2-D PAGE Map Analysis

Exploring the 2-D gel mapping field, the chapters in this book are separated into four different categories: Part I talks about 2-D maps reproducibility and maps modeling; Part II describes the image analysis tools that provide spot volume datasets; Part III is about the statistical methods applied to spot volume datasets to identify candidate biomarkers; and Part IV discusses differential analysis from direct image analysis tools. 2-D PAGE Map Analysis: Methods and Protocols provides a unique approach to 2-D gel mapping, in that it helps users avoid drawbacks due to ignorance of the basic theoretical mechanisms underlying the technique, including data handling and proper tools for spot analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, 2-D PAGE Map Analysis: Methods and Protocols, is a useful resource for any scientist or researcher, with a mathematical background, who is interested in 2-D gel mapping.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts Includes supplementary material: sn.pub/extras

Autorentext
Dr Elisa Robotti, PhD Dip. Scienze e Innovazione Tecnologica Università del Piemonte Orientale Viale Michel 11 15121 Alessandria Tel: +39 0131 360272 Fax: +39 0131 360250 e-mail: elisa.robotti@mfn.unipmn.it Emilio Marengo Department of Environmental and Life Sciences, University of Eastern Piedmont, Alessandria, Italy. marengoe@tin.it

Inhalt

Sources of Experimental Variation in 2D-Maps: The Importance of Experimental Design in Gel-Based Proteomics.- Decoding 2D-Maps by Autocovariance Functions.- Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages.- Comparative Evaluation of Software Features and Performances.- Image Pretreatment Tools I: Algorithms for Maps Denoising and Background Subtraction Methods.- Image Pretreatment Tools II: Normalization Techniques for 2DE and 2D-DIGE.- Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information.- Algorithms for Warping of 2D-PAGE Maps.- 2-DE Gel Analysis: The Spot Detection.- GENOCOP Algorithm and Hierarchical Grid Transformation for Image Warping of Two Dimensional Gel Electrophoretic Maps.- Detection and Quantification of Protein Spots by Pinnacle.- A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots.- Multiple Testing and Pattern Recognition in 2DE Proteomics.- Chemometric Multivariate Tools for Candidate Biomarkers Identification: LDA, PLS-DA, SIMCA, Ranking-PCA.- The Use of Legendre and Zernike Moment Functions for the Comparison of 2D-PAGE Maps.- Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data.- Differential Analysis of 2D-Maps by Pixel-Based Approaches.