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SPS' Digest

Issue 27, 2-Feb-2006

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Quick jumps to articles in: Bioinformatics (26) / Biological applications (37) / Biomedical and clinical applications (43) / Eukaryotic Cells And Tissues (19) / Prokaryotes (12) / Pharmacology and Toxicology (9) / Protein Array (4) / Protein Characterization - PTMs (13) / Protein-protein interaction (4) / Quantitation (9) / Review (21) / Methodology (21) / Books (1) / Meeting (2) / Other (3) /

In this issue, 222 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 (26) / Biological applications (37) / Biomedical and clinical applications (43) / Eukaryotic Cells And Tissues (19) / Prokaryotes (12) / Pharmacology and Toxicology (9) / Protein Array (4) / Protein Characterization - PTMs (13) / Protein-protein interaction (4) / Quantitation (9) / Review (21) / Methodology (21) / Books (1) / Meeting (2) / Other (3) /

Bioinformatics

Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments
Adam Rauch, Matthew Bellew, Jimmy Eng, Matthew Fitzgibbon, Ted Holzman, Peter Hussey, Mark Igra, Brendan Maclean, Chen Wei Lin, Andrea Detter, Ruihua Fang, Vitor Faca, Phil Gafken, Heidi Zhang, Jeffrey Whitaker, David States, Sam Hanash, Amanda Paulovich, and Martin W. McIntosh
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 112-121

PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns
McLaughlin T, Siepen JA, Selley J, Lynch JA, Lau KW, Yin H, Gaskell SJ, Hubbard SJ
Nucl Acids Res (2006) 34(Suppl 1): D649-54

TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi
Aguero F, Zheng W, Weatherly DB, Mendes P, Kissinger JC
Nucl Acids Res (2006) 34(Suppl 1): D428-31

Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes
Koning LJ, Kasper PT, Back JW, Nessen MA, Vanrobaeys F, Van Beeumen J, Gherardi E, Koster CG, Jong L
FEBS J (2006) 273(2): 281-91

LOCATE: a mouse protein subcellular localization database
Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD
Nucl Acids Res (2006) 34(Suppl 1): D213-7

The Universal Protein Resource (UniProt): an expanding universe of protein information
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'donovan C, Redaschi N, Suzek B
Nucl Acids Res (2006) 34(Suppl 1): D187-91

Does the proteome encode organellar pH?
Brett CL, Donowitz M, Rao R
FEBS Lett Early Edition: published 12-Jan-2006

Self-regulating gene: An exact solution
Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic JN, Wolynes PG
Phys Rev E Stat Nonlin Soft Matter Phys (2005) 72(5 Pt 1): 051907

The UCSC Genome Browser Database: update 2006
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ
Nucl Acids Res (2006) 34(Suppl 1): D590-8

MitoP2: the mitochondrial proteome database--now including mouse data
Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger T
Nucl Acids Res (2006) 34(Suppl 1): D705-11

Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis
Pall F Jonsson , Tamara Cavanna , Daniel Zicha and Paul A Bates
BMC Bioinformatics (2006) 7(1): 2

Counting the Zinc-Proteins Encoded in the Human Genome
Claudia Andreini , Lucia Banci , Ivano Bertini , and Antonio Rosato
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 196-201

Comparison of Software Tools to Improve the Detection of Carcinogen Induced Changes in the Rat Liver Proteome by Analyzing SELDI-TOF-MS Spectra
Suse Beyer, Yvonne Walter, Juergen Hellmann, Peter-Juergen Kramer, Annette Kopp-Schneider, Michaela Kroeger, and Carina Ittrich
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Human protein reference database--2006 update
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, Pandey A
Nucl Acids Res (2006) 34(Suppl 1): D411-4

Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis
Marengo E, Robotti E, Bobba M, Liparota MC, Rustichelli C, Zamo A, Chilosi M, Righetti PG
Electrophoresis Early Edition: published 21-Dec-2005

LMPD: LIPID MAPS proteome database
Cotter D, Maer A, Guda C, Saunders B, Subramaniam S
Nucl Acids Res (2006) 34(Suppl 1): D507-10

The PeptideAtlas project
Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R
Nucl Acids Res (2006) 34(Suppl 1): D655-8

PRIDE: a public repository of protein and peptide identifications for the proteomics community
Jones P, Cote RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R
Nucl Acids Res (2006) 34(Suppl 1): D659-63

WholePathwayScope: A comprehensive pathway-based analysis tool for high-throughput data
Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM
BMC Bioinformatics (2006) 7(1): 30

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice
Li F, Li M, Xiao Z, Zhang P, Li J, Chen Z
BMC Bioinformatics (2006) 7(1): 13

pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M
Nucl Acids Res (2006) 34(Suppl 1): D527-34

Predicting Protein-Protein Interactions from Sequences in a Hybridization Space
Kuo-Chen Chou and Yu-Dong Cai
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/23/2005

A biological approach to computational models of proteomic networks
Janes KA, Lauffenburger DA
Curr Opin Chem Biol Early Edition: published 4-Jan-2006

Bioinformatic methods to exploit mass spectrometric data for proteomic applications
Chalkley RJ, Hansen KC, Baldwin MA
Methods Enzymol (2005) 402: 289-312

dbPTM: an information repository of protein post-translational modification
Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, and Tzu-Hao Wang
Nucl. Acids Res. (2006) 34(Suppl 1): D622-D627

NOPdb: Nucleolar Proteome Database
Leung AK, Trinkle-Mulcahy L, Lam YW, Andersen JS, Mann M, Lamond AI
Nucl Acids Res (2006) 34(Suppl 1): D218-20

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Biological applications

Characterization of Local Polarity and Hydrophobic Binding Sites of -Lactoglobulin by Using N-Terminal Specific Fluorescence Labeling
Su-Ying Dong, Zhen-Wen Zhao, and Hui-Min Ma
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 26-31

Strain-dependent expression of signaling proteins in the mouse hippocampus
Pollak DD, John J, Schneider A, Hoeger H, Lubec G
Neuroscience Early Edition: published 14-Dec-2005

Proteomic Analysis of Rice Leaf Sheath during Drought Stress
Ghulam Muhammad Ali and Setsuko Komatsu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Organelle proteomics reveals cargo maturation mechanisms associated with golgi-like encystation vesicles in the early-diverged protozoan giardia lamblia
Stefanic S, Palm D, Svard SG, Hehl AB
J Biol Chem Early Edition: published 3-Jan-2006

Cloning and characterization of a third isoform of corazonin in the honey bee Apis mellifera
Verleyen P, Baggerman G, Mertens I, Vandersmissen T, Huybrechts J, Lommel AV, Loof AD, Schoofs L
Peptides Early Edition: published 6-Jan-2006

Perspectives in Proteomics: Structural Folds of a Predicted and an Experimentally Determined Cation Channel
Mager, Peter P.; Weber, Anje; Walter, Horst; Wirkner, Kerstin; Illes, Peter
Current Proteomics (2005) 2(4): 319-324

Proteomics of boar seminal plasma current studies and possibility of their application in biotechnology of animal reproduction
Strzezek J, Wysocki P, Kordan W, Kuklinska M
Reprod Biol (2005) 5(3): 279-90

hnRNP K: An HDM2 Target and Transcriptional Coactivator of p53 in Response to DNA Damage
Moumen A, Masterson P, O'connor MJ, Jackson SP
Cell (2005) 123(6): 1065-78

Peptidomics of Caenorhabditis elegans: in search of neuropeptides
Husson SJ, Clynen E, Baggerman G, De Loof A, Schoofs L
Commun Agric Appl Biol Sci (2005) 70(2): 153-6

Isolation of a latent polyphenol oxidase from loquat fruit (Eriobotrya japonica Lindl.): Kinetic characterization and comparison with the active form
Selles-Marchart S, Casado-Vela J, Bru-Martinez R
Arch Biochem Biophys Early Edition: published 27-Dec-2005

A Proteomics Approach to Identify Long-Term Molecular Changes in Rat Medial Prefrontal Cortex Resulting from Sucrose Self-Administration
Michel C. Van den Oever, Sabine Spijker, Ka Wan Li, Connie R. Jiménez, Eisuke Koya, Roel C. Van der Schors, Yvonne Gouwenberg, Rob Binnekade, Taco J. De Vries, Anton N. M. Schoffelmeer, and August B. Smit
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 147-154

Proteomic Analysis of Mice Hippocampus in Simulated Microgravity Environment
Poonam Sarkar, Shubhashish Sarkar, Vani Ramesh, Barbara E. Hayes, Renard L. Thomas, Bobby L. Wilson, Helen Kim, Stephen Barnes, Anil Kulkarni, Neal Pellis, and Govindarajan T. Ramesh
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/27/2006

The GYF domain
Kofler MM, Freund C
FEBS J (2006) 273(2): 245-56

Proteome analysis: a successful approach for functional research in recalcitrant non-model crops
Carpentier S, Witters E, Laukens K, Panis B, Swennen R
Commun Agric Appl Biol Sci (2005) 70(2): 3-4

A proteomic approach to the identification and characterisation of protein composition in wheat germ
Mak Y, Skylas DJ, Willows R, Connolly A, Cordwell SJ, Wrigley CW, Sharp PJ, Copeland L
Funct Integr Genomics Early Edition: published 12-Jan-2006

Proteomic Analysis of the Yeast Mitochondrial Outer Membrane Reveals Accumulation of a Subclass of Preproteins
Zahedi RP, Sickmann A, Boehm AM, Winkler C, Zufall N, Schonfisch B, Guiard B, Pfanner N, Meisinger C
Mol Biol Cell Early Edition: published 11-Jan-2006

Uncoupling protein 1 affects the yeast mitoproteome and oxygen free radical production
Douette P, Gerkens P, Navet R, Leprince P, De Pauw E, Sluse FE
Free Radic Biol Med (2006) 40(2): 303-15

Integrating Cytomics and Proteomics
Tytus Bernas, Gerald Gregori, Eli K. Asem, and J. Paul Robinson
Mol Cell Proteomics (2006) 5(1): 2-13

Proteomics of Bovine Myelin Sheath: Characterization of a Truncated Form of P0 by MALDI-TOF/TOF Mass Spectrometry
Qualtieri A, Urso E, Le Pera M, Scornaienchi M, Quattrone A, Di Donna L, Napoli A, Sindona G
J Am Soc Mass Spectrom Early Edition: published 7-Jan-2006

Quantitation of adenovirus type 5 empty capsids
Takahashi E, Cohen SL, Tsai PK, Sweeney JA
Anal Biochem Early Edition: published 28-Nov-2005

Anion channels transport ATP into the Golgi lumen
Thompson RJ, Akana HC, Finnigan C, Howell KE, Caldwell JH
Am J Physiol Cell Physiol (2006) 290(2): C499-514

Identification of peptides in antimicrobial fractions of cheese extracts by electrospray ionization ion trap mass spectrometry coupled to a two-dimensional liquid chromatographic separation
Losito I, Carbonara T, De Bari MD, Gobbetti M, Palmisano F, Rizzello CG, Zambonin PG
Rapid Commun Mass Spectrom (2006) 20(3): 447-455

Sex-based individual variation of snake venom proteome among eighteen Bothrops jararaca siblings
Menezes MC, Furtado MF, Travaglia-Cardoso SR, Camargo AC, Serrano SM
Toxicon Early Edition: published 19-Dec-2005

Identification of a New Spore Wall Protein from Encephalitozoon cuniculi
Xu Y, Takvorian P, Cali A, Wang F, Zhang H, Orr G, Weiss LM
Infect Immun (2006) 74(1): 239-47

Alterations in syncytiotrophoblast cytokine expression following treatment with lipopolysaccharide
Ma Y, Mor G, Abrahams VM, Buhimschi IA, Buhimschi CS, Guller S
Am J Reprod Immunol (2006) 55(1): 12-8

Cryopreservation and abiotic stress tolerance in potato: a proteomic approach
Criel B, Panta A, Carpentier S, Renaut J, Swennen R, Panis B, Hausman JF
Commun Agric Appl Biol Sci (2005) 70(2): 83-6

Mycoplasma gallisepticum hemagglutinin V1hA, pyruvate dehydrogenase PdhA, lactate dehydrogenase, and elongation factor Tu share epitopes with Mycoplasma imitans homologues
Lavric M, Bencina D, Narat M
Avian Dis (2005) 49(4): 507-13

The Oligomeric Stromal Proteome of Arabidopsis thaliana Chloroplasts
Jean-Benoit Peltier, Yang Cai, Qi Sun, Vladimir Zabrouskov, Lisa Giacomelli, Andrea Rudella, A. Jimmy Ytterberg, Heidi Rutschow, and Klaas J. van Wijk
Mol Cell Proteomics (2006) 5(1): 114-133

Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular Dynamics and Molecular Field Analysis
Tingjun Hou, William McLaughlin, Benzhuo Lu, Ken Chen, and Wei Wang
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 32-43

Identification of Differentially Expressed Proteins during Larval Molting of Helicoverpa armigera
Xiao-Fan Zhao, Hong-Juan He, Du-Juan Dong, and Jin-Xing Wang
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 164-169

Proteomic analysis of individual human embryos to identify novel biomarkers of development and viability
Katz-Jaffe MG, Gardner DK, Schoolcraft WB
Fertil Steril (2006) 85(1): 101-7

Flightless I Homolog Negatively Modulates the TLR Pathway
Wang T, Chuang TH, Ronni T, Gu S, Du YC, Cai H, Sun HQ, Yin HL, Chen X
J Immunol (2006) 176(3): 1355-62

Rice Proteomics: A Step Toward Functional Analysis of Stress Responses
Komatsu, Setsuko
Current Proteomics (2005) 2(4): 325-333

Responses to Nickel in the Proteome of the Hyperaccumulator Plant Alyssum lesbiacum
Ingle RA, Smith JA, Sweetlove LJ
Biometals (2005) 18(6): 627-41

Comparative Profiling of the Mammalian Mitochondrial Proteome: Multiple Aconitase-2 Isoforms Including N-formylkynurenine Modifications as Part of a Protein Biomarker Signature for Reactive Oxidative Species
Christian Hunzinger, Wojciech Wozny, Gerhard P. Schwall, Slobodan Poznanovi , Werner Stegmann, Helmut Zengerling, Rainer Schoepf, Karlfried Groebe, Michael A. Cahill, Heinz D. Osiewacz, Nora Jägemann, Monika Bloch, Norbert A. Dencher, Frank Krause, and André Schrattenholz
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/27/2006

Proteomic analysis of microglial contribution to mouse strain-dependent dopaminergic neurotoxicity
McLaughlin P, Zhou Y, Ma T, Liu J, Zhang W, Hong JS, Kovacs M, Zhang J
Glia Early Edition: published 17-Jan-2006

Screening of entomopathogenic Metarhizium anisopliae isolates and proteomic analysis of secretion synthesized in response to cowpea weevil (Callosobruchus maculatus) exoskeleton
Murad AM, Laumann RA, Lima TD, Sarmento RB, Noronha EF, Rocha TL, Valadares-Inglis MC, Franco OL
Comp Biochem Physiol C Toxicol Pharmacol Early Edition: published 6-Jan-2006

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Biomedical and clinical applications

Decoding Serological Response to Candida Cell Wall Immunome into Novel Diagnostic, Prognostic, and Therapeutic Candidates for Systemic Candidiasis by Proteomic and Bioinformatic Analyses
Aida Pitarch, Antonio Jimenez, Cesar Nombela, and Concha Gil
Mol Cell Proteomics (2006) 5(1): 79-96

Selenium binding protein 1 in ovarian cancer
Huang KC, Park DC, Ng SK, Lee JY, Ni X, Ng WC, Bandera CA, Welch WR, Berkowitz RS, Mok SC, Ng SW
Int J Cancer Early Edition: published 27-Dec-2005

Novel peptides secreted from human neuroblastoma: useful clinical tools?
Sandoval JA, Hoelz DJ, Woodruff HA, Powell RL, Jay CL, Grosfeld JL, Hickeyd RJ, Malkas LH
J Pediatr Surg (2006) 41(1): 245-51

Identification of disease markers in human cerebrospinal fluid using lipidomic and proteomic methods
Fonteh AN, Harrington RJ, Huhmer AF, Biringer RG, Riggins JN, Harrington MG
Dis Markers (2006) 22(1-2): 247-72

Genomic and proteomic approaches highlight phagocytosis of living and apoptotic human cells by the parasite Entamoeba histolytica
Marion S, Guillen N
Int J Parasitol Early Edition: published 28-Nov-2005

Proteomics of Human Pulmonary Surfactant Proteins
He, Chang
Current Proteomics (2005) 2(4): 303-318

Preliminary study on proteomics of gastric carcinoma and its clinical significance
Qian HG, Shen J, Ma H, Ma HC, Su YH, Hao CY, Xing BC, Huang XF, Shou CC
World J Gastroenterol (2005) 11(40): 6249-53

Identification of putative oncogenes in lung adenocarcinoma by a comprehensive functional genomic approach
Li R, Wang H, Bekele BN, Yin Z, Caraway NP, Katz RL, Stass SA, Jiang F
Oncogene Early Edition: published 12-Dec-2005

Proteomic analysis of the CSF in unmedicated patients with major depressive disorder reveals alterations in suicide attempters
Brunner J, Bronisch T, Uhr M, Ising M, Binder E, Holsboer F, Turck CW
Eur Arch Psychiatry Clin Neurosci (2005) 255(6): 438-440

Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome
Rodriguez-Ortega MJ, Norais N, Bensi G, Liberatori S, Capo S, Mora M, Scarselli M, Doro F, Ferrari G, Garaguso I, Maggi T, Neumann A, Covre A, Telford JL, Grandi G
Nat Biotechnol Early Edition: published 15-Jan-2006

Comparison of the Protein Profile of Established and Regressed Hypertension-Induced Left Ventricular Hypertrophy
Julio Gallego-Delgado, Alberto Lazaro, Julio I. Osende, Maria G. Barderas, Maria C. Duran, Fernando Vivanco, # and Jesus Egido
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/30/2005

Analysis of Glioma Cell Platinum Response by Metacomparison of Two-dimensional Chromatographic Proteome Profiles
Christine Billecke, Imran Malik, Ashley Movsisyan, Syed Sulghani, Azita Sharif, Tom Mikkelsen, Nicholas P. Farrell, and Oliver Bogler
Mol Cell Proteomics (2006) 5(1): 35-42

A proteomic approach to assess intraneuronal inclusions associated with neurodegenerative disorders
Kawaja MD
Curr Opin Mol Ther (2005) 7(6): 565-8

Structural analysis of the human neuroblastoma DNA replication complex: insights into faulty proliferation
Sandoval JA, Grosfeld JL, Hickey RJ, Malkas LH
J Pediatr Surg (2006) 41(1): 266-70

Identification of nitrated proteins in Alzheimer's disease brain using a redox proteomics approach
Sultana R, Poon HF, Cai J, Pierce WM, Merchant M, Klein JB, Markesbery WR, Butterfield DA
Neurobiol Dis Early Edition: published 22-Dec-2005

Differential proteomic serum pattern of low molecular weight proteins expressed by adenocarcinoma lung cancer patients
Maciel CM, Junqueira M, Paschoal ME, Kawamura MT, Duarte RL, Carvalho Mda G, Domont GB
J Exp Ther Oncol (2005) 5(1): 31-8

Activity profiling of deubiquitinating enzymes in cervical carcinoma biopsies and cell lines
Rolen U, Kobzeva V, Gasparjan N, Ovaa H, Winberg G, Kisseljov F, Masucci MG
Mol Carcinog Early Edition: published 9-Jan-2006

Comparative Proteomics of Nasal Fluid in Seasonal Allergic Rhinitis
B. Ghafouri, K. Irander, J. Lindbom, C. Tagesson, and M. Lindahl
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/13/2006

Biomarker Discovery from Pancreatic Cancer Secretome Using a Differential Proteomic Approach
Mads Gronborg, Troels Zakarias Kristiansen, Akiko Iwahori, Rubens Chang, Raghunath Reddy, Norihiro Sato, Henrik Molina, Ole Norregaard Jensen, Ralph H. Hruban, Michael G. Goggins, Anirban Maitra, and Akhilesh Pandey
Mol Cell Proteomics (2006) 5(1): 157-171

Protein Dysregulation in Mouse Hippocampus Polytransgenic for Chromosome 21 Structures in the Down Syndrome Critical Region
Joo-Ho Shin, Talin Gulesserian, Emmanuelle Verger, Jean-Maurice Delabar, and Gert Lubec
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 44-53

The quest for brain disorder biomarkers(*)
Turck CW, Maccarrone G, Sayan-Ayata E, Jacob AM, Ditzen C, Kronsbein H, Birg I, Doertbudak CC, Haegler K, Lebar M, Teplytska L, Kolb N, Uwaje N, Zollinger R
J Med Invest (2005) 52 Suppl: 231-5

Adipocyte Fatty Acid-Binding Protein Is a Plasma Biomarker Closely Associated with Obesity and Metabolic Syndrome
Xu A, Wang Y, Xu JY, Stejskal D, Tam S, Zhang J, Wat NM, Wong WK, Lam KS
Clin Chem Early Edition: published 19-Jan-2006

Inhibition of tumor metastasis in vivo by combination of paclitaxel and hyaluronic acid
Yin DS, Ge ZQ, Yang WY, Liu CX, Yuan YJ
Cancer Lett Early Edition: published 5-Jan-2006

Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome
Pang RT, Poon TC, Chan KC, Lee NL, Chiu RW, Tong YK, Wong RM, Chim SS, Ngai SM, Sung JJ, Lo YM
Clin Chem Early Edition: published 19-Jan-2006

Investigation of early protein changes in the urinary bladder following partial bladder outlet obstruction by proteomic approach
Kim HJ, Sohng I, Kim DH, Lee DC, Hwang CH, Park JY, Ryu JW
J Korean Med Sci (2005) 20(6): 1000-5

Proteomic Analysis of Serum Associated Fucosylated Glycoproteins in the Development of Primary Hepatocellular Carcinoma
Mary Ann Comunale , Melissa Lowman, Ronald E. Long, Jonathan Krakover, Ramila Philip, Steven Seeholzer, Alison A. Evans, Hie-Won L. Hann, # Timothy M. Block, and Anand S. Mehta
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Endotoxins in the Prostatic Secretions of Chronic Prostatitis Patients: a Need for Further Biomarkers Through the Use of Proteomics
Kommu SS, Reiss S
Asian J Androl (2006) 8(1): 123-124

Proteomic Analysis of Lysosomal Acid Hydrolases Secreted by Osteoclasts: Implications for Lytic Enzyme Transport and Bone Metabolism
Cornelia Czupalla, Hannu Mansukoski, Thilo Riedl, Dorothee Thiel, Eberhard Krause, and Bernard Hoflack
Mol Cell Proteomics (2006) 5(1): 134-143

Examining the proteins of functional retinal lipofuscin using proteomic analysis as a guide for understanding its origin
Warburton S, Southwick K, Hardman RM, Secrest AM, Grow RK, Xin H, Woolley AT, Burton GF, Thulin CD
Mol Vis (2005) 11: 1122-34.

Proteomic evaluation of milk from different mammalian species as a substitute for breast milk
D'auria E, Agostoni C, Giovannini M, Riva E, Zetterstrom R, Fortin R, Greppi GF, Bonizzi L, Roncada P
Acta Paediatr (2005) 94(12): 1708-13

Functional proteomic screens in therapeutic protein drug discovery
Ilag LL
Curr Opin Mol Ther (2005) 7(6): 538-42

Proteome Analysis of Isolated Perfused Organ Effluent as a Novel Model for Protein Biomarker Discovery
John M. Koomen, Christopher R. Wilson, Patrick Guthrie, Matthew J. Androlewicz, Ryuji Kobayashi, and Heinrich Taegtmeyer
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 177-182

Surveillance for recurrent bladder cancer using a point-of-care proteomic assay
Grossman HB, Soloway M, Messing E, Katz G, Stein B, Kassabian V, Shen Y
JAMA (2006) 295(3): 299-305

Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold
Liotta LA, Petricoin EF
J Clin Invest (2006) 116(1): 26-30

Mitochondria as a target for early detection and diagnosis of cancer
Kagan J, Srivastava S
Crit Rev Clin Lab Sci (2005) 42(5): 453-72

Application of surface-enhanced laser desorption/ionization time-of-flight-based serum proteomic array technique for the early diagnosis of prostate cancer
Pan YZ, Xiao XY, Zhao D, Zhang L, Ji GY, Li Y, Yang BX, He DC, Zhao XJ
Asian J Androl (2006) 8(1): 45-51

Systematic Evaluation of Sample Preparation Methods for Gel-Based Human Urinary Proteomics: Quantity, Quality, and Variability
Visith Thongboonkerd, Somchai Chutipongtanate, and Rattiyaporn Kanlaya
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 183-191

Proteomic Identification of Lower Apolipoprotein A-I in Alzheimer's Disease
Liu HC, Hu CJ, Chang JG, Sung SM, Lee LS, Yuan RY, Leu SJ
Dement Geriatr Cogn Disord (2006) 21(3): 155-161

Proteomic profiles of serum inflammatory markers accurately predict atherosclerosis in mice
Tabibiazar R, Wagner RA, Deng A, Tsao PS, Quertermous T
Physiol Genomics Early Edition: published 17-Jan-2006

Proteomic study of plasma proteins in pregnant women with asthma
Murphy VE, Johnson RF, Wang YC, Akinsanya K, Gibson PG, Smith R, Clifton VL
Respirology (2006) 11(1): 41-8

Insulin-dependent Interactions of Proteins with GLUT4 Revealed through Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)
Leonard J. Foster, Assaf Rudich, Ilana Talior, Nish Patel, Xudong Huang, L. Michelle Furtado, Philip J. Bilan, Matthias Mann, and Amira Klip
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 64-75

Transcending the biomarker mindset: deciphering disease mechanisms at the single cell level
Danna EA, Nolan GP
Curr Opin Chem Biol Early Edition: published 4-Jan-2006

The inflammatory transcriptome of reactive murine astrocytes and implications for their innate immune function
Falsig J, Porzgen P, Lund S, Schrattenholz A, Leist M
J Neurochem Early Edition: published 9-Jan-2005

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Eukaryotic Cells And Tissues

Proteomic Analysis of Different Mutant Genotypes of Arabidopsis Led to the Identification of 11 Proteins Correlating with Adventitious Root Development
Sorin C, Negroni L, Balliau T, Corti H, Jacquemot MP, Davanture M, Sandberg G, Zivy M, Bellini C
Plant Physiol Early Edition: published 23-Dec-2005

A proteomics approach to characterizing human submandibular gland cell lines by fluorescent two-dimensional differential in-gel electrophoresis
Kasamatsu A, Uzawa K, Nakashima D, Kouzu Y, Endo Y, Koike H, Yokoe H, Harada K, Sato M, Tanzawa H
Int J Mol Med (2006) 17(2): 253-60

Plasticity-related regulation of the hippocampal proteome
McNair K, Davies CH, Cobb SR
Eur J Neurosci (2006) 23(2): 575-80

Saccharomyces cerevisiae Mitoproteome Plasticity in Response to Recombinant Alternative Ubiquinol Oxidase
Grégory Mathy, Rachel Navet, Pascal Gerkens, Pierre Leprince, # Edwin De Pauw, Claudine M. Sluse-Goffart, Francis E. Sluse, and Pierre Douette
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/23/2005

Identification of Novel Centrosomal Proteins in Dictyostelium discoideum by Comparative Proteomic Approaches
Yvonne Reinders, Irene Schulz, Ralph Gräf, and Albert Sickmann
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/27/2006

Proteomic analysis of Myrmecia pilosula (jack jumper) ant venom
Wiese MD, Chataway TK, Davies NW, Milne RW, Brown SG, Gai WP, Heddle RJ
Toxicon Early Edition: published 22-Dec-2005

Proteomics of Rac GTPase signaling reveals its predominant role in elicitor-induced defense response of cultured rice cells
Fujiwara M, Umemura K, Kawasaki T, Shimamoto K
Plant Physiol Early Edition: published 29-Dec-2005

Transcriptomic and Proteomic Approach for Understanding the Molecular Basis of Adaptation of Saccharomyces cerevisiae to Wine Fermentation
Zuzuarregui A, Monteoliva L, Gil C, Del Olmo ML
Appl Environ Microbiol (2006) 72(1): 836-47

A preliminary proteomic survey of the in vitro excretory/secretory products of fourth-stage larval and adult Teladorsagia circumcincta
Craig H, Wastling JM, Knox DP
Parasitology Early Edition: published 3-Jan-2006

Proteome analysis of the silkworm (Bombyx mori. L) colleterial gland during different development stages
Jin Y, Chen Y, Jiang Y, Xu M
Arch Insect Biochem Physiol (2005) 61(1): 42-50

Proteomics of early zebrafish embryos
Link V, Shevchenko A, Heisenberg CP
BMC Dev Biol (2006) 6(1): 1

Proteomic studies of Plasmodium knowlesi SICA variant antigens demonstrate their relationship with P. falciparum EMP1
Korir CC, Galinski MR
Infect Genet Evol (2006) 6(1): 75-9

The synapse proteome and phosphoproteome: a new paradigm for synapse biology
Grant SG
Biochem Soc Trans (2006) 34(Pt 1): 59-63

Cell Wall Proteome in the Maize Primary Root Elongation Zone. I. Extraction and Identification of Water-Soluble and Lightly Ionically Bound Proteins
Zhu J, Chen S, Alvarez S, Asirvatham VS, Schachtman DP, Wu Y, Sharp RE
Plant Physiol Early Edition: published 23-Dec-2005

Proteome analysis of gametophores identified a metallothionein involved in various abiotic stress responses in Physcomitrella patens
Cho SH, Hoang QT, Kim YY, Shin HY, Ok SH, Bae JM, Shin JS
Plant Cell Rep Early Edition: published 6-Jan-2006

Differentiation-dependent expression of hypothetical proteins in the neuroblastoma cell line N1E-115
Oh JE, Karlmark KR, Shin J, Hengstschlager M, Lubec G
Proteins Early Edition: published 19-Jan-2006

Use of a proteomics approach to identify favourable conditions for production of good quality lambskin leather
Deb Choudhury S, Allsop T, Passman A, Norris GE
Anal Bioanal Chem Early Edition: published 3-Jan-2006

Proteomic profiling of mature CD10+ B-cell lymphomas
Fan G, Molstad M, Braziel RM, Standley M, Huang J, Rodgers W, Nagalla S
Am J Clin Pathol (2005) 124(6): 920-9

New Insights into Molecular Mechanisms of Phagocytosis in Entamoeba histolytica by Proteomic Analysis
Okada M, Nozaki T
Arch Med Res (2005) 37(2): 244-251

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Prokaryotes

Identification of Proteins from a Cell Wall Fraction of the Diatom Thalassiosira pseudonana: Insights into Silica Structure Formation
Luciano G. Frigeri, Timothy R. Radabaugh, Paul A. Haynes, and Mark Hildebrand
Mol Cell Proteomics (2006) 5(1): 182-193

Mass Spectrometry-Based Proteomics Combined with Bioinformatic Tools for Bacterial Classification
Jacek P. Dworzanski, Samir V. Deshpande, Rui Chen, Rabih E. Jabbour, A. Peter Snyder, Charles H. Wick, and Liang Li
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 76-87

Anaerobic Survival of Pseudomonas aeruginosa by Pyruvate Fermentation Requires an Usp-Type Stress Protein
Schreiber K, Boes N, Eschbach M, Jaensch L, Wehland J, Bjarnsholt T, Givskov M, Hentzer M, Schobert M
J Bacteriol (2006) 188(2): 659-68

Quantitative Proteomic Analysis of Drug-Induced Changes in Mycobacteria
Minerva A. Hughes, Jeffrey C. Silva, Scott J. Geromanos, and Craig A. Townsend
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 54-63

Halophile Aldehyde Dehydrogenase from Halobacterium salinarum
Hyo-jeong Kim, Won-A Joo, Chang-Won Cho, and Chan-Wha Kim
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 192-195

How does Pasteurella multocida respond to the host environment?
Boyce JD, Adler B
Curr Opin Microbiol Early Edition: published 4-Jan-2006

Expression Analysis of Up-Regulated Genes Responding to Plumbagin in Escherichia coli
Chen JW, Sun CM, Sheng WL, Wang YC, Syu WJ
J Bacteriol (2006) 188(2): 456-63

Emerging Corynebacterium glutamicum systems biology
Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W
J Biotechnol Early Edition: published 5-Jan-2006

ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis
Cho SH, Goodlett D, Franzblau S
Tuberculosis (Edinb) Early Edition: published 19-Dec-2005

Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under Its Major Metabolic States
Nathan C. VerBerkmoes, Manesh B. Shah, Patricia K. Lankford, Dale A. Pelletier, Michael B. Strader , David L. Tabb , W. Hayes McDonald, John W. Barton , Gregory B. Hurst, Loren Hauser, Brian H. Davison, J. Thomas Beatty, Caroline S. Harwood, # F. Robert Tabita, Robert L. Hettich, and Frank W. Larimer
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Comparative proteomic analysis of B. henselae Houston and B. henselae Marseille by two-dimensional gel electrophoresis
Zhao SQ, Cai YF, Zhu ZY
Biomed Environ Sci (2005) 18(5): 341-4

Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome
Carapito C, Muller D, Turlin E, Koechler S, Danchin A, Van Dorsselaer A, Leize-Wagner E, Bertin PN, Lett MC
Biochimie Early Edition: published 5-Dec-2005

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Pharmacology and Toxicology

Proteomic analysis of iron overload in human hepatoma cells
Petrak J, Myslivcova D, Man P, Cmejla R, Cmejlova J, Vyoral D
Am J Physiol Gastrointest Liver Physiol Early Edition: published 12-Jan-2006

Proteomic analysis of chemoresistance to 5-fluorouracil in colon cancer in vitro
Mader RM, Schmidt WM, Mitterer G, Gerner C
Int J Clin Pharmacol Ther (2005) 43(12): 599-600

Cytosolic and Nuclear Protein Targets of Thiol-Reactive Electrophiles
Dennehy MK, Richards KA, Wernke GR, Shyr Y, Liebler DC
Chem Res Toxicol (2006) 19(1): 20-29

Genetic mechanisms of scorpion venom peptide diversification
Zhijian C, Feng L, Yingliang W, Xin M, Wenxin L
Toxicon Early Edition: published 29-Dec-2005

Proteomic Profiling for Cellular Responses to Different Concentrations of N-Methyl-N'-nitro-N-nitrosoguanidine
Jing Shen, Meiping Wu, and Yingnian Yu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Chemical Effects in Biological Systems (CEBS) object model for toxicology data, SysTox-OM: design and application
Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ 3rd, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD
Bioinformatics Early Edition: published 12-Jan-2006

Proteomic profiling in the sera of workers occupationally exposed to arsenic and lead: identification of potential biomarkers
Zhai R, Su S, Lu X, Liao R, Ge X, He M, Huang Y, Mai S, Lu X, Christiani D
Biometals (2005) 18(6): 603-13

Pharmacoproteomics of 4-Phenylbutyrate-Treated IB3-1 Cystic Fibrosis Bronchial Epithelial Cells
Om V. Singh, Neeraj Vij, Peter J. Mogayzel, Jr., Cathy Jozwik, Harvey B. Pollard, and Pamela L. Zeitlin
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/27/2006

Proteomics analysis of the actions of grape seed extract in rat brain: Technological and biological implications for the study of the actions of psychoactive compounds
Kim H, Deshane J, Barnes S, Meleth S
Life Sci Early Edition: published 13-Jan-2006

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Protein Array

A novel mass spectrometry-based assay for GSK-3beta activity
Bowley E, Mulvihill E, Howard JC, Pak BJ, Gan BS, O'gorman DB
BMC Biochem (2005) 6(1): 29

Changes in the serum proteome associated with the development of hepatocellular carcinoma in hepatitis C-related cirrhosis
Ward DG, Cheng Y, N'kontchou G, Thar TT, Barget N, Wei W, Billingham LJ, Martin A, Beaugrand M, Johnson PJ
Br J Cancer Early Edition: published 10-Jan-2006

Serum proteomic signature for cystic fibrosis using an antibody microarray platform
Srivastava M, Eidelman O, Joswik C, Paweletz C, Huang W, Zeitlin PL, Pollard HB
Mol Genet Metab Early Edition: published 5-Jan-2006

Biomarker discovery for ovarian cancer using SELDI-TOF-MS
Zhang H, Kong B, Qu X, Jia L, Deng B, Yang Q
Gynecol Oncol Early Edition: published 3-Jan-2006

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Protein Characterization / PTMs

SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures
Hao G, Derakhshan B, Shi L, Campagne F, Gross SS
Proc Natl Acad Sci U S A Early Edition: published 17-Jan-2006

Mapping Post-translational Modifications of the Histone Variant MacroH2A1 Using Tandem Mass Spectrometry
Feixia Chu, Dmitri A. Nusinow, Robert J. Chalkley, Kathrin Plath, Barbara Panning, and Alma L. Burlingame
Mol Cell Proteomics (2006) 5(1): 194-203

Top Down Mass Spectrometry of <60-kDa Proteins from Methanosarcina acetivorans Using Quadrupole FTMS with Automated Octopole Collisionally Activated Dissociation
Steven M. Patrie, Jonathan T. Ferguson, Dana E. Robinson, Dave Whipple, Michael Rother, William W. Metcalf, and Neil L. Kelleher
Mol Cell Proteomics (2006) 5(1): 14-25

Hyperphosphorylation of JNK-interacting Protein 1, a Protein Associated with Alzheimer Disease
Chiara D'Ambrosio, Simona Arena, Gabriella Fulcoli, Meir H. Scheinfeld, Dawang Zhou, Luciano D'Adamio, and Andrea Scaloni
Mol Cell Proteomics (2006) 5(1): 97-113

Analysis of Total N-Glycans in Cell Membrane Fractions of Cancer Cells Using a Combination of Serotonin Affinity Chromatography and Normal Phase Chromatography
Ryosuke Naka, Satoru Kamoda, Aya Ishizuka, Mitsuhiro Kinoshita, and Kazuaki Kakehi
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 88-97

Global Identification of O-GlcNAc-Modified Proteins
Nandi A, Sprung R, Barma DK, Zhao Y, Kim SC, Falck JR, Zhao Y
Anal Chem (2006) 78(2): 452-8

Phosphorylation Analysis by Mass Spectrometry: Myths, Facts, and the Consequences for Qualitative and Quantitative Measurements
Hanno Steen, Judith A. Jebanathirajah, John Rush, Nicolas Morrice, andMarc W. Kirschner
Mol Cell Proteomics (2006) 5(1): 172-181

Quantitative Phosphoproteomic Analysis of the Tumor Necrosis Factor Pathway
Greg T. Cantin, John D. Venable, Daniel Cociorva, and John R. Yates, III
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 127-134

Monocarboxylate transporter MCT1 is a target for immunosuppression
Murray CM, Hutchinson R, Bantick JR, Belfield GP, Benjamin AD, Brazma D, Bundick RV, Cook ID, Craggs RI, Edwards S, Evans LR, Harrison R, Holness E, Jackson AP, Jackson CG, Kingston LP, Perry MW, Ross AR, Rugman PA, Sidhu SS, Sullivan M, Taylor-Fishwick DA, Walker PC, Whitehead YM, Wilkinson DJ, Wright A, Donald DK
Nat Chem Biol (2005) 1(7): 371-6

Phosphoproteomic Analysis of Rat Liver by High Capacity IMAC and LC-MS/MS
Katrin Moser and Forest M. White
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 98-104

The S. cerevisiae proteome of oxidized protein-thiols:Contrasted functions for the thioredoxin and GSH pathways
Le Moan N, Clement G, Le Maout S, Tacnet F, Toledano MB
J Biol Chem Early Edition: published 17-Jan-2006

Identification of Candidate Regulators of Embryonic Stem Cell Differentiation by Comparative Phosphoprotein Affinity Profiling
Lawrence G. Puente, Douglas J. Borris, Jean-Francois Carriere, John F.Kelly, and Lynn A. Megeney
Mol Cell Proteomics (2006) 5(1): 57-67

Mass spectrometric characterization of lipid-modified peptides for the analysis of acylated proteins
Hoffman MD, Kast J
J Mass Spectrom Early Edition: published 18-Jan-2006

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Protein-protein interaction

Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis
Pall F Jonsson , Tamara Cavanna , Daniel Zicha and Paul A Bates
BMC Bioinformatics (2006) 7(1): 2

Interactome networks: the state of the science
Guy J Warner , Yeyejide A Adeleye and Trey Ideker
Genome Biology (2006) 7(1): 301

Phosphate Stabilization of Intermolecular Interactions
Shelley N. Jackson, Hay-Yan J. Wang, Alfred Yergey, and Amina S. Woods
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 122-126

Effect of Protein Backbone Folding on the Stability of Protein-Ligand Complexes
Ernesto Estrada, Eugenio Uriarte, and Santiago Vilar
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 105-111

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Quantitation

Two-dimensional mass spectrometric mapping
Roesli C, Elia G, Neri D
Curr Opin Chem Biol Early Edition: published 4-Jan-2006

Combined Chemical and Enzymatic Stable Isotope Labeling for Quantitative Profiling of Detergent-Insoluble Membrane Proteins Isolated Using Triton X-100 and Brij-96
Josip Blonder, Li-Rong Yu, Galina Radeva, King C. Chan, David A. Lucas, Timothy J. Waybright, Haleem J. Issaq, Frances J. Sharom, and Timothy D. Veenstra
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Comparison of Two Proteomics Techniques Used to Identify Proteins Regulated by Gibberellin in Rice
Setsuko Komatsu, Xin Zang, and Naoki Tanaka
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/30/2005

Recent Progress in Quantitative Proteomics Using Stable Isotope Labeling, Multidimensional Liquid Chromatography and Mass Spectrometry
Hsu, Jue-Liang; Chen, Shu-Hui
Current Proteomics (2005) 2(4): 287-302

An Optimized Strategy for ICAT Quantification of Membrane Proteins
Claire Ramus, Anne Gonzalez de Peredo, Cecile Dahout, Maighread Gallagher, and Jerome Garin
Mol Cell Proteomics (2006) 5(1): 68-78

Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms
Bettina M. Mayr, Oliver Kohlbacher, Knut Reinert, Marc Sturm, Clemens Gröpl, Eva Lange, Christoph Klein, and Christian G. Huber
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

Absolute Quantification of Proteins by LCMSE: A Virtue of Parallel ms Acquisition
Jeffrey C. Silva, Marc V. Gorenstein, Guo-Zhong Li, Johannes P. C. Vissers, and Scott J. Geromanos
Mol Cell Proteomics (2006) 5(1): 144-156

Mass spectrometry-based proteomics turns quantitative
Ong SE, Mann M
Nat Chem Biol (2005) 1(5): 252-62

Synthesis of Acid-Cleavable Light Isotope-Coded Affinity Tags (ICAT-L) for Potential Use in Proteomic Expression Profiling Analysis
Fauq AH, Kache R, Khan MA, Vega IE
Bioconjug Chem (2006) 17(1): 248-54

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Review

The application of inductively coupled plasma mass spectrometry in pharmaceutical and biomedical analysis
Huang J, Hu X, Zhang J, Li K, Yan Y, Xu X
J Pharm Biomed Anal Early Edition: published 15-Dec-2005

The amplified peptidome: the new treasure chest of candidate biomarkers
Geho DH, Liotta LA, Petricoin EF, Zhao W, Araujo RP
Curr Opin Chem Biol Early Edition: published 14-Jan-2006

Alzheimer's disease cerebrospinal fluid biomarker discovery: a proteomics approach
D'Ascenzo M, Relkin NR, Lee KH
Curr Opin Mol Ther (2005) 7(6): 557-64

Fungal pathogens research: novel and improved molecular approaches for the discovery of antifungal drug targets
Tournu H, Serneels J, Van Dijck P
Curr Drug Targets (2005) 6(8): 909-22

Advances, Challenges, and Limitations in Serum-Proteome-Based Cancer Diagnosis
Matthias P. A. Ebert, Murray Korc, Peter Malfertheiner, and Christoph Röcken
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 19-25

Protein analysis in human cerebrospinal fluid: Physiological aspects, current progress and future challenges
Huhmer AF, Biringer RG, Amato H, Fonteh AN, Harrington MG
Dis Markers (2006) 22(1-2): 211-34

Metabolomics reviewed: a new "omics" platform technology for systems biology and implications for natural products research
Rochfort S
J Nat Prod (2005) 68(12): 1813-20

Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics
Lee HJ, Lee EY, Kwon MS, Paik YK
Curr Opin Chem Biol Early Edition: published 14-Jan-2006

Targeted discovery tools: proteomics and chromatin immunoprecipitation-on-chip
LE Guezennec X, Brinkman AB, Vermeulen M, Denissov SG, Gazziola C, Lohrum ME, Stunnenberg HG
BJU Int (2005) 96(Suppl 2): 16-22

Understanding platelets. Lessons from proteomics, genomics and promises from network analysis
Dittrich M, Birschmann I, Stuhlfelder C, Sickmann A, Herterich S, Nieswandt B, Walter U, Dandekar T
Thromb Haemost (2005) 94(5): 916-25

Systems biology. When proteomes collide
Bader JS, Chant J
Science (2006) 311(5758): 187-8

Capillary electrophoresis at the omics level: Towards systems biology
Babu C V S, Song EJ, Babar SM, Wi MH, Yoo YS
Electrophoresis (2006) 27(1): 97-110

Proteomic research in renal transplantation
Clarke W
Ther Drug Monit (2006) 28(1): 19-22

A control theoretic paradigm for cell signaling networks: a simple complexity for a sensitive robustness
Araujo RP, Liotta LA
Curr Opin Chem Biol Early Edition: published 12-Jan-2006

Proteomics: applications relevant to transfusion medicine
Page MJ, Griffiths TA, Bleackley MR, Macgillivray RT
Transfus Med Rev (2006) 20(1): 63-74

Proteomics: a paradigm shift
Kalia A, Gupta RP
Crit Rev Biotechnol (2005) 25(4): 173-98

Proteomics in tumor progression and metastasis
Everley PA, Zetter BR
Ann N Y Acad Sci (2005) 1059: 1-10.

Practical proteomic biomarker discovery: taking a step back to leap forward
Listgarten J, Emili A
Drug Discov Today (2005) 10(23-24): 1697-702

Fluorescent labels for proteomics and genomics
Waggoner A
Curr Opin Chem Biol Early Edition: published 14-Jan-2006

Multiplexed Protein Array Platforms for Analysis of Autoimmune Diseases
Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ
Annu Rev Immunol Early Edition: published 16-Jan-2006

Peptidomics: Identification and quantification of endogenous peptides in neuroendocrine tissues
Fricker LD, Lim J, Pan H, Che FY
Mass Spectrom Rev Early Edition: published 10-Jan-2006

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Methodology

A practical approach to maximizing peak capacity by using long columns packed with pellicular stationary phases for proteomic research
Wang X, Barber WE, Carr PW
J Chromatogr A Early Edition: published 9-Jan-2006

Multidimensional Liquid Chromatography Separation of Intact Proteins by Chromatographic Focusing and Reversed Phase of the Human Serum Proteome: Optimization and Protein Database
Simon Sheng, Dawn Chen, and Jennifer E. Van Eyk
Mol Cell Proteomics (2006) 5(1): 26-34

Performance of a linear ion trap-orbitrap hybrid for Peptide analysis
Yates JR, Cociorva D, Liao L, Zabrouskov V
Anal Chem (2006) 78(2): 493-500

On-line microdevice for stress proteomics
Tabuchi M, Nagata H, Nomura M, Katsube S, Sawada A, Joko A, Hatta K, Hagiwara N, Kobayashi K, Tomita F, Miki S, Arai K, Ishiguro T, Baba Y
J Med Invest (2005) 52 Suppl: 225-7

Protein interactions with subcutaneously implanted biosensors
Gifford R, Kehoe JJ, Barnes SL, Kornilayev BA, Alterman MA, Wilson GS
Biomaterials Early Edition: published 15-Dec-2005

Integration of Multidimensional Chromatographic Protein Separations with a Combined "Top-Down" and "Bottom-Up" Proteomic Strategy
Kevin M. Millea, Ira S. Krull, Steven A. Cohen, John C. Gebler, and Scott J. Berger
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 135-146

Current Progress in Sample Preparation for Two-Dimensional Electrophoresis in Proteomics
Cai, Zhen; Chiu, Jen-Fu; He, Qing-Yu
Current Proteomics (2005) 2(4): 259-268

Combining Low and High Mass Ion Accumulation for Enhancing Shotgun Proteome Analysis by Accurate Mass Measurement
Wong RL, Amster IJ
J Am Soc Mass Spectrom Early Edition: published 10-Jan-2006

Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)
Emily I. Chen, Johannes Hewel, Brunhilde Felding-Habermann, and John R. Yates, III
Mol Cell Proteomics (2006) 5(1): 53-56

Pre-extraction Sample Handling by Automated Frozen Disruption Significantly Improves Subsequent Proteomic Analyses
R. Hussain Butt and Jens R. Coorssen
JOURNAL OF PROTEOME RESEARCH Early Edition: published 12/23/2005

Classification of Cancer Cell Lines Using an Automated Two-dimensional Liquid Mapping Method with Hierarchical Clustering Techniques
Yanfei Wang, Rong Wu, Kathleen R. Cho, Kerby A. Shedden, Timothy J. Barder, and David M. Lubman
Mol Cell Proteomics (2006) 5(1): 43-52

Peptide sequencing by MALDI 193-nm photodissociation TOF MS
Morgan JW, Hettick JM, Russell DH
Methods Enzymol (2005) 402: 186-209

In vivo protein sampling using capillary ultrafiltration semi-permeable hollow fiber and protein identification via mass spectrometry-based proteomics
Huang CM, Wang CC, Kawai M, Barnes S, Elmets CA
J Chromatogr A Early Edition: published 22-Dec-2005

Sample Preparation Techniques for Mass Spectrometry in Proteomics Using Recently Developed Highly Selective Materials
Huck, Christian W.; Bakry, Rania; Bonn, Gunther K
Current Proteomics (2005) 2(4): 269-285

Protein conformations, interactions, and H/D exchange
Maier CS, Deinzer ML
Methods Enzymol (2005) 402: 312-60

One-Step Fractionation of Complex Proteomes Enables Detection of Low Abundant Analytes Using Antibody-Based Microarrays
Johan Ingvarsson, Malin Lindstedt, Carl A. K. Borrebaeck, and Christer Wingren
JOURNAL OF PROTEOME RESEARCH (2006) 5(1): 170-176

Protein depletion from blood plasma using a volatile buffer
Sitnikov D, Chan D, Thibaudeau E, Pinard M, Hunter JM
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 13-Jan-2006

Comprehensive Protein Profiling by Multiplexed Capillary Zone Electrophoresis Using Cross-Linked Polyacrylamide Coated Capillaries
Shaorong Liu, Lin Gao, Qiaosheng Pu, Joann J. Lu, and Xingjia Wang
JOURNAL OF PROTEOME RESEARCH Early Edition: published 01/06/2006

The process chain for peptidomic biomarker discovery
Schrader M, Selle H
Dis Markers (2006) 22(1-2): 235-45

Optimisation of a 2-D gel electrophoresis protocol for the human-pathogenic fungus Aspergillus fumigatus
Kniemeyer O, Lessing F, Scheibner O, Hertweck C, Brakhage AA
Curr Genet Early Edition: published 17-Dec-2005

First Annual Symposium on Proteome Fractionation
John Hobbs
Mol Cell Proteomics (2006) 5(1): 1

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Books

Review of "The Ten Most Wanted Solutions in Protein Bioinformatics"
Anna Tramontano
BioMedical Engineering OnLine (2006) 5(1): 1

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Meeting

Interactome networks: the state of the science
Guy J Warner , Yeyejide A Adeleye and Trey Ideker
Genome Biology (2006) 7(1): 301

The 24th International Specialized Symposium on Yeasts (ISSY 24) "Cell surface: a genomic and proteomic approach" Oropesa del Mar (Castellon, Spain), 28 September-2 October 2005
Gola S, Pla J
FEMS Yeast Res (2006) 6(1): 143-7

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Other

Metaproteomics: studying functional gene expression in microbial ecosystems
Wilmes P, Bond PL
Trends Microbiol Early Edition: published 6-Jan-2006

Checking and fixing the cellular nanomachinery: towards medical nanoscopy
Peters R
Trends Mol Med Early Edition: published 5-Jan-2006

Proteomics
Stults JT, Arnott D
Methods Enzymol (2005) 402: 245-89

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