chapter 1 Chapter 1 -- chapter 2 Chapter 2 -- chapter 3 Creating a National Virtual Knowledge Environment for Proteomics and Information Management -- chapter 4 Public Protein Databases and Interfaces -- chapter 5 Proteomics Knowledge Databases: Facilitating Collaboration and Interaction between Academia, Industry, and Federal Agencies -- chapter 6 Proteome Knowledge Bases in the Context of Cancer -- chapter 7 Data Standards in Proteomics: Promises and Challenges -- chapter 8 Data Standardization and Integration in Collaborative Proteomics Studies -- chapter 9 Informatics Tools for Functional Pathway Analysis Using Genomics and Proteomics -- chapter 10 Data Mining in Proteomics -- chapter 11 Protein Expression Analysis -- chapter 12 Nonparametric, Distance-Based, Supervised Protein Array Analysis -- chapter 13 Protein Identification by Searching Collections of Sequences with Mass Spectrometric Data -- chapter 14 Bioinformatics Tools for Differential Analysis of Proteomic Expression Profiling Data from Clinical Samples -- chapter 15 Sample Characterization Using Large Data Sets -- chapter 16 Computational Tools for Tandem Mass Spectrometry–Based High-Throughput Quantitative Proteomics -- chapter 17 Pattern Recognition Algorithms and Disease Biomarkers -- chapter 18 Statistical Design and Analytical Strategies for Discovery of Disease-Specific Protein Patterns -- chapter 19 Image Analysis in Proteomics.