This detailed book provides a set of protocols necessary for the development of a variety of microchip-based electrophoretic assays. It compiles a range of such electrophoretic methods by leading researchers in the field, covering subjects such as microfluidic device fabrication, on-chip sample preparation, theoretical/simulation protocols for assessing these separation methods, as well as common practices followed when applying them to important real world applications. The contents of the book range from protocols for classical assays to those involving pioneering separation techniques recently developed by the scientific community for advancing our analytical capabilities. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.