Polymer-based microfluidic systems have received considerable attention for high throughput chemical analysis. Recently, the ongoing development of microfluidics interfacing to high-accuracy mass spectrometry to identify large molecules had an important impact on biochemistry. A primary goal of this dissertation is the development of a microfluidic apparatus for performing microscale gel electrophoresis, coupled with integrated electrospray tips for either direct interfacing to mass spectrometry through ESI-MS, or coupling to MALDI-MS through the deposition of separated analyte onto a MALDI target for offline analysis. In this dissertation, microfabrication techniques for polymer-based microchip are developed. A novel electrospray interface is demonstrated with good performance. The optimization of multi-channel electrospray tips for multiplexed analysis from a single microfluidic chip was demonstrated. Gas-phased electrophoretic protein/peptide concentration on a pre-structured MALDI target was further demonstrated via theoretical and experimental analysis. The results for developing μGE-ES using linear polymer gel validate the underlined principles and specify challenges involved in coupling μGE to MS. Finally, cross-linked polyacrylamide gel was explored and characterized using in-situ photo- polymerization method in microchannels.