Interest in microfluidic platforms has surged as an alternative for sample preparation in the past two decades, with the potential for miniaturization, portability, automation, integration and parallelism driving this research. However, it is still very challenging to develop an integrated microfluidic device for proteomic preparation for mass spectrometry analysis. My thesis work is focused on the development of a valve-based microfluidic platform interfaced with electrospray ionization mass spectrometry for multiplexed proteomic analysis. First, techniques are developed for the fabrication and packing of multiple beds in a polydimethylsiloxane (PDMS) microdevice, which is compatible with the integration of multilayer microvalves. A soft lithography technique was used to fabricate stable weirs in microchips and new bead introduction techniques were explored for the elimination of bead introduction channels in the design. Such a combination provides a convenient, efficient and effective way for multiple bed preparation in a complex design. Next, detailed studies were carried out on the design parameters and performance of multilayer PDMS microvalves in the presence of high electric fields. These studies guided the integration of electrophoresis methods with valve-based fractionation. Finally, a coupled CE-fractionation-SPE-ESIMS peptide analysis on a totally integrated valve-based microchip is presented. We show the design and operation of a system that performs electrokinetic separation, followed by fractionation into multiple channels, SPE extraction and sample cleanup on packed reaction beds, using a multiplexed, hydraulically valved system, with subsequent mass spectral (MS) analysis. This coupled multiple channel CE-Fractionation-SPE-ESIMS platform on valve-based microchip was successfully applied to peptide analysis.

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