Web-Based Tools for the Interpretation of Chain-Like Protein Spot Patterns on Two-Dimensional Gels

Two-dimensional gel electrophoresis is a standard tool of proteomic analysis, consisting of first dimensional protein separation according to the respective protein's isoelectric point, and the second dimensional separation according to the protein's molecular weight. In these gels, “chain-like” protein spots of equal molecular weight but different isoelectric points are common observations. When identified by mass spectrometry, these chain-like protein spots are identified as the same protein entry in the databases, thus representing “protein species” in the proteomic literature. In this review, we will discuss the factors responsible for the occurrence of multiple protein species, which mostly depend on posttranslational modifications (PTMs) such as phosphorylation and glycosylation and others. Additionally, we will show how internet-based prediction tools can be used for comparing the theoretical models to the actual gel pattern. This may present useful tools for the validation of biomarkers in health and disease.