Contents: Proteomics 3/2009

CONTENTS Volume 9? Issue 3

February 2009

Proteomics 9 (3) 499–800 (2009)

REGULAR

REPORT 499 Managing the Data Explosion

A Report on the HUPO-PSI Workshop

August 2008, Amsterdam, The Netherlands

Sandra Orchard, Christine Hoogland, Amos Bairoch,Martin Eisenacher, Hans-Joachim Kraus and Pierre-Alain Binz

502 HUPO World Congress Publication Committee Meeting

August 2008, Amsterdam, The Netherlands

Sandra Orchard and Peipei Ping

Research Articles

504 Differential protein expression in heart in UT-B null mice with cardiac

conduction defects

Hao Yu, Yan Meng, Li-Shun Wang, Xian Jin, Li-Fang Gao,Lei Zhou, Kun Ji, Yang Li, Li-Juan Zhao, Guo-Qiang Chen,Xue-Jian Zhao and Baoxue Yang

512 Multivariate analysis of single quadrupole LC-MS spectra for routine

characterization and quantification of intact proteins

Francois-Thomas Michaud, Alain Garnier, Lise Lemieuxand Carl Duchesne

521 Proteomic profiling of tumor cells after induction of telomere dysfunction

Stefan Zimmermann, Martin L. Biniossek, Milena Pantic,Dietmar Pfeifer, Hendrik Veelken and Uwe M. Martens

Supporting information see www.proteomics-journal.com

535 Identification of secreted proteins regulated by cAMP in glioblastoma cells

using glycopeptide capture and label-free quantification

Jennifer J. Hill, Maria J. Moreno, Jean C. Y. Lam, Arsalan S. Haqqaniand John F. Kelly


550 Highly sensitive saturation labeling reveals changes in abundance of cell

cycle-associated proteins and redox enzyme variants during oocyte

maturation in vitro

Frank J. Berendt, Thomas Fröhlich, Patrick Bolbrinker,Marc Boelhauve, Tuna Güngör, Felix A. Habermann,Eckhard Wolf and Georg J. Arnold


© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com

Proteomics 2009, 9

565 The proteome of Salmonella Typhimurium grown under in vivo-mimicking

conditions

Kathleen A. J. Sonck, Gwendoline Kint, Geert Schoofs,Corinne Vander Wauven, Jos Vanderleyden andSigrid C. J. De Keersmaecker


580 Proteome profiling of aging in mouse models: Differential expression of

proteins involved in metabolism, transport, and stress response in kidney

Bulbul Chakravarti, Beerelli Seshi, Wongrat Ratanaprayul,Neville Dalal, Lawrence Lin, Alpan Raval and Deb N. Chakravarti

598 A bioanalytical method for the proteome wide display and analysis of

protein complexes from whole plant cell lysates

Noor Remmerie, Luc Roef , Eveline Van De Slijke, Jelle Van Leene,Geert Persiau, Dominique Eeckhout, Hilde Stals, Kris Laukens,Filip Lemière, Eddy Esmans, Harry Van Onckelen, Dirk Inzé,Geert De Jaeger and Erwin Witters


610 Chitosan treatment induces changes of protein expression profile and

stilbene distribution in Vitis vinifera cell suspensions

Maura Ferri, Annalisa Tassoni, Marina Franceschetti, Laura Righetti,Mike J. Naldrett and Nello Bagni

625 Mass spectrometric characterization of membrane integral low molecular

weight proteins from photosystem II in barley etioplasts

Matthias Plöscher, Bernhard Granvogl, Mikael Zoryan,Veronika Reisinger and Lutz Andreas Eichacker

636 Dissimilar hepatic protein expression profiles during the acute and flow

phases following experimental thermal injury

Xunbao Duan, Francois Berthiaume, David M. Yarmushand Martin L. Yarmush

648 Analysis of outer membrane porin complexes of Neisseria meningitidis in

wild-type and specific knock-out mutant strains

Juan Marzoa, Ana Abel, Sandra Sánchez, Hannah Chan, Ian Feavers,María Teresa Criado and Carlos M. Ferreirós

657 Insights into yeast adaptive response to the agricultural fungicide

mancozeb: A toxicoproteomics approach

Pedro M. Santos, Tânia Simões and Isabel Sá-CorreiaSupporting information see www.proteomics-journal.com

671 Proteomic profiling of antisense-induced exon skipping reveals reversal of

pathobiochemical abnormalities in dystrophic mdx diaphragm

Philip Doran, Steve D. Wilton, Sue Fletcher and Kay Ohlendieck

686 A chip-based amide-HILIC LC/MS platform for glycosaminoglycan

glycomics profiling

Gregory O. Staples, Michael J. Bowman, Catherine E. Costello,Alicia M. Hitchcock, James M. Lau, Nancy Leymarie, Christine Miller,Hicham Naimy, Xiaofeng Shi and Joseph Zaia



Proteomics 2009, 9

696 A comprehensive evaluation of imidazole-zinc reverse stain for current

proteomic researches

Ching-Yu Lin, Vinchi Wang, Hao-Ai Shui, Rong-Huay Juang,Ai-Ling Hour, Pei-Sing Chen, Hui-Ming Huang, Szu-Yu Wu,Jen-Chieh Lee, Tzung-Lin Tsai and Han-Min Chen


710 Chemical de-O-glycosylation of glycoproteins for application in LC-based

proteomics

Franz-Georg Hanisch, Sebastian Teitz, Tilo Schwientekand Stefan Müller

720 Yeast protein expression profile during acetic acid-induced apoptosis

indicates causal involvement of the TOR pathway

Bruno Almeida, Steffen Ohlmeier, Agostinho J. Almeida, FrankMadeo, Cecília Leão, Fernando Rodrigues and Paula Ludovico

733 Analysis of the subproteomes of proteinases and heparin-binding toxins of

eight Bothrops venoms

Adriana F. Paes Leme, Eduardo S. Kitano, Maria F. Furtado,Richard H. Valente, Antonio C. M. Camargo, Paulo L. Ho, Jay W. Foxand Solange M. T. Serrano

746 Unintended molecular interactions in transgenic plants expressing

clinically useful proteins: The case of bovine aprotinin traveling the potato

leaf cell secretory pathway

M. Amine Badri, Daniel Rivard, Karine Coenen andDominique Michaud


757 Effects of green tea extract on lung cancer A549 cells: Proteomic identifi-

cation of proteins associated with cell migration

Qing-Yi Lu, Yanan Yang, Yu Sheng Jin, Zuo-Feng Zhang, David Heber,Frederick P. Li, Steven M. Dubinett, Melissa A. Sondej, Joseph A. Looand Jian Yu Rao

768 Mass spectrometric and computational analysis of cytokine-induced

alterations in the astrocyte secretome

Sarah Dunn Keene, Todd M. Greco, Ioannis Parastatidis,Seon-Hwa Lee, Ethan G. Hughes, Rita J. Balice-Gordon,David W. Speicher and Harry Ischiropoulos


Technical Brief

783 Improved protein sequence coverage by on resin deglycosylation and

cysteine modification for biomarker discovery

Haruhiko Kamada, Tim Fugmann, Dario Neri and Christoph RoesliSupporting information see www.proteomics-journal.com


Proteomics 2009, 9

Dataset Briefs

788 The neuropeptidome of Rhodnius prolixus brain

Sheila Ons, Florian Richter, Henning Urlaub andRolando Rivera Pomar


793 Comparative proteomics of leaf, stem, and root tissues of synthetic

Brassica napus

Warren Albertin, Olivier Langella, Johann Joets, Luc Négroni,Michel Zivy, Catherine Damerval and Hervé Thiellement

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Contents: Proteomics 3/2009