation
Marek ?ebela, Tat'ána ?tosová, Jan Havli?, Natalie Wielsch, Henrik Thomas, Zbyn?k Zdráhal, Andrej Shevchenko
PROTEOMICS (2006) 6(10): 2959-2963

Four Stage Liquid Chromatographic Selection of Methionyl Peptides for Peptide-Centric Proteome Analysis: The Proteome of Human Multipotent Adult Progenitor Cells
Kris Gevaert, Jef Pinxteren, Hans Demol, Koen Hugelier, An Staes, Jozef Van Damme, Lennart Martens, and Joël Vandekerckhove
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/05/2006

High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell
Hughes SR, Riedmuller SB, Mertens JA, Li XL, Bischoff KM, Qureshi N, Cotta MA, Farrelly PJ
Proteome Sci (2006) 4(1): 10

Fractionation of Serum Components Using Nanoporous Substrates
Geho D, Ming-Cheng Cheng M, Killian K, Lowenthal M, Ross S, Frogale K, Nijdam J, Lahar N, Johann D, Herrmann P, Whiteley G, Ferrari M, Petricoin E, Liotta L
Bioconjug Chem (2006) 17(3): 654-661

Competition between bound and free peptides in an ELISA-based procedure that assays peptides derived from protein digests
Braitbard O, Glickstein H, Bishara-Shieban J, Pace U, Stein W
Proteome Sci (2006) 4(1): 12

Peak capacity optimization of Peptide separations in reversed-phase gradient elution chromatography: fixed column format
Wang X, Stoll DR, Schellinger AP, Carr PW
Anal Chem (2006) 78(10): 3406-16

Depletion of abundant proteins from non-human primate serum for biomarker studies
Willard M. Freeman, Melinda E. Lull, Michael T. Guilford, Kent E. Vrana
PROTEOMICS (2006) 6(10): 3109-3113

Efficient and non-denaturing membrane solubilization combined with enrichment of membrane protein complexes by detergent/polymer aqueous two-phase partitioning for proteome analysis
Everberg H, Leiding T, Schioth A, Tjerneld F, Gustavsson N
J Chromatogr A Early Edition: published 5-May-2006

A novel Bicine running buffer system for doubled sodium dodecyl sulfate - polyacrylamide gel electrophoresis of membrane proteins
Williams TI, Combs JC, Thakur AP, Strobel HJ, Lynn BC
Electrophoresis Early Edition: published 22-May-2006

Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column
Joachim Brand, Tobias Haslberger, Werner Zolg, Gabriele Pestlin, Stefan Palme
PROTEOMICS (2006) 6(11): 3236-3242

Enhancement of the StreptoTag method for isolation of endogenously expressed proteins with complex RNA binding targets
John A. Dangerfield, Nikolai Windbichler, Brian Salmons, Walter H. Günzburg, Renée Schröder
ELECTROPHORESIS (2006) 27(10): 1874-1877

Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid
Guerreiro N, Gomez-Mancilla B, Charmont S
Proteome Sci (2006) 4: 7

Isolation of Escherichia coli inner membranes by metal affinity two-phase partitioning
Everberg H, Clough J, Henderson P, Jergil B, Tjerneld F, Ramirez IB
J Chromatogr A Early Edition: published 26-Apr-2006

Isolation and Characterization of Glycosylphosphatidylinositol-Anchored Peptides by Hydrophilic Interaction Chromatography and MALDI Tandem Mass Spectrometry
Omaetxebarria MJ, Hagglund P, Elortza F, Hooper NM, Arizmendi JM, Jensen ON
Anal Chem (2006) 78(10): 3335-3341

Selective binding and enrichment for low-molecular weight biomarker molecules in human plasma after exposure to nanoporous silica particles
Rosa Terracciano, Marco Gaspari, Flaviano Testa, Luigi Pasqua, Pierosandro Tagliaferri, Mark Ming-Cheng Cheng, A. Jasper Nijdam, Emanuel F. Petricoin, Lance A. Liotta, Giovanni Cuda, Mauro Ferrari, Salvatore Venuta
PROTEOMICS (2006) 6(11): 3243-3250

Optimising ovine cerebrospinal fluid preparation for two-dimensional gel electrophoresis
Ruo Li Chen, Elizabeth A. Sage, Michael J. Dunn, Robin Wait, Jane E. Preston
PROTEOMICS (2006) 6(10): 3170-3175

Systematical evaluation of the effects of sample collection procedures on low-molecular-weight serum/plasma proteome profiling
Sen-Yung Hsieh, Ren-Kung Chen, Yi-Hsin Pan, Hai-Lun Lee
PROTEOMICS (2006) 6(10): 3189-3198

Optimizing UV laser focus profiles for improved MALDI performance
Holle A, Haase A, Kayser M, Hohndorf J
J Mass Spectrom Early Edition: published 22-May-2006

Development of an on-line immobilized-enzyme reversed-phase HPLC method for protein digestion and peptide separation
Lim LW, Tomatsu M, Takeuchi T
Anal Bioanal Chem Early Edition: published 25-May-2006

Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
Takamoto K, Chance MR
Annu Rev Biophys Biomol Struct (2006) 35: 251-76

2-D native-PAGE/SDS-PAGE visualization of an oligomer's subunits: Application to the analysis of IgG
Leticia Gonzalez, Juan J. Bustamante, Edwin J. Barea-Rodriguez, Andrew O. Martinez, Luis S. Haro
ELECTROPHORESIS (2006) 27(10): 2016-2023

Resolution and characterisation of multiple isoforms of bovine ?-casein by 2-DE following a reversible cysteine-tagging enrichment strategy
John W. Holland, Hilton C. Deeth, Paul F. Alewood
PROTEOMICS (2006) 6(10): 3087-3095

Progress in capillary electrophoresis coupled to matrix-assisted laser desorption/ionization - time of flight mass spectrometry
Christian W. Huck, Rania Bakry, Lukas A. Huber, Günther K. Bonn
ELECTROPHORESIS (2006) 27(11): 2063-2074

N-terminal H(3)/D(3)-acetylation for improved high-throughput peptide sequencing by matrix-assisted laser desorption/ionization mass spectrometry with a time-of-flight/time-of-flight analyzer
Noga MJ, Asperger A, Silberring J
Rapid Commun Mass Spectrom (2006) 20(12): 1823-1827

High Recovery HPLC Separation of Lipid Rafts for Membrane Proteome Analysis
James Martosella, Nina Zolotarjova, Hongbin Liu, Susanne C. Moyer, Patrick D. Perkins, and Barry E. Boyes
JOURNAL OF PROTEOME RESEARCH Early Edition: published 05/19/2006

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Books

A Review of: "Surrogate Tissue Analysis: Genomic, Proteomic and Metabolomic Approaches"
Aaron S
Int J Toxicol (2006) 25(3): 229-30

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Meeting

Meeting report: The Plasma Proteome: High Abundance versus Low Abundance
Hui Zhang
Expert Review of Proteomics (2006) 3(2): 175-178

Meetings Diary: Proteomics 11/2006
PROTEOMICS (2006) 6(11): 3477-3479

Editorial: Report from the 2nd Annual US HUPO Meeting on the HUPO Human Plasma Proteome Project
Gilbert S Omenn
Expert Review of Proteomics (2006) 3(2): 165-168

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Other

Variation among species in proteomic sulphur content is related to environmental conditions
Bragg JG, Thomas D, Baudouin-Cornu P
Proc Biol Sci (2006) 273(1591): 1293-300

Correspondence regarding Schwend and Gustafsson, "False positives in MALDI-TOF detection of ERbeta in mitochondria"
Yang SH, Prokai L, Simpkins JW
Biochem Biophys Res Commun Early Edition: published 8-May-2006

A set of amino acids found to occur more frequently in human and fly than in plant and yeast proteomes consists of non-essential amino acids
Prosdocimi F, Mudado MA, Ortega JM
Comput Biol Med Early Edition: published 27-Apr-2006

Proteomics: moving beyond the human genome
Formanek R Jr
FDA Consum (2005) 39(6): 18-27

Publishing proteomic data
Latterich M
Proteome Sci (2006) 4(1): 8

News in Brief
Expert Review of Proteomics (2006) 3(2): 169-174

Enamel proteomics and protein interactions
Hubbard M
Eur J Oral Sci (2006) 114(Suppl 1): 285-6

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