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SPS' Digest

Issue 09, 4-Aug-2004

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In this issue, 123 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 (16) / Biological applications (8) / Biomedical applications (23) / Clinical applications (20) / Eukaryotic Cells And Tissues (1) / Prokaryotes (2) / Protein Array (2) / Protein Characterization (11) / Protein-protein interaction (3) / Quantitation (4) / Review (4) / Methodology (29) / Books (3) / Meeting (1) / Other (6) /

Bioinformatics

Towards developing a protein infrared spectra databank (PISD) for proteomics research
Joachim A. Hering, Peter R. Innocent, Parvez I. Haris
PROTEOMICS (2004) 4(8): 2310-2319

Mining mass spectra for diagnosis and biomarker discovery of cerebral accidents
Julien Prados, Alexandros Kalousis, Jean-Charles Sanchez, Laure Allard, Odile Carrette, Melanie Hilario
PROTEOMICS (2004) 4(8): 2320-2332

In vitro and in silico processes to identify differentially expressed proteins
Nadia Allet, Nicolas Barrillat, Thierry Baussant, Celia Boiteau, Paolo Botti, Lydie Bougueleret, Nicolas Budin, Denis Canet, Stéphanie Carraud, Diego Chiappe, Nicolas Christmann, Jacques Colinge, Isabelle Cusin, Nicolas Dafflon, Benoît Depresle, Irène Fasso, Pascal Frauchiger, Hubert Gaertner, Anne Gleizes, Eduardo Gonzalez-Couto, Catherine Jeandenans, Abderrahim Karmime, Thomas Kowall, Sophie Lagache, Eve Mahé, Alexandre Masselot, Hassan Mattou, Marc Moniatte, Anne Niknejad, Marianne Paolini, Frédéric Perret, Nicolas Pinaud, Frédéric Ranno, Sylvain Raimondi, Samia Reffas, Pierre-Olivier Regamey, Pierre-Antoine Rey, Patricia Rodriguez-Tomé, Keith Rose, Gérald Rossellat, Cédric Saudrais, Camille Schmidt, Matteo Villain, Catherine Zwahlen
PROTEOMICS (2004) 4(8): 2333-2351

SWISS-2DPAGE, ten years later
Christine Hoogland, Khaled Mostaguir, Jean-Charles Sanchez, Denis F. Hochstrasser, Ron D. Appel
PROTEOMICS (2004) 4(8): 2352-2356

Towards data management of the HUPO Human Brain Proteome Project pilot phase
Martin Blüggel, Sonja Bailey, Gerhard Körting, Christian Stephan, Kai A. Reidegeld, Herbert Thiele, Rolf Apweiler, Michael Hamacher, Helmut E. Meyer
PROTEOMICS (2004) 4(8): 2361-2362

Advances in the development of common interchange standards for proteomic data
Sandra Orchard, Chris F. Taylor, Henning Hermjakob, Weimin-Zhu, Randall K. Julian Jr., Rolf Apweiler
PROTEOMICS (2004) 4(8): 2363-2365

Bioinformatics in proteomics: application, terminology, and pitfalls.
Wiemer JC, Prokudin A
Pathol Res Pract (2004) 200(2): 173-8.

Bioinformatics strategies for proteomic profiling.
White CN, Chan DW, Zhang Z
Clin Biochem (2004) 37(7): 636-41.

Open Mass Spectrometry Search Algorithm
Lewis Y. Geer, Sanford P. Markey, Jeffrey A. Kowalak, Lukas Wagner, Dawn M. Maynard, Xiaoyu Yang, Wenyao Shi, and Stephen H. Bryant
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/02/2004

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, Gordon A. Anderson, Yufeng Shen, Jon M. Jacobs, David G. Camp II, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/09/2004

Improving Reproducibility and Sensitivity in Identifying Human Proteins by Shotgun Proteomics
Katheryn A. Resing, Karen Meyer-Arendt, Alex M. Mendoza, Lauren D. Aveline-Wolf, Karen R. Jonscher, Kevin G. Pierce, William M. Old, Hiu T. Cheung, Steven Russell, Joy L. Wattawa, Geoff R. Goehle, Robin D. Knight, and Natalie G. Ahn
ANALYTICAL CHEMISTRY (2004) 76(13): 3556-3568

A Tool To Visualize and Evaluate Data Obtained by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry
Xiao-jun Li, Patrick G. A. Pedrioli, Jimmy Eng, Dan Martin, Eugene C. Yi, Hookeun Lee, and Ruedi Aebersold
ANALYTICAL CHEMISTRY (2004) 76(13): 3856-3860

Application of the GA/KNN method to SELDI proteomics data
Leping Li, David M. Umbach, Paul Terry, and Jack A. Taylor
Bioinformatics (2004) 20(10): 1638-1640

Automatic Quality Assessment of Peptide Tandem Mass Spectra
Marshall Bern, David Goldberg, W. Hayes McDonald, and John R. Yates, III
Bioinformatics (2004) 20(suppl_1): i49-i54

Analysis of domain correlations in yeast protein complexes
Doron Betel, Ruth Isserlin, and Christopher W. V. Hogue
Bioinformatics (2004) 20(suppl_1): i55-i62

Predicting protein-peptide interactions via a network-based motif sampler
David J. Reiss and Benno Schwikowski
Bioinformatics (2004) 20(suppl_1): i274-i282

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Biological applications

Quantitative proteome profiling during the fermentation process of pleiotropic Bacillus subtilis mutants
Haike Antelmann, Ron Sapolsky, Brian Miller, Eugenio Ferrari, Gopal Chotani, Walter Weyler, Alfred Gaertner, Michael Hecker
PROTEOMICS (2004) 4(8): 2408-2424

Proteomic response to amino acid starvation inCandida albicans and Saccharomyces cerevisiae
Zhikang Yin, David Stead, Laura Selway, Janet Walker, Isabel Riba-Garcia, Tracey Mclnerney, Simon Gaskell, Stephen G. Oliver, Philip Cash, Alistair J. P. Brown
PROTEOMICS (2004) 4(8): 2425-2436

Proteome analysis of barley seeds: Identification of major proteins from two-dimensional gels (pI 4-7)
Ole Østergaard, Christine Finnie, Sabrina Laugesen, Peter Roepstorff, Birte Svennson
PROTEOMICS (2004) 4(8): 2437-2447

UDP-Glucose pyrophosphorylase is upregulated in carriers of the porcine RN- mutation in the AMP-activated protein kinase
Jakob Hedegaard, Per Horn, René Lametsch, Hanne Søndergaard Møller, Peter Roepstorff, Christian Bendixen, Emøke Bendixen
PROTEOMICS (2004) 4(8): 2448-2454

Proteome analysis of apoptotic cells
Bernd Thiede, Thomas Rudel
Mass Spectrometry Reviews (2004) 23(5): 333-349

Identification of New Intrinsic Proteins in Arabidopsis Plasma Membrane Proteome
Anne Marmagne, Marie-Aude Rouet, Myriam Ferro, Norbert Rolland, CarineAlcon, Jacques Joyard, Jerome Garin, Helene Barbier-Brygoo, and Genevieve Ephritikhine
Mol Cell Proteomics (2004) 3(7): 675-691

Identification of the Linker-SH2 Domain of STAT as the Origin of the SH2 Domain Using Two-dimensional Structural Alignment
Qian Gao, Jian Hua, Rich Kimura, Jeffery J. Headd, Xin-yuan Fu, and Y.Eugene Chin
Mol Cell Proteomics (2004) 3(7): 704-714

A Proteomic Analysis of Human Bile
Troels Zakarias Kristiansen, Jakob Bunkenborg, Mads Gronborg, Henrik Molina, Paul J. Thuluvath, Pedram Argani, Michael G. Goggins, Anirban Maitra, and Akhilesh Pandey
Mol Cell Proteomics (2004) 3(7): 715-728

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Biomedical applications

Cystatin C as a potential cerebrospinal fluid marker for the diagnosis of Creutzfeldt-Jakob disease
Jean-Charles Sanchez, Elisabeth Guillaume, Pierre Lescuyer, Laure Allard, Odile Carrette, Alex Scherl, Jennifer Burgess, Garry L. Corthals, Pierre R. Burkhard, Denis F. Hochstrasser
PROTEOMICS (2004) 4(8): 2229-2233

Identification of post-mortem cerebrospinal fluid proteins as potential biomarkers of ischemia and neurodegeneration
Pierre Lescuyer, Laure Allard, Catherine G. Zimmermann-Ivol, Jennifer A. Burgess, Séverine Hughes-Frutiger, Pierre R. Burkhard, Jean-Charles Sanchez, Denis F. Hochstrasser
PROTEOMICS (2004) 4(8): 2234-2241

ApoC-I and ApoC-III as potential plasmatic markers to distinguish between ischemic and hemorrhagic stroke
Laure Allard, Pierre Lescuyer, Jennifer Burgess, Kit-Yi Leung, Malcolm Ward, Nadia Walter, Pierre R. Burkhard, Garry Corthals, Denis F. Hochstrasser, Jean-Charles Sanchez
PROTEOMICS (2004) 4(8): 2242-2251

Expression of heat shock protein 27 in human renal cell carcinoma
Cecilia Sarto, Cristina Valsecchi, Fulvio Magni, Lucia Tremolada, Carmelo Arizzi, Nicoletta Cordani, Stefano Casellato, Giancarlo Doro, Paolo Favini, Roberto A. Perego, Francesca Raimondo, Stefano Ferrero, Paolo Mocarelli, Marzia Galli-Kienle
PROTEOMICS (2004) 4(8): 2252-2260

Radioresistance-related proteins in rectal cancer
Abdelkarim S. Allal, Thilo Kähne, Alexandra K. Reverdin, Hans Lippert, Werner Schlegel, Marc-André Reymond
PROTEOMICS (2004) 4(8): 2261-2269

Effect of high-fat diet on the expression of proteins in muscle, adipose tissues, and liver of C57BL/6 mice
Gerhard M. Schmid, Véronique Converset, Nadia Walter, Matthew V. Sennitt, Kit-Yi Leung, Helen Byers, Malcolm Ward, Denis F. Hochstrasser, Michael A. Cawthorne, Jean-Charles Sanchez
PROTEOMICS (2004) 4(8): 2270-2282

Pleiotropic molecular effects of the pro-apoptotic dietary constituent flavone in human colon cancer cells identified by protein and mRNA expression profiling
Angelika Herzog, Birgit Kindermann, Frank Döring, Hannelore Daniel, Uwe Wenzel
PROTEOMICS (2004) 4(8): 2455-2464

Proteomic Analysis of Human Leukemic U937 Cells Incubated with Conditioned Medium of Mononuclear Cells Stimulated by Proteins from Dietary Mushroom of Agrocybe aegerita
Yuh-Tai Wang, Zhu-Jun Huang, and Hung-Min Chang
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/02/2004

Aberrant expression of acute-phase reactant proteins in sera and breast lesions of patients with malignant and benign breast tumors
Saeid R. Doustjalali, Rohana Yusof, Cheng-Har Yip, Lai-Meng Looi, Bhanumathy Pillay, Onn H. Hashim
ELECTROPHORESIS (2004) 25(14): 2392-2401

Improved capillary electrophoresis method for the determination of carbohydrate-deficient transferrin in patient sera
Christian Lanz, Martina Kuhn, Veronika Deiss, Wolfgang Thormann
ELECTROPHORESIS (2004) 25(14): 2309-2318

Virtual two-dimensional gel electrophoresis of high-density lipoproteins
Rachel R. Ogorzalek Loo, Lang Yam, Joseph A. Loo, Verne N. Schumaker
ELECTROPHORESIS (2004) 25(14): 2384-2391

A Proteomic Analysis of Human Bile
Troels Zakarias Kristiansen, Jakob Bunkenborg, Mads Gronborg, Henrik Molina, Paul J. Thuluvath, Pedram Argani, Michael G. Goggins, Anirban Maitra, and Akhilesh Pandey
Mol Cell Proteomics (2004) 3(7): 715-728

Identification of swiprosin 1 in human lymphocytes
Françoise Vuadens, Nathalie Rufer, Annegret Kress, Patricia Corthésy, Philippe Schneider, Jean-Daniel Tissot
PROTEOMICS (2004) 4(8): 2216-2220

Antioxidant role of human haptoglobin
Chi Feng Tseng, Chia Ching Lin, Hsing Yi Huang, Huei Chun Liu, Simon J. T. Mao
PROTEOMICS (2004) 4(8): 2221-2228

Identification of proteins in activated human neutrophils susceptible to tyrosyl radical attack. A proteomic study using a tyrosylating fluorophore
Diana Avram, Edwin P. Romijn, Everard H. W. Pap, Albert J. R. Heck, Karel W. A. Wirtz
PROTEOMICS (2004) 4(8): 2397-2407

Proteomics of buccal squamous cell carcinoma: The involvement of multiple pathways in tumorigenesis
Jia Chen, Qing-Yu He, Anthony Po-Wing Yuen, Jeng-Fu Chiu
PROTEOMICS (2004) 4(8): 2465-2475

Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: A strategy for identification of candidate cancer biomarkers
Haixing Wang, Maureen T. Kachman, Donald R. Schwartz, Kathleen R. Cho, David M. Lubman
PROTEOMICS (2004) 4(8): 2476-2495

Array technology and proteomics in autoimmune diseases.
Krenn V, Petersen I, Haupl T, Koepenik A, Blind C, Dietel M, Konthur Z, Skriner K
Pathol Res Pract (2004) 200(2): 95-103.

Proteomics in pathology, research and practice.
Rocken C, Ebert MP, Roessner A
Pathol Res Pract (2004) 200(2): 69-82.

Proteomic Analysis of the Soluble Fraction from Human Corneal Fibroblasts with Reference to Ocular Transparency
Henrik Karring, Ida B. Thogersen, Gordon K. Klintworth, Jan J. Enghild, and Torben Moller-Pedersen
Mol Cell Proteomics (2004) 3(7): 660-674

Quantitative Cancer Proteomics: Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) as a Tool for Prostate Cancer Research
Patrick A. Everley, Jeroen Krijgsveld, Bruce R. Zetter, and Steven P. Gygi
Mol Cell Proteomics (2004) 3(7): 729-735

Profiling of rat plasma by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, a novel tool for biomarker discovery in nutrition research
Thomas Linke, A.Catharine Ross and Earl H Harrison
Journal of Chromatography A (2004) 1043(1): 65-71

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Clinical applications

Lessons from Kitty Hawk: From feasibility to routine clinical use for the field of proteomic pattern diagnostics
Emanuel F. Petricoin, David A. Fishman, Thomas P. Conrads, Timothy D. Veenstra, Lance A. Liotta
PROTEOMICS (2004) 4(8): 2357-2360

Proteomics of buccal squamous cell carcinoma: The involvement of multiple pathways in tumorigenesis
Jia Chen, Qing-Yu He, Anthony Po-Wing Yuen, Jeng-Fu Chiu
PROTEOMICS (2004) 4(8): 2465-2475

Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: A strategy for identification of candidate cancer biomarkers
Haixing Wang, Maureen T. Kachman, Donald R. Schwartz, Kathleen R. Cho, David M. Lubman
PROTEOMICS (2004) 4(8): 2476-2495

Cystatin C as a potential cerebrospinal fluid marker for the diagnosis of Creutzfeldt-Jakob disease
Jean-Charles Sanchez, Elisabeth Guillaume, Pierre Lescuyer, Laure Allard, Odile Carrette, Alex Scherl, Jennifer Burgess, Garry L. Corthals, Pierre R. Burkhard, Denis F. Hochstrasser
PROTEOMICS (2004) 4(8): 2229-2233

Identification of post-mortem cerebrospinal fluid proteins as potential biomarkers of ischemia and neurodegeneration
Pierre Lescuyer, Laure Allard, Catherine G. Zimmermann-Ivol, Jennifer A. Burgess, Séverine Hughes-Frutiger, Pierre R. Burkhard, Jean-Charles Sanchez, Denis F. Hochstrasser
PROTEOMICS (2004) 4(8): 2234-2241

ApoC-I and ApoC-III as potential plasmatic markers to distinguish between ischemic and hemorrhagic stroke
Laure Allard, Pierre Lescuyer, Jennifer Burgess, Kit-Yi Leung, Malcolm Ward, Nadia Walter, Pierre R. Burkhard, Garry Corthals, Denis F. Hochstrasser, Jean-Charles Sanchez
PROTEOMICS (2004) 4(8): 2242-2251

Differential proteomic analysis of human hepatocellular carcinoma cell line metastasis-associated proteins
Cui JF, Liu YK, Pan BS, Song HY, Zhang Y, Sun RX, Chen J, Feng JT, Tang ZY, Yu YL, Shen HL, Yang PY
J Cancer Res Clin Oncol Early Edition: published 09-July-2004

Clinical proteomics in lung diseases.
Waldburg N, Kahne T, Reisenauer A, Rocken C, Welte T, Buhling F
Pathol Res Pract (2004) 200(2): 147-54.

Capillary electrophoresis coupled to mass spectrometer for automated and robust polypeptide determination in body fluids for clinical use
Thorsten Kaiser, Stefan Wittke, Ingo Just, Ronald Krebs, Sebastian Bartel, Danilo Fliser, Harald Mischak, Eva M. Weissinger
ELECTROPHORESIS (2004) 25(13): 2044-2055

Proteomics in myocardial diseases.
Bukowska A, Lendeckel U, Kahne T, Goette A
Pathol Res Pract (2004) 200(2): 135-45.

Proteomics and chronic inflammatory bowel diseases.
Felley-Bosco E, Andre M
Pathol Res Pract (2004) 200(2): 129-33.

Expression and functional proteomics studies in colorectal cancer.
Reymond MA, Steinert R, Kahne T, Sagynaliev E, Allal AS, Lippert H
Pathol Res Pract (2004) 200(2): 119-27.

Proteomics in cancer cell research: an analysis of therapy resistance.
Lage H
Pathol Res Pract (2004) 200(2): 105-17.

Proteomics and cancer diagnosis: the potential of mass spectrometry.
Rodland KD
Clin Biochem (2004) 37(7): 579-83.

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 and Biomarker Discovery.
Johann DJ Jr, McGuigan MD, Patel AR, Tomov S, Ross S, Conrads TP, Veenstra TD, Fishman DA, Whiteley GR, Petricoin EF 3rd, Liotta LA
Ann N Y Acad Sci (2004) 1022: 295-305.

Cancer Proteomics: Serum Diagnostics for Tumor Marker Discovery.
Rai AJ, Chan DW
Ann N Y Acad Sci (2004) 1022: 286-294.

Circulating Nucleic Acids and Proteomics of Plasma/Serum: Clinical Utility.
Taback B, Hoon DS
Ann N Y Acad Sci (2004) 1022: 1-8.

Refining the results of a whole-genome screen based on 4666 microsatellite markers for defining predisposition factors for multiple sclerosis
René Gödde, Viktoria Nigmatova, Peter Jagiello, Eckhart Sindern, Michael Haupts, Sebastian Schimrigk, Jörg T. Epplen
ELECTROPHORESIS (2004) 25(14): 2212-2218

Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry
Giuseppina Maccarrone, Dale Milfay, Isabel Birg, Marcus Rosenhagen, Florian Holsboer, Rudolf Grimm, Jerome Bailey, Nina Zolotarjova, Christoph W. Turck
ELECTROPHORESIS (2004) 25(14): 2402-2412

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Eukaryotic Cells And Tissues

Epithelial cell preparation for proteomic and transcriptomic analysis in human pancreatic tissue.
Kellner U, Steinert R, Seibert V, Heim S, Kellner A, Schulz HU, Roessner A, Kruger S, Reymond M
Pathol Res Pract (2004) 200(2): 155-63.

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Prokaryotes

Application of capillary electrophoresis/ electrospray ionization-mass spectrometry to subcellular proteomics of Escherichia coli ribosomal proteins
Mehdi Moini, Hsiaoling Huang
ELECTROPHORESIS (2004) 25(13): 1981-1987

Identification of Biomarkers of Whole Coxiella burnetii Phase I by MALDI-TOF Mass Spectrometry
Edward I. Shaw, Hercules Moura, Adrian R. Woolfitt, Maria Ospina, Herbert A. Thompson, and John R. Barr
ANALYTICAL CHEMISTRY (2004) 76(14): 4017-4022

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Protein Array

Micropatterned agarose gels for stamping arrays of proteins and gradients of proteins
Michael Mayer, Jerry Yang, Irina Gitlin, David H. Gracias, George M. Whitesides
PROTEOMICS (2004) 4(8): 2366-2376

Development of a Protein Chip: A MS-Based Method for Quantitation of Protein Expression and Modification Levels Using an Immunoaffinity Approach
Erin N. Warren, Phillip J. Elms, Carol E. Parker, and Christoph H. Borchers
ANALYTICAL CHEMISTRY (2004) 76(14): 4082-4092

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Protein Characterization

Glycoproteomics of cerebrospinal fluid in neurodegenerative disease
Carina Sihlbom, Pia Davidsson, Mark R. Emmett, Alan G. Marshall and Carol L. Nilsson
International Journal of Mass Spectrometry (2004) 234(1-3): 145-152

Identification of swiprosin 1 in human lymphocytes
Françoise Vuadens, Nathalie Rufer, Annegret Kress, Patricia Corthésy, Philippe Schneider, Jean-Daniel Tissot
PROTEOMICS (2004) 4(8): 2216-2220

Antioxidant role of human haptoglobin
Chi Feng Tseng, Chia Ching Lin, Hsing Yi Huang, Huei Chun Liu, Simon J. T. Mao
PROTEOMICS (2004) 4(8): 2221-2228

Identification of proteins in activated human neutrophils susceptible to tyrosyl radical attack. A proteomic study using a tyrosylating fluorophore
Diana Avram, Edwin P. Romijn, Everard H. W. Pap, Albert J. R. Heck, Karel W. A. Wirtz
PROTEOMICS (2004) 4(8): 2397-2407

Proteomic tools to characterize the protein fraction of Equidae milk
Guy Miranda, Marie-Françoise Mahé, Christine Leroux, Patrice Martin
PROTEOMICS (2004) 4(8): 2496-2509

Investigation of intact protein complexes by mass spectrometry
Albert J. R. Heck, Robert H. H. van den Heuvel
Mass Spectrometry Reviews (2004) 23(5): 368-389

'Signature Sets', Minimal Fragment Sets for Identifying Protein Disulfide Structures with Cyanylation-Based Mass Mapping Methodology
Wei Wu, Wei Huang, Jianfeng Qi, Yi-Te Chou, Eric Torng, and J. Throck Watson
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/09/2004

Using Immobilized Metal Affinity Chromatography, Two-Dimensional Electrophoresis and Mass Spectrometry to Identify Hepatocellular Proteins with Copper-Binding Ability
Scott D. Smith, Yi-Min She, Eve A. Roberts, # and Bibudhendra Sarkar
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/16/2004

Enrichment of Cysteine-Containing Peptides from Tryptic Digests Using a Quaternary Amine Tag
Diya Ren, Samir Julka, Halina D. Inerowicz, and Fred E. Regnier
ANALYTICAL CHEMISTRY (2004) 76(15): 4522-4530

Vectorial proteomics reveal targeting, phosphorylation and specific fragmentation of PTRF (polymerase I and transcript release factor) at the surface of caveolae in human adipocytes.
Aboulaich N, Vainonen JP, Stralfors P, Vener AV
Biochem J. Early Edition: published 09-July-2004

Activity-based probes for the proteomic profiling of metalloproteases
Alan Saghatelian, Nadim Jessani, Arul Joseph, Mark Humphrey, and Benjamin F. Cravatt
PNAS (2004) 101(27): 10000-10005

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Protein-protein interaction

Studying the interactome with the yeast two-hybrid system and mass spectrometry
Barry Causier
Mass Spectrometry Reviews (2004) 23(5): 350-367

Analysis of alpha -synuclein-associated proteins by quantitative proteomics.
Zhou Y, Gu G, Goodlett DR, Zhang T, Pan C, Montine TJ, Montine KS, Aebersold RH, Zhang J
J Biol Chem. Early Edition: published 01-July-2004

Polyunsaturated Fatty Acids Including Docosahexaenoic and Arachidonic Acid Bind to the Retinoid X Receptor {alpha} Ligand-binding Domain
Johan Lengqvist, Alexander Mata de Urquiza, Ann-Charlotte Bergman, Timothy M. Willson, Jan Sjovall, Thomas Perlmann, and William J. Griffiths
Mol Cell Proteomics (2004) 3(7): 692-703

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Quantitation

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 Early Edition: published 07/16/2004

Absolute Quantification of Specific Proteins in Complex Mixtures Using Visible Isotope-Coded Affinity Tags
Yu Lu, Patricia Bottari, Frantisek Turecek, Ruedi Aebersold, and Michael H. Gelb
ANALYTICAL CHEMISTRY (2004) 76(14): 4104-4111

Absolute Quantitation of Proteins by a Combination of Acid Hydrolysis and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
Olga A. Mirgorodskaya, Roman Körner, Alexander Novikov, and Peter Roepstorff
ANALYTICAL CHEMISTRY (2004) 76(13): 3569-3575

Depth of Proteome Issues: A Yeast Isotope-Coded Affinity Tag Reagent Study
Kenneth C. Parker, Dale Patterson, Brian Williamson, Jason Marchese, Armin Graber, Feng He, Allan Jacobson, Peter Juhasz, and Stephen Martin
Mol Cell Proteomics (2004) 3(7): 625-659

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Review

State-of-the-art of the hyphenation of capillary electrochromatography with mass spectrometry
Elena Barceló-Barrachina, Encarnación Moyano, M. Teresa Galceran
ELECTROPHORESIS (2004) 25(13): 1927-1948

Capillary electrophoresis-mass spectrometry for glycoscreening in biomedical research
Alina Zamfir, Jasna Peter-Katalini?
ELECTROPHORESIS (2004) 25(13): 1949-1963

MALDI: more than peptide mass fingerprints.
Stuhler K, Meyer HE
Curr Opin Mol Ther (2004) 6(3): 239-48.

The potentials of MS-based subproteomic approaches in medical science: The case of lysosomes and breast cancer
Agnès Journet, Myriam Ferro
Mass Spectrometry Reviews (2004) 23(6): 393-442

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Methodology

Development of a monolithic silica extraction tip for the analysis of proteins
Shota Miyazaki, Kei Morisato, Norio Ishizuka, Hiroyoshi Minakuchi, Yukihiro Shintani, Masahiro Furuno and Kazuki Nakanishi
Journal of Chromatography A (2004) 1043(1): 19-25

Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts
Charlotta Agaton, Ronny Falk, Ingmarie Hoiden Guthenberg, Lovisa Gostring, Mathias Uhlen and Sophia Hober
Journal of Chromatography A (2004) 1043(1): 33-40

Strategies for automating top-down protein analysis with Q-FTICR MS
Steven M. Patrie, Dana E. Robinson, Fanyu Meng, Yi Du and Neil L. Kelleher
International Journal of Mass Spectrometry (2004) 234(1-3): 175-184

Effect of ionization mode in the analysis of proteolytic protein digests
Paul M. Bigwarfe Jr. and Troy D. Wood
International Journal of Mass Spectrometry (2004) 234(1-3): 185-202

High pressure MALDI-FTMS: implications for proteomics
Bogdan A. Budnik, Susanne C. Moyer, Jason L. Pittman, Vera B. Ivleva, Ulf Sommer, Catherine E. Costello and Peter B. O'Connor
International Journal of Mass Spectrometry (2004) 234(1-3): 203-212

Monoliths for microfluidic devices in proteomics
Severine Le Gac, Julien Carlier, Jean-Christophe Camart, Cecile Cren-Olive and Christian Rolando
Journal of Chromatography B (2004) 808(1): 3-14

Utilization of newly developed immobilized enzyme reactors for preparation and study of immunoglobulin G fragments
Lucie Korecka, Zuzana Bilkova, Michal Holeapek, Josef Kralovsky, Milan Benes, Jioi Lenfeld, Nicolas Minc, Roxana Cecal, Jean-Louis Viovy and Michael Przybylski
Journal of Chromatography B (2004) 808(1): 15-24

Differential proteome analysis and mass spectrometric characterization of germ line development-related proteins of Caenorhabditis elegans
Marcus Bantscheff, Bruno Ringel, András Madi, Ralf Schnabel, Michael O. Glocker, Hans-Jürgen Thiesen
PROTEOMICS (2004) 4(8): 2283-2295

Purification of biotinylated proteins on streptavidin resin: A protocol for quantitative elution
Jascha-N. Rybak, Simone B. Scheurer, Dario Neri, Giuliano Elia
PROTEOMICS (2004) 4(8): 2296-2299

High resolution mass spectrometric alveolar proteomics: Identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients
Yu Bai, Dmitry Galetskiy, Eugen Damoc, Christian Paschen, Zhiqiang Liu, Mathias Griese, Shuying Liu, Michael Przybylski
PROTEOMICS (2004) 4(8): 2300-2309

Preprocessing of two-dimensional gel electrophoresis images
Krzysztof Kaczmarek, Beata Walczak, Sijmen de Jong, Bernard G. M. Vandeginste
PROTEOMICS (2004) 4(8): 2377-2389

Atomic force microscopy revelation of molecular complexes in the multiprotein cytochrome P450 2B4-containing system
Vadim Yu. Kuznetsov, Yuri D. Ivanov, Alexander I. Archakov
PROTEOMICS (2004) 4(8): 2390-2396

Analysis of Murine Natural Killer Cell Microsomal Proteins Using Two-Dimensional Liquid Chromatography Coupled to Tandem Electrospray Ionization Mass Spectrometry
Josip Blonder, Maria C. Rodriguez-Galan, King C. Chan, David A. Lucas, Thomas P. Conrads, Haleem J. Issaq, Howard A. Young, and Timothy D. Veenstra
JOURNAL OF PROTEOME RESEARCH Early Edition: published 07/16/2004

NMR for structural proteomics of Thermotoga maritima: Screening and structure determination.
Peti W, Etezady-Esfarjani T, Herrmann T, Klock HE, Lesley SA, Wuthrich K
J Struct Funct Genomics (2004) 5(3): 205-15.

Intracellular antibodies for proteomics.
Visintin M, Meli GA, Cannistraci I, Cattaneo A
J Immunol Methods (2004) 290(1-2): 135-53.

Two-dimensional liquid chromatography-capillary zone electrophoresis-sheathless electrospray ionization-mass spectrometry: Evaluation for peptide analysis and protein identification
George M. Janini, King C. Chan, Thomas P. Conrads, Haleem J. Issaq, Timothy D. Veenstra
ELECTROPHORESIS (2004) 25(13): 1973-1980

Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis
Jie Zhang, Hualing Hu, Mingxia Gao, Pengyuan Yang, Xiangmin Zhang
ELECTROPHORESIS (2004) 25(14): 2374-2383

Two-step elution of human serum proteins from different glass-modified bioactive surfaces: A comparative proteomic analysis of adsorption patterns
Agnese Magnani, Rolando Barbucci, Stefania Lamponi, Antonio Chiumento, Alessandro Paffetti, Lorenza Trabalzini, Paola Martelli, Annalisa Santucci
ELECTROPHORESIS (2004) 25(14): 2413-2424

Localization of the O-Glycosylated Sites in Peptides by Fixed-Charge Derivatization with a Phosphonium Group
Xavier Czeszak, Willy Morelle, Guy Ricart, Daniel Tétaert, and Jérôme Lemoine
ANALYTICAL CHEMISTRY (2004) 76(15): 4320-4324

Detection of Oligosaccharides Labeled with Cyanine Dyes Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
Akihiko Kameyama, Yuko Kaneda, Hidenori Yamanaka, Hiroshi Yoshimine, Hisashi Narimatsu, and Yasuro Shinohara
ANALYTICAL CHEMISTRY (2004) 76(15): 4537-4542

Selective Isolation at the Femtomole Level of Phosphopeptides from Proteolytic Digests Using 2D-NanoLC-ESI-MS/MS and Titanium Oxide Precolumns
Martijn W. H. Pinkse, Pauliina M. Uitto, Martijn J. Hilhorst, Bert Ooms, and Albert J. R. Heck
ANALYTICAL CHEMISTRY (2004) 76(14): 3935-3943

Divinyl Sulfone as a Postdigestion Modifier for Enhancing the a1 Ion in MS/MS and Postsource Decay: Potential Applications in Proteomics
Emily S. Boja, Edward A. Sokoloski, and Henry M. Fales
ANALYTICAL CHEMISTRY (2004) 76(14): 3958-3970

A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics
Hongbin Liu, Rovshan G. Sadygov, and John R. Yates, III
ANALYTICAL CHEMISTRY (2004) 76(14): 4193-4201

Needle in a haystack: microdissecting the proteome of a tissue
H. J. Ball, N. H. Hunt
Amino Acids Early Edition: published 14-July-2004

Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI TOF-MS) and ProteinChip technology in proteomics research.
Seibert V, Wiesner A, Buschmann T, Meuer J
Pathol Res Pract (2004) 200(2): 83-94.

Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
John E. P. Syka, Joshua J. Coon, Melanie J. Schroeder, Jeffrey Shabanowitz, and Donald F. Hunt
PNAS (2004) 101(26): 9528-9533

MALDI MS Peptide Mapping Performance by In-Gel Digestion on a Probe with Prestructured Sample Supports
Tina Guldberg Klen , Christian Maal v Andreasen, Helle Ørsted Kjeldal, Lise R nnedal Leonardsen, Thomas Nylandsted Krogh, Per Franklin Nielsen, Marianne Vind S rensen, and Ole N rregaard Jensen
ANALYTICAL CHEMISTRY (2004) 76(13): 3576-3583

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
Journal of The American Society for Mass Spectrometry (2004) 15(7): 1099-1108

Optimum concentration of trifluoroacetic acid for reversed-phase liquid chromatography of peptides revisited
Y. Chen, A.R. Mehok, C.T. Mant and R.S. Hodges
Journal of Chromatography A (2004) 1043(1): 9-18

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Books

Book Reviews: Protein Purification Protocols, Second Edition. By Paul Cutler (Editor)
Cecilia Sarto
PROTEOMICS (2004) 4(8): 2510

Book Reviews: Protein Arrays, Biochips, and Proteomics. Edited by Joanna S. Albala and Ian Humphrey-Smith
Thomas Joos
PROTEOMICS (2004) 4(8): 2510-2512

Book Reviews: Biomedical Applications of Proteomics. By J.-C. Sanchez, G. L. Corthals, D. F. Hochstrasser (Eds.)
Hana Kovarova
PROTEOMICS (2004) 4(8): 2512-2513

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Meeting

Meetings: Proteomics 8/2004
PROTEOMICS (2004) 4(8): 2514

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Other

Quantify this! Report on a round table discussion on quantitative mass spectrometry in proteomics
Manfredo Quadroni, Axel Ducret, Reto Stöcklin
PROTEOMICS (2004) 4(8): 2211-2215

If you can lose a driving licence, why not a PhD?
Adam G. Hart
Nature (2004) 430(6999): 503

Bioanalysis: Its past, present, and some future
Pier Giorgio Righetti
ELECTROPHORESIS (2004) 25(14): 2111-2127

Britain decides 'open access' is still an open issue
Declan Butler
Nature (2004) 430(6998): 390

Proteomics in pathology, research and practice: ethical considerations.
Beck N
Pathol Res Pract (2004) 200(2): 179-80.

Responsible authorship of papers in PNAS
Nicholas R. Cozzarelli
PNAS (2004) 101(29): 10495

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