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SPS' Digest

Issue 10, 14-Sep-2004

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Quick jumps to articles in: Bioinformatics (7) / Biological applications (18) / Biomedical and clinical applications (26) / Eukaryotic Cells And Tissues (18) / Prokaryotes (4) / Pharmacology and Toxicology (1) / Protein Array (3) / Protein Characterization - PTMs (15) / Protein-protein interaction (5) / Quantitation (5) / Review (14) / Methodology (30) / Meeting (2) / Other (1) /

In this issue, 142 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 (7) / Biological applications (18) / Biomedical and clinical applications (26) / Eukaryotic Cells And Tissues (18) / Prokaryotes (4) / Pharmacology and Toxicology (1) / Protein Array (3) / Protein Characterization - PTMs (15) / Protein-protein interaction (5) / Quantitation (5) / Review (14) / Methodology (30) / Meeting (2) / Other (1) /

Bioinformatics

Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
Eduardo Sontag, Anatoly Kiyatkin, and Boris N. Kholodenko
Bioinformatics (2004) 20(12): 1877-1886

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry
Yan Fu, Qiang Yang, Ruixiang Sun, Dequan Li, Rong Zeng, Charles X. Ling, and Wen Gao
Bioinformatics (2004) 20(12): 1948-1954

Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0
Rune Matthiesen, Jakob Bunkenborg, Allan Stensballe, Ole N. Jensen, Karen G. Welinder, Guy Bauw
PROTEOMICS (2004) 4(9): 2583-2593

Automated methods for improved protein identification by peptide mass fingerprinting
Fredrik Levander, Thorsteinn Rögnvaldsson, Jim Samuelsson, Peter James
PROTEOMICS (2004) 4(9): 2594-2601

Tree analysis of mass spectral urine profiles discriminates transitional cell carcinoma of the bladder from noncancer patient.
Zhang YF, Wu DL, Guan M, Liu WW, Wu Z, Chen YM, Zhang WZ, Lu Y
Clin Biochem (2004) 37(9): 772-9

A software utility for creating interactive maps for 2D gel-based proteomics.
Li J, Liu S, Osterman T, Zhang Y, Coppage H, Pedrick N, Witzmann FA
Anal Biochem (2004) 332(1): 187-90

Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum.
Anderle M, Roy S, Lin H, Becker C, Joho K
Bioinformatics Early Edition: published 29-July-2004

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Biological applications

Proteome analysis of human mesothelial cells during epithelial to mesenchymal transitions induced by shed menstrual effluent
Ay?e Y. Demir, Hans Demol, Magda Puype, Anton F. P. M. de Goeij, Gerard A. J. Dunselman, Andreas Herrler, Johannes L. H. Evers, Joël Vandekerckhove, Patrick G. Groothuis
PROTEOMICS (2004) 4(9): 2608-2623

Multidimensional Protein Profiling Technology and Its Application to Human Plasma Proteome
Kiyonaga Fujii, Tomoyo Nakano, Takeshi Kawamura, Fumihiko Usui, Yasuhiko Bando, Rong Wang, and Toshihide Nishimura
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 712-718

Analyzing Alkaline Proteins in Human Colon Crypt Proteome
Xin-Ming Li, Bhavinkumar B. Patel, Elena L. Blagoi, Maketa D. Patterson, Steven H. Seehozer, Tao Zhang, Shirish Damle, Zhenqiang Gao, Bruce Boman, and Anthony T. Yeung
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 821-833

Quantitative Mass Spectrometric Immunoassay of Insulin Like Growth Factor 1
Randall W. Nelson, Dobrin Nedelkov, Kemmons A. Tubbs, and Urban A. Kiernan
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 851-855

Surface-enhanced laser desorption/ionization-time of flight-mass spectrometry approach to biomarker discovery in blue mussels (Mytilus edulis) exposed to polyaromatic hydrocarbons and heavy metals under field conditions
Thomas Knigge, Tiphaine Monsinjon, Odd-Ketil Andersen
PROTEOMICS (2004) 4(9): 2722-2727

Proteome Analysis of Gastric Cancer Metastasis by Two-Dimensional Gel Electrophoresis and Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry for Identification of Metastasis-Related Proteins
Jie Chen, Thilo Kähne, Christoph Röcken, Tobias Götze, Jun Yu, Minhu Chen, # Pinjin Hu, # Peter Malfertheiner, and Matthias P. A. Ebert
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/06/2004

Analysis of Signal-dependent Changes in the Proteome of Drosophila Blood Cells During an Immune Response
Olga Loseva and Ylva Engstrom
Mol Cell Proteomics (2004) 3(8): 796-808

Proteomic signature of human cancer cells
Masahiro Seike, Tadashi Kondo, Kazuyasu Fujii, Tesshi Yamada, Akihiko Gemma, Shoji Kudoh, Setsuo Hirohashi
PROTEOMICS (2004) 4(9): 2776-2788

Impact of sewage sludges on Medicago truncatula symbiotic proteome.
Bestel-Corre G, Gianinazzi S, Dumas-Gaudot E
Phytochemistry (2004) 65(11): 1651-9

Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification.
Wienkoop S, Zoeller D, Ebert B, Simon-Rosin U, Fisahn J, Glinski M, Weckwerth W
Phytochemistry (2004) 65(11): 1641-9

Environmental and transgene expression effects on the barley seed proteome.
Finnie C, Steenholdt T, Roda Noguera O, Knudsen S, Larsen J, Brinch-Pedersen H, Bach Holm P, Olsen O, Svensson B
Phytochemistry (2004) 65(11): 1619-27

A proteomic approach to studying plant response to crenate broomrape (Orobanche crenata) in pea (Pisum sativum).
Angeles Castillejo M, Amiour N, Dumas-Gaudot E, Rubiales D, Jorrin JV
Phytochemistry (2004) 65(12): 1817-28

Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and [Formula: see text] -gene mediated resistance.
Jones AM, Thomas V, Truman B, Lilley K, Mansfield J, Grant M
Phytochemistry (2004) 65(12): 1805-16

Proteomic approach to characterize the supramolecular organization of photosystems in higher plants.
Heinemeyer J, Eubel H, Wehmhoner D, Jansch L, Braun HP
Phytochemistry (2004) 65(12): 1683-92

A proteomic approach to cisplatin resistance in the ­cervix squamous cell carcinoma cell line A431
Annalisa Castagna, Paolo Antonioli, Hubert Astner, Mahmoud Hamdan, Sabina Carla Righetti, Paola Perego, Franco Zunino, Pier Giorgio Righetti
PROTEOMICS Early Edition: published 9 Aug 2004

Expressional pattern of known and predicted signaling proteins in seven human cell lines
Daniela Pollak, Kurt Krapfenbauer, Michael Fountoulakis, Andreas Peyrl and Gert Lubec
J Chromatogr B (2004) 808(2): 185-208

Proteomic Studies of Lipopolysaccharide-induced Polypeptides in the Silkworm, Bombyx mori.
Wang Y, Zhang P, Fujii H, Banno Y, Yamamoto K, Aso Y
Biosci Biotechnol Biochem (2004) 68(8): 1821-3

Proteomics in reproductive medicine: the technology for separation and identification of proteins.
Hachey DL, Chaurand P
J Reprod Immunol (2004) 63(1): 61-73.

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Biomedical and clinical applications

Identification of metastasis-associated proteins in a human tumor metastasis model using the mass-mapping technique
Paweena Kreunin, Virginia Urquidi, David M Lubman, Steve Goodison
PROTEOMICS (2004) 4(9): 2754-2765

Identification of tumor-associated plasma biomarkers using proteomic techniques: From mouse to human
Hsueh-Fen Juan, Jenn-Han Chen, Wei-Tse Hsu, Su-Ching Huang, Shui-Tein Chen, John Yi-Chung Lin, Yu-Wang Chang, Chih-Yin Chiang, Li-Li Wen, De-Chuan Chan, Yao-Chi Liu, Yu-Ju Chen
PROTEOMICS (2004) 4(9): 2766-2775

Proteomic signature of human cancer cells
Masahiro Seike, Tadashi Kondo, Kazuyasu Fujii, Tesshi Yamada, Akihiko Gemma, Shoji Kudoh, Setsuo Hirohashi
PROTEOMICS (2004) 4(9): 2776-2788

Mitochondrial proteome: Cancer-altered metabolism associated with cytochrome c oxidase subunit level variation
René C. Krieg, Ruth Knuechel, Elliot Schiffmann, Lance A. Liotta, Emanuel F. Petricoin III, Paul C. Herrmann
PROTEOMICS (2004) 4(9): 2789-2795

OvaCheck: doubts voiced soon after publication.
Diamandis EP
Nature (2004) 430(7000): 611

Proteomic analysis of differential protein expression in neuropathic pain and electroacupuncture treatment models
Ho Joong Sung, Yoon Suk Kim, In Sik Kim, Sung-Wuk Jang, Yoon Rim Kim, Doe Sun Na, Ki Hoon Han, Byung Gil Hwang, Dong Suk Park, Jesang Ko
PROTEOMICS (2004) 4(9): 2805-2813

Proteomic analysis of proteins altered by dibenzoylmethane in human prostatic cancer LNCaP cells
Monica C. Frazier, Kimberly M. Jackson, Ewa Jankowska-Stephens, Mark G. Anderson, Wayne B. Harris
PROTEOMICS (2004) 4(9): 2814-2821

OvaCheck: let's not dismiss the concept.
Villanueva J, Tempst P
Nature (2004) 430(7000): 611

Mining the proteome.
Chapman T
Nature (2004) 430(6995): 109

Evaluation of Metabolic Labeling for Comparative Proteomics in Breast Cancer Cells
Marion L. Gehrmann, Yetrib Hathout, and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/20/2004

Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT-ICR mass spectrometry.
Bergen HR 3rd, Vasmatzis G, Cliby WA, Johnson KL, Oberg AL, Muddiman DC
Dis Markers (2004) 19(4-5): 239-49

SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers.
Laronga C, Becker S, Watson P, Gregory B, Cazares L, Lynch H, Perry RR, Wright GL Jr, Drake RR, Semmes OJ
Dis Markers (2004) 19(4-5): 229-38

Characterization of plasma membrane proteins from ovarian cancer cells using mass spectrometry.
Springer DL, Auberry DL, Ahram M, Adkins JN, Feldhaus JM, Wahl JH, Wunschel DS, Rodland KD
Dis Markers (2004) 19(4-5): 219-28

Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.
Yu LR, Zhou M, Conrads TP, Veenstra TD
Dis Markers (2004) 19(4-5): 209-18

Novel approaches to visualization and data mining reveals diagnostic information in the low amplitude region of serum mass spectra from ovarian cancer patients.
Johann DJ Jr, McGuigan MD, Tomov S, Fusaro VA, Ross S, Conrads TP, Veenstra TD, Fishman DA, Whiteley GR, Petricoin EF, Liotta LA
Dis Markers (2004) 19(4-5): 197-207

Serum protein expression profiling for cancer detection: validation of a SELDI-based approach for prostate cancer.
Grizzle WE, Adam BL, Bigbee WL, Conrads TP, Carroll C, Feng Z, Izbicka E, Jendoubi M, Johnsey D, Kagan J, Leach RJ, McCarthy DB, Semmes OJ, Srivastava S, Srivastava S, Thompson IM, Thornquist MD, Verma M, Zhang Z, Zou Z
Dis Markers (2004) 19(4-5): 185-95

The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis.
Van QN, Klose JR, Lucas DA, Prieto DA, Luke B, Collins J, Burt SK, Chmurny GN, Issaq HJ, Conrads TP, Veenstra TD, Keay SK
Dis Markers (2004) 19(4-5): 169-83

Proteomic analysis of an orthotopic neuroblastoma xenograft animal model
Natascia Campostrini, Jennifer Pascali, Mahmoud Hamdan, Hubert Astner, Danilo Marimpietri, Fabio Pastorino, Mirco Ponzoni and Pier Giorgio Righetti
J Chromatogr B (2004) 808(2): 279-286

A mouse serum two-dimensional gel map: Application to profiling burn injury and infection
Xunbao Duan, David M. Yarmush, François Berthiaume, Arul Jayaraman, Martin L. Yarmush
ELECTROPHORESIS (2004) 25(17): 3055-3065

Identification and proteomic profiling of exosomes in human urine
Trairak Pisitkun, Rong-Fong Shen, and Mark A. Knepper
PNAS (2004) 101(36): 13368-13373

Expression, by functional proteomics, of spontaneous tolerance in rat orthotopic liver transplantation.
Pan TL, Wang PW, Huang CC, Goto S, Chen CL
Immunology (2004) 113(1): 57-64

A serum proteomics approach to the diagnosis of ectopic pregnancy.
Gerton GL, Fan XJ, Chittams J, Sammel M, Hummel A, Strauss JF, Barnhart K
Ann N Y Acad Sci (2004) 1022: 306-16

Clinical proteomics: Applications for prostate cancer biomarker discovery and detection.
Petricoin EF, Ornstein DK, Liotta LA
Urol Oncol (2004) 22(4): 322-8.

Diagnosis of intra-amniotic infection by proteomic profiling and identification of novel biomarkers.
Gravett MG, Novy MJ, Rosenfeld RG, Reddy AP, Jacob T, Turner M, McCormack A, Lapidus JA, Hitti J, Eschenbach DA, Roberts CT Jr, Nagalla SR
JAMA (2004) 292(4): 462-9.

Detection of differentially expressed proteins in early-stage melanoma patients using SELDI-TOF mass spectrometry.
Wilson LL, Tran L, Morton DL, Hoon DS
Ann N Y Acad Sci (2004) 1022: 317-22

Proteomics to display tissue repair opposing injury response to LPS-induced liver injury.
Liu XW, Lu FG, Zhang GS, Wu XP, You Y, Ouyang CH, Yang DY
World J Gastroenterol (2004) 10(18): 2701-5

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Eukaryotic Cells And Tissues

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?
Rodrigo A Gutiérrez , Pamela J Green, Kenneth Keegstra and John B Ohlrogge
Genome Biology (2004) 5(8): R53

Wheat leaf proteome analysis using sequence data of proteins separated by two-dimensional electrophoresis
Nasser Bahrman, Luc Negroni, Odile Jaminon, Jacques Le Gouis
PROTEOMICS (2004) 4(9): 2672-2684

Proteomic analysis of aneuploid lines in the homeologous group 1 of the hexaploid wheat cultivar Courtot
Jérôme Dumur, Joseph Jahier, Emmanuelle Bancel, Michel Laurière, Michel Bernard, Gérard Branlard
PROTEOMICS (2004) 4(9): 2685-2695

New targets of Arabidopsis thioredoxins revealed by proteomic analysis
Christophe Marchand, Pierre Le Maréchal, Yves Meyer, Myroslawa Miginiac-Maslow, Emmanuelle Issakidis-Bourguet, Paulette Decottignies
PROTEOMICS (2004) 4(9): 2696-2706

A two-dimensional proteome map of maize endosperm.
Mechin V, Balliau T, Chateau-Joubert S, Davanture M, Langella O, Negroni L, Prioul JL, Thevenot C, Zivy M, Damerval C
Phytochemistry (2004) 65(11): 1609-18

Mapping of the Physcomitrella patens proteome.
Sarnighausen E, Wurtz V, Heintz D, Van Dorsselaer A, Reski R
Phytochemistry (2004) 65(11): 1589-607

Untangling multi-gene families in plants by integrating proteomics into functional genomics.
Sappl PG, Heazlewood JL, Millar AH
Phytochemistry (2004) 65(11): 1517-30

Proteomic analysis of small heat shock protein isoforms in barley shoots.
Sule A, Vanrobaeys F, Hajos G, Van Beeumen J, Devreese B
Phytochemistry (2004) 65(12): 1853-63

Identification of oxidised proteins in the matrix of rice leaf mitochondria by immunoprecipitation and two-dimensional liquid chromatography-tandem mass spectrometry.
Kristensen BK, Askerlund P, Bykova NV, Egsgaard H, Moller IM
Phytochemistry (2004) 65(12): 1839-51

A proteomic analysis of plant programmed cell death.
Swidzinski JA, Leaver CJ, Sweetlove LJ
Phytochemistry (2004) 65(12): 1829-38

Proteomics of curcurbit phloem exudate reveals a network of defence proteins.
Walz C, Giavalisco P, Schad M, Juenger M, Klose J, Kehr J
Phytochemistry (2004) 65(12): 1795-804

Evaluation of an integrated strategy for proteomic ­profiling of skeletal muscle
Marie-Catherine Le Bihan, Edward Tarelli, Gary R. Coulton
PROTEOMICS Early Edition: published 9 Aug 2004

Proteomics-based sequence analysis of plant gene expression - the chloroplast transcription apparatus.
Loschelder H, Homann A, Ogrzewalla K, Link G
Phytochemistry (2004) 65(12): 1785-93

The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions.
Brugiere S, Kowalski S, Ferro M, Seigneurin-Berny D, Miras S, Salvi D, Ravanel S, D'Herin P, Garin J, Bourguignon J, Joyard J, Rolland N
Phytochemistry (2004) 65(12): 1693-707

Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture
Eberhard Durr, Jingyi Yu, Karolina M Krasinska, Lucy A Carver, John R Yates III, Jacqueline E Testa, Phil Oh & Jan E Schnitzer
Nat Biotechnol (2004) 22(8): 985-992

System-based proteomic analysis of the interferon response in human liver cells
Wei Yan, Hookeun Lee, Eugene C Yi, David Reiss, Paul Shannon, Bartlomiej K Kwieciszewski, Carlos Coito, Xiao-jun Li, Andrew Keller, Jimmy Eng, Timothy Galitski, David R Goodlett, Ruedi Aebersold and Michael G Katze
Genome Biology (2004) 5(8): R54

The proteomic approach to analysis of human milk fat globule membrane.
Cavaletto M, Giuffrida MG, Conti A
Clin Chim Acta (2004) 347(1-2): 41-8

Two-dimensional polyacrylamide gel electrophoresis for platelet proteomics.
Marcus K, Meyer HE
Methods Mol Biol (2004) 273: 421-34

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Prokaryotes

Use of surface-enhanced laser desorption/ionization -time of flight to explore bacterial proteomes
Dagania Barzaghi, Jenefir D. Isbister, Kimberly P. Lauer, Timothy L. Born
PROTEOMICS (2004) 4(9): 2624-2628

Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics
Pedro M. Santos, Dirk Benndorf, Isabel Sá-Correia
PROTEOMICS (2004) 4(9): 2640-2652

Identification of Bacillus anthracis proteins associated with germination and early outgrowth by proteomic profiling of anthrax spores
Chun-Ming Huang, K. Wade Foster, Tivanka S. DeSilva, Kent R. Van Kampen, Craig A. Elmets, De-chu C. Tang
PROTEOMICS (2004) 4(9): 2653-2661

Protein composition of Paracoccus denitrificans cells grown on various electron acceptors and in the presence of azide
Pavel Bouchal, Petra P?ececht?lová, Zbyn?k Zdráhal, Igor Ku?era
PROTEOMICS (2004) 4(9): 2662-2671

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Pharmacology and Toxicology

Pharmacoproteomic approach to the study of drug mode of action, toxicity, and resistance: applications in diabetes and cancer.
Chapal N, Molina L, Molina F, Laplanche M, Pau B, Petit P
Fundam Clin Pharmacol (2004) 18(4): 413-22

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Protein Array

Evaluation of an integrated strategy for proteomic profiling of skeletal muscle
Marie-Catherine Le Bihan, Edward Tarelli, Gary R. Coulton
PROTEOMICS (2004) 4(9): 2739-2753

Antibodies Immobilized as Arrays to Profile Protein Post-translational Modifications in Mammalian Cells
Stanimir S. Ivanov, Alicia S. Chung, Zheng-long Yuan, Ying-jie Guan, Katherine V. Sachs, Jonathan S. Reichner, and Y. Eugene Chin
Mol Cell Proteomics (2004) 3(8): 788-795

Identification of barley CK2alpha targets by using the protein microarray technology.
Kramer A, Feilner T, Possling A, Radchuk V, Weschke W, Burkle L, Kersten B
Phytochemistry (2004) 65(12): 1777-84

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Protein Characterization / PTMs

Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics.
Blagoev B, Ong SE, Kratchmarova I, Mann M
Nat Biotechnol (2004) 22(9): 1139-45

Large-scale characterization of HeLa cell nuclear phosphoproteins
Sean A. Beausoleil, Mark Jedrychowski, Daniel Schwartz, Joshua E. Elias, Judit Villen, Jiaxu Li, Martin A. Cohn, Lewis C. Cantley, and Steven P. Gygi
PNAS (2004) 101(33): 12130-12135

New Approach for Analysis of the Phosphotyrosine Proteome and Its Application to the Chicken B Cell Line, DT40
Melissa D. Zolodz, Karl V. Wood, Fred E. Regnier, and Robert L. Geahlen
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 743-750

The identification of Dictyostelium phosphoproteins altered in response to the activation of RasG
David M. Secko, Robert H. Insall, George B. Spiegelman, Gerry Weeks
PROTEOMICS (2004) 4(9): 2629-2639

Lectin Affinity as an Approach to the Proteomic Analysis of Membrane Glycoproteins
Dhiman Ghosh, Oleg Krokhin, Mihaela Antonovici, Werner Ens, Kenneth G. Standing, Ronald C. Beavis, and John A. Wilkins
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 841-850

Automated methods for improved protein identification by peptide mass fingerprinting
Fredrik Levander, Thorsteinn Rögnvaldsson, Jim Samuelsson, Peter James
PROTEOMICS (2004) 4(9): 2594-2601

Thioredoxin targets of developing wheat seeds identified by complementary proteomic approaches.
Wong JH, Cai N, Balmer Y, Tanaka CK, Vensel WH, Hurkman WJ, Buchanan BB
Phytochemistry (2004) 65(11): 1629-40

Investigation of cationic peanut peroxidase glycans by electrospray ionization mass spectrometry.
Zhang C, Doherty-Kirby A, Huystee Rv R, Lajoie G
Phytochemistry (2004) 65(11): 1575-88

Proteome analysis differentiates between two highly homologues germin-like proteins in Arabidopsis thaliana ecotypes Col-0 and Ws-2.
Schlesier B, Berna A, Bernier F, Mock HP
Phytochemistry (2004) 65(11): 1565-74

Improved Molecular Weight-Based Processing of Intact Proteins for Interrogation by Quadrupole-Enhanced FT MS/MS
Yi Du, Fanyu Meng, Steven M. Patrie, Leah M. Miller, and Neil L. Kelleher
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 801-806

Protein Tyrosine-O-Sulfation Analysis by Exhaustive Product Ion Scanning with Minimum Collision Offset in a NanoESI Q-TOF Tandem Mass Spectrometer
Mogjiborahman Salek, Sabine Costagliola, and Wolf D. Lehmann
ANALYTICAL CHEMISTRY Early Edition: published 08/06/2004

Profiling treatment-specific post-translational modifications in a complex proteome with subtractive substrate phage display
Angela Tenzer, Barbara Hofstetter, Christelle Sauser, Stephan Bodis, August P. Schubiger, Christophe Bonny, Martin Pruschy
PROTEOMICS (2004) 4(9): 2796-2804

Antibodies Immobilized as Arrays to Profile Protein Post-translational Modifications in Mammalian Cells
Stanimir S. Ivanov, Alicia S. Chung, Zheng-long Yuan, Ying-jie Guan, Katherine V. Sachs, Jonathan S. Reichner, and Y. Eugene Chin
Mol Cell Proteomics (2004) 3(8): 788-795

A tagging-via-substrate technology for detection and proteomics of farnesylated proteins
Yoonjung Kho, Sung Chan Kim, Chen Jiang, Deb Barma, Sung Won Kwon, Jinke Cheng, Janis Jaunbergs, Carolyn Weinbaum, Fuyuhiko Tamanoi, John Falck, and Yingming Zhao
PNAS (2004) 101(34): 12479-12484

A proteomic approach for the discovery of protease substrates.
Bredemeyer AJ, Lewis RM, Malone JP, Davis AE, Gross J, Townsend RR, Ley TJ
Proc Natl Acad Sci U S A Early Edition: published 27-July-2004

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Protein-protein interaction

Kinetics of regulated protein-protein interactions revealed with firefly luciferase complementation imaging in cells and living animals
Kathryn E. Luker, Matthew C. P. Smith, Gary D. Luker, Seth T. Gammon, Helen Piwnica-Worms, and David Piwnica-Worms
PNAS (2004) 101(33): 12288-12293

A critical and integrated view of the yeast interactome
Michael Cornell, Norman W. Paton, Stephen G. Oliver
Comparative and Functional Genomics (2004) 5(5): 382-402

A proteomic approach for the discovery of protease substrates
Andrew J. Bredemeyer, Renate M. Lewis, James P. Malone, Alan E. Davis, Julia Gross, R. Reid Townsend, and Timothy J. Ley
PNAS (2004) 101(32): 11785-11790

Biochemical Characterization of Protein Complexes from the Helicobacter pylori Protein Interaction Map: Strategies for Complex Formation and Evidence for Novel Interactions Within Type IV Secretion Systems
Laurent Terradot, Nathan Durnell, Min Li, Ming Li, Jeremiah Ory, AgnesLabigne, Pierre Legrain, Frederic Colland, and Gabriel Waksman
Mol Cell Proteomics (2004) 3(8): 809-819

Determination of protein-protein interactions through aldehyde-dextran intermolecular cross-linking
Manuel Fuentes, Rosa L. Segura, Olga Abian, Lorena Betancor, Aurelio Hidalgo, Cesar Mateo, Roberto Fernandez-Lafuente, Jose M. Guisan
PROTEOMICS (2004) 4(9): 2602-2607

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Quantitation

Characterization of a digested protein complex with quantitative aspects: An approach based on accurate mass chromatographic analysis with Fourier transform-ion cyclotron resonance mass spectrometry
Takemichi Nakamura, Naoshi Dohmae, Koji Takio
PROTEOMICS (2004) 4(9): 2558-2566

Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics.
Whitelegge JP, Katz JE, Pihakari KA, Hale R, Aguilera R, Gomez SM, Faull KF, Vavilin D, Vermaas W
Phytochemistry (2004) 65(11): 1507-15

Proteomic capacity of recent fluorescent dyes for protein staining.
Chevalier F, Rofidal V, Vanova P, Bergoin A, Rossignol M
Phytochemistry (2004) 65(11): 1499-506

Quantitative Mass Spectrometric Immunoassay of Insulin Like Growth Factor 1
Randall W. Nelson, Dobrin Nedelkov, Kemmons A. Tubbs, and Urban A. Kiernan
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 851-855

Quantitative Proteomic and Transcriptional Analysis of the Response to the p38 Mitogen-activated Protein Kinase Inhibitor SB203580 in Transformed Follicular Lymphoma Cells
Zhaosheng Lin, David K. Crockett, Stephen D. Jenson, Megan S. Lim, andKojo S. J. Elenitoba-Johnson
Mol Cell Proteomics (2004) 3(8): 820-833

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Review

Advances in pituitary pathology: use of novel techniques.
Lloyd RV
Front Horm Res (2004) 32: 146-74.

Functional genomics studied by proteomics.
Honore B, OStergaard M, Vorum H
Bioessays (2004) 26(8): 901-15.

Proteomics in pathology research.
Lim MS, Elenitoba-Johnson KS
Lab Invest Early Edition: published 2004 Aug 16

Proteomics and ovarian cancer: implications for diagnosis and treatment: a critical review of the recent literature.
Posadas EM, Davidson B, Kohn EC
Curr Opin Oncol (2004) 16(5): 478-84

Tackling the plant proteome: practical approaches, hurdles and experimental tools.
Rose JK, Bashir S, Giovannoni JJ, Jahn MM, Saravanan RS
Plant J (2004) 39(5): 715-33

Multivariate approaches in plant science.
Gottlieb DM, Schultz J, Bruun SW, Jacobsen S, Sondergaard I
Phytochemistry (2004) 65(11): 1531-48

Technical aspects of functional proteomics in plants.
Hirano H, Islam N, Kawasaki H
Phytochemistry (2004) 65(11): 1487-98

Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments.
Newton RP, Brenton AG, Smith CJ, Dudley E
Phytochemistry (2004) 65(11): 1449-85

Proteomics: empowering systems biology in plants.
Paul Bolwell G, Slabas AR, Whitelegge JP
Phytochemistry (2004) 65(11): 1443-7

Biomarker discovery and validation: technologies and integrative approaches
Sergey E Ilyin, Stanley M Belkowski and Carlos R Plata-Salaman
Trends in Biotechnology (2004) 22(8): 411-416

Capillary electrochromatography of peptides and proteins
Dirk Bandilla and Cameron D Skinner
J Chromatogr A (2004) 1044(1-2): 113-129

Review coupling of capillary electrochromatography to mass spectrometry
Christian W Klampfl
J Chromatogr A (2004) 1044(1-2): 131-144

Proteomics of calcium-signaling components in plants.
Reddy VS, Reddy AS
Phytochemistry (2004) 65(12): 1745-76

Rice proteomics: recent developments and analysis of nuclear proteins.
Khan MM, Komatsu S
Phytochemistry (2004) 65(12): 1671-81

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Methodology

A method for proteomic identification of membrane-bound proteins containing Asn-linked oligosaccharides.
Fan X, She YM, Bagshaw RD, Callahan JW, Schachter H, Mahuran DJ
Anal Biochem (2004) 332(1): 178-86

Homology-based functional proteomics by mass spectrometry: Application to the Xenopus microtubule-associated proteome
Adam J. Liska, Andrei V. Popov, Shamil Sunyaev, Peg Coughlin, Bianca Habermann, Anna Shevchenko, Peer Bork, Eric Karsenti, Andrej Shevchenko
PROTEOMICS (2004) 4(9): 2707-2721

Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry
Eric F. Strittmatter, Lars J. Kangas, Konstantinos Petritis, Heather M. Mottaz, Gordon A. Anderson, Yufeng Shen, Jon M. Jacobs, David G. Camp II, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 760-769

Improved Molecular Weight-Based Processing of Intact Proteins for Interrogation by Quadrupole-Enhanced FT MS/MS
Yi Du, Fanyu Meng, Steven M. Patrie, Leah M. Miller, and Neil L. Kelleher
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 801-806

Potential for False Positive Identifications from Large Databases through Tandem Mass Spectrometry
Benjamin J. Cargile, Jonathan L. Bundy, and James L. Stephenson, Jr
JOURNAL OF PROTEOME RESEARCH Early Edition: published 08/20/2004

A method for the rapid depletion of albumin and immunoglobulin from human plasma
Carrie Greenough, Rosalind E. Jenkins, Neil R. Kitteringham, Munir Pirmohamed, B. Kevin Park, Stephen R. Pennington
PROTEOMICS Early Edition: published 23 Jul 2004

Global Differential Non-Gel Proteomics by Quantitative and Stable Labeling of Tryptic Peptides with Oxygen-18
An Staes, Hans Demol, Jozef Van Damme, Lennart Martens, Joël Vandekerckhove, and Kris Gevaert
JOURNAL OF PROTEOME RESEARCH (2004) 3(4): 786-791

A Proteome Strategy for Fractionating Proteins and Peptides Using Continuous Free-Flow Electrophoresis Coupled Off-Line to Reversed-Phase High-Performance Liquid Chromatography
Robert L. Moritz, Hong Ji, Frédéric Schütz, Lisa M. Connolly, Eugene A. Kapp, Terence P. Speed, and Richard J. Simpson
ANALYTICAL CHEMISTRY (2004) 76(16): 4811-4824

Analysis of the Low Molecular Weight Fraction of Serum by LC-Dual ESI-FT-ICR Mass Spectrometry: Precision of Retention Time, Mass, and Ion Abundance
Kenneth L. Johnson, Christopher J. Mason, David C. Muddiman, and Jeanette E. Eckel
ANALYTICAL CHEMISTRY Early Edition: published 08/06/2004

High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-peptide Enrichment Technology
Tao Liu, Wei-Jun Qian, Eric F. Strittmatter, David G. Camp, II, Brian D. Thrall, and Richard D. Smith
ANALYTICAL CHEMISTRY Early Edition: published 08/06/2004

Optimization of Two-Dimensional Off-Line LC/MS Separations To Improve Resolution of Complex Proteomic Samples
Martin Vollmer, Patric Hörth, and Edgar Nägele
ANALYTICAL CHEMISTRY Early Edition: published 08/06/2004

Automated, on-line two-dimensional nano liquid ­chromatography tandem mass spectrometry for rapid analysis of complex protein digests
Goran Mitulovi?, Christoph Stingl, Marek Smoluch, Remco Swart, Jean-Pierre Chervet, Ines Steinmacher, Christopher Gerner, Karl Mechtler
PROTEOMICS Early Edition: published 9 Aug 2004

Automated methods for improved protein identification by peptide mass fingerprinting
Fredrik Levander, Thorsteinn Rögnvaldsson, Jim Samuelsson, Peter James
PROTEOMICS Early Edition: published 24 Jun 2004

Development of a bioreactor based on trypsin immobilized on monolithic support for the on-line digestion and identification of proteins
E. Calleri, C. Temporini, E. Perani, C. Stella, S. Rudaz, D. Lubda, G. Mellerio, J.-L. Veuthey, G. Caccialanza and G. Massolini
J Chromatogr A (2004) 1045(1-2): 99-109

Construction of a hybrid quadrupole/fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa
Steven M Patrie, Jay P Charlebois, David Whipple, Neil L Kelleher, Christopher L Hendrickson, John P Quinn, Alan G Marshall and Biswarup Mukhopadhyay
J Am Soc Mass Spectrom (2004) 15(7): 1099-1108

Techniques: The application of accelerator mass spectrometry to pharmacology and toxicology
Ian N.H. White and Karen Brown
Trends in Pharmacological Sciences (2004) 25(8): 442-447

High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification.
Mooney BP, Thelen JJ
Phytochemistry (2004) 65(12): 1733-44

Sub-cellular proteomic analysis of a Medicago truncatula root microsomal fraction.
Valot B, Gianinazzi S, Eliane DG
Phytochemistry (2004) 65(12): 1721-32

Proteomics of Medicago sativa cell walls.
Watson BS, Lei Z, Dixon RA, Sumner LW
Phytochemistry (2004) 65(12): 1709-20

A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues
Ramu S. Saravanan, Jocelyn K. C. Rose
PROTEOMICS (2004) 4(9): 2522-2532

Parallel isoelectric focusing chip
Gleb Zilberstein, Leonid Korol, Shmuel Bukshpan, Emanuil Baskin
PROTEOMICS (2004) 4(9): 2533-2540

A peptide preconcentration approach for nano-high-performance liquid chromatography to diminish memory effects
Heike Schaefer, Jean-Pierre Chervet, Christian Bunse, Cornelia Joppich, Helmut E. Meyer, Katrin Marcus
PROTEOMICS (2004) 4(9): 2541-2544

Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests
Goran Mitulovi?, Christoph Stingl, Marek Smoluch, Remco Swart, Jean-Pierre Chervet, Ines Steinmacher, Christopher Gerner, Karl Mechtler
PROTEOMICS (2004) 4(9): 2545-2557

High reproducibility of large-gel two-dimensional electrophoresis
Kiran Kumar Challapalli, Claus Zabel, Johannes Schuchhardt, Angela M. Kaindl, Joachim Klose, Hanspeter Herzel
ELECTROPHORESIS (2004) 25(17): 3040-3047

A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis
Ian R. White, Russell Pickford, John Wood, J. Mark Skehel, Bevan Gangadharan, Paul Cutler
ELECTROPHORESIS (2004) 25(17): 3048-3054

Characterization of a digested protein complex with quantitative aspects: An approach based on accurate mass chromatographic analysis with Fourier transform-ion cyclotron resonance mass spectrometry
Takemichi Nakamura, Naoshi Dohmae, Koji Takio
PROTEOMICS (2004) 4(9): 2558-2566

Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification
Isam Rais, Michael Karas, Hermann Schägger
PROTEOMICS (2004) 4(9): 2567-2571

New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast and versatile fractionation strategy.
Peltier JB, Ytterberg AJ, Sun Q, Van Wijk KJ
J Biol Chem Early Edition: published 2004 Aug 20

Evaluation of a Novel, Integrated Approach Using Functionalized Magnetic Beads, Bench-Top MALDI-TOF-MS with Prestructured Sample Supports, and Pattern Recognition Software for Profiling Potential Biomarkers in Human Plasma.
Zhang X, Leung SM, Morris CR, Shigenaga MK
J Biomol Tech (2004) 15(3): 167-75

Development of a monolithic silica extraction tip for the analysis of proteins.
Miyazaki S, Morisato K, Ishizuka N, Minakuchi H, Shintani Y, Furuno M, Nakanishi K
J Chromatogr A (2004) 1043(1): 19-25

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Meeting

Meetings Diary: Proteomics 9/2004
PROTEOMICS (2004) 4(9): 2823

Calendar
Mol Cell Proteomics (2004) 3(8): 841-842

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Other

A human proteome project with a beginning and an end
Ian Humphery-Smith
PROTEOMICS (2004) 4(9): 2519-2521

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