ABSTRACT
SECTION 1 ANALYZING 2DE-DERIVED DATA 286 Part I Introduction 286
1. Two-Dimensional Gel Electrophoresis: What Is It and Why Is It Useful? 286 2. What Is Involved in Performing Analyses of 2DE Gels? 287 3. 2DE Gel Analysis Software 289
Part II Step-By-Step Tutorial 290 1. TT900 Warping 290 2. Progenesis Analysis 292
Part III Sample Data 302 SECTION 2 ANALYZING MASS-SPECTROMETRY-DERIVED DATA 303
Part I Introduction 303 1. The Scientific Utility of Mass Spectrometry and Mass Spectrometry Database Search Programs 303 2. What Is Involved in Mass-Spectrometry-Derived Data Analysis? 303 3. Some Commonly Used Mass Spectrometry Database Search Programs 306
Part II Step-By-Step Tutorial 308
1. Setting Up a Database Search 308 2. View and Interpret the Results 311
Part III Sample Data 317 SECTION 3 ANALYZING DATA DERIVED FROM PROTEIN MICROARRAYS 318
Part I Introduction 318 1. Types of Protein Microarrays 318 2. Why Is Protein Microarray Analysis Important? 319 3. Procedures in Executing Protein Microarray Data Analysis 319 4. Examples of Protein Microarray Analysis Programs 323
Part II Step-By-Step Tutorial 324 1. Agilent Technologies: GeneSpring GX 324
Part III Sample Data 330
Proteomics is an emerging scientific field that involves the identification, characterization, and quantification of proteins in cells, tissues, or body fluids. Protein characterization, in an ideal situation, includes amino acid sequence analysis, determination of specific splice variant, polymorphism, and posttranslational modifications (PTMs), identification of protein binding partners, cellular localization, and its potential function. Twodimensional gel electrophoresis (2DE), mass spectrometry, and protein microarrays are important technologies in proteomics, and the related data analysis tools allow us to interpret the data and get meaningful information. In this chapter, proteomic data analysis, specifically, analysis of 2DE-derived data, mass-spectrometry-derived data, and data derived from protein microarrays will be reviewed. In each section, the basic steps and commonly used data analysis programs will be reviewed, and a step-bystep tutorial of how to use the most popular program will be given.
