Marengo E., Robotti E. (Eds.) 2-D PAGE Map Analysis. Methods and Protocols

Humana Press, 2016 — 331p. — (Methods in Molecular Biology 1384) — ISBN: 978-1-4939-3255-9 (eBook), 978-1-4939-3254-2 (Hardcover).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.Sources of Experimental Variation in 2-D Maps: The Importance of Experimental Design in Gel-Based Proteomics
Decoding 2-D Maps by Autocovariance Function
Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages
Comparative Evaluation of Software Features and Performances
Image Pretreatment Tools I: Algorithms for Map Denoising and Background Subtraction Methods
Image Pretreatment Tools II: Normalization Techniques for 2-DE and 2-D DIGE
Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information
Algorithms for Warping of 2-D 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 2-D Gel Electrophoresis Saturated Protein Spots
Multiple Testing and Pattern Recognition in 2-DE Proteomics
Chemometric Multivariate Tools for Candidate Biomarker Identification: LDA, PLS-DA, SIMCA, Ranking-PCA
The Use of Legendre and Zernike Moment Functions for the Comparison of 2-D PAGE Maps
Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data
Differential Analysis of 2-D Maps by Pixel-Based Approaches