PROTEOMICS

The supplementary issue series PRACTICAL PROTEOMICS focuses on all the practical aspects of proteome research. It serves the purposes of education & training and provides the information source for the current trends in the standardization process in the fi eld.

PRACTICAL PROTEOMICS shows the proper usage
of laboratory and computer methods in proteome research.
PRACTICAL PROTEOMICS covers all methodological steps
from sample preparation through 2-D gel electrophoresis, liquid chromatography, mass spectrometry, protein arrays and bioinformatics.
PRACTICAL PROTEOMICS guides newcomers
through the jungle of the numerous methods to be found in the scientific literature.
PRACTICAL PROTEOMICS gives problem-oriented practical instructions
on how to obtain reliable and reproducible research results.
PRACTICAL PROTEOMICS serves as a publication platform
for contributions resulting from the HUPO and EuPA Training & Education activities.

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 Editorial

Focus on the Practical Aspects
Hans-Joachim Kraus

2

 Education & Training

How to Analyze Protein Complexes by 2D Blue Native SDS-PAGE
Veronika Reisinger and Lutz Andreas Eichacker
Supporting information

6

High-performance Proteomics as a Tool in Biomarker Discovery
Helmut E. Meyer and Kai Stühler

18

 Standardization

Submit Your Interaction Data the IMEx Way
A Step by Step Guide to Trouble-free Deposition
Sandra Orchard, Samuel Kerrien, Philip Jones, Arnaud Ceol, Andrew Chatr-aryamontri, Lukasz Salwinski, Jason Nerothin and Henning Hermjakob

28

 Standardization Report

An Update on Data Standards for Gel Electrophoresis
Andrew R. Jones and Frank Gibson

35

 Statistical Tools

Design and Analysis Issues in Quantitative Proteomics Studies
Natasha A. Karp and Kathryn S. Lilley

42

Extracting Protein Regulatory Networks with Graphical Models
Marco Grzegorczyk

51

 Wet Lab

Frequently Made Mistakes in Electrophoresis
Reiner Westermeier

60

 Practical Reviews

Lyophilization, a Practical Way to Store and Transport Tissues Prior to Protein Extraction for 2DE Analysis?
Sebastien C. Carpentier, Koen Dens, Ines Van den Houwe, Rony Swennen and Bart Panis

64

Separation-based Glycoprofiling Approaches using Fluorescent Labels
Paula Jane Domann, Ana Carmen Pardos-Pardos, Daryl Ludger Fernandes, Daniel Ian Richard Spencer, Catherine Mavis Radcliffe, Louise Royle, Raymond Allen Dwek and Pauline Mary Rudd
Supporting information

70

Serum Peptide Profiling using MALDI Mass Spectrometry
Avoiding the Pitfalls of Coated Magnetic Beads using Well-established ZipTip Technology
Ali Tiss, Celia Smith, Stephane Camuzeaux, Musarat Kabir, Simon Gayther, Usha Menon, Mike Waterfi eld, John Timms, Ian Jacobs and Rainer Cramer
Supporting information

77

 Report

Promoting Proteomics Knowledge in Europe
Report on the Activities of the EuPA Education Committee 2006-2007
Juan Pablo Albar, Garry L. Corthals, Concha Gil, Peter James, Ole N. Jensen, Patricia M. Palagi and Deborah Penque

90