2-D PAGE Map Analysis: Methods and Protocols

Part I: 2D-Maps Reproducibility and Maps Modeling

1. Sources of Experimental Variation in 2D-Maps: The Importance of Experimental Design in Gel-Based Proteomics
Cristina-Maria Valcu and Mihai Valcu

2. Decoding 2D-Maps by Autocovariance Functions
Maria Chiara Pietrogrande, Nicola Marchetti, and Francesco Dondi

3. Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages
Martin H. Maurer

Part II: Image Analysis Tools to Provide Spot Volume Datasets

4. Comparative Evaluation of Software Features and Performances
Daniela Cecconi

5. Image Pretreatment Tools I: Algorithms for Maps Denoising and Background Subtraction Methods
Carlo Vittorio Cannistraci and Massimo Alessio

6. Image Pretreatment Tools II: Normalization Techniques for 2DE and 2D-DIGE
Emilio Marengo and Elisa Robotti

7. Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information
Hua-Mei Xin and Yuemin Zhu

8. Algorithms for Warping of 2D-PAGE Maps
Marcello Manfredi, Elisa Robotti, and Emilio Marnego

9. 2-DE Gel Analysis: The Spot Detection
Simona Martinotti and Elia Ranzato

10. GENOCOP Algorithm and Hierarchical Grid Transformation for Image Warping of Two Dimensional Gel Electrophoretic Maps
Elisa Robotti, Marco Demartini, and Emilio Marengo

11. Detection and Quantification of Protein Spots by Pinnacle
Jeffrey S. Morris and Howard B. Gutstein

12. A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots
Massimo Natale, Alfonso Caiazzo, and Elisa Ficarra

Part III: Statistical Methods Applied to Spot Volume Datasets to Identify Candidate Biomarkers

13. Multiple Testing and Pattern Recognition in 2DE Proteomics
Sebastien C. Carpentier

14. Chemometric Multivariate Tools for Candidate Biomarkers Identification: LDA, PLS-DA, SIMCA, Ranking-PCA
Elisa Robotti and Emilio Marengo

Part IV: Differential Analysis from Direct Image Analysis Tools

15. The Use of Legendre and Zernike Moment Functions for the Comparison of 2D-PAGE Maps
Elisa Robotti, Marco Demartini, and Emilio Marengo

16. Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data
Massimo Alessio and Carlo Vittorio Cannistraci

17. Differential Analysis of 2D-Maps by Pixel-Based Approaches
Emilio Marengo and Elisa Robotti